Defending the Christian Worldview, Creationism, and Intelligent Design
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Defending the Christian Worldview, Creationism, and Intelligent Design

This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, and biodiversity


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Defending the Christian Worldview, Creationism, and Intelligent Design » Origin of life » Abiogenesis: The factory maker argument

Abiogenesis: The factory maker argument

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1Abiogenesis: The factory maker argument Empty Abiogenesis: The factory maker argument Tue Dec 15, 2015 5:27 am

Otangelo


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The factory maker argument

https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument

Barbieri (2012): Modern Biology describes the cell as an ‘autopoietic’ system, a “system that fabricates itself”. The concept of autopoiesis, or self-production, describes the ability of living systems to produce their own components and eventually to produce copies of themselves.
https://link.springer.com/content/pdf/10.1007/s12304-012-9162-4.pdf

Cells have a codified description of themselves in digital form stored in genes and have the machinery to transform that blueprint through information transfer from genotype to phenotype, into an identical representation in analog 3D form, the physical 'reality' of that description. The cause leading to a machine’s and factory's functionality has only been found in the mind of the engineer and nowhere else.

All historical, observational, testable, and repeatable examples have demonstrated that information and operational functionality come from intelligent sources.

G. F. Joyce, L. E. Orgel: Prospects for Understanding the Origin of the RNA World 1993
A blueprint cannot produce a car all by itself without a factory and workers to assemble the parts according to the instructions contained in the blueprint; in the same way, the blueprint contained in RNA cannot produce proteins by itself without the cooperation of other cellular components which follow the instructions contained in the RNA.

Paul Davies: How did stupid atoms spontaneously write their own software … ? Nobody knows … … there is no known law of physics able to create information from nothing.

Life has only been observed to come from life. Never from nonlife, by unguided means. 

Life is based on enormously complex engineering principles where information manages, choreographs, coordinates, controls, regulates, and directs the making and employment of incredibly efficient nanomachines and chemical production lines, working with extraordinary efficiency and operating very close to thermodynamic perfection, using energy made by almost 100% efficient molecular energy turbines. It is like an entire city of exquisitely designed processes all interlinked and coordinated into a functionally integrated system with a coherent outcome. Those that stick to a non-designed explanation, must propose a sequential stepwise process, each in itself very unlikely,  in which each product must have been a chemical compound with some beneficial advantage over the system as a whole, providing more fitness for survival ( even if not alive yet).  It is difficult to envisage how a cell, such an intricately complex system could have arisen from nonliving elements in that way, in a long gradual incrementally complexifying process. Extremely improbable events would have had to take place to create a self-replicating cell. Each step in the direction of making a living cell is remotely probable because there are so many possible reactions that a disorganized chemical system could undergo. One is oxygen reaction species (ROS) destroying the stem. Modern cells have protection mechanisms to prevent this). 

An essential characteristic of living cells, homeostasis, is the ability to maintain a steady and more-or-less constant chemical balance in a changing environment. Cell survival requires appropriate proportions of molecular oxygen and various antioxidants. Reactive products of oxygen, called Reactive Oxygen Species ( ROS) are amongst the most potent and omnipresent threats faced by cells. Cells, damaged by ROS, are irreversibly turned functionless.

Could all these steps required to make a self-replicating cell have occurred simultaneously by non-guided means? This is most unlikely because they would have had to occur in a big sweep - each reaction being highly improbable, and the origin of the system would be the sum of all individual highly unlikely reactions. Such an integrated system can only be rationally explained all in one go and suddenly, like a phase transition in physics where everything came together and was created at once. 

Cells have a codified description of themselves in digital form stored in genes and have the machinery to transform it through information transfer and the injection of energy into the physical 'reality' of that description. To suggest that a physical non-designed process can create instructional assembly information, a recipe, or a blueprint, is like suggesting that throwing ink on paper will create a blueprint. It is never going to happen. On top of that, believing that somehow information transmission networks will emerge by chance, that will encode, transmit, and decode that information, and subsequently, somehow, add energy, non-intelligent mechanisms will direct the assembly process of complex machines, interconnect them, and produce a self-replicating factory through that information is extremely unlikely. There might be a chance, you might say. If one wins 1000 times the lottery in a row, there might-yes, statistically be a chance, but it is so unlikely, that it makes more sense to believe that someone cheated.

Specified complexity observed in genes dictates and directs the making of irreducible complex molecular machines, robotic molecular production lines, and chemical cell factories. If this is not evidence of design, what is it?

Analogous effects have analogous causes
Isaac Newton’s First and Second Rules of Reasoning in Philosophy; in particular, his second, states, “…to the same natural effects we must, as far as possible, assign the same causes.”
Sir Isaac Newton:  Mathematical Principles of Natural Philosophy, trans. Andrew Motte (1729)

Hume wrote in the form of a dialogue between three characters. Philo, Cleanthes, and Demea. The design argument is spoken by Cleanthes in Part II of the Dialogues:
The curious adapting of means to ends, throughout all nature, resembles exactly, though much exceeds, the production of human contrivance, or human design, the thought, wisdom and intelligence. Since therefore the effects resemble each other, we are led to infer, by all the rules of analogy, that the causes also resemble; and that the Author of nature is somewhat similar to the mind of man; though possesses of much large faculties, proportioned to the grandeur of the work executed. By this argument a posteriori, and by this argument alone, do we prove at once the existence of a Deity, and his similarity to human mind and intelligence. ...
https://philosophy.lander.edu/intro/introbook2.1/x4211.html

John Frederick William Herschel: A Preliminary Discourse on the Study of Natural Philosophy, page 149, 1830
If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.
https://3lib.net/book/1196808/dad956

A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.

Abiogenesis: The factory maker argument Hersch10


Abiogenesis: The factory maker argument Gggdfg10

1. Living Cells are information-driven factories. They store very complex epigenetic and genetic information through the genetic code, over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms.  The information drives the operation in a manner analogous to how software in a computer drives computer hardware. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advances and sophistication.
2. Humans routinely create blueprints containing instructional assembly information, and fabricate complex machines and interlinked factories based on these instructions, which produce goods for specific purposes.
3. Since the manufacturing process of biological cells is analogous, having a codified description of themselves in digital form stored in genes and use their machinery to transform that blueprint through information transfer into an identical representation in analog 3D form, the physical 'reality' of that description, that process is best explained by the action of an intelligent designer, who created life for his own purposes.


Michael Denton Evolution: A Theory in Crisis 1985
The inference to design is a purely a posteriori induction based on a ruthlessly consistent application of the logic of analogy.
http://library.lol/main/326ED7C1E370B55C902D447EB1A891F4

DNA Is Called The Blueprint Of Life: Here’s Why OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/

BIOTOL, B.C. CurrellThe Molecular Fabric of Cells   1991
Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompasses chemically simple compounds such as ethanol and carbon dioxide as well as the extremely complex proteins, carbohydrates, lipids, nucleic acids and secondary products. Furthermore: Self-replication is the epitome of manufacturing advance and achievements, far from being realized by man-made factories.  
http://library.lol/main/AD1B3F4370D3A95CE59520193B4383FC

Self-replication had to emerge and be implemented first, which raises the unbridgeable problem that DNA replication is irreducibly complex. Evolution is not a capable driving force to make the DNA replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.

Chance of intelligence to set up life: 
100% We KNOW by repeated experience that the origin of blueprints containing instructional complex assembly information, dictating the fabrication of complex machines, robotic production lines, computers, transistors, turbines, energy plants,  and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup. 

Chance of unguided random natural events doing it, that is:

Let's suppose, we have a fully operational raw material, and the genetic language upon which to store genetic information. Only now, we can ask: Where did the information come from to make the first living organism? Various attempts have been made to lower the minimal information content to produce a fully working operational cell. Often, Mycoplasma is mentioned as a reference to the threshold of the living from the non-living. Mycoplasma genitalium is held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ).  As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence the bacteria do not need the genes for producing such compounds themselves. As such, it does not require the same complexity of biosynthesis pathways to manufacturing all nutrients as a free-living bacterium. 

The simplest free-living bacteria is Pelagibacter ubique. It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. 2

This probability is hard to imagine but an illustration may help. Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^55. 

The likelihood is far less than finding a red atom amongst all atoms in the universe (10^80) by luck. The luck to find the right sequence would exhaust by far the maximal number of possible simultaneous interactions in the entire history of the universe (10^139) It would exhaust all probabilistic resources of this Universe, or a collection of 5194 of them!

Furthermore, what good would functional proteins be good for, if not transported to the right site in the Cell, inserted in the right place, and interconnected to start the fabrication of chemical compounds used in the Cell?  It is clear, that life had to start based on fully operating cell factories, able to self replicate, adapt, produce energy, regulate its sophisticated molecular machinery.

Wilhelm Huck chemist , professor at Radboud University Nijmegen
A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity
https://sixdaysblog.com/2013/07/06/protocells-may-have-formed-in-a-salty-soup/

Objection: Cells are not factories
Answer: Cells are factories in a literal sense:
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#6959

When you see a blueprint of a factory, with the precise instructions to make all machines, subparts, how to assemble each machine, interconnect them into production lines, organized production compartments, gates to permit the right materials to get in, and the end products go through error check and repair, and export, and then see the functional factory-build precisely upon the blueprint which you saw previously, and the operation of the factory close to  perfection, controlled and directed by computers, directing thousands of processes simultaneously and adapting the production output by its demands, but have no clue of how both, the blueprint, and the factory, came to be: What is the obvious answer:

a) That an intelligent team of engineers, machine designers, etc. made the project, and skilled, intelligent labor workers, carpenters, masons, electricians, machine builders, etc. constructed the factory, or
b) that natural forces somehow made the blueprint, and random unguided forces brought the building materials together, and by luck, the factory was assembled precisely based on the blueprint instructions and started its production ? or
c) you have no way to conclude anything meaningful and feel justified to say: " I don't know"?

If we sum up the total number of amino acids for a minimal Cell, there would have to be 560 proteins x 400 amino acids  =  224.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^224.000 possibilities !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible. 

Peptide Bond Formation of amino acids in prebiotic conditions: an insurmountable problem of protein synthesis on early earth: 

1. The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of pre-biological ( chemical) evolution.
2. The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life. 
3. The best one can hope for from such a scenario is a racemic polymer of proteinous and non-proteinous amino acids with no relevance to living systems.
4. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed.
5. Even if there were billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates, even if, as is claimed, there was no oxygen in the prebiotic earth, then there would be no protection from UV light, which would destroy and disintegrate prebiotic organic compounds. Secondly, even if there would be a sequence, producing a functional folding protein, by itself, if not inserted in a functional way in the cell, it would absolutely no function. It would just lay around, and then soon disintegrate. Furthermore, in modern cells proteins are tagged and transported on molecular highways to their precise destination, where they are utilized. Obviously, all this was not extant on the early earth.
6. To form a chain, it is necessary to react bifunctional monomers, that is, molecules with two functional groups so they combine with two others. If a unifunctional monomer (with only one functional group) reacts with the end of the chain, the chain can grow no further at this end. If only a small fraction of unifunctional molecules were present, long polymers could not form. But all ‘prebiotic simulation’ experiments produce at least three times more unifunctional molecules than bifunctional molecules. 1

Now let us suppose that all these problems would be overcome, and random shuffling would take place:

Calculations of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

https://reasonandscience.catsboard.com/t2508-abiogenesis-calculations-of-life-beginning-through-unguided-natural-random-events#6665

Proteins are the result of the DNA blueprint, which specifies the complex sequence necessary to produce functional 3D folds of proteins. Both improbability and specification are required in order to justify an inference of design.
1. The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins. 
2. According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8
3. Each of the 400 positions in the amino acid polypeptide chains could be occupied by any one of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would fold into a functional 3D protein would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number. 
4. Since we need in the order of  1354 proteins total to make a first free-living living cell, we would have to repeat the shuffle 1354 times, to get all proteins required for life. The probability would be therefore 1354/10^520.  We arrive at a probability far beyond  of 1 in 10^722.000  ( A proteome set with 239 proteins yields odds of approximately 1/10^119.614 ) 7
Granted, the calculation does not take into consideration nor give information on the probabilistic resources available. But the sheer gigantic number os possibilities throw any reasonable possibility out of the window. 

If we sum up the total number of amino acids for a minimal Cell, there would have to be 1300 proteins x 400 amino acids  =  520.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 10^722.000.000 possibilities !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible. 

We can take an even smaller organism, which is regarded as one of the smallest possible, and the situation does not change significantly:
The simplest known free-living organism, Mycoplasma genitalium,  has the smallest genome of any free-living organism, has a genome of 580,000 base pairs. This is an astonishingly large number for such a ‘simple’ organism. It has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451. If we calculate the entire proteome, then the odds are 470 x 347 = 163090 amino acids, that is odds of 20^164090 , if we disconsider that nature had to select only left-handed amino acids and bifunctional ones. 

Denton, p. 329.
We would see [in cells] that nearly every feature of our own advanced machines had its analog in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late-twentieth-century technology.
    “What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory that would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle.”


Science confirms:

Abiogenesis is virtually impossible
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-virtually-impossible

Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

No scientific experiment has been able to come even close to synthesize the basic building blocks of life, and reproduce a  self-replicating Cell in the Laboratory through self-assembly and autonomous organization. Scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative agency. The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true.

“There’s a huge chasm between the origins of life and the last common ancestor,”
https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/

Scientists are learning that what is required for life seems to be much greater than what is possible by natural process.  This huge difference has motivated scientists to creatively construct new theories for reducing requirements and enhancing possibilities, but none of these ideas has progressed from speculation to plausibility. The simplest "living system" we can imagine, involving hundreds of components interacting in an organized way to achieve energy production and self-replication, would be extremely difficult to assemble by undirected natural process.  And all of this self-organization would have to occur before natural selection (which depends on self-replication) was available.

Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance:  page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of  the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.

125 reasons to believe in God
https://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

Abiogenesis: The factory maker argument JL02zBk

Someone wrote that following argument signals the death knell of atheism.
From Wikipedia
“A Death Knell was the ringing of a bell immediately after a death to announce it. Historically it was the second of three bells rung around death; the first being the "Passing Bell" to warn of impending death, and the last was the "Lych Bell", or "Corpse Bell", which survives today as the Funeral toll.”


When you see a blueprint, instructional information, containing the manual to make machines, production lines, computers, and factories, and subsequently, a factory containing computers and machines, precisely fabricated upon the blueprint but have no clue of how both, the blueprint, and the factory, came to be: What is the obvious answer:
a) That an intelligent team of engineers made the project, and skilled, intelligent labor workers, machine builders, etc. constructed the factory, or
b) that natural forces somehow made the blueprint, and random unguided forces brought the building materials together, and by luck, the factory was assembled precisely based on the blueprint instructions and started its production ? or
c) you have no way to conclude anything meaningful and feel justified to say: " I don't know"?


1. Blueprints, instructional information and master plans, and the making of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  

2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks.

3. The Blueprint and instructional information stored in DNA and epigenetics, which directs the making of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

You find a nanofactory, packed with miniature chemical processors, computing, and robotics, able to self-replicate, and the blueprint upon which the factory was made. Is this  most likely the product of:

a) intelligence
b) random unguided forces  
c) physical necessity
c) or you feel justified to say: " I don't know"?

Why don't you go with Richard Dawkins?
If you look at the um at the details of biochemistry molecular biology you might find a signature of some sort of designer
https://www.youtube.com/watch?v=AbpCefr5_Ac

Abiogenesis: The factory maker argument Factor10

Abiogenesis: The factory maker argument Nanofa10

How to recognize high-tech intelligent design in biology, if no he is a construction analogous to the products of human technology?
Such molecular machines, such as engine or bacterial and ATP synthase is almost analogy engines manufactured by man. In other words, they have all the characteristics of advanced technical devices intelligently designed.
Some molecular machines have all the characteristics of high-tech projects, but do not have counterparts in human technology. For example, polymerase, helicase, vesicular transport or the most complex biological machine ribosome.

The living cell is a chemical factory, analogous to human-made factories. On the lowest level, it contains minuscule pumps, levers, motors, rotors, turbines, propellers, scissors, and many other instruments that we are familiar with from a human workshop. But also more complex functional components like molecular machines, production lines producing a myriad of chemical compounds, and energy turbines to generate energy, all of them exquisite examples of the highest sophisticated nanotechnology. Like human factories that are organized in compartments, each performing a specific step in the manufacturing process, so do living cells have compartments called organelles.

Paul Davies, The Goldilocks enigma page 203
The living cell contains minuscule pumps, levers, motors, rotors, turbines, propellers, scissors, and many other instruments familiar from a human workshop, all of them exquisite examples of nanotechnology. The entire assemblage runs itself with great efficiency, sometimes autonomously, sometimes in collaboration with other cells through a sophisticated network of intercellular communication based on chemical signaling. The command and control functions of the cell are encoded in its DNA database, which implements instructions through intermediary molecules using an optimal mathematical code to convert software instructions into hardware products with customized functionality. And this is just one cell. In a larger organism, vastly many cells get together and cooperate to form organs such as eyes, ears, brains, livers, and kidneys, many of them immensely elaborate in their structure and function. The human brain alone has more cells than there are stars in the Milky Way galaxy. So it all adds up to a package of marvels that boggles the mind.
https://3lib.net/book/5903498/82353b

1. Intelligent minds make blueprints of factories full of machines with specific functions, set up for specific purposes. Each factory eventually will be full of robotic production lines where the product of one factory is handed over to the next for further processing until the end product is made. Each of the intermediate steps is essential. If any is mal or non-functioning, like energy supply, or supply of the raw materials, the factory as a whole ceases its production.
2. Biological cells are a factory complex of interlinked high-tech fabrics, fully automated and self-replicating, hosting up to over 2 billion molecular machines like Ribosomes & chemical production lines, full of protein machines that act like robots, each with a specific task or function, and completing each other, the whole system has the purpose to survive and perpetuate life. At least 1350 proteins and a fully setup genome, metabolome, and interactome is required, and they are interdependent. The probability, that such complex nano-factory complex could have emerged by unguided chemical reactions, no matter in what primordial environment, is beyond the chance of one to
10^750000. The universe hosts about 10^80 atoms.  
3. Biological Cells are of unparalleled gigantic complexity and adaptive design, vastly more complex and sophisticated than any man-made factory complex. Self-replicating cells are, therefore, with extremely high probability, the product of an intelligent agency with purpose and intent.

Albert Voie (2006): Life expresses both function and sign systems. Due to the abstract character of function and sign systems, life is not a subsystem of natural laws. This suggests that our reason is limited in respect to solving the problem of the origin of life and that we are left accepting life as an axiom.

Computer programs and machines are subsystems of the mind 
It seems that it is generally accepted as emphasized by Hoffmeyer and Emmeche [8], that "No natural law restricts the possibility-space of a written (or spoken) text". Yet, it is under strict control, following abstract rules. Formal systems are indeed abstract, non-physical, and it is really easy to see that they are subsystems of the human mind and belong to another category of phenomena than subsystems of the laws of nature, such as a rock, or a pond. Another similar set of subsystems is functional objects.

In general (not in the mathematical but in the engineering sense), a function is a goal-oriented property of an entity. Function (according to the TOGA meta-theory is not a physical property of a system, it depends how this system (a distinguished process) is used. The carrier of a function is a process; therefore, the same function is possible to realize using different physical processes, and one process can be a carrier of different functions. For example, a clock's main function, i.e. a presentation of time, can be realized by different physical processes, such as atomic, electronic, mechanical, or water movement.

A machine, for example, cannot be explained in terms of physics and chemistry. Machines can go wrong and break down - something that does not happen to laws of physics and chemistry. In fact, a machine can be smashed and the laws of physics and chemistry will go on operating unfailingly in the parts remaining after the machine ceases to exist. Engineering principles create the structure of the machine which harnesses the laws of physics and chemistry for the purposes the machine is designed to serve. Physics and chemistry cannot reveal the practical principles of design or coordination which are the structure of the machine.

The engineer can manipulate inanimate matter to create the structure of the machine, which harnesses the laws of physics and chemistry for the purposes the machine is designed to serve. The cause leading to a machine’s functionality is found in the mind of the engineer and nowhere else.

The interdependency of biological function and sign systems In life there is interdependency between biological function and sign systems. To secure the transmission of biological function through time, biological function must be stored in a “time-independent” sign system. Only an abstract sign-based language can store the abstract information necessary to build functional biomolecules. In the same manner, the very definition of the genetic code depends upon biological function. This is the origin of life problems and it penetrates deeper than just the fact that organisms observed today have such a design.

Von Neumann believed that life was ultimately based on logic, and so there should be a logical construct that should be able to support the reproduction that is observed in life. In order to solve the implication of Gödel’s incompleteness theorem, von Neumann had to introduce a blueprint of the machine. The trick is to employ representations or names of objects, a code, which can be smaller than the objects themselves and can indeed be contained within that object. Von Neumann’s abstract machine consisted of two central elements: a Universal Computer and a Universal Constructor. The Universal Constructor builds another Universal Constructor based on the directions contained in the Universal Computer. When finished, the Universal Constructor copies the Universal Computer and hands the copy to its descendant. As a model of a self-replicating system, it has its counterpart in life where the Universal Computer is represented by the instructions contained in the genes, while the Universal Constructor is represented by the cell and its machinery. In order to replicate, the necessity of a symbolic self-reference is a general premise in logic. Can we really apply logical terms such as “paradox” and “consistent” to biological systems in the same manner as we do to formal systems? 

The function of biological bodies is determined by their three-dimensional structure and how this structure relates to a whole. However, in order to copy them one would require access their internal sequence of amino acids (or nucleic acids if the body is a ribozyme), which would then interfere with their structure and function. For instance, for an enzyme to replicate itself, it would need to have the intrinsic property of self-replication "by default". Otherwise, it would have to be able to assemble itself from a pool of existing parts, but for this, it would have to "unfold" so that its internal parts could be reconstituted for the copy to be produced. Thus, instead of using terms such as “paradox” and “consistent,” it is more relevant to speak of what is physically and practically possible when it comes to physical construction. These constraints require the categorical distinction between the machine that reads the instructions and the description of the machine.

Memory-stored controls transform symbols into physical states. Von Neumann made no suggestion as to how these symbolic and material functions in life could have originated. He felt, "That they should occur in the world at all is a miracle of the first magnitude."
https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.94.171&rep=rep1&type=pdf

Abiogenesis: The factory maker argument Von_ne10


On the one side, there is the computer storing the data, on the other, the construction machines. The construction machines build/replicate and make another identical construction machine, based on the data stored in the computer. Once finished, the construction machines copy the computer and the data and hand it down to the descendant.

As a model of a self-replicating system, it has its counterpart in life where the computer is represented by the instructions contained in the genes, while the construction machines are represented by the cell and its machinery that transcribes, translates, and replicates the information stored in genes.  RNA polymerase transcribes, and the ribosome translates the information stored in DNA and produces a Fidel reproduction of the cell and all the machinery inside of the cell. Once done, the genome is replicated, and handed over to the descendant replicated cell, and the mother cell has produced a daughter cell.    

The entire process of self-replication is data-driven and based on a sequence of events that can only be instantiated by understanding and knowing the right sequence of events. There is an interdependence of data and function. The function is performed by machines that are constructed based on the data instructions.

The cause to instantiate such a sequence of events and state of affairs can only be a mind.



1. https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664
2. https://web.archive.org/web/20170423032439/http://creationsafaris.com/epoi_c06.htm#ec06f25



Last edited by Otangelo on Thu Jul 28, 2022 3:24 pm; edited 255 times in total

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2Abiogenesis: The factory maker argument Empty Are Cells factories in a literal sense? Tue Dec 15, 2015 10:08 am

Otangelo


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Are Cells factories in a literal sense?

https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#4490

Comparing the Cell to a Factory
(modified from A Busy Factory, Imagine a busy factory making the latest must-have toy. Whether they make bicycles, cell phones, or hot air balloons, most factories are set up the same way. All factories have outside walls that protect and support them and inside walls that create different work areas. They usually have a production line where a product is put together and an executive department that decides what product is made. A finishing department processes and prepares the product for shipping, and a packaging department wraps the product. In addition, a factory has a receiving department that brings in the parts it needs to make its product, a communications department that allows it to contact suppliers, and a power plant that provides the energy it needs to run. Finally, a custodial staff keeps everything clean and in good working order. Cells are similar to factories. To stay alive and function properly, cells have a division of labor similar to that found in factories. All eukaryotic cells are composed of a plasma membrane, a nucleus, and cytoplasm. These structures can be compared with a factory's departments.
https://www.portolams.org/apps/pages/index.jsp?uREC_ID=343690&type=d

Objection: cells are not factories in a literal sense.
Answer: Cells are not just equivalent to human-made factories. Cells are better described as an entire High-Tech Industry Quartier, an entire city of chemical factories, smart in the sense that they are fully interconnected and flexible. Cells use real-time production based on inventory data, leveraging to adapt to the changing environment. It even changes its surrounding environment to fit better its needs. That's called niche construction.  Cells self-optimize performance based on input from the signaling network, self-adapt to and learn from new conditions in real or near-real time, and autonomously run entire production processes.

Cells adapt far more sophisticated and complex manufacturing procedures than any human-made factory, producing the basic building blocks of life in the right quantities, which is strictly regulated and controlled, with sophisticated recycling mechanisms, and using these basic building blocks to make ultracomplex molecular machines, which perform all kind of essential tasks, interlinked into veritable production lines, producing all kind of products necessary for maintaining all life-essential functions: reproduction, metabolism, nutrition, growth, development, permanence and change. On top of that, they self-replicate, which is the epitome of manufacturing advances and achievements, far from being realized by man-made factories. 

Cells contain inside of them up to over 2 billion individual factories ( Human cells ) analogous to human-made factories, so we can draw an analogy. Cells contain literally billions of factories, not factory-like, or just similar in a distant way. Cells are the MOST ADVANCED factories in the universe, far more complex than ANY man-made factory. There are vast scientific literature, science papers, and books, which mention Cells as factories in a literal sense. 

Factory is from Latin, and means fabricare, or make. Produce, manufacture. A factory or manufacturing plant is a site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where, in fully automated factories, for example, pre-programmed robots, manufacture goods or operate machines processing one product into another. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex machine processing, computing, etc. They produce all organelles, proteins, membranes, parts, they make a copy of themselves. Self-replication is a marvel of engineering. the most advanced method of manufacturing. And fully automated. No external help is required. If we could make factories like that, we would be able to create a society where machines do all the work for us, and we would have time only to entertain ourselves, no work, or money needed anymore..... And if factories could evolve to produce subsequently better, more adapted products, that would add even further complexity, and point to even more requirements of pre-programming to get the feat done.

Alberts: Molecular biology of the Cell 6th ed.: Cells are chemical factories 
The surface of our planet is populated by living things—curious, intricately organized chemical factories that take in matter from their surroundings and use these raw materials to generate copies of themselves.

Each cell can be viewed as a tiny chemical factory, performing many millions of reactions every second. The Nucleolus Is a ribosome-producing factory. The nucleolus can be thought of as a large factory at which different noncoding RNAs are transcribed, processed, and assembled with proteins to form a large variety of ribonucleoprotein complexes. mRNA production is made more efficient in the nucleus by an aggregation of the many components needed for transcription and pre-mRNA processing, thereby producing a specialized biochemical factory. The extensive ER network serves as a factory for the production of almost all of the cell’s lipids. DNA repair is observed to congregate in discrete foci inside the nucleus, creating “repair factories”.  . In response to DNA damage, they rapidly converge on the sites of DNA damage, become activated, and form “repair factories” where many lesions are apparently brought together and repaired. And nuclei often contain hundreds of discrete foci representing factories for DNA or RNA synthesis. mRNA is made by production factories and DNA by replication factories. Subnuclear structures (including Cajal bodies and interchromatin granule clusters) are sites where components involved in RNA processing are assembled, stored, and recycled. The high concentration of components in such “factories” ensures that the processes being catalyzed are rapid and efficient. 

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
The central theme of both of these texts is to consider cells as biological factories. Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompasses chemically simple compounds such as ethanol and carbon dioxide as well as extremely complex proteins, carbohydrates, lipids, nucleic acids, and secondary products. 

Membranes represent the walls of the cellular factory. Membranes control what comes into the factory and what leaves. We may view the cytoplasm and its surrounding plasma membrane as being the workshop of the chemical factory. The Golgi apparatus, another membranous structure embedded in the cytoplasm, is also involved in the processing of macromolecules made within the cell. Its special properties are for modifying cell products so that they can be exported from the cell. In our chemical factory, they are the packaging and exporting department. Enzymes are indeed rather like the workers in a large complex industrial process. Each is designed to carry out a specific task in a specific area of the factory.

Understanding how a factory operates requires knowledge of the tools and equipment available within the factory and how these tools are organized. We might anticipate that our biological factories will be comprised of structural and functional elements.


Cell Factory Engineering MARCH 22, 2017
While industrial biotechnology has a long history, it was not until the arrival of genetic engineering that it became possible to modify the DNA of the cell factories to improve production. Native metabolites are here compounds naturally produced by the cell factory, either intracellularly or (preferably) a secreted compound. Examples are amino and nucleic acids, antibiotics, vitamins, enzymes, bioactive compounds, and proteins produced from anabolic pathways of cells

The future of biologically inspired next‐generation factories for chemicals online 2017 Aug 14
Biomanufacturing processes may be performed using cell factories, cell‐free processes or biocatalytic routes. The cell factory route uses microbial cells and is presently the most advanced technology and preferred route for the large‐scale production of chemicals that require several enzymatic transformation reactions. Microorganisms have a long tradition as cell factories and are used for the large‐scale production of commodity chemicals such as organic acids, amino acids and bioactive compounds like antibiotics.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5609277/

Science matters, Robert M.Hazen
http://gen.lib.rus.ec/book/index.php?md5=87EC7C6B467B05243CFD3A9BF9E9D29D
Pg.239 Cells act as chemical factories, taking in materials from the environment, processing them, and producing “finished goods” to be used for the cell’s own maintenance and for that of the larger organism of which they may be part. In a complex cell, materials are taken in through specialized receptors (“loading docks”), processed by chemical reactions governed by a central information system (“the front once”), carried around to various locations (“assembly lines”) as the work progresses, and finally sent back via those same receptors into the larger organism. The cell is a highly organized, busy place, whose many different parts must work together to keep the whole functioning. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply.
Pg. 242 Nucleic acids. These molecules (DNA and RNA) carry the blueprint that runs the cell’s chemical factories, and also are the vehicle for inheritance
Pg. 243 Carbohydrates. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply. The basic building blocks of carbohydrates are sugars—small ring-
Pg. 245 Like any factory, each cell has several essential systems. It must have a front office, a place to store information, and issue instructions to the factory door to guide the work in progress. It must have bricks and mortar—a building with walls and partitions where the actual work goes on. Its production system must include the various machines that produce finished goods as well as the transportation network that moves raw materials and finished products from place to place. And finally, there must be an energy plant to power the machinery.
Pg. 246 Cellular factories consist of walls, partitions, and loading docks.
Pg. 249 Every living thing is composed of one or more cells, each of which has a complex anatomy. A “generic” cell contains many structures and organelles—tiny chemical factories.
Pg. 263 The sequence of the bases along the double helix of DNA contains the genetic code—all the information a cell needs to reproduce itself and run its chemical factories, all the characteristics and quirks that make you unique. 
Pg. 309 Shortly thereafter, the glucose is processed in cellular chemical factories to form part of the cellulose fibers that support each grass blade. The carbon atom has become an integral part of the structure of grass.

