Intelligent Design, the best explanation of Origins

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Abiogenesis: The factory maker argument

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

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The factory maker argument

https://www.youtube.com/watch?v=f8oGda1JxKw

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.”

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 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.”

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/

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: 


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

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

Abiogenesis: The factory maker argument JL02zBk

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



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2Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Tue Dec 15, 2015 10:08 am

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

http://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. 

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.”


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? 

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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
http://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
http://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. 

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

Analogy Viewed from Science
http://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

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. 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. 

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. 

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Objection: cells are not factories in a literal sense.
Answer: 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 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.

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
http://libgen.io/search.php?req=The+Molecular+Fabric+of+Cells&lg_topic=libgen&open=0&view=simple&res=25&phrase=1&column=def

 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 encompass chemically simple compounds such as ethanol and carbon dioxide as well as the 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.

To understand 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.

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

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

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.
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/

Abiogenesis: The factory maker argument QEJ4DJ9




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



Abiogenesis: The factory maker argument WB4FVEm

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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 : 

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. 

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

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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.  


Ed Croteau
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.


DNA - the instructional blueprint of life
http://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

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 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.

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

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

http://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.



 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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."

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."

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

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

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.

Abiogenesis: The factory maker argument The_fa11



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/



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Organic Production Systems: What the Biological Cell Can Teach Us About Manufacturing
https://ink.library.smu.edu.sg/cgi/viewcontent.cgi?article=2060&context=lkcsb_research

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.  A final concern is that the biological cell is the result of evolution, not design. Consider the cell’s technology, which stabilized about two billion years ago. 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.


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.

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...


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

Quantum biology 6
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. 


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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.

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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.

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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.

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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

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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.

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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.

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

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

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.

Abiogenesis: The factory maker argument Mm5QlIC


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




Information Management for Factory Planning and Design 

Manufacturing   and Factory  location:
In a human factory:
The term manufacturing location represents the external perspective. Within the scope of developing business sectors, market offers, and necessary processes, a suitable manufacturing location has to be selected from a global perspective. Sometimes a web of different manufacturing companies produces subparts at different locations and countries, each factory at a different place producing different parts, which then are sent to a central assembly factory. The whole process must be coordinated and managed. The factories communicate with each other to coordinate the whole manufacturing process. In order to quickly seize opportunities for a complex product or system, a number of factories
can temporarily join together for a project and bundle their processes and resources.
In the cell:
In a developing animal embryo, the four fundamental processes are happening in a kaleidoscopic variety of ways, as they give rise to different parts of the organism. 4 Like the members of an orchestra, the cells in the embryo have to play their individual parts in a highly coordinated manner. In the embryo, however, there is no conductor—no central authority—to direct the performance. Instead, development is a self-assembly process in which the cells, as they grow and proliferate, organize themselves into increasingly complex structures. Each of the millions of cells has to choose for itself how to behave, selectively utilizing the genetic instructions in its chromosomes. The mechanism that sets up the basic body plan of the developing fly is surprisingly precise. ( that is, that coordinates where the individual cells have to be )  Question : had these instructions not have to be pre-programmed through a intelligent  mind?


Morphology of Factory Types
In a human factory:
Various types of factories can be made, depending on the requirement of production. The choosing and decision making of which factory type is required is a mental process.

In the cell:
In developmental biology, cellular differentiation is the process of a cell changing from one cell type to another. Most commonly this is a less specialized type becoming a more specialized type, such as during cell growth. Differentiation occurs numerous times during the development of a multicellular organism as it changes from a simple zygote to a complex system of tissues and cell types. 5
The Development of Multicellular Organisms Requires the OrchestratedDifferentiation of Cells 6
Each multicellular organism begins as a single cell. For this cell to develop into a complex organism, the embryonic cells must follow an intricate program of regulated gene expression, cell division, and cell movement. Programming is throughout a mental process.  The developmental program relies substantially on the responses of cells to the environment created by neighboring cells. Cells in specific positions within the developing embryo divide to form particular tissues, such as muscle.

Factory planning:
Factory planning covers all activities in the fold-out, except the installation parts, when developing a (new) factory. It extends from investigating the feasibility of the factory.

Factory design:  
The main result from the factory design is the factory layout.

Information management within factory planning and design:
This part focuses on the information that needs to be managed within factory planning and has a deeper focus on factory design. Information management in this research is not about PLM (Product Lifecycle Management) as many people will relate to. Information management in this research means how all the information within a domain can/should be organized, structured, represented and presented for the best use and reuse, both for humans and applications. This is also the foundation for a good realization of PLM or rather MLM (Manufacturing lifecycle management) in this case.

