E-mail debates

This e-mail list was started to exchange scientific information that either instantiates intelligent designer(s)/God(s) or not. Anyone can participate. When replying, please reply to all. Representatives of both sides are included in the list. New participants can be added by anyone.  If you do not wish to receive the e-mails, you can block and unfollow.

DK: The better explanation is the formation of the bridge peptide.
In your paper, you state: We assume that the factor determining the time of encoding of a particular amino acid could only be its physicochemical properties related to the survival of the living structures.
In the conclusion of your paper, you write: : the amino acids that possess GC-rich codons were the very first to be included in the initial living complex. 
Question:  What living complex was that, if life depends on the full set up of the genetic code, ( and all tRNA's, mRNA, the ribosome, aminoacyl tRNA synthetase, etc? https://mmbr.asm.org/content/68/3/518  )  

At point 4. you write: Order of Codon Establishment—GC-Rich Were Early and AU Late

I don't get how you conclude that GC would be early, and AU late, in face of what I already replied: DNA’s capacity to convey information actually requires freedom from chemical determinism or constraint, in particular, in the arrangement of the nucleotide bases. If the bonding properties of nucleotides determine their arrangement, the capacity of DNA to convey information would be destroyed. In that case, the bonding properties of each nucleotide would determine each subsequent nucleotide and thus, in turn, the sequence of the molecular chain. Under these conditions, a rigidly ordered pattern would emerge as required by their bonding properties and then repeat endlessly, forming something like a crystal. If DNA manifested such redundancy, it would be impossible for it to store or convey function bearing information. Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page.

Please elucidate.

DK: “The selection” and “unguided means” those two terms are used not correctly. The selection is the guide toward survival.
Reply: There was no survival. We are talking about things prior to when life started. Life is characterized in my understanding as done by Davies:
https://reasonandscience.catsboard.com/t1435-paul-davies-what-is-life

DK:Also, the new formed Darwinian selection (evolution) was formed at the level of already formed short RNA and peptides. Until that moment you have just chemistry. Although some blocks of life may be more stable this is not information-based selection = life.
Reply: Koonin, the logic of chance, page 246 Evolution by natural selection and drift can begin only after replication with sufficient fidelity is established.

DK: RNA building blocks and RNA is quite stable especially in acidic conditions. I can boil RNA and will stay intact (proven thousands of times). Also, what kind of argument is this? Just a recent paper from prof Williams shows that RNA is even more stable with peptide interactions.
Reply: Nucleic acid instability challenges RNA world hypothesis 26 SEPTEMBER 2016
RNA and DNA have very different abilities to withstand chemical changes like depurination, deamination, and hydrolysis. The chemical stability of these two nucleic acids should also be considered when thinking about how they could become incorporated into the earliest forms of life.
https://www.chemistryworld.com/news/nucleic-acid-instability-challenges-rna-world-hypothesis/1017458.article

The stability of the RNA bases: Implications for the origin of life MATTHEW LEVY AND STANLEY L. MILLER , July 1998
High-temperature origin-of-life theories require that the components of the first genetic material are stable. We, therefore, have measured the half-lives for the decomposition of the nucleobases. They have been found to be
short on the geologic time scale. At 100°C, the growth temperatures of the hyperthermophiles, the half-lives are too short to allow for the adequate accumulation of these compounds (t1/2 for A and G ~ 1 yr; U = 12 yr; C = 19 days).
Therefore, unless the origin of life took place extremely rapidly (<100 yr), we conclude that a high-temperature origin of life may be possible, but it cannot involve adenine, uracil, guanine, or cytosine.
https://www.pnas.org/content/pnas/95/14/7933.full.pdf

PREBIOTIC RIBOSE SYNTHESIS: A CRITICAL ANALYSIS ROBERT SHAPIRO d 9 February, 1987
The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.
https://sci-hub.st/https://link.springer.com/article/10.1007/BF01808782

Robert Shapiro:
The presumption that “the bases, adenine, cytosine, guanine and uracil were readily available on the early earth” is “not supported by existing knowledge of the basic chemistry of these substances. The RNA-world hypothesis faces an even more acute, but related, obstacle—a kind of catch-22. The presence of the nitrogen-rich chemicals necessary for the production of nucleotide bases prevents the production of ribose sugars. Yet both ribose and the nucleotide bases are needed to build RNA.

Dean Kenyon explains
“The chemical conditions proposed for the prebiotic synthesis of purines and pyrimidines [the bases] are sharply incompatible with those proposed for the synthesis of ribose.”

Shapiro concludes:
“The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.”

Ot: “Ribozymes Are Poor Substitutes for Proteins” DK: Please accept my apology for the note, but what is this? Argument or joke? There are so many different proteins with a variety of activities including interaction with RNA. Frankly, I have no idea where you are going with this argument!
Reply: Naturally occurring RNA molecules possess very few of the specific enzymatic properties of proteins. Science has shown that ribozymes can perform a few of the inumerous functions performed by proteins. Some RNA molecules can cleave other RNA molecules (at the phosphodiester bond) (hydrolysis). Ribosomal (rRNA) performs peptide-bond formation in the peptidyl transferase center, though only in association with an additional chemical catalyst. Beyond that, RNA can perform only a few minor functional roles and then usually as the result of engineering in the laboratory. Claiming that catalytic RNA could replace proteins in the earliest stages of chemical evolution is not evidence-based.

Ot: “An RNA-based Translation and Coding System Is Implausible” DK: Just the biological process “Translation” means transfer of information from RNA to protein. Of course, if you have only RNA there will not be a translation by default. I’m assuming, you refer to the RNA world hypothesis which has to explain the transition from RNA only system to RNA-protein system. I agree it is difficult by the RNA world hypothesis.
Reply:  How do you go from an RNA based world, to produce proteins? That is a huge, unsolved gap. In order to do so, you need the molecular machines that do so. The primitive replicator would need to produce RNA molecules capable of performing the functions of proteins involved in translation.

Determination of the Core of a Minimal Bacterial Gene Set
A  bacterial cell depends upon a translation and coding system consisting of 106 distinct but functionally integrated proteins as well several distinct types of RNA molecules (tRNAs, mRNAs, and rRNAs) The minimal number of ribosomal proteins required for proper functioning of the ribosome corresponds to the gene set present in M. genitalium, which includes 31 proteins for the large ribosomal subunit and 19 proteins for the small one.
https://mmbr.asm.org/content/68/3/518

These RNA molecules would need to perform the functions of the twenty specific tRNA synthetases, tRNA's, among the many others involved in translation. 
How do you go to substitute supposed ribozymes with proteins, that later would do the same job? That's a far fetched just so scenario, which bears no evidence that such a transition could/would occur. In other words, the evolving RNA world would need to develop a coding and translation system based entirely on RNA and also generate the information necessary to build the proteins that later would be needed to replace it.

Ot: “The RNA World Doesn’t Explain the Origin of Genetic Information” DK: What do you mean? Genetic information or genetic code. Actually, the RNA world explains well the origin of stable RNA sequences (information) but has difficulties to explain genetic code. Yes, I agree indeed RNA world hypothesis have a huge difficulty to explain origin of genetic code or the process of polymer transition. HOWEVER, OTANGELO NONE OF MY PAPERS ADVOCATES RNA WORLD HYPOTHESIS BUT RNA-PEPTIDE WORLD HYPOTHESIS AND THIS IS VERY DIFFERENT. It looks like that you do not make differences between those two different types of hypotheses. My view is that the RNA world hypothesis is a history.
Reply:1. Algorithms, prescribing functional instructions, digital programming, using symbols and coding systems are abstract respresentations and non-physical, and originate always from thought—from conscious or intelligent activity. 
2. Genetic and epigenetic information is characterized containing prescriptive codified information, which result in functional outcomes due to the right particular specified complex sequence of triplet codons and ultimately the translated sequencing of amino acid building blocks into protein strings.  The sequencing of nucleotides in DNA also prescribes highly specific regulatory micro RNAs and other epigenetic factors.
3. Therefore, genetic and epigenetic information comes from an intelligent mind. Since there was no human mind present to create life, it must have been a supernatural agency.

https://biosemiosis.net/?fbclid=IwAR1xTZ-JWsSeSaTHqN5MmsaXpPN6dlFQz4liWCcOYzt6ugib-TVWv9y8YIE
Information is not a tangible entity, it has no energy and no mass, it is not physical,  it is conceptual.

- Life is a software / information driven process.
- Information is not physical it is conceptual.
- The only known source of semiotic information is prior intelligence.
- Life is therefore the direct product of a deliberate creative intellectual processes.

Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating a conceptual semiotic information is a conscious intelligent mind.
Life is no accident, the vast quantity of semiotic information in life provides powerful positive evidence that we have been designed.
To quote one scientist working at the cutting edge of our understanding of the programing information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

DK: Here we go again “irreducible complexity” and our friend Otangelo. Please, stop it and try to understand the living systems (organisms or cells or whatever) evolved in a step by step co-evolution upgrade. 
Reply:  This is your claim. There is no evidence to back it up.

DK: Every single moment whatever is built is self sufficient for the ALREADY existing system. Every single bio-process can be reconstituted outside of the cell. If I accept your argument for “irreducible complexity” I have to accept also that there is not in existence simpler and more complicated organisms and all organisms are with the same level of complexity. YOU KNOW, I KNOW, EVERYBODY KNOWS THAT IS NOT CORRECT. Otangelo, that was the last time that I’m explaining “irreducible complexity” not anymore.
Reply:   Michael Behe's Original Definition — [an irreducibly complex system is] "a single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning." (Darwin's Black Box, page 39, 1996)

This means, before starting an inquiry if a complex system ( biological or not ) is irreducible, we need to set the minimal target function. In our case, it is LIFE. If you disagree, then we should be able to reduce the complexity of Pelagibacter ubique to a bunch of subatomic particles, which should be able to perform the same basic functions as a prokaryotic cell. That will of course not gonna happen. The threshold  

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

Erika: I think you may need to take the time to look into what I said a bit more because isochron dating makes no assumptions about any past conditions or starting material. This alone precludes Young Earth Creationism, full stop.
Reply:I think you are over confident in your assertions, Erika. As it seems, this issue is not as bulletproof as you attempt to say.
The Iconic Isochron: Radioactive Dating, Part 2
In the end, the isochron model for radioactive dating is only a hypothesis and a rather poor one at that. Models, no matter how elegant their mathematics, are only as good as the assumptions that go into them and how well they reproduce reality through observation and experimental data.
Conclusion: The scientific method simply does not allow isochron-model dating to be presented as scientific fact.
https://www.icr.org/article/iconic-isochron-radioactive-dating

Erika: Additionally, the law of radioactive decay is a law. It is a mathematical certainty. There is no guesswork on how elements decay, and there are no known means by which decay rates can be naturally sped up. This was confirmed by Creationist Geologists of the Rate team, which was discontinued in 2005.
Reply: If these clocks are based on faulty assumptions and yield unreliable results, then scientists should not trust or promote the claimed radioactive “ages” of countless millions of years, especially since they contradict the true history
https://answersingenesis.org/geology/radiometric-dating/radiometric-dating-problems-with-the-assumptions/

Erika: You and I are both apes, but since you presented nothing to counter the support I collected for you, I suppose you accept that.
Reply: If God exists, and if it is the God of the Bible, and he told us that we are made upon his image, and distinct from apes, who is to trust more: Your assertions, science, or the one that made everything, and gave us his special revelation? If the foundation is not solid, the entire house will not be. How do you know that we can exist without a creator? There are many reasons why your claims are not compelling, Erika, and there are very intelligent and well informed professional scientists like Marcos Eberlin, who disagree with you. It's great to have credentials, but what in the end is relevant, is the evidence.

Chimps, our brothers?
https://reasonandscience.catsboard.com/t2272-chimps-our-brothers

Erika: (Otangelo, you have still not presented a model. I think you need to look into what constitutes one in a legitimate analysis)
Reply:  Science has invented over 40 hypotheses and models in regards of the origins of life, and ALL failed. Where do you go from this? My "model" does not fail, because it has been already shown
that intelligence can make what we see in nature. But what we see in nature, requires FAR more intelligence than ours.

1. The essential parts of a living cell cohere only because they have a function such as membrane proteins ( factory portals ), DNA ( hardware ), the genetic code and instructional complex information stored in DNA (software), RNA polymerase ( information retrieval/encoding ) messenger RNA ( transmission ) Ribosome ( translation/decoding ) proteins ( complex machines ) dynein, kinesin ( taxis ) tubulins ( molecular highways ) mitochondria ( power generating plants ) ATP synthase ( power turbines ) the metabolic network ( electric circuits ) and so on, which are found forming an integrated interdependent system because they make it possible together for the cell to self-replicate, adapt, and remain alive.
2. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a hardware store could not assemble a watch.)
3. These chemicals, building blocks, and macromolecules must have a designer who designed them with their function in mind: just as a watch implies a watchmaker, a machine implies a machine designer. Living cells were not created by human designers. Therefore, living cells must have had a non-human intelligent designer

The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator.
Since there is being, being has always been. Beginning requires a beginner. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer.Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator. Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, Factories require a factory-maker, Objective moral values come from a moral giver. The "God of the gaps" argument is invalid. And so, that there is no evidence for God(s).

If God exists, is it not far more reliable to ask and trust HIM who made everything, rather than fallible humans?

Taylor:   Even playing back the fastest lunar recession model, linear, the moon would be nowhere near the limit where its orbit could not be sustained.  
Reply: Laser-ranging experiments show that the moon is receding from Earth at the rate of 3.8 centimeters per year 1

Explicitly modelled deep-time tidal dissipation and its implication for Lunar history
It is very likely that the Earth-Moon system is unusually dissipative at present. Consequently, the Moon’s recession rate was slower in the deep past than predicted using PD dissipation rates, supporting the old-age Earth-Moon model.
As always, we creationists should be careful not to overstate our case. creationists should concede that the lunar recession argument against an old Earth isn’t necessarily airtight.
So this might not be an argument worth to be mentioned as a case for a young earth. I, at least, will not use it anymore

Taylor: You don't seem to have put much effort into understanding what a paradox is, it's just an apparent contradiction, not an actual contradiction.  This is because lots of possible solutions are known to be able to heat the earth even with 70% of the sunlight output.  These have been successfully mathematically modeled, and lots of options work themselves or in tandem with others.  The only question is which one actually happened.  This is nowhere near evidence for a young earth.  
Reply: The faint young sun paradox
https://reasonandscience.catsboard.com/t2549-the-faint-young-sun-paradox
Another uniqueness of the Earth is the temperatures suitable for life. If the solar system were billions of years old, the formation of the solar system, the Sun would have had to be nearly one-third less luminous than it is now. If the sun were 25% less bright than it is today, the earth would simply be too cold to support life. In fact, it would be too cold to have liquid water present in any reasonable amount. This is a serious problem, however, because there is ample evidence that there has been significant amounts of liquid water on the earth during the earliest parts of its history. 4 So if the nuclear reactions in the sun play by the same rules as those in the lab, there shouldn’t have been liquid water on the earth billions of years ago. Nevertheless, there was.

Taylor: why do most of your claims (especially those concerning the flood and ark) have ZERO academic and scholarly sourcing?  If historians really confirmed the ark, you should be able to cite something other than a creationist website.  It seems like you just accept all creationist claims no matter how spurious, as fact.
Reply:  First of all, reasonandscience.catsboard.com is my personal virtual library, where I collect information. I cited in my previous response Josephus. But in the links are plenty of resources and information. 
The second like is about the finding of a wooden structure at 4100mts and 4900mts. There is a LOT of information, and videos. It is powerful evidence that the Ark has been found with high probability on Mount Ararat. Since Philip Williams is in the e-mail list, anyone can ask questions to him as he has been there, and made the videos below:

Noah's Ark has been found with high probability on Mount Ararat
https://reasonandscience.catsboard.com/t2940-noah-s-ark-has-been-found-with-high-probability-on-mount-ararat

First American Visit to the Mount Ararat Discovery
https://www.youtube.com/watch?v=IAO_0E-J1lw

Second Deck Noah's Ark
https://www.youtube.com/watch?v=bNxwCnfpQwE

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959131/
2. https://sci-hub.st/https://www.sciencedirect.com/science/article/pii/S0012821X16307518
3. https://www.icr.org/article/lunar-recession-in-the-news

The Recession of the Moon and the Age of the Earth-Moon System
http://www.talkorigins.org/faqs/moonrec.html

Taylor: OR you're a Dunning Krugerite who makes demonstrably false statements like "Information is a non-material entity, which cannot be produced by material processes,"
Reply: 1. Algorithms, prescribing functional instructions, digital programming, using symbols, and coding systems are abstract representations and non-physical and originate always from thought—from conscious or intelligent activity. 
2. Genetic and epigenetic information is characterized containing prescriptive codified information, which results in functional outcomes due to the right particular specified complex sequence of triplet codons and ultimately the translated sequencing of amino acid building blocks into protein strings.  The sequencing of nucleotides in DNA also prescribes highly specific regulatory micro RNAs and other epigenetic factors.
3. Therefore, genetic and epigenetic information comes from an intelligent mind. Since there was no human mind present to create life, it must have been a supernatural agency.

https://biosemiosis.net/?fbclid=IwAR1xTZ-JWsSeSaTHqN5MmsaXpPN6dlFQz4liWCcOYzt6ugib-TVWv9y8YIE
Information is not a tangible entity, it has no energy and no mass, it is not physical,  it is conceptual.

- Life is a software/information-driven process.
- Information is not physical it is conceptual.
- The only known source of semiotic information is prior to intelligence.
- Life is therefore the direct product of a deliberate creative intellectual process.

Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process.
This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry... it is never going to happen!  Physics and chemistry alone do not possess the tools to create a concept. The only cause capable of creating conceptual semiotic information is a conscious intelligent mind.
Life is no accident, the vast quantity of semiotic information in life provides powerful positive evidence that we have been designed.
To quote one scientist working at the cutting edge of our understanding of the programming information in biology, he described what he saw as an “alien technology written by an engineer a million times smarter than us”

If you convert the idea to a sentence to communicate (as I do here) or to remember it, that sentence may be physical, yet is dependent upon the non-physical idea, which is in no way dependent upon it.

Information is not physical
https://arxiv.org/pdf/1402.2414.pdf
Information is a disembodied abstract entity independent of its physical carrier. ”Information is always tied to a physical representation. It is represented by engraving on a stone tablet, a spin, a charge, a hole in a punched card, a mark on paper, or some other equivalent. This ties the handling of information to all the possibilities and restrictions of our real physical word, its laws of physics and its storehouse”. However, the legitimate questions concern the physical properties of information carriers like ”stone tablet, a spin, a charge, a hole in a punched card, a mark on paper”, but not the information itself.  Information is neither classical nor quantum, it is independent of the properties of physical systems used for its processing.

An algorithm is a finite sequence of well-defined, computer-implementable instructions resulting in precise intended functions. A prescriptive algorithm in biological context can be described as performing control operations using  rules, axioms and coherent instructions. These instructions are performed, using a linear, digital, cybernetic string of symbols representing syntactic, semantic and pragmatic prescriptive information. 

Three subsets of sequence complexity and their relevance to biopolymeric information
https://link.springer.com/article/10.1186/1742-4682-2-29
An algorithm is a finite sequence of well-defined, computer-implementable instructions. Genetic algorithms instruct sophisticated biological organization. Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC). FSC alone provides algorithmic instruction.  A linear, digital, cybernetic string of symbols representing syntactic, semantic and pragmatic prescription; each successive sign in the string is a representation of a decision-node configurable switch-setting – a specific selection for function. Selection, specification, or signification of certain "choices" in FSC sequences results only from nonrandom selection.

Nucleotides are grouped into triplet Hamming block codes, each of which represents a certain amino acid. No direct physicochemical causative link exists between codon and its symbolized amino acid in the physical translative machinery. Physics and chemistry do not explain why the "correct" amino acid lies at the opposite end of tRNA from the appropriate anticodon. Physics and chemistry do not explain how the appropriate aminoacyl tRNA synthetase joins a specific amino acid only to a tRNA with the correct anticodon on its opposite end. Genes are not analogous to messages; genes are messages. Genes are literal programs. They are sent from a source by a transmitter through a channel.   Prescriptive sequences are called "instructions" and "programs." They are not merely complex sequences. They are algorithmically complex sequences. They are cybernetic.

The capabilities of chaos and complexity.
http://europepmc.org/article/PMC/2662469
Do symbol systems exist outside of human minds?
Molecular biology’s two-dimensional complexity (secondary biopolymeric structure) and three-dimensional complexity (tertiary biopolymeric structure) are both ultimately determined by linear sequence complexity (primary structure; functional sequence complexity, FSC).  The codon table is arbitrary and formal, not physical. The linking of each tRNA with the correct amino acid depends entirely upon on a completely independent family of tRNA aminoacyl synthetase proteins. Each of these synthetases must be specifically prescribed by separate linear digital programming, but using the same MSS. These symbol and coding systems not only predate human existence, they produced humans along with their anthropocentric minds.

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14    That would be the size of a book with 400 pages, each page with 3000 characters.  They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000.

Leading scientists have calculated that the statistical probability of life emerging by random unguided events, is far beyond the limit of Borel's law, which is in the order of 1 in 10^50.

This probability is hard to imagine but an illustration may help. Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^50. In other words, the evidence that our universe is designed is overwhelming!

1. The more statistically improbable something is, the less it makes sense to believe that it just happened by blind chance.
2. Statistically, it is practically impossible, that the primordial genome, proteome, and metabolome of the first living cell arose by chance.
3. Furthermore, we see in biochemistry purposeful design.  
4. Therefore, an intelligent Designer is by far the best explanation of origins. 


Taylor:  Information is a physical phenomenon that can only exist on material, or be converted to energy.
Reply: Near Death experience , evidence of dualism
https://reasonandscience.catsboard.com/t1284-dualism-near-death-experience

In a study of NDE  after cardiac arrest and successful resuscitation, almost 20% included out of body experiences.  OBE’s were at first considered a psychosis, or depersonalization, but this is not consistent with current research.

Jon Lieff MD psychiatrist, with specialities in geriatric psychiatry and neuropsychiatry, writes :

The fact that OBE’s can be stimulated in the laboratory clearly demonstrates that the sense of “I”, the self-identity, can be separated from the body consciousness.  Studies of body maps are also consistent with this view because they show that body consciousness is constantly changing through neuroplasticity. Therefore, ultimately, the sense of self is independent of the body sense, although normally extremely associated with it. The sense of “I,” or identity, is also ordinarily very attached to the self perceptions involving our professions, families, and other strongly held beliefs and feelings.