The cell's journey: from metaphorical to literal factory
https://www.sciencedirect.com/science/article/abs/pii/S0160932707000312

And it is at this time – the early twentieth century – when biochemical investigations came to dominate the attention of cytologists that the description of the cell as a chemical factory began to rise in popularity.
Today there are professional journals specifically devoted to research into cell factories. A recent article appearing in one such publication explained further the opportunities for the engineered improvement of the cell’s innate manufacturing ability:

The bag or the spindle: the cell factory at the time of systems' biology
https://microbialcellfactories.biomedcentral.com/articles/10.1186/1475-2859-3-13
Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes . . . or small gene clusters are improved and expressed in a variety of hosts. New techniques derived from functional genomics . . . now allow users to shift from this single-gene approach to amore integrated view of the cell, where it is more and more considered as a
factory. One can expect in the near future that bacteria will be entirely reprogrammed, and perhaps even created de novo from bits and pieces, to constitute man-made cell factories. This will require exploration of the landscape made of neighbourhoods of all the genes in the cell. Present work is already paving the way for that futuristic viewof bacteria in industry

Abiogenesis: The factory maker argument 111111

Cells are nature’s factories
Cells – the smallest functional units of any living organism – are tiny factories that build biological products, or molecules
https://sitn.hms.harvard.edu/flash/2020/an-introduction-to-ribosomes-natures-busiest-molecular-machines/

The scientific impact of microbial cell factories
https://core.ac.uk/download/pdf/8251128.pdf

The bag or the spindle: the cell factory at the time of systems' biology
https://microbialcellfactories.biomedcentral.com/articles/10.1186/1475-2859-3-13

Dr. Tour on the Origin of Life at Syracuse University Cru  min: 22:31
A  cell is an absolute Factory
https://www.youtube.com/watch?v=-Gsa58Rm8Sk&feature=youtu.be

Plant Cells as Chemical Factories: Control and Recovery of Valuable Products
https://link.springer.com/chapter/10.1007/978-94-017-0641-4_14

Microbial cell factory is an approach to bioengineering  which considers microbial  cells as a production facility in which the optimization process largely depends on metabolic engineering
https://en.wikipedia.org/wiki/Microbial_cell_factory

Microbial Cell Factories is an open access peer-reviewed journal that covers any topic related to the development, use and investigation of microbial cells as producers of recombinant proteins and natural products
https://microbialcellfactories.biomedcentral.com/

Fine Tuning our Cellular Factories: Sirtuins in Mitochondrial Biology
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111451/

Cells As Molecular Factories
Eukaryotic cells are molecular factories in two senses: cells produce molecules and cells are made up of molecules.
http://serendip.brynmawr.edu/exchange/bioactivities/cellmolecular

Cells are nature’s factories
https://sitn.hms.harvard.edu/flash/2020/an-introduction-to-ribosomes-natures-busiest-molecular-machines/

Michael Denton: Evolution: A Theory In Crisis:
The cell is a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world. 

Ribosome: Lessons of a molecular factory construction
https://link.springer.com/article/10.1134/S0026893314040116

VijayKumar Introduction to ribosome factory, origin, and evolution of translation
https://www.sciencedirect.com/science/article/pii/B9780128163641000020?via%3Dihub

The protein factory
https://www.ebi.ac.uk/pdbe/about/news/protein-factory

Ribosome: The cell city's factories 16th May 2002
FACTORY:  New goods and products are continually being manufactured from raw materials. In cities this takes place in workshops and factories. Raw materials are transformed, usually in a sequence of steps on a production line, into finished products. The process is governed by a clear set of instructions or specifications. In some cases the final products are for immediate or local use, in others they are packaged for export.
https://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories

O. V. Sergeeva Ribosome: Lessons of a molecular factory construction 15 August 2014
https://sci-hub.3800808.com/10.1134/S0026893314040116

Ever wondered how your cells work? They’re like tiny factories.
All the parts need to work together for your body to stay in business.
https://www.washingtonpost.com/lifestyle/kidspost/ever-wondered-how-your-cells-work-theyre-like-tiny-factories/2017/05/26/135da89a-30d8-11e7-8674-437ddb6e813e_story.html


Nucleolus: the ribosome factory
https://www.ncbi.nlm.nih.gov/pubmed/18712681

Ribosome: The cell city's factories
http://www.open.edu/openlearn/nature-environment/natural-history/ribosome-the-cell-citys-factories
In the cell, there are production lines, in this case, manufacturing new proteins of many different sorts. New goods and products are continually being manufactured from raw materials. In cities this takes place in workshops and factories. Raw materials are transformed, usually in a sequence of steps on a production line, into finished products. The process is governed by a clear set of instructions or specifications. In some cases the final products are for immediate or local use, in others they are packaged for export.

The Cell's Protein Factory in Action
What looks like a jumble of rubber bands and twisty ties is the ribosome, the cellular protein factory.
https://www.livescience.com/41863-ribosomes-protein-factory-nigms.html

Chloroplasts are the microscopic factories on which all life on Earth is based.
https://www.quora.com/What-is-chloroplast-For-what-it-is-used

Visualization of the active expression site locus by tagging with green fluorescent protein shows that it is specifically located at this unique pol I transcriptional factory.
http://www.nature.com/nature/journal/v414/n6865/full/414759a.html

There are millions of protein factories in every cell. Surprise, they’re not all the same
http://www.sciencemag.org/news/2017/06/there-are-millions-protein-factories-every-cell-surprise-they-re-not-all-same

Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane.
https://en.wikibooks.org/wiki/Cell_Biology/Print_version

Endoplasmic reticulum: Scientists image 'parking garage' helix structure in protein-making factory
https://www.sciencedaily.com/releases/2013/07/130718130617.htm

Theoretical biologists at Los Alamos National Laboratory have used a New Mexico supercomputer to aid an international research team in untangling another mystery related to ribosomes -- those enigmatic jumbles of molecules that are the protein factories of living cells.
https://phys.org/news/2010-12-scientists-ratchet-cellular-protein-factory.html

The molecular factory that translates the information from RNA to proteins is called the "ribosome"
https://phys.org/news/2014-08-key-worker-protein-synthesis-factory.html

Quality control in the endoplasmic reticulum protein factory
The endoplasmic reticulum (ER) is a factory where secretory proteins are manufactured, and where stringent quality-control systems ensure that only correctly folded proteins are sent to their final destinations. The changing needs of the ER factory are monitored by integrated signalling pathways that constantly adjust the levels of folding assistants.

The cell is a mind-bogglingly complex and intricate marvel of nano-technology.  Every one of the trillions of cells in your body is not “like” an automated nano-factory. It is an automated nano-factory.
https://uncommondescent.com/intelligent-design/pardon-me-if-i-am-not-impressed-dr-miller/

The self-synthesizing ribosome
As the cell's protein factory, the ribosome is the only natural machine that manufactures its own parts.
https://www.sciencedaily.com/releases/2020/05/200521102052.htm

Jens Nielsen: Engineering Cellular Metabolism  2016
Engineering a cell factory involves several rounds of the so-called ‘‘design-build-test’’ cycle, in which a certain metabolic design is implemented and improved through genetic engineering and thereafter tested.
https://sci-hub.ren/10.1016/j.cell.2016.02.004


BIOTOL The Molecular Fabric of Cells
https://3lib.net/book/2280229/06f5b1


José Manuel Otero: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory January 21, 2013
Saccharomyces cerevisiae is the most well-characterized eukaryote, the preferred microbial cell factory
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054144

Abiogenesis: The factory maker argument QEJ4DJ9


Syllogisms of the factory argument

The Factory maker Argument
1. Factories are the result of intelligent design
2. Biological cells are factories
3. Therefore, biological cells are designed. 

1. Blueprints and buildings made upon its instructions are always sourced back to an intelligent cause.
2. The instructional information stored in DNA directs the make of biological cells and organisms.
3. DNA, biological Cells and organisms are therefore most probably the result of intelligent design.

1. The implementation and construction of factory parks for specific goals depends always on planning, elaborating blueprints and codified specified instructions.
2. The make and development of cells which are literally self-replicating factories are due to blueprints, genetic instructions,  stored in DNA. 
3. All information storage devices, code languages, blueprints, information transmission systems, translation cyphers, with the purpose to make factories, are of intelligent origin. Biological cells are therefore the result of Intelligent design.

1. The more complex a machine, the more likely it was created rather than self-assembled.
2. Science is uncovering more and more levels of complexity in physical and biochemical systems.
3. Science is therefore leading to an increased likelihood that things are created rather than self-assembled.

1. Factories produce  products and artifacts based on pre-existing goals, utilizing complex machines and production lines  ( machine = an apparatus using or applying mechanical power and having several parts, each with a definite function and together performing a particular task) and such things require planning intelligence for setup
2. Cells are complex factories importing raw materials, transforming them into basic building blocks, machines that make machines, and in the end, products through complex, interconnected machines and machine complexes.
3. Cells require intelligent design

1. Blueprints, instructional information and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  
2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks. 
2. The Blueprint and instructional information stored in DNA and epigenetics, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

1. Blueprints, instructional information and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  
2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks. 
3. The Blueprint and instructional information stored in DNA and epigenetics, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

1. Manufacturing facilities operate by intelligent design.
2. The operating structure within cells is the same as a manufacturing facility.
3. Therefore, cells are intelligently designed.

1. Blueprints and codified instructions are required to make factories with specific goals
2. DNA is an information storage molecule which stores the blueprint, the genetic instructions for the development and function of living things.
3. All information storage devices, blueprints and factories known, are of intelligent origin.
4. Therefore, biological cells are the result of Intelligent design.

1. Factory portals - factory compartments - a library index and fully automated information classification systems, storage and retrieval programs - molecular computers - hardware ( DNA )- software, a language using signs and codes like the alphabet, an instructional blueprint - information retrieval - transmission - translation - signaling - the make of complex machines - taxis - transport highways - tagging programs - factory assembly lines - error check and repair systems - recycling methods - waste grinders and management  - power generating plants - power turbines - electric circuits - machines - robots - fully automated manufacturing production lines - transport carriers - turbines - transistors - computers - and factories are always set up by intelligent designers.
2. Science has discovered, that cells are literally chemical nano factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, neuron transistors, and computers.
3. Therefore, with extremely high probability, cell factory complexes containing all those things are the product of an intelligent designer.

1. Intelligent minds make factory plants full of machines with specific functions, set up for specific purposes. Each fabric can be full of robotic production lines where the product of one factory is handed over to the next for further processing until the end product is made. Each of the intermediate steps is essential. If any is mal or non-functioning, like energy supply, or supply of the raw materials, the factory as a whole ceases its production. 
2. Biological cells are a factory complex of interlinked high-tech fabrics, fully automated and self-replicating, hosting up to over 2 billion molecular fabrics like Ribosomes & chemical production lines, full of proteins that act like robots, each with a specific task, function or goal, and completing each other, the whole system has the purpose to survive and perpetuate life. At least 560 proteins and a fully setup metabolome and genome is required, and they are interdependent. If even one of these proteins were missing, life could not kick-start. For example, without helicase, DNA replication would not be possible, and life could not perpetuate. The probability, that such complex nano-factory plant could have emerged by unguided chemical reactions, no matter in what primordial environment, is beyond the chance of one to 10^150.000. The universe hosts about 10^80 atoms.  
3. Biological Cells are of unparalleled gigantic complexity and purposeful adaptive design, vastly more complex and sophisticated than any man-made factory plant. Self-replicating cells demonstrate, therefore extremely strong indicators that the deliberate action of a conscious intelligent designer was involved in creating living cells.

1. Intelligent minds produce large manufacturing plants composed of many interconnected factories, using advanced computers and robotic production lines to fulfil specific purposes. To construct them, Architects, engineers etc. purposefully plan, draw, project, design and elaborate buildings, or complex machines,  production lines, factories or interconnected factory complexes, based on the specific requirements, and elaborate the necessary blueprints. Computer software programs ( ex.autocad ) is used to draw the blueprints, which are saved in the HD of the computer. Not rarely, thousands of blueprints are required, to specify the individual parts, and others describe the higher order of the object(s), and instruction manuals about how to assemble the individual parts in the right sequence and order to a functional complex device of various well-matched, interacting parts. All the blueprints must be stored in folders, which are tagged, for easy retrieval. Once the blueprints are made, they can be sent for example by email to the country where the object(s) of the blueprint is manufactured. Some places may be located in other countries, where other languages are spoken, and also the writing system is different. In order for the factory workers to be able to decipher the blueprints, translation software is used to make the translation. Once done, the factory workers can read the blueprints in their own languages, and based on the specific instructions, make the artefacts.
2. Biological living cells resemble human-made factories but are vastly more complex. They ARE literally interconnected High-Tech factory complexes, hosting in case of human cells over 2 billion proteins which are, each of them, manufacturing devices by their own,  like ribosomes.  Other molecular machines - some are powerful and highly specific catalysts like uridine monophosphate, have enormous catalytic capacities and speed up processes “absolutely essential” in creating the building blocks of DNA and RNA which would take 78 million years, in milliseconds. Others are even faster, speeding up the process over 2 billion years. Cells have the purpose to reproduce, metabolize food, grow and develop, pass their genes to the next generation, adapt to the changing environment, and survive. The production flow of Cells resembles one of human-made factories. The gene regulatory network (dGRN's) is a pre-programmed information extraction system, like a library classification system, fully automated. It is a collection of molecular regulators that interact with each other and with other substances in the cell to orchestrate the expression of DNA.  dGRN's operate based on logic gates and their networks process chemical input signals similar to computers. These encoded instructions are based on boolean logic. DNA stores information based on a code system, and codified, complex, instructional information, with the same function as a blueprint. Cells use sophisticated information transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding & translation ( Ribosome ) systems. The Ribosome enzyme that translates a cell’s mRNA message into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To the further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction is “shocking” and reveals just how much of a stickler (insisting) the ribosome is about high-fidelity protein synthesis.  Interactions between molecules are not simply matters of matching electrons with protons.  Instead, large structural molecules form machines with moving parts.  These parts experience the same kinds of forces and motions that we experience at the macro level: stretching, bending, leverage, spring tension, ratcheting, rotation and translocation.  The same units of force and energy are appropriate for both – except at vastly different levels. To make proteins, and direct and insert them to the right place where they are needed, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps are required. Each step requires extremely complex molecular machines composed of numerous subunits and co-factors, which require to be made, the very own processing procedure which they perform, which makes its origin an irreducible catch22 problem: DNA makes RNA which makes proteins, which make DNA and RNA.
3. Cells components are part of a complex system that is useful only in the completion of that much larger system. If unguided processes would have to meet the challenge, since we need 560 proteins total to make a first living cell, we would have to repeat the shuffle 560 times, to get all proteins required for life. The probability would be therefore 560/10520.  We arrive at a probability far beyond of [size=13]1 in 10^100.000
  ( A proteome set with 239 proteins yields odds of approximately 1/10^119614 ) Basic building blocks and intermediate biosynthesis products do have no biochemical function on their own: Why would random occurrences produce these in the first place?  A discrete minimal size of each individual molecular machine, aka. proteins and holo-protein complexes made of multiple subunits and cofactors are necessary for these to be functional. Each protein and holo-protein requires a minimal size and complexity to be functional. And it has only function interdependently, and correct precise energy supply, and when interconnected with other molecules in the Cell. Irreducibility and interdependence cannot evolve but depend on intelligence with foreknowledge on how to build discrete parts with a distant goal. A minimal estimate of the proteins of a supposed theoretical last universal common ancestor would require to be composed of Replication/recombination/repair/modification, Transcription/regulation, Translation through the ribosome, RNA processing, Transport/membrane, Electron transport, and vastly complex Metabolic network performing anabolism and catabolism.  The origin of a library index and fully automated information classification, storage and retrieval program, complex, codified, specified, instructional information stored in the genome and epigenetic codes, the origin of the genetic Code itself, nearly optimal for allowing additional information within protein-coding sequences, more robust than 1 million alternative possible codes, over a dozen epigenetic codes, the origin of the information transmission system, that is the origin of the genetic code itself, encoding, transmission, decoding and translation, the origin of the genetic cypher/translation, from digital ( DNA / mRNA ) to analogue ( Protein ), the origin of the hardware, that is DNA, RNA, amino acids, and carbohydrates for fuel generation, the origin of the replication/duplication of the DNA, the origin of the signal recognition particle, and the origin of the tubulin Code for correct direction to the final destination of proteins, last not least, the origin of entire irreducible and interdependent biological Cell factory complexes cannot be explained by evolution since evolution depends on fully setup DNA replication. It is most plausible that biological Cell factory complexes are the product of a powerful and vastly intelligent designer who created life.
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Last edited by Otangelo on Thu Jun 09, 2022 10:56 am; edited 60 times in total

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Objections to the claim that Cells are factories

Objection:  Cells are Self-replicating, while human-made factories are not. 
Answer: This is a self-defeating argument because it is not taken into consideration, that self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories. 
The fact that cells self-replicate substantiates and reinforces the inference of intelligent design gigantically.

There are currently 593 proteins known to be required to assure high fidelity of human DNA replication and to prevent disease.
What a stunning revelation! Without these proteins operating in concert, our DNA would degenerate rapidly and completely within a matter of a few generations. The vital question...how did these proteins, required for DNA replication emerge in the first place. They are paramount to intelligent design. Performing seeming miracles with every cell division.

If man were able to make self-replicating, fully automated robotic factories using in-situ resources, that would be a game-changing technology for all of humanity. This is a monumental challenge. The number of processes involved and parts to build complex machinery is very large. We don't have any factory without human control or intervention.
That would be a smart factory and a huge leap forward from more traditional automation to a fully connected and flexible system - one that can use a constant stream of data from connected operations and production systems to learn and adapt to new demands as biological cells are.

And even if we eventually get there one day,  raw material inputs would still have to be managed by man. Cells have sophisticated gates in the membrane, which sort out what materials can be permitted to get in, and waste products out of the cell. They have even sophisticated machines on the membrane surface, like amazing molecular assembly lines called nonribosomal peptide synthetase, which are protein nanofactories. They detect, attract, and transform iron in the environment into siderophores, which is iron in form that can be mobilized, uptaken and imported into the cell to manufacture protein co-factors, Iron-sulfur cores used as the catalyzers of enzyme reactions in the core pocket of proteins.

Each factory would also need the means to replicate and copy the information storage device, the hard disk, equivalent to the DNA molecule, and the information content. That is staggeringly complex.

Self-replication had to emerge and be implemented first, which rises the unbridgeable problem that DNA replication is irreducibly complex : 

Evolution is not a capable driving force to make the dna replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.

In fact, the highest degree of manufacturing  performance, excellence, precision, energy efficiency, adaptability to external change, economy, refinement and intelligence of production automatization ( at a scale from 1 -100,  = 100 )  we find in proceedings adopted by  each cell,  analogous to a factory , and biosynthesis pathways and processes in biology.  A cell uses a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. 

And furthermore, there ARE actually man-made self-replicating factories : 
Von Neumann universal constructor
John von Neumann's Universal Constructor is a self-replicating machine in a cellular automata (CA) environment. It was designed in the 1940s, without the use of a computer. The fundamental details of the machine were published in von Neumann's book Theory of Self-Reproducing Automata, completed in 1966 by Arthur W. Burks after von Neumann's death.Von Neumann's goal was to specify an abstract machine which, when run, would replicate itself. In his design, the machine consists of three parts: a 'blueprint' for itself, a mechanism that can read any blueprint and construct the machine (sans blueprint) specified by that blueprint, and a 'copy machine' that can make copies of any blueprint. After the mechanism has been used to construct the machine specified by the blueprint, the copy machine is used to create a copy of that blueprint, and this copy is placed into the new machine, resulting in a faithful replication of the original machine.

============================================================================================================================================

Objection:  I don't believe you. Demonstrate your god, and I'll accept it as a POSSIBLE cause of DNA. Until then, no. Everything you've said amounts to "I've invented this magic guy who can do anything. He could be the answer to that!".
Response:  I do not have to demonstrate God. We do not need direct observed empirical evidence to infer design. Origins of reality cannot be explained through testing experiments of operational science, but one can extrapolate what we see today back to times that we cannot see today, and therefore these extrapolations cannot be confirmed via the empirical method.   It is enough that I provide the inference to the best explanation of causation of the natural. We have empirically observed facts and experience that intelligence can and does produce information storage devices like computer hard disks, software codes and languages, and specifying complex information, and instructional blueprints which serve to instruct to make complex machines, production lines and factories for purposeful goals, upon the specific, precise specification of the machines, production lines, factories, and interdependent and irreducible factory plants, and the whole manufacturing process in a correct sequential manner. 

In practice, we have just one competitor to intelligence, and that competing explanation can be knocked down with one straightforward and judicious blow. The spontaneous generation and self-assembly by trial and error by orderly aggregation and sequentially correct manner without the external direction of hardware/software, communication systems and factory parks has never been observed, and the probability of such assemblage by trial and error is far beyond anything that is within the realm of the possible and conceivable. We have never observed that unguided random events can produce the same, and no reason to believe they ever could. Probability calculations have shown that even to make a minimal protein set for a functional Cell is one in 10^150000 attempts. That is in the realm of the impossible.  

DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living things.
https://www.sciencedaily.com/terms/dna.htm

A Busy Factory
http://www.esalq.usp.br/lepse/imgs/conteudo_thumb/Cells-a-busy-factory.pdf

Are factories made by intelligent professionals or unguided unconscious random processes?
https://reasonandscience.catsboard.com/t2799-are-factories-made-by-intelligent-professionals-or-unguided-unconscious-random-processes




Atheist: "  I just believe in one God less than you. God only exists in the believers imagination and is based on blind faith.
Answer: " Engineers, Programmers, Machine designers are required to make blueprints of Factories, machines, and computers.
Information transmission systems are required to send the blueprints from the engineering department to the assembly sites of the factories.
Carpenters, electricians, masons, machinists etc. are required to construct machines, factories, assembly lines, robots etc. "
 
Atheist: " We don't know. We know that people do build factories, but there is no empirical proof that God created life. There were billions of years, enough time for trial and error."
Answer: Biological cells are veritable micro-miniaturized industrial park of various interlinked factories containing millions of exquisitely designed pieces of intricate molecular machinery. Biological Cells do not resemble factories, they ARE an industrial park of high-tech factories, working in conjunction. Is it a rational proposition to defend and advocate that computers, hardware, software, a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits could emerge randomly, by unguided, accidental events ? That is  the ONLY causal alternative, once intelligent planning, invention, design, and implementation are excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories.

Atheist: " We don't know. We know that people do build factories, but there is no empirical proof that God created life. There were billions of years, enough time for trial and error."
Answer: 
The Cell is  a Factory
https://reasonandscience.catsboard.com/t2245-the-cell-is-a-factory

The central dogma of intelligent design
https://reasonandscience.catsboard.com/t2714-the-central-dogma-of-intelligent-design

Book Excerpt: A Factory That Builds Factories That Build Factories That…
https://evolutionnews.org/2020/05/book-excerpt-a-factory-that-builds-factories-that-build-factories-that/?fbclid=IwAR2atWrgS-MzfAtV_bRX3HkI6O7MN9ZcOZNmJuEZ5Gn-BA8fVWP9h-bJy-o

“The Activity of a Cell Is Like That of a Factory”
“At the cellular level, biology concerns the operation of the cell in its pursuit of life, not simply the molecular infrastructure that forms the physiochemical underpinnings of life. The activity of a cell is like that of a factory, where machines manufacture products, energy is consumed, information is stored, information is processed, decisions are made, and signals are sent to maintain proper factory organization and operation.12 Once a factory exceeds a very small number of interconnected components, coordinating its operations goes beyond a commonsense, nonmathematical approach. Cells have massive numbers of interconnected components.” [Emphasis added.]
https://evolutionnews.org/2020/05/the-activity-of-a-cell-is-like-that-of-a-factory/?fbclid=IwAR2xLG_NGjSFmkRa-fVPt7hQ53s93pN-JazYOFa2fU2j1bmkHkSfvncWKGM

More about the physiology of the human cell
In order to function properly, each cell in our body has very specific raw materials requirements. These nutrient raw materials enable each cell to perform its specific metabolic task. As a result of healthy and normal metabolism, each cell produces beneficial products, and each cell also produces waste products that are detrimental and toxic to the host cell.
These toxic waste products must be identified, neutralized, and eliminated on a regular basis or the host cell will get sick, degenerate, and die. If the cell replicates (divides or gives birth to offspring cells) in a condition of unresolved toxicity, or unrepaired damage, or if it is weak, sick, or diseased, it will pass on these irregularities to the offspring cells. This situation can lead to the continuous replication of abnormal or irregular cells within tissues and organs of the body.
Vigilant quality control - in the form of conscientious monitoring of the incoming raw materials and the outgoing products and waste products of our little cellular factories - is one of the keys to health. 
The cells of our body are constantly sending messages to the cells of our brain to make sure the brain is aware of how all factories are doing. Think of the brain as the inspector general for all those trillion plus factories. Are we listening? Are we in communication with the inspector general in our own body/brain/mind? How do we respond to the various calls we get on a daily basis from the cells to the inspector general? How are we communicating with our own internal cellular communication system?
http://www.healthyfutures.net/ADD-Plus/products/betternutrition/factory.php

https://www.youtube.com/watch?v=zm-3kovWpNQ

06:38
now this next picture is showing you a more realistic bigger protein molecule most protein molecules are bigger than the one I just showed you they often look something like this and now I want to switch from talking about the folding problem per se to talking about mechanisms and functions and the case I want to make for you is that proteins are machines you have 20,000 different types of machines in your body and then other kinds of living organisms have other kinds of protein machines there's tens of thousands to hundreds of thousands of different machines and the first case I want to make for you is that these are real machines that's not a metaphor they use energy they spin around they pump they act to cause force and motion

It is now clear that most functions in the cell are not carried out by single protein enzymes, colliding randomly within the cellular jungle, but by macromolecular complexes containing multiple subunits with specific functions (Alberts 1998). Many of these complexes are described as “molecular machines.” Indeed, this designation captures many of the aspects characterizing these biological complexes: modularity, complexity, cyclic function, and, in most cases, the consumption of energy. Examples of such molecular machines are the replisome, the transcriptional machinery, the spliceosome, and the ribosome.

Claim:  The natural is known and the supernatural is not so natural explanations are the appropriate null
Answer:  
1. It is known that complex machines and factories are intelligently designed
2. Biological cells are factories full of complex machines
3. Biological cells are intelligently designed...

Objection:  Cells are Self-replicating, while human-made factories are not. 
Answer: This is a self-defeating argument, because it is not taken into consideration, that self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories. 

Self-replication had to emerge and be implemented first, which rises the unbridgeable problem that DNA replication is irreducibly complex : 

DNA replication, and its mind boggling nano technology  that defies naturalistic explanations
http://reasonandscience..catsboard.com/t1849-dna-replication-of-prokaryotes
Evolution is not a capable driving force to make the dna replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.

Infact, the highest degree of manufacturing  performance, excellence, precision, energy efficiency, adaptability to external change, economy, refinement and intelligence of production automatization ( at a scale from 1 -100,  = 100 )  we find in proceedings adopted by  each cell,  analogous to a factory , and biosynthesis pathways and processes in biology.  A cell uses a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. 
http://reasonandscience..catsboard.com/t1987-information-biosynthesis-analogy-with-human-programming-engeneering-and-factory-robotic-assembly-lines

And furthemore, ther ARE actually man-made selfreplicating factories : 
Von Neumann universal constructor
John von Neumann's Universal Constructor is a self-replicating machine in a cellular automata (CA) environment. It was designed in the 1940s, without the use of a computer. The fundamental details of the machine were published in von Neumann's book Theory of Self-Reproducing Automata, completed in 1966 by Arthur W. Burks after von Neumann's death.Von Neumann's goal was to specify an abstract machine which, when run, would replicate itself. In his design, the machine consists of three parts: a 'blueprint' for itself, a mechanism that can read any blueprint and construct the machine (sans blueprint) specified by that blueprint, and a 'copy machine' that can make copies of any blueprint. After the mechanism has been used to construct the machine specified by the blueprint, the copy machine is used to create a copy of that blueprint, and this copy is placed into the new machine, resulting in a faithful replication of the original machine.
https://en.wikipedia.org/wiki/Von_Neumann_universal_constructor

Objection: DNA isn't a code
Answer: true, it STORES the genetic code. its the hardware, compared to a HD. DNA stores literally coded information

https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information

Paul Davies, Origin of Life, page 18
Biological complexity is instructed complexity or, to use modern parlance, it is information-based complexity. Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being. Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being.  The message isn't written in ink or type, but in atoms, strung together in an elaborately arranged sequence to form DNA, short for deoxyribonucleic acid. It is the most extraordinary molecule on Earth.

Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint, or more accurately an algorithm or instruction manual, for building a living, breathing, thinking human being. We share this magic molecule with almost all other life forms on Earth. From fungi to flies, from bacteria to bears, organisms are sculpted according to their respective DNA instructions. Each individual's DNA differs from others in their species (with the exception of identical twins), and differs even more from that of other species. But the essential structure – the chemical make-up, the double helix architecture – is universal.