Factory layout planning:
it is also about the information needed to develop a factory layout. Factory layout can be manufacturing system layout, building layout, or safety layout. flow simulation, scheduling and optimization for fine tuning of the layout.

Equipment supply:  
management of equipment and raw material supply

Process planning:
The focus of process planning is how a part or product should be manufactured in a machine or a manufacturing system. The planning handles the selection of the right type of process, sequence planning, measurement planning, appropriate fixture design etc.

Production Planning and Control

Abiogenesis: The factory maker argument Produc10

In a human factory:
The control loop, as depicted above, is well suited as a model for planning the production.  Based on these a production planning and control system (PPC) uses various
methods to generate a production plan that is then further broken down into in-house production plans, procurement plans, and supply plans. The key tasks of production planning and control include planning the production program, planning the production requirements, and planning and control of external procurements and in-house manufactured items. Production program planning determines which products should be produced in which quantities during the next planning periods.
In the cell: 
This separation of the DNA from the protein synthesis machinery provides eukaryotic cells with more intricate regulatory control over the production of proteins and their RNA intermediates.

Communication:
In a human factory:
Communication networks must be established and kept during factory operation as well. Material and communication flows, need to be re-integrated constantly. Communication has become a decisive production factor. Whereas mistakes in the physical material flow become evident sooner or later, those in the mental communication flow usually remain hidden.
In the cell:
the relevance of cell communication is quite vast, but major areas of fundamental research are often divided between the study of signals at the cell membrane and the study of signals within and between intracellular compartments.Cell signaling (cell signalling in British English) is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity as well as normal tissue homeostasis. Errors in cellular information processing are responsible for diseases such as cancer, autoimmunity, and diabetes.

Quantity and Variant Flexibility
In a human factory:
one of the predominant characteristics of production in a turbulent market is strong demand fluctuations and a simultaneous increase in the number of variants and their components. Whereas up until now it was possible to at least partially counter the variant problem with a skillful modular construction, the increasing quantity fluctuations pose a dilemma for enterprises. 
There are two basic production concepts :
A rigid production concept, characterized by extensively automated individual processes, linked workstations, long setup times and a small workforce usually operated in 2 or 3 shifts is defined by two limits in the output quantity
The aim of a flexible volume production concept is to cover the volume fluctuations in the market as well as possible by first extending the economic upper and lower limits 

Abiogenesis: The factory maker argument Produc11

By doing so, an economic production is even then possible when the sales volume is small—most likely due to an adjustable degree of automation. Moreover, it aims to quickly
adjust the technical upper limit, e.g., through modular workstations.

The planning of either a rigid or flexible volume concept is a mental process. 
In the cell:
The environments in which cells grow often change rapidly.6 For example, cells may consume all of a particular food source and must utilize others. To survive in a changing world, cells evolved have designed mechanisms for adjusting their biochemistry in response to signals indicating the environmental change. The adjustments can take many forms, including changes in the activities of preexisting enzyme molecules, changes in the rates of synthesis of new enzyme molecules, and changes in membrane transport processes.Filamentous Structures and Molecular Motors Enable Intracellular and Cellular Movement The development of the ability to move was another important stage in the evolution of cells  design invention  capable of adapting to a changing environment. Without this ability, nonphotosynthetic cells might have starved after consuming the nutrients available in their immediate vicinity.

Networking and Cooperation
External physical network and cooperation:
Of a human factory:
A clear ability to network externally with respect to logistics, organizational aspects, and communications technology has to be ensured in order to effectively co-operate with suppliers, development partners, and customers. Cooperations include development partners (for sub-systems), production partners (for part and component families) as well as logistic partners (for supplying parts, distributing goods and interim storage).
Of the cell:
Signals are transduced within cells or in between cells and thus form complex signaling networks. For instance, in the MAPK/ERK pathway is transduced from the cell surface to the cell nucleus by a series of protein-protein interactions, phosphorylation reactions, and other events. Signaling networks typically integrate protein-protein interaction networks, gene regulatory networks, and metabolic networks.
Internal networking and cooperation:
In a human factory:
The functional factory is organized into areas using the same technology through which a number of different products are routed e.g., mechanical processing, electronic manufacturing, and assembly.
In the cell:
Enzymes work in teams, with the product of one enzyme becoming the substrate for the next. The result is an elaborate network of metabolic pathways that provides the cell with energy and generates the many large and small molecules that the cell needs  8
The metabolic balance of a cell is amazingly stable. Whenever the balance is perturbed, the cell reacts so as to restore the initial state. The cell can adapt and continue to function during starvation or disease. Mutations of many kinds can damage or even eliminate particular reaction pathways, and yet—provided that certain minimum requirements are met—the cell survives. It does so because
an elaborate network of control mechanisms regulates and coordinates the rates of all of its reactions. These controls rest, ultimately, on the remarkable abilities of proteins to change their shape and their chemistry in response to changes in their immediate environment.
Proteins in the cell never act alone. Even the simplest cellular functions, such as transport of a molecule across the cellular membrane or defining the site of future cell division, are normally executed by groups of interacting proteins. These groups are best represented as protein networks, where nodes correspond to individual proteins and edges represent their interactions. The more complex the task, the larger and more complex is the underlying network, and ultimately all functional networks can be connected into a cell-wide network. 9
The structure of composite functional modules containing co-transcriptional regulation interaction and protein-protein interaction reflected the cooperation of transcriptional regulation and protein function implementation and was indicative of their important roles in essential cell functions. In addition, their structural and functional characteristics were closely related and suggesting the complexity of the cell regulatory system. 10