Idealism, dualism, or materialism? The Mind is Not The Brain
https://reasonandscience.catsboard.com/t1662-dualism-the-mind-is-not-the-brain

Argument from consciousness
1. Existing fundamentals—space, time, mass, charge can’t explain consciousness, which itself is something fundamental, and essentially different than physical things.
2. Consciousness englobes the mind, "qualia", intellectual activity, calculating, thinking, forming abstract ideas, imagination, introspection, cognition, memories, awareness, experiencing, intentions, free volition, free creation, invention, generation of  information. It classifies, recognizes and judges behavior, good and evil. It is aware of beauty, and feels sensations and emotions. Those are all fundamental discrete indivisible non-quantifiable qualities of immaterial substance, a different identity from hard physical objects, matter and space. Perception, understanding, and evaluation of things adds a quality beyond and absent from natural physical matter and states, and can, therefore, not be reduced to known physical principles.
3.  Hard objects are never observed spontaneously to transform themselves into abstract ideas. The mind cannot be an emergent property of the brain. To ascribe to the electrons in our brain the property to generate consciousness, and not to ascribe the same property to the electrons moving in a bulb, is in contradiction with quantum physics, which establishes that all electrons are equal and indistinguishable, that is they have all exactly the same properties. The mind is to the brain what a pianist is to a piano. The former (the pianist) is not reducible to the latter (the piano).
4. Therefore, dualism is true, and since the universe had a beginning, the mind precedes and exists beyond the universe. That mind is God.


Taylor:  https://link.springer.com/chapter/10.1007%2F978-3-030-03633-1_13 -A Universe Built of Information
Reply: Decoding reality - Information is fundamental 
https://reasonandscience.catsboard.com/t3035-decoding-reality-information-is-fundamental

"As a man who has devoted his whole life to the most clear-headed science, to the study of matter, I can tell you as a result of my research about atoms this much: There is no matter as such. All matter originates and exists only by virtue of a force that brings the particle of an atom to vibration and holds this most minute solar system of the atom together. We must assume behind this force the existence of a conscious and intelligent mind. This mind is the matrix of all matter."
“Das Wesen der Materie” (The Nature of Matter), speech at Florence, Italy, 1944 (from Archiv zur Geschichte der Max-Planck-Gesellschaft, Abt. Va, Rep. 11 Planck, Nr. 1797)

Werner Heisenberg
“The atoms or elementary particles themselves are not real; they form a world of potentialities or possibilities rather than one of things or facts.”

I think that modern physics has definitely decided in favor of Plato. In fact, the smallest units of matter are not physical objects in the ordinary sense; they are forms, ideas which can be expressed unambiguously only in mathematical language.

Of course, we all know that our own reality depends on the structure of our consciousness; we can objectify no more than a small part of our world. But even when we try to probe into the subjective realm, we cannot ignore the central order…In the final analysis, the central order, or 'the one' as it used to be called and with which we commune in the language of religion, must win out.

Sir James Hopwood Jeans
Today there is a wide measure of agreement, which on the physical side of science approaches almost to unanimity, that the stream of knowledge is heading towards a non-mechanical reality; the universe begins to look more like a great thought than like a great machine. Mind no longer appears as an accidental intruder into the realm of matter; we are beginning to suspect that we ought rather to hail it as a creator and governor of the realm of matter... 5

Quantum physicists discovered that physical atoms are made up of vortices of energy that are constantly spinning and vibrating, each one radiating its own unique energy signature. This is also known as "the Vacuum" or "The Zero-Point Field."

Our reality is ultimately made up of information. 1

Information (and not matter or energy) is the building block on which everything is constructed. 1 
Information can be used to explain the origin and behavior of microscopic interactions such as energy and matter. As pointed out by Deutsch and Wheeler, however, whatever candidate is proposed for the fundamental building block of the Universe, it still needs to explain its ‘own’ ultimate origin too. In other words, the question of everything from nothing, creation ex nihilo, is key. So if, as I claim, information is this common thread, the question of creation ex nihilo reduces to explaining how some information arises out of no information.

The big question, of course, is how much can we connect – is it feasible that there is one ultimate law, one master magician’s trick, that describes the whole Universe? Within this discourse, surely the most exciting and fundamental question of all has to be: why is there a reality at all and where does it come from? In other words, before we can even speak about why things are connected, we need to ask ourselves why things exist in the first place. The notion of ‘information’ gives us the answer to both questions. Information is a far more fundamental quantity in the Universe than matter or energy. If we look at reality in terms of ‘bits of information’, it is interesting that both the existence of reality and its inherent connectivity become completely transparent.

Towards an Informationist Post-Metaphysic 6
I see matter as described by the Standard Model of Physics as a kind of epiphenomenon arising out of an informational substrate. I call this theory “informationism” to distinguish it from materialism.

Forget Space-Time: Information May Create the Cosmos 2   May 23, 2015
What are the basic building blocks of the cosmos? Atoms, particles, mass energy? Quantum mechanics, forces, fields? Space and time — space-time? Tiny strings with many dimensions?

Are we living in a hologram? 5
The idea that we live in a holographic universe is very real. With the invention of quantum computers, physicists should soon be able to prove this beyond a reasonable doubt. So, what does it mean that we live in a holographic universe generated by some kind of quantum computer? It means that the Universe was created by an intelligent creator, and therefore it was not created by accident. In other words, the Prime Creator exists!

A new candidate is "information," which some scientists claim is the foundation of reality. The late distinguished physicist John Archibald Wheeler characterized the idea as "It from bit" — "it" referring to all the stuff of the universe and "bit" meaning information.  

Davies, director of BEYOND:
"Historically, matter has been at the bottom of the explanatory chain, and information has been a sort of secondary derivative of it," Davies said. Now, he added, "there's increasing interest among at least a small group of physicists to turn this upside down and say, maybe at rock bottom, the universe is about information and information processing, and it's matter that emerges as a secondary concept.

The universe written in binary
Seth Lloyd, an MIT professor specializing in quantum information, defends this idea by likening the universe to a computer, 
"a physical system that breaks up information into bits, and flips those bits in a systematic fashion."
He explained that electrons have spins, which are described by the laws of quantum mechanics. Electrons can take only two distinguishable values: spinning up or spinning down — the same binary characters as computer bits. So, at rock bottom, Lloyd said, the universe consists of information; every elementary particle carries information.
"So, what is the universe?" Lloyd asked. "The universe is a physical system that contains and processes information in a systematic fashion and that can do everything a computer can do."
To Lloyd, information is not just a way of appreciating or approximating how the universe works, but the literal, most fundamental way it actually works. He sees the universe not like a computer as an explanatory metaphor; it really is a computer as scientific fact. As such, he claims that all changes in the universe are "computations."

The claim is monumental.
Physicist Stephen Wolfram, founder of Mathematica and Wolfram Alpha, calls information "the most prominent thing of our times" and posits that "simple rules… generate what we see in nature." He described "an ultimate representation of the universe" in terms of "simple rules," which "govern fundamentally" and are "best conceptualized in terms of computation."

INFORMATION– CONSCIOUSNESS–REALITY James B. Glattfelder page 531
The first crazy idea is that consciousness is fundamental. Physicists sometimes take some aspects of the universe as fundamental building blocks: space and time and mass. They postulate fundamental laws governing them, like the laws of gravity or of quantum mechanics. These fundamental properties and laws aren’t explained in terms of anything more basic. Rather, they’re taken as primitive, and you build up the world from there. Now sometimes, the list of fundamentals expands. In the 19th century, Maxwell figured out that you can’t explain electromagnetic phenomena in terms of the existing fundamentals—space, time, mass, Newton’s laws—so he postulated fundamental laws of electromagnetism and postulated electric charge as a fundamental element that those laws govern. I think that’s the situation we’re in with consciousness.

If you can’t explain consciousness in terms of the existing fundamentals—space, time, mass, charge—then as a matter of logic, you need to expand the list. The natural thing to do is to postulate consciousness itself as something fundamental, a fundamental building block of nature. This doesn’t mean you suddenly can’t do science with it. This opens up the way for you to do science with it. […]

A deeper motivation comes from the idea that perhaps the most simple and powerful way to find fundamental laws connecting consciousness to physical processing is to link consciousness to information. Wherever there’s information processing, there’s consciousness. Complex information processing, like in a human, complex consciousness. Simple information processing, simple consciousness.  

Physicists and philosophers have often observed that physics is curiously abstract. It describes the structure of reality using a bunch of equations, but it doesn’t tell us about the reality that underlies it. As Stephen Hawking puts it, what puts the fire into the equations?  That’s what physics really is ultimately doing, describing the flux of consciousness. On this view, it’s consciousness that puts the fire into the equations. 

Martin Rees
In the beginning there were only probabilities. The universe could only come into existence if someone observed it.

1. DECODING REALITY THE UNIVERSE AS QUANTUM INFORMATION VLATKO VEDRAL
2.  https://www.space.com/29477-did-information-create-the-cosmos.html
3.  https://www.discovermagazine.com/the-sciences/the-biocentric-universe-theory-life-creates-time-space-and-the-cosmos-itself
4.  https://iai.tv/articles/the-code-of-the-cosmos-auid-531
5.  https://medium.com/@MahmoudNafousi/the-role-of-information-in-the-working-of-the-universe-5a63e44cedb5
6.  https://philosophadam.wordpress.com/2018/12/30/towards-an-informationist-post-metaphysic/

Rulon: Thank you for reacting exactly the way I expected you to, which was not to think about the question, just dismissing technical work as mere "mambo jambo".  This is why creationism has no credibility (and why YOU have no credibility).  It is useless, not a model at all, but only a foot-stamping anti-model.
Reply: What you are doing, is called blame-shifting. You are unable to provide a consistent compelling model based un unguided natural causes, and complain when this is being pointed out.

The Onset of Information on Earth
Life on earth is the product of information recorded inside the cell. When this information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth. The mystery of life’s origin is therefore equal to the mystery of information. Where did the information come from that organized the very first living cell on earth? Did this information come together as an incredible chance event in chemical history, or was it the result of a deliberate act of design? To organize the first living cell, one set of objects must encode the information in a series of representations, and the other set of objects must specify what is being represented. This is how a "recipe" for the cell can exist in a universe where no object inherently means (represents or specifies) any other object. It requires both a representation and the means to interpret it.

But there is a third requirement. The organization of the system must also preserve the natural discontinuity that exists between the representations and their effects. By doing so, a group of arbitrary relationships are established that otherwise wouldn't exist. That set of relationships is what we now call The Genetic Code. The unique physical conditions described here are the universal requirements of translation. They were proposed in theory, confirmed by experiment, and are not even controversial. They are also something that the living cell shares with every other instance of translated information ever known to exist. The genetic translation system provides objective physical evidence of the first irreducible organic system on earth, and from it, all other organic systems follow. Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life's capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity.

And as a final indication of just how profound the appearance of this system was, an almost impossible observation remains – not only must these objects arise from a non-information (inanimate) environment, but the details of their construction must also be simultaneously encoded in the very information that they make possible. Without these things, life on earth would simply not exist.
https://web.archive.org/web/20170715000000*/http://biosemiosis.org

The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin

1. The assignment of a word to represent something, like the word chair to an object to sit down, is always of mental origin.
2. The translation of a word in one language, to another language, is always of mental origin. For example the assignment of the word chair, in English, to xizi, in Chinese, can only be made by intelligence upon common agreement of meaning.
3. In biology the genetic code is the assignment and convention ( a cipher) of 64 triplet codons corresponding to 20 amino acids. It functions as a higher-level constraint distinct from the laws of physics and chemistry, much like a grammatical convention in a human language.
4. Since we know only of intelligence to be able to do so, this assignment is best explained by the deliberate, arbitrary action of a non-human intelligent agency.

1. The origin of the genetic cipher 
1.Triplet codons must be assigned to amino acids to establish a genetic cipher.  Nucleic-acid bases and amino acids don’t recognize each other directly but have to deal via chemical intermediaries ( tRNA's and  Aminoacyl tRNA synthetase ), there is no obvious reason why particular triplets should go with particular amino acids.
2. Other translation assignments are conceivable, but whatever cipher is established, the right amino acids must be assigned to permit polypeptide chains, which fold to active functional proteins. Functional amino acid chains in sequence space are rare.  There are two possibilities to explain the correct assignment of the codons to the right amino acids. Chance, and design. Natural selection is not an option, since DNA replication is not set up at the stage prior to a self-replicating cell, but this assignment had to be established before.
3. If it were a lucky accident that happened by chance, luck would have hit the jackpot through trial and error amongst 1.5 × 10^84 possible genetic code tables. That is the number of atoms in the whole universe. That puts any real possibility of chance providing the feat out of question. Its, using  Borel's law, in the realm of impossibility. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that's universal. Put simply, the chemical lottery lacks the time necessary to find the universal genetic code. 
4. We have not even considered that there are also over 500 possible amino acids, which would have to be sorted out, to get only 20, and select all L amino and R sugar bases......
5. We know that minds do invent languages, codes, translation systems, ciphers, and complex, specified information all the time. 
6. Put it in other words: The task compares to invent two languages, two alphabets, and a translation system, and the information content of a book ( for example hamlet)  being created and written in English, and translated to Chinese, through the invention and application of an extremely sophisticated hardware system. 
7. The genetic code and its translation system are best explained through the action of an intelligent designer. 

2. The software and hardware of the cell are irreducibly complex 
1. The cell contains a complex information storage medium through DNA.
2. The cell has a complex information processing system ( through  RNA polymerase, transcription factors, a spliceosome, a  ribosome,  chaperone enzymes, specialized transport proteins, and ATP
3. The cell contains a genetic code that is at or very close to a global optimum for error minimization across plausible parameter space
4. The cell stores complex, specified, coded information ( the software ) 
5. The cell has a complex translation system through a universal cipher, which assigns 61 codons (4x4x4=64-3 stop and start=64) to 20 amino acids and permits the translation of the genetic code into functional proteins
6. This constitutes a logical structure of information processing: DNA>>RNA>>>Protein, based on software and hardware. Both aspects must be explained.
7. There is no reason for information processing machinery to exist without the software, and vice versa.
8. Systems of interconnected software and hardware are irreducibly complex.
9. A irreducible complex system can not arise in a stepwise, evolutionary manner. 
10. Only minds are capable to conceptualise and implement  instructional information control systems transformed into molecular dynamics
11. Therefore, an intelligent designer exists.

“Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source — from a mind or personal agent.”
– Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).

“As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information.”
– Stephen Meyer

“A code system is always the result of a mental process (it requires an intelligent origin or inventor). It should be emphasized that matter as such is unable to generate any code. All experiences indicate that a thinking being voluntarily exercising his own free will, cognition, and creativity, is required. ,,,there is no known law of nature and no known sequence of events which can cause information to originate by itself in matter.
Werner Gitt 1997 In The Beginning Was Information pp. 64-67, 79, 107.”
(The retired Dr Gitt was a director and professor at the German Federal Institute of Physics and Technology (Physikalisch-Technische Bundesanstalt, Braunschweig), the Head of the Department of Information Technology.)

“Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
Donald E. Johnson – Bioinformatics: The Information in Life

“The genetic code’s error-minimization properties are far more dramatic than these (one in a million) results indicate. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This means of 10^18 codes few, if any have an error-minimization capacity that approaches the code found universally throughout nature.”
Fazale Rana – From page 175; ‘The Cell’s Design’

The genetic code could not be the product of evolution, since it had to be fully operational when life started ( and so, DNA replication, upon which evolution depends ). The only alternative to design is that random unguided events originated it.

Barbieri: Code Biology:
"...there is no deterministic link between codons and amino acids because any codon can be associated with any amino acid.  This means that the rules of the genetic code do not descend from chemical necessity and in this sense they are arbitrary." "...we have the experimental evidence that the genetic code is a real code, a code that is compatible with the laws of physics and chemistry but is not dictated by them."
https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C

[Comment on other biological codes]: "In signal transduction, in short, we find all the essential components of a code: (a) two independents worlds of molecules (first messengers and second messengers), (b) a set of adaptors that create a mapping between them, and (c) the proof that the mapping is arbitrary because its rules can be changed in many different ways."

Why should or would molecules promote designate, assign, dictate, ascribe, correspond, correlate, specify anything at all? How does that make sense?  This is not an argument from incredulity. The proposition defies reasonable principles and the known and limited, unspecific range of chance, physical necessity, mutations, and natural selection. What we need, is giving a *plausible* account of how it came about to be in the first place. 
It is in ANY scenario a far stretch to believe that unguided random events would produce a functional code system and arbitrary assignments of meaning. That's simply putting far too much faith into what molecules on their own are capable of doing.

RNA's, ( if they were extant prebiotically anyway), would just lay around and then disintegrate in a short period of time. If we disconsider that the prebiotic synthesis of RNA's HAS NEVER BEEN DEMONSTRATED IN THE LAB, they would not polymerize. Clay experiments have failed. Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  the literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where molecule complexification emerged spontaneously from a pool of random chemicals. It is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the world of the “living”. 

Alberts: The Molecular Biology of the Cell et al, p367
The relationship between a sequence of DNA and the sequence of the corresponding protein is called the genetic code…the genetic code is deciphered by a complex apparatus that interprets the nucleic acid sequence.
Genes VIII, by Lewin, p21-22

…the conversion of the information in [messenger] RNA represents a translation of the information into another language that uses quite different symbols.

The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases 28 July 2020
One of the most profound open questions in biology is how the genetic code was established. The emergence of this self-referencing system poses a chicken-or-egg dilemma and its origin is still heavily debated

https://www.nature.com/articles/s41598-020-69100-0

Comparison of translation loads for standard and alternative genetic codes
The origin and universality of the genetic code is one of the biggest enigmas in biology. Soon after the genetic code of Escherichia coli was deciphered, it was realized that this specific code out of more than 1084 possible codes is shared by all studied life forms (albeit sometimes with minor modifications). The question of how this specific code appeared and which physical or chemical constraints and evolutionary forces have shaped its highly non-random codon assignment is subject of an intense debate. In particular, the feature that codons differing by a single nucleotide usually code for either the same or chemically very similar amino acid and the associated block structure of the assignments is thought to be a necessary condition for the robustness of the genetic code both against mutations as well as against errors in translation.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909233/

Taylor: Mitochondrial DNA is as close to absolute proof that there is NO creator that I can think of.  This is an absolute death knell to creationism.  Why would God create a different code, and a different location, and a different structure, close to that of bacteria, which supports endocytosis theory, when there are organisms with mitochondrial DNA IN their nuclear DNA?  God can clearly make organisms with DNA for the mitochondrial organelle inside the nucleus, those organisms exist, so you CANNOT say it is a necessary design feature that most eukaryotes have their mitochondrial DNA SEPARATE from their nucleus, as we'd expect if mitochondria evolved from prokaryotic organisms.

 The standard nuclear code can clearly assemble mitochondrial proteins, there are organisms that do this, and yet god makes most eukaryotes to look evolved instead, even though this choice is not necessary.  Does God put deception in his creation?  Why does he consistently go out of his way to do things that only fit an evolutionary model?   Sure, you can just SAY god did it, and did it for a reason, since he can technically do anything, and you won't question the reason, just assert that there is one, but this is NOT a scientific model, since it supports no predictive conclusion one way or the other... in other words, you don't have a set of rules to tell you what to expect, which we can test, you just assume that ALL results are chosen by God, for some unknowable good reason, but you cannot PREDICT the results.  Going loosely, with a designer, one should expect a universal code and a centrally controlled genetic hub, but we see only what we'd expect if cells adapted to live inside other cells.

Reply: There are variants of the standard genetic code. These variants are used for instance in the mitochondria of many species, and they consist in the modification of one or several codons of the standard genetic code.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909233/

Richard Dawkins has claimed that the genetic code is universal across all organisms on earth. This is “near-conclusive proof,” he writes, that every living thing on this planet “descended from a single common ancestor” (1986, p. 270) at the root of Darwin’s universal tree of life. More recently, Dawkins repeated the claim in his bestseller The Greatest Show On Earth (2009, p. 409):

…the genetic code is universal, all but identical across animals, plants, fungi, bacteria, archaea and viruses. The 64-word dictionary, by which three letter DNA words are translated into 20 amino acids and one punctuation mark, which means ‘start reading here’ or ‘stop reading here,’ is the same 64-word dictionary wherever you look in the living kingdoms (with one or two exceptions too minor to undermine the generalization).

Let’s look at the reason Dawkins gives for why the code must be universal:

The reason is interesting. Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster. (2009, p. 409-10)

And now, see here:

https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes

• 1. The Standard Code
  
• 2. The Vertebrate Mitochondrial Code
  
• 3. The Yeast Mitochondrial Code
  
• 4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code
  
• 5. The Invertebrate Mitochondrial Code
  
• 6. The Ciliate, Dasycladacean and Hexamita Nuclear Code
  
• 9. The Echinoderm and Flatworm Mitochondrial Code
  
• 10. The Euplotid Nuclear Code
  
• 11. The Bacterial, Archaeal and Plant Plastid Code
  
• 12. The Alternative Yeast Nuclear Code
  
• 13. The Ascidian Mitochondrial Code
  
• 14. The Alternative Flatworm Mitochondrial Code
  
• 16. Chlorophycean Mitochondrial Code
  
• 21. Trematode Mitochondrial Code
  
• 22. Scenedesmus obliquus Mitochondrial Code
  
• 23. Thraustochytrium Mitochondrial Code
  
• 24. Rhabdopleuridae Mitochondrial Code
  
• 25. Candidate Division SR1 and Gracilibacteria Code
  
• 26. Pachysolen tannophilus Nuclear Code
  
• 27. Karyorelict Nuclear Code
  
• 28. Condylostoma Nuclear Code
  
• 29. Mesodinium Nuclear Code
  
• 30. Peritrich Nuclear Code
  
• 31. Blastocrithidia Nuclear Code
  
• 33. Cephalodiscidae Mitochondrial UAA-Tyr Code
  

Simple counting question: does “one or two” equal 33? That’s the number of known variant genetic codes compiled by the National Center for Biotechnology Information (NCBI). By any measure, Dawkins is off by an order of magnitude.



In human cells, the codon UGA codes for “stop,” meaning the end of an open reading frame (i.e., section of DNA coding for a protein). When the ribosome, the molecular machine that constructs proteins, encounters UGA in the messenger RNA of a human cell, it ceases translation. Not so in Mycoplasma, where UGA codes for the amino acid tryptophan. On encountering UGA in an mRNA strand, the Mycoplasma ribosome would insert a tryptophan (in the protein the ribosome is assembling) and keep chugging right along with translation, through the following codons, until it met a Mycoplasma stop codon. Human and Mycoplasma cells do not read their DNA in the same way.

Genomics: Evolution of the Genetic Code 1
Understanding how this code originated and how it affects the molecular biology and evolution of life today are challenging problems, in part because it is so highly conserved — without variation to observe it is difficult to dissect the functional implications of different aspects of a character. 

It is tempting to think that a system so central to life should be elegant, but of course that’s not how evolution works; the genetic code was not designed by clever scientists, but rather built through a series of contingencies. The ‘frozen accident’, as it was described by Crick, that ultimately emerged is certainly non-random, but is more of a mishmash than an elegant plan, which led to new ideas about how the code may have evolved in a series of steps from simpler codes with fewer amino acids. So the code was not always thus, but once it was established before the last universal common ancestor of all extant life (LUCA) it has remained under very powerful selective constraints that kept the code frozen in nearly all genomes that subsequently diversified.

My comment:  A series of contingencies !!! a mishmash than an elegant plan !!! Contingent means accidental, incidental, adventitious, casual, chance. So, in other words, luck. A fortuitous accident. Is that a rational proposition ? 

The genetic codons are assigned to amino acids. Why should or would molecules promote designate, dictate, ascribe, correspond, correlate, specify anything at all ? How does that make sense?