Feature The digital code of DNA
The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: its digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes. The discovery of the double helix in 1953 immediately raised questions about how biological information isencoded in DNA. A remarkable feature of the structure is that DNA can accommodate almost any sequence of base pairs — any combination of the bases adenine (A), cytosine (C), guanine (G) and thymine (T) — and, hence any digital message or information. During the following decade it was discovered that each gene encodes a complementary RNA transcript, called messenger RNA (mRNA), made up of A, C, G and uracil (U), instead of T. The four bases of the DNA and RNA alphabets are related to the 20 amino acids of the protein alphabet by a triplet code — each three letters (or ‘codons’) in a gene encodes one amino acid. For example, AGT encodes the amino acid serine. The dictionary of DNA letters that make up the amino acids is called the genetic code. There are 64 different triplets or codons, 61 of which encode an amino acid (different triplets can encode the same amino acid), and three of which are used for ‘punctuation’ in that they signal the termination of the growing protein chain. The molecular complementary of the double helix — whereby each base on one strand of DNA pairs with its complementary base on the partner strand (A with T, and C with G) — has profound implications for biology. As implied by James Watson and Francis Crick in their landmark paper, base pairing suggests a template copying mechanism that accounts for the fidelity in copying of genetic material during DNA replication . It also underpins the synthesis of mRNA from the DNA template, as well as processes of repairing damaged DNA.
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html

DNA Is Multibillion-Year-Old Software
Nature invented (sic) software billions of years before we did. “The origin of life is really the origin of software,” says Gregory Chaitin. Life requires what software does (it’s foundationally algorithmic).
1. “DNA is multibillion-year-old software,” says Chaitin (inventor of mathematical metabiology). We’re surrounded by software, but couldn’t see it until we had suitable thinking tools.
2. Alan Turing described modern software in 1936, inspiring John Von Neumann to connect software to biology. Before DNA was understood, Von Neumann saw that self-reproducing automata needed software. We now know DNA stores information; it's a biochemical version of Turning’s software tape, but more generally: All that lives must process information. Biology's basic building blocks are processes that make decisions.
http://bigthink.com/errors-we-live-by/dna-is-multibillion-year-old-software


Objection: Cells aren't factories, but it's helpful for students to understand. cells are not factories, and the analogy fails.
Answer: Cells are MORE than just ONE factory. Biological cells are like an industrial park of various interconnected factories, working in conjunction. Factory is from Latin, and means fabricare, or make. Produce, manufacture. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex molecular machine processing, computing etc.
Therefore, they had most probably a mind as a causal agency.
The claim is falsified and topped, once someone can demonstrate a factory that can self-assemble, without the requirement of intelligence.

Factory is from latin, and means fabricare, or make. Produce, manufacture. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex machine processing, computing etc. They produce all organelles, proteins, membranes, parts, they make a copy of themselves. Self-replication is a marvel of engineering. the most advanced method of manufacturing. And fully automated. No external help required. If we could make factories like that, we would be able to create a society where machines do all the work for us, and we would have time only to entertain us, no work, nor money needed anymore..... And if factories could evolve to produce subsequently better, more adapted products, that would add even further complexity, and point to even more requirement of pre- programming to get the feat done.

Fine Tuning our Cellular Factories: Sirtuins in Mitochondrial Biology
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111451/

Cells As Molecular Factories
Eukaryotic cells are molecular factories in two senses: cells produce molecules and cells are made up of molecules.
http://serendip.brynmawr.edu/exchange/bioactivities/cellmolecular

Michael Denton: Evolution: A Theory In Crisis:
The cell is a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world.

Ribosome: Lessons of a molecular factory construction
https://link.springer.com/article/10.1134/S0026893314040116

Visualization of the active expression site locus by tagging with green fluorescent protein shows that it is specifically located at this unique pol I transcriptional factory.
http://www.nature.com/nature/journal/v414/n6865/full/414759a.html

There are millions of protein factories in every cell. Surprise, they’re not all the same
http://www.sciencemag.org/news/2017/06/there-are-millions-protein-factories-every-cell-surprise-they-re-not-all-same

Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane.
https://en.wikibooks.org/wiki/Cell_Biology/Print_version

Endoplasmic reticulum: Scientists image 'parking garage' helix structure in protein-making factory
https://www.sciencedaily.com/releases/2013/07/130718130617.htm

Theoretical biologists at Los Alamos National Laboratory have used a New Mexico supercomputer to aid an international research team in untangling another mystery related to ribosomes -- those enigmatic jumbles of molecules that are the protein factories of living cells.
https://phys.org/news/2010-12-scientists-ratchet-cellular-protein-factory.html

The molecular factory that translates the information from RNA to proteins is called the "ribosome"
https://phys.org/news/2014-08-key-worker-protein-synthesis-factory.html

Quality control in the endoplasmic reticulum protein factory
The endoplasmic reticulum (ER) is a factory where secretory proteins are manufactured, and where stringent quality-control systems ensure that only correctly folded proteins are sent to their final destinations. The changing needs of the ER factory are monitored by integrated signalling pathways that constantly adjust the levels of folding assistants.
http://sci-hub.cc/10.1038/nature02262

The cell is a mind-bogglingly complex and intricate marvel of nano-technology.  Every one of the trillions of cells in your body is not “like” an automated nano-factory. It is an automated nano-factory.
https://uncommondescent.com/intelligent-design/pardon-me-if-i-am-not-impressed-dr-miller/


Objection: Mitochondria aren't power plants, but it's a useful metaphor.
Answer: Mitochondria are unusual organelles. They act as the power plants of the cell, are surrounded by two membranes, and have their own genome.
https://www.nature.com/scitable/topicpage/mitochondria-14053590

Mitochondria are the cell's powerplant due to their massive ATP generation.
https://www.sciencedirect.com/science/article/pii/S2468867317300238



Last edited by Otangelo on Wed Jun 23, 2021 10:15 am; edited 12 times in total

https://reasonandscience.catsboard.com

Otangelo


Admin

Biological Cell factories point overwhelmingly to set up by intelligent design

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7761

- factory building that protects the factory from the weather and hostile external environment ( cell membranes)
factory portals with fully automated security checkpoints and control ( membrane proteins )
factory compartments ( organelles )
a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
molecular computers, hardware ( DNA )
software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
information retrieval ( RNA polymerase )
transmission ( messenger RNA )
translation ( Ribosome )
signaling ( hormones )
complex machines ( proteins )
taxis ( dynein, kinesin, transport vesicles )
molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
recycling methods ( endocytic recycling )
waste grinders and management  ( Proteasome Garbage Grinders )  
power generating plants ( mitochondria )
power turbines ( ATP synthase )
electric circuits ( the metabolic network )

1. Factory portals - factory compartments - a library index and fully automated information classification systems, storage and retrieval programs - molecular computers - hardware ( DNA )- software, a language using signs and codes like the alphabet, an instructional blueprint - information retrieval - transmission - translation - signaling - the make of complex machines - taxis - transport highways - tagging programs - factory assembly lines - error check and repair systems - recycling methods - waste grinders and management  - power generating plants - power turbines - electric circuits - machines - robots - fully automated manufacturing production lines - transport carriers - turbines - transistors - computers - and factories are always set up by intelligent designers.
2. Science has discovered, that cells are literally chemical nano factories, that operate based on molecular machines, protein robots, kinesin protein carriers, autonomous self-regulated production lines, generate energy through turbines, neuron transistors, and computers.
3. Therefore, with extremely high probability, cell factory complexes containing all those things are the product of an intelligent designer.

Engineering requires an engineer. An artificial cell or minimal cell is an engineered particle that mimics one or many functions of a biological cell. Mimicking a living cell requires engineers. 1
Architecture requires an architect.  Biological Cells demonstrate a complex architectural structure like a factory complex in a building  2
Orchestration requires a director. Gene regulatory networks orchestrate the expression of genes 3
Organization requires an organizer. Cells are organized into tissues, which are organized into organs, which are organized into organ systems 4
Programming languages are always set up by programmersGenes together form the master DNA program 5
Translation programs are always set up by translation programmers. 64 Codons of the genetic code are assigned to 20 amino acids during translation in the Ribosome.  6
Communication systems require network engineers. Cells give and receive messages with its environment and with itself. 7
Electrical networks require electrical engineers. Biological cells contain bioelectric circuits 8
Logistics require a logistic specialist. The cytoskeleton and microtubules serve as tracks for motor protein-based intracellular transport 9
Modular organization requires a modular project manager. Proteins and protein complexes organize intracellular interactions into networks of modules 10
Setting up recycling systems require a recycling technician. Cells sort out usable proteins for recycling 11
Setting up power plants requires systems engineers of power plants. Mitochondria are unusual organelles. They act as the power plants of the cell 12
Nanoscale technology requires nano processes, development engineers Living systems use biological nanomotors to build life’s essential molecules—such as DNA and proteins 13
Product planning and control require a production control coordinator. Eukaryotic cells have intricate regulatory control over the production of proteins and their RNA intermediates. 14
Product Quantity and Variant Flexibility control require product management engineers. Cells are extremely good at making products with high robustness, flexibility, and efficiency. 15
Waste disposal and management require a waste logistics manager.   Cells use proteasomes as "garbage disposal," 16
Creating a language requires intelligence. Cells use a remarkable variety of languages and communication methods 17
Creating Instructional information requires intelligent specialistsSoluble cues, cell-cell contact-dependent signals coordinate, encode and transmit regulatory information to instruct single-cell behavior18
Coordination requires a coordinator Circadian clocks are cell-autonomous timing mechanisms that organize and coordinate cell functions in a 24-h periodicity.19
Setting up strategies requires a strategist.    Cells use strategies to minimize energy consumption, by employing a number of common metabolic pathways for a variety of intermediate products before the pathway splits into different final products.  20
Regulation requires a regulator.  Regulatory circuits responsible for the function of individual genes or gene sets are at the lowest regulatory level. Then, there are circuits underlying the functions of cells, tissues, organs, and entire organisms. Endocrine and nervous systems are the regulatory circuits of the highest hierarchical level. 21
Controlling requires intelligence that sets up and programs the automatic control functions. Various cell cycle regulators control the Cell Cycle. 22
Recruiting requires intelligence which instructs autonomous programs how to do it. Proteins are for example recruited to fix DNA lesions. 23
Interpretation and response require intelligence which creates an interpretation program.  Cells monitor, interpret and respond to internal and external cues. 24
Setting up switch mechanisms based on logic gates with on and off states require intelligent setup. DNA binding proteins work based on circuit principles and logic gates 25
Setting up transport highways requires  Transportation Development engineers. Microtubules can act as specific transport roads for the trafficking of signaling factors 26
Controlled factory implosion programming requires an Explosive Safety Specialist Apoptosis is a form of programmed cell death that occurs in multicellular organisms. 27

1. Does inventing computer programs and using them to store instructional assembly information require a programmer? Genes together form the master DNA program 
https://www.quantamagazine.org/how-the-dna-computer-program-makes-you-and-me-20180405/
2. Does inventing a translation program require someone with intelligence to invent and implement that program? 64 Codons of the genetic code are assigned to 20 amino acids during translation in the Ribosome.  
https://pubmed.ncbi.nlm.nih.gov/29870756/
3. Does inventing machines for specific purposes require engineers? Proteins are nano-machines, each one of them designed to perform a specific task.
https://www.nanowerk.com/nanotechnology-news/newsid=46811.php
4. Does invent and constructing factories for specific purposes require a team of specialized engineers? Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products.
https://www.sciencedirect.com/science/article/abs/pii/S0160932707000312
5. Does the implementation of electrical networks require electrical engineers ?  Biological cells contain bioelectric circuits 
https://www.ncbi.nlm.nih.gov/books/NBK549549/
6. Does setting up recycling systems require recycling system engineers? Cells sort out usable proteins for recycling 
https://phys.org/news/2020-01-cells-recycle-components.html
7. Does implementing engineered artifacts require engineers?  Engineering principles such as integral control and robustness were found to be implemented in biological cells. 
https://www.cell.com/cell-systems/pdf/S2405-4712(16)00009-0.pdf
8. Does the making of an Architecture project require architects?  Biological Cells demonstrate a complex architectural structure like a factory complex in a building  
https://www.nature.com/articles/nrm2460
9. Does orchestrate in order to configure, coordinate, and manage require a director?  Gene regulatory networks orchestrate the expression of genes 
https://www.nature.com/articles/nrm2428
10. Does organizing require an organizer? Cells are organized into tissues, which are organized into organs, which are organized into organ systems 
https://flexbooks.ck12.org/cbook/ck-12-biology-flexbook-2.0/section/2.10/primary/lesson/organization-of-cells-bio
11. Does create a language require intelligence? Cells use a remarkable variety of languages and communication methods 
http://jonlieffmd.com/blog/the-remarkable-language-of-cells
12. Does creating communication systems require network engineers?  Cells give and receive messages with its environment and with itself. 
[url= https://www.nature.com/scitable/topic/cell-communication-14122659/]https://www.nature.com/scitable/topic/cell-communication-14122659/[/url]
13. Does setting up systems that work in a coordinated fashion require intelligent engineers that set them up? Circadian clocks are cell-autonomous timing mechanisms that organize and coordinate cell functions in a 24-h periodicity.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057284/
14. Does setting up power plants require systems engineers of power plants? Mitochondria are unusual organelles. They act as the power plants of the cell 
https://www.nature.com/scitable/topicpage/mitochondria-14053590/
15. Does setting up strategies to reach specific goals require a strategist? Cells use strategies to minimize energy consumption, by employing a number of common metabolic pathways for a variety of intermediate products before the pathway splits into different final products.  
http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033

Genes together form the master DNA program.  Translation in the Ribosome depends on 64 Codons of the genetic code that are assigned to 20 amino acids. Amino acid strands form proteins which are nano-machines, each one of them designed to perform a specific task in the cell. Proteins are the working horses of the Cells, which are outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. Biological cells contain bioelectric circuits. Cells sort out usable proteins for recycling. Engineering principles such as integrated control and robustness were found to be implemented in biological cells. Biological Cells demonstrate a complex architectural structure like a factory complex in a building.
Gene regulatory networks orchestrate the expression of genes. Cells are organized into tissues, which are organized into organs, which are organized into organ systems. Cells use a remarkable variety of languages and communication methods. Cells give and receive messages with their environment and with themselves. Circadian clocks are cell-autonomous timing mechanisms that organize and coordinate cell functions in a 24-h periodicity. Mitochondria are unusual organelles. They act as the power plants of the cell. Cells use strategies to minimize energy consumption. 




Actions like engineering, architecting, orchestrating, organizing, programming, translating, setting up communication channels, electric networks, logistic networks, organizing modular systems, recycling systems, making power plants in nanoscale dimensions, product planning and control, establishing product quality and variant flexibility, setting up waste disposal and management systems, creating languages and instructional information, coordinating, setting up strategies, regulating, controlling, recruiting, interpreting and responding, setting up switch mechanisms based on logic gates, setting up transport highways and GPS systems, and controlled factory implosion, are ALWAYS and EXCLUSIVELY assigned to the action of intelligent agents. No exceptions

We can conclude, therefore, that biological systems, which cleverly perform all the demanding, multifaceted job activities described above, are most likely due to the set up of an intelligent designer(s). It is extraordinarily unlikely, statistically, and chemically, that blind fortune would be up to the task. Only a master player with foresight guided by superb chemical wisdom, putting all those systems together in a proper way is an explanation that makes sense.

1. https://en.wikipedia.org/wiki/Artificial_cell
2. https://www.nature.com/articles/nrm2460
3. https://www.nature.com/articles/nrm2428
4. https://flexbooks.ck12.org/cbook/ck-12-biology-flexbook-2.0/section/2.10/primary/lesson/organization-of-cells-bio
5. https://www.quantamagazine.org/how-the-dna-computer-program-makes-you-and-me-20180405/
6. https://pubmed.ncbi.nlm.nih.gov/29870756/
7. https://www.nature.com/scitable/topic/cell-communication-14122659/
8. https://www.ncbi.nlm.nih.gov/books/NBK549549/
9. https://sci-hub.tw/https://www.annualreviews.org/doi/full/10.1146/annurev-cellbio-100818-125149
10. https://www.pnas.org/content/100/3/1128
11. https://phys.org/news/2020-01-cells-recycle-components.html
12. https://www.nature.com/scitable/topicpage/mitochondria-14053590/
13. https://www.researchgate.net/profile/Viola_Vogel/publication/23154570_Harnessing_Biological_Motors_to_Engineer_Systems_for_Nanoscale_Transport_and_Assembly/links/551ab0590cf2bb754076cac6/Harnessing-Biological-Motors-to-Engineer-Systems-for-Nanoscale-Transport-and-Assembly.pdf
14. https://www.nature.com/scitable/topicpage/eukaryotic-cells-14023963/
15. https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=2060&context=lkcsb_research
16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3524306/
17. http://jonlieffmd.com/blog/the-remarkable-language-of-cells
18. https://advances.sciencemag.org/content/6/12/eaay5696
19. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057284/
20. http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033
21. http://www.bionet.nsc.ru/meeting/bgrs_proceedings/papers/1998/27/index.html
22. https://courses.lumenlearning.com/suny-biology1/chapter/control-of-the-cell-cycle/
23. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317637/
24. https://europepmc.org/article/med/27856508
25. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230274/
26. https://jcs.biologists.org/content/126/11/2319
27. https://en.wikipedia.org/wiki/Apoptosis

One of the silliest propositions is to claim that movement and change require no prime mover, beginning no cause, existence, no necessary eternally existent being, creation no creator, power, no powerful source, design, no designer, laws, no lawgiver, mathematics no mathematician, fine-tuning no fine-tuner, codes no coder, selection, no selector, translation no translator, logic, no logic source, consciousness, no conscious source, setting up prescriptive information, no agency with intent, will, foresight, and know-how, machine blueprints, no machine-designer, architecture, no architect, coordination no coordinator, recruiting no recruiter, regulation, no regulator, controlling, no controller, factories no factory-makers,   engineering no engineer, orchestration no director, organization no organizer, elaborating a strategy, no strategist, setting up programming languages no programmers,  translation programs no translators,  logistics no manager, creating a language no intelligence.

Do communication systems require network engineers? electrical networks electrical engineers? the modular organization modular project managers? Setting up recycling systems recycling technicians?  setting up power plants systems engineers of power plants?  nanoscale technology nano processes, development engineers?  product planning and control production control coordinators? product quantity and variant flexibility control, product management engineers?  waste disposal and management, managers? interpretation, and response, intelligence which creates an interpretation program? setting up switch mechanisms based on logic gates, intelligent setup?  setting up transport highways, transportation development engineers? controlled factory implosion, explosive safety specialist? Does setting up irreducibly complex systems require agency? Yes or no?

The origin of life depends on most things mentioned above. Does life require no creator of life? To create and instantiate the things above requires know-how, foresight, intention, and will. The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator, and that unguided, blind, random stochastic events can bring forward all these things.

Abiogenesis: The factory maker argument Image010



Last edited by Otangelo on Sun Jun 12, 2022 7:56 am; edited 14 times in total

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Otangelo


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Do biological cells host codes, machines, factories, power plants in a literal sense, or is it just an analogy? 

https://reasonandscience.catsboard.com/t2245-the-cell-is-a-factory#6003

Atheists are often totally unprepared and uneducated to debate or argue about molecular biology. A common objection forwarded by them is that: 

1. DNA is not a code
2. Cells are not factories in a literal sense
3. Mitochondria aren't power plants, they are just like power plants

above are all just analogies. The real situation however is that DNA is a true information carrier, like a hard disk, and stores a genetic information through a genetic code, and that code is a code in a literal sense, in the same manner as an alphabet, a morse code, or the notes of a partiture, or a binary computer code. Cells are not LIKE factories, but an industrial park of various interconnected factories, working in conjunction. And Mitochondria are the cell's powerplant due to their massive generation of ATP, the energy currency in the cell.  

The argumentation of atheists goes usually as follows: 

" You rely on analogies then claim the object of comparison in the analogy is the same as the object under discussion. DNA isn't a code, it's just helpful to describe it as such to high school kids. Cells aren't factories, but it's helpful for students to understand. Mitochondria aren't power plants, but it's a useful metaphor. Besides, as you've just said, intelligent design should be status quo "in your view". Great. That's your opinion. I have mine. But they're all the same, cause it's just our views ".

" Your reason for defining cells as factories is literally based in etymology, not the actual English definition of factories. Your comment on mitochondria is exactly what I said, the fact they are weird doesn't make the a power plant, that's a description of their function. I'm well aware of how DNA functions. Do the patterns matter yes, so do the patterns of ripples in sand dunes, they even contain information about how that dune was formed and the interactions of wind and water on the dune. Is that a code? Atoms bond in specific patterns due to the arrangement of electrons, and there's information in the specific energy structure of the atom, is that a code? "

Objection: DNA isn't a code
Answer: true, it STORES the genetic code. its the hardware, compared to a HD. DNA stores literally coded information

https://reasonandscience.catsboard.com/t1281-dna-stores-literally-coded-information

Paul Davies, Origin of Life, page 18
Biological complexity is instructed complexity or, to use modern parlance, it is information-based complexity. Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being. Inside each and every one of us lies a message. It is inscribed in an ancient code, its beginnings lost in the mists of time. Decrypted, the message contains instructions on how to make a human being.  The message isn't written in ink or type, but in atoms, strung together in an elaborately arranged sequence to form DNA, short for deoxyribonucleic acid. It is the most extraordinary molecule on Earth.

Although DNA is a material structure, it is pregnant with meaning. The arrangement of the atoms along the helical strands of your DNA determines how you look and even, to a certain extent, how you feel and behave. DNA is nothing less than a blueprint, or more accurately an algorithm or instruction manual, for building a living, breathing, thinking human being. We share this magic molecule with almost all other life forms on Earth. From fungi to flies, from bacteria to bears, organisms are sculpted according to their respective DNA instructions. Each individual's DNA differs from others in their species (with the exception of identical twins), and differs even more from that of other species. But the essential structure – the chemical make-up, the double helix architecture – is universal.

Feature The digital code of DNA
The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: its digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes. The discovery of the double helix in 1953 immediately raised questions about how biological information isencoded in DNA. A remarkable feature of the structure is that DNA can accommodate almost any sequence of base pairs — any combination of the bases adenine (A), cytosine (C), guanine (G) and thymine (T) — and, hence any digital message or information. During the following decade it was discovered that each gene encodes a complementary RNA transcript, called messenger RNA (mRNA), made up of A, C, G and uracil (U), instead of T. The four bases of the DNA and RNA alphabets are related to the 20 amino acids of the protein alphabet by a triplet code — each three letters (or ‘codons’) in a gene encodes one amino acid. For example, AGT encodes the amino acid serine. The dictionary of DNA letters that make up the amino acids is called the genetic code. There are 64 different triplets or codons, 61 of which encode an amino acid (different triplets can encode the same amino acid), and three of which are used for ‘punctuation’ in that they signal the termination of the growing protein chain. The molecular complementary of the double helix — whereby each base on one strand of DNA pairs with its complementary base on the partner strand (A with T, and C with G) — has profound implications for biology. As implied by James Watson and Francis Crick in their landmark paper, base pairing suggests a template copying mechanism that accounts for the fidelity in copying of genetic material during DNA replication . It also underpins the synthesis of mRNA from the DNA template, as well as processes of repairing damaged DNA.
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html

DNA Is Multibillion-Year-Old Software
Nature invented (sic) software billions of years before we did. “The origin of life is really the origin of software,” says Gregory Chaitin. Life requires what software does (it’s foundationally algorithmic).
1. “DNA is multibillion-year-old software,” says Chaitin (inventor of mathematical metabiology). We’re surrounded by software, but couldn’t see it until we had suitable thinking tools.
2. Alan Turing described modern software in 1936, inspiring John Von Neumann to connect software to biology. Before DNA was understood, Von Neumann saw that self-reproducing automata needed software. We now know DNA stores information; it's a biochemical version of Turning’s software tape, but more generally: All that lives must process information. Biology's basic building blocks are processes that make decisions.
http://bigthink.com/errors-we-live-by/dna-is-multibillion-year-old-software


Objection: Cells aren't factories, but it's helpful for students to understand. cells are not factories, and the analogy fails.
Answer: Cells are MORE than just ONE factory. Biological cells are like an industrial park of various interconnected factories, working in conjunction. Factory is from Latin, and means fabricare, or make. Produce, manufacture. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex molecular machine processing, computing etc.
Therefore, they had most probably a mind as a causal agency.
The claim is falsified and topped, once someone can demonstrate a factory that can self-assemble, without the requirement of intelligence.

Factory is from latin, and means fabricare, or make. Produce, manufacture. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex machine processing, computing etc. They produce all organelles, proteins, membranes, parts, they make a copy of themselves. Self-replication is a marvel of engineering. the most advanced method of manufacturing. And fully automated. No external help required. If we could make factories like that, we would be able to create a society where machines do all the work for us, and we would have time only to entertain us, no work, nor money needed anymore..... And if factories could evolve to produce subsequently better, more adapted products, that would add even further complexity, and point to even more requirement of pre- programming to get the feat done.

Fine Tuning our Cellular Factories: Sirtuins in Mitochondrial Biology
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111451/

Cells As Molecular Factories
Eukaryotic cells are molecular factories in two senses: cells produce molecules and cells are made up of molecules.
http://serendip.brynmawr.edu/exchange/bioactivities/cellmolecular

Michael Denton: Evolution: A Theory In Crisis:
The cell is a veritable micro-miniaturized factory containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world.

Ribosome: Lessons of a molecular factory construction
https://link.springer.com/article/10.1134/S0026893314040116

Visualization of the active expression site locus by tagging with green fluorescent protein shows that it is specifically located at this unique pol I transcriptional factory.
http://www.nature.com/nature/journal/v414/n6865/full/414759a.html

There are millions of protein factories in every cell. Surprise, they’re not all the same
http://www.sciencemag.org/news/2017/06/there-are-millions-protein-factories-every-cell-surprise-they-re-not-all-same

Rough ER is also a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane.
https://en.wikibooks.org/wiki/Cell_Biology/Print_version

Endoplasmic reticulum: Scientists image 'parking garage' helix structure in protein-making factory
https://www.sciencedaily.com/releases/2013/07/130718130617.htm

Theoretical biologists at Los Alamos National Laboratory have used a New Mexico supercomputer to aid an international research team in untangling another mystery related to ribosomes -- those enigmatic jumbles of molecules that are the protein factories of living cells.
https://phys.org/news/2010-12-scientists-ratchet-cellular-protein-factory.html

The molecular factory that translates the information from RNA to proteins is called the "ribosome"
https://phys.org/news/2014-08-key-worker-protein-synthesis-factory.html

Quality control in the endoplasmic reticulum protein factory
The endoplasmic reticulum (ER) is a factory where secretory proteins are manufactured, and where stringent quality-control systems ensure that only correctly folded proteins are sent to their final destinations. The changing needs of the ER factory are monitored by integrated signalling pathways that constantly adjust the levels of folding assistants.
http://sci-hub.cc/10.1038/nature02262

The cell is a mind-bogglingly complex and intricate marvel of nano-technology.  Every one of the trillions of cells in your body is not “like” an automated nano-factory. It is an automated nano-factory.
https://uncommondescent.com/intelligent-design/pardon-me-if-i-am-not-impressed-dr-miller/


Objection: Mitochondria aren't power plants, but it's a useful metaphor.
Answer: Mitochondria are unusual organelles. They act as the power plants of the cell, are surrounded by two membranes, and have their own genome.
https://www.nature.com/scitable/topicpage/mitochondria-14053590

Mitochondria are the cell's powerplant due to their massive ATP generation.
https://www.sciencedirect.com/science/article/pii/S2468867317300238

Abiogenesis is impossible. Science moves forward recognizing this more and more

No scientific experiment has been able to come even close to synthesize the basic building blocks of life, and reproduce
self-replicating Cell in the Laboratory through self-assembly and autonomous organization

Observation: 
The origin of life depends on biological cells, which perpetuate life upon the complex action of 

- factory building that protects the factory from the weather and hostile external environment ( cell membranes)
- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA )
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome )
- signalling ( hormones )
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
- recycling methods ( endocytic recycling )
- waste grinders and management  ( Proteasome Garbage Grinders ) 
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )

Biological cells are a veritable micro-miniaturized industrial park full of interlinked and interdependent factories containing millions of exquisitely designed
pieces of intricate molecular machinery. Biological  Cells do not resemble factory parks, they ARE an industrial park of various interconnected factories, working in conjunction.

Hypothesis (Prediction):
Complex machines and interconnected factory parks are intelligently designed. Biological cells are intelligently designed. Factories can not self-assemble spontaneously
by orderly aggregation and sequentially correct manner without external direction. The claim can be falsified, once someone can demonstrate that factories
can self-assemble spontaneously by orderly aggregation and sequentially correct manner without external direction.

Experiment: 
Since origin of life experiments began, nobody was able to bring up an experiment, replicating the origin of life by natural means.

Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance:
" The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of
the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique
events are not conducive to scientific study.

A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the
multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have
coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were
not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives
for the origin of life. " Scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a
conscious creative agency. The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life…
is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview
of who wants naturalism to be true.

Conclusion: 
Upon the logic of mutual exclusion,  design and non-design are mutually exclusive (it was one or the other) so we can use eliminative logic: if non-design is highly
improbable, then design is highly probable. The evaluative status of non-design (and thus design) can be decreased or increased by observable empirical evidence, so
a theory of design is empirically responsive and is testable, so, by applying  Bayesian probability, we can conclude that Life is most probably intelligently designed.

Abiogenesis: The factory maker argument N1rcruX

" The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 252
The origin of life is one of the hardest problems in all of science, but it is also one of the most important. Origin-of-life research has evolved into a lively, interdisciplinary field, but other scientists often view it with skepticism and even derision. This attitude is understandable and, in a sense, perhaps justified, given the “dirty,” rarely mentioned secret: Despite many interesting results to its credit, when judged by the straightforward criterion of reaching (or even approaching) the ultimate
goal, the origin of life field is a failure—we still do not have even a plausible coherent model, let alone a validated scenario, for the emergence of life on Earth. Certainly, this is due not to a lack of experimental and theoretical effort, but to the extraordinary intrinsic difficulty and complexity of the problem. A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle.

Which of the following is better explained by design, rather than non-design?

Probability theory is the logic of science, dingdong. You do not need to prove everything absolutely for it to make sense within reason. What you need is a tendency for it to
be true statistically. That means evidence of it working repeatedly with low error.

Design can be tested using scientific logic.  How? Upon the logic of mutual exclusion, design and non-design are mutually exclusive (it was one or the other) so
we can use eliminative logic: if non-design is highly improbable, then design is highly probable.  Thus, evidence against non-design (against production of a feature by
undirected natural process) is evidence for design.  And vice versa. The evaluative status of non-design (and thus design) can be decreased or increased by observable
empirical evidence, so a theory of design is empirically responsive and is testable.

Upon applying above logic, how is the following better explained, by design, or non-design ?