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


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/



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4Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Tue Jun 20, 2017 8:31 pm

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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.


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


Factory and machine planning and design, and what it tells us about cell factories and molecular machines

http://reasonandscience.catsboard.com/t2245-factory-and-machine-planning-and-design-and-what-it-tells-us-about-cell-factories-and-molecular-machines

Some steps to consider in regard of factory planning, design and operation

All text in red requires INTELLIGENCE :

Choosing Manufacturing   and Factory location
Selecting Morphology of Factory Types
Factory planning
Factory design
Information management within factory planning and design
Factory layout planning
Equipment supply
Process planning
Production Planning and Control
establishing various internal and external  Communication networks 
Establishing Quantity and Variant Flexibility
The planning of either a rigid or flexible volume concept depending of what is required
Establishing Networking and Cooperation
Establishing Modular organization
Size and internal factory space organization, compartmentalization and layout 
Planning of recycling Economy
Waste management
Controlled factory implosion programming

All these procedures and operational steps are required and implemented in human factories, and so in biological cells which operate like factories. It takes a lot of faith to believe, human factories require intelligence, but cells, far more complex and elaborated, do not require intelligence to make them, and intelligent programming to work in a self sustaining and self replicating manner, and to self disctruct, when required.  

Molecular machines: 

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

The engineering design process is a methodical series of steps that engineers use in creating functional products and processes. 2

All text in red requires INTELLIGENCE 


[b]Biological cells and their extraordinary manufacturing capabilities


It surprises me that the following paper has not been discovered by the ID community yet. A proponent of ID could not have made a better case for ID, than authors of following mainstream science paper did, comparing humanly-made factories and production lines to  Biological cells, which are examples of ID par excellence. The advanced production solutions implemented in cells excel human-made factories, machines, and production lines by far and so point to an intelligent designer/creator. For that reason, I don't think cells are LIKE factories, but they ARE in a literal sense the most advanced factories known in many ways, which following paper outlines extraordinary well. A must read for any advocate and proponent   of ID: following is a resume, the whole paper can be read at the link below at the end:

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

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 change. Speed 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. For example, in the biosynthesis of aromatic amino acids, a number of common precursors are synthesized before the pathway splits into different final products.  A final concern is that the biological cell is the result of evolution, not design. Consider the cell’s technology, which stabilized about two billion years ago. 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.

Factory and machine planning and design, and what it tells us about cell factories and molecular machines
The Cell is  a Factory
http://reasonandscience.heavenforum.org/t2245-factory-and-machine-planning-and-design-and-what-it-tells-us-about-cell-factories-and-molecular-machines



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5Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Sat Aug 12, 2017 12:48 pm

Admin


Admin
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.
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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6Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Sat Dec 09, 2017 12:57 pm

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

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.


Production Equipment Is Added, Removed, or Renewed Instantly
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.

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7Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Thu May 24, 2018 6:51 pm