The genetic code could not be the product of evolution, since it had to be fully operational when life started ( and so, DNA replication, upon which evolution depends ). The only alternative to design is that random unguided events originated it.

Barbieri: Code Biology:
"...there is no deterministic link between codons and amino acids because any codon can be associated with any amino acid.  This means that the rules of the genetic code do not descend from chemical necessity and in this sense they are arbitrary." "...we have the experimental evidence that the genetic code is a real code, a code that is compatible with the laws of physics and chemistry but is not dictated by them."
https://www.sciencedirect.com/journal/biosystems/vol/164/suppl/C

[Comment on other biological codes]: "In signal transduction, in short, we find all the essential components of a code: (a) two independents worlds of molecules (first messengers and second messengers), (b) a set of adaptors that create a mapping between them, and (c) the proof that the mapping is arbitrary because its rules can be changed in many different ways."

RNA's, ( if they were extant prebiotically anyway), would just lay around and then disintegrate in a short period of time ( a month or so). If we disconsider that the prebiotic synthesis of RNA's HAS NEVER BEEN DEMONSTRATED IN THE LAB, they would not polymerize. Clay experiments have failed. And even IF they would bind in GC rich configurations to small peptides, they would as well simply lay around, and disintegrate. It is in ANY scneario a far stretch to believe that unguided events would produce randomly codes. That's simply putting far too much faith into what molecules on their own are capable of doing.

My comment:  Without stop codons, the translation machinery would not know where to end the protein synthesis, and there could/would never be functional proteins, and no life on earth. At all.

These characteristics may render such changes more statistically probable, less likely to be deleterious, or both. However, most non-canonical genetic codes are inferred from DNA sequence alone, or occasionally DNA sequences and corresponding tRNAs. 

We must bear in mind that most non-canonical codes evolved independently from the others, and so may have evolved through different steps

My comment:  It is evident why the authors make that claim. As Dawkins wrote: Any mutation in the genetic code itself (as opposed to mutations in the genes that it encodes) would have an instantly catastrophic effect, not just in one place but throughout the whole organism. If any word in the 64-word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster.

And Dr.Wile: Someone can assume that while invertebrates evolved into vertebrates, their mitochondria also evolved to use a different genetic code. However, I am not really sure how that would be possible. After all, the invertebrates spent millions of years evolving, and through all those years, their mitochondrial DNA was set up based on one code. How could the code change without destroying the function of the mitochondria? At minimum, this adds another task to the long, long list of unfinished tasks necessary to explain how evolution could possibly work.

Even in a genome that has only 30-50 proteins, each protein is very long and uses the same amino acid multiple times. It would have to be shown how it is possible for four codons to go completely out of use. Then, how they can get reassigned in order to go from the “universal” code to the vertebrate mitochondrial code. Also, how did this happened only at the base of the vertebrate tree?

Why alternative genetic codes?
One reason why there are alternative genetic codes is the reduction of the number of tRNA needed. Furthermore, one alternative genetic code (the 'Echinoderm and Flatworm Mitochondrial Code') that seems to be better at reducing mutation and translation loads, and particularly yields better translation load except for very small AT content (approx. 20% AT content or less).

Of course, science literature claims that there was an adaptive advantage and improvement of fitness of these alternative codes, but how the transition could have happened is an open question.

The implications are significant: If the origin of the universal genetic code is an enigma, imagine another 33 different ones, that had to emerge independently !!!! This is simply evidence that the best explanation is an intelligent designer which created and generated different codes for different life forms separately. And it means, that the tree of life is bunk. 

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes 17 April 2006
If a change in the translation system occurs in an organism such that a codon is reassigned, most of the occurrences of this codon will still be at places where the old amino acid was preferred. We would expect the changes causing the codon reassignment to be strongly disadvantageous and to be eliminated by selection.

My comment:  A reassignment means, that the tRNA's amino acid binding site would have to change to reassign a different amino acid. 

The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases 28 July 2020
https://www.nature.com/articles/s41598-020-69100-0
One of the most profound open questions in biology is how the genetic code was established.  The correct read-out of genetic information is a delicate interplay between the composition of the binding site, non-covalent interactions, error correction mechanisms, and steric effects.

A glimpse into nature's looking glass -- to find the genetic code is reassigned: Stop codon varies widely
We were surprised to find that an unprecedented number of bacteria in the wild possess these codon reassignments, from "stop" to amino-acid encoding "sense," up to 10 percent of the time in some environments," said Rubin.
Another observation the researchers made was that beyond bacteria, these reassignments were also happening in phage, viruses that attack bacterial cells. Phage infect bacteria, injecting their DNA into the cell and exploiting the translational machinery of the cell to create more of themselves, to the point when the bacterial cell explodes, releasing more progeny phage particles to spread to neighboring bacteria and run amok.
https://www.sciencedaily.com/releases/2014/05/140522141422.htm

The genetic translation system provides objective physical evidence of the first irreducible organic system on earth, and from it, all other organic systems follow. Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life’s capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity.


It is possible for mutations to cause disappearance of the codon in its original positions and reappearance in positions where the new amino acid is preferred. Mutations throughout the genome are required for it to readjust to the change in the genetic code. The problem is therefore to understand how codon reassignments can become fixed in a population despite being apparently deleterious in the intermediate stage before the genome has time to readjust.

Different genetic codes are strong evidence that they were designed.

Craig Venter vs Richard Dawkins:
It’s instructive to watch a fascinating exchange between Dawkins and genome guru J. Craig Venter, which occurred during a science forum held at Arizona State University. The question for discussion at the forum was “What is life?” Most of the panelists agreed that all organisms on Earth represent a single kind of life — a sample of one — because all organisms have descended from a last universal common ancestor (LUCA). This “sample of one” problem is strong motivation, panelist and NASA scientist Chris McKay argued, for exploring Mars and other planets (or their moons) in our solar system, to try to find a second example of life, unrelated to Earth organisms.
Venter disagreed — in a remarkable way (start at the 9:00 minute mark). “I’m not so sanguine as some of my colleagues here,” he said, “that there’s only one life form on this planet. We have a lot of different types of metabolism, different organisms. I wouldn’t call you [Venter said, turning to physicist Paul Davies, on his right] the same life form as the one we have that lives in pH 12 base, that would dissolve your skin if we dropped you in it.”
“Well, I’ve got the same genetic code,” said Davies. “We’ll have a common ancestor.”
“You don’t have the same genetic code,” replied Venter. “In fact, the Mycoplasmas [a group of bacteria Venter and his team have used to engineer synthetic chromosomes] use a different genetic code that would not work in your cells. So there are a lot of variations on the theme…”
Here Davies, a bit alarmed, interrupts Venter: “But you’re not saying it [i.e., Mycoplasma] belongs to a different tree of life from me, are you?”
“The tree of life is an artifact of some early scientific studies that aren’t really holding up…So there is not a tree of life.”
Dawkins is Flabbergasted
Fast forward to 11:23, when moderator Roger Bingham turns the microphone over to Dawkins:
“I’m intrigued,” replies Dawkins, “at Craig saying that the tree of life is a fiction. I mean…the DNA code of all creatures that have ever been looked at is all but identical.”
WHOPPER. Venter just told the forum that Mycoplasma read their DNA using a different coding convention than other organisms (for “stop” and tryptophan). But Dawkins is undaunted:
“Surely that means,” he asks Venter, “that they’re all related? Doesn’t it?”
As nearly as we can tell from the video, Venter only smiles.

https://www.youtube.com/watch?v=xIHMnD2FDeY

1. https://sci-hub.st/https://www.sciencedirect.com/science/article/pii/S0960982216309174

Erika:  To note that yes, the literature, not youtube atheists, has not reached a consensus on the nature of the genetic code being a "real" code. The literature, to remind you, is composed of folks with experience and expertise from dozens of fields. It is normal for consensus-reaching to be difficult, especially with a subject as new as the genetic code.

Dr. Sy Garte and Dr. Carter know their stuff to be sure. What I am saying is that other folks out there with relevant degrees and work disagree with them. You can quibble all day on who is correct, but as stated above it doesn't matter with regard to the actual question being asked. 

Reply: You might be right in the sense that there is a diversity of views about the genetic code, but if you look into the authors who make the claim that the genetic code isn't so in a real sense, they are linguists, historians, philosophers, one medical doctors without expertise in the field of genetics.

 Can you quote ONE biology or biochemistry textbook which, as you, questions if the genetic code IS a code in a literal sense, and confesses that the issue is ambiguous?
Because, in my book, this is not an issue. AT ALL. It is settled in science. It is just from the materialist camp, FOR DECADES now, that claim that the genetic code is an actual code is fallacious, an error committed only by those ID rubes with an agenda. But, of course, not only is this untrue, it is easily shown to be untrue. There are numerous examples of materialists insisting that the “code” part of “genetic code” refers to a real code; it is not an analogy nor the sloppy use of language. 

It is clear why atheists dispute that fact for decades.
The genetic code is at the heart of the cell’s functionality, and is thus an enabling causal factor for cell based life. That code implies a code/protocol based communication system (as Yockey expands) and is inherently linguistic. Language is a characteristic of intelligence and so ID proponents have good reasons to infer intelligence and design as the most case-adequate cause of cell based life.

For Larry Moran, for example, there is no ambiguity.

This is the genetic code. It shows the relationship between a sequence of nucleotides in messenger RNA (mRNA), or DNA, and the amino acids that are inserted into a growing polypeptide chain.
We do not say that the string of dots and dashes is the Morse Code. We say that it’s a message encrypted using the Morse Code. Similarly, we do not say that a string of nucleotides is the genetic code. It’s the message that’s translated using the Genetic Code.
https://sandwalk.blogspot.com/2007/02/real-genetic-code.html

That the genetic code is an actual semiotic code is not disputed by any serious person. Just Google “genetic code semiotic” and dozens of scholarly articles will pop up discussing how the genetic code is semiotic all the way down and not, as Ortho insists, merely chemical. It turns out that the real question is not whether the genetic code is a semiotic code. That is glaringly obvious and taken for granted by scientists who have studied the matter. No, the real question is what motivates the materialists who stuff our combox to deny the science.

Crick’s letter
Notice,  Cricks wrote: “. . . D.N.A. is a code.”


This was then drawn out by the early 1970’s, yielding several Nobel Prizes along the way, and it is now a commonplace from primary school on. 
Technically, he is wrong. DNA is a semantophoretic molecule that stores genetic information using the genetic code. 


The Genetic code uses three-letter codons to specify the sequence of AA’s in proteins and specifying start/stop

And here is an excerpt from the website Biosemiosis:
Life on earth is the product of information recorded inside the cell. When this information is translated by cellular machinery, it organizes inanimate matter (carbon, hydrogen, nitrogen, etc) into all the living things on earth. The mystery of life’s origin is therefore equal to the mystery of information. Where did the information come from that organized the very first living cell on earth? Did this information come together as an incredible chance event in chemical history, or was it the result of a deliberate act of design?  To organize the first living cell, one set of objects must encode the information in a series of representations, and the other set of objects must specify what is being represented. This is how a "recipe" for the cell can exist in a universe where no object inherently means (represents or specifies) any other object. It requires both a representation and the means to interpret it.

But there is a third requirement. The organization of the system must also preserve the natural discontinuity that exists between the representations and their effects. By doing so, a group of  arbitrary relationships are established that otherwise wouldn't exist. That set of relationships is what we now call The Genetic Code. The unique physical conditions described here are the universal requirements of translation. They were proposed in theory, confirmed by experiment, and are not even controversial. They are also something that the living cell shares with every other instance of translated information ever known to exist. The genetic translation system provides objective physical evidence of the first irreducible organic system on earth, and from it, all other organic systems follow. Moreover, this system is not the product of Darwinian evolution. Instead, it is the source of evolution (i.e. the physical conditions that enable life's capacity to change and adapt over time) and as the first instance of specification on earth, it marks the rise of the genome and the starting point of heredity.

And as a final indication of just how profound the appearance of this system was, an almost impossible observation remains – not only must these objects arise from a non-information (inanimate) environment, but the details of their construction must also be simultaneously encoded in the very information that they make possible. Without these things, life on earth would simply not exist.

There are two distinct categories of semiotic systems. One category uses representations where the arrangement of the medium (like a pheromone) is reducible to the physical properties of the medium itself; the other uses representations that have a spatial (dimensional) orientation and are not reducible to their physical make-up (like the words on this page). The first type is found throughout the living kingdom. The second type is found nowhere but in recorded language and mathematics  (and in the genetic code).

This leads to an undeniable observation of physical reality; the singularly-unique material conditions required for dimensional semiosis, which would ostensibly not exist on Earth until the rise of human intelligence, were entirely evident at the very origin of life. They are the physical means by which the living cell became organized.
https://web.archive.org/web/20170715000000*/http://biosemiosis.org

Rulon: Ooh, more deliciously ironic authority quotes from the likes of Steve Meyer or Faz Rana who do NOT in any way whatsoever embrace your young earth creationism.  So convince THEM first that life originated only 6000 years ago, then get back to us.
Reply:   The origin of the genetic code has NOTHING to do with the quest if the Earth is young or old. 


Speed: Yockey is not an ID'r. Nor is Barbieri. Same with about 99% of the biosemiotics guys. Why do you think they wrote the books on biosemiotics and they do not agree with you?
Reply: Because they apply methodological naturalism to historical sciences, which is arbitrary and unjustified. And because they have a personal commitment to atheism/materialism. That constitutes considerable barriers. In most cases, the never "get" it, and die with their lifelong hold belief, despite being wrong.
A rare case is Anthony Flew.

In the last half of the twentieth century, the world’s most famous unbeliever was an English philosopher named Antony Flew. Long before Dawkins, Dennett, Hitchens, and Harris attacked God and religion, Flew was the leading spokesman for the atheist movement. An honorary member of the New Zealand Association of Rationalists and Humanists, and a fellow of the Committee for Skeptical Inquiry, Flew received many honors from the intellectual community, including the In Praise of Reason Award, in recognition of his “long-standing contributions to the use of methods of critical inquiry, scientific evidence, and reason in evaluating claims to knowledge and solving
social problems.”6 Then, in 2004, the unthinkable happened. Flew shocked the world by announcing he had come to believe in God. His defection threw atheists into a frenzy. They immediately turned on him and began to
question whether his conversion might be due to his declining mental capacities.7 Flew, however, remained sharp as a whip. When asked why he had become a believer, he calmly replied:

There were two factors in particular that were decisive. One was my growing empathy with the insight of Einstein and other noted scientists that there had to be an Intelligence behind the integrated complexity of the physical Universe. The second was my own insight that the integrated complexity of life itself—which is far more complex than the physical Universe—can only be explained in terms of an Intelligent Source. I believe that the origin of life and reproduction simply cannot be explained from a biological standpoint despite numerous efforts to do so. With every passing year, the more that was discovered about the richness and inherent intelligence of life, the less it seemed likely that a chemical soup could magically generate the genetic code. The difference between life and non-life, it became apparent to me, was ontological and not chemical. The best confirmation of this radical gulf is Richard Dawkins’ comical effort to argue in The God Delusion that the origin of life can be attributed to a “lucky chance.” If that’s the best argument you have, then the game is over. No, I did not hear a Voice. It was the evidence itself that led me to this conclusion.

Doesn’t sound much like “declining mental capacities,” does it? Nevertheless, atheists unleashed a storm of invective against Flew (that’s what they do best), and to this day they are licking their wounds.

Anthony DeStefano, Inside the atheist mind, page 82

Rulon James: "First, it would seem that the early codons need have used only two bases (which could code for up to 16 amino acids); but a subsequent change to three bases (to accommodate 20) would seriously disrupt the code."

Says who on that?  We OBSERVE the wobbly nature of the third codon, many organisms have already changed the assignment of the third codon without disruption.  By all means direct us to the current science work insisting the physical impossibility of a third codon attaching to the system.
Reply: Paul Davies,The fifth miracle,  page 105  
It would be far simpler to employ sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over.  As in all translations, there must be someone, or something, that is bilingual, in this case to turn the coded instructions written in nucleicacid language into a result written in amino-acid language. The British biologist John Maynard Smith has described the origin of the code as the most perplexing problem in evolutionary biology. With collaborator Eörs Szathmáry he writes: “The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.”
Darwinian evolution works in incremental steps, accumulating small advantages over many generations. In the case of the code, this won’t do. Changing even a single assignment would normally prove lethal, because it alters not merely one but a whole set of proteins. Among these are the proteins that activate and facilitate the translation process itself. So a change in the code risks feeding back into the very translation machinery that implements it, leading to a catastrophic feedback of errors that would wreck the whole process.

My comment: There are many things about the translation process which science has unraveled and discovered, but materialists take it as granted, that natural/unguided processes would have come up with such an extraordinary feat, and it seems it does not pass in their mind, that it could be better explained by design. No matter, how complex/counter intuitive. And so,  unguided random events become almost super powerful/intelligent, and are able to produce without goal nor any direction machines and factories of unparalleled complexity, without equal in the manmade world. That justifies to ask questions, which seem to be tabu in science papers, because it becomes almost begging the question just to ask these questions. As for example:

Questions:
How did such a system working equal to a 3D printer, using the genetic code, arise at all?
If, as commonly argued, life started with the RNA world, and so translation, how about the fact that RNA Building Blocks Are Hard to Synthesize ( it has never been shown in the lab to be possible without enzymes) and the fact that tey are easy to destroy and disintegrate in 30 to 40 days?
Ribozymes Are Poor Substitutes for Proteins
How/why did the genetic code emerge at all, and discover a solution to the numerical mismatch from the four alphabet A, G, C, T, to 20 amino acids used to make proteins?
Why/how should there be a reason that particular triplets should map a specific set of 20 amino acids amongst hundreds supposedly existing on early earth?
How/why were 20 canonical amino acids selected for the protein synthesis, in special finely tuned to be one of the best sets ?
(Out of 100 million different sets of twenty amino acids, only six are better able to explore "chemistry space" than the twenty amino acids that life uses)
How/why would there have been a selection process AT ALL?
Is it reasonable to claim a "Frozen accident"? Life simply got stuck with these numbers? Just so? How is that a satisfying answer?
How/why should molecules have the "urge" to complexify AT ALL, as we see in translation?
How/why could a bottom-up process generate the genetic code encoding a functionally optimal set of amino acids? ( If less, a mix permitting functional proteins, from hydrophobic polar, to intermediate, and very polar side chains would not be generated?)
How/why is the standard Genetic Code  exceedingly highly ordered with respect to the polar requirement, with large coherent domains for hydrophobic, intermediate, and polar amino acids? (Polar amino acids are those with side-chains that prefer to reside in an aqueous (i.e. water) environment.) The Standard Genetic Code division into a few coherent regions is especially striking. See the paper: Evolution of the standard genetic code, Michael Yarus February 25, 2020
How/why is the genetic code represented by the four bases A, T(U), G, and C, and not just binary?
How/why did tRNA adapter molecules emerge prebiotically at all, fit so fantastically as an intermediate/adapter molecule?
How/why did the set of about 45 tRNA's anticodon/amino acids emerge to match/fit (lock and key) and be recognized by a set of 20 Aminoacyl-tRNA synthetases?
How/why does the genetic code have a triplet structure?
How/why is the genetic code not overlapping, that is, why does the translation apparatus of a cell, which transcribes information, have a discrete equaling to three, but not to one?
How/why does the degeneracy number of the code vary from one to six for various amino acids?
How/why could translation have emerged, in face of the fact that several hundreds of parts are required to assemble the individual participant proteins/ribozymes, and operate translation?
How/why did error check and repair mechanisms of translation emerge? ( i have enumerated 13 mechanisms in translation that work in a joint venture to assure accurate translation)
How/why could the entire system get "off the hook", if amino-acid misincorporations during translation have to minimized to a tolerable rate ? ( It is estimated to occur once in every 1,000 to 10,000 codons translated)

 Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life’s employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise. Do random chemical reactions have knowledge to arrive at a optimal conclusion, or a " good compromise" ?  
An even tougher problem concerns the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly, but have to deal via chemical intermediaries, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance.

That frozen accident means, that good old luck would have  hit the jackpot  trough trial and error.
Hubert P. Yockey Information Theory and Molecular Biology 1992
Natural selection would have to explore 1.40 x 1070 different genetic codes to discover the universal genetic code found in nature. Yockey estimated 6.3 x 10^15 seconds (200 million years) is the maximum time available for the code to originate. Natural selection would have to evaluate roughly 10^55 codes per second to find the universal genetic code. And even if the search time was extended for the entire duration of the universe’s existence, it still would require searching through 10^52 codes per second to find nature’s genetic code. Put simply, natural selection lacks the time to find the universal genetic code.

To claim that deterministic chemical affinities explain the origin of the genetic code lacks empirical foundation. In order for the translation system to be operational, and the genetic code to bear any function,

The discovery of thirty-one variant genetic codes in mitochondria, and a plethora of prokaryotes indicates that the chemical properties of the relevant monomers allow more than a single set of codon–amino acid assignments. That means: the chemical properties of amino acids and nucleotides do not determine a single universal genetic code; since there is not just one code, “it” cannot be inevitable.

DNA’s capacity to convey information actually requires freedom from chemical determinism or constraint, in particular, in the arrangement of the nucleotide bases. If the bonding properties of nucleotides determines their arrangement, the capacity of DNA to convey information would be destroyed. In that case, the bonding properties of each nucleotide would determine each subsequent nucleotide and thus, in turn, the sequence of the molecular chain. Under these conditions, a rigidly ordered pattern would emerge as required by their bonding properties and then repeat endlessly, forming something like a crystal. If DNA manifested such redundancy, it would be impossible for it to store or convey function bearing information. Whatever may be the origin of a DNA configuration, it can function as a code only if its order is not due to the forces of potential energy. It must be as physically indeterminate as the sequence of words is on a printed page.

There are no differential bonding affinities between oligonucleotides. There is not just an absence of differing bonding affinities; there are no bonds at all between the critical information-bearing bases in DNA. There are neither bonds nor bonding affinities—differing in strength or otherwise—that can explain the origin of the base sequencing that constitutes the information in the DNA molecule. Differing chemical attractions between nucleotide bases does not exist within the DNA molecule. All four bases are acceptable; none is chemically favored. This means there is nothing about either the backbone of the molecule or the way any of the four bases attached to it that make any sequence more likely to form than another.

There are no significant differential affinities between any of the four bases and the binding sites along the sugar-phosphate backbone. The properties of nucleic acids indicate that all the combinatorially possible nucleotide patterns of a DNA are, from a chemical point of view, equivalent. two features of DNA ensure that “self-organizing” bonding affinities cannot explain the specific arrangement of nucleotide bases in the molecule:
(1) there are no bonds between bases along the information-bearing axis of the molecule and
(2) there are no differential affinities between the backbone and the specific bases that could account for variations in sequence.

The Ribosome and its two subunits, the over 200 assembly and scaffold proteins for the biogenesis of the ribosome, initiation, elongation, and release factors,  the signal recognition particle, the error check and repair machinery to ensure minimization of translation errors,  the matching pool of the  tRNA's, amino acyl tRNA synthetases, mRNA's, all twenty amino acids used in proteins, would have to arise together.