- Components of a complex system that are only useful in the completion of a much larger system and their orderly aggregation in a sequentially correct manner.
- Intermediate sub-products which have by its own no use of any sort unless they are correctly assembled in a larger system.  
- Instructional complex information which is required for to make these sub-products and parts,  to mount them correctly in the right order and at the right place, and interconnected correctly in a larger system.  
- The making of computer hardware, and highly efficient information storage devices.
- Creating software, based on a language using signs and codes like the alphabet, an instructional blueprint.
- Information retrieval, transmission, signalling, and translation
- The make of machine parts with highly specific structures, which permit to form the aggregation into complex machines, production line complexes, autonomous robots with error check functions and repair mechanisms, electronic circuit - like networks, energy production factories, power generating plants, energy turbines, recycle mechanisms and methods, waste grinders and management, organized waste disposal mechanisms, and self distruction when needed to reach a higher end, and veritable micro-miniaturized factories where all before-metioned systems and parts are required in order for that factory to be self- replicating, and being functional.
- Establishment of advanced communication systems. Signal relay stations. Signal without recognition is meaningless.  Communication implies a signaling convention (a “coming together” or agreement in advance) that a given signal means or represents something: e.g., that S-O-S means “Send Help!”   A transmitter and receiver system made of physical materials, with a functional purpose, performing an algorithm that is not itself a product of the materials or the blind forces acting on them, acting as information processing system ( the interaction of a software program and the hardware )
- Selecting the most optimal and efficient code information system and ability to minimize the effects of errors.
- A system which uses a cipher, translating instructions through one language,  which contains Statistics, Syntax, Semantics, Pragmatics, and Apobetics, and assign the code of one system to the code of another system.
- The make of complicated, fast high-performance production systems,  and technology with high robustness, flexibility, efficiency, and responsiveness, and quality-management techniques.
- The setup of 1,000–1,500 manufacturing proceedings in parallel by a series of operations and flow connections to reach a common end-goal, the most complex industry-like production networks known.
- The implementation of a product making system,  only in response to actual demand, not in anticipation of forecast demand, thus preventing overproduction.
- Creating machines, production lines and factories that are more complex than man-made things of the sort.
- The organization of software exhibiting logical functional layers - regulatory mechanisms -  and control networks and systems.
- Error check and detection,  inspection processes, quality assurance procedures, information error proofreading and repair mechanisms.
- Foolproofing, applying the key-lock principle to guarantee a proper fit between product and machine.
- Complex production lines which depend on precise optimization and fine-tuning.
- Create complex systems which are able to adapt to variating conditions.

Self-replication with variation is what makes the accumulation of complexity possible - but self-replication had to emerge first


Objection:  Cells are Self-replicating, while human-made factories are not. 
Answer: This is a self-defeating argument because it is not taken into consideration, that self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories. 

Self-replication had to emerge and be implemented first, which raises the unbridgeable problem that DNA replication is irreducibly complex : 

The machinery for DNA replication is irreducibly complex
In prokaryotic cells, DNA replication involves more than thirty specialized proteins to perform tasks necessary for building and accurately copying the genetic molecule.
Each of these proteins is essential and required for the proper replicating process. Not a single one of these proteins can be missing, otherwise, the whole process breaks down, and is unable to perform its task correctly. DNA repair mechanisms must also be in place,  fully functional and working properly, otherwise, the mutation rate will be too high, and the cell dies. 18
The individual parts and proteins require by themselves complex assembly proteins to be built.
The individual parts, assembly proteins, and proteins individually would have no function on their own. They have only function interconnected in the working whole. 
The individual parts must be readily available on the construction site of the RNA replication complex, being correctly interlocked, interlinked, and have the right interface compatibility to be able to interact correctly together. All this requires information and meta information ( information that directs the expression of the genomic information for construction of the individual proteins, and correct timing of expression, and as well the information of the correct assembly sequence. )
Evolution is not a capable driving force to make the DNA replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.
DNA replication requires coded, complex, specified information and meta-information, and the DNA replication process is irreducibly complex.
Therefore, DNA replication is best explained through design. 

In fact, the highest degree of manufacturing  performance, excellence, precision, energy efficiency, adaptability to external change, economy, refinement and intelligence of production automatization ( at a scale from 1 -100,  = 100 )  we find in proceedings adopted by  each cell,  analogous to a factory , and biosynthesis pathways and processes in biology.  A cell uses a complex web of metabolic pathways, each composed of chains of chemical reactions in which the product of one enzyme becomes the substrate of the next. In this maze of pathways, there are many branch points where different enzymes compete for the same substrate. The system is so complex that elaborate controls are required to regulate when and how rapidly each reaction occurs. Like a factory production line, each enzyme catalyzes a specific reaction, using the product of the upstream enzyme, and passing the result to the downstream enzyme. 

And furthermore, there ARE actually man-made self-replicating factories : 
Von Neumann universal constructor
John von Neumann's Universal Constructor is a self-replicating machine in a cellular automata (CA) environment. It was designed in the 1940s, without the use of a computer. The fundamental details of the machine were published in von Neumann's book Theory of Self-Reproducing Automata, completed in 1966 by Arthur W. Burks after von Neumann's death.Von Neumann's goal was to specify an abstract machine which, when run, would replicate itself. In his design, the machine consists of three parts: a 'blueprint' for itself, a mechanism that can read any blueprint and construct the machine (sans blueprint) specified by that blueprint, and a 'copy machine' that can make copies of any blueprint. After the mechanism has been used to construct the machine specified by the blueprint, the copy machine is used to create a copy of that blueprint, and this copy is placed into the new machine, resulting in a faithful replication of the original machine.
https://en.wikipedia.org/wiki/Von_Neumann_universal_constructor

The Large Hadron Collider (LHC) VS Biological High-tech Fabrics

The Large Hadron Collider (LHC) is the world's largest machine in the world.

10 mind-blowing facts about the CERN Large Collider
https://www.rt.com/op-ed/313922-cern-collider-hadron-higgs/amp/

It took over 10,000 scientists and hundreds of universities to build it. The size of the LHC constitutes an exceptional engineering challenge. If you never heard about the LHC, but someone would approach and show it to you, describe its complexity, and ask: How do you think, was the LHC most probably made? And you had two options to chose from:

1. Given enough time, billions of years of random shuffling and luck, it might self-assemble by an unexpected accident
2. It's evident, it was made by intelligence.

Which of the two options would you choose?

The origin of life depends on biological cells. They are a veritable miniaturized high-tech park of interlinked and interdependent, fully automated pre-programmed self-replicating factories, containing millions, in case of human cells, each individual cell over two billion of exquisitely designed pieces of intricate molecular machinery working in a conjoined and coordinated fashion together. They form a hierarchically formed structure, where one compartment, a central hub, manufactures the essential basic building blocks, and ATP energy. The machines on the lowest level must perform their functions in the correct manner, in order to make the end - higher goal and function viable. In order to economize, cells have decision-making checkpoints in order to economize, where basic building blocks are either recycled through catabolism or newly generated in anabolic networks.

There is an interdependence between the lowest level and the top level. If one of the lower level functions or availability of building blocks is missing or the manufacturing machinery does not work properly, global mal-function, disease, is the consequence or no function at all and cell death. Many individual machines are essential, and if one, like topoisomerase II or helicase proteins is missing, no DNA replication - no life perpetuation. Cells are gigantic irreducible complex constructs. Some of the protein machines are veritable molecular computers, with elaborated control regulation systems, allosteric feedback inhibition mechanisms, substrate concentration sensing, on and off state instructions etc.

Another enzyme, OMP decarboxylase, is an extraordinarily efficient catalyst capable of accelerating the uncatalyzed reaction rate by an impressive factor of 10^17. To put this in perspective, a reaction that would take 78 million years in its absence takes 18 milliseconds when it is enzyme catalyzed. If that enzyme were not existent, the pyrimidine synthesis pathway would not be complete, and cytosine, uracil and thymine nucleotides, essential for life, could not be made, and DNA base-pairing would not be possible, and so, no molecular hard disk for information storage and RNA messaging.

Cells do not resemble a factory park. Each Cell IS a High-tech fabric complex with an overarching goal to develop, self-replicate, adapt to the environment, get food, produce energy, and perpetuate life. They do also fully autonomously regulate, govern, control, orchestrate all relevant molecular processes, they do recognize manufacturing errors along and during all manufacturing and assembly line production processes. They have a complex network of regulatory proteins that trigger the different events of the Cell Cycle. There are 20 essential checkpoints; they have inbuilt circadian rhythms, pre-programmed clocks which determine when certain processes have to be turned on or off. Cells are preprogrammed to coordinate their growth and get the exact right cell size.

Cells do error repair, adapt to the environment and food sources, regenerate, and reproduce.  The action of multicellular organisms adds enormously in complexity. For example, in the case of the human body, 3,7 trillion cells need to be specified in their specific function, position and place in the body, interconnected, communicate together, adhere one to each other precisely with cell-cell adhesion molecules, self-destruct and self-implode at the right moment etc.

Each single cell needs:

- factory building that protects the factory from the weather and hostile external environment ( cell membranes)
- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA )
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome )
- signalling ( hormones )
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
- recycling methods ( endocytic recycling )
- waste grinders and management  ( Proteasome Garbage Grinders )  
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )

If I asked you the same as in regards to the LHC. What would you answer to the question, how cells most probably emerged?

1. I don't know, but given enough time, billions of years of random shuffling and luck, it might self-assemble by an unexpected accident
2. It's evident, it was made by intelligence.

In case you did opt for the first option, 1:

Why would you say in regards to the LHC: It's evident, it was made by intelligence. But in regards of biological cells which are far more complex, they do not resemble factory parks, they ARE a High-tech park of various factories, working in conjunction:  " I don't know how they most probably came to be"?

The Cell is  a Factory
https://reasonandscience.catsboard.com/t2245-the-cell-is-a-factory

Abiogenesis: The factory maker argument 0waymit

Are factories made by intelligent professionals, or unguided unconscious random processes ? 

https://reasonandscience.catsboard.com/t2799-are-factories-made-by-intelligent-professionals-or-unguided-unconscious-random-processes

Do we need to see architects, engineers, programmers, coordinators, instructors, managers, specialists, regulators, fine-tuners, interpreters etc. in action, building factories,  to conclude a factory was made by intelligent professionals? Or can we conclude design and intelligent setup as the best explanation when we see a factory in operation?

Engineering requires an engineer
Architecture requires an architect
An orchestra requires a Director
Organization requires an organizer
Setting up a programming language requires a programmer
Setting up Information selection programs require Search and Selection Programming engineers
Setting up translation programs requires translation programmers
Creating communication systems require  Network engineers
Electrical networks require electrical engineers
Logistics require a logistic specialist
Modular organization requires a Modular project manager
Setting up recycling systems require a recycling technician
Setting up power plants requires Systems Engineers of Power Plants
The make of Nanoscale technology requires Nano Process Development Engineers
Product planning and control require a Production Control Coordinator
Establishing product Quantity and Variant Flexibility require product management engineers
Waste management require a waste logistics manager
Creating a language requires intelligence
Creating Instructional information requires an Instructor
Coordination requires a coordinator
Setting up strategies requires a strategist
Regulation requires a regulator
Controlling requires intelligence that sets up and programs the automatic control functions
Recruiting requires intelligence which instructs autonomous programs how to do it.
Interpretation requires intelligence which creates an interpretation program.
Setting up switch mechanisms with on and off states require intelligent setup.
Setting up transport highways requires  Transportation Development engineers
Controlled factory implosion programming requires an Explosive Safety Specialist

Biological Cells do all above described, but no intelligence to set up all these things is required?

Objection: We have never observed a being of any capacity creating biological systems and life.  
Answer: We do not need direct observed empirical evidence to infer design. As anyone who has watched TV's Crime Scene Investigation knows, scientific investigation of a set of data (the data at the scene of a man's death) may lead to the conclusion that the event that produced the data (the death) was not the product of natural causes not an accident, in other words but was the product of an intelligence a perpetrator.
But of course, the data at the crime scene usually can't tell us very much about that intelligence. If the data includes fingerprints or DNA that produces a match when cross-checked against other data fingerprint or DNA banks it might lead to the identification of an individual. But even so, the tools of natural science are useless to determine the I.Q. of the intelligence, the efficiency vs. the emotionalism of the intelligence, or the motive of the intelligence. That data, analyzed by only the tools of natural science, often cannot permit the investigator to construct a theory of why the perpetrator acted.  Sherlock Holmes can use chemistry to figure out that an intelligence a person did the act that killed the victim, even if he can't use chemistry to figure out that the person who did it was Professor Moriarty, or to figure out why Moriarty did the crime.
Same when we observe the natural world. It gives us hints about how it could have been created. We do not need to present the act of creation to infer creationism / Intelligent design.

Atheists err when asking for material evidence to prove God's existence
https://reasonandscience.catsboard.com/t2256-atheists-err-when-asking-for-material-evidence-to-prove-god-s-existence

Question for an atheist. Are you a non-believer because you cannot see, hear or touch God? or is it for other reasons?
If it is because you cannot prove there is a God, I want to propose another question.
But first, try this out.
Say "I love tasty food," but don't actually try to physically make an effort to say it. Use your mind to say it.
Okay, what exactly did you just do and how is it that you can hear yourself so clearly in your own mind. There is an action (you saying the statement) and its existence is clear to you, but to us that sentence that you just said "out loud" in your head doesn't exist to us.
Matter of fact I will ask you, right now, to prove to me that you just said, "I love tasty food," in your head.
Telling me you said that statement isn't showing me evidence as to its existence. Some of you may say, "Hey, well it is dumbass." Ok, I understand how that can be a compelling argument. Now lets consider that I may lie to you and tell you that I did say I love tasty food consciously, but I actually didn't. Well then, the physical act of telling someone you thought something isn't the most viable way of showing evidence as to what you actually thought. Therefore isn't proving anything.
To get to the point, I want to say that there are probably lots of things that don't physically exist in our world, but have an existence. Just because you can't prove something doesn't mean it doesn't exist.
hopefully food for thought.



Last edited by Otangelo on Sun Jun 12, 2022 7:58 am; edited 9 times in total

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Otangelo


Admin

Job in the FactoryCell OrganelleFunction of the organelle
Shipping/Receiving DepartmentPlasma membraneRegulates what enters and leaves the cell; where cell makes contact with the external environment
Chief Executive Officer (CEO)NucleusControls all cell activity; determines what proteins will be made
Factory floorCytoplasmContains the organelles; site of most cell activity
Assembly line (where workers do their work)Endoplasmic Reticulum (ER)Where ribosomes do their work
Workers in the assembly lineRibosomesBuild the proteins
Finishing/packaging departmentGolgi apparatusPrepares proteins for use or export
Maintenance crewLysosomesResponsible for breaking down and absorbing materials taken in by the cell
Support beams (walls, ceilings, floorsCytoskeletonMaintains cell shape
Power plantMitochondria/chloroplastsTransforms one form of energy into another

https://reasonandscience.catsboard.com

7Abiogenesis: The factory maker argument Empty The factory maker argument Thu Mar 14, 2019 10:16 am

Otangelo


Admin

The factory maker argument

https://reasonandscience.catsboard.com/t2245-abiogenesis-biological-cells-are-equal-to-a-complex-of-millions-of-interlinked-factories#6686

1. Blueprints, instructional information and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  

2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks.

2. The Blueprint and instructional information stored in DNA and epigenetics, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life

DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/

Biological Cells are equal to a complex of millions of interlinked factories
https://reasonandscience.catsboard.com/t2245-biological-cells-are-like-an-industry-complex-full-of-interlinked-factories

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompass chemically simple compounds such as ethanol and carbon dioxide as well as the extremely complex proteins, carbohydrates, lipids, nucleic acids and secondary products. Furthermore: Self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories.  


Self-replication had to emerge and be implemented first, which raises the unbridgeable problem that DNA replication is irreducibly complex. Evolution is not a capable driving force to make the DNA replicating complex, because evolution depends on cell replication through the very own mechanism we try to explain. It takes proteins to make DNA replication happen. But it takes the DNA replication process to make proteins. That’s a catch 22 situation.


Chance of intelligence to set up life: 
100% We KNOW by repeated experience that intelligence does elaborate blueprints and constructs complex factories and machines with specific purposes.

Chance of unguided random natural events doing it:

Chance of random chemical reactions to setup amino-acid polypeptide chains to produce  functional proteins on early earth external to cellular biosynthesis:
1 in 10^200.000 That's virtually the same as 0%. There are 10^80 atoms in the universe.

Peptide Bond Formation of amino acids in prebiotic conditions: an insurmountable problem of protein synthesis on early earth: 
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664


1. The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of pre-biological ( chemical) evolution.
2. The formation of amide bonds without the assistance of enzymes poses a major challenge for theories of the origin of life. 
3. The best one can hope for from such a scenario is a racemic polymer of proteinous and non-proteinous amino acids with no relevance to living systems.
4. Polymerization is a reaction in which water is a product. Thus it will only be favoured in the absence of water. The presence of precursors in an ocean of water favours depolymerization of any molecules that might be formed.
5. Even if there were billions of simultaneous trials as the billions of building block molecules interacted in the oceans, or on the thousands of kilometers of shorelines that could provide catalytic surfaces or templates, even if, as is claimed, there was no oxygen in the prebiotic earth, then there would be no protection from UV light, which would destroy and disintegrate prebiotic organic compounds. Secondly, even if there would be a sequence, producing a functional folding protein, by itself, if not inserted in a functional way in the cell, it would absolutely no function. It would just lay around, and then soon disintegrate. Furthermore, in modern cells proteins are tagged and transported on molecular highways to their precise destination, where they are utilized. Obviously, all this was not extant on the early earth.
6. To form a chain, it is necessary to react bifunctional monomers, that is, molecules with two functional groups so they combine with two others. If a unifunctional monomer (with only one functional group) reacts with the end of the chain, the chain can grow no further at this end. If only a small fraction of unifunctional molecules were present, long polymers could not form. But all ‘prebiotic simulation’ experiments produce at least three times more unifunctional molecules than bifunctional molecules. 1

Now let us suppose that all these problems would be overcome, and random shuffling would take place:

Calculations of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events

https://reasonandscience.catsboard.com/t2508-abiogenesis-calculations-of-life-beginning-through-unguided-natural-random-events#6665

Proteins are the result of the DNA blueprint, which specifies the complex sequence necessary to produce functional 3D folds of proteins. Both improbability and specification are required in order to justify an inference of design.
1. According to the latest estimation of a minimal protein set for the first living organism, the requirement would be about 560 proteins, this would be the absolute minimum to keep the basic functions of a cell alive.  
2. According to the Protein-length distributions for the three domains of life, there is an average between prokaryotic and eukaryotic cells of about 400 amino acids per protein. 8
3. Each of the 400 positions in the amino acid polypeptide chains could be occupied by any one of the 20 amino acids used in cells, so if we suppose that proteins emerged randomly on prebiotic earth, then the total possible arrangements or odds to get one which would fold into a functional 3D protein would be 1 to 20^400 or 1 to 10^520. A truly enormous, super astronomical number. 
4. Since we need 560 proteins total to make a first living cell, we would have to repeat the shuffle 560 times, to get all proteins required for life. The probability would be therefore 560/10^520.  We arrive at a probability far beyond  of 1 in 10^200.000  ( A proteome set with 239 proteins yields odds of approximately 1/10^119.614 ) 7
Granted, the calculation does not take into consideration nor give information on the probabilistic resources available. But the sheer gigantic number os possibilities throw any reasonable possibility out of the window. 

If we sum up the total number of amino acids for a minimal Cell, there would have to be 560 proteins x 400 amino acids  =  224.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^224.000 possibilities !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible. 

We can take an even smaller organism, which is regarded as one of the smallest possible, and the situation does not change significantly:
The simplest known free-living organism, Mycoplasma genitalium,  has the smallest genome of any free-living organism, has a genome of 580,000 base pairs. This is an astonishingly large number for such a ‘simple’ organism. It has 470 genes that code for 470 proteins that average 347 amino acids in length. The odds against just one specified protein of that length are 1:10^451. If we calculate the entire proteome, then the odds are 470 x 347 = 163090 amino acids, that is odds of 20^164090 , if we disconsider that nature had to select only left-handed amino acids and bifunctional ones. 

Science confirms:

Abiogenesis is virtually impossible
https://reasonandscience.catsboard.com/t1279-abiogenesis-is-virtually-impossible

Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

No scientific experiment has been able to come even close to synthesize the basic building blocks of life, and reproduce a  self-replicating Cell in the Laboratory through self-assembly and autonomous organization. Scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative agency. The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true.

“There’s a huge chasm between the origins of life and the last common ancestor,”
https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/

Scientists are learning that what is required for life seems to be much greater than what is possible by natural process.  This huge difference has motivated scientists to creatively construct new theories for reducing requirements and enhancing possibilities, but none of these ideas has progressed from speculation to plausibility. The simplest "living system" we can imagine, involving hundreds of components interacting in an organized way to achieve energy production and self-replication, would be extremely difficult to assemble by undirected natural process.  And all of this self-organization would have to occur before natural selection (which depends on self-replication) was available.

Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance:  page 351:
The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of  the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.

125 reasons to believe in God
https://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

Abiogenesis: The factory maker argument The_fa10

The factory maker argument
1. Blueprints, instructional information and master plans, and the making of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  
2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signaling networks.
3. The Blueprint and instructional information stored in DNA and epigenetics, which directs the making of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena is very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

A factory with machines and production lines, controlled by informatics and computers and advanced information transmission systems based on languages and codes, performing all following actions listed below, certainly must have been devised, projected, imagined,  engineered, thought out, installed, implemented, constructed and created by an agency equipped with intelligence, able to plan, think, set distant goals with specific purposes.  

Adapting,
choreographing,
communicating,
controlling product quality,  
coordinating,
constructing,
cutting,  
duplicating,
elaborating strategies,    
engineering,
error checking and detecting, and minimizing,
expressing,
fabricating,
fine-tuning,  
foolproof,
governing,
guiding,    
implementing,
information processing,
interpreting,    
interconnecting,
intermediating,
instructing,  
logistics organizing,
managing,
monitoring,
optimizing,
orchestrating,
organizing,
positioning,
quality monitoring and managing,
regulating,
recruiting,
recognizing,  
recycling,
repairing,
retrieving,
shuttling,
separating,    
self-destructing,
selecting,
signaling,
stabilizing,
storing,
translating,
transcribing,
transmitting,
transporting,
waste managing,

Self-replicating Cell factories perform all tasks described above on a molecular level with exquisite precision in a fully autonomous preprogrammed robot-like manner with high-performance, high ability of adaptation to the environment.

Cells do error repair, adapt to the environment and food sources, regenerate, and reproduce.  The action of multicellular organisms adds enormously in complexity. For example, in the case of the human body, 3,7 trillion cells need to be specified in their specific function, position and place in the body, interconnected, communicate together, adhere one to each other precisely with cell-cell adhesion molecules, self-destruct and self-implode at the right moment, etc.

Each single cell needs:

factory building that protects the factory from the weather and hostile external environment ( cell membranes)
- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA )
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome )
- signaling ( hormones )
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines were to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
- recycling methods ( endocytic recycling )
- waste grinders and management  ( Proteasome Garbage Grinders )  
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )

Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, proteins that act like robots that work as teams in production lines, fully automated and self-replicating, directed by genes and epigenetic languages and signaling networks. The Blueprint and instructional information stored in DNA and epigenetics, which directs the making of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

What is the better explanation for the origin of the following things?

https://reasonandscience.catsboard.com/t2245p25-abiogenesis-the-factory-maker-argument#7912

- factory portals with fully automated security checkpoints and control
- factory compartments
- a library index and fully automated information classification, storage, and retrieval program
- computer hardware
- software, a language using signs and codes like the alphabet, an instructional blueprint,
- information retrieval systems
- information transmission systems
- translation systems
- complex robotlike machines
- taxis adapted for cargo transport and delivery, with GPS systems
- highways
- tagging programs informing taxis were to transport goods
- factory assembly lines
- error check and repair systems, electric scanning
- recycling machines
- waste grinders and management
- power generating plants
- power turbines
- electric circuits

Chance, or intelligent design?

- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA )
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome )
- signaling ( hormones )
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, actins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems, electric scanning  ( exonucleolytic proofreading, strand-directed mismatch repair )
- recycling methods ( endocytic recycling )
- waste grinders and management  ( Proteasome Garbage Grinders )  
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )

The cell is a factory 

1. Computer hard-drives with high capacity of digital data storage, software programs based on languages using statistics, syntax, semantics, pragmatics, and apobetics, and the elaboration of complex instructional blueprints through those software programs, and data transmission systems (encoding, sending, decoding), all operated through computers and interlinked computer networks, which prescribe, drive, direct, operate and control interlinked compartmentalized factory parks making products for specific purposes, full of autonomous, robotlike high-tech production lines, high-efficiency power plants, complex high-tech robots with autoregulation and feedback loops, producing products with minimal error rates, that are transported through GPS driven transport carriers to their destination, all driven through energy made by high rotative turbines and power plants, are always set up by intelligent agents designing those things for purposeful goals.

2. Science has unraveled, that cells, strikingly, contain, and operate through all those things. Cells are cybernetic, ingeniously crafted cities full of factories. Cells contain information, which is stored in genes (books), and libraries (chromosomes). Cells have superb, fully automated information classification, storage, and retrieval programs ( gene regulatory networks ) which orchestrate strikingly precise and regulated gene expression. Cells also contain hardware - a masterful information-storage molecule ( DNA ) - and software, more efficient than millions of alternatives ( the genetic code ) - ingenious information encoding, transmission, and decoding machinery ( RNA polymerase, mRNA, the Ribosome ) - and highly robust signaling networks ( hormones and signaling pathways ) - awe-inspiring error check and repair systems of data ( for example mind-boggling Endonuclease III which error checks and repairs DNA through electric scanning ). Information systems, which prescribe, drive, direct, operate, and control interlinked compartmentalized self-replicating cell factory parks that perpetuate and thrive life. Large high-tech multimolecular robotlike machines ( proteins ) and factory assembly lines of striking complexity ( fatty acid synthase, non-ribosomal peptide synthase ) are interconnected into functional large metabolic networks. In order to be employed at the right place, once synthesized, each protein is tagged with an amino acid sequence, and clever molecular taxis ( motor proteins dynein, kinesin, transport vesicles ) load and transport them to the right destination on awe-inspiring molecular highways ( tubulins, actin filaments ). All this, of course, requires energy. Responsible for energy generation are high-efficiency power turbines ( ATP synthase )- superb power generating plants ( mitochondria ) and electric circuits ( highly intricate metabolic networks ). When something goes havoc, fantastic repair mechanisms are ready in place. There are protein folding error check and repair machines ( chaperones), and if molecules become non-functional, advanced recycling methods take care ( endocytic recycling ) - waste grinders and management ( Proteasome Garbage Grinders )

3. Chemist Wilhelm Huck, professor at Radboud University, Netherlands: A working cell is more than the sum of its parts. "A functioning cell must be entirely correct at once, in all its complexity. Cells, containing all those things are irreducibly complex. Without energy, information, or the basic building blocks fully synthesized, there would be no life. All this is best explained as a product of a super-intellect, an agency equipped with unfathomable intelligence - through the direct intervention, creative force, and activity of an intelligent cognitive agency, a powerful creator.

I don't choose to be a theist. I don't have enough faith to be an atheist. 
I just can not force my brain to accept the claim that Biological cells which are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signaling networks, could emerge by no guiding intelligence, but random unguided lucky accidents.

Intelligent design theory is like a sword with two edges
It wins using eliminative induction based on the fact that its competitors are false. Materialism explains basically nothing consistently in regards to origins but is based on unwarranted consensus and scientific materialism, a philosophical framework, that should never have been applied to historical sciences. Evidence should be permitted to lead wherever it is. Also, eventually, to an intelligent agency as the best explanation of origins.

And intelligent design wins based on abductive reasoning, using inference to the best explanation, relying on positive evidence, on the fact that basically all-natural phenomena demonstrate the imprints and signature of intelligent input and setup. We see an unfolding plan, a universe governed by laws, that follows mathematical principles, finely adjusted on all levels, from the Big Bang, to the earth, to permit life, which is governed by instructional complex information stored in genes and epigenetically, encoding, transmitting and decoding information, used to build, control and maintain irreducible complex and interdependent machines, robots, fully automated manufacturing production lines, transport carriers, turbines, transistors, computers, and factory parks, employed to give rise to a wide range, millions of species, of unimaginably complex multicellular organisms.

Abiogenesis: The factory maker argument Unname10

1. https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664



Last edited by Otangelo on Sun Jun 12, 2022 7:59 am; edited 3 times in total

https://reasonandscience.catsboard.com

Otangelo


Admin

We do not need a model to predict and test if intelligence is a capable potent causal principle and agency to make life and biodiversity. We KNOW by repeated experience that following things are both always the result of intelligent setup. 

1. Blueprints containing instructional complex assembly information, dictating the 
2. fabrication of complex machines, robotic production lines, computers, transistors, turbines, energy plants,  and interlinked factories based on these instructions, which produce goods for specific purposes. 


We see all these things in biochemistry, and biology, and much more.....

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7761

factory portals with fully automated security checkpoints and control ( membrane proteins )
factory compartments ( organelles )
a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
molecular computers, hardware ( DNA )
software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes )
information retrieval ( RNA polymerase )
transmission ( messenger RNA )
translation ( Ribosome )
signaling ( hormones )
complex machines ( proteins )
taxis ( dynein, kinesin, transport vesicles )
molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
recycling methods ( endocytic recycling )
waste grinders and management  ( Proteasome Garbage Grinders )  
power generating plants ( mitochondria )
power turbines ( ATP synthase )
electric circuits ( the metabolic network )

https://reasonandscience.catsboard.com

Otangelo


Admin

Biological Cells are equal to a complex of millions of interlinked factories

https://reasonandscience.catsboard.com/t2245-biological-cells-are-like-an-industry-complex-full-of-interlinked-factories

1. Blueprints, instructional information and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  
2. Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks. 
3. The Blueprint and instructional information stored in DNA and epigenetics, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

Blueprints, instructional information and master plans, and the make of complex machines and factories upon these are both always tracked back to an intelligent source which made them for purposeful, specific goals.  
The Blueprint and instructional information stored in DNA, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

When you see a blueprint of a complex factory, and the factory made accordingly to the blueprint, but have no information about the origin of both, do you think and infer that rather both, the blueprint, and the factory, were invented, designed, and implemented by intelligence, or not? what makes more sense?

By repeated experience, observation, knowledge and understanding, we know that only intelligence can elaborate master plans, manuals of constructions, blueprints, technical drawings of machines, buildings, complex factories, and these things made accordingly to these blueprints and instructions. Is that correct?  If we see both but have no information about the origin of them, is it obvious to think, that somebody made them, or not? 

==========================================================================================================================================

The Factory maker argument
Imagine you find a book and at the first pages the picture of an Autocad 3D factory blueprint. The drawing contains the precisely detailed instructions to make 560 complex  robotic fully automated machines and the instructions how to interconnect each one of them in a specific complex functional network into sophisticated production-lines, in order to make the components of a larger factory complex with a specific purpose, where each of these components individually would be useful only in the completion of that much larger factory complex. Then, you give a further look while scrolling the book and discover a picture of the fully implemented and installed factory complex, exactly how the blueprint did specify how it had to be done.  The book gives no information about what or who made the blueprint, when and how the project and 3D blueprint was elaborated, nor any information or pictures of the building process. Upon our past experience, we know how to detect when something has been intelligently designed and implemented, rather than not, and based on that knowledge, we can infer logically, that intelligence was required to make the blueprints and the factory upon their instructions.  

We can detect intelligent design when we see things that were made based on mathematical principles, the intelligent design of a blueprint usually precedes the assembly of parts in accordance with the blueprint or preconceived instructional blueprint, objects purposefully made for specific goals, specified and organized complexity, codified messages, systems and networks functioning based on logic gates, irreducible complex and interdependent systems or artefacts composed of several interlocked, well-matched parts contributing to a higher end of a complex system that would be useful only in the completion of that much larger system, order or orderly patterns, and fine-tuning. Upon these criteria, even if the book above mentioned does not give any information of how the blueprint and the implementation of the factory came to be, we can make logically and rationally the inference to the best explanation, that the origin of blueprint and factory is best explained by abductive reasoning concluding that intelligent elaboration and setup is far more likely, than unguided, random events.