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Hello and welcome to 10 craziest things
00:09
cells do. My name is Wallace Marshall and I teach at
00:11
UCSF, the University of California, San Francisco.
00:14
In today's talk, we're going to tackle the myth that
00:18
cells are small, simple, and stupid. Why do we all
00:21
tend to think that? It arises from the idea of cell theory.
00:24
And so cell theory is built on two premises,
00:27
one is that cells are small, simple building blocks,
00:29
similar to atomictheory. And also the second part of
00:33
cell theory is that cells are separate compartments of living
00:36
matter, and that's why they're called "cels."
00:38
So typically when we learn about cells in school,
00:41
we learn some picture like this shown here, where it's
00:43
a relatively simple bag or box full of watery enzyme
00:47
with a few parts in it, but pretty simple and kind of boring.
00:50
And the general view about cells is that they're
00:53
not very exciting, they're relatively simple, like the lego
00:57
block. And the only way to build anything interesting
01:00
is to have lots and lots of cells.
01:02
It turns out, though, when you look at real cells, they're not
01:06
necessarily simple at all. They can be very complicated and
01:09
make beautiful shapes. So I've just shown here a few examples of
01:12
cells, both free living cells and also cells from the bodies of animals
01:16
and plants, in which the cells are much more complicated than
01:19
just a little bag of enzymes. No one knows where all the
01:22
shape comes from, but it makes you think that maybe cells
01:24
could do much more complicated things than just sit there
01:27
and be building blocks. So today's lecture, we're going to talk about
01:30
10 crazy things that cells can do.
01:33
One thing that cells can do that's crazy is get really big.
01:37
It's not crazy that you get big, but it's crazy how big they can
01:40
get. Here's one example, Gromia sphaerica. It's a round amoeba
01:45
that lives on the ocean floor, and a single cell can be 1.5 inches
01:49
in diameter, the size of a large grape or small ping pong ball.
01:53
And as you can see here, they're comparable in size to an
01:57
animal, here are several Gromias shown next to a shrimp.
02:00
And I love this picture, because it looks as though the cells
02:02
are actually chasing the shrimp down and trying to kill it.
02:04
They aren't really doing that, but it just gives you that impression.
02:07
But another nice thing about this image is that you see
02:09
how the cells can leave behind trails in the dirt.
02:12
And there's an ongoing controversy now in people who study
02:15
trace fossils, who want to know when did hard-bodied animals
02:19
first evolve. They've often based those arguments on seeing traces
02:23
and tracks in the dirt that have been fossilized, and it's now thought
02:26
some of those tracks could be things like Gromia that
02:28
were big enough to leave trails, even though they were just
02:31
single cells. Gromia's big, but it's not the biggest
02:34
cell we know. One really big kind of cell is Acetabularia, it's a green
02:38
algae. And this is a clump of them. Each individual cell
02:41
looks like a plant, it's got a root at the base, a stalk, and then
02:44
this flower-like cap, you see. Each single cell could be 10cm
02:48
long. You could hold these cells in your hand like little
02:51
flowers and even make a bouquet out of them.
02:53
So this is extremely large, these are among the largest
02:56
single cells we know that have just one nucleus.
03:00
If you let cells have lots of nuclei, then there's even bigger
03:02
examples. This is an example of Caulerpa, which is a multinucleate
03:08
syncytial cell. This bush-like plant here, is actually one single cell
03:13
that makes many branches and fronds and leaves, but it's all
03:16
just one cell. And it can be larger than a human being.
03:18
And just one cell. So cells can be crazily large,
03:22
so that's crazy thing number 10 that cells can do.
03:24
Some cells, though, can be extremely small. And this example
03:30
is Ostreococcus tauri, which is only about a micron in diameter
03:34
and is so small that it only has one of everything. So the entire
03:38
cytoskeleton is just one microtubule.
03:40
Number 9, cells that walk. We're used to thinking about
03:44
cells moving by crawling along a surface like an amoeba,
03:48
or we think about cells that can swim through pond water.
03:50
But cells have many other ways that they can move, for example,
03:53
this kind of cell here, Stylonychia, is a type of ciliate that's able
03:57
to walk. It walks using clusters of cilia on the bottom surface of the
04:01
cell. And as shown in the picture on the right, it can actually walk
04:04
along leaves and branches inside the pond.
04:07
So this is one remarkable way the cell can walk.
04:09
And if you didn't know better when you see these things moving,
04:11
you would think they were little insects like cockroaches,
04:13
but it's just one cell. But there are other varieties of motile
04:18
behaviors that cells can do beyond just walking. For example,
04:22
there are cells like Dileptus shown here, that are basically
04:25
vampire cells. They have a sharp little needle they can poke
04:28
into other cells and then drink their cytoplasm. There's also
04:32
cells that can open up mouths that they have, into gigantic
04:34
mouths that can swallow other cells whole. For example,
04:37
here is Didinium swallowing a Paramecium whole.
04:40
So there's a wide variety of movements that cells can do,
04:44
moving and also attacking other cells.
04:46
Number 8, cells that go left. So I've talked about weird ways that
04:53
cells can move by walking and by opening their mouths,
04:56
but even among cells that crawl the normal way, there's
04:59
very strange things that certain cells do. For example, there was a
05:02
beautiful paper by Xu et al, showing that white blood cells
05:06
tend to move left. So what they did was they looked at cells
05:11
in the absence of any chemical attractive signal, just sitting on
05:14