Producing the molecular complexes necessary for translation requires coupling multiple tricks—multiple crucial reactions—in a closely integrated (and virtually simultaneous) way. True enzyme catalysts do this. RNA and
small-molecule catalysts do not.

The British biologist John Maynard Smith has described the origin of the code as the most perplexing problem in evolutionary biology. With collaborator Eörs Szathmáry he writes:
“The existing translational machinery is at the same time so complex, so universal, and so essential that it is hard to see how it could have come into existence, or how life could have existed without it.” To get some idea of why the code is such an enigma, consider whether there is anything special about the numbers involved. Why does life use twenty amino acids and four nucleotide bases? It would be far simpler to employ, say, sixteen amino acids and package the four bases into doublets rather than triplets. Easier still would be to have just two bases and use a binary code, like a computer. If a simpler system had evolved, it is hard to see how the more complicated triplet code would ever take over. The answer could be a case of “It was a good idea at the time.” A good idea of whom ?  If the code evolved at a very early stage in the history of life, perhaps even during its prebiotic phase, the numbers four and twenty may have been the best way to go for chemical reasons relevant at that stage. Life simply got stuck with these numbers thereafter, their original purpose lost. Or perhaps the use of four and twenty is the optimum way to do it. There is an advantage in life’s employing many varieties of amino acid, because they can be strung together in more ways to offer a wider selection of proteins. But there is also a price: with increasing numbers of amino acids, the risk of translation errors grows. With too many amino acids around, there would be a greater likelihood that the wrong one would be hooked onto the protein chain. So maybe twenty is a good compromise. Do random chemical reactions have knowledge to arrive at a optimal conclusion, or a " good compromise" ?   An even tougher problem concerns the coding assignments—i.e., which triplets code for which amino acids. How did these designations come about? Because nucleic-acid bases and amino acids don’t recognize each other directly, but have to deal via chemical intermediaries, there is no obvious reason why particular triplets should go with particular amino acids. Other translations are conceivable. Coded instructions are a good idea, but the actual code seems to be pretty arbitrary. Perhaps it is simply a frozen accident, a random choice that just locked itself in, with no deeper significance.

 The task compares to invent two languages, two alphabets, and a translation system, and the information content of a book (for example hamlet)  being written in English translated  to Chinese  in an extremely sophisticated hardware system. The conclusion that an intelligent designer had to set up the system follows not based on missing knowledge (argument from ignorance). We know that minds do invent languages, codes, translation systems, ciphers, and complex, specified information all the time.  The genetic code and its translation system is best explained through the action of an intelligent designer.

The attribution of the design has to be to God or purely materialistic mechanisms. The gigantic pull to swallow in the second case is the fact that the output is the product of code, and that the molecular machinery needed to replicate the code (for inheritance/perpetuation), transcribe it, translate it into protein with many intermediate steps requiring highly specific operations, and to repair it in the foreseen event that it is damaged (to preserve/protect it) or destroy it in the event that it suffers irreparable damage (to forestall cancer) is just too big to swallow. DNA had an intentional purpose. That's the only reasonable conclusion I can come to.

Stephen Meyer, Signature in the Cell,  page 18:
As the information theorist Hubert Yockey observes, the “genetic code is constructed to confront and solve the problems of communication and recording by the same principles found…in modern communication and computer codes.”

There is no physical reason why any particular codon should be paired up with any specific amino acid. any codon could have been assigned to any amino acid, since there are no direct physical interactions between them:
Chemical affinities between nucleotide codons and amino acids do not determine the correspondences between codons and amino acids that define the genetic code. From the standpoint of the properties of the constituents that comprise the code, the code is physically and chemically arbitrary. All possible codes are equally likely; none is favored chemically. . . . To claim that deterministic chemical affinities made the origin of this system inevitable lacks empirical foundation.

If there is no direct chemical interaction between the codon and binding site of the amino acid on the tRNA, but there is an intermediate space, then there is no evidence that chemical interactions could have selected the assignment based on chemical affinities. Rather, this state of affairs, is evidence that the “genetic code” is in fact a genuine, arbitrary code, such as a designer would create from scratch.

In order to explain the origin of the genetic code, a bottom-up narrative is required.

 Koonin, the logic of chance, page 237
The origin of translation: The key ideas and models
During the 40 years since the discovery of the translation mechanism and deciphering of the genetic code, numerous theoretical (inevitably, speculative, sometimes far-fetched, often highly ingenious) models of the origin and evolution of various components of the translation apparatus and different aspects of the translation process have been proposed. It is unrealistic to provide here a thorough critical review of these models. Instead, I consider a few central ideas that are germane to the thinking about the origin of translation and then discuss in somewhat greater detail the only two coherent scenarios I am aware of. The main general point about the evolution of translation is that selection for protein synthesis could not have been the underlying cause behind the origin of the translation system. To evolve this complex system via the Darwinian route, numerous steps are required, but proteins appear only at the last steps; until that point, an evolving organism “does not know” how good proteins could be.

Can the Origin of the Genetic Code Be Explained by Direct RNA Templating? August 24, 2011 Stephen C. Meyer, Paul A. Nelson 
The three main naturalistic concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physico-chemical affinity between amino acids and the cognate codons (anticodons). 

The genetic code as we observe it today is a semantic (symbol- based) relation between (a) amino acids, the building blocks of proteins, and (b) codons, the three-nucleotide units in messenger RNA specifying the identity and order of different amino acids in protein assembly.  The actual physical mediators of the code, however, are transfer RNAs (tRNAs) that, after being charged with their specific amino acids by aminoacyl tRNA synthetases (aaRSs), present the amino acids for peptide bond formation in the peptidyl-transferase (P) site of the ribosome, the molecular machine that constructs proteins. 

When proteins are produced in cells based on the "genetic code" of codons, there is a precise process under which molecules called transfer RNA (tRNA) bind to specific amino acids and then transport them to cellular factories, ribosomes, where the amino acids are placed together, step by step, to form a protein. Mistakes in this process, which is mediated by enzymes called synthetases, can be disastrous, as they can lead to improperly formed proteins. Thankfully, the tRNA molecules are matched to the proper amino acids with great precision, but we still lack a fundamental understanding of how this selection takes place. 4

The secondary structure of a typical tRNA see figure below, reveals the coding (semantic) relations that Yarus et al. are trying to obtain from chemistry alone - a quest Yockey has compared to latter-day alchemy 


At the end of its 3' arm, the tRNA binds its cognate amino acid via the universally conserved CCA sequence. Some distance away—about 70 Å—in loop 2, at the other end of the inverted cloverleaf, the anticodon recognizes the corresponding codon in the mRNA strand.  (The familiar ‘cloverleaf’ shape represents only the secondary structure of tRNA; its three-dimensional form more closely resembles an “L” shape, with the anticodon at one end and an amino acid at the other.)Thus, in the current genetic code, there is no direct chemical interaction between codons, anticodons, and amino acids. The anticodon triplet and amino acid are situated at opposite ends of the tRNA: the mRNA codon binds not to the amino acid directly, but rather to the anticodon triplet in loop 2 of the tRNA. 

Since all twenty amino acids, when bound to their corresponding tRNA molecules, attach to the same CCA sequence at the end of the 3’ arm, the stereochemical properties of that nucleotide sequence clearly do not determine which amino acids attach, and which do not. The CCA sequence is indifferent, so to speak, to which amino acids bind to it

Nevertheless, tRNAs are informationally (i.e., semantically) highly specific: protein assembly and biological function—but not chemistry—demand such specificity. As noted, in the current code, codon-to-amino acid semantic mappings are mediated by tRNAs, but also by the enzymatic action of the twenty separate aminoacyl-tRNA synthetases 

This is a functionally interdependent system of highly specific molecules, including mRNA, a suite of tRNAs, and twenty specific aaRS enzymes, each of which is itself constructed from information stored on the very DNA strands that the system as a whole decodes.

The DNA - Enzyme System is Irreducibly Complex 
An often undiscussed aspect of complexity is how the tRNA get assigned to the right amino acids. For the DNA language to be translated properly, each tRNA codon must be attached to the correct amino acid. If this crucial step in DNA replication is not functional, then the language of DNA breaks down. Aminoacyl - tRNA synthetases (aaRSs) ensure that the proper amino acid is attached to a tRNA with the correct codon through a chemical reaction called "aminoacylation." Accurate translation requires not only that each tRNA be assigned the correct amino acid, but also that it not be aminoacylated by any of the aaRS molecules for the other 19 amino acids. One biochemistry textbook notes that because all aaRSs catalyze similar reactions upon various similar tRNA molecules, it was thought they "evolved from an common ancestor and should therefore be structurally related." (Voet and Voet pg. 971-975) However, this was not the case as the, "aaRSs form a diverse group of [over 100] enzymes … and there is little sequence similarity among synthetases specific for different amino acids." (Voet and Voet pg. 971-975) Amazingly, these aaRSs themselves are coded for by the DNA: this forms the essence of a chicken-egg problem. The enzymes themselves build help perform the very task which constructs them! 

http://www.ideacenter.org/contentmgr/showdetails.php/id/845

In the cell,  Aminoacyl-tRNA-synthetase recognizes the triplet anticodon of the tRNA and attach the equivalent amino acid to the tRNA. How could random chemical reactions have produced this recognition? Let's suppose rather than intelligence, the chance was the mechanism. The imaginary cell would have to select randomly any of the amino acids, restrict by an unknown mechanism to the 20 used for life, since there are more out there, select by an unknown mechanism only left-handed ones, and make a test drive and produce a polynucleotide and see what happens. Some theories try to explain the mechanism, but they all remain unsatisfactory. Obviously. Furthermore, Aminoacyl-tRNA- synthetase is complex enzymes. For what reason would they have come to be, if the final function could only be employed after the whole translation process was set in place, with a fully functional ribosome being able to do its job? Remembering the catch22 situation, since they are by themselves made through the very own process in question?

Question: what good would the ribosome be for without tRNAs? without amino acids, which are the product of enormously complex chemical processes and pathways? What good would the machinery be good for, if the code was not established, and neither the assignment of each codon to the respective amino acid? had the software and the hardware not have to be in place at the same time? Were all the parts not only fully functional if fully developed, interlocked, set-up, and tuned to do its job with precision like a human-made motor? 

And even it lets say, the whole thing was fully working and in place, what good would it be for without all the other parts required, that is, the DNA double helix, its compactation through histones and chromatins and chromosomes, its highly complex mechanism of information extraction and transcription into mRNA?  Had the whole process, that is   INITIATION OF TRANSCRIPTION, CAPPING,  ELONGATION,  SPLICING, CLEAVAGE, POLYADENYLATION, AND TERMINATION, EXPORT FROM THE NUCLEUS TO THE CYTOSOL, INITIATION OF PROTEIN SYNTHESIS (TRANSLATION), COMPLETION OF PROTEIN SYNTHESIS AND PROTEIN FOLDING, and its respective machinery not have to be all in place? Does that not constitute an interdependent and irreducibly complex system? 

Redundancy of the genetic code enables translational pausing 2014 Mar 27
A new peer-reviewed paper in the journal Frontiers in Genetics, "Redundancy of the genetic code enables translational pausing ," finds that so-called "redundant" codons may actually serve important functions in the genome. Redundant (also called "degenerate") codons are those triplets of nucleotides that encode the same amino acid. For example, in the genetic code, the codons GGU, GGC, GGA, and GGG all encode the amino acid glycine. While it has been shown that such redundancy is actually optimized to minimize the impact of mutations resulting in amino acid changes, it is generally assumed that synonymous codons are functionally equivalent. They just encode the same amino acid, and that's it.  

The ribosome is capable of reading both sets of commands -- as they put it, "the ribosome can be thought of as an autonomous functional processor of data that it sees at its input." To put it another way, the genetic code is "multidimensional," a code within a code. This multidimensional nature exceeds the complexity of computer codes generated by humans, which lack the kind of redundancy of the genetic code. As the abstract states:

The codon redundancy ("degeneracy") found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of Translational Pausing TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.

The paper even suggests, "Cause-and-effect physical determinism...cannot account for the programming of sequence-dependent biofunction."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4033003/

The Wobble hypothesis points to intelligent set up!
1. In translation, the wobble hypothesis is a set of four relationships. The first two bases in the codon create the coding specificity, for they form strong Watson-Crick base pairs and bond strongly to the anticodon of the tRNA.
2. When reading 5' to 3' the first nucleotide in the anticodon (which is on the tRNA and pairs with the last nucleotide of the codon on the mRNA) determines how many nucleotides the tRNA actually distinguishes.
If the first nucleotide in the anticodon is a C or an A, pairing is specific and acknowledges original Watson-Crick pairing, that is: only one specific codon can be paired to that tRNA. If the first nucleotide is U or G, the pairing is less specific and in fact, two bases can be interchangeably recognized by the tRNA. Inosine displays the true qualities of wobble, in that if that is the first nucleotide in the anticodon then any of three bases in the original codon can be matched with the tRNA.
3. Due to the specificity inherent in the first two nucleotides of the codon, if one amino acid is coded for by multiple anticodons and those anticodons differ in either the second or third position (first or second position in the codon) then a different tRNA is required for that anticodon.
4. The minimum requirement to satisfy all possible codons (61 excluding three stop codons) is 32 tRNAs. That is 31 tRNAs for the amino acids and one initiation codon. Aside from the obvious necessity of wobble, that our bodies have a limited amount of tRNAs and wobble allows for broad specificity, wobble base pairs have been shown to facilitate many biological functions. This has another AMAZING implication which points to intelligent set up:  The science paper: The genetic code is one in a million, confesses: If we employ weightings to allow for biases in translation, then only 1 in every million random alternative codes generated is more efficient than the natural code. We thus conclude not only that the natural genetic code is extremely efficient at minimizing the effects of errors, but also that its structure reflects biases in these errors, as might be expected were the code the product of selection.
5. This, all, by all means, screams out literally of intelligent DESIGN !!

Hundreds of unrelated proteins, chaperones, co-factors, ribozymes are needed (plus several special RNA polymers) to assemble the translation machinery, and process the encoded information. Without them the genetic code won’t work, but generating such complex molecular 3D printer requires that the code already be functional.

Rulon James: That you have no model is not irrelevant, to the contrary, its why antievolutionists aren't taken seriously at the science table, they haven't earned a spot.  Merely taking pot shots at what is claimed has not been explained is not an open door for you to slip in your meaningless and useless "creation" notions.  You don't perceive it that way--we get that--but don't imagine others are obliged not to see it that way on your behalf.

Reply: Observe how you change the subject again (and that is what you always do. When you are cornered on one issue, you move on to the next) While in your previous e-mail you complain that creationism/ID is not useful in productive ways (that was never the goal, to begin with), now you complain that ID has no predictive model. That was also a claim made by Erika. 
We do not need a model to predict and test if intelligence is a capable potent causal principle and agency to make life and biodiversity. We KNOW by repeated experience that following things are both always the result of intelligent setup. 

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

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

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

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

1. The essential parts of a living cell cohere only because they have a function such as membrane proteins ( factory portals ), DNA ( hardware ), the genetic code and instructional complex information stored in DNA (software),  RNA polymerase ( information retrieval/encoding )  messenger RNA ( transmission ) Ribosome ( translation/decoding ) proteins ( complex machines )  dynein, kinesin ( taxis ) tubulins ( molecular highways )  mitochondria ( power generating plants ) ATP synthase ( power turbines ) the metabolic network ( electric circuits )  and so on, which are found forming an integrated interdependent system because they make it possible together for the cell to self-replicate, adapt, and remain alive.
2. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a junk yard could not assemble a 747.) It is extraordinarily unlikely, statistically, and chemically, that blind fortune would be up to the task.
3. Actions like engineering, architecting, orchestrating, organizing, programming, translating, setting up communication channels, electric networks, logistic networks, organizing modular systems, recycling systems, making power plants in nanoscale dimensions, product planning and control, establishing product quality and variant flexibility, setting up waste disposal and management systems, creating languages and instructional information, coordinating, setting up strategies, regulating, controlling, recruiting, interpreting and responding, setting up switch mechanisms based on logic gates, setting up transport highways and GPS systems, and controlled factory implosion, are ALWAYS and EXCLUSIVELY assigned to the action of intelligent agents. No exceptions. We see all those things being performed in living cells. 
4. We can conclude, therefore, that biological systems, which cleverly perform all the demanding, multifaceted job activities described above, are most likely due to the set up of an intelligent designer(s).  Only a master player with foresight guided by superb chemical wisdom, putting all those systems together in a proper way is an explanation that makes sense.These chemicals, building blocks, and macromolecules must have a designer who designed them with their function in mind: just as a watch implies a watchmaker, a machine implies a machine designer. Living cells were not created by human designers. Therefore, living cells must have had most likely a non-human intelligent designer


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

Tony Reed: He presented a falsifiable argument.
You either CAN reduce the structure to disprove his argument, or you CAN NOT reduce the structure.
There is nothing stopping you from doing this.
Reply: No. He did send me two science papers, and expects me to decipher and understand what the point is that he is making. That's not how it works. It's not my job to make the argument.
Its his. Or, actually, if that would REALLY be an argument, it would have been an argument from an ID theorist in the first place, and then refuted by whoever it is.

Tony Reed:This was YOUR debate.
I don't ask you to do MY homework. Don't ask me to do yours.
Reply: Correct. But you immediately endorsed my opponents views. I am still questioning if you even understand the point which is supposedly being made.


Tony Reed: If your definition for "irreducibly complex" is such that only IC proponents can use it, then you don't have a definition and the entire IC argument is moot.
Reply: You are correct in the sense that, yes, opponents can also formulate an IC argument, and then shoot it down. But thats not how it usually goes. Normally, an ID theorist elaborates an argument, and opponents attempt to falsify the claim.

Tony Reed:You wrote - "I also still have NO CLUE what the lizard placenta has to do with IC."
Can you, or can't you, reduce it?
Reply: I created my own challenge. What emerged first, the placenta, or the embryo? Now i am giving you a job......

Tony Reed:You wrote - "But I can make an IC claim in regard to the placenta by my own. What evolved first: The embryo, or the placenta ?
That's not a claim. That's a question.
Reply: Its a question, and an implicit claim. There would be no function for a placenta without an embryo. And an embryo depends on the placenta to develop. They are irreducible, and interdependent. Prove me wrong.

Tony Reed: Before I answer, are you proposing that the combination of the placental system and the embryo comprise an Irreducibly complex system?
Reply: Yes. In the same sense, the relationship goes as well to the question of what came first: The chicken, or the egg. I have yet to see an alternative explanation to: God created the chicken and the cock, they had some fun together, and then came the egg and the embryo started its development.

Conversations with Dimiter Kunnev about the Ribosome

https://reasonandscience.catsboard.com/t1661p25-translation-through-ribosomes-amazing-nano-machines#8008

In reply to my email

How ribosomes are like Russian dolls
https://reasonandscience.catsboard.com/t1661-translation-through-ribosomes-amazing-nano-machines#8006

Dimiter Kunnev did send me following reply:
Hi guys, please note that in order for Ribosome to function as protein synthesis needs only PTC even in a primitive form and something to hold it. I'm sending several papers to consider. The entire concept for the irreducibly complex ribosome is only wishful thinking. Enjoy

It is nice first to read the papers and then give answers. From your answer, it is clear that you don't know what you are talking about. Here is the evidence that in order to have peptide synthesis you need only short RNA. Also, I'm sending the 2012 and 2016 Anolles papers where is presented IN DETAILS loop by loop, helix by helix entire evolution of the ribosome. You can see that the ribosomal RNA and tRNA are coevolved EXACTLY as suppose to be according to step by step evolutionary development. ALL DATA CLEARLY SUGGESTS THAT THE RIBOSOME IS NOT IRREDUCEBLY COMPLEX. Your hypothesis for SUDDEN ID dependent formation is NOT supported at all. Please do not answer unprepared and after all, please acknowledge the data even that contradicts your view.

Following science papers were annexed in the first reply:
Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins
https://www.sciencedirect.com/science/article/pii/S1047847717300606
Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features
https://www.sciencedirect.com/science/article/pii/S1047847717300606
Could a Proto-Ribosome Emerge Spontaneously in the Prebiotic World?
https://europepmc.org/article/med/27941673
History of the ribosome and the origin of translation
https://www.pnas.org/content/112/50/15396

Here my reply & comments:

Claim: in order for Ribosome to function as protein synthesis needs only PTC even in a primitive form 
Reply: The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses
https://www.mdpi.com/2075-1729/10/8/134
The PTC region has been considered crucial in the understanding about the origins of life. It has been described as the most significant trigger that engendered a mutualistic behavior between nucleic acids and peptides, allowing the emergence of biological systems.

Mutational characterization and mapping of the 70S ribosome active site
03 February 2020
https://academic.oup.com/nar/article/48/5/2777/5721209
The ribosome's active site accurately and efficiently processes α-amino acid monomers using catalytic rRNA, that we would expect to exhibit high levels of conservation and would be less permissible, or flexible, to mutation. In fact, previous work has demonstrated in vivo that many nucleotide changes to highly-conserved nucleotides are detrimental , but the ribosome can still withstand some changes at select positions

As expected, the entire PTC active site (PTC-ring, A-loop, and P-loop) exhibited a high-level of conservation, with ∼75% of the nucleotide positions possessing a Shannon Entropy value at or near zero.

My comment: This is hard evidence, that a stepwise, gradative evolution of the Peptidyl Transferase Center is not supported by the empirical data provided in this paper.

Claim: The emergence of this proto-PTC is a prerequisite to couple a chemical symbiosis between RNAs and peptides that further evolved both to (i) become the large subunit of the ribosome by the principle of accretion and (ii) to allow the emergence of the genetic code. Its importance cannot be challenged as it composes the central core of the decoding language of biology.
Reply: There is no selection pressure why  this highly complex system would/should emerge without the genetic code, and vice versa. 

Claim: Caetano-Anollés and Sun used structural analyses to provide evidence that tRNAs were older than ribosomes and were coopted to operate in the translation machinery.
Reply: Before the translation machinery can operate, ALL essential players must be fully formed an in place. In the same sense, as an automobile can only fulfill its function, if all parts are working together once fully formed, constituting a device of integrated complexity, the same is the case for the ribosome, where , if even one tiny peace is missing, nothing goes. Imagine, you have a fully operational translation machinery, and instead of all aminoacyl tRNA synthetases are present, what would happen? The entire translation process would absolutely brake down, and any polypeptide product would be non-functional, and not fold into functional 3D forms. 

Claim: Farias et al. reconstructed a 3D structure of the PTC based on an ancestral sequence of tRNAs and observed a structural similarity of 92% when compared to the PTC of the bacteria Thermus thermophilus. Together, all these data make evident a scenario for the origin of life in which an evolutionary and chronological connection can be observed between these two essential components of the translation system: tRNAs and rRNAs.
Reply: This makes no sense whatsoever. How do they make the jump from the evidence to the conclusion? How would PTC and tRNA's come to a functional relationship and organization without all other players in place, and the genetic code set up? 