Biological cells are a factory park of unparalleled gigantic complexity and purposeful adaptive design of interlinked high-tech fabrics, proteins that act like robots which work as teams in production lines, fully automated and self-replicating, directed by genes and epigenetic languages and signalling networks. The Blueprint and instructional information stored in DNA and epigenetics, which directs the make of biological cells and organisms - the origin of both is, therefore, best explained by an intelligent designer which created life for his own purposes.

Herschel 1830 1987, p. 148:
“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

DNA - the instructional blueprint of life
https://reasonandscience.catsboard.com/t2544-dna-the-instructional-blueprint-of-life

DNA Is Called The Blueprint Of Life: Here’s Why
OCTOBER 26, 2017
DNA is called the blueprint of life because it is the instruction manual to create, grow, function and reproduce life on Earth similar to a blueprint of a house. 10
https://sciencetrends.com/dna-called-blueprint-life-heres/

Biological Cells are equal to a complex of millions of interlinked factories
https://reasonandscience.catsboard.com/t2245-biological-cells-are-like-an-industry-complex-full-of-interlinked-factories

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompass chemically simple compounds such as ethanol and carbon dioxide as well as the extremely complex proteins, carbohydrates, lipids, nucleic acids and secondary products. Furthermore: Self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories. 

By the turn of the twentieth century, the cell was being variously characterized as “a little engine with admirably adapted parts”( Conn, 1899 , p. 126), a “chemical machine”ca- pable of “automatically developing, preserving, and reproduc- ing [itself]”( Loeb, 1906 , p. 1), and “a battery, with a series of resistances and condensers, made up of conductors and di- electrics”( Matthews, 1924 , p. 15). But most influential of all was the understanding of the cell as a “small chemical laboratory”( Hertwig, 1895 , p. 126) or a miniature factory, with proteins and other macromolecules arranged like machine tools on an assembly line 

=============================================================================================================================================


How to recognize the signature of (past) intelligent actions
https://reasonandscience.catsboard.com/t2805-how-to-recognize-intelligently-made-artefacts

Analogy Viewed from Science
https://reasonandscience.catsboard.com/t2809-analogy-viewed-from-science

If the causes are known that are efficacious in those other, similar phenomena, then this may give us clues concerning the causes in the phenomenon under consideration. Of course, whether this strategy works depends on the availability of closely analogous phenomena that are already explained (Herschel [1830] 1987, p. 148). Herschel (ibid., p. 149) wrote:

“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

A “good argument.” is one which (i) is logically valid; (ii) has true premises; and (iii) has conclusions which are more plausible than their negations. 17

Helicases are astonishing motor proteins which rotational speed is up to 10,000 rotations per minute, and are life essential. They are a class of enzymes vital to all living organisms. Their main function is to unpackage an organism's genes. They require 1000 left-handed amino acids in the right specified sequence. Each of the 1000 amino acids must be the right amongst 20 to chose from.  How did they emerge by natural processes? The chance to get them by random chemical reactions is 1 to 20^1000..... there are 10^80 atoms in the universe. 

If we sum up the total number of amino acids for a minimal Cell, there would have to be 560 proteins x 400 amino acids  =  224.000 amino acids, which would have to be bonded in the right sequence, choosing for each position amongst 20 different amino acids, and selecting only the left-handed, while sorting out the right-handed ones. That means each position would have to be selected correctly from 40 variants !! that is 1 right selection out of 40^224.000 possibilities !! Obviously, a gigantic number far above any realistic probability to occur by unguided events. Even a trillion universes, each hosting a trillion planets, and each shuffling a trillion times in a trillionth of a second, continuously for a trillion years, would not be enough. Such astronomically unimaginably gigantic odds are in the realm of the utmost extremely impossible. 

===============================================================================================================================================

Knut Eichler Organic Production Systems: What the Biological Cell Can Teach Us About Manufacturing 2004
Biological cells run complicated and sophisticated production systems. The study of the cell’s production technology provides us with insights that are potentially useful in industrial manufacturing. When comparing cell metabolism with manufacturing techniques in industry, we find some striking commonalitiesLike today’s well-run factories, the cell operates a very lean production system, assures quality at the source, and uses component commonality to simplify production. While we can certainly learn from how the cell accomplishes these parallels, it is even more interesting to look at how the cell operates differently. In biological cells, all products and machines are built from a small set of common building blocks that circulate in local recycling loops. Production equipment is added, removed, or renewed instantly when needed. The cell’s manufacturing unit is highly autonomous and reacts quickly to a wide range of changes in the local environment. Although this “organic production system” is very different from existing manufacturing systems, some of its principles are applicable to manufacturing, and indeed, a few can even be seen emerging today. Thus, the organic production system can be viewed as a possible scenario for the future of manufacturing.
http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033


Abiogenesis: The factory maker argument WB4FVEm


Are factories made by intelligent professionals or unguided unconscious random processes? 

https://reasonandscience.catsboard.com/t2799-are-factories-made-by-intelligent-professionals-or-unguided-unconscious-random-processes

Do we need to see architects, engineers, programmers, coordinators, instructors, managers, specialists, regulators, fine-tuners, interpreters etc. in action, building factories,  to conclude a factory was made by intelligent professionals? Or can we conclude design and intelligent setup as the best explanation when we see a factory in operation?

Engineering requires an engineer
Architecture requires an architect
An orchestra requires a Director
Organization requires an organizer
Setting up a programming language requires a programmer
Setting up Information selection programs require Search and Selection Programming engineers
Setting up translation programs requires translation programmers
Creating communication systems require  Network engineers
Electrical networks require electrical engineers
Logistics require a logistic specialist
Modular organization requires a Modular project manager
Setting up recycling systems require a recycling technician
Setting up power plants requires Systems Engineers of Power Plants
The make of Nanoscale technology requires Nano Process Development Engineers
Product planning and control require a Production Control Coordinator
Establishing product Quantity and Variant Flexibility require product management engineers
Waste management require a waste logistics manager
Creating a language requires intelligence
Creating Instructional information requires an Instructor
Coordination requires a coordinator
Setting up strategies requires a strategist
Regulation requires a regulator
Controlling requires intelligence that sets up and programs the automatic control functions
Recruiting requires intelligence which instructs autonomous programs how to do it.
Interpretation requires intelligence which creates an interpretation program.
Setting up switch mechanisms with on and off states require intelligent setup.
Setting up transport highways requires  Transportation Development engineers
Controlled factory implosion programming requires an Explosive Safety Specialist

Biological Cells: 
- a project department ( ? )
- computers which store the projects and blueprints of manufacturing ( DNA )

- factory portals with fully automated security checkpoints and control ( membrane proteins )
- factory compartments ( organelles )
- a library index and fully automated information classification, storage and retrieval program ( chromosomes, and the gene regulatory network )
- molecular computers, hardware ( DNA ) 
- software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and at least 23 different epigenetic codes, some more complex than DNA )
- information retrieval ( RNA polymerase )
- transmission ( messenger RNA )
- translation ( Ribosome ) 
- signalling ( hormones ) 
- complex machines ( proteins )
- taxis ( dynein, kinesin, transport vesicles )
- molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
- tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
- factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
- error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair ) 
- recycling methods ( endocytic recycling )
- waste grinders and management  ( Proteasome Garbage Grinders )  
- power generating plants ( mitochondria )
- power turbines ( ATP synthase )
- electric circuits ( the metabolic network )

Organic Production Systems: What the Biological Cell Can Teach Us About Manufacturing
http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033

What is a factory ?
Factory is from latin, and means fabricare, or make. Produce, manufacture. A factory or manufacturing plant is a site, usually consisting of buildings and machinery, or more commonly a complex having several buildings, where, in fully automated factories, for example, pre-programmed robots, manufacture goods or operate machines processing one product into another. A factory is a place where materials or products are produced or created. A factory is a manufacturing unit for manufacture/production of an article or thing.

Manufacturing:
Engineers, Programmers, Machine designers make blueprints of various goods or things: Factories, machines, and computers. Information transmission systems can be utilized to send the blueprints from the engineering department to the assembly sites of the factories. Carpenters, electricians, masons, machinists etc. construct machines, factories, assembly lines, robots etc. " Factories are usually full of machines, interlinked assembly lines that manufacture various kind of products. 

A factory is a place containing
- a project department
- computers which store the projects and blueprints of manufacturing
- a library index and fully automated information classification, storage and retrieval program 
- material Storage Units
- Alpha and Beta Testers
- security guards
- a control office
- support structures of the building of the factory
- factory portals with fully automated security checkpoints and control 
- factory compartments 
- computers, hardware 
- software, a language using signs and codes like the alphabet, and instructional blueprints and production manuals
- information retrieval 
- information transmission channels
- information translation systems 
- complex machines
- internal factory material delivery vehicles
- factory passageways and highways 
- various compartments, production departments and sections
- tagging programs 
- factory assembly lines 
- manufacturing error check and repair systems  
- recycling methods 
- waste grinders and management  
- power generating plants 
- power turbines 
- electric circuits 
- feedback loops 

Factories run complicated and sophisticated production systems and are composed of high-performance manufacturing systems, by employing production principles, making products with high robustness, flexibility, and efficiency, responsiveness. Factories can run various reactions in parallel. Raw materials are transformed into final products in a series of operations.  Factories use production flow, advanced technology, and production networks. Production systems need to be fast, efficient, and responsiveSpeed and range of response, as well as the efficiency of its production systems, are clearly critical to success.

Factories do respond to actual demand, not in anticipation of forecast demand, thus preventing overproduction.  Operating with little waste, even in regulating its production linesproduction planning and quality assurance.  quality-management techniques. Factories invest in defect prevention at various stages, using 100% inspection processes, quality assurance procedures, and foolproofing techniques. quality assurance, critical for proper functioning. Apply of key-lock principle to guarantee a proper fit between the machine and the product being manufactured, i.e., product and machine. The substrate fits into a pocket like a key into a lock, ensuring that only one particular product can be processed. 

This is comparable with poka-yoke systems in manufacturing. An everyday example of poka-yoke is the narrow opening for an unleaded gasoline tank in a car. It prevents you from inserting the larger leaded fuel nozzle. Factory pathways are designed in such a way that different end products often share a set of initial common steps. Factories can use just a few recyclable components, and upon these, an enormous variety of products in the appropriate quantities could be produced when they are needed.  The constant renewal eliminates the need for other types of “machine maintenance.” Assembly and disassembly of machines, fast and frictionless that they allow a scheme of constant machine renewal.  A factory that is able of completely recycle the machines that are taken out of production. The components derived from this recycling process can be used not only to create other machines of the same type, but also to create different machines if that is what is needed in the “plant.” This way of handling its machines has some clear advantages. New capacity can be installed quickly to meet current demand. At the same time, there are never idle machines around taking up space or hogging important building blocks. Maintenance is a positive “side effect” of the continuous machine renewal process, thereby guaranteeing the quality of output. Finally, the ability to quickly build new production lines from scratch has allowed  to take advantage of a big library of contingency plans that allow it to quickly react to a wide range of circumstances.



1) https://en.wikipedia.org/wiki/Molecular_machine
2) https://docs.google.com/presentation/d/1wKdTv5AeYQuVF4AcK6jhIhnSUYWEut_8m2dGQrjDXOo/edit#slide=id.g3217d827_0_49
3) http://www.nature.com/scitable/topic/cell-communication-14122659
4) http://reasonandscience..catsboard.com/t2229-development-of-multicellular-organisms?highlight=multicellular
5) https://en.wikipedia.org/wiki/Cellular_differentiation
6) http://www.nature.com/ncomms/2015/150908/ncomms9224/abs/ncomms9224.html
7) Genetics, Analysis and Principles, 4th edition, page 690
8  Molecular biology of the cell, B.Alberts, 6th ed. page 141
9) https://www.mpg.de/9271053/annual-report-2014-sourjik.pdf
10) http://www.biomedcentral.com/1752-0509/4/82
11) Molecular biology of the cell, B.Alberts, 6th ed. page 737
12) http://reasonandscience..catsboard.com/t2193-apoptosis-cell-s-essential-mechanism-of-programmed-suicide-points-to-design?highlight=apoptosis[/size]
13) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003694/
14) https://cordis.europa.eu/biotech/src/ab-1.htm
15) https://cellbiology.med.unsw.edu.au/cellbiology/index.php/Cell_Export_-_Exocytosis
16. https://prezi.com/h6wxkvzbvfgs/cell-analogy-to-a-computer/
17. https://www.reasonablefaith.org/writings/question-answer/the-leibnizian-cosmological-argument/
18. https://sci-hub.st/10.1016/j.jtbi.2019.06.002



Last edited by Otangelo on Wed Jul 14, 2021 1:19 pm; edited 2 times in total

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10Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument Wed Jun 23, 2021 10:13 am

Otangelo


Admin

The origin of life can not be explained through biological nor chemical evolution. Adaptation, mutation, and natural selection depend on DNA replication. Heredity is guaranteed by faithful DNA replication whereas evolution depends upon errors accompanying DNA replication.
Neither can it be explained through physical laws. Life depends on codes and instructional complex information. This information can only be generated by when the arrangement of the code is free and unconstrained, and any of the four bases of the genetic code can be placed in any of the positions in the sequence to generate the information.
The only alternative, if the action of a creative agency is excluded, would be spontaneous self-assembly by orderly aggregation of prebiotic elements and building blocks in a sequentially correct manner without external direction.

Abiogenesis Observation:
The origin of life depends on biological cells, which perpetuate life upon the complex action of  molecular computers, hardware ( DNA ), software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes ) information retreavel ( RNA polymerase ) transmission ( messenger RNA ) translation ( Ribosome ) signaling ( hormones ) complex machines ( proteins ), factory assembly lines ( fatty acid synthase, non ribosomal peptide synthase ), error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair ) , recycling methods ( endocytic recycling ), waste grinders and management  ( Proteasome Garbage Grinders )  , power generating plants ( mitochondria ), power turbines ( atp synthase ), and electric circuits ( the metabolic network ).  Biological cells are veritable micro-miniaturized factories containing thousands of exquisitely designed pieces of intricate molecular machinery. Biological Cells do not resemble factories, they ARE an industrial park of various interconnected factories, working in conjunction.

Hypothesis (Prediction):
Complex machines and interconnected factory parks are intelligently designed. Biological cells are intelligently designed. Factories can not self-assemble spontaneously by orderly aggregation and sequentially correct manner without external direction.The claim can be falsified, once someone can demonstrate that factories can self-assemble spontaneously by orderly aggregation and sequentially correct manner without external direction.

Experiment:
Since origin of life experiments began, nobody was able to bring up an experiment, replicating the origin of life by natural means.
Eugene Koonin, advisory editorial board of Trends in Genetics, writes in his book: The Logic of Chance:
" The Nature and Origin of Biological Evolution, Eugene V. Koonin, page 351:The origin of life is the most difficult problem that faces evolutionary biology and, arguably, biology in general. Indeed, the problem is so hard and the current state of the art seems so frustrating that some researchers prefer to dismiss the entire issue as being outside the scientific domain altogether, on the grounds that unique events are not conducive to scientific study.
A succession of exceedingly unlikely steps is essential for the origin of life, from the synthesis and accumulation of nucleotides to the origin of translation; through the multiplication of probabilities, these make the final outcome seem almost like a miracle. The difficulties remain formidable. For all the effort, we do not currently have coherent and plausible models for the path from simple organic molecules to the first life forms. Most damningly, the powerful mechanisms of biological evolution were not available for all the stages preceding the emergence of replicator systems. Given all these major difficulties, it appears prudent to seriously consider radical alternatives for the origin of life. "
Scientists do not have even the slightest clue as to how life could have begun through an unguided naturalistic process absent the intervention of a conscious creative agency.
The total lack of any kind of experimental evidence leading to the re-creation of life; not to mention the spontaneous emergence of life… is the most humiliating embarrassment to the proponents of naturalism and the whole so-called “scientific establishment” around it… because it undermines the worldview of who wants naturalism to be true.

Conclusion:
Upon the logic of mutual exclusion,  design and non-design are mutually exclusive (it was one or the other) so we can use eliminative logic: if non-design is highly improbable, then design is highly probable. The evaluative status of non-design (and thus design) can be decreased or increased by observable empirical evidence, so a theory of design is empirically responsive and is testable, so, by applying  Bayesian probability, we can conclude that Life is most probably intelligently designed.

A factory is a facility where goods are manufactured for export.  A factory consumes raw materials and energy in an effort to sustain its workers and provide resources to others.  This is analogous to the functioning of a cell

Molecular machines in biology
https://reasonandscience.catsboard.com/t1289-molecular-machines-in-biology

Quantum biology :One of the simplest and most well-studied examples is the light-harvesting apparatus of green-sulphur bacteria (Fig. 1)

The Cell is a factory.
the Nucleus is the control office.  The cell membrane the security guard and wall. The cytoskeleton is like the support structures.The Cytoplasm is like the Air and the Factory FloorThe endoplasmic reticulum is like the Assembly Line. Ribosomes are information translation devices.  The Golgi Apparatus is like the Alpha and Beta Testers. Lysosomes are like the Janitors. Vacuoles are the Storage Units. The Mitochondria is the Powerplant. Chloroplasts are like the Solar Panels.

Proteins are true nanomachines in charge of most biological roles in living cells, a feat they accomplish by self-assembling into sophisticated 3D structures that exploit thermal, and on occasion chemical, energy to change shape in response to stimuli. 13

Factories, full of machines and production lines and computers, originate from intelligent minds. No exception.
Biological cells are like a industrial park of various interconnected factories, working in conjunction.
Factory is from Latin, and means fabricare, or make. Produce, manufacture. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex machine processing, computing etc. 
Therefore, they had most probably a mind as a causal agency. 
The claim is falsified and topped, once someone can demonstrate  a factory that can self-assemble, without the requirement of intelligence. 


=============================================================================================================================================

By repeated observation and testing, it has always and exclusively been observed and demonstrated, that  computers, hardware, software, a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits, which are finely tuned, regulated, in a homeostatic environment,  only and always, no exception, are the result of intelligent planning, invention, design, and implementation. Proponents of naturalism have a case, once they meet the challenge, and are able to demonstrate by testing and experiment, that random,  unguided, accidental events can produce these things by self-assembly spontaneously by orderly aggregation and sequentially correct manner without external direction. That is the ONLY causal alternative, once intelligent set up is excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories full of machines and information, and codified blueprint storage and retrieval devices.

=============================================================================================================================================

Nobody in its sane mind would defend and advocate that computers, hardware, software, a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits could emerge randomly, by unguided, accidental events. That is, however, the ONLY causal alternative, once intelligent planning, invention, design, and implementation are excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories.

Is it a rational proposition to defend and advocate that computers, hardware, software, a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits could emerge randomly, by unguided, accidental events ? That is  the ONLY causal alternative, once intelligent planning, invention, design, and implementation are excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories.

==========================================================================================================================================

Gods existence is a fact, as much as the fact that factories do not self-assemble spontaneously by orderly aggregation and sequentially correct manner without external direction.
But who knows, and Wikipedia, a commonly known anti ID website, is right ?? They claim:
The most famous example of self-assembly phenomenon is the occurrence of the life on Earth. It is plausible to hypothesize that it happens because the sun generates a strong temperate gradient in its environment. Does that make sense ?

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Let's suppose you arrive at a huge abandoned city, and there you see many interlinked factory facilities, with offices where projects were elaborated, full of complex supercomputers, integrated and connected to production halls with manufacturing assembly lines, energy disposals, error check and repair mechanisms, waste recycle mechanisms, solar panels, and batteries for energy storage. Would you intuitively conclude, that

1. wind, basic building materials, bauxite iron, sulfur, stones, bricks etc. over a long period of time assembled these factories spontaneously by orderly aggregation and sequentially correct manner without external direction, or rather that
2. the city was previously habited by people, which constructed the factories by intelligent planning,  invention, setting distant goals, elaboration of blueprints, design, and then implementation by the precise guidance of these instructional blueprints?
What would you choose? Option one, or two ?

Nobody in its sane mind would defend and advocate that  computers, hardware, software, a language using signs and codes like the alphabet, an instructional blueprint, complex machines, factory assembly lines, error check and repair systems, recycling methods, waste grinders and management, power generating plants, power turbines, and electric circuits could emerge randomly, by unguided, accidental events. That is, however, the ONLY causal alternative, once intelligent planning,  invention, design, and implementation are excluded, to explain the origin of biological Cells, which are literally miniaturized, ultracomplex, molecular, self-replicating factories.

We know empirically, that intelligence can and does invent, elaborates, projects, and makes blueprints of complex machines, production lines, and factories, and is capable of implementing them. We do have no example of any alternative causal mechanism able of the same feat. Denton describes biological cells as " veritable micro-miniaturized factories containing thousands of exquisitely designed pieces of intricate molecular machinery, made up altogether of one hundred thousand million atoms, far more complicated than any machine built by man and absolutely without parallel in the non-living world ". The claim is falsified and topped, once someone can demonstrate a factory that can self-assemble, without the requirement of intelligence.

==========================================================================================================================================

Know-how is required to create a language, a code system, an information transmission system, a signaling code and transmission and recognition,  translation systems, an information storage device, and use it to store a blueprint to make complex factories, machines and production lines, which depend on a minimal number of parts, which by their own, without being interconnected in a meaningful manner, have no function, are not useful. Intelligent foresight is required to invent and create components of a complex system which have only purpose in the completion of that much larger system. Hardware, software, production lines, factories full of machines, error check and repair programs, recycle system and waste bins, and auto-destruction systems when required, have only been observed to originate from inventive, goal oriented intelligent minds. No exception.
Biological cells are like an industrial park of various interconnected factories, working in conjunction.
Factory is from Latin, and means fabricare, or make. Produce, manufacture. And that's PRECISELY what cells do. They produce other cells through self-replication, through complex molecular machine processing, computing etc.
Therefore, they had most probably a mind as a causal agency.
The claim is falsified and topped, once someone can demonstrate a factory that can self-assemble, without the requirement of intelligence.

B.Alberts, The Cell as a Collection Overview of Protein Machines: Preparing the Next Generation of Molecular Biologists
“Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”  Many of these structures are just as amazing, and more so, as the flagellum.  For a few examples, see the spliceosome, RNA polymerase, and ATP Synthase.  Another article posted yesterday on EurekAlert uses the word “machine” seven times as it discusses “an intricately complex protein machine” that adjusts the connections between neurons.
https://brucealberts.ucsf.edu/publications/BAPub157.pdf

Developing Bacillus spp. as a cell factory for production of microbial enzymes
We highlight the limitations and challenges in developing Bacillus spp. as a robust and efficient production host, and we discuss in the context of systems and synthetic biology the emerging opportunities and future research prospects in developing Bacillus spp. as a microbial cell factory.
https://www.researchgate.net/publication/237095038_Developing_Bacillus_spp_as_a_cell_factory_for_production_of_microbial_enzymes_and_industrially_important_biochemicals_in_the_context_of_systems_and_synthetic_biology

Organic Production Systems: What the Biological Cell Can Teach Us About Manufacturing
Biological cells run complicated and sophisticated production systems. The study of the cell’s production technology provides us with insights that are potentially useful in industrial manufacturing. When comparing cell metabolism with manufacturing techniques in the industry, we find some striking commonalities assures quality at the source, and uses component commonality to simplify production.  The organic production system can be viewed as a possible scenario for the future of manufacturing. 
http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033

Cells are very similar to factories. To stay alive and function properly, cells have a division of labor similar to that found in factories.
https://www.slcschools.org/departments/curriculum/science/Grade-7-to-8/Grade-7/documents/s3-o2-lesson-cell-as-a-factory-website-pdf.pdf

Comparing a Cell to a Factory: Answer Key
Science NetLinks is a project of the Directorate for Education and Human Resources Programs of the American Association for the Advancement of Science.
http://sciencenetlinks.com/student-teacher-sheets/comparing-cell-factory-answer-key/

The scientists from Stuttgart may have already identified the first words in the programming language for living cells. For example, in their experiments with certain tissue cells, fibroblasts, they discovered that they were, in fact, able to switch their protein-making factory between two production modes by varying the contact distance. In a 58-nanometer gold pattern, the cells produce a different kind of tissue adhesive from the extensive family of fibronectin proteins compared with what they produce when the distance between contacts is 73 nanometers.
https://www.mpg.de/794120/F003_Focus_032-037.pdf

John Kendrew uses this fitting comparison:
Any living thing can be likened to a giant factory, a factory producing chemicals, producing energy and motion, indeed reproducing itself too (which most factories cannot do!) and if one thinks of the way in which assembly lines are organized in factories one realizes immediately that all this complex of operations could not be carried out unless they were in some way organized, separated into compartments, not higgledy-piggledy.  In other words, there must be some kind of organization in the structure of an animal to enable it to carry out these processes in an orderly way. In that parallel, the DNA would be like the manuals and blueprints that prescribe in detail just how each operation is to be done, and in what order of timing. The coded information in DNA, then, would obviously be absolutely essential.  It would also be absolutely helpless unless it had the entire system of the manufacturing plant, including people or computers to read and put into action its instructions.  The DNA master copy of the production blueprints must be kept protected.  What is required first of all is a way to make working copies of just the sections needed at the moment.  These temporary copies can then be taken out into the rough-and-tumble of the production area, leaving the DNA original safely in the office.  When no longer needed, the copies are destroyed.

Cells are entire FACTORY COMPLEXES; rather just one big factory, an agglomeration of MANY factories, that together form a giant manufacturing complex. So we can distinguish the Ribosome factory, the Endoplasmic reticulum factory, the transcription factory, mitochondria as the energy production factory, etc.

The scientists from Stuttgart may have already identified the first words in the programming language for living cells. For example, in their experiments with certain tissue cells, fibroblasts, they discovered that they were, in fact, able to switch their protein-making factory between two production modes by varying the contact distance. In a 58-nanometer gold pattern, the cells produce a different kind of tissue adhesive from the extensive family of fibronectin proteins compared with what they produce when the distance between contacts is 73 nanometers.
https://www.mpg.de/794120/F003_Focus_032-037.pdf

Cell Factories
The primary objective of research on Cell Factories is to reach a better understanding of how living cells manage to be productive, and how the industry can use these cellular processes to further design and operate safe, efficient, reproducible and sustainable bioprocesses. 14  Information is transferred from stable stored information (DNA) converted to an intermediate (mRNA, rRNA, tRNA) of variable stability, exported from the nucleus to the cytoplasm where mRNA is then translated into Protein. This is gene expression, the products of this process are used either within the cell, exported (exocytosis) or used to replace worn out components. 15

The cell is a factory, that has various computer like hierarchically organized systems of  hardware and software, various language based  informational systems, a translation system, huge amounts of precise instructional/specified, complex information stored and extract systems to make all parts needed to produce the factory and replicate itself, the scaffold structure, that permits the build of the indispensable protection wall, form and size of its building, walls with  gates that permits  cargo in and out, recognition mechanisms that let only the right cargo in, has specific sites and production lines, "employees", busy and instructed to produce all kind of necessary products, parts and subparts  with the right form and size through the right materials, others which mount the parts together in the right order, on the right place, in the right sequence, at the right time,   which has sophisticated check and error detection mechanisms all along the production process, the ability to compare correctly produced parts to faulty ones and discard the faulty ones, and repeat the process to make the correct ones;

highways and cargo carriers that have tags which recognize where to drop the cargo where it's needed,  cleans up waste and has waste bins and sophisticated recycle mechanisms, storage departments, produces its energy and shuttles it to where it's needed, and last not least, does reproduce itself. The salient thing is that the individual parts and compartments have no function by their own. They had to emerge ALL AT ONCE, No stepwise manner is possible, all systems are INTERDEPENDENT and IRREDUCIBLE. And it could not be through evolution, since evolution depends on fully working self-replicating cells, in order to function.  How can someone rationally argue that the origin of the most sophisticated factory in the universe would be probable to be based on natural occurrence, without involving any guiding intelligence?  To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

It was not until the relatively recent advent of advanced microscopes that we could peer deeply into a cell.  What scientists found amazed them!  They found a micro-city.  The nucleus is like the city hall, directing the cells activities.  The mitochondria is the cell’s power plant, giving the cell its energy to work.   Every city needs grocery stores and that is the job of the Golgi bodies.  Golgi bodies store supplies of chemicals which the cell makes.  Whenever proteins or fats are needed in another part of the cell, the Golgi body wraps it up and sends it to where it is needed.   The endoplasmic reticulum transports things within the cell – like a mailman.  It also acts like a garbage collector, picking up waste so the cell does not become polluted.  The lysomes are the cell’s police force protecting it by destroying invaders (like bacteria).  They also send trash out through the city wall (the cell membrane).  Darwin never knew all the activity was going on within a microscopic cell.  It really is like a miniature city abuzz with activity. 3

A Cell Is Like A Computer 16
Around plant cells,there is a cell wall. It is a strong wall to protect the cell and give it its shape. Cell Wall vs. Computer Case Around a computer, there is a protective casing called the computer case. It protects the computer and keeps everything together. Both the cell wall and the computer case are physical barriers that support and protect the delicate and complicated contents within. 
The cell wall is to a plant cell as a computer case is to a computer. 
Chloroplast vs. Power Chord 
The chloroplast is the organelle in a cell that captures energy from the sun and turns it into glucose, which the plant can then use as food. A computer's power chord takes energy from a socket in the wall. It enables the computer to have the power needed to function. Both the chloroplasts and the power chord for the computer take in energy from an outside source. The energy that the chloroplasts take in allows the cell to function and the energy that the power chord takes in allows the computer to function. A chloroplast is to a cell as a power cable is to a computer. 
Cytoskeleton Vs Wire Casing 
The cytoskeleton is a structure in the cytoplasm of a cell that holds the cytoplasm together and keeps it from collapsing. The rubber casing around the wires in a computer holds together the wire strands, keeps their shape, and protects them. Both the cytoskeleton and the casing around the wires in computers keep the shape of the means by which transportation occurs.In cells, transportation occurs within the cytoplasm. Molecules move between organelles through the cytoplasm. The cytoskeleton keeps the cytoplasm from collapsing. In a computer, electrical charges move around the computer via a network of wires. The rubber casing around the wires hold the wires together and keep them from falling apart. Both wire casing and the cytoskeleton support the means of transportation in computers and cells respectively. That's why the cytoskeleton is to cells as wire casing is to computers. 
DNA Vs. Computer 
Code DNA is the code held within every cell from which all protein is synthesized and that determines how a cell functions. Computer code is written to determine what a computer program does and exactly how it operates. Both DNA and computer code are extensive codes that determine exactly what either the cell or the computer program is supposed to do.That's why DNA is to a cell's function as computer code is to a computer's function. 
Golgi Apparatus Vs Computer Processor 
The Golgi Apparatus receives, sorts and packages smaller molecules into bigger molecules for either storage or to be sent out of the cell. A computer processor processes the data given to it by the hard drive and sends it out for use in other parts of the computer. Both the Golgi Apparatus and the computer processor take something (whether it's molecules or data) and process it and then send it out. The golgi apparatus is to the cell as the computer processor (cpu) is to the computer. 
Mitochondrion Vs Computer battery 
The mitochondria turn energy stored as food into energy that's usable to the cell (ATP) through a process called cellular respiration. The battery of a computer holds the energy brought into the computer by the power cable. It also releases the energy in a form usable to power the computer. Both the mitochondria and the battery of a computer turn the energy that was captured from an external source and make it usable for the cell or computer. The mitochondria are to the cell as the battery is to the computer. 
Lysosome Vs Recycle bin 
A lysosome is full of enzymes. It uses these enzymes to digest unwanted or harmful molecules. The recycle bin in a computer holds files that are useless or potentially dangerous. Then it gets rid of them. The Lysosome gets rid of molecules that the cell doesn't want and the recycle bin gets rid of files that the computer doesn't want. Both get rid of potetially dangerous things. The lysosome is to the cell as the recycle bin is to the computer. 
Nucleus Vs Hard Drive Disk 
The nucleus is like the cell's brain. It contains DNA and RNA and also controls eating, movement, reproduction and more. The Hard Drive Disk creates and controls all of a computer's activities. Both the nucleus and the hard drive are like the brain or control center in their cell or computer. They control all the activities. The nucleus is to the cell as the hard drive is to the computer. 
Plasma Membrane vs Firewall 
The plasma membrane surrounds the cell just inside of the cell wall. It is selectively permeable meaning that it regulates the entry and exit of molecules into and out of the cell. A firewall selectively allows or blocks inbound traffic to a computer's network. It allows or blocks specific devices from accessing the content on a network. Both the plasma membrane and a firewall allow the things that are meant to come into the cell or computer network, to come in and both keep out thing that are potentially dangerous to the cell or computer. The plasma membrane is to the cell as a firewall is to a computer network. 
Ribosomes Vs Transistors 
Ribosomes construct proteins in cells by attaching amino acids together and building long protein chains. Transistors are used to do calculations by building different codes of ones and zeros. Ribosomes and Transistors are both small builders that occur in quantity in the cell or computer. Ribosomes build proteins and transistor build/manipulate code. Also, it is consistent with the analogy because the endoplasmic reticulum brings the ribosome made proteins to the golgi apparatus and the front side local bus (which I liken to the endoplasmic reticulum) brings the transistors to the processor (which I likened to the golgi apparatus). That's why the ribosomes are to the cell as transistors are to a computer. 
Endoplasmic Reticulum Vs Front Side Bus 
The endoplasmic reticulum packs, stores and carries steroids, ions, and proteins. Specifically, one of its functions is to give ribosome made proteins to the golgi apparatus. The front side bus brings the transistors to the computer's processing core. The Endoplasmic reticulum brings protein synthesized by the ribosomes to the golgi apparatus just as the front side bus brings the transistors (which I likened to the ribosomes) to the processing core (which I likened to the golgi apparatus). That's why the endoplasmic reticulum is to the cell as the front side bus is to a computer. 
Vacuole Vs RAM 
The vacuole in a cell stores water, food, waste, and more until they are used or gotten rid of. The RAM stores data from software. It doesn't store things permanently. Files on the RAM are either saved to the hard drive or disposed of. Both the vacuole and the RAM store things that are necessary in carrying the cell or computer's tasks. Also, they both hold things that they need to be rid of (waste). Finally, neither stores things permanently. They both are used for short-term storage. That's why the vacuole is to the cell as the RAM is to the computer. A cell is like a computer because the main components of each are comparable.