the dish. And they drew a line from the nucleus to the centrosome,
05:18
basically giving you an idea of the axis that the cell is oriented in,
05:21
and so they show that line in these graphs here with this red arrow.
05:24
They then added a chemoattractant everywhere in the media,
05:28
so the cell has to pick a random direction to start moving in.
05:31
And the remarkable thing, as shown by the blue dots, is that
05:34
most of the cells will move to the left of their original direction.
05:37
So these cells know left from right. How does a watery bag of
05:41
enzymes know which way is left and which way is right?
05:44
It's really not clear. The one structure in the cell that does
05:47
have a left and right handedness to it, though, is the centriole.
05:50
So as shown here, the centrosome contains a pair of
05:53
centrioles, that are basically barrel like structures made of microtubule
05:56
triplets. And those microtubule triplets have a certain handedness
05:59
as they go around the centriole. So you could imagine that this
06:02
might be a source of left or right handedness in a cell.
06:05
And in fact, in this paper, when they ablated the centriole,
06:08
they were able to eliminate the leftward bias of the motion.
06:11
So this just tells us that the ability of cells to move and the
06:15
decisions that they make while they're moving are probably
06:17
a lot more complicated and crazier than we ever would've thought.
06:20
Number 7, tunneling nanotubes. A fundamental part of cell
06:27
theory is that each cell is a totally separate entity disconnected
06:30
from all the others. That's why they were called cells in the first
06:33
place. But in fact, we know that cells are often connected
06:35
with each other. This is well known in plants, you've probably heard
06:38
about plasmodesmata, shown at the bottom. Which are tubes
06:41
connecting plant cells after they divide. But it's also true
06:44
in animal cells, so one thing that we've discovered in the past decade
06:47
is that many animal cells can be joined by very narrow
06:50
connections called tunneling nanotubes. Which allow cells
06:54
to join to each other and exchange various chemicals
06:57
and maybe even organelles. So even though they look separate,
07:00
the cells are really connected at a small enough scale.
07:03
Tunneling nanotubes are a specific case of the more general
07:07
idea that cells are not as separated from each other as one
07:10
might think. And there are many different examples that have
07:12
come to light. For example, shown on the top here is the
07:15
phenomenon of leukocyte transcellular migration. In this case,
07:19
white blood cells or leukocytes in the bloodstream want to escape
07:22
from the blood vessel and attack invading organisms in your
07:26
tissue. So they have to get through this epithelial layer, but the
07:30
epithelial cells are very tightly connected to each other. And actually,
07:33
the leukocytes cannot squeeze through them. So instead,
07:35
they just dive right through the cells. So you can have a leukocyte
07:38
crawling inside another cell, and this is happening all the time
07:41
right now in your bodies. So you can have cells inside of other
07:45
cells. You also can have cells that let go of membrane vesicles
07:49
which can then be taken up by other cells and passed from one
07:52
cell to another like a bucket brigade, and these are called
07:54
argosomes, shown here on the bottom. An even more
07:57
weird example, which I feel is weirder than argosomes,
08:00
is kleptoplasty. This is a phenomenon whereby the cells of
08:04
one organism can eat another cell and digest it and then
08:08
save the organelles from that cell and put them inside
08:10
of itself. So here we see a sea slug, the reason why the
08:14
sea slug is green is because the cells of these sea slugs
08:17
contain chloroplast that they stole from green algae that
08:20
this organism was feeding on. So that's why they call it
08:25
kleptoplasty, the stealing of plastids or organelles.
08:28
So all these examples just show that cells really are not
08:31
as disconnected as one tends to believe and they're constantly
08:34
exchanging material in ways that we're only now beginning
08:37
to understand.
08:40
Number 6, cytoplasts. What a cytoplast is, is under certain
08:45
conditions, for example, by heat shock, a piece of the cell
08:48
-- a piece of the cytoplasm will just decide to take off by itself.
08:51
And that's shown here, you have a little piece of cytoplasm
08:54
that's just crawled away from the rest of the cell. These cell
08:57
fragments can move by themselves, they leave behind the nucleus,
09:00
the centrosome, the golgi, most of the components of the cell are
09:03
left behind. But yet, this little fragment of cytoplasm is still
09:06
able to move and it can still do chemotaxis. The main reason
09:10
why researchers study these is because it allows you to ask
09:13
what behaviors can a cell do without the other organelles?
09:17
And in particular, you can show that you don't need the nucleus
09:20
or genes to do chemotaxis. So it's been very useful to rule out
09:25
transcription as an important factor in many behaviors. But on
09:29
some level, formation of cytoplasts is still a laboratory artifact.
09:32
However, it points to the ability of other cell types to naturally
09:36
fragment. The really classic example being platelets.
09:39
So platelets are structures that float in your blood that are
09:42
important for wound healing, for promoting a blood clot.
09:44
But what platelets actually are is tiny fragments of a much
09:48
larger cell called a megakaryocyte. And as shown in this
09:51
cartoon, the megakaryocyte grows and grows, sends out
09:54
long, long fibrils, which then fragment to make lots of tiny
09:58
little pieces, and those are the platelets. So this again
10:01
speaks to the exceptions to cell theory that we need to think
10:05
about. Normally, we think about the cell as being the minimal
10:07
unit of biological function. But here's an example where the
10:10
important unit of function is actually a tiny little fragment of the
10:13