Observation: Besides, as we were interested in understanding the relevance of the PTC to the early origin of life, we decided to exclude eukaryotic sequences from the analyses. Eukaryotes are now known to have originated from archaeal organisms coming from the phylum Lokiarchaeota, subphylum Asgard, therefore being derivate clades and having no substantial role in early origins of life
Reply: The authors implicitly admit that there is no homologous sequence of the eukaryotic and prokaryotic ribosome. This is a deal killer form common ancestry ( and there are many other points relevant to this observation, listed later )



Claim: The entire concept for the irreducibly complex ribosome is only wishful thinking. From your answer, it is clear that you don't know what you are talking about. Here is the evidence that in order to have peptide synthesis you need only short RNA. Also, I'm sending the 2012 and 2016 Anolles papers where is presented IN DETAILS loop by loop, helix by helix entire evolution of the ribosome. You can see that the ribosomal RNA and tRNA are coevolved EXACTLY as suppose to be according to step by step evolutionary development. ALL DATA CLEARLY SUGGESTS THAT THE RIBOSOME IS NOT IRREDUCEBLY COMPLEX. Your hypothesis for SUDDEN ID dependent formation is NOT supported at all. Please do not answer unprepared and after all, please acknowledge the data even that contradicts your view.


Response: Handwaving the claim away and glossing over will not solve the point in question, and refute the made observation. If abiogenesis researchers want to be taken seriously, they need to address the objections in a consistent manner, and if a threshold is reached, where natural mechanisms don't suffice, or conceptual problems are pointed out that cannot be overcome, than it is expected that they acknowledge the status quo, and the facts presented. Observing and reasoning about the many intricate patterns in nature requires that one is able to recognize the boundaries of what unguided, random, non-intelligent mechanisms can achieve, and when complexity is observed in the natural world that implodes that range, design should be expected to be inferred as the more case adequate explanation. As we see today, science is unravelling more and more biomechanical complexity, and multilayered information systems working conjoined and in a teamwork.  Unfortunately, as it seems, rarely evolutionary biologists are open-minded enough to do so because evolutionary scenarios are ingrained in their thinking from young age and through education, so giving a second thought on the matter is usually not on the table, but evolutionary assertions are asserted over and over, and considered as the only viable and acceptable scenario, while intelligent design is derisen and ridiculed as unscientific, and incredulity is in most cases the only answer.

Fact remains, that translation ONLY works with all parts involved working in an integrated fashion together, in a joint venture.

According to Darwins Theory, the mechanism of natural selection is survival of the fittest. Leaving the fact on side, that there was no life when the Ribosome emerged, ( life depends on the ribosome, andself-replication), the question is:

1. What function would each of the following molecules have on their own?

1. The Ribosome
Conserved nucleotides in the peptidyl-transferase center (PTC) and its proximity may play a key role in peptide-bond formation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1592644/
2. Aminoacyl -tRNA synthetases
3. tRNA's
4. mRNA
5. A SELECTED pool of 20 amino acids ( as used in life, from hundreds supposedly existing on early earth )

The functionality of translation would not be maintained  after any of the listed parts have been removed. I would go a step further and say, that even changing a few amino acids or ribonucleotides near the peptidyl transferase center, and the entire translation system would absolutely break down.

Claim:The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code 2019 Mar 1
This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains.
Response: How is this not a made-up just so hypothetical scenario that has no real world plausiblity? Why should unguided events lead to hiearchies and emergence at all, rather than racemisation and asphaltization of molecules? The thing is, there's no driver for any of the pieces to evolve individually because single parts confer no advantage in and of themselves. Assembling things in the right order leading to functional integrated machine-like complexity, where    

why would any natural unguided events come up with any of the four molecules, if individually, there would be no function whatsoever for them ? This cannot be pointed out clear enough. 

Soren Lovtrup, professional biologist in Sweden, said
"...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous."

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 ?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overall design goal.
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.

But on top of that: The Ribosome requires over 200 scaffold proteins, chaperones, and 75 cofactors for its assembly. tRNA's also require a very complex biosynthesis pathway. Arguing that natural stepwise, gradual unguided processes produced all these molecular machines resulting in the making of the ribosome which cannot function unless all other parts are there and interconnected, is far from being a reasonable, plausible, and logical assertion and inference. 

Translation is just a small part of the entire irreducible chain to make functional proteins: Each individual of the 25 unimaginably complex holoproteins have only function when everything works together:

The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins

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 the very own processing procedure described below, which makes its origin an irreducible  catch22 problem:

THE GENE REGULATORY NETWORK "SELECTS" WHEN, WHICH GENE IS TO BE EXPRESSED
INITIATION OF TRANSCRIPTION BY RNA POLYMERASE
TRANSCRIPTION ERROR CHECKING BY CORE POLYMERASE AND TRANSCRIPTION FACTORS
RNA CAPPING
ELONGATION
SPLICING
CLEAVAGE
POLYADENYLATION AND TERMINATION
EXPORT FROM THE NUCLEUS TO THE CYTOSOL
INITIATION OF PROTEIN SYNTHESIS (TRANSLATION) IN THE RIBOSOME
COMPLETION OF PROTEIN SYNTHESIS  
PROTEIN FOLDING
MATURATION
PROTEIN TARGETING TO THE RIGHT CELLULAR COMPARTMENT
ENGAGING THE TARGETING MACHINERY BY THE PROTEIN SIGNAL SEQUENCE
CALL CARGO PROTEINS TO LOAD/UNLOAD THE PROTEINS TO BE TRANSPORTED
ASSEMBLY/DISASSEMBLY OF THE TRANSLOCATION MACHINERY
VARIOS CHECKPOINTS FOR QUALITY CONTROL AND REJECTION OF INCORRECT CARGOS
TRANSLOCATION TO THE ENDOPLASMIC RETICULUM
POSTRANSLATIONAL PROCESS OF PROTEINS IN THE ENDOPLASMIC RETICULUM OF TRANSMEMBRANE PROTEINS AND WATER-SOLUBLE PROTEINS
GLYCOSILATION OF MEMBRANE PROTEINS IN THE ER ( ENDOPLASMIC RETICULUM )
ADDITION OF OLIGOSACCHARIDES
INCORRECTLY FOLDED PROTEINS ARE EXPORTED FROM THE ER, AND DEGRADED IN THE CYTOSOL
TRANSPORT OF THE PROTEIN CARGO TO THE END DESTINATIONS AND ASSEMBLY

Claim: Add a part. Make it necessary. That is the heart of Mullerian two-step process.
Reply: Müller introduced this concept way back in 1918, and did so in the following scientific paper: Genetic Variability, Twin Hybrids and Constant Hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)

Here is the relevant quote :

Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary. 

Reply: The problem is always explaining how biological information or function is built up in the first place.

First paper linked in the email by Dimiter: 
Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins

As a first part of my reply, here to the lucid parts of the paper which partially agree with:
Observation: Most peptides, even those composed of the 20 proteinogenic amino acids, are of no structural and functional use to RNA, placing a premium on synthesizing only useful forms and passing the information on to the next generation. Given the broad spectrum of steps needed to fulfill even the basic requirements of an information-bearing chemical system capable of autocatalytic replication, it seems clear that the RNA-peptide world must have achieved considerable complexity well before its transition to the DNA-protein world we observe today. In making this transition, the RNA-peptide world faced a considerable challenge: whereas the chemistry of the RNA-to-DNA transition seems unproblematic (Ritson and Sutherland, 2014), there is a major obstacle on the path from peptides to proteins, known as the protein folding problem.
Reply:  Origin and Evolution of DNA and DNA Replication Machineries 
https://www.ncbi.nlm.nih.gov/books/NBK6360/
Scientists are struggling to answer major questions such as: how did the DNA/Protein world come about, why would such partition of tasks evolve in the RNA world, and which came first, DNA or Protein? Again, we find the ‘chicken and egg’ problem.

Ribonucleotide reductase (RNR) which are the main player in the transition from RNA to DNA are ENORMOUSLY COMPLEX proteins. It takes these enzymes to make DNA. But it takes DNA to make these enzymes. What came first?

From RNA to DNA impossible
https://reasonandscience.catsboard.com/t1784-from-rna-to-dna-impossible

Formation of Deoxyribonucleotides
https://reasonandscience.catsboard.com/t2028-the-dna-double-helix-evidence-of-design#3432

The protein folding problem from an evolutionary perspective
Protein structure, in contrast, is an altogether more complex property and the process by which proteins reach their structure (folding) is easily disrupted and readily undone by even minor changes in temperature or the chemical environment. Once denatured, proteins tend to aggregate and can either not be renatured, or only with large loss of material, making denaturation a substantially irreversible process. The easy loss of structure in most proteins is due to the low free energy of folding (often equivalent to just a few hydrogen bonds), which places them energetically close to the unfolded state. Their tendency to aggregate upon denaturation is due to the dominant role of the hydrophobic effect in folding, which leads folded proteins to mainly segregate hydrophobic residues to the protein core and hydrophilic residues to the surface. When the hydrophobic residues of the core become exposed in the denatured state, they tend to coalesce into heterogeneous tangles, which are generally impossible to resolve and must be degraded. The closeness of the structured and unstructured states in most proteins and the many problems arising to living beings from this are documented in the elaborate protein quality control and degradation systems that are universal to life

Forces Stabilizing Proteins - essential for their correct folding
https://reasonandscience.catsboard.com/t2692-forces-stabilizing-proteins-essential-for-their-correct-folding

Even biophotons!! are involved in protein folding: 
The mechanism and properties of bio-photon emission and absorption in protein molecules in living systems
https://aip.scitation.org/doi/10.1063/1.4709420

Quantum mechanic communication in cells: A paradigm shift in biology
https://www.youtube.com/watch?v=9x32MF79AkA
https://reasonandscience.catsboard.com/t3021-awe-inspiring-biophoton-cell-cell-communication-points-to-design#7981

Claim: Proteins from peptides: The staggering size of protein sequence space and the low incidence of folded exemplars within it essentially preclude an origin of folded domains by random concatenation of amino acids. An alternative scenario proposes that the first folded domains did not arise from random processes, but from the increased complexity of the peptides that had evolved in the RNA world
Reply: This is an entirely UNSUPPORTED claim. 

No evidence that RNA molecules ever had the broad range of catalytic activities
https://reasonandscience.catsboard.com/t2243-no-evidence-that-rna-molecules-ever-had-the-broad-range-of-catalytic-activities

The origin of replication and translation and the RNA World
https://reasonandscience.catsboard.com/t2234-the-origin-of-replication-and-translation-and-the-rna-world
The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that, to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could evolve is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual.

Claim:For the most part, contemporary proteins can be traced back to a basic set of a few thousand domain prototypes, many of which were already established in the Last Universal Common Ancestor of life on Earth, around 3.5 billion years ago. 
Response:  Common descent, the tree of life, a failed hypothesis
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis

1. The DNA replication machinery is not homologous in the 3 domains of life. The bacterial core replisome enzymes do not share a common ancestor with the analogous components in eukaryotes and archaea.
2. Bacteria and Archaea differ strikingly in the chemistry of their membrane lipids. Cell membrane phospholipids are synthesized by different, unrelated enzymes in bacteria and archaea, and yield chemically distinct membranes.
3. Sequences of glycolytic enzymes differ between Archaea and Bacteria/Eukaryotes. There is no evidence of a common ancestor for any of the four glycolytic kinases or of the seven enzymes that bind nucleotides.
4. There are at least six distinct autotrophic carbon fixation pathways. If common ancestry were true, an ancestral Wood–Ljungdahl pathway should have become life's one and only principle for biomass production.
5. There is a sharp divide in the organizational complexity of the cell between eukaryotes, which have complex intracellular compartmentalization, and even the most sophisticated prokaryotes (archaea and bacteria), which do not.
6. A typical eukaryotic cell is about 1,000-fold bigger by volume than a typical bacterium or archaeon, and functions under different physical principles: free diffusion has little role in eukaryotic cells but is crucial in prokaryotes
7. Subsequent massive sequencing of numerous, complete microbial genomes have revealed novel evolutionary phenomena, the most fundamental of these being: pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept
8. RNA Polymerase differences: Prokaryotes only contain three different promoter elements: -10, -35 promoters, and upstream elements.  Eukaryotes contain many different promoter elements
9. Ribosome and ribosome biogenesis differences: Although we could identify E. coli counterparts with comparable biochemical activity for 12 yeast ribosome biogenesis factors (RBFs), only 2 are known to participate in bacterial ribosome assembly. This indicates that the recruitment of individual proteins to this pathway has been largely independent in the bacterial and eukaryotic lineages. 22


Observation: The origin of these domain prototypes, however, remains poorly understood.
Response: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14  That would be the size of a book with 400 pages, each page with 3000 characters.  They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. 


Claim: One hypothesis posits that they arose from an ancestral set of peptides, which acted as cofactors of RNAmediated catalysis and replication.
Response: 
(Big!)problem 1: New technologies to analyse protein function: an intrinsic disorder perspective
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014577/

The corresponding DNA sequences dictate the amino acid sequences. Specific functionality of a given protein is defined by a unique spatial positioning of its amino acid side chains and prosthetic groups, suggesting that such a specific spatial arrangement of functional groups in biologically active proteins is defined by their unique 3D structures predetermined by the unique amino acid sequences encoded in unique genes.

Basic molecules need to polymerize to become information-bearing genomes and proteins with specific functions and come into a functional relationship and interdependence. An organizational structure would have to be established between the domain of information and computation ( the genome and epigenetic information orchestrating gene expression ) and the mechanistic domain, where proteins and enzymes work based on the direction and information flow of the beforementioned blueprint-like information. The puzzle lies with the problem of creating a causal organization, the interrelationship of informational and mechanical aspects into interdependent narratives. One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and control of molecular mechanical dynamics. 
In modern cells, to make proteins, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps through large multimolecular machines are required. Each step requires exquisitely engineered molecular machines composed of an enormous number of subunits and co-factors, which require the very own processing procedure described, which makes its origin an irreducible  catch22 problem.

Problem 2: Peptide Bond Formation of amino acids in prebiotic conditions: another unsurmountable problem of protein synthesis on early earth
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins#6664

The Role of Lipid Membranes in Life’s Origin
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
A plausible mechanism for synthesis of peptide bonds and ester bonds on the prebiotic Earth continues to be a major gap in our understanding of the origin of life.

Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life
Claudia Huber and Guenter Waechtershaeuser
Under the dilute aqueous conditions most relevant for the origin of life, activation of the amino acids by coupling with hydrolysis reactions notably of inorganic polyphosphates has been suggested. It is, however, not clear how under
hot aqueous conditions such hydrolytically sensitive coupling compounds, if geochemically available at all, could resist rapid equilibration.
http://fire.biol.wwu.edu/cmoyer/zztemp_fire/biol345_S99/huber2.pdf


Problem 3:  the prevalence of protein sequences adopting functional enzyme folds.
Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10(77), adding to the body of evidence that functional folds require highly extraordinary sequences.
https://www.ncbi.nlm.nih.gov/pubmed/15321723?fbclid=IwAR2WqQIOoD3Opw1tmhd6Z5K76yAcJ-w_DbwlWnPml5jVxM34YxC9l7N3PHw

Chemical evolution of amino acids and proteins ? Impossible !!
https://reasonandscience.catsboard.com/t2887-chemical-evolution-of-amino-acids-and-proteins-impossible

Claim: Initially, these peptides were entirely dependent on the RNA scaffold for their structure, but as their complexity increased, they became able to form structures by excluding water through hydrophobic contacts, making them independent of the RNA scaffold.
Reply: How does the author know that there were RNA scaffolds on prebiotic earth?

Claim: ability to fold was thus an emergent property of peptide-RNA coevolution. The ribosome is the main survivor of this primordial RNA world and offers an excellent model system for retracing the steps that led to the folded proteins of today, due to its very slow rate of change. Close to the peptidyl transferase center, which is the oldest part of the ribosome, proteins are extended and largely devoid of secondary structure; further from the center, their secondary structure content increases and supersecondary topologies become common, although the proteins still largely lack a hydrophobic core; at the ribosomal periphery, supersecondary structures coalesce around hydrophobic cores, forming folds that resemble those seen in proteins of the cytosol. Collectively, ribosomal proteins thus offer a window onto the time when proteins were acquiring the ability to fold.
Reply: These are unsupported claims.

Observation: It seems impossible that this elaborate interplay of complex macromolecules could have emerged de novo from abiotic processes
Reply: ABSOLUTELY AGREED. 

Claim: it is generally accepted that life must have started in a simpler form, which has been the subject of much theorizing and some experimentation. Among the possibilities considered, by far the most popular and best supported has been that of RNA forming the first systems capable of autocatalytic replication, acting as both the information bearer and the agent of catalysis. The RNA world is now well established and
widely considered to have been the direct precursor to the DNAprotein world of today.
Reply: The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated
https://reasonandscience.catsboard.com/t2997-the-problem-of-the-origin-of-the-hardware-and-software-in-the-cell-is-far-greater-than-commonly-appreciated

The very origin of the first organisms presents at least an appearance of a paradox because a certain minimum level of complexity is required to make self-replication possible at all; high-fidelity replication requires additional functionalities that need even more information to be encoded.  The crucial question is how the Darwin-Eigen cycle could have started—how was the minimum complexity that is required to achieve the minimally acceptable replication fidelity attained? In even the simplest modern systems, such as RNA viruses, replication is catalyzed by complex protein polymerases. The replicase itself is produced by translation of the respective mRNA(s), which is mediated by the immensely complex ribosomal apparatus. Hence, the dramatic paradox of the origin of life is that to attain the minimum complexity required for a biological system to start on the Darwin-Eigen spiral, a system of a far greater complexity appears to be required. How such a system could emerge is a  puzzle that defeats conventional evolutionary thinking, all of which is about biological systems moving along the spiral; the solution is bound to be unusual. The origin of life—or, to be more precise, the origin of the first replicator systems and the origin of translation—remains a huge enigma, and progress in solving these problems has been very modest—in the case of translation, nearly negligible.4

Second paper linked in the email by Dimiter: 
Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features 


Claim: Similar catalytic rates but different primary sequences and different metal ion requirements. One of these ribozymes has now been re-engineered to catalyze intermolecular peptide-bond formation using an aminoacylated nucleotide and an amino-acid-linked oligonucleotide as substrates. Our results demonstrate that a ribozyme can catalyze peptide-bond formation reactions analogous to the action of the ribosome and, most surprisingly, appears to use similar sequence and structure motifs. These findings provide evidence for the feasibility of the 
Reply: The authors confess re-engineering. That means ===>>> Intelligent design !! Case closed. 


Third paper linked in the email by Dimiter:
Could a Proto-Ribosome Emerge Spontaneously in the Prebiotic World? 


Observation: An indispensable prerequisite for establishing a scenario of life emerging by natural processes is the requirement that the first simple proto-molecules could have had a realistic probability of self-assembly from random molecular polymers in the prebiotic world.
Reply: There is more than enough evidence demonstrating that protein synthesis by unguided random events is not possible at all. 
https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesis

Claim: Three concentric structural elements of different magnitudes, having a dimeric nature derived from the symmetrical region of the ribosomal large subunit, were suggested to constitute the vestige of the proto-ribosome. It is assumed to have materialized spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and simple elongation. 
Reply: The problem of chain termination
https://reasonandscience.catsboard.com/t2130-peptide-bonding-of-amino-acids-to-form-proteins-and-its-origins
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. Formic acid (HCOOH) is by far the commonest organic product of Miller-type simulations. Indeed, if it weren’t for evolutionary bias, the abstracts of the experimental reports would probably state nothing more than: ‘An inefficient method for production of formic acid is here described …’ Formic acid has little biological significance except that it is a major component of ant (Latin formica) stings.

Observation: Even the sequence of a simple ribozyme of 40 nucleotides has 10^24 possible compositions. To represent all of these compositions at least once, and thus to establish a certainty that this simple ribozyme could have materialized, requires 27 kg of RNA chains, which classifies spontaneous emergence as a highly implausible event.
Reply: We are in FULL AGREEMENT with the observation :=)) 

Observation:  probability of spontaneous occurrence of the DPR sequence, obtained under the notion of limited sequence specificity, may be too optimistic, but even a significantly lower probability is still acceptable, taking into consideration that the emergence of life is believed to have occurred just once. Given optimal, yet unknown environmental conditions and sufficient time, a small pond with a relatively low concentration of random RNA chains of about 70 mer may have provided feasible likelihood for the materialization of a prebiotic apparatus catalyzing non-coded peptide-bond formation and simple elongation. 
Reply: So what is it now? Highly implausible, or feasible likelihood ? The paper is in contradiction with itself !! 

Observation: The first true alternative to terrestrial biology will be found on an extrasolar planet, in a rock from Mars, or within an extreme environment on Earth. More likely, it will be the handiwork of an intelligent species that has discovered the principles of Darwinian evolution and learned to devise chemical systems that have the capacity to generate bits on their own.
Reply: Or maybe a superpowerful intelligent creator was involved ? Seems the most likely scenario to me.

Fourth paper provided by Dimiter: 
History of the ribosome and the origin of translation

Intro: We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA.
Reply:  When naturalistic explanations are short coming, it is not rare that the authors resort ad-hoc to a "frozen accident". The intro of the paper resorts as well to that "escape", and as such, it is a implicit admission that rational evidence based , plausible and logical explanations are lacking.

Science-based on materialism resorting to frozen accidents.
https://reasonandscience.catsboard.com/t2889-science-based-on-materialism-resorting-to-frozen-accidents

Claim:  Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization.
Reply: Why should stochastic unguided natural events " evolve" capabilities in a orderly sequenced fashion ? This is streching far too far the capabilities of unguided random chemical reactions!! How is it possible, that the authors are not realizing this VERY OBVIOUS fact? Not only that, but they outline what it is, namely: RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. WOW!!! I mean: Really ???!! I mean: How can the authors make such a huge claim, shamelessly, without a blinker of an eye? This is just ad-hoc speculation without a SHRED of evidence to back up the claims. This is not science. This is PSEUDO-SCIENTIFIC hogwash !! How can people not realize this?? 

In regards of the origin of tRNAs: 



Piecemeal Buildup of the Genetic Code, Ribosomes, and Genomes from Primordial tRNA Building Blocks
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5198078/

Claim: tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation.
Reply: Why should tRNA's define the genetic code? There is no reason, why unguided events would have selected a set of 20 amino acids, nor their cognate aminoacyl-tRNA synthetases, and even less, that these molecules would have frozen somehow the triplet codon set of RNA's or DNA. Simply said: This is baseless speculation without a shred of evidence to back up the claim. Its a made-up story.

Claim: We propose that these nucleic acid loops were capable of interacting stereochemically with evolving protein structure and responding to their molecular makeup.
Reply: Claiming that proteins are the product of evolution is unsupported. There is no evidence for this.

Claim: Increases in these interactions canalized both the appearance of genetic memory and building blocks (modules) of RNA with which to construct processive biosynthetic machinery on one hand and genomic memory storage on the other.
Reply: One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and control of molecular mechanical dynamics.