The Nucleus is like the control office.
Stores the information for our body/ the factory
controls the cell/factory
most important part of the cell/company

The cell membrane is like the security guard
only lets certain things enter and leave the cell/factory
makes sure the things the cell/factory needs comes in.
makes sure the things that would be bad for the cell/factory can't come in

The cytoskeleton/ the cell wall is like the support structures
Gives support to the building
Gives the building a shape

The Cytoplasm is like the Air and the Factory Floor
Takes up most of the cell's volume
Covers almost all of where the work is being done

The endoplasmic reticulum is like the Assembly Line
The E.R. serves as the site of production for proteins
The assembly line is where all of the products are made

Ribosomes are like the Employees on the Floor
Ribosomes make the proteins, so they are the employees of the cell
The Employees on the floor are the people who make all of the products that are shipped out

The Golgi Apparatus is like the Alpha and Beta Testers
The Golgi Apparatus makes sure the Products put out by the E.R. will work
The alpha and Beta testers are there to make sure the Factory's products come out the way they should

Lysosomes are like the Janitors
The Lysosomes contain digestive enzymes to clean up the cell and get rid of waste
The Janitors always make sure the factory is clean

Vacuoles are like the Storage Units
The vacuole is there for storage
The storage units in a factory store the thing that will be needed for future use

The Mitochondria are like the Powerplant
The Mitochondria break down food molecules to create energy for the cell
The Powerplant of the factory creates energy for the Factory

The Chloroplasts are like the Solar Panels
The chloroplasts are only in some cells (plant cells) and they create energy from sunlight
Not everyone has Solar Panels, and they soak up the energy made by the sun

https://docs.google.com/presentation/d/1wKdTv5AeYQuVF4AcK6jhIhnSUYWEut_8m2dGQrjDXOo/edit#slide=id.g3217d827_0_49




Abiogenesis: The factory maker argument Networ10


Modular organization
Of a human factory:
Starting with adapting the resources primarily in view of reducing overhead costs, business processes were radically reorganized along the value adding chain. Largely autonomous mini-factories were created within the factory from a number of product/ market combinations. Consequently, products and processes were also frequently redesigned to be more modular.

In the cell:
Many proteins, particularly those found in eukaryotic species, have a modular structure composed of two or more domains with different functions. For example, certain transcription factors have discrete domains involved with hormone binding, dimerization, and DNA binding. 7

Abiogenesis: The factory maker argument J5r0E9O

Abiogenesis: The factory maker argument Ltp7Fyk

Abiogenesis: The factory maker argument Cell_f10

Abiogenesis: The factory maker argument Wt1NssV

Abiogenesis: The factory maker argument The_ce10

Abiogenesis: The factory maker argument Mm5QlIC

Abiogenesis: The factory maker argument The_fa11


1) https://en.wikipedia.org/wiki/Molecular_machine
2) https://en.wikipedia.org/wiki/Engineering_design_process

3. http://creationevidenceexpo.org/2013/06/04/a-cell-is-a-city/



Last edited by Otangelo on Wed Jun 23, 2021 10:24 am; edited 1 time in total

https://reasonandscience.catsboard.com

11Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument Wed Jun 23, 2021 10:22 am

Otangelo


Admin

Size and internal factory space organization, compartmentalization and layout 
In a human factory:
The compartmentalization of production functions and requirements into operational units that can be manipulated between alternate production schemes to achieve the optimal arrangement to fit a given set of needs. In a reconfigurable manufacturing system, many components are typically modular (e.g., machines, axes of motion, controls, and tooling – see example in the Figure below). When necessary, the modular components can be replaced or upgraded to better suit new applications. 
Abiogenesis: The factory maker argument Factor10

In the cell:
Abiogenesis: The factory maker argument Animal10



Compartmentalization increases the efficiency of many subcellular processes by concentrating the required components to a confined space within the cell. Where a specific condition is required to facilitate a given subcellular process, this may be locally contained so as not to disrupt the function of other subcellular compartments. For example, lysosomes require a lower pH in order to facilitate degradation of internalized material. Membrane bound proton pumps present on the lysosome maintain this condition.

Recycling Economy
In a human factory:
The products themselves should also be designed so that they consume as few as possible resources that are detrimental to the environment during their use. Moreover, the components and materials contained in them should be reused as much as possible or recycled.


In the cell:
Recycling Endosomes Regulate Plasma Membrane Composition 
most receptors are recycled and returned to the same plasma membrane domain from which they came; some proceed to a different domain of the plasma membrane, thereby mediating transcytosis; and some progress to lysosomes, where they are degraded. Cells can regulate the release of membrane proteins from recycling endosomes, thus adjusting the flux of proteins through the transcytotic pathway according to need. This regulation, the mechanism of which is uncertain, allows recycling endosomes to play an important part in adjusting the concentration of specific plasma membrane proteins.


Waste bin:
In a human factory:
Attention should be paid to manufacturing waste, e.g., metal chips as well as the ancillary and operating materials related to them such as emulsions, lubricants, grease, acids, alkaline solutions, etc.
In the cell:
Improperly processed mRNAs and other RNA debris (excised intron sequences, for example) are retained in the nucleus, where they are eventually degraded by the nuclear exosome, a large protein complex whose interior is rich in 3ʹ-to-5ʹ RNA exonucleases


Controlled factory implosion
Of a human factory:
Sometimes, factories are imploded to provide space for new buildings and new developments. 
In the cell:
apoptosis, programmed cell death
Like engineers carefully blowing up a bridge, cells have intricate, programmed suicide mechanisms. The signal is sent and an apparatus of destruction is activated. But suicide hardly fits the evolutionary narrative. Wasn’t this all about survival, reproductive advantages and leaving more offspring? Why would a cell evolve intricate and complex suicide machinery? 12

The make of machines and factories, and what it tells us in regard of molecular machines in the cell
The most complex molecular machines are proteins found within cells. 1 These include motor proteins, such as myosin, which is responsible for muscle contraction, kinesin, which moves cargo inside cells away from the nucleus along microtubules, and dynein, which produces the axonemal beating of motile cilia and flagella. These proteins and their nanoscale dynamics are far more complex than any molecular machines that have yet been artificially constructed.

Probably the most significant biological machine known is the ribosome. Other important examples include ciliary mobility. A high-level abstraction summary is that, "[i]n effect, the [motile cilium] is a nanomachine composed of perhaps over 600 proteins in molecular complexes, many of which also function independently as nanomachines." Flexible linker domains allow the connecting protein domains to recruit their binding partners and induce long-range allostery via protein domain dynamics. 

Engineering design process
All text in red requires INTELLIGENCE.  

Research
A significant amount of time is spent on locating information and researchConsideration should be given to the existing applicable literature, problems and successes associated with existing solutions, costs, and marketplace needs.


The source of information should be relevant, including existing solutions. Reverse engineering can be an effective technique if other solutions are available on the market. Other sources of information include the Internet, local libraries, available government documents, personal organizations, trade journals, vendor catalogs and individual experts available.[/h3]


Feasibility

At first, a feasibility study is carried out after which schedules, resource plans and, estimates for the next phase are developed. The feasibility study is an evaluation and analysis of the potential of a proposed project to support the process of decision making. It outlines and analyses alternatives or methods of achieving the desired outcome. The feasibility study helps to narrow the scope of the project to identify the best scenario. A feasibility report is generated following which Post Feasibility Review is performed.
The purpose of a feasibility assessment is to determine whether the engineer's project can proceed into the design phase. This is based on two criteria: the project needs to be based on an achievable idea, and it needs to be within cost constraints. It is important to have engineers with experience and good judgment to be involved in this portion of the feasibility study.


Conceptualization

Following Feasibility, a concept study (conceptualization, conceptual engineering) is performed. A concept study is the phase of project planning that includes producing ideas and taking into account the pros and cons of implementing those ideas. This stage of a project is done to minimize the likelihood of error, manage costs, assess risks, and evaluate the potential success of the intended project.
Once an engineering issue is defined, solutions must be identified. These solutions can be found by using ideation, the mental process by which ideas are generated. The following are the most widely used techniques:
trigger word - a word or phrase associated with the issue at hand is stated, and subsequent words and phrases are evoked.

morphological chart - independent design characteristics are listed in a chart, and different engineering solutions are proposed for each solution. Normally, a preliminary sketch and short report accompany the morphological chart.

synectics - the engineer imagines him or herself as the item and asks, "What would I do if I were the system?" This unconventional method of thinking may find a solution to the problem at hand. The vital aspects of the conceptualization step is synthesis. Synthesis is the process of taking the element of the concept and arranging them in the proper way. Synthesis creative process is present in every design.

brainstorming - this popular method involves thinking of different ideas, typically as part of a small group, and adopting these ideas in some form as a solution to the problem

Design requirements
Establishing design requirements is one of the most important elements in the design process, and this task is normally performed at the same time as the feasibility analysis. The design requirements control the design of the project throughout the engineering design process. Some design requirements include hardware and software parameters, maintainability, availability, and testability

Preliminary design
The preliminary design, or high-level design (also called FEED), bridges the gap between the design concept and the detailed design phase. In this task, the overall system configuration is defined, and schematics, diagrams and layouts of the project will provide early project configuration. During detailed design and optimization, the parameters of the part being created will change, but the preliminary design focuses on creating the general framework to build the project on.


Detailed design

Following FEED is the Detailed Design (Detailed Engineering) phase which may consist of procurement as well. This phase builds on the already developed FEED, aiming to further elaborate each aspect of the project by complete description through solid modeling,drawings as well as specifications.

Some of the said specifications include:
Operating parameters
Operating and nonoperating environmental stimuli
Test requirements
External dimensions
Maintenance and testability provisions
Materials requirements
Reliability requirements
External surface treatment
Design life
Packaging requirements
External marking

Computer-aided design (CAD) programs have made the detailed design phase more efficient. This is because a CAD program can provide optimization, where it can reduce volume without hindering the part's quality. It can also calculate stress and displacementusing the finite element method to determine stresses throughout the part. It is the engineer's responsibility to determine whether these stresses and displacements are allowable, so the part is safe.

Production planning and tool design
The production planning and tool design consist in planning how to mass-produce the project and which tools should be used in the manufacturing of the part. Tasks to complete in this step include selecting the material, selection of the production processes, determination of the sequence of operations, and selection of tools, such as jigs, fixtures, metal cutting and metal forming tools. This task also involves testing a working prototype to ensure the created part meets qualification standards.

Production
With the completion of 
qualification testing and prototype testing, the engineering design process is finalized. The part must now be manufactured, and the machines must be inspected regularly to make sure that they do not break down and slow production.


locating information and research
feasibility study 
evaluation and analysis of the potential of a proposed project 
process of decision making. Outlines and analyses alternatives or methods of achieving the desired outcome
feasibility report is generated 
determine whether the engineer's project can proceed into the design phase
the project needs to be based on an achievable idea
concept study (conceptualization, conceptual engineering
project planning 
solutions must be identified
ideation, the mental process by which ideas are generated
morphological chart - independent design characteristics are listed in a chart, and different engineering solutions are proposed for each solution. Normally, a preliminary sketch and short report accompany the morphological chart.
the engineer imagines him or herself as the item and asks, "What would I do if I were the system?" 
Synthesis is the process of taking the element of the concept and arranging them in the proper way. 
Synthesis creative process is present in every design.
thinking of different ideas, typically as part of a small group, and adopting these ideas in some form as a solution to the problem
Establishing design requirements is one of the most important elements in the design process
feasibility analysis
Some design requirements include hardware and software parameters, maintainability, availability, and testability
the overall system configuration is defined, and schematics, diagrams, and layouts of the project will provide early project configuration. 
detailed design and optimization
the preliminary design focuses on creating the general framework to build the project on.
further elaborate each aspect of the project by complete description through solid modeling,drawings as well as specifications.
Some of the said specifications include:
Operating parameters
Operating and nonoperating environmental stimuli
Test requirements
External dimensions
Maintenance and testability provisions
Materials requirements
Reliability requirements
External surface treatment
Design life
considering packaging requirements and implant them
External marking

production planning and tool design


planning how to mass-produce the project and which tools should be used in the manufacturing of the part. 
selecting the material, selection of the production processes, determination of the sequence of operations, and selection of tools, such as jigs, fixtures, metal cutting and metal forming tools. 
start of manufactoring

the machines must be inspected regularly to make sure that they do not break down and slow production


Someone can object and say, that human invented machines do nor replicate, and therefor the comparison is invalid. Fact is however, that replication adds further complexity , since humans have not been able to construct self replicating machines in large scale. This is imho what every living cell is able and programmed to do. In order to so so, extremely complex celluar mechanisms are required, like DNA replication. 


Imagine you would be the most genius inventor of all time, more intelligent than the ten most brilliant and intelligent men of all time, Faraday, Spinoza, DaVinci, Descartes, Galilei, Leibnitz, Newton, Einstein, Goethe, and Terence Tao ( i.Q 230 ) and responsible for the creation  of:

-The Sunway TaihuLight - the most powerful and fastest supercomputer on Earth, installed in China, with 125 petaflops, 10,649,600 cores, and 1.31 petabytes of primary memory, using 10.6 million cores, and five times faster than the fastest supercomputer in u.s.a.
-the world's smallest hard disk' with 500x more storage space than best hard drive,  manipulating chlorine atoms in order to store a kilobyte of data on a microscopic storage drive
-some of the most advanced computer programming languages, like Rust, which runs incredibly fast, SQL, JAVA, Python, C++, and a few more.
-the most Technologically Advanced, extreme Power Plant in the world, a hydropower plant like no other, able to generate as much electricity as a nuclear power plant and, at the flip of a switch, act as a giant battery.
-inventor of the World's largest concentrated solar plant, the Noor complex in Morocco
-the inventor and builder  of the most advanced manufacturing facility in der world, today Tesla's  NUMMI Plant in Fremont, California, accommodating 14000 workers, which on top would have the ability to self-replicate ( which adds a huge quantity of more complex processes ) with fully automated recognition mechanisms and gates that permit  only the right cargo in and out, which has sophisticated check and error detection mechanisms all along the production process,  the ability to compare correctly produced parts to faulty ones and discard the faulty ones, and repeat the process to make the correct ones ( no recall is ever required ) and all this process fully automated and pre-programmed,
- the Most Complicated Watch Ever Made, the Vacheron Constantin Reference 57260 pocket watch with 57 distinct complications, sold for a record of us$ 11 million

now imagine this creator would give you all his inventions as a free gift. And you would not only not recognize him for what he is, did, and gave you for free,  but deny and ignore him completely, as if he would not exist.
Furthermore, you would DESTRUCT his free gift, and blame him for a unperfect job.  

How do you think would he feel with your behavior?

God is that inventor. He made your body and each single cell with:

- a gene regulatory and expression network and a transcription factor code, a  specific and pre-programmed code of gene expression which knows when, where and how to turn a gene on or off to be expressed, transcribed, and translated to produce specific cell products required in the cell for various tasks
- a nucleus, which stores DNA,  the smallest storage device possible and known, a trillion times denser than a CD, and far denser than the world's smallest hard disk,
- the genetic code, equivalent to a computer language, but 1 million times more robust than any comparable code, and less prone to errors
- encoding, transmission, and decoding of the information stored in DNA through a ultracomplex molecular machinery, like RNA polymerase, the Ribosome, chaperones etc.
- mitochondria, the power plant in the cell, which provides energy to your cells, with its amazing, almost 100% efficient ATP synthase machines,  far surpassing even the most advanced human technology
- photosynthesis, about 95% efficient when it comes to the first step of capturing light’s energy, far ahead of any human invented  solar photovoltaic system
- the cell, the most advanced factory,  the most detailed and concentrated organizational structure known to humanity
- circadian clocks, or circadian oscillators, are a biochemical oscillator that oscillates with a stable phase relationship to solar time

his inventive and creative power exceeds anything we could ever imagine or fathom. But we misuse our body, many destroy it with drugs, alcohol, various kinds of addictions, and forget completely about our creator and forget, that our body is not ours, but we are only administrators of it, besides our time, and all goods we receive. We are accountable for all we do.

Its not for nothing, that the apostle Paul writes in 1.Corinthians 3:
16 Do you not know that you are the temple of God and that the Spirit of God dwells in you? 17 If anyone defiles the temple of God, God will destroy him. For the temple of God is holy, which temple you are.

But God in his foreknowledge knew we would decide against him, and provided a solution for all destruction he knew we would provoke.  The bible says that this universe one day will be destructed in flames, and he will create a new place, that is eternal.  And he invites you to become a resident there in the future. All depends on you if you want to go there, or not.

All Things Made New
Apocalypse 21 Now I saw a new heaven and a new earth, for the first heaven and the first earth had passed away. Also, there was no more sea. 2 Then I, John,[a] saw the holy city, New Jerusalem, coming down out of heaven from God, prepared as a bride adorned for her husband. 3 And I heard a loud voice from heaven saying, “Behold, the tabernacle of God is with men, and He will dwell with them, and they shall be His people. God Himself will be with them and be their God. 4 And God will wipe away every tear from their eyes; there shall be no more death, nor sorrow, nor crying. There shall be no more pain, for the former things have passed away.” 5 Then He who sat on the throne said, “Behold, I make all things new.” And He said to me, “Write, for these words are true and faithful.” 6 And He said to me, “It is done![c] I am the Alpha and the Omega, the Beginning and the End. I will give of the fountain of the water of life freely to him who thirsts. 7

Lieven DEMEESTER: Organic Production Systems: What the Biological Cell Can Teach Us About Manufacturing September 23, 2010
Biological cells run complicated and sophisticated production systems. The study of the cell’s production technology provides us with insights that are potentially useful in industrial manufacturing. When comparing cell metabolism with manufacturing techniques in industry, we find some striking commonalitiesLike today’s well-run factories, the cell operates a very lean production system, assures quality at the source, and uses component commonality to simplify production. While we can certainly learn from how the cell accomplishes these parallels, it is even more interesting to look at how the cell operates differently. In biological cells, all products and machines are built from a small set of common building blocks that circulate in local recycling loops. Production equipment is added, removed, or renewed instantly when needed. The cell’s manufacturing unit is highly autonomous and reacts quickly to a wide range of changes in the local environment. Although this “organic production system” is very different from existing manufacturing systems, some of its principles are applicable to manufacturing, and indeed, a few can even be seen emerging today. Thus, the organic production system can be viewed as a possible scenario for the future of manufacturing.

Can we say anything about possible directions that the changes in manufacturing might take? We try to do so in this paper by studying a high-performance manufacturing system that is two billion years old—namely, the biological cell. A careful examination of the production principles used by the biological cell reveals that cells are extremely good at making products with high robustness, flexibility, and efficiency. Using the biological cell as an analogy, we describe an alternative manufacturing system that we call the “organic production system,” and we argue that it holds useful ideas for possible future trends in manufacturing. Our argument is organized as follows. 

Section 2
provides a review of related literature and introduces the methodology of learning from analogies. 

Section 3
describes the basic metaphor of this article, the biological cell as a production system, and shows that the cell is subject to similar performance pressures.

Section 4
further deepens the metaphor by pointing out the similarities between the biological cell and a modern manufacturing system. We then point to the limits of the metaphor in §5 before we identify, in §6, four important production principles that are sources of efficiency and responsiveness for the biological cell, but that we currently do not widely observe in industrial production. Analogical reasoning then leads to §7, in which we formulate and illustrate the principles of an “organic production system,” based on those four distinctive principles. We also show that partial examples of its application already exist. In the final section, we discuss the relevance of this innovative production system for possible future trends in manufacturing.

First, nature manufactures its materials under life-friendly conditions (e.g., no chemical baths or high pressure or high temperature). 
Two, nature makes materials in an orderly hierarchical structure (e.g., self-similar fractals across dimensions, which arise from growing structures from the ground up). 
Three, nature relies on self-assembly—no central logic, but decentralized growth according to local rules. Four, nature customizes materials through the use of templates; the genes are templates for proteins, which become templates for material growth. The templates can be varied, so materials are made as needed and required by the environmental challenge, with little waste.

The Cell Metabolism as a Manufacturing System

The cell is quite clearly a manufacturing system. It uses a small set of inputs to “manufacture” a wide range of compounds that help it to interact appropriately with its environment, and eventually allow it to reproduce itself . The cell manages this production in a complex network of several thousands of biochemical reactions. For example, the intestinal bacterium, Escherichia coli,  runs 1,000–1,500 biochemical reactions in parallel. Just as in manufacturing, cell metabolism can be represented by flow diagrams in which raw materials are transformed into final products in a series of operations. Figure 1, for example, shows part of a biochemical pathway, which is the equivalent of a production line, in which enzymes, which are the cell’s machines, perform operations on the different types of work-in-process inventory.

Abiogenesis: The factory maker argument Enzyme10

As in manufacturing, each of these operations has a certain capacity, and the amount of production at each step is controlled directly by signals or indirectly by limiting the material flow. With its thousands of biochemical reactions and high number of flow connections, the complexity of the cell’s production flow matches even the most complex industrial production networks we can observe today.  The performance pressures operating on the cell’s production system also exhibit clear parallels with manufacturing. Both production systems need to be fast, efficient, and responsive to environmental changeSpeed and range of response, as well as efficiency of its production systems, are clearly critical to the biological cell. Biologists have made the argument that the evolution of the basic structure of modern cells has largely been driven by “alimentary efficiency,” or the input-output efficiency of turning available nutrients into energy and basic building blocks. In addition, it is clear that in dynamic environments, the ability of the cell to react quickly and decisively is vital to ensure survival and reproduction. An important type of response, indeed, is the cell’s biosynthetic response, i.e., the response of its production systems. The cell has  competencies that allow for efficiency through energy and building block conservation, while maximizing responsiveness to environmental changes. As it is for the cell in biology, a lack of operational efficiency or responsiveness can lead to a company’s demise in industry. As has been argued by the Business Process Reengineering movement, the fate of a company may be decided by the quality of its operations rather than by its strategy. Examples abound of companies that struggled or went bankrupt because of poor operations management: Harley Davidson was on the brink of bankruptcy in 1981 because of poor product quality, high inventories, and high manufacturing costs. Boeing lost market share to Airbus in 1998 because of its inability to manufacture its backlog of ordered planes on time. Kmart filed for bankruptcy in 2000 because of poor logistics and inef- ficient supply chain management. And so on. Given the “manufacturing” nature of cell biochemistry and the comparable performance pressures on it, one should not be surprised to find interesting solutions developed by the cell that are applicable in manufacturing—especially since “cell technology” is much older and more mature than any human technology.

Commonalities Between the Cell and Manufacturing 
Although a cell and a manufacturing plant are, of course, very different organisms , we have argued that at least some of the pressures for efficiency and responsiveness that act on the biological cell’s production systems are similar to those acting upon industrial production systems. Many solutions that these two systems have developed are similar as well. We may, therefore, expect that the biological cell holds some useful lessons for manufacturing systems, in spite of the differences. The cell has not served as a role model in the historical development of manufacturing, so we should not expect to find similarities as a result of imitation or copying. However, the cell applies many of the mechanisms that can also be observed in modern manufacturing: lean production, quality at the source, and postponement. The cell carries out a very lean operation: By using pull systems and excess capacity, the storage of intermediates is kept to a minimum within the pathways. The cell also assures quality at the source, avoiding rework loops for the repair of “broken” molecules. Finally, the cell takes advantage of modularity, component commonality and postponement in its biochemical pathways. Using Pull Systems to Avoid Overproduction In biochemical pathways, production occurs only when triggered by a downstream shortage. Or, inversely, any build-up of downstream product will immediately halt further production. As long as there is still final product available, the first enzyme or “machine” of the pathway is physically blocked by an interaction between the final product and the enzyme, a mechanism called “feedback inhibition”. When the final product of a pathway is depleted by high “demand,” the first enzyme is unblocked. As it opens up for production, it gets hold of a piece of raw material and starts processing it. The cell never forecasts demand; it achieves responsiveness through speed, not through inventories. The limits to responsiveness depend only on the capacity limits of the enzymes in a particular pathway. The corresponding mechanism in manufacturing is referred to as a pull system. It produces only in response to actual demand, not in anticipation of forecast demand, thus preventing overproduction.

Minimizing Work in Process by Using Bottlenecks to Control the Release Rate In virtually all biochemical pathways, the first enzyme is the bottleneck that limits the entry rate, as illustrated in Figure 2.

Abiogenesis: The factory maker argument Enzyme11

The enzymes within the pathway can process products much faster than the entry rate and, as a result, the level of intermediate products is kept to a minimum. In manufacturing, the principle of using the bottleneck to control the release of jobs into a production line is also well known. As both the pull mechanism and the upfront bottleneck are known to simplify production control in manufacturing, it is interesting to check the amount of control and regulation overhead in the two analogous systems. Escherichia coli, for instance, is known to dedicate about 11% of its genes to regulation and control. While it is difficult to make direct comparisons with manufacturing plants, some case examples illustrate that the cell operates with little waste, even in regulating its pathways. In a U.S. electric-connectors factory in the early 1990s, 28.6% of plant labor was devoted to control and materials handling, while the figure was 14.9% in a simpler and leaner Japanese plant. In a house-care products plant, a cost analysis revealed that at least 14% of production costs were incurred by production planning and quality assurance. With its 11% of regulatory genes, the cell seems to set a pretty tight benchmark for regulation efficiency.

Using Excess Capacity to Simplify Control and Lower Work in Process
It is important for the cell to keep intermediates at a low level in order to save energy and building blocks. Work in process, in the form of intermediates, is costly—first, because space comes at a premium in the cell, and second, because inventory may degrade and represents unproductive use of material. The question is whether the cell pays a price for keeping the level of intermediates at such a low level. It does have excess capacity for all but the first enzyme in its pathways, and one may wonder whether this is efficient. In manufacturing, such excess capacity may be too costly. However, if capacity becomes more flexible and more affordable, and responsiveness more important, one may see more factories in which some safety capacity, in all operations but the first, is used to lower work in process, simplify control, and increase responsiveness to sudden market changes. The clothing retailer Zara, for example, known for its quick response capabilities, is seen to use excess capacity in its distribution systems to ensure short leadtimes and to avoid costly build-up of inventories in its warehouses.

Managing Quality at the Source 
The cell also uses quality-management techniques used in manufacturing today. The cell invests in defect prevention at various stages of its replication process, using 100% inspection processes, quality assurance procedures, and foolproofing techniques. An example of the cell inspecting each and every part of a product is DNA proofreading. As the DNA gets replicated, the enzyme DNA polymerase adds new nucleotides to the growing DNA strand, limiting the number of errors by removing incorrectly incorporated nucleotides with a proofreading function.

An example of quality assurance can be found in the use of helper proteins, also called “chaperones.” These make sure that newly produced proteins fold themselves correctly, which is critical to their proper functioning. Finally, as an example of foolproofing, the cell applies the key-lock principle to guarantee a proper fit between substrate and enzyme, i.e., product and machine. The substrate fits into a pocket of the enzyme like a key into a lock, ensuring that only one particular substrate can be processed. This is comparable with poka-yoke systems in manufacturing. An everyday example of poka-yoke is the narrow opening for an unleaded gasoline tank in a car. It prevents you from inserting the larger leaded fuel nozzle.