cell that's been shattered and is now freely moving around
10:16
in the blood.
10:18
Number 5, cells that can sense electricity.
10:21
So now we're starting to get into the realm of the truly crazy.
10:24
So when you look at a mitotic spindle, just visually, the
10:28
microtubules of the spindle look an awful lot like the lines
10:31
of magnetic force around a bar magnet. Now there's absolutely
10:35
no similarity between these two phenomena whatsoever,
10:39
they just look similar. Nevertheless, the fact they look similar
10:42
tends to make you want to think about, could there be electric
10:44
fields doing something important in biology, in cell biology?
10:48
And in fact, this has led to a variety of proposals and inventions,
10:52
including several patents for equipment that would use
10:55
electric fields to change the behaviors themselves. It's not
10:59
entirely clear whether these would actually work. They're considered
11:02
a little bit on the fringe of what we know, but nevertheless,
11:06
there is one very clear case where electricity is affecting what
11:09
cells do. And that's the phenomenon of galvanotaxis.
11:13
So this is illustrated in this slide here, where we see
11:16
keratocytes from a fish, which are moving in the direction
11:19
of an applied electric field. And this is a well known
11:21
phenomenon, galvanotaxis. Why would cells care about
11:25
electric fields? Well, it turns out, epithelial layers like
11:28
your skin, have an electric potential across them.
11:32
So the cells in the skin are constantly pumping ions back
11:35
and forth, and if you were to punch a hole in your skin,
11:38
for example, if you get cut or wounded, that would now
11:41
produce an electric field that varies from position to position
11:43
across the skin. This then gives an electrical cue for the
11:47
keratocytes to move towards the site of the wound, so they
11:50
can fill in the hole. So galvanotaxis is not only a real
11:53
phenomenon, it's actually really important for your ability
11:56
to heal wounds.
11:57
Number 4, cells that can solve mazes.
12:01
Part of cell theory is that we think cells are relatively
12:05
stupid, because they're so simple and they need to be used
12:07
as building blocks. So therefore an individual cell probably
12:10
can't do that much. That's not necessarily true, and in fact,
12:13
we really don't know how much computation one cell can
12:15
perform. People have done various interesting experiments
12:19
to ask whether cells can do problem solving, one classic
12:22
example, is can cells solve mazes?
12:24
So here I'm showing two examples of maze solving by cells.
12:27
One is Physarum, which is a syncytial slime mold. So a single
12:31
cell will fill up a maze and it will eventually grow such that the
12:36
fibers of the cell will find the shortest path between the
12:40
entrance and exit of the maze, between two chunks of
12:42
food. So, in this sense, Physarum is able to solve the maze.
12:46
Filamentous fungi can also solve mazes, as shown on the
12:49
bottom. They can send little filaments into the maze
12:51
and those filaments make choices about which way to move
12:54
when they hit a corner or intersection. And it's been shown
12:57
that the choices that the single cell makes are better than
13:00
just random. So it is somehow solving the maze.
13:02
Cells can also solve a well-known problem in computer science
13:06
called the "traveling salesman" problem.
13:08
So the traveling salesman problem is, if you're a salesman
13:11
and you want to visit a number of cities in defined locations, how
13:14
do you decide which order to visit those cities so you minimize
13:17
the total traveling that you do? It's known from computer science
13:20
theory that many different problems can be shown to be
13:23
equivalent to traveling salesmen. So if you can solve this
13:25
problem, you can solve many problems in computer science.
13:27
Turns out that single cells can solve this problem of traveling
13:31
salesmen. Here's an example of the Physarum, and again this is
13:34
syncytial slime mold. And what the experiment done here was
13:37
researchers put chunks of food in a pattern that mimics the
13:40
location of cities and villages surrounding Tokyo. They then let a
13:44
single cell of physarum grow until it built various filaments connecting
13:48
these food sources. They then found that the pattern of these food
13:52
sources, not only is optimal, in terms of matching the traveling
13:56
salesman problem, it also very closely mimics the actual
13:59
railway map of the greater Tokyo area. Arguing that the single
14:03
cell can do the same kind of problem solving that human
14:06
engineers would do when they plan out a railway map.
14:09
So this all shows that cell are probably a lot smarter than we
14:12
think they are. And we probably are only beginning to scratch
14:14
the surface of what kind of problems they can solve.
14:16
Cells can also learn, and they can show simple types of learning.
14:20
Here's an example, where we see Stentor coeruleus, this is a
14:24
pond-dwelling ciliate that normally stretches out into the shape
14:27
of a cone. And as it's stretched out as a cone, it can filter
14:30
feed. So it's eating bacteria and algae. But while it's stretched
14:33
out, it's vulnerable to other organisms eating it. So something
14:36
touches it, it contracts down into a ball, shown here.
14:39
Once it's contracted though, now it can't feed anymore.
14:42
So the cell has to decide when something touches it,
14:45
is it really dangerous or not? How does it know it's dangerous?
14:48
It does the same way human does, by experience.
14:50
If something happens all the time, you learn that it's safe.
14:53
For example, if you live near a railway track, you don't get scared
14:55
when the train goes by anymore. So that's habituation.
14:58
It's a common form of learning that all animals do.
15:00
And actually, the Nobel prize was awarded to Eric Kandel for studying
15:03
this exact kind of learning in Aplysia, the sea slug.
15:06
As shown in the graph here, if you tap Stentor cells
15:10
again and again and again, they will gradually learn to