1. Whenever there are things that cohere only because of a purpose or function (for example, all the complicated parts of a watch that allow it to keep time), we know that they had a designer who designed them with the function in mind; they are too improbable to have arisen by random physical processes. (A hurricane blowing through a hardware store could not assemble a watch.)
2. The essential parts of a living cell cohere to a functional whole. They are found forming an integrated complex system because they make it possible together for the cell to self-replicate, adapt, and remain alive. There is an organizational structure between the domain of specified complex information that cleverly directs the making all functional parts and controls molecular mechanical dynamics and self-replication.
3. The functional organization which makes chemicals, building blocks, and macromolecules must have a designer who designed the system with the function in mind: just as a watch implies a watchmaker, a machine implies a machine designer, and a factory, a factory maker. Living cell factories full of machines made through the instructional genetic information were not created by human designers. Therefore, living cells must have had a non-human intelligent designer

Transfer RNA, and its biogenesis, best explained through design
https://reasonandscience.catsboard.com/t2070-transfer-rna-and-its-biogenesis

tRNA's are very specific molecules, and the " made of " follows several steps, requiring a significant number of proteins and enzymes, which are often made of several subunits and ainded by essential co-factors and metals.

The challenge for evolution to the fact, that biological systems incorporate several essential parts, that cannot be eliminated without losing the core function of the system in question, and that these parts have no function of their own and could therefore not be product of natural mechanisms, of gradual evolutionary steps, is in my view more severe than most philosophers of science and scientists like Behe exemplify. In systems of enormous biological complexity like the cell, thousands of parts are essential , many more parts, than the well known examples like the flagellum. Irreducibility is found from the highest level of biological organisation and systems, to a single DNA deoxyribonucleotide, which loses function if reduced to its single components, the bases, phosphate or sugar. Just take off one, and the molecule loses its function. Same goes for the cell. Take off one building block, like the spindle apparatus, and mitosis and cell division is not possible, and life could not reproduce itself.

The make of proteins is similar to the make of cars in a car factory. If the grinder machine to make the motor pistons has a mal function, the pistons cannot be finished, the car's motor block cannot be assembled with all parts, and the motor would not function without that essential part. Amongst thousands of parts, just a tiny one will compromise the function of the whole system. In biological nano-factories, the solutions to overcome problems like damage must all be pre-programmed, and the repair "working horses" to resolve the problem must be ready in place and "know" what to do how, and when. If a roboter in a factory assembly line fails, employees are ready to detect the error and make the repair . In the cell, the mal function of any part even as tiny and irrelevant as it might seem, can be fatal, and if the repair mechanisms are not functioning correctly and fully in place right from the start, the repair can't be done, and life ceases. These repair enzymes which cleave, join, add, replace etc. must be programmed in order to function properly right from the start. Aberrantly processed pre-tRNAs for example are eliminated through a nuclear surveillance pathway by degradation of their 3′ ends, whereas mature tRNAs lacking modifications are degraded from their 5′ends in the cytosol. 




1. https://www.frontiersin.org/articles/10.3389/fmolb.2019.00123/full
2. https://pubmed.ncbi.nlm.nih.gov/28454764/

Central Dogma & Origin of the Ribosome
https://www.youtube.com/watch?v=x2DaEyfN0Ws

The ribosome works like a factory and machine, and requires like a printing machine precisely fitting parts to work together. And those parts cannot be the result of evolution, since individually, those parts confer no function. 

Video comment: life the greatest story ever told life on earth originated about four billion years ago the origin of life was a transition from simple chemistry to complex biochemistry the first branching of the tree of life created bacteria and archaea later a third branch Eukarya split off from archaea
Reply: This claim is falsified alone by the fact that the bacterial ribosome and eukaryotic ribosome are not homologous:

Mutational characterization and mapping of the 70S ribosome active site
03 February 2020
https://academic.oup.com/nar/article/48/5/2777/5721209

Observation: Besides, as we were interested in understanding the relevance of the PTC to the early origin of life, we decided to exclude eukaryotic sequences from the analyses. Eukaryotes are now known to have originated from archaeal organisms coming from the phylum Lokiarchaeota, subphylum Asgard, therefore being derivate clades and having no substantial role in early origins of life
Reply: The authors implicitly admit that there is no homologous sequence of the eukaryotic and prokaryotic ribosome. This is a deal killer form common ancestry ( and there are many other points relevant to this observation, listed later )

Video comment:  polymers are replicated transcribed and translated the rules that govern the information flow during these processes are known as the central dogma of molecular biology the central dogma says that RNA can be replicated to make new RNA. RNA can be reversed transcribed to make DNA. DNA can be replicated to make new DNA. DNA can be transcribed to make RNA and RNA can be translated to make protein. biology contains what we call molecular symbiotic these are different types of polymers that rely entirely on one another RNA is one type of molecular symbiotic RNA is synthesized by protein protein is the other molecular symbiotic protein is synthesized by RNA in every cell of every organism RNA and protein depend on each other for synthesis

Reply: An organizational structure would have to be established between the domain of information and computation ( the genome and epigenetic information orchestrating gene expression ) and the mechanistic domain, where proteins and enzymes work based on the direction and information flow of the beforementioned blueprint-like information. The puzzle lies with the problem of creating a causal organization, the interrelationship of informational and mechanical aspects into interdependent narratives. One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and control of molecular mechanical dynamics.  In modern cells, to make proteins, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps through large multimolecular machines are required. Each step requires exquisitely engineered molecular machines composed of an enormous number of subunits and co-factors, which require the very own processing procedure described, which makes its origin an irreducible  catch22 problem.

Video comment: the synthesis of protein by the ribosome is called translation the ribosome is the most ancient and universal macro molecular assembly in the biological world the ribosome has a small subunit that reads the mRNA the ribosome also contains a large subunit that links amino acids in the correct sequence

Reply: First, there would have to be the entire pathway starting from the genome, having a genetic code, and information using the genetic code, to store the information in DNA. Secondly , there would have to be the messenger RNA, and the entire pathway including transcription, and the hyper complex holo protein complex that transcribes the information from RNA to messenger DNA. And there would have to exist already the set of 20 amino acids, synthesized and available in the cell for polymerization. This is a simplified explanation, but the entire pathway is in reality immensy complex, and requires a myriad of complex macromolecules and molecular machines. 

The interdependent and irreducible structures required to make proteins
https://reasonandscience.catsboard.com/t2039-the-interdependent-and-irreducible-structures-required-to-make-proteins

Now, EVEN IF we convey that all those things were already fully extant and evolved, linking the right amino acids together in the correct sequence is far from a simple task. It is a very precise, coordinated process which requires the ribosomal subunits to work together in a coordinated and exquisitely controlled process, where also error check and repair is absolutely essential, and a right balance between speed of translation and error rate must be just right. There is no feasible way how the right speed of polymerization of about 20 amino acids per second could be established by trial and error.  

tRNAs deliver amino acids to the ribosome the evolution of the prokaryotic ribosomes was essentially complete by the last Universal common ancestor or Luca

Video comment: Evolution and natural selection  was in play prior DNA replication began, NOT BEFORE:

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 abetted by chemical selection, such as the preferential survival of stable RNA species.

Functional proteins from a random-sequence library
Anthony D. Keefe & Jack W. Szostak
Functional primordial proteins presumably originated from random sequences
https://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Keefe_Szostak_Nature_01.pdf?fbclid=IwAR0giOg_aZfFRKQALk7CB22nVIx32ShiN0Vp78cwtAYwmwQ_0RJicfxpR1M
The possible mechanisms to explain the origin of life
https://reasonandscience.catsboard.com/t2515-abiogenesis-the-possible-mechanisms-to-explain-the-origin-of-life

The ribosome works like a factory and machine, and requires like a printing machine precisely fitting parts to work together. And those parts cannot be the result of evolution, since individually, those parts confer no function.

Video comment: ribosome is around four billion years old even though it is extremely ancient we have developed methods for reconstructing the evolution of the ribosome in phase one the LSU and SSU both begin as small RNA stem loops folding to stem loops protects the RNA from chemical degradation
Reply: This is smuggling teleology into the argument. There is no urge for matter to prevent itself to degrade!! This is borrowing from a worldview where intent was at play to make the Ribosome. Something, a materialist cannot resort to !! 

Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.

Video comment: in Phase two the LSU our RNA from the peptidyl transferase center the SSU our RNA function is less certain in Phase three the peptidyl transferase center is encased and rigidify and the exit pore is extended into a short tunnel

Reply: The entrance and exit tunnel of the Ribosome are ABSOLUTELY ESSENTIAL in order for the mRNA's, tRNA's, aminoacyl-tRNA-synthetases to get in, and the growing polymerized strand to get out. How did this precise configuration and position be positioned for correct operation? These tunnels require the right size, directing to the peptidyl transferase center, and the right size of the cavity of the PTC, how were they figured out without intelligence ? Random trial and error until the thing was set up right ? Furthermore.

The ribosomal peptidyl transferase center: structure, function, evolution, inhibition
https://pubmed.ncbi.nlm.nih.gov/16257828/
Functions of the two ribosomal subunits are very distinct. The small subunit deals exclusively with an RNA template (mRNA) on which it assembles complementary RNA entities (tRNA anticodons). The large subunit, in contrast, deals primarily with amino acids that are activated by esterification to the tRNA 3 -hydroxyl of the terminal ribose.

Question: Both subunits are performing  absolutely essential distinguished tasks, which are complementary. Both subunits have no function by themselves. If evolutionary processes would be generating these subunits, it would/should be expected that iterative rounds of random mutations and  selection would "discover" new and useful ribozymes & proteins subunits. In this case, that would however not be the case:

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 ?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overall design goal. 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.

According to following science paper:
The Ancient History of Peptidyl Transferase Center Formation as Told by Conservation and Information Analyses 
https://www.mdpi.com/2075-1729/10/8/134

The PTC has been recognized as the earliest ribosomal part and its origins embodied the First Universal Common Ancestor (FUCA).



 the SSU terminated associate with formation of the central pseudoknot by the end of phase three the LSU and the SSU associate in phase four and the LSU the tunnel is further developed the SSU gains well-defined binding pockets for the T RNAs and phase five the ratcheting system is acquired the genetic code begins to optimize and expand in Phase six the prokaryotic ribosomes is finalized with a fully optimized genetic code the ribosomal surface is an integrated patchwork of RNA and mature ribosomal proteins the ribosome grew by accretion of new RNA on old RNA like nested Russian dolls

My response (Otangelo) to Dimiter

Dimiter: Hello, look carefully, where did you see “no homologous sequence of the eukaryotic and prokaryotic ribosome”. Your interpretation of the claim in the paper is in your way, but it not what the authors say. There is sequence homology in some more and some less and this is normal to explain from the evolutionary model. But let’s go to a more fundamental problem: THE MODEL
Reply: Ok. But there ARE particles that are not homologous, like the 5.8S RNA which is unique to eukaryotes

Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation
https://www.ncbi.nlm.nih.gov/books/NBK22531/

Questioning that so many differences could be explained by evolutionary means is more than justified.

Otangelo: it is the answer to Caetano-Anollés: “Before the translation machinery can operate, ALL essential players must be fully formed and in place. In the same sense, as an automobile can only fulfill its function, if all parts are working together once fully formed, constituting a device of integrated complexity, the same is the case for the ribosome, where, if even one tiny piece is missing, nothing goes. Imagine, you have fully operational translation machinery, and instead of all aminoacyl tRNA synthetases are present, what would happen? The entire translation process would absolutely break down, and any polypeptide product would be non-functional, and not fold into functional 3D forms
Dimiter: This is fundamentally wrong. I’m surprised that after so many hours spent together explaining how the evolution functions and how the biological systems may be reduced in some conditions and how reduced variants make sense in a more simple system, you continue to put the same an argument over and over again and again.

Reply: Yes, you keep saying that. I gave a closer look at your paper ( see a short review below), and there are good reasons why I am not convinced that your claims are rational and justifiable. We are dealing with the origin of probably THE most complex macromolecular factory in the cell, central to explain the origin of life. 

Otangelo: Look your sentence “Before the translation machinery can operate, ALL essential players must be fully formed and in place.” 
Dimiter: OK, who says that? 
Reply: The relevant question is not WHO says it, but if the evidence points to that direction. I think it does. For example:

The elongation phase of the ribosome-catalyzed translation requires:
1. mRNA
2. a complete set of tRNA's 
3. elongation factor EF-Tu complexed with GTP 
4. a complete set of aminoacyl-tRNA's 
5. elongation factor EF-G dependent on GTP

If ANY of those players is missing, elongation cannot occur. Demonstrate how ANY of the individual molecules would have functions on their own, and explain why, for what reasons, unguided random events would evolve them. 

Dimiter: It comes from your model, not mine
Reply: Your evolutionary model is not true by default. You need to DEMONSTRATE why a down-up approach is conceptually feasible and compelling. Just asserting that it is a better approach than intelligent design based on a preconceived engineering model depending on intelligent action is not enough. 

Dimiter: your pre-set thinking from your irreducible fantasy. I spend enough time explaining that the very first event during the formation of Darwinian evolution was the formation of primitive translation, not the other way around.
Reply: Correct. I appreciate your efforts, and I gave a sincere effort not only to understand your model, but also to think about it, if it makes sense, and if it is feasible and compelling. Does the mere fact that you explained it means, that I would have to swallow it without giving a closer look at your assertions and accept them because you have a P.hD, or because you feel you are a ribosomologist authority? I mean, the mere fact that you spend years reading and studying science papers on the subject, does that mean automatically mean, that your philosophical inferences drawn ( without a shred of empirical evidence to back up your claims ) must be true by default?
If you expected that, then I suppose, you know better by now?!

Dimiter: This translation contains only a few aa and an only a short set of RNAs. Although this claim is not proven directly experimentally, it is supported by numerous experimental data: Yarus, every day PCRs, Arg interactions, Caetano-Anollés model (from 2012) for step by step, loop by loop, helix by helix evolutionary conclusions, and so on.
Reply:  Once again, I do not need to resort to creationist papers and articles, but to your peer, Koonin, which is very honest about the status quo and situation:

Koonin, the logic of chance, page 376
Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name!

Dimiter: It is supported by numerous co-observations that fit the model (look my second paper for example). The peptidyl transfer can occur even without PTC in some conditions and a primitive ribosome can work well enough for simple pre-LUCA forms. PTC center dramatically increases the efficiency and the entire ribosome assembly, but it is NOT an absolute requirement to have peptide synthesis. But no, you of course do not appreciate that. You continue to paste the same argument that if you remove something nothing can work. “…if even one tiny piece is missing, nothing goes. Imagine, you have fully operational translation machinery, and instead of all aminoacyl tRNA synthetases are present, what would happen? The entire translation process would absolutely break down…..” Yes, in your steady imaginary world you are correct, but I give you enough arguments that this MODEL is wrong and the world is NOT steady.
The sad notion is that just because you desperately want your model to be correct, you are IGNORING to acknowledge what the data are for. 
Reply: 
I am sorry, Dimiter, but you have not provided ANY DATA whatsoever to back up your model. It's all just conjecture based on the presupposition that evolution even operates abiotically ( which, funny, tough, even Aron Ra pointed out ) is not true. Darwinian evolution works when life and DNA replication starts. There is PLENTY of scientific literature pointing that out !!

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

Dimiter: If you would like to play as a scientist, please follow the scientific way AND do not pick up only the text phrases that suited your view and interpret it wrongly.
I know you are feeling yourself in a mission to distribute the biblical TRUTH.
Reply:  In our interactions, Dimiter, did in NOWHERE cite or propose my religious beliefs for anything. All I infer is that intelligent design is a far better and more case-adequate explanation than unguided evolutionary explanations. The mere fact that you mention this, demonstrates your PREJUDICE AGAINST religion, and in special, our model. Should a scientist not be as unbiased as possible, and PERMIT the scientific evidence to lead wherever it is, EVEN IF it does not fit the preconceived outcome? That's NOT what you seem to do. You seem rather like a veteran evolutionary biologist, which is unable to look outside of your evolutionary thinking, and try to force your ideas and models to others, and feel frustrated, when there is no success.... why is that so?

Dimiter: As the Indian Jones told me: “archeology (understand as science) does not work with the TRUTH, it works with FACTS”. 
Reply:  That's fine in operational science, where the quest is to find out how things factually work in the molecular world. But investigators of history do not have a time machine to travel back in the past and see what happened. So we apply the inference to the best explanation. Which you, unfortunately, have yet to provide, since the glaring gaps that your model still has, are not reasonably filled with materialism.

Dimiter: So to say, science is not about TRUTH, but about FACTS.  Ask yourself: if the Bible is correct and if the science is correct, why those two should contradict? Does not make sense. 
Reply:  Is science correct by default? No. Is the Bible correct by default IF the God of the Bible exists, and if he IS indeed the creator of life, and IF he is truthful? YES.
But that's NOT what I have done all along. I have started from the premise of what is, the evidence seen in the natural world, and FROM THERE, drawn meaningful conclusions. I do not adopt a presupposition in my scientific endeavor and thinking ( despite being a Christian, and, yes, of course, I have a bias as well ), but that is precisely what methodological naturalism forces scientists to do: To FORCE natural explanations, even IF the evidence does not support the explanations.

Historical sciences, and methodological naturalism
https://reasonandscience.catsboard.com/t1692-historical-sciences-and-methodological-naturalism

Possible Emergence of Sequence-Specific RNA Aminoacylation via Peptide Intermediary to Initiate Darwinian Evolution and Code through Origin of Life
Dimiter Kunnev: 2018 Oct 2 1

Observation: An overarching need is to establish interactions between the carrier of genetic information and that of structure/function. It is unclear how the initial relationships between RNA and proteins came to being, bearing in mind that RNA needs proteins to replicate and proteins need RNA to be coded (a problem known as “chicken and egg dilemma”).
Reply: Correct. And how was this established by unguided events? The relationship of information systems directing and controlling the making and operating of machines and factories is ALWAYS tracked back to intelligence.

An organizational structure would have to be established between the domain of information and computation ( the genome ) and the mechanistic domain, where proteins and enzymes work based on the direction and information flow of the beforementioned instructional genetic information. The puzzle lies with the problem of creating a causal organization, the interrelationship of informational and mechanical aspects into interdependent narratives. One of the challenges of life’s origin is thus to explain how instructional information control systems emerge naturally and spontaneously from mere chemical interactions and start taking over the clever making and direction of molecular mechanical dynamics. In modern cells, to make proteins, at least 25 unimaginably complex biosyntheses and production-line like manufacturing steps through large multimolecular machines are required to make proteins. Each step along the way requires exquisitely engineered molecular machines composed of an enormous number of subunits and co-factors. These molecular machines require by their own synthesis through complex multistep assembly processes using many scaffold proteins, co-factors, and chaperones, which orchestrate the biogenesis and assembly of these macromolecular highly complex holoprotein complexes. Machines, making machines, that make machines. How could all this come about by natural means? Incredulity that unguided mechanisms could come with this is justified.  

Paul Davies, the fifth miracle page 53:
Since most large molecules needed for life are produced only by living organisms and are not found outside the cell, how did they come to exist originally, without the help of a meddling scientist? Could we seriously expect a Miller-Urey type of soup to make them all at once, given the hit-and-miss nature of its chemistry?

The four interdependent requirements to have an information transmission system
https://reasonandscience.catsboard.com/t3030-the-four-interdependent-requirements-to-have-an-information-transmission-system
Information is what is conveyed or represented by a particular arrangement or sequence of things. To have an information transmission system, the following things are indispensable, essential, and required ( if any of those is missing, information transmission cannot be established - all have to be precisely defined in advance before any form of communication can be possible at all):

1. A language, 2. the information (message) produced upon that language, 3. an information storage mechanism ( a hard disk, paper, etc.), 4. an information transmission system, that is: encoding - sending and decoding, and eventually fifth ( not essential): 5. translation

Claim: In strong support of the RNA world are the many ribozymes selected under laboratory conditions for almost all the steps of translation.
Reply: No evidence that RNA molecules ever had a broad range of catalytic activities
https://reasonandscience.catsboard.com/t2243-no-evidence-that-rna-molecules-ever-had-the-broad-range-of-catalytic-activities

Another point not considered in this paper is the fact that either in bacteria or the nucleolus in eukaryotic cells, the make of ribosomes is encapsulated in a protected environment through the membrane. The nucleolus is a huge aggregate of macromolecules, including the rRNA genes themselves, precursor rRNAs, mature rRNAs, rRNA-processing enzymes, snoRNPs, a large set of assembly factors (including ATPases, GTPases, protein kinases, and RNA helicases), ribosomal proteins, and partly assembled ribosomes. Those are concentrated and at disposition for the ribosome assembly. The close association of all these components allows the assembly of ribosomes to occur rapidly and smoothly. This environment was not extant on the prebiotic earth unless someone posits that the basic molecules involved in translation were concentrated somehow into a lipid vesicle. How that concentration could have occurred is beyond my imagination nor understanding, and considerable skepticism that it is feasible is in my view justified.

Dimiter: Hello, look carefully, where did you see “no homologous sequence of the eukaryotic and prokaryotic ribosome”. Your interpretation of the claim in the paper is in your way, but it not what the authors say. There is sequence homology in some more and some less and this is normal to explain from the evolutionary model. But let’s go to a more fundamental problem: THE MODEL
Reply: Ok. But there ARE particles that are not homologous, like the 5.8S RNA which is unique to eukaryotes

Eukaryotic Protein Synthesis Differs from Prokaryotic Protein Synthesis Primarily in Translation Initiation
https://www.ncbi.nlm.nih.gov/books/NBK22531/

Questioning that so many differences could be explained by evolutionary means is more than justified.

Another point in question: If there were an evolutionary transition from a more simple prokaryotic ribosome, to a more complex ribosome in eukaryotes, not only the evolution and transition from a simpler to a more complex ribosome would have to be explained, but also the origin of the nucleolus and eventual possible evolution of orchestration of import of the two ribosomal subunits which attain their final functional form only after each is individually transported through the nuclear pores into the cytoplasm. Other ribonucleoprotein complexes, including telomerase, are also assembled in the nucleolus.

My comment: How was this transport programmed and orchestrated? By unguided, nonintelligent processes? Trial and error? How likely and feasible is that? 



All information storage devices, code languages, blueprints, information transmission systems, translation ciphers, with the purpose to make factories, and interdependent factory parks made upon those instructions are of intelligent origin. The Ribosome signaling networks are therefore the result of Intelligent design.

This machinery is consistent with the idea that positioning of the reactive groups is the critical factor for catalysis, but does not exclude assistance from ribosomal or substrate moieties. Hence, by offering the frame for correct substrate positioning, as well as for catalytic contribution of the P-site tRNA 2′-hydroxyl group, it became evident that the ribosomal architectural frame governs the positional requirements and provides the means for substrate-mediated chemical catalysis.

Observation:  Any architectural conformation that is not precisely as the fully developed one will by non-functional. A stepwise evolutionary emergence is therefore not feasible. Architecting a precise functional position requires foresight and engineering skills which only intelligent agents are capable of.

The transition state for formation of the peptide bond in the ribosome
https://www.pnas.org/content/103/36/13327

 50 atoms are important in the peptide formation mechanism.  This ribosomal elaborate architectural design guides the process of peptide-bond reaction by forcing a rotational motion consistent with the 2-fold rotation axis.  In all respects, it makes good chemical sense, in terms of formation of a peptide bond, the translocation of A-site tRNA to the P site, and P-site tRNA separation from the elongated chain. The chemical sense, after the mathematical criteria, is what corroborates the TS.  The TS is characterized mathematically by normal mode frequencies that are all positive, except for exactly one, which is negative and corresponds to a vibration along the reaction coordinate sending the old reactants into the new products.