Exploiting Postponement and Platform Strategies 
The cell’s pathways are designed in such a way that different end products often share a set of initial common steps (as is shown in Figure 2). For example, in the biosynthesis of aromatic amino acids, a number of common precursors are synthesized before the pathway splits into different final products. This commonality reduces the number of enzymes needed to synthesize amino acids, thus conserving energy and building blocks. It postpones the decision of which amino acid, and how much of it, to synthesize. Another striking example of commonality is steroids, a class of common molecules in microorganisms, plants, and animals. Steroids help in performing various biological functions, such as regulation (hormones) or solubilization of fat (bile acids). Their basic structure is a sterane skeleton, which is modified by side chains and functional groups that give the particular molecule its specific biological activity. Steroids perfectly match the industrial definition of a platform—a set of subsystems and interfaces that form a common structure from which a stream of derivative products can be efficiently developed

Limits of the Metaphor Between the Cell and Manufacturing
In the previous section, we described a set of similarities between the cell’s production principles and modern manufacturing, providing evidence of convergent evolution for both systems.

The difference is IMHO that human production lines are not resulting of evolution, but intelligent design.....

We now examine what insights and lessons we can derive from examining some of the differences between biochemical pathways and current manufacturing systems. Before turning to insight-generating differences (§6), we must first recognize the limits of the metaphor, or fundamental differences that could invalidate parts of it or prevent the transfer of the cell’s production principles to manufacturing.  First, many differences between a cell and industrial manufacturing fall outside the scope of the metaphor—many simply reflect differences in size or materials used and cannot be clearly linked with performance, or are not meaningful within the context of industrial production. For example, the enzymatic reactions in cells all exploit basic chemical equilibria and are, in principle, reversible. This is not true in manufacturing, but since the cell does not really employ this feature in a way that makes it more efficient or more responsive, we did not explore this characteristic further. For other characteristics of cell production, the difference is real and perhaps significant, but their implications would be difficult to imagine or analyze. For example, in biological cells, the basic form of energy, the ATP molecule, is so prevalent that one is tempted to attach meaning to the lack of a clear analogous element, a “currency,” in industrial production. While noteworthy, we did not include an analysis of this difference because it did not lead to clear implications. Second, the cell faces important constraints that limit the usefulness of some otherwise clear analogies. First, as mentioned in the previous section, there are physical constraints on the maximum size of the biological cell, so we have to be careful not to draw any direct conclusions about the right scale of a manufacturing unit. A second constraint faced by one-cellular organisms is that they cannot rely on contract law or memory-enabled reciprocity to establish cooperation among multiple individuals or units. Cells may, therefore, have a stronger need to be autonomous than factories or plants. We take both of these constraints into account when proposing lessons for manufacturing in §7. A final concern is that the biological cell is the result of evolution, not design.

This is evidently false since cells had to emerge fully operational prior DNA replication took place, and consequently, evolution. 

This could raise questions about the usefulness of the cell’s production principles for manufacturing. Consider the cell’s technology, which stabilized about two billion years ago. Before that time, many technologies competed for survival: for example, RNA molecules instead of DNA for the storage of genetic information, ribozymes instead of proteins for biocatalysis, and chemosynthesis as the primary mode of energy production versus photosynthesis today. However, around two billion years ago, the fundamental “cell technology,” with its production system, reached a mature design— i.e., a stable configuration of system components and their interactions. This mature design gained a dominant “market share” of biomass on the planet and has not fundamentally changed since, as it has not been outcompeted by any other technology (although countless numbers of mutations arose). This does not mean this design is perfect; on the contrary, it is known in biology that many basic elements of cells and organisms are evolutionary relics and could be improved upon, but they are stable because they are part of the system. The quirks of evolution may indeed put some limits on the applicability of the cell’s production principles. However, these limits should not be overstated. First, even if evolution comes with some constraints, it does not mean that its solutions should be disregarded. Second, human technologies also display characteristics of evolutionary systems. Take the recent evolution of software as an example. There are still some “Stone Age” routines hidden deep down in modern software (commonly referred to as legacy code) that were written 40 years ago on card punchers, were embedded in large systems, ported to new languages, cross-linked with interfaces, and made invisible to users with layers of user interfaces. These modules may no longer be optimal or efficient; system performance could be improved if they were reengineered. The reason for retention is that reengineering has been infeasible because either the improvements would have to be implemented everywhere (impossible), or the improved versions would lose compatibility and cross-sharing (debilitating). The same is true for manufacturing systems, which contain ancient relics as well (see, for example, the discussion of today’s railway-track-width standard, which may stem ultimately from the Roman warrior chariots, Fine 1998, pp. 40–41). Thus, it seems that manufacturing systems are also constrained by evolution, which should only increase the relevance of the biological cell as a useful template.

Products and Machines Are Built from a Small Set of Common Building Blocks
The cell uses a small set of basic materials to produce an extremely wide variety of tools and products. As production technologies become more advanced, manufacturing may see a similar convergence around a common set of versatile materials. Four nucleotides, twenty amino acids, some saccharides, and fatty acids are the basic building blocks that are used for the synthesis of major cell molecules: DNA, proteins, polysaccharides, and lipids, respectively. These ingredients of life are so universal that nucleotides, amino acids, saccharides, and fatty acids can easily be exchanged across species, usually when they devour one another. A second, lower level of commonality is found in the central metabolism. Here, a limited number of about 30 intermediates can be identified, which serve as precursors for the abovementioned nucleotides, amino acids, saccharides, fatty acids, and many other biomolecules. Interestingly, the intermediates used for “products” and “machines” (enzymes) are identical. In other words, the cell can easily degrade an enzyme into its component amino acids and use these amino acids to synthesize a new enzyme (a “machine”), replenish the central metabolism, or make another molecule (a “product”), e.g., a biogenic amine. It seems an amazing achievement by the cell to build the complexity and variety of life with such a small number of components. Imagine that all industrial machines were made of only 20 different modules, corresponding to the 20 amino acids from which all proteins are made. As we further explain below, this modular approach allows the cell to be remarkably efficient and responsive at the same time. Basically, with both products and machines being built from just a few recyclable components, the cell can efficiently produce an enormous variety of products in the appropriate quantities when they are needed. In industry, parts commonality and material versatility are on the rise, but at a very rudimentary level. For example, supply chains are designed with common processes upfront and the differentiating operations at the end . The Franco-German company, SEW, produces small and medium-size electric motors for a wide range of industrial applications. For a certain line of motors, there are 50 million customer-specific variants, but by clever localization of the customized parts in a few modules of the motor, fewer than a thousand different parts suffice to yield this amount of variety.

https://reasonandscience.catsboard.com

12Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument Wed Jun 23, 2021 10:26 am

Otangelo


Admin

Cells use sophisticated high-performance molecular machines to process the data stored in genes. They copy it for future generations, and also, transfer it through transcription and translation, to then express it to create, manufacture, and produce complex molecular machines for purposeful function. This is miniaturized technology of the highest sophistication, operating with extreme accuracy and precision, high robustness, flexibility, and efficiency. The entire process is constantly being monitored, error-checked, the products are 100% inspected, fool proved,  and what is possible, being repaired. Quality assurance is achieved by helper proteins, called chaperones. These make sure that newly produced proteins fold themselves correctly, which is critical for proper functioning. Useless products are discarded and recycled and reused. For example, cells can easily degrade an enzyme into its component amino acids and use these amino acids to synthesize a new enzyme. The constant renewal eliminates the need for other types of “machine maintenance.” Assembly and disassembly of the cell’s machines are so fast and frictionless that they allow a scheme of constant machine renewal. 

KUMAR SELVARAJOO: Production Equipment Is Added, Removed, or Renewed Instantly 
The cell has pushed this principle even further. First, it does not even wait until the machine fails, but replaces it long before it has a chance to break down. And second, it completely recycles the machine that is taken out of production. The components derived from this recycling process can be used not only to create other machines of the same type, but also to create different machines if that is what is needed in the “plant.” This way of handling its machines has some clear advantages for the cell. New capacity can be installed quickly to meet current demand. At the same time, there are never idle machines around taking up space or hogging important building blocks. Maintenance is a positive “side effect” of the continuous machine renewal process, thereby guaranteeing the quality of output. Finally, the ability to quickly build new production lines from scratch has allowed the cell to take advantage of a big library of contingency plans in its DNA that allow it to quickly react to a wide range of circumstances.
https://ink.library.smu.edu.sg/lkcsb_research/1061/

Even "simple" bacteria, like Escherichia coli,  run 1,000–1,500 biochemical reactions in parallel and compete with the most complex industrial production networks we can observe today. In order to respond to different environmental conditions, cells do not store large energy-consuming inventories but respond through speed of production. Economy of energy expenditure is also achieved through production of little waste through regulation efficiency. 

The genome of E. coli encodes approximately 4,000 proteins, that of yeast 6,000; Most staggering is man. There are about 37.2 Trillion Cells in the human Body. That is 37,200,000,000,000 Cells Each contains 2,3 Billion ( 2,300000000) Proteins That sums up to 85560000000000000000000 Proteins. That is 8,556^21 Proteins. That is 8,5 Vigintillion Proteins. That is about the number of stars in the entire universe. 

In the book of Psalms, David writes in chapter 139 verses 13 and 14: “for it was You who created my inward parts; you knit me together in my mother's womb. I will praise You because I have been fearfully and wonderfully made”.

Lieven DEMEESTER Organic Production Systems: What the Biological Cell Can Teach Us About Manufacturing 3-2004
Biological cells run complicated and sophisticated production systems. The study of the cell’s production technology provides us with insights that are potentially useful in industrial manufacturing. When comparing cell metabolism with manufacturing techniques in the industry, we find some striking commonalities assures quality at the source, and uses component commonality to simplify production.  The organic production system can be viewed as a possible scenario for the future of manufacturing. We try to do so in this paper by studying a high-performance manufacturing system - namely, the biological cell. A careful examination of the production principles used by the biological cell reveals that cells are extremely good at making products with high robustness, flexibility, and efficiency. Section 1 describes the basic metaphor of this article, the biological cell as a production system, and shows that the cell is subject to similar performance pressures. Section 4 further deepens the metaphor by pointing out the similarities between the biological cell and a modern manufacturing system. We then point to the limits of the metaphor in §5 before we identify, in §6, four important production principles that are sources of efficiency and responsiveness for the biological cell, but that we currently do not widely observe in industrial production. For example, the intestinal bacterium, Escherichia coli,  runs 1,000–1,500 biochemical reactions in parallel. Just as in manufacturing, cell metabolism can be represented by flow diagrams in which raw materials are transformed into final products in a series of operations. 

With its thousands of biochemical reactions and high number of flow connections, the complexity of the cell’s production flow matches even the most complex industrial production networks we can observe today.  The performance pressures operating on the cell’s production system also exhibit clear parallels with manufacturing. Both production systems need to be fast, efficient, and responsive to environmental changeSpeed and range of response, as well as efficiency of its production systems, are clearly critical to the biological cell. Biologists have made the argument that the evolution of the basic structure of modern cells has largely been driven by “alimentary efficiency,” or the input-output efficiency of turning available nutrients into energy and basic building blocks. In addition, it is clear that in dynamic environments, the ability of the cell to react quickly and decisively is vital to ensure survival and reproduction.  Given the “manufacturing” nature of cell biochemistry and the comparable performance pressures on it, one should not be surprised to find interesting solutions developed by the cell that are applicable in manufacturing—especially since “cell technology” is much older and more mature than any human technology. The cell never forecasts demand; it achieves responsiveness through speed, not through inventories.

The limits to responsiveness depend only on the capacity limits of the enzymes in a particular pathway. The corresponding mechanism in manufacturing is referred to as a pull system. It produces only in response to actual demand, not in anticipation of forecast demand, thus preventing overproduction. While it is difficult to make direct comparisons with manufacturing plants, some case examples illustrate that the cell operates with little waste, even in regulating its pathways. In a U.S. electric-connectors factory in the early 1990s, 28.6% of plant labor was devoted to control and materials handling, while the figure was 14.9% in a simpler and leaner Japanese plant. In a house-care products plant, a cost analysis revealed that at least 14% of production costs were incurred by production planning and quality assurance. With its 11% of regulatory genes, the cell seems to set a pretty tight benchmark for regulation efficiency. The cell also uses quality-management techniques used in manufacturing today. The cell invests in defect prevention at various stages of its replication process, using 100% inspection processes, quality assurance procedures, and foolproofing techniques. An example of the cell inspecting each and every part of a product is DNA proofreading. As the DNA gets replicated, the enzyme DNA polymerase adds new nucleotides to the growing DNA strand, limiting the number of errors by removing incorrectly incorporated nucleotides with a proofreading function. An example of quality assurance can be found in the use of helper proteins, also called “chaperones.” These make sure that newly produced proteins fold themselves correctly, which is critical to their proper functioning. Finally, as an example of foolproofing, the cell applies the key-lock principle to guarantee a proper fit between substrate and enzyme, i.e., product and machine. The substrate fits into a pocket of the enzyme like a key into a lock, ensuring that only one particular substrate can be processed.

This is comparable with poka-yoke systems in manufacturing. An everyday example of poka-yoke is the narrow opening for an unleaded gasoline tank in a car. It prevents you from inserting the larger leaded fuel nozzle. The cell’s pathways are designed in such a way that different end products often share a set of initial common steps (as is shown in Figure 2). For example, in the biosynthesis of aromatic amino acids, a number of common precursors are synthesized before the pathway splits into different final products.   Interestingly, the intermediates used for “products” and “machines” (enzymes) are identical. In other words, the cell can easily degrade an enzyme into its component amino acids and use these amino acids to synthesize a new enzyme (a “machine”), replenish the central metabolism, or make another molecule (a “product”), e.g., a biogenic amine. It seems an amazing achievement by the cell to build the complexity and variety of life with such a small number of components. Imagine that all industrial machines were made of only 20 different modules, corresponding to the 20 amino acids from which all proteins are made. As we further explain below, this modular approach allows the cell to be remarkably efficient and responsive at the same time.

Basically, with both products and machines being built from just a few recyclable components, the cell can efficiently produce an enormous variety of products in the appropriate quantities when they are needed.  At any moment, synthesis and breakdown for each enzyme happen in the cell. The constant renewal eliminates the need for other types of “machine maintenance.” Assembly and disassembly of the cell’s machines are so fast and frictionless that they allow a scheme of constant machine renewal.  The cell has pushed this principle even further. First, it does not even wait until the machine fails, but replaces it long before it has a chance to break down. And second, it completely recycles the machine that is taken out of production. The components derived from this recycling process can be used not only to create other machines of the same type, but also to create different machines if that is what is needed in the “plant.” This way of handling its machines has some clear advantages for the cell. New capacity can be installed quickly to meet current demand. At the same time, there are never idle machines around taking up space or hogging important building blocks. Maintenance is a positive “side effect” of the continuous machine renewal process, thereby guaranteeing the quality of output. Finally, the ability to quickly build new production lines from scratch has allowed the cell to take advantage of a big library of contingency plans in its DNA that allow it to quickly react to a wide range of circumstances.
https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=2060&context=lkcsb_research


KUMAR SELVARAJOO: Production Equipment Is Added, Removed, or Renewed Instantly 22 October 2008
The capacity of the cell’s pathways can be adjusted almost immediately if the demand for its products changes. If the current capacity of a pathway is insufficient to meet demand, additional enzymes are “expressed” to generate more capacity within a certain range. Once the demand goes down, these enzymes are broken down again into their basic amino acids. This avoids waste as the released amino acids are then used for the synthesis of new proteins. At any moment, synthesis and breakdown for each enzyme happen in the cell. The constant renewal eliminates the need for other types of “machine maintenance.” Assembly and disassembly of the cell’s machines are so fast and frictionless that they allow a scheme of constant machine renewal. In some industrial manufacturing settings, we are also witnessing signs of the emergence of flexible capacity. Some of these companies do not repair their manufacturing equipment, but have it replaced. Take, for example, a contract manufacturer in Singapore that provides semiconductor assembly and test services for INTEL, AMD, and others. Its manufacturing equipment includes die bonders, wire bonders, and encapsulation and test equipment, all organized in pools. As soon as one machine goes down, the managers work with the equipment supplier to make a one-to-one replacement. All this goes very rapidly indeed. This policy makes sense because the low cost of a machine compared to the cost of downtime makes it economically feasible to have a couple of machines idle in the somewhat longer repair cycle. One can imagine this practice spreading as manufacturing equipment becomes more standardized and less expensive, and as the cost of a capacity shortage increases. In this scenario, machines are still repaired, although at the supplier site rather than on the manufacturing floor. The cell has pushed this principle even further. First, it does not even wait until the machine fails, but replaces it long before it has a chance to break down. And second, it completely recycles the machine that is taken out of production. The components derived from this recycling process can be used not only to create other machines of the same type, but also to create different machines if that is what is needed in the “plant.” This way of handling its machines has some clear advantages for the cell. New capacity can be installed quickly to meet current demand. At the same time, there are never idle machines around taking up space or hogging important building blocks. Maintenance is a positive “side effect” of the continuous machine renewal process, thereby guaranteeing the quality of output. Finally, the ability to quickly build new production lines from scratch has allowed the cell to take advantage of a big library of contingency plans in its DNA that allow it to quickly react to a wide range of circumstances.
https://ink.library.smu.edu.sg/lkcsb_research/1061/

CAN COMPLEX CELLULAR PROCESSES BE GOVERNED BY SIMPLE LINEAR RULES?
Complex living systems have shown remarkably well-orchestrated, self-organized, robust, and stable behavior under a wide range of perturbations. Simple linear rules govern the response behavior of biological networks in an ensemble of cells. It is daunting to know why such simplicity could hold in a complex heterogeneous environment. Provided physical reasons can be explained for these phenomena, major advancement in the understanding of basic cellular processes could be achieved. Cellular systems are characterized by the complex interplay of DNA, RNA, proteins, and metabolites to achieve specific goals: cell division, differentiation, apoptosis, etc.

My comment: Specific goals. That is pure teleology. And these specific goals had to emerge, if naturalism is true, by random, unguided accidents.

Although this is valuable advancement in modern biology, cellular properties such as growth, ageing, morphology, and immune response still remain largely elusive.

My comment: If morphology remains elusive, evolution remains elusive too. Evolution influences directly morphology, Cell shape, body shape and form, and if the mechanisms that determine these things are not understood in the first place, how they can change, cannot be known either.

To understand such complex and dynamic behavior of living systems, which may be governed by key regulatory principles, the development of systems biology approaches which integrates theoretical concepts with experimental methodologies is required. Typically, random deletions, mutations, or duplications of genes have been shown not to affect the overall network behavior or phenotypic outcome of living systems, revealing the persistence of stable and robust behavior under diverse perturbations. Biological networks are not connected randomly, but centers around a small proportion of “hub” and “connector” elements. Catastrophic failure can occur due to the lost of function of such crucial family of “hub/connector” molecules. Well-defined signal transduction module in living systems cannot result through random collisions or interactions.

Several studies have indicated that ensemble of cells display collective behavior which is deterministic (averaging), robust, highly predictable, and stable under drastic environment perturbations. Under these circumstances, we have reviewed that simple linear rules derived from the first-order mass-action response equations can be used to determine the causal relationships between biological networks. This simplicity surprisingly holds in a highly anticipated complex heterogeneous environment.
https://sci-hub.ren/https://www.worldscientific.com/doi/abs/10.1142/S0219720009003947?subid1=20210624-0013-5180-91f4-1c52cb31ffdb

Franklin M. Harold: in The Way of the Cell (Oxford: Oxford University Press, c. 2001, 205.)
Evolution of the fact of Intelligent Design
The truth of Intelligent Design is passing through three stages. First, it was ridiculed ( past ) Second, it is violently opposed ( present ). Third, it is accepted as being self-evident. ( future )

“At the cellular level, we find an incredibly intricate and “Who-ish” world where each single-celled organism is a high-tech factory complete (as one scientist described it) with artificial languages and their decoding systems, memory banks for in formation storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proofreading devices utilized for quality control, assembly processes involving the principles of prefabrication and modular construction…”

We may think of a cell as an intricate and sophisticated chemical factory. Matter, energy and information enter the cell from the environment, while waste products and heat are discharged. The object of the entire exercise is to replicate the chemical composition and organization of the original cell, making two cells grow where there was one before. Even in the simplest cells, this calls for the collaborative interactions of many thousands of molecules large and small, and requires hundreds of concurrent chemical reactions.These break down foodstuff, extract energy, manufacture precursors, assemble constituents, note and execute genetic instructions and keep all this frantic activity coordinated. The term “metabolism” designates the sum total of all these chemical processes, derived from the Greek word for “change.” Biochemistry, then, is the study of the chemical basis of all biological activity.

Enzymes derive meaning from being parts of a larger whole, the metabolic web. How enzymes perform their catalytic feats, greater by many orders of magnitude than those of inorganic catalysts, has long been one of the central questions in biochemistry. The heart of the matter is the specific, intimate, and tight binding of the substrate (or substrates) to the enzyme. Proteins (and virtually all enzymes are proteins) are not shapeless blobs, but sculptured objects, equipped with crannies and cavities that admit particular molecules, while excluding others. Binding commonly entails changes in the configuration of both substrate and enzyme, inducing stresses and strains that contribute to the mechanism of catalysis. Besides, the catalytic site supplies chemically active groups in the form of amino acid side-chains that actually participate in the reaction. The catalytic site is tailored, as it were, to its particular task, linking its structure to its function.

The genome of E. coli encodes approximately 4,000 proteins, that of yeast 6,000; it takes 3.000,000 proteins or more to make a man. What do they all do? Many proteins are enzymes, but by no means all. Some proteins serve as the building blocks of structural scaffolding. Some make tracks for the movement of organelles, itself mediated by motor proteins. Proteins act as receptors for signals from within the cell or from the outer world; they transport nutrients, waste products and viruses across membranes. Proteins also commonly modulate the activities of other proteins, or of genes. The general principle is that, except for the storage and transmission of genetic information and the construction of compartments, almost all that cells do is done by proteins. The explanation for the functional versatility of proteins is not chemical so much as physical. Amino acid chains can fold into a variety of shapes, globular and fibrous, each determined by the sequence of the amino acids that make up the protein in question. As they fold, each generates a unique contour with its own pattern of structural features: rods and hinges, platforms and channels, holes and crevices. Moreover, proteins are flexible and dynamic constructs that commonly change shape when they interact with ligands or with each other. The range of stable configurations that amino acid chains can assume is wider than that of other classes of macromolecules, nucleic acids in particular; and their flexibility permits all sorts of mechanical actions demanded of molecular machines.

Proteins, as catalysts and structural elements, are part of biochemical tradition; more recently we have come to see many of them as mechanical devices that rely on energized motion to perform their tasks. Even enzymes can be profitably looked at from this point of view: with the growing catalogue of enzyme structures has come the recognition that active sites and their elements commonly undergo rearrangement as part of the catalytic cycle and its regulation. Other proteins are there to bring about overt movement, either of molecules or of larger objects. Transport carriers reorient the binding site from one membrane surface to the other, and back again; sometimes the mechanical cycle is coupled to an energy source, turning the carrier into a pump. Students of eukaryotic cells are finding ever more motor proteins that translocate vesicles, chromosomes, or elements of the cytoskeleton from one place to another. The most familiar example is myosin, whose cyclic change of conformations underlies muscle contraction and some instances of cell motility. And bear in mind ribosomes and the polymerases that transcribe and replicate genetic information: energized movements are central to their operations. As we unravel the molecular workings of life, the cell presents itself as an assemblage of tiny machines; mundane mechanical engineering looms as large as the subtle flow of energy and information.



Last edited by Otangelo on Fri Dec 31, 2021 8:07 am; edited 3 times in total

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The factory maker argument


1. Blueprints containing instructional complex assembly information, dictating the 
2. fabrication of complex machines, robotic production lines, computers, transistors, turbines, energy plants,  and interlinked factories based on these instructions, which produce goods for specific purposes. 

Is intelligence required to make:


- a software program, a language using signs and codes like the alphabet? 
- a blueprint containing instructional assembly information ( the genetic and over a dozen epigenetic codes )
- a translation program that translates a language into another, like English to chinese ( Ribosome )
computers, hardware ( DNA )
complex machines ( proteins )
power turbines ( ATP synthase )
power generating plants ( mitochondria )
factory assembly lines ( fatty acid synthase, non-ribosomal peptide synthase )
electric circuits ( the metabolic network )
error check and repair systems  ( exonucleolytic proofreading, strand-directed mismatch repair )
factory portals with fully automated security checkpoints and control ( membrane proteins )
factory compartments ( organelles )
a library index and fully automated information classification, storage, and retrieval program ( chromosomes, and the gene regulatory network )
information retrieval ( RNA polymerase )
transmission ( messenger RNA )
translation ( Ribosome )
signaling ( hormones )
taxis ( dynein, kinesin, transport vesicles )
molecular highways ( tubulins, used by dynein and kinesin proteins for molecular transport to various destinations )
tagging programs ( each protein has a tag, which is an amino acid sequence ) informing other molecular transport machines where to transport them.
recycling methods ( endocytic recycling )
waste grinders and management  ( Proteasome Garbage Grinders )  

3. The agency that made living cells must be a super intelligent programmer, inventor, architect, director, organizer, strategist, and a formidable, electric, recycling systems, network, and systems engineer, 


Genes form a marvelous master DNA program.  Translation in the Ribosome depends on 64 Codons of the genetic code that are assigned to 20 amino acids. Amino acid strands form proteins which are incredible nano-machines, each one of them designed to perform a specific task in the cell. Proteins are the working horses of the Cells, which are outstanding machines, and some are ingeniously crafted factories. Each cell type takes in its own set of chemicals and making its own collection of products. Biological cells contain striking bioelectric circuits. Cells have exquisitely engineered recycling mechanisms. They sort out usable proteins for recycling. Clever engineering principles such as integrated control and robustness are found to be implemented in biological cells. Biological Cells demonstrate a complex architectural structure like a factory complex in a building. Gene regulatory networks carefully and precisely orchestrate the expression of genes. Cells are organized into tissues, which are organized into organs, which are organized into wonderful organ systems. Cells use a remarkable variety of languages and communication methods. Cells give and receive messages with their environment and with themselves. Circadian clocks are cell-autonomous timing mechanisms that organize and coordinate cell functions in a 24-h periodicity. Mitochondria are unusual organelles. They act as the power plants of the cell. Cells use strategies to minimize energy consumption. 

Is intelligence required to make:
1. a blueprint containing instructional assembly information to make machines full of machines?
2. machines that produce things with specific purposes ?
3. assembly lines with several robots lined up to make products for specific purposes? 
4. an entire factory producing things for specific purposes? 
5. an entire city full of interlinked factories producing things for specific purposes? 

1. Does creating a factory full of machines for a specific function using instructional assembly information require intelligence? Genes store instructional information to make proteins, which machines and cells, which are factories. 
https://www.quantamagazine.org/how-the-dna-computer-program-makes-you-and-me-20180405/
2. Does inventing a translation program require an inventor with intelligence to invent and implement that program? 64 Codons of the genetic code are assigned to 20 amino acids during translation in the Ribosome.  
https://pubmed.ncbi.nlm.nih.gov/29870756/
3. Does inventing machines for specific purposes require engineers? Proteins are nano-machines, each one of them designed to perform a specific task.
https://www.nanowerk.com/nanotechnology-news/newsid=46811.php
4. Does invent and constructing factories for specific purposes require a team of specialized engineers? Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products.
https://www.sciencedirect.com/science/article/abs/pii/S0160932707000312
5. Does the implementation of electrical networks require electrical engineers ?  Biological cells contain bioelectric circuits 
https://www.ncbi.nlm.nih.gov/books/NBK549549/
6. Does setting up recycling systems require recycling system engineers? Cells sort out usable proteins for recycling 
https://phys.org/news/2020-01-cells-recycle-components.html
7. Does implementing engineered artifacts require engineers?  Engineering principles such as integral control and robustness were found to be implemented in biological cells. 
https://www.cell.com/cell-systems/pdf/S2405-4712(16)00009-0.pdf
8. Does the making of an Architecture project require architects?  Biological Cells demonstrate a complex architectural structure like a factory complex in a building  
https://www.nature.com/articles/nrm2460
9. Does orchestrate in order to configure, coordinate, and manage require a director?  Gene regulatory networks orchestrate the expression of genes 
https://www.nature.com/articles/nrm2428
10. Does organizing require an organizer? Cells are organized into tissues, which are organized into organs, which are organized into organ systems 
https://flexbooks.ck12.org/cbook/ck-12-biology-flexbook-2.0/section/2.10/primary/lesson/organization-of-cells-bio
11. Does create a language require intelligence? Cells use a remarkable variety of languages and communication methods 
http://jonlieffmd.com/blog/the-remarkable-language-of-cells
12. Does creating communication systems require network engineers?  Cells give and receive messages with its environment and with itself. 
[url= https://www.nature.com/scitable/topic/cell-communication-14122659/]https://www.nature.com/scitable/topic/cell-communication-14122659/]https://www.nature.com/scitable/topic/cell-communication-14122659/[/url][/url]
13. Does setting up systems that work in a coordinated fashion require intelligent engineers that set them up? Circadian clocks are cell-autonomous timing mechanisms that organize and coordinate cell functions in a 24-h periodicity.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057284/
14. Does setting up power plants require systems engineers of power plants? Mitochondria are unusual organelles. They act as the power plants of the cell 
https://www.nature.com/scitable/topicpage/mitochondria-14053590/
15. Does setting up strategies to reach specific goals require a strategist? Cells use strategies to minimize energy consumption, by employing a number of common metabolic pathways for a variety of intermediate products before the pathway splits into different final products.  
http://pubsonline.informs.org/doi/pdf/10.1287/msom.1030.0033

Abiogenesis: The factory maker argument Cell_f10

Cells as computers: Looking upon cells with an information processing perspective
https://www.i2cell.science



Last edited by Otangelo on Thu Jan 13, 2022 3:34 pm; edited 5 times in total

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Do these machines have counterparts in human technology. Do they have all the characteristics of intelligent design? :
http://haha.nu/…/simple-animation-to-explain-complex-princ…/
http://commons.wikimedia.org/…/Category:Animations_of_engin…
http://twistedsifter.com/…/animated-gifs-that-explain-how-…/
https://www.lhup.edu/~dsimanek/museum/machines/machines.htm
http://explain3d.com/
BIOLOGICAL MACHINE. Some of them have analogous counterparts in human and advanced technology others do not. However, they all have the characteristics of high-tech devices and intelligently designed. There are many criteria that allow the recognition of intelligent design in nature.
Helicase:
https://www.youtube.com/watch?v=h9OZL0jOmTU
http://bioslawek.files.wordpress.com/…/helikazxa-z-mareckim…
https://www.youtube.com/watch?v=bePPQpoVUpM
https://www.youtube.com/watch?v=pgLEnjkNNlA
DNA replication:
https://www.youtube.com/watch?v=4jtmOZaIvS0
https://www.youtube.com/watch?v=OnuspQG0Jd0
https://www.youtube.com/watch?v=27TxKoFU2Nw
Sytnhase ATP:
https://www.youtube.com/watch?v=9kP79bTd5aA
https://www.youtube.com/watch?v=PjdPTY1wHdQ
http://bioslawek.files.wordpress.com/…/silnik-desygnat-pomp…
http://bioslawek.files.wordpress.com/…/mc582yn-wodny-dyskus…
Flagellum:
https://www.youtube.com/watch?v=Ey7Emmddf7Y
Spliceosome:
https://www.youtube.com/watch?v=FVuAwBGw_pQ
Bacteriophage:
https://www.youtube.com/watch?v=Dfl4F1R0Hv0
https://www.youtube.com/watch?v=qyaM577oaG4
https://www.youtube.com/watch?v=4PnPNkkfCt4
Vesicular transport:
https://www.youtube.com/watch…
https://www.youtube.com/watch?v=eRslV6lrVxY
https://www.youtube.com/watch?v=q-Er5sEaj2U
https://www.youtube.com/watch?v=u2lieHDDYPY
Kinesin-'molecular truck':
https://www.youtube.com/watch?v=y-uuk4Pr2i8
http://bioslawek.files.wordpress.com/2014/02/t1.jpg…
Mechanical stress activated channels (mechanoreceptors) in the auditory cells (the hairy cells):
https://www.youtube.com/watch?v=1VmwHiRTdVc
http://www.cochlea.eu/…/ouverture-des-canaux-de-transductio…
http://bioslawek.files.wordpress.com/…/cellule-ciliee-d-une…
Ribosomes:
https://www.youtube.com/watch?v=Jml8CFBWcDs
https://www.youtube.com/watch?v=q_n0Ij3K_Ho
https://www.youtube.com/watch?v=ID7tDAr39Ow
https://www.youtube.com/watch?v=D5vH4Q_tAkY

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God reveals Himself to us through the languages implemented in nature

The origin of:

- The language of mathematics
- The language of genetics
- The intra and extracellular signaling languages
- The languages in epigenetics
- The languages in animal communication
- The language of humans
- Boolean logic in gene regulation
- Logic in human communication

by cosmic, chemical, and biological evolution, or design? 


