Intelligent Design, the best explanation of Origins

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Paley’s Watchmaker and Arguing with Creationists

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Paley’s Watchmaker and Arguing with Creationists

http://www.patheos.com/blogs/tippling/2018/08/09/paleys-watchmaker-and-arguing-with-creationists/

Jonathan MS Pearce (JP) wrote a lengthy refutation on one of my Facebook posts. I will respond here.

" Then there is Darwin:
The old argument of design in nature, as given by Paley, which formerly seemed to me so conclusive, fails, now that the law of natural selection had been discovered. "

Answer:
Jonathan asked me for the best shot to evidence God. I answered with the following syllogism:

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...

The argument is a problem about the origin of life, not evolution. As such, there are only two possible causal agencies that can be considered: 

1. Self-assembly spontaneously by orderly aggregation and sequentially correct manner without external direction

2. Intelligent planning, invention, design, direction, manufacturing, and implementation.

Evolution does NOT explain the origin of life, since it depends on DNA replication, as Eugene Koonin writes:

Koonin, the logic of chance, page 266
Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established. Even at that stage, the evolution of translation remains highly problematic. The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible . The synthesis of nucleotides and (at least) moderate-sized polynucleotides could not have evolved biologically and must have emerged abiogenically—that is, effectively by chance 

The possible mechanisms to explain the origin of life
http://reasonandscience.catsboard.com/t2515-the-possible-mechanisms-to-explain-the-origin-of-life

JP:
Only living organisms are made of organic material, only artefacts show signs of artificial production, and only organisms reproduce.

Objection: "Factories and machines can be made of all kind of materials, and  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, 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.

Only organisms reproduce
Answer: This is a self-defeating argument, because it is not taken into consideration, that self-replication is the epitome of manufacturing advance and achievement, far from being realized by man-made factories. 

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

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

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

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

Objection:
A watch is complex
A watch has a watchmaker
The universe is also complex
Therefore the universe has a watchmaker

But this logic can also be applied as follows:

Leaves are complex cellulose structures
Leaves grow on trees
Money bills are also complex cellulose structures
Therefore, bills of money grow on trees (which, according to the idiom, they don’t)

Answer: that is a strawman argument, which does equal nor refute my syllogism above.
Furthermore, the argument is not based solely on the fact that Cell factories and machines are complex, but:

Confirmation of intelligent design predictions
http://reasonandscience.catsboard.com/t1659-confirmation-of-intelligent-design-predictions

Observation: Intelligent agents act frequently with an end goal in mind, constructing functional irreducibly complex multipart-machines, and make exquisitely integrated circuits that require a blueprint to build the object. Furthermore, Computers integrate software/hardware and store high levels of instructional complex coded information. In our experience, systems that either a)require or b)store large amounts of specified instructional complex information such as codes and languages, and which are constructed in an interdependence of hard and software invariably originate from an intelligent source. No exception.

Hypothesis (Prediction): Natural structures will be found that contain many parts arranged in intricate patterns, metabolic pathways similar to electronic circuits, and irreducible structures that perform specific functions -- indicating high levels of  Information, irreducible complexity, and interdependence, like hard/software.

Experiment: Experimental investigations of DNA, epigenetic codes, and metabolic circuits indicate that biological molecular machines and factories ( Cells ) are full of information-rich, language-based codes and code/blueprint-based structures. Biologists have performed mutational sensitivity tests in proteins and determined that their amino acid sequences, in order to provide function, require highly instructional complex coded information stored in the Genome.   Additionally, it has been found out, that cells require and use various epigenetic codes, namely  Splicing Codes,  Metabolic Codes,  Signal Transduction Codes,  Signal Integration Codes Histone Codes, Tubulin Codes, Sugar Codes, and The Glycomic Code. Furthermore, all kind of irreducibly complex molecular machines and biosynthesis performing and metabolic pathways have been found, which could not keep their basic functions without a minimal number of parts and complex inter-wined and interdependent structures. That indicates these biological machines and pathways had to emerge fully operational, all at once. A stepwise evolutionary manner is not possible. Furthermore, knockout experiments of all components of the flagellum have shown that the flagellum is irreducibly complex.

Conclusion: Unless someone can falsify the prediction, and point out a non-intelligent source of  Information as found in the cell, the high levels of instructional complex coded information, irreducible complex and interdependent molecular systems and complex metabolic circuits and biosynthesis pathways, their origin is best explained by the action of an intelligent agent.

Objection:
As David Schwartz writes:

But let’s think about this for a moment. If you look at a watch lying on the ground and think to yourself, “Oh, this must be designed,” what are you comparing the watch to in order to make that judgment?

Answer: 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.

Objection: False Analogy II: In a further example of how this is a false analogy. We need to understand that humans designing and making a watch is not at all like God designing and making anything.

Answer:  My syllogism is not resorting to an analogy, that is: Biological Cells can be compared to Factories full of machines. My premise is that: Biological Cells ARE factories full or machines. In a literal sense. 
This is more than enough evidenced in secular science papers and books. As for example:

The Molecular Fabric of Cells
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.

http://libgen.io/search.php?req=The+Molecular+Fabric+of+Cells&lg_topic=libgen&open=0&view=simple&res=25&phrase=1&column=def




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

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: In his ruling, the judge stated that the use of the argument from design by intelligent design proponents “is merely a restatement of the Reverend William Paley’s argument applied at the cell level”[20] and that the argument from design is subjective.[21]
This objection goes in line with the argument: We have never observed a being of any capacity creating biological systems and life.  