Observation:  Even if the claim is that just 50 atoms would be important for the peptide formation mechanism, the odds to have that conformation by random chance would be fare beyond what random shuffling in this vast sequence space would be capable of achieving.

https://www.nature.com/collections/gjbhcpwgss
Understanding how the simple molecules present on the early Earth may have given rise to the complex systems and processes of contemporary biology is widely regarded as one of chemistry's great unsolved questions

Quantum mechanic glimpse into peptide bond formation within the ribosome shed light on origin of life
https://link.springer.com/article/10.1007/s11224-017-0980-5

The structure of the Peptidyl Transferase Center pocket  seems to be ingeniously built for accommodating the 3′ ends of the A- and P-site tRNAs

The preservation of RNA activity in performing the extremely important process of genetic code translation indicates that RNA is capable of handling the complexity of the current cellular life, which requires a highly controlled sophisticated regulatory mechanism. Obviously, translation is much more complicated than accidental peptide bond formation. 

Remarkably, within the contemporary ribosomes, the distances between the regions involved in the ribosome’s function are far beyond the possibility of any direct Bchemical talk^ (70–140 A). The symmetrical region is located at the heart of the ribosome and chemically connects to all of the ribosome functional centers involved in translation. Hence, it can transmit signals between them. 

Observation: Signaling means communication. 

The four interdependent requirements to have an information transmission system
https://reasonandscience.catsboard.com/t3030-the-four-interdependent-requirements-to-have-an-information-transmission-system

Information is what is conveyed or represented by a particular arrangement or sequence of things. To have an information transmission system, the following things are indispensable, essential, and required ( if any of those is missing, information transmission cannot be established - all have to be precisely defined in advance before any form of communication can be possible at all):  1. A language, 2. the information (message) produced upon that language,  the 3 .information storage mechanism ( a hard disk, paper, etc.), 4. an information transmission system, that is: encoding - sending and decoding) and eventually fifth ( not essential): 5. translation. 

All information storage devices, code languages, blueprints, information transmission systems, translation ciphers, with the purpose to make factories, and interdependent factory parks made upon those instructions are of intelligent origin. The Ribosome signaling networks are therefore the result of Intelligent design.

This machinery is consistent with the idea that positioning of the reactive groups is the critical factor for catalysis, but does not exclude assistance from ribosomal or substrate moieties. Hence, by offering the frame for correct substrate positioning, as well as for catalytic contribution of the P-site tRNA 2′-hydroxyl group, it became evident that the ribosomal architectural frame governs the positional requirements and provides the means for substrate-mediated chemical catalysis.

Observation:  Any architectural conformation that is not precisely as the fully developed one will by non-functional. A stepwise evolutionary emergence is therefore not feasible. Architecting a precise functional position requires foresight and engineering skills which only intelligent agents are capable of.

The transition state for formation of the peptide bond in the ribosome
https://www.pnas.org/content/103/36/13327

 50 atoms are important in the peptide formation mechanism.  This ribosomal elaborate architectural design guides the process of peptide-bond reaction by forcing a rotational motion consistent with the 2-fold rotation axis.  In all respects, it makes good chemical sense, in terms of formation of a peptide bond, the translocation of A-site tRNA to the P site, and P-site tRNA separation from the elongated chain. The chemical sense, after the mathematical criteria, is what corroborates the TS.  The TS is characterized mathematically by normal mode frequencies that are all positive, except for exactly one, which is negative, and corresponds to a vibration along the reaction coordinate sending the old reactants into the new products.  

On origin of life
The high conservation of the proto-ribosome nucleotide sequence is suggestive of its robustness under diverse environmental conditions and hence hints at its prebiotic origin.
My comment: It is also evidence that a gradual, evolutionary, step-wise evolution of the sequence would be non-functional, and indication, that the Ribosome had to emerge from the start, fully functional and operational, "as is".

The A andP sites are close enough together for their two tRNA molecules to be forced to form base pairs with adjacent codons on the mRNA molecule. This feature of the ribosome maintains the correct reading frame on the mRNA.
Comment: that means, in order to maintain the correct reading frame on the mRNA, the configuration of the A and P sites to be close enough together IS VITAL. How could this configuration have emerged randomly? Trial and error? This tiny fact means, there is no tolerance here. It is an all or nothing business. The configuration HAS TO BE RIGHT just from the beginning. A down up development to get the right distance will be always non-functional. Another important evidence that demonstrates that evolutionary means are not adequate to explain the feat in question.  

On origin of life
The high conservation of the proto-ribosome nucleotide sequence is suggestive of its robustness under diverse environmental conditions and hence hints at its prebiotic origin.
My comment: It is also evidence that a gradual, evolutionary, step-wise evolution of the sequence would be non-functional, and indication, that the Ribosome had to emerge from the start, fully functional and operational, "as is".

The Ribosome is one of the greatest wonders of molecular nanotechnology ever devised by our amazing unfathomable creator.
Koonin, the logic of chance, page 376
Breaking the evolution of the translation system into incremental steps, each associated with a biologically plausible selective advantage is extremely difficult even within a speculative scheme let alone experimentally. Speaking of ribosomes, they are so well structured that when broken down into their component parts by chemical catalysts (into long molecular fragments and more than fifty different proteins) they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carry on working.  Design some machinery which behaves like this and I personally will build a temple to your name!
My comment: Fortunately, people that recognize the magnificence of the creator of the Ribosome, build him churches and temples all over the globe, and give HIM glory.

Molecular biology of the Cell, Alberts, 6th ed. pg. 369
Producing an overall speed of translation of 20 amino acids incorporated per second in bacteria. Mutant bacteria with a specific alteration in the small ribosomal subunit have longer delays and translate mRNA into protein with an accuracy considerably higher than this; however, protein synthesis is so slow in these mutants that the bacteria are barely able to survive.

Question: How could the right speed have been obtained with trial and error, if slow mutants do not survive? Had the speed not to be right from the beginning?

Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
https://sci-hub.st/https://science.sciencemag.org/content/292/5518/897

The ribosome recognizes the geometry of codon anticodon base pairing in a way that would discriminate against near-cognate tRNAs. The minor groove of the first and second base pairs between the codon and anticodon is closely monitored by a set of interactions that are induced by the binding of cognate tRNA. These interactions would be disrupted by mismatches, so that the induced structural changes would no longer be energetically favorable. The third or “wobble” position has less stringent constraints, and therefore can allow a broader range of base-pairing geometries, consistent with the requirements of the genetic code. 

My comment: Monitoring and taking action when something is wrong requires "knowledge" of the correct state, "knowledge" of the wrong state, and know how to correct the wrong state. Knowledge, monitoring, error recognition and repair are actions only known to be performed by intelligence. 

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316189/

https://leagueofreason.org.uk/index.php?threads/on-irreducible-complexity-otangelo-rationalist-is-clueless-on-the-falsification-principle.16637/

Claim: 


Reply: There are basically just two worldviews

(a) time, chance, and the natural properties of matter; or
(b) design, creation, and the undeniable properties of organization and mind.

There are following possible  causing agents of origins and the universe as a whole:

There are 4 possibilities we are faced with regarding the beginning of the universe:

1. The universe is an illusion and none of this exists
2. The universe is "self-created"
3. The universe is "self-existent/eternal"
4. The universe was created by someone who is "self-existent/eternal"

1. The universe and the physical laws: an intelligent creator, or random unguided natural events
2. The fine-tuning of the universe  and the origin of life: an intelligent creator, random natural events, and physical necessity


The origin of life can be explained by just TWO possible mechanisms:

The origin of life
Either life emerged by a fortuitous accident, spontaneously through self-organization by unguided stochastic coincidence, natural events that turned into self-organization in an orderly manner without external direction, chemical non-biological, purely physico-dynamic kinetic processes and reactions influenced by environmental parameters, or through the direct intervention, creative force and activity of an intelligent cognitive agency, a powerful creator.

Biodiversity: 
above three, and evolution


Claim: you are OBVIOUSLY making a false dichotomy - that is, you are considering ONLY TWO options - namely, random chance, or a god. Have you considered that there may be OTHER explanations?
Reply: Extraordinary claims require extraordinary evidence. If the claim is that other worldviews exist, the claimer must be able to back up the claim, otherwise, it can be dismissed without evidence.

Claim:  Argument from incredulity
Reply: "Incredulous" basically means "I don't believe it". Well, why should someone believe a "just so" story about HOW reality came to exist? That is the THING that we are incredulous about - a *certain scenario* ( naturalism, cosmological, chemical, and biological evolution, abiogenesis, and Neo-Darwinism, and that irreducibly complex biological system, coded, instructed or specified complex information, and entire factory complexes composed of myriads of interconnected factories, full of computers and robotic production lines could emerge naturally ) that's only *imagined* about how various amazing abilities of animals and plants happened all by themselves, defying known and reasonable principles of the limited range of chance, physical necessity, mutations, and  Natural selection. There are busy little molecular machines that let it untangle, replicate, and build according to plan. A large cadre of researchers continues to make new discoveries on a regular basis. Our mythology is that it explains life, but the system is far, far too complex to occur by accident, and requires that features to support many processes are required, making a path for its evolution very hard to surmise. DNA isn't the secret to life. It's a whole bunch of puzzles we don't have answers for. The proponent of naturalism is "incredulous" that an intelligent creator/designer could exist, beyond and behind our entire space-time continuum, who is our Creator. But there is nothing ridiculous about that - especially if you can't personally examine reality to that depth - how do you know nature is all that exists? What IS ridiculous (IMO) is trying to imagine a *naturalistic origin* of these things.  What we need, is giving a *plausible* account of how it came about to be in the first place, and the " No-God hypothesis" simply doesn't cut the cake.



Claim:  Once IC has been falsified with one example, one can use inductive reasoning and generalize, and the hypothesis has to be modified.
Reply: I cane see your point. In the meantime, I do not acknowledge that IC has been falsified through the two examples given in the debate with Dapper, until he provides a FORMAL argument, using the scientific papers provided as the premise. It is not my job to read the papers in an attempt to discover the argument that is being made. That is the job of the proponent. Also, in the debate, all I got, were assertions. I am still waiting for a formal argument to be analyzed. Once this has been done, i will see how and where i go from this.



Claim: If ONE system claimed to be IC has been observed to evolve, then the hypothesis has been falsified.
Reply:  Ok. I will agree with that point.



Claim: The VPu protein has evolved a novel function
Vpu tetherin antagonism:
https://jvi.asm.org/content/91/6/e02177-16#:~:text=To%20promote%20virus%20release%20from,region%20adjacent%20to%20this%20deletion.

Reply:  HIV comes from SIV. Some forms of SIV also has a VPU protein that counteracts tetherin. So this isn't the evolution of a new function. It's regaining an existing function. Although it regained the function through a different mutational pathway.
"Vpu protein of SIVgsn [SIV in Greater Spot-nosed Monkeys] has been shown to counteract greater spot-nosed monkey tetherin."[2]
For more info, see the VPU section of my HIV evolution article.[1]

1. http://bereanarchive.org/articles/biology/hiv-evolution#vpu
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/

Dr.Dan Cardinale: It’s 100% a new function. The hiv-1 group m together in antagonism is via a completely new mechanism. All the siv forms of the tetherin antagonism, via NEF or VPU, involve targeting the intracellular domain of tetherin, and human tetherin is missing most of this domain, so none of those mechanisms work. It’s completely new. I'll also note that this is a good example of "you need to read the whole paper". They've done the experimental work on this. SIV VPU *that antagonizes tetherin in other apes* fails in humans, because our tetherin is shorter. Also, HIV-1 group M evolved from SIV-cpz, not SIV-gsn.

Reply: The scientists use language indicating it got back its function rather than acquired a new function:
"the vpu gene did not diverge to the extent that the activity could not be RESCUED."
"When SIVcpz crossed the species barrier to infect humans... Vpu subsequently REGAINED its tetherin-antagonizing function."
If you want to call it a new function, ok.  It all depends on how different something has to be before you call it "new." In the article
http://bereanarchive.org/articles/biology/hiv-evolution#vpu
it can be seen in the diagram that shows what changed, and a description below that about the three amino acids that changed for the anti-tetherin function.
If you take an irreducibly complex mousetrap and replace the metal hammer with a metal spike, does that disprove irreducible complexity?

Dr.Dan Cardinale: Look, this is cut and dry. I’m right about this and I’m not gonna waste more time pretending there’s a debate here. You can either do your homework and see that I’m right, or read just enough to tell yourself I’m wrong. If you want to be taken seriously, pick a better hill to die on.

Claim:  https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.11011 
Reply: In this paper they found a lizard that uses placenta, and assumed it evolved. There was no evolution observed. This is evidence against Darwin's tree of life because only eutherian mammals should have placenta.



Claim: If we move the goalpost to A, B, C, etc. the claim becomes unfalsifiable.
Reply: Agreed. But permit me the Tu Quoque here.

Falsification of evolution is impossible

https://reasonandscience.catsboard.com/t1713-the-theory-of-evolution-cannot-be-falsified

The great problem with evolution theory, as many writers have pointed out, is that it cannot be falsified. Nothing can falsify it, and that makes it an article of faith. It also puts it on a par with faith in God. Now that I regard as serious.

I say that it cannot be falsified for the following reasons:

1 If it has been seen to occur (it never has, as far as I know) that's proof of evolution(see, it happened!)
2 If it has not been seen to occur, that's proof too. (Never mind, we know it did, pat pat).
3 If it can account for the origin of anything, that's proof. (see, that's proof!)
4 If it can't, then that's proof too. (Ah the evidence hasn't emerged as yet).

It simply cannot be falsified and therefore it is not a scientific theory. Popper says so.

One patronising criticism one hears is 'that's found on a creationist site' as if that invalidates a fact! If one were to say, it's found on talkorigins, and is therefore invalidated, then who knows what wrath will descend? There's a double standard here.

Claim: you keep saying the same thing over and over again, and when the flaws are pointed out, you just double-down and re-explain the same thing again, as if we don't understand what you are saying (we do) or that you explaining it again will convince us (it won't).   Repeating the same bad argument won't help.  
Reply:  https://reasonandscience.catsboard.com/t3087-e-mail-debates#8401
Claim: The VPu protein has evolved a novel function
Vpu tetherin antagonism:
[url=https://jvi.asm.org/content/91/6/e02177-16#:~:text=To promote virus release from,region adjacent to this deletion.]https://jvi.asm.org/content/91/6/e02177-16#:~:text=To%20promote%20virus%20release%20from,region%20adjacent%20to%20this%20deletion.[/url]

Reply:  HIV comes from SIV. Some forms of SIV also has a VPU protein that counteracts tetherin. So this isn't the evolution of a new function. It's regaining an existing function. Although it regained the function through a different mutational pathway.
"Vpu protein of SIVgsn [SIV in Greater Spot-nosed Monkeys] has been shown to counteract greater spot-nosed monkey tetherin."[2]
For more info, see the VPU section of my HIV evolution article.[1]

1. http://bereanarchive.org/articles/biology/hiv-evolution#vpu
2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935100/

Dr.Dan Cardinale: It’s 100% a new function. The hiv-1 group m together in antagonism is via a completely new mechanism. All the siv forms of the tetherin antagonism, via NEF or VPU, involve targeting the intracellular domain of tetherin, and human tetherin is missing most of this domain, so none of those mechanisms work. It’s completely new. I'll also note that this is a good example of "you need to read the whole paper". They've done the experimental work on this. SIV VPU *that antagonizes tetherin in other apes* fails in humans, because our tetherin is shorter. Also, HIV-1 group M evolved from SIV-cpz, not SIV-gsn.

Reply: The scientists use language indicating it got back its function rather than acquired a new function:
"the vpu gene did not diverge to the extent that the activity could not be RESCUED."
"When SIVcpz crossed the species barrier to infect humans... Vpu subsequently REGAINED its tetherin-antagonizing function."
If you want to call it a new function, ok.  It all depends on how different something has to be before you call it "new." In the article
http://bereanarchive.org/articles/biology/hiv-evolution#vpu
it can be seen in the diagram that shows what changed, and a description below that about the three amino acids that changed for the anti-tetherin function.
If you take an irreducibly complex mousetrap and replace the metal hammer with a metal spike, does that disprove irreducible complexity?

Dr.Dan Cardinale: Look, this is cut and dry. I’m right about this and I’m not gonna waste more time pretending there’s a debate here. You can either do your homework and see that I’m right, or read just enough to tell yourself I’m wrong. If you want to be taken seriously, pick a better hill to die on.

Claim:  https://onlinelibrary.wiley.com/doi/abs/10.1002/jmor.11011  
Reply: In this paper they found a lizard that uses placenta, and assumed it evolved. There was no evolution observed. This is evidence against Darwin's tree of life because only eutherian mammals should have placenta.

Claim:I know John Maddox explained a few times that he dislikes hearing the same rebuttals over and over, but that's because he does similar too - he argues the same points over and over, which are just as easily rebutted, yet he feels superior to the rebuttals because he's heard them all before.   
Reply: Those that disagree with John Maddox are either a) not understanding what he is talking about, or b) too arrogant to conceide that he is right. DNA is not a code, but is stores instructional complex assembly information using the genetic code. There is no controversy in science about this topic, only, as it seems, amongst uninformed YouTube atheists.

https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin#8253

The codon bases have a non-random correlation with the kind of amino acids which they code for.  The first of the three letters relate to the kind of amino acid the codon stands for, giving the language a consistent meaning.

Any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information.
https://www.nature.com/articles/s41598-020-69100-0

The order of the three input bases is arbitrary and interchangeable (i.e. the model does not include uneven distribution of assignment uncertainty due to a third base ‘wobble’). There is no codon ambiguity; each codon maps uniquely to one amino acid. To create signal-meaning pairs, for each selected amino acid to be transferred we had to determine its codon assignment according to the donor’s code.
https://www.nature.com/articles/s41598-018-21973-y

The Genetic Code (B): Basic Features and Codon Assignments
The assignment of codons to different amino acids was essentially completed by applying the trinucleotide binding technique discovered by Nirenberg and Leder to all the 64 possible synthetic ribotrinucleotides.
https://www.worldscientific.com/doi/abs/10.1142/9789812813626_0008

A survey of codon assignments for 20 amino acids.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC219908/

In translation, 64 genetic codons are ascribed to 20 amino acids

In the standard genetic code table, of the 64 triplets or codons, 61 codons correspond to the 20 amino acids
https://www.dovepress.com/synonymous-codons-influencing-gene-expression-in-organisms-peer-reviewed-fulltext-article-RRBC

The Universal Genetic Code and Non-Canonical Variants
Genetic code refers to the assignment of the codons to the amino acids, thus being the cornerstone template underling the translation process.
https://www.sciencedirect.com/topics/neuroscience/genetic-code

A new integrated symmetrical table for genetic codes
For the formation of proteins in living organism cells, it is found that each amino acid can be specified by either a minimum of one codon or up to a maximum of six possible codons. In other words, different codons specify the different number of amino acids. A table for genetic codes is a representation of translation for illustrating the different amino acids with their respectively specifying codons, that is, a set of rules by which information encoded in genetic material (RNA sequences) is translated into proteins (amino acid sequences) by living cells.  There are a total of 64 possible codons, but there are only 20 amino acids specified by them.
https://arxiv.org/ftp/arxiv/papers/1703/1703.03787.pdf

A specification often refers to a set of documented requirements to be satisfied by a material, design, product, or service. A specification is often a type of technical standard.
https://en.wikipedia.org/wiki/Specification_(technical_standard)

Claim: Metaphors and analogies are not evidence.  They are comparisons used to simplify or explain ideas.   When you use them, they only help explain the idea you have.  They do not provide any evidence or any substantive reason to believe in your assertion.  
Reply:  Agreed. They just help to undersand the point which is being made.

Claim:  Biological systems do resemble mechanical systems.  No question.  There are whole scientific fields (as you know) like biomechanical engineering and biomimetics that deal in that area.  So what?   Humans are trying to understand how to live longer, healthier, more productive lives, and using what we have to understand biology and replicate it is important.  We see efficiency in nature, and we replicate it.  We have been looking at nature for a whole lot longer than we have been looking at factories and computers, and of course developing the ideas of factories and computers had to come from somewhere.  So it's completely unremarkable that we have engineered such things.
Reply: Information directing the make of factories has always mental origin
1. Cells are cybernetic, ingeniously crafted cities full of interlinked fully autonomous chemical nano factories. They host large high-tech macromolecular machines, superb power plants, and striking nano-robots. Wonderful arrays of fully automated manufacturing production lines, transport carriers, generate energy through incredibly efficient turbines, neuron transistors, miniaturized Computers. All those things are made based on algorithmic specified instructional complex information, which prescribes how all those things have to be made, controlled, assembled, and work together in an integrated fashion.  
2. The emergence of cities full of interlinked factories full of computer directed machines, assembly lines made of a series of robots working in a joint venture,  energy turbines, transistors, circuit boards, logic gates for specific purposes,directed by prescribed, instructional complex assembly information have only been observed to come from intelligent minds.  Semiotic functional information is not a tangible entity, and as such, it is beyond the reach of, and cannot be created by any undirected physical process. This is not an argument about probability. Conceptual semiotic information is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic codes, and upon it, instructional information, is like suggesting that a rainbow can write poetry... it is never going to happen!
3. Therefore, most probably, cell factories containing all those things are the product of an intelligent designer.

Claim:  Conversely, what we have engineered is what we best understand.  Nature still holds many mysteries, as we didn't create it ourselves.   We are products of nature.  
Reply:The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator.
Since there is being, being has always been. Beginning requires a cause. Movement and change a prime mover. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer. Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator.  Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, machines require a machine-maker.  Factories require a factory-maker.  Objective moral values come from a moral giver. The "God of the gaps" is an invalid refutation of arguments for the existence of God. And so, that there is no evidence for God(s).

Claim:   I mentor and coach robotics teams, and although I'm not an engineer, I am around and work with engineers and engineering students all the time.  We draw inspiration from anywhere we can to build complex competition robots.  We had to figure out how to make a robot climb a rope, accurately shoot projectiles, sense targets, balance, hook onto and carry other robots, do many autonomous tasks, etc.
Reply: Dinoflagellates with multi-barrel Gatling guns
1. Nematodinium Dinoflagellates are the coolest cells. They are among the most complex single-celled organisms we know of.They have ballistic "nematocyst" organelles. The weaponry is complicated, savage, and unlike what’s seen in animals. These bugs are basically the battle tanks of the microbial world, with armor-piercing, multi-barrel Gatling guns capturing them with their harpoon-like weapons that pierce the prey and drag them in to be consumed. They have  intricate weapons—including a microscopic version of a Gatling gun—to harpoon their dinners.    They are hunters that eat other dinoflagellates, which themselves are bristling with armor, microscopic munitions and even chemical weapons.  The tiny weapons are a unique invention
2. In order for their ballistic organelle to function, a capsule or nematocyst is required, which is composed of 9 essential elementary parts that compose the Gatling gun. This is an integrated interdependent system, where all parts must be in place in order to reach the higher end, that is to catch prey.
3. The origin of these sophisticated ballistic organelles that exceed those of animals in complexity are best explained through intelligent design.
https://reasonandscience.catsboard.com/t3055-a-dinoflagellate-protist-which-has-eyes-like-in-vertebrates-and-ballistic-multi-barrel-guns-for-taking-out-prey-by-design-or-evolution


Claim: The point is that we know what we are doing has a mind behind it.  It's ours, it's demonstrable, and that's very clear.  But because nature resembles what we have engineered doesn't mean that nature has a mind behind it. 
Reply:  If it quacks like a duck, it's probably a duck. If it looks designed, it's probably designed.