15:12
ignore the tap, showing that they do in fact do habituation.
15:15
So this shows the cells not only can solve problems like mazes,
15:18
they can also learn like animals. It really raises the question,
15:21
how much thinking can a cell actually do?
15:24
Number 3, cells that can see.
15:29
In a series of controversial papers, Gunter Albrecht-Buehler
15:32
argued that cells possess some kind of eye that allows them
15:35
to detect information at a distance. Several experiments he did
15:39
showed that cells can move toward infrared light sources,
15:42
and perhaps more controversially, that cells can align to each
15:46
other, even if they're on opposite sides of the glass coverslip.
15:49
Now this is not something that everyone necessarily
15:52
thinks is true, I'm not aware of any careful attempts to reproduce
15:55
this by anyone. Because I think most people think this is just
15:57
so unusual, unexpected, and crazy. But doesn't mean it's not true,
16:01
however. And in fact, there are clear cases where cells are able
16:04
to sense and use light, and effectively see. This is quite common
16:09
in algae, so Chlamydomonas is a green alga that swims with two
16:12
flagella, as shown here. Has a eyespot that can detect light
16:15
coming from particular directions. So as it swims, it's scanning
16:18
for light and it can go directly toward the light source very quickly.
16:22
This is just a very simple eye spot, it's just a patch of photoreceptors.
16:25
But there are more complex eyes, for example, dinoflagellates
16:28
form a reflecting lens that actually focuses light outside of the
16:32
cell body, right onto the interior of its flagellum, where the
16:35
photoreceptor molecules are located. Other dinoflagellates
16:38
like Warnowia, form actually a clear lens just like the human
16:43
eye has, and it uses the lens to focus light onto its
16:46
photoreceptors. So cells definitely do have eyes, what we don't
16:50
know yet is how much information they get from that
16:52
light, whether it's just the intensity of the light or just the spatial
16:55
information. That's still, I think, an open question.
16:58
Number 2, exploding cells.
17:03
There's nothing more extreme that you can do than to explode.
17:06
And there are cells that do just that. Here's an example,
17:10
this is Magnaporthe grisea, also known as the rice blast fungus.
17:13
It causes the disease that destroys rice crops.
17:16
And the way it infects a plant cell is, it has to get through
17:19
the tough wall of the plant cell. How does it do that?
17:22
It does it by forming this structure here called the appressorium,
17:25
and shown in high-mag down here. Where it's a protrusion of the
17:28
cell that becomes surrounded by a thick cell wall and it fills up
17:32
with melanin, creating a very strong osmotic pressure.
17:35
Actually, the pressure that builds up inside this thing is 10 Mpa,
17:38
the same pressure of a bullet. When the cell builds the appressorium
17:43
on top of the plant surface, it then suddenly ruptures at just
17:46
one point, releasing this massive pressure into a tiny little
17:50
spot on the plant cell, punching a hole into it. Like shooting
17:53
it with a bullet from a gun. So by exploding, this cell produces
17:56
a breach in the defenses of the plant and allows the fungus
17:59
to invade that plant. This is a relatively extreme example.
18:03
Most cells do not explode in this dramatic manner, but many
18:07
cells do actually take advantage of hydrostatic pressure
18:10
in order to move. And this is a phenomenon called blebbing.
18:14
So as shown here, cells will sometimes have the cell membrane
18:17
let go from the actin cortex, and then hydrostatic pressure will then
18:21
push out this bleb of the membrane, which can then
18:24
fill in with more actin. And that allows the cell to then move a little
18:26
bit forward. And cells can move forward progressively
18:29
by these blebbing events, and there are beautiful theories showing
18:32
how the hydrostatic pressure is enough to provide the force
18:35
for this motion. So this shows that even very extreme phenomenon
18:39
like cells exploding, often point to very fundamental and universal
18:43
cellular behaviors that most cells actually do.
18:46
Number 1, the craziest thing that I'm aware of is cells
18:50
that can eat your brain and control your mind.
18:53
The cells we're talking about are Toxoplasma, shown here in
18:56
this image, they have this conoid organ that they can use
19:00
to puncture and move inside of other cells. And if they get into
19:04
your brain, they will actually eat holes in your brain. Now
19:07
it turns out, this isn't really that bad for you. Many people,
19:09
many of us, have toxoplasmosis. We have these organisms
19:13
that have eaten holes in our brain, you can get it from your
19:15
cats if you're pregnant or immunocompromised. Or if you
19:18
eat a lot of raw meat like carpaccio or beef tartare,
19:20
you can get toxoplasma infections. It doesn't cause really
19:23
overt symptoms, it doesn't kill you, but interestingly enough,
19:27
a researcher called Jaroslav Flegr, shown here, has combined
19:31
personality tests with immunoassays for toxoplasma infection.
19:35
And what he finds is that individuals who have had toxoplasma
19:39
infect their brain, tend to have a variety of personality
19:43
traits. So for men, it tends to correlate with dressing sloppily.
19:46
For women, it tends to correlate with dressing overly neatly.
19:49
For both men and women, it tends to correlate with suicide,
19:51
reckless driving, and introverted personalities. So this is a case
19:56
where a single cell is somehow able to get into our brains and not just
20:00
eat random holes, but somehow actually control the way
20:03
our mind works. And if that's not crazy, I don't know what is.
20:06
So I hope you've enjoyed today's lecture. I hope it shows you
20:10
that cells are not as simple as we think they are. They're
20:12
incredibly complex, they can do crazy things, and I believe
20:15
we've only scratched the surface of what cells are capable of.
20:18
Thank you.