Answer: 
Every explanation about origins is based on Bayesian probabilities. 
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.

Objection: many theists, particularly creationists, live in a bubble whereby they will only read books by apologists concerning the area of evolution. Therefore, they deny evolution without ever having read a book on evolution by an evolutionary biologist!

Answer: As stated previously, my syllogism deals with the quest of the origin of life, not biodiversity and how it came to be. And, as what can be said about the knowledge of creationists, making generalisations and attacking the knowledge of an opponent has never been a good method to establish truth:

Critizism about the opponents knowledge
http://reasonandscience.catsboard.com/t2114-personal-attacks#3759

Whoever belittles his neighbor lacks sense,But a man of understanding remains silent.-Proverbs 11:12

Critizising the opponents knowledge, intelligence or education is not the best way to establish a point. I hear often critiques like You need basic understanding of science, you don't understand evolution, take a science class, we're trying to educate you, you are spouting ignorance of the subject,  you refuse to learn, Head well and truly in the sand, willful ignorance is your decision, you don't understand what you're copying and pasting, or go over to explicit insults of various forms and degrees. Mock and ridicule with contempt are not new to me. That are responses put forward frequently by Atheists in the attempt to hide their own ignorance, and avoid providing substance. Rather than address the specific issues in question, and provide compelling scenarios that would underline their own views, they resort to that implicit personal attacks and try to discredit the opponent. Not only does it hide their ignorance on the subject, but they expose also their ignorance of their opponents knowledge and education, which cannot be known after a few sentences and posts made on a specific topic.   Fact is, even IF their opponent were ignorant on the issue, that would not make their views become more credible or correct. That's a logical fallacy. The best way for them to deal with the arguments brought forward by proponents of ID/creationism, is 1. educate themselves about the issue in question, and 2. if they disagree with the inference drawn, provide a better explanation based on their views.

And if JP would like to discuss if the Theory of Evolution is sound, he is free to start a new topic. This is what he has to consider :

Why Darwins theory of evolution does not explain biodiversity
http://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity

Objection: Paley’s version of the argument, however, is generally thought to have been refuted by Charles Darwin’s competing explanation for complex organisms.
Answer: Paleys argument can be applied not only towards the quest of biodiversity, but also abiogenesis. But if applied to the Theory of Evolution, there are many lines of reasoning, that lead to the conclusion that design tops evolution in explanatory power. One reason is the fact that irreducible complexity and interdependence can be observed in syntrophy of ecological cycles, ecology, energy cycles, multicellular organisms on every level, from micro to macro.

The existence of irreducible interdependent structures in biology is an undeniable fact
http://reasonandscience.catsboard.com/t1468-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact

Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.
In other words : Why would natural selection select an intermediate biosynthesis product, which has by its own no use for the organism, unless that product keeps going through all necessary steps, up to the point to be ready to be assembled in a larger system ?   A minimal amount of instructional complex information is required for a gene to produce useful proteins. A minimal size of a protein is necessary for it to be functional.   Thus, before a region of DNA contains the requisite information to make useful proteins, natural selection would not select for a positive trait and play no role in guiding its evolution.

Objection: Contemporary biologist, Richard Dawkins (1986), uses a programming problem to show that the logic of the process renders the Darwinian explanation significantly more probable than the design explanation. Dawkins considers two ways in which one might program a computer to generate the following sequence of characters: METHINKS IT IS LIKE A WEASEL.

Answer: The Two Most Obvious Problems
https://evolutionnews.org/2016/09/dawkinss_weasel/

First, on its evolutionary journey from gibberish to the line from Shakespeare, the program passes through and builds from utterly dysfunctional intermediates. That’s a problem because the Darwinian process of natural selection tends to eliminate dysfunctional offspring.

Second, the computer simulation has been programmed to aim for a particular distant goal — the weasel line from Hamlet. That’s a problem because Darwinian evolution doesn’t work toward particular distant goals. It isn’t mindful but mindless, not seeing but blind.

The problem of the fact that life is based on information, goes much deeper than Dawkins says. It is not only an evolution problem but essentially of the origin of life.

Main topics on complex, specified/instructional coded information in biochemical systems and life
http://reasonandscience.catsboard.com/t2625-main-topics-on-complex-specified-instructional-coded-information-in-biochemical-systems-and-life

The problem of information

It has to be explained:

- The origin of the complex, codified, specified, instructional information stored in the genome and epigenetic codes to make the first living organism
- The origin of the genetic Code
- How it got nearly optimal for allowing additional information within protein-coding sequences
- How it got more robust than 1 million alternative possible codes
- The origin of the 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 cipher/translation, from digital ( DNA / mRNA ) to analog ( 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
- The origin of the tubulin Code for correct direction to the final destination of proteins

none of the above items can be explained by evolution since evolution depends on all this.

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