The universe, the physical laws, and matter have a description of themselves that can be expressed in the language of mathematics.

Cells have a codified description of themselves in digital form stored in genes and have the machinery to transform that blueprint through information transfer into an identical representation in analog 3D form, the physical 'reality' of that description.

According to the naturalist perspective, these self-replicating cells became an agglomerate of socializing cells, creating another higher language to process information, based on communication through signaling. They started to talk to each other using sophisticated signaling networks.

Not enough, they started to differentiate, giving rise to a multicellular organism, creating tissues, organs, organ systems, and bodies that could sense the environment.
And they created an additional 45 different languages, used to orchestrate cell differentiation, cell migration, cell adaptation, a protective immune system, and the ability to adapt to different environmental conditions.

Here, they also advanced by applying logic during gene expression, and smart as they are, programmed using boolean logic, the software, to select the right genes, to be expressed at the right time during development.   

And last not least, this complex agglomeration of self-replicating cells created neurons, tiny computers, then created a brain, and that brain created another emergent property, called consciousness, and another language, based on words and using logic.

Since that was not enough, the organism created sense perception. It created hearing, seeing, smelling, tasting, and feeling. 

Different degrees of communications were implemented in the natural world. Animals use courtship calls. Dolphins use echolocation to hunt prey. Trees talk to each other through pheromones and other scent signals. 
Animals use visual or acoustic communication, chemical signals, magnetic field orientation, etc.

Then, man evolved from lower primates. The human conscious mind was able to evolve using language, to detect, and describe itself, and its environment. Amazing.

Able to discover and describe the mathematical language used to create the laws of physics, atoms, the genetic language to make living cells, epigenetic languages to make multicellular organisms, itself, and even to philosophize how all that was a product of a fortunate accident. That was an unfortunate accident. That it was able to come to false conclusions, based on wishful thinking. Putting will ahead of reason.

Obviously, the language of mathematics, genetics, epigenetics, boolean logic, human language, and the logic applied to the human language, could only be the product of a pre-existing mind, using its innate eternal language and logic to create things similar to himself.

Whenever there is a mechanism implemented that is able to process information, it has to be implemented by consciousness using intelligence.  

In the beginning, was the Word, and the Word was with God, and the Word was God. In him was life. Through him all things were made; without him, nothing was made that has been made.
Consciousness came first and is fundamental.  That a living being, conscious and able to communicate with words using language and logic, was able to instantiate all language systems described above using language. We call it God. The God of the Bible.  I AM. An eternal being, superintelligent and conscious. We are his thoughts. All started from the mind of God.

That higher conscious being instantiated also communication with his creatures. Us. God talks to us, and we can talk to him. He has expressed his love through Christ, and we can love Him back, believing, and obeying Him.

Isn't that awesome?!!

Decoding reality - Information is fundamental
https://reasonandscience.catsboard.com/t3035-decoding-reality-information-is-fundamental

Abiogenesis: The factory maker argument Indexs10

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16Abiogenesis: The factory maker argument Empty I have been fearfully and wonderfully made Fri Dec 31, 2021 8:08 am

Otangelo


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I have been fearfully and wonderfully made

https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#9065

Cells use sophisticated high-performance molecular machines to process the data stored in genes. They copy it for future generations, and also, transfer it through transcription and translation, to then express it to create, manufacture, and produce complex molecular machines for purposeful function. This is miniaturized technology of the highest sophistication, operating with extreme accuracy and precision, high robustness, flexibility, and efficiency. The entire process is constantly being monitored, error-checked, the products are 100% inspected, fool proved,  and what is possible, being repaired. Quality assurance is achieved by helper proteins, called chaperones. These make sure that newly produced proteins fold themselves correctly, which is critical for proper functioning. Useless products are discarded and recycled and reused. For example, cells can easily degrade an enzyme into its component amino acids and use these amino acids to synthesize a new enzyme. The constant renewal eliminates the need for other types of “machine maintenance.” Assembly and disassembly of the cell’s machines are so fast and frictionless that they allow a scheme of constant machine renewal.

KUMAR SELVARAJOO: Production Equipment Is Added, Removed, or Renewed Instantly
The cell has pushed this principle even further. First, it does not even wait until the machine fails, but replaces it long before it has a chance to break down. And second, it completely recycles the machine that is taken out of production. The components derived from this recycling process can be used not only to create other machines of the same type, but also to create different machines if that is what is needed in the “plant.” This way of handling its machines has some clear advantages for the cell. New capacity can be installed quickly to meet current demand. At the same time, there are never idle machines around taking up space or hogging important building blocks. Maintenance is a positive “side effect” of the continuous machine renewal process, thereby guaranteeing the quality of output. Finally, the ability to quickly build new production lines from scratch has allowed the cell to take advantage of a big library of contingency plans in its DNA that allow it to quickly react to a wide range of circumstances.
https://ink.library.smu.edu.sg/lkcsb_research/1061/

Even "simple" bacteria, like Escherichia coli,  run 1,000–1,500 biochemical reactions in parallel and compete with the most complex industrial production networks we can observe today. In order to respond to different environmental conditions, cells do not store large energy-consuming inventories but respond through speed of production. Economy of energy expenditure is also achieved through production of little waste through regulation efficiency.

The genome of E. coli encodes approximately 4,000 proteins, that of yeast 6,000; Most staggering is man. There are about 37.2 Trillion Cells in the human Body. That is 37,200,000,000,000 Cells Each contains 2,3 Billion ( 2,300000000) Proteins That sums up to 85560000000000000000000 Proteins. That is 8,556^21 Proteins. That is 8,5 Vigintillion Proteins. That is about the number of stars in the entire universe.

In the book of Psalms, David writes in chapter 139 verses 13 and 14: “for it was You who created my inward parts; you knit me together in my mother's womb. I will praise You because I have been fearfully and wonderfully made”.

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I have never seen random, irregular, undetermined, undirected, stochastic, accidental, events driven by no mechanism or agent, but by pure luck and chance/probability on its favor, hitting the jackpot, creating a hardware like a harddisk, a information storage device, and in parallel, creating the accompanying software, composed of a language with alphabet, statistics, grammar, syntax and apobetics, a collection of punctuation marks and regulatory sites, , sharing 10 of the 13 characteristics of human language, furthermore a translation mechanism, cipher or code, information transmission systems that encode, transmit, decode through transcription and translation.

Then, furthermore, using that computer-like information system to create a digital blueprint, complex specified instructional assembly information instituted through the function bearing sequence of the words of that language, stored in that information storage device, and transforming it into an identical representation in analog 3D form, the physical 'reality' of that description. That information directing the making and operation of thousands of machines, each composed of several irreducibly complex parts, and many interlinked in the right way to create robot-like production lines, resulting in a self-replicating factory of highest technological sophistication, robust, error-prone, and able to adapt to the most varigated external conditions.

All this, driven by energy turbines, that permit the operation of the factory. Making a factory depends on hardware/software, buiding blocks, and energy, that bear no function on their own. All three need to work in a joint venture, and if one component is missing, nothing functions.

Concluding that unguided stochastic events are not a plausible explanation for the origin of all above described, which is what analogously living cells are, is not an argument from incredulity or ignorance. When we have two competing alternatives, intelligence, and non-intelligence, and we have repeated experience that intelligence can instantiate all this, while we have never observed non-intillgence being capable of doing it, we are rationally warranted to conclude that intelligent design is the more case-adequate explanation.

Abiogenesis: The factory maker argument Abioge12

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If you'd go to mars, and find an abandoned city, you would immediately conclude: Aliens made it.
Science unraveled the cell as a city full of interlinked factories, full of machines, production lines, energy turbines, but conclude: Nobody made it?
How does that make sense?

Cell Analogies “A Cell is like a city …..”.
https://slideplayer.com/slide/8019227/

1. All things that are made for specific purposes are first conceptualized in the mind, then a blueprint is made, and the end product is assembled based on the instructional blueprint. It starts with a mind and ends with the product.
2. Living cells, the smallest unit of life, analogously, have the purpose to perpetuate life through self-replication. Each of them has a codified description of themselves in digital form stored in genes and have the machinery to transform that blueprint through information transfer into an identical representation in analog 3D form, the physical 'reality' of that description.
3. That is analogous to human-made things with purpose. “If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”
4. Therefore, we can logically infer and conclude, that an intelligent mind was at the beginning to create life.

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Timothy R. Stout Information-Driven Machines and Predefined Specifications: Implications for the Appearance of Organic Cellular Life April 8, 2019

https://osf.io/qz7bn/?fbclid=IwAR1AaVWUvLokPTbYsbsy5bdCyqEZLUUITJIrAa6vk6TvQhCczFBA8zI26UA


The actual appearance on Earth of a living cell required an intelligent being to work outside of natural law in order to arrange molecules and atoms into dynamic relationships with each other in accordance with a predefined specification, one which was developed through intelligence and apart from natural processes. There is a word we use to call an extremely intelligent being who can move molecules and atoms into predetermined, dynamic relationships at will—God. This paper has plausibly demonstrated how unsuppressed, unbiased scientific observation leads to a Being with the characteristics of God as the source of the physical life we see around us.

One purpose of scientific investigation is to determine the scope and limits of physical processes. This is particularly true for abiogenesis because this field of study is dedicated to reconstructing a possible explanation for the origin of life on the basis of processes we see today at work in physics, chemistry, geology, and biology. A proper understanding of the scope and limitations of available processes is essential for legitimate attempts at historical reconstruction. A living cell may be viewed as an information-driven machine. A body of information is stored in a genome within the cell. Cellular “hardware” then reads, decodes, and uses the information. The information drives the operation in a manner analogous to how software in a computer drives computer hardware. In both cases, proper information needs to be available for use by functioning hardware which in turn is controlled by it. The gradual step-by-step developmental processes characteristic of evolution are not compatible with the first appearance of a computer. There is a minimum amount of functioning information required for computer operation. There is a minimum amount of functioning hardware required for computer operation. The information and hardware must interact with each other in a very intricate, intertwined manner. The minimum amounts required for each are staggeringly complex. In industry, a computer needs to be designed before it is fabricated. The probability is virtually zero for an unguided, random combination of logic gates to form a functioning computer, complete with internal memory, memory address logic, data registers, a central processing unit, data input, and output components, control signal inputs, and outputs, and connections between internal components. Beyond this, there are no known means for random combinations of logic to generate a body of information tailored to work with a specific form of computer hardware. There are no known means for such information to be stored for use by the computer and to be accessible by it. Computers are the product of deliberate intelligent action, not random processes. Since computers and living cells are both information-driven machines, this suggests the possibility that the difficulties facing initial computer fabrication could also apply to initial cell fabrication. If this suggestion proves valid, it poses serious issues concerning the adequacy of natural processes being adequate to account for the information-driven physical life we see around us. There is another aspect of this problem that has particular significance. In industry, both computers and processer-driven applications ranging from microwave ovens to self-driving automobiles start with a predefined system specification.

Typically, this will define an overall task for the machine to accomplish. Some tasks may be done in hardware or software. Typically, the software is cheaper and more readily adapts to a wide range of possible variations in operation. However, hardware is faster and requires minimal input to trigger its operation. The specification determines whether a particular task is to be done in hardware or software. It also determines how the software and the hardware interact with each other to accomplish a given task. A major objective of the system specification is to define a software specification describing what the software needs to do and a hardware specification defining what the hardware needs to do. In industry, separate hardware and software design engineering teams then design a product meeting their specified goals. In an ideal world, the system specification will be so complete and accurate and the proficiency of the software and hardware engineers in implementing their specifications will likewise be so complete and accurate that the system will work the first time the power is turned on and the two are brought together. In real life, this is not typical.

Concluding Analyses
If a living cell is more complex than a physical computer and if debug of computer design typically is an extremely difficult task, this suggests that a living cell must have its origin in a being so intelligent that it can anticipate all of the behaviors of the various arrangements of building block amino acids and nucleotides. The first cell must appear in working form without needing debug. This is particularly the case since special test equipment for identifying design problems would not be available in a prebiotic scenario. Although mutation and natural selection can have use in adapting an already living cell to changing environmental conditions, they appear inadequate to meet the requirements of initial cellular appearance. A slight modification of an existing, already working design is trivial compared to the difficulties of implementing an initial design. During my experience as an industrial design engineer, I was active on many design projects that were canceled for various reasons. I have worked on designs that were ready for a prototype to be built, but funds were not provided to make it. There is a difference between having a paper design, no matter how good it might be, and actually having resources to build the product. It is insufficient for an intelligent being to design a living cell capable of survival in the environment in which it will appear. Since the design specification appears outside of natural law, its physical implementation must also take place outside of natural law. Natural processes have no ability to implement non-material plans.

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Timothy R. Stout A Natural Origin-of-Life: Every Hypothetical Step Appears Thwarted by Abiogenetic Randomization May 5, 2019

https://osf.io/p5nw3/?fbclid=IwAR0vAV5jVQR7Z-IT_S1fQzJQ_fMonIgUW9xvj0quKIOFdgWWwcnzPPStXIc

This is not a paper on metaphysics. No solution is offered to these problems posed by the conclusion presented; they are beyond the scope of the paper. However, it appears that nature itself provides conclusive evidence that natural processes are incapable of assembling a living cell. Wherever one looks there are problems.

Prebiotic processes naturally randomize their feedstock. This has resulted in the failure of every experimentally tested hypothetical step in abiogenesis beginning with the 1953 Miller-Urey Experiment and continuing to the present. Not a single step has been demonstrated that starts with appropriate supply chemicals, operates on the chemicals with a prebiotic process, and yields new chemicals that represent progress towards life and which can also be used in a subsequent step as produced. Instead, the products of thousands of experiments over more than six decades consistently exhibit either increased randomization over their initial composition or no change. We propose the following hypothesis of Abiogenetic Randomization as the root cause for most if not all of the failures: 1) prebiotic processes naturally form many different kinds of products; life requires a few very specific kinds. 2) The needs of abiogenesis spatially and temporally are not connected to and do not change the natural output of prebiotic processes. 3) Prebiotic processes naturally randomize feedstock. A lengthy passage of time only results in more complete randomization of the feedstock, not eventual provision of chemicals suitable for life. The Murchison meteorite provides a clear example of this. 4) At each hypothetical step of abiogenesis, the ratio of randomized to required products proves fatal for that step. 5. The statistical law of large numbers applies, causing incidental appearances of potentially useful products eventually to be overwhelmed by the overall, normal product distribution. 6) The principle of emergence magnifies the problems: the components used in the later steps of abiogenesis become so intertwined that a single-step first appearance of the entire set is required. Small molecules are not the answer. Dynamic self-organization requires from the beginning large proteins for replication, metabolism, and active transport. Many steps across the entire spectrum of abiogenesis are examined, showing how the hypothesis appears to predict the observed problems qualitatively. There is broad experimental support for the hypothesis at each observed step with no currently known exceptions.

Just as there are no betting schemes that allow a person to overcome randomness in a casino, there appear to be no schemes able to overcome randomness using prebiotic processes. We suggest that an unwillingness to acknowledge this has led to the sixty plus years of failure in the field. There is a large body of evidence—essentially all experiments in abiogenesis performed since its inception sixty plus years ago—that appear to be consistent with the hypothesis presented in this paper. Randomization prevails.

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God is the best explanation for the existence of life

https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#9226

Life depends on instructional complex information stored in a stable DNA molecule, that has the function of a computer hard drive. Information that is encoded, transmitted, and decoded by very complex molecular machines.  That information governs the making and operating of irreducibly complex machines, production lines, metabolic pathways,  and the operation of self-replicating and reproducing cell factories, able to adapt to the environment and keep their internal homeostatic milieu. It depends on the four basic specified complex building blocks, and energy in the form of complex ATP molecules, the energy currency in the cell. It depends on the ability to the uptake of nutrition, and ability of waste disposal, and recycling. It depends on the program that knows how to direct the growth and development, permanence, and change. All these features are irreducible, and each of them is life essential. If one is missing, no life.

Let me make a confession here. I am incredulous that such a staggeringly complex molecular chemical factory could emerge by unguided random events on the early earth, without the input of an intelligent agent, super-powerful, with intelligence, goals, foresight, will, and purpose, to bring forth biological life, which is essentially composed of parts, that are all only functional if summed up, contributing to the higher-order, but individually, have no function at all. I am credulous that intelligence is capable, non-intelligence is not, and that only intelligence can instantiate the transition from chemical non-life, to biological life.

Denton: Evolution, A Theory in Crisis, page 249
We now know not only of the existence of a break between the living and non-living world but also that it represents the most dramatic and fundamental of all the discontinuities of nature. Between a living cell and the most highly ordered non-biological system, such as a crystal or a snowflake, there is a chasm as vast and absolute as it is possible to conceive.

Lynn Margulis:
To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium.

Of course, if someone is desperate to deny a creator, like Richard Dawkins, that person can resort to aliens. But then the enigma is just pushed back a step further. Who or what made these aliens?

This is also not an argument from ignorance. To say: There are swirling potatoes surrounding mars, prove me wrong - that is an argument from ignorance. I make up a claim that I cannot back up - and ask others to disprove it. No. I am saying that we know by our own experience as beings like us equipped with intelligence, that we are capable of instantiating a codified description of a device for specific purposes in digital form, a blueprint,  stored on a hard disk, and the know-how to instantiate the information transition machinery that encodes, transmits, and decodes the information to transform that information of the blueprint into an identical representation in analog 3D form, the physical 'reality' of that description.  There is no need to make predictions and test if it is possible. We already know it is by our own experience.

Cells have a codified description of themselves in digital form stored in genes and have the machinery to transform that blueprint through information transfer into an identical representation in analog 3D form, the physical 'reality' of that description. Using Bayesian probability, or abductive reasoning, an intelligent cause is the best explanation.

You can also object that we have never seen God creating life. That's true. Neither have we, that natural causes did it. What is, is the path to the cause. We can make logical inferences to the best explanation.

“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.”

We can infer, using logical, rational reasoning, that intelligence is the more case-adequate causal principle, rather than unguided stochastic, random events. Asking, HOW God did it, is asking for an explanation of the explanation.

What's the Mechanism of Intelligent Design?

https://reasonandscience.catsboard.com/t1794-how-exactly-did-god-create-the-universe-and-the-world-what-process-was-involved

W.L.Craig: First, in order to recognize an explanation as the best, one needn't have an explanation of the explanation. This is an elementary point concerning inference to the best explanation as practiced in the philosophy of science. If archaeologists digging in the earth were to discover things looking like arrowheads and hatchet heads and pottery shards, they would be justified in inferring that these artifacts are not the chance result of sedimentation and metamorphosis, but products of some unknown group of people, even though they had no explanation of who these people were or where they came from. Similarly, if astronauts were to come upon a pile of machinery on the backside of the moon, they would be justified in inferring that it was the product of intelligent, extra-terrestrial agents, even if they had no idea whatsoever who these extra-terrestrial agents were or how they got there. In order to recognize an explanation as the best, one needn't be able to explain the explanation. In fact, so requiring would lead to an infinite regress of explanations, so that nothing could ever be explained and science would be destroyed. So in the case at hand, in order to recognize that intelligent design is the best explanation of the appearance of design in the universe, one needn't be able to explain the designer.

I have not enough faith to be an atheist. Why do you?

The factory maker argument
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument

Abiogenesis: The factory maker argument Last_u11

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REBECCA MCCLELLAN: Stanford researchers gain insight into how cells avoid assembly-line mistakes NOVEMBER 4, 2021

Molecular assembly lines maintain their precise control while shepherding growing molecules through a complex, multi-step construction process. Every cell is a master builder, able to craft useful and structurally complex molecules, time and again and with astonishingly few mistakes.  There are thousands of these assembly lines in nature, and they all make unique compounds.   These molecular assembly lines maintain their precise control while shepherding growing molecules through a complex, multi-step construction process. Cells, for example, synthesize polyketides through molecular assembly lines called synthases. Each synthase contains anywhere between three to 30 “modules,” groups of active proteins, or enzymes, organized sequentially. Each module is a station in the assembly line that is responsible for adding a piece to a growing molecular chain and then installing chemical modifications to that unit. Passing from module to module, a polyketide grows in size and complexity until it eventually rolls off the conveyor belt in its final form. This assembly line, like others, always manages to push the growing molecule in the right direction, a feat that the laws of thermodynamics can’t fully explain. The assembly line looks like BMW plant. These are amazingly complex molecular machines. There are so many components that have to come together at the right place and the right time, in a highly orchestrated way.  Each module is made up of a pair of enzymes, each of which has a molecular arm that extends out from the module’s sides. It was widely thought that these arms mirror one another in their poses. One arm extends out while the second arm flexed downward. The structure is the module in action and the bent arm could be the key to the assembly line’s directionality. Each module can only work on two molecules at a time. It's a “turnstile” mechanism, with each module closing itself off to incoming chains until it releases one it’s working on. This flexed arm acts as the arm of the turnstile. The turnstile arm appears to have two jobs. First, it acts as a gatekeeper and physically blocks incoming molecules from entering while one is being processed. Second, the contortion of the enzyme into that asymmetric pose requires energy, which gets stored in the flex of the arm. The relaxation of the arm back to its “normal” state, which releases the pent-up energy, helps propel the molecule under construction to the next stage of the assembly line. These enzymes are capturing energy in these amazing contortions, and they use that energy to power something else.

SAKET R. BAGDE Modular polyketide synthase contains two reaction chambers that operate asynchronously 4 Nov 2021 2

Type I modular polyketide synthases are multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and keto-group modification reactions.  These structures revealed how the constituent domains are positioned relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific interactions formed between the domains. Lsd14 contains two reaction chambers, but only one chamber has the full complement of catalytic domains, indicating that only one chamber produces the polyketide product at any given time. Polyethers are generated via a common three-stage biosynthetic scheme. Stage 1: construction of the polyketide backbone by modular polyketide synthases (PKSs). Stage 2: stereoselective epoxidation of the polyene intermediate by a monooxygenase. Stage 3: formation of the hallmark cyclic ether groups by one or more epoxide hydrolases. Multiple modules act successively in an assembly line-like fashion where each module performs a single round of chain extension followed by β-keto group modification reaction and then transfers the growing polyketide chain to the next module. The final PKS module in the biosynthesis pathway typically contains a thioesterase (TE) domain that catalyzes release of the fully extended polyketide product.

My comment:  Isn't that an amazing example of ingeniosity of its finest at a molecular level? We see here machine-like operations, that depends on several modules operating in an assembly line-like fashion, as a joint venture together. Only intelligence invents machines and assembly lines. It has never been demonstrated otherwise. 

1. https://news.stanford.edu/2021/11/04/cells-avoid-molecular-assembly-line-mistakes/
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8689591/

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Alberts: Molecular biology of the Cell 6th ed. 2015
The surface of our planet is populated by living things—curious, intricately organized chemical factories that take in matter from their surroundings and use these raw materials to generate copies of themselves.  
All cells function as biochemical factories dealing with the same basic molecular building blocks.
When DNA is damaged by irradiation, the set of enzymes needed to carry out  DNA repair is observed to congregate in discrete foci inside the nucleus, creating “repair factories”
Cells host mRNA production factories and DNA replication factories  1

B.C. Currell: The Molecular Fabric of Cells October 22, 2013
The central theme of both of these texts is to consider cells as biological factories. Cells are, indeed, outstanding factories. Each cell type takes in its own set of chemicals and making its own collection of products. The range of products is quite remarkable and encompasses chemically simple compounds such as ethanol and carbon dioxide as well as extremely complex proteins, carbohydrates, lipids, nucleic acids, and secondary products. 2 

Robert M.Hazen:  Science Matters: Achieving Scientific Literacy 2009
Pg.239 Cells act as chemical factories, taking in materials from the environment, processing them, and producing “finished goods” to be used for the cell’s own maintenance and for that of the larger organism of which they may be part. In a complex cell, materials are taken in through specialized receptors (“loading docks”), processed by chemical reactions governed by a central information system (“the front once”), carried around to various locations (“assembly lines”) as the work progresses, and finally sent back via those same receptors into the larger organism. The cell is a highly organized, busy place, whose many different parts must work together to keep the whole functioning. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply.
Pg. 242 Nucleic acids. These molecules (DNA and RNA) carry the blueprint that runs the cell’s chemical factories, and also are the vehicle for inheritance
Pg. 243 Carbohydrates. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply. The basic building blocks of carbohydrates are sugars—small ring-
Pg. 245 Like any factory, each cell has several essential systems. It must have a front office, a place to store information, and issue instructions to the factory door to guide the work in progress. It must have bricks and mortar—a building with walls and partitions where the actual work goes on. Its production system must include the various machines that produce finished goods as well as the transportation network that moves raw materials and finished products from place to place. And finally, there must be an energy plant to power the machinery.
Pg. 246 Cellular factories consist of walls, partitions, and loading docks.
Pg. 249 Every living thing is composed of one or more cells, each of which has a complex anatomy. A “generic” cell contains many structures and organelles—tiny chemical factories.
Pg. 263 The sequence of the bases along the double helix of DNA contains the genetic code—all the information a cell needs to reproduce itself and run its chemical factories, all the characteristics and quirks that make you unique.
Pg. 309 Shortly thereafter, the glucose is processed in cellular chemical factories to form part of the cellulose fibers that support each grass blade. The carbon atom has become an integral part of the structure of grass. 3

Andrew Reynolds: The cell's journey: from metaphorical to literal factory  June 2007
All living things are made from cells, the chemical factories of life. Cells act as chemical factories, taking in materials from the environment, processing them, and producing ‘‘finished goods’’ to be used for the cell’s own maintenance and for that of the larger organism of which they may be part. Today in the twenty-first century, metaphorical imagery has become a reality, with cells acting as chemical factories for the synthesis of commercially valuable bio-products. Recent techniques and knowledge in molecular biology and genetics mean that living cells – from bacteria to man – are now becoming real ‘factories’.  One can expect in the near future that bacteria will be entirely reprogrammed, and perhaps even created de novo from bits and pieces, to constitute man-made cell factories. 4

Antoine Danchin: The bag or the spindle: the cell factory at the time of systems' biology 10 November 2004
Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes . . . or small gene clusters are improved and expressed in a variety of hosts. New techniques derived from functional genomics . . . now allow users to shift from this single-gene approach to amore integrated view of the cell, where it is more and more considered as a
factory. One can expect in the near future that bacteria will be entirely reprogrammed, and perhaps even created de novo from bits and pieces, to constitute man-made cell factories. This will require exploration of the landscape made of neighbourhoods of all the genes in the cell. Present work is already paving the way for that futuristic viewof bacteria in industry 5

Francesca Tomasi: An Introduction to Ribosomes: Nature’s busiest molecular machines OCTOBER 13, 2020
Cells – the smallest functional units of any living organism – are tiny factories that build biological products, or molecules 6

Antoine Danchin: The bag or the spindle: the cell factory at the time of systems' biology 10 November 2004
New techniques derived from functional genomics (transcriptome, proteome and metabolome studies) now allow users to shift from this single-gene approach to a more integrated view of the cell, where it is more and more considered as a factory. More than 40,000 pages are indexed in the WWW Browser Engine Google for the keyword "cell factory". ( In 2022, over 2 Mio )    7

José Manuel Otero: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory January 21, 2013
Saccharomyces cerevisiae is the most well-characterized eukaryote, the preferred microbial cell factory 8



1. Alberts: Molecular biology of the Cell 6th ed. 2015 https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/dp/0815345240
2. B.C. Currell: The Molecular Fabric of Cells  October 22, 2013 https://www.amazon.com./Molecular-Fabric-Biotechnology-Learning-English-ebook/dp/B01E3ICWPU
3. Robert M.Hazen:  Science Matters: Achieving Scientific Literacy 2009 https://www.amazon.com/Science-Matters-Achieving-Scientific-Literacy/dp/0307454584
4. Andrew Reynolds: The cell's journey: from metaphorical to literal factory June 2007 https://www.sciencedirect.com/science/article/abs/pii/S0160932707000312
5. Antoine Danchin: The bag or the spindle: the cell factory at the time of systems' biology 10 November 2004 https://microbialcellfactories.biomedcentral.com/articles/10.1186/1475-2859-3-13
6. Francesca Tomasi: An Introduction to Ribosomes: Nature’s busiest molecular machines OCTOBER 13, 2020 https://sitn.hms.harvard.edu/flash/2020/an-introduction-to-ribosomes-natures-busiest-molecular-machines/
7. Antoine Danchin: bag or the spindle: the cell factory at the time of systems' biology 10 November 2004 https://microbialcellfactories.biomedcentral.com/articles/10.1186/1475-2859-3-13
8. José Manuel Otero: Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory January 21, 2013 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054144

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24Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument Mon Jul 18, 2022 12:30 pm

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Specified complex information using a genetic language ( consistent of codon "words", start and stop signs) dictates and directs the making and operation of irreducible complex molecular machines, (proteins), robotic molecular production lines (metabolic pathways), energy turbines (ATP synthase), and chemical self-replicating factories (cells). What alternative mechanism to intelligence do you propose to explain the origin of all this?

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