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

http://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

http://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
http://www.nature.com/nature/journal/v421/n6921/full/nature01410.html
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.

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

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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.


http://sci-hub.tw/https://www.worldscientific.com/doi/abs/10.1142/S0219720009003947

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10Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Mon Aug 06, 2018 6:32 pm

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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

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11Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Wed Oct 24, 2018 7:07 am

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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, signaling, 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.

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12Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Fri Oct 26, 2018 8:36 am

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Objection: Cells are not factories, and the analogy fails.
Answer: 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 
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. 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.

The Molecular Fabric of Cells  BIOTOL, B.C. Currell and R C.E Dam-Mieras (Auth.)
Cells are indeed, biological, 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 as well as the 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. 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. To understand 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.

Abiogenesis: The factory maker argument 4oODbDc

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

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

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.
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/

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13Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Fri Oct 26, 2018 9:27 am

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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.

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14Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Fri Oct 26, 2018 10:15 am

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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
a  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 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.



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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

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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 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
http://reasonandscience.catsboard.com/t2245-the-cell-is-a-factory

Abiogenesis: The factory maker argument 0waymit

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17Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Thu Dec 20, 2018 11:03 am

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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.



Franklin M. Harold in The Way of the Cell (Oxford: Oxford University Press, c. 2001, 205.)

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18Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Sun Feb 03, 2019 6:00 am

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

http://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
http://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.

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19Abiogenesis: The factory maker argument Empty The factory maker argument on Thu Mar 14, 2019 10:16 am

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The factory maker argument

http://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
http://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
http://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: 
http://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

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

Abiogenesis: The factory maker argument The_fa10

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

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20Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Thu Mar 28, 2019 5:00 pm

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The factory maker argument

https://www.youtube.com/watch?v=yUyzXe1mzcM&t=101s

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.”

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21Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Wed Apr 03, 2019 10:11 am

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The factory maker argument

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.”

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 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.”

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 or 10^378.000 !! 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.

https://www.youtube.com/watch?v=yUyzXe1mzcM&t=101s



Last edited by Admin on Sat Apr 13, 2019 12:02 pm; edited 2 times in total

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22Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Tue Apr 09, 2019 6:13 am

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                       Following argument signals the death knell of atheism

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.”

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.”

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23Abiogenesis: The factory maker argument Empty Re: Abiogenesis: The factory maker argument on Thu May 09, 2019 8:36 am

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Blueprints and factories are always and only purposefully built.
Cells are factories made based on the blueprint stored in DNA.
Therefore, cells built based on the blueprint stored in DNA were made with a purpose.
Only conscious agents act with purpose and foresight.
Therefore, biological Cells and life were made by a conscient agent with purpose.
That agent was with the highest probability, God.

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