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

Claim: Nature is what we draw inspiration from, not the other way around.   Just because what we create has a mind doesn't mean that the best explanation is that nature was designed too.   You think it does, but all you have are statements like, "the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who created life for his own purposes."   When you make that statement, you do so with no evidence.
Reply: Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

Chance of unguided random natural events producing just a minimal functional proteome, not considering all other essential things to get a first living self-replicating cell,is:

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

Mycoplasma are not primitive but instead descendants of soil-dwelling proteobacteria, quite possibly the Bacillus, which evolved into parasites. In becoming obligate parasites, the organisms were able to discard almost all biosynthetic capacity by a strategy of gaining biochemical intermediates from the host or from the growth medium in the case of laboratory culture.

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. Leading scientists have calculated that the statistical probability of life emerging by random unguided events, is far beyond the limit of Borel's law, which is in the order of 1 in 10^50.

This probability is hard to imagine but an illustration may help. Imagine covering the whole of the USA with small coins, edge to edge. Now imagine piling other coins on each of these millions of coins. Now imagine continuing to pile coins on each coin until reaching the moon about 400,000 km away! If you were told that within this vast mountain of coins there was one coin different to all the others. The statistical chance of finding that one coin is about 1 in 10^50. In other words, the evidence that our universe is designed is overwhelming!

1. The more statistically improbable something is, the less it makes sense to believe that it just happened by blind chance.
2. Statistically, it is practically impossible, that the primordial genome, proteome, and metabolome of the first living cell arose by chance.
3. Furthermore, we see in biochemistry purposeful design.  
4. Therefore, an intelligent Designer is by far the best explanation of origins.  

Claim:  You need to have evidence that it exists.  Otherwise, who cares?   Sure, nature might be the product of creation as you assert, but if we don't have evidence of a creator's existence, it's a moot point.  We already know that the watchmaker analogy fails on the same basis.  The tornado in a junk yard fails on the same basis.  And your factory analogy fails on the same basis.  Just saying that everything appears created, therefore a creator exists, is not evidence.  It's flawed reasoning, and we will keep pointing it out if you keep asserting it.
Reply: 1. The mechanisms required to build complex organismal form is preprogrammed instructional complex information encoded in various genetic and at least 41 epigenetic codes and languages and communication by various signalling pathways through various physicochemical signalling networks.
2. Science has demonstrated, that evolution by mutations and natural selection genetic drift, and gene flow result in entropy, deteriorate the genome, rather than increasing information and organismal complexity.
3. The origin of instructional complex information ( analogous to blueprints ) and signalling networks is always tracked back to intelligence setting them up with specific purposes.
4. Therefore, biodiversity and organismal architecture are better explained by an intelligent creator, rather than mindless evolution.

1. Regulating, governing, controlling, recruiting, interpreting, recognising, orchestrating, choreographing, elaborating strategies, guiding, instructing, fine-tuning, monitoring, organizing, are all tasks of the gene regulatory network, which are ultrasophisticated communication networks, analogous to electric circuits in man-made devices.
2. In the same sense as copper, plastic, basic electronic parts do not turn into a printed circuit board randomly, molecular regulators, transcription factors, on/off switches, feedback loops do not turn into a gene regulatory network by unguided processes. Communication networks and signal transmission systems, similar as seen in gene regulatory networks, highly flexible, and able to rapidly reconfigure to deliver different outputs can only be implemented and pre-programmed by intelligence.
3. Therefore, most probably, the gene regulatory network was implemented and programmed by an intelligent agency.

Claim:  If you want to impress me, then bring evidence for a creator.  Otherwise, when you wheel out the same arguments over and over, don't be surprised to get the same pushback.  You're just repeating yourself, and since your arguments are not convincing, we'll keep on repeating the same rebuttals as they refute your argument each time.
Reply: 125 reasons to believe in God
https://reasonandscience.catsboard.com/t1276-125-reasons-to-believe-in-god

The obviousness of Creation is hidden from those who reject God. There is no evidence that we can exist without a creator. Since there is being, being has always been. Beginning requires a cause. Movement and change a prime mover. Contingent beings depend on a necessary cause. Creation requires a creator. Design requires a designer. Laws require a lawmaker. Mathematics requires a mathematician. Fine-tuning requires a fine-tuner, Codes require a coder. Information requires an Informer. Translation requires a translator.  Life has only been observed to come from life. Logic comes from logic, Consciousness comes from consciousness, machines require a machine-maker.  Factories require a factory-maker.  Objective moral values come from a moral giver. The "God of the gaps" is an invalid refutation of arguments for the existence of God. And so, that there is no evidence for God(s). 

Dimiter,

thanks for your reply. 

in order to start a plausible narrative of how life could have emerged from nonlife, one has to start from the beginning. You have not answered in regards to the ( in my opinion ) unbridgeable problem to synthesize RNA prebiotically, without enzymes. The papers which you quoted, did not provide a solution to the problems exposed. But we can go even a bit further.

One major problem is that there was NO prebiotic selection process of the functional nucleobases for Watson-Crick basepairing amongst myriads of possible configurations. THIS ALONE is a check-mate situation for the unguided abiotic origin of life hypotheses. 

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#7700

As following paper reports:

Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides May 18, 2020
https://sci-hub.st/https://pubs.acs.org/doi/10.1021/acs.chemrev.0c00069

Even if the noncanonical nucleotides present on the prebiotic Earth were not able to achieve the functions that would have allowed for the action of evolution to push these molecules along the path to the extant nucleotides, the work reviewed earlier on possible prebiotic syntheses of the canonical nucleotides, primarily by the groups of Carell, Sutherland, and Powner, also raises the possibility that the prebiotic importance of noncanonical nucleosides was simply their mechanistic intermediacy en route to canonical nucleosides. 

Question: Why should that be the case? Did noncanonical nucleosides have the anthropomorphic "urge" or goal to become complex semantophoretic macromolecules that carry genetic information ? 

An enormous amount of effort has been put into finding the prebiotic origins of the extant nucleotides and our opinion that the journey is not yet complete.

My comment: And upon my understanding, the simple fact that there was no SELECTION MECHANISM of the dearly needed basic building blocks of life, and the fact that Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  ( Steven A. Benner  https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/25608919  ) makes ANY unguided abiogenesis hypothesis untenable and unlikely to the extreme. Using my pharising, i keep saying, impossible !! 

The trajectory from a prebiotic synthesis of the basic building blocks of life, to the sophisticated synthesis by cell factories: an unsolved riddle
https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible#7650

Nucleotides are building blocks for DNA and RNA. Three Pyrimidines and Two Purines Are Commonly Found in Cells.
The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP.
The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes. 1 
De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP. 

Question:  How would you go from a prebiotic synthesis of RNA, to enzymatic synthesis, required all the enzymes mentioned above?

The DNA double helix, evidence of design
https://reasonandscience.catsboard.com/t2028-biosynthesis-of-the-dna-double-helix-evidence-of-design

Enzyme expert Dr Richard Wolfenden, of the University of North Carolina, showed in 1998 that a reaction ‘“absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years in water’, but was speeded up 10^18 times by an enzyme.1 This was orotidine 5′-monophosphate decarboxylase, responsible for de novo synthesis of uridine 5′-phosphate, an essential precursor of RNA and DNA, by decarboxylating orotidine 5′-monophosphate (OMP).

Wolfenden said,
‘Without catalysts, there would be no life at all, from microbes to humans. It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction.’

Question:  In order to make RNA and DNA, prebiotic earth without this enzyme would have needed to wait 78 million years to yield Uridine monophosphate to make RNA. by natural processes......

The problems do not end here. In order to make nucleobases, carbon and nitrogen

DK: RNA-peptide hypothesis for the origin of life is based on well-known facts like Watson/Crick base pair interactions
Reply: As previously elucidated, Watson-Crick base-pairing depends on the very specific isomeric arrangement of nucleobases, in special carbon and nitrogen.

But carbon and nitrogen were not ready available on early earth. That is another huge, unsolved problem. 

Availability of nitrogen and ammonia on early earth
https://reasonandscience.catsboard.com/t2689-availability-of-nitrogen-and-ammonia-on-early-earth

Where did Glucose come from in a prebiotic world ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#8116

DK: Let me give you an example of fantasy: Assembly of the complicated organism “out of blue” due to some unknown force of intelligent designer. No previous scientific data, no physico-chemical interaction no laws allowing this. The explanation that comes from irreducible complexity or  “I believe so” is not a scientific explanation, therefore we are talking about fantasy.  
Having this in mind to criticize that something IS JUST HYPOTHESIS is unfair, especially if you have an alternative fantasy.
Reply: Chance of intelligence to set up life: 
100% We KNOW by repeated experience that intelligence produces all the things, as follows:
factory portals  ( membrane proteins ) factory compartments ( organelles ) a library index ( chromosomes, and the gene regulatory network ) molecular computers, hardware ( DNA ) software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes ) information retrieval ( RNA polymerase ) transmission ( messenger RNA ) translation ( Ribosome ) signaling ( hormones ) complex machines ( proteins ) taxis ( dynein, kinesin, transport vesicles ) molecular highways ( tubulins ) tagging programs ( each protein has a tag, which is an amino acid sequence  informing other molecular transport machines were to transport them.) factory assembly lines ( fatty acid synthase ) error check and repair systems  ( exonucleolytic proofreading ) recycling methods ( endocytic recycling ) waste grinders and management  ( Proteasome Garbage Grinders )   power generating plants ( mitochondria ) power turbines ( ATP synthase ) electric circuits ( the metabolic network ) computers ( neurons ) computer networks ( brain ) all with specific purposes.

Chance of unguided random natural events producing just a minimal functional proteome, not considering all other essential things to get a first living self-replicating cell,is:

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

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14   That would be the size of a book with 400 pages, each page with 3000 characters.  They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.  

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

DK: evolution of proto-aaRS is based on aaRS phylogenetic DATA.
Reply:  How can there be a phylogenetic tree about proteins that must be there all at once, and on top of that, prebiotically,  in order for the translation machinery to work? There is NO evidence that a smaller genetic code, as for example using two, rather three nucleotides, and a smaller set of amino acids would/could confer functional proteins. Also, how do you explain the selection of an optimal amino acid set?

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids
https://www.nature.com/articles/srep09414
Additional factors beyond selection for the three properties principally considered in our test contributed to the adaptability of the coded set as a LUCA organism colonized habitable spaces on Earth. Given that each additional criterion greatly reduces the number of better sets, it would seem that adding functional criteria would only make the coded set even more unusual, and possibly reflect the truly limited set of possibilities that life has to choose from.

Not considering, that proteins by their own have no use, and no function, unless embedded and working in a joint venture with other proteins, as in metabolic pathways, productionline-like arrangements to make complex macromolecules, to generate energy etc.

Homology: A Concept in Crisis
https://reasonandscience.catsboard.com/t1454-homology-a-concept-in-crisis
Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account.

Structural similarities among automobiles, even similarities between older and newer models are due to construction according to pre-existing patterns, i.e., to design. Ironically, even striking similarities are not sufficient to exclude design-based explanations. In order to demonstrate naturalistic evolution, it is necessary to show that the mechanism by which organisms are constructed (unlike the mechanism by which automobiles are constructed) does not involve design.

DK: PREBIOTICALLY nothing complicated can come to be. The complication comes AFTER the formation of Darwinian evolution. There is an initial function of short peptides (not fully formed aaRS) to stabilized RNA-peptide complex (experimentally proven fact). After that, the short peptides EVOLVED into longer peptides accepting step by step more functions in a step by step more complicated life system until you have a fully developed translation system.
Reply: You keep ASSERTING that. Please give me good reasons why I should take your claim at face value. 

Proteins and Protein synthesis
https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesis

How Did Protein Synthesis Evolve?
The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place. As attractive as the RNA world idea is for envisioning early life, it does not explain how the modern-day system of protein synthesis arose.
Molecular biology of the cell, 6th ed. pg. 365

Kind regards

Otangelo

E-mail as an answer to John Peterson's stream at The Rage, to which his only answer was: Why would you think I would read this? You really are a clown. LMBO! Muting you now.
https://reasonandscience.catsboard.com/t3087-e-mail-debates#8504

https://www.youtube.com/watch?v=psq7PNtOnZc&t=108s
Immutable: 29:13: which is that um he will bring up a source that says that he thinks says he's right and if you actually read it which he never does it directly contradicts him.
Reply:  You DO NOT KNOW THAT!! STOP making unwarranted claims which you cannot know. The EVIDENCE cited in the paper of royal society IS THE RELEVANT PART.

The inference drawn by the authors is IRRELEVANT, and not only that: It actually DEMONSTRATES what I said several times. Namely that science is BIASED AGAINST creationism.

The authors write in the end: We hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.
Nobel Laureate Christian de Duve: ‘Scientific inquiry rests on the notion that all manifestations in the universe are explainable in natural terms, without supernatural intervention.
Steven Weinberg said:  ‘The world needs to wake up from the long nightmare of religion... Anything we scientists can do to weaken the hold of religion should be done

If a claim based on those ideas is merely assumed to be true (as is the case across biology today), and if that assumption is then used to institutionalize the attack on a valid
scientific alternative, then that practice is not only illogical, but is a clear abuse of scientific practice. In fact, it is the ultimate “science stopper”.
As it stands right now, if materialism is not true, there is no way under current practices for science to correct itself.
And in a perfect irony, it is this concept of self-correction that materialists routinely use to promote their dominance over the institution.

Lewontin: we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations,
no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, so we cannot allow a Divine Foot in the door.”

Claim from the paper: To further support this idea of a reduced alphabet of amino acids, there are also very plausible suggestions that the original amino acid repertoire consisted of only four or five amino acids
like those found in the Miller–Urey experiments and the Murchison meteorite (Miller et al. 1976), and that the genetic code was initially limited to these few amino acids
Reply: This is a totally UNWARRANTED claim. Amino acids need to be a mix of polar and non-polar in order to be hydrophilic and hydrophobic in order to have functional proteins

John: if were to go control f on my keyboard right now it'll bring up a little tab and it'll ask me like what i want to search for within the current one and that's what a Otangelo often does with the papers isn't
it that he is looking for specific phrases or words that he believes to make his argument for him
Immutable: yeah it's either that or he's getting it from like discovery institute or some creationist knockoff
Reply: Do you not feel ashamed, Immutable, to make totally things up about me ?? How can you even know how I perform my scientific research? You can't.

Immutable: but the theory itself is kind of addressing uh scientific means that are that seem plausible to get there
Reply: Can you give an example? Because the scientific papers that I read in regards to the topic come to an entirely different conclusion.

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

Some of the worlds leading scientists in the field of synthetic chemistry, biochemistry, and computational biology, like James Tour, Graham Cairns-Smith, Eugene Koonin and Steve Benner have stated that solving the mystery of the origin of life is categorically not possible, that science has no clue how to solve the riddle, that abiogenesis research is a failure, and the most difficult problem that faces evolutionary biology and, arguably, biology in general.

Eugene V. Koonin: The Logic of Chance: page 252:
" 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.

Steve Benner:  Paradoxes in the origin of life
Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken
together) suggest that the “origins problem” cannot be solved.

Graham Cairns-Smith: Genetic takeover, page 66:
Now you may say that there are alternative ways of building up nucleotides, and perhaps there was some geochemical way on the early Earth. But what we know of the experimental difficulties in nucleotide synthesis speaks strongly against any such supposition. However it is to be put together, a nucleotide is too complex and metastable a molecule for there to be any reason to expect an easy synthesis.

Garrett: Biochemistry, 6th ed,  page 665
Key compounds, such as arginine, lysine, and histidine; the straight-chain fatty acids; porphyrins; and essential coenzymes, have not been convincingly synthesized under simulated prebiotic conditions.

Robert Shapiro: A Replicator Was Not Involved in the Origin of Life
A profound difficulty exists, however, with the idea of RNA, or any other replicator, at the start of life. Existing replicators can serve as templates for the synthesis of additional copies of themselves, but this device cannot be used for the preparation of the very first such molecule, which must arise spontaneously from an unorganized mixture. The formation of an information-bearing homopolymer through undirected chemical synthesis appears very improbable.

Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

Immutable: somewhat so so what i see sometimes is that certain experiments go to um where they do form components that are needed for um they do form components needed for cell like a lipid or nucleotides or amino acids that will react to form
Reply: Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life

https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

1. Life requires the use of a limited set of complex biomolecules, a universal convention and unity which is composed of the four basic building blocks of life ( RNA and DNA's, amino acids, phospholipids, and carbohydrates). They are of a very specific complex functional composition and made by cells in extremely sophisticated orchestrated metabolic pathways, which were not extant on the early earth. If abiogenesis were true, these biomolecules had to be prebiotically available and naturally ocurring ( in non enzyme-catalyzed ways by natural means ) and then somehow join in an organized way and form the first living cells. They had to be available in big quantities, and concentrated at one specific building site. 
2. Making things for a specific purpose, for a distant goal, requires goal-directedness. And that's a big problem for naturalistic explanations of the origin of life. There was a potentially unlimited variety of molecules on the prebiotic earth. Competition and selection among them would never have occurred at all, to promote a separation of those molecules that are used in life, from those that are useless. Selection is a scope and powerless mechanism  to explain all of the living order, and even the ability to maintain order in the short term, and to explain the emergence, overall organization, and long-term persistence of life from non-living precursors. It is an error of false conceptual reduction to suppose that competition and selection  will thereby be the source of explanation for all relevant forms of the living order.
3. We know that a) unguided random purposeless events are unlikely to the extreme to make specific purposeful elementary components to build large integrated macromolecular systems, and b) intelligence has goal-directedness. Bricks do not form from clay by themselves, and then line up to make walls. Someone made them. Phospholipids do not form from glycerol, a phosphate group, and two fatty acid chains by themselves, and line up to make cell membranes. Someone made them. That is God.

Immutable: you uh you know what the constituents of the cake are uh you have an idea of how to make the cake um but you don't know what the oven is
Reply: 1. Making a cake needs a recipe (information) and the right ingredients (matter) and a stove (energy).
2. Living cells require a recipe (Instructional assembly information stored in DNA); the right building blocks (nucleotides, RNA and DNA, 20 amino acids, phospholipids and carbohydrates) and energy in the form of ATP.
3. Making the recipe, selecting and preparing the ingredients (in the right quantity), and generating energy always requires an intelligent source. Therefore, life requires an intelligent designer.

John: like you alluded to earlier we can't know for sure unless we get a time machine go back there and there could have been like some phenomenon some uh you know process that that uh had a part in the first life that we just can't detect at all with our current science it could have been something that was a flash in the pan and there's no leftover evidence of it you know
Reply: Do you know what materialism of the gaps fallacy is? It is when you have no clue how life could have formed, but your pressupose that once science finds out, it will be natural mechanisms. 

John: the paper he just brought up is not the paper in question to the incident i was referring to
Reply: Ok. I remember now. That issue was in regards of there were other life hosting planets in the universe.

Life on other planets, a real possibility?
https://reasonandscience.catsboard.com/t232-life-on-other-planets-a-real-possibility

The data demonstrate that the probability of finding even one planet with the capacity to support extraterrestrial intelligence ( Peti ) falls short of one chance in 10^122 (that number is 1 followed by 122 zeros).

THE LOG LOG PRIOR FOR THE FREQUENCY OF EXTRATERRESTRIAL INTELLIGENCES September 21, 2016
This log log prior can handle a very wide range of PETI values, from 1 to 1010^122 while remaining responsive to evidence about extraterrestrial societies.
https://arxiv.org/pdf/1609.05931.pdf

Exotic Life Sites: The Feasibility of Far-Out Habitats
The data demonstrate that the probability of finding even one planet with the capacity to support life falls short of one chance in 10^140 (that number is 1 followed by 140 zeros)
https://reasons.org/explore/publications/facts-for-faith/read/facts-for-faith/2001/10/01/exotic-life-sites-the-feasibility-of-far-out-habitats

As it comes out, the second paper gives an estimate even higher, namely of one to 10^140. So I was not lying. My point stands. 

John: they're going to find where it does not say anything that uh tangelo is claiming and it's just it's just beautiful
Reply: I actually said EXACTLY what the abstract said: 

How much of protein sequence space has been explored by life on Earth?
A typical estimate of the size of sequence space is 20^100 (approx. 10^130) for a protein of 100 amino acids in which any of the normally occurring 20 amino acids can be found. This number is indeed gigantic
https://royalsocietypublishing.org/doi/10.1098/rsif.2008.0085

The evidence is indisputable ( and that is what I demonstrated ), but the CONCLUSION is biased.  

The inference drawn by the authors is IRRELEVANT, and not only that: It actually DEMONSTRATES what I said many times. Namely that science is BIASED AGAINST creationism.

The authors write in the end: We hope that our calculation will also rule out any possible use of this big numbers ‘game’ to provide justification for postulating divine intervention.
Nobel Laureate Christian de Duve: ‘Scientific inquiry rests on the notion that all manifestations in the universe are explainable in natural terms, without supernatural intervention.
Steven Weinberg said:  ‘The world needs to wake up from the long nightmare of religion... Anything we scientists can do to weaken the hold of religion should be done

Lewontin: we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations,
no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, so we cannot allow a Divine Foot in the door.”

Claim of the paper to show what i am saying: To further support this idea of a reduced alphabet of amino acids, there are also very plausible suggestions that the original amino acid repertoire consisted of only four or five amino acids like those found in the Miller–Urey experiments and the Murchison meteorite (Miller et al. 1976), and that the genetic code was initially limited to these few amino acids
Reply: This is a totally UNWARRANTED claim. Amino acids need to be a mix of polar and non-polar in order to be hydrophilic and hydrophobic in order to have functional proteins.

Mike: now Axe himself had a paper from 1996 where he showed 25 of one sequence space that he studied had functional proteins. there's 10 to 130 different possible proteins out of those probably 10 to the 90th are functional they will do something they will perform some function according to douglas axe. douglas act said uh 10 to the 70 74th were functional out of a protein space of 10 to the 150th
Me replying in the chat: no no no no what i understood in history
John: yeah uh yeah that's not what he read in the paper because he didn't read the whole paper
Reply:  Axe disproves what Speed claimed in the live chat, and confirms what I said. Yes, John, I did actually read the paper, contrary to your false accusations.  

Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds  
The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain  
https://sci-hub.ren/10.1016/j.jmb.2004.06.058

This is the email that I did send to Speed today, and got no answer. Silence. Why?

Speed, 

your claim in the live chat was that Axe's paper calculated 10^150 possible different outcomes/possible sequences in protein sequence space, and of these, about half, you said about 10^75 or so were functional. I don't know where you got that from, That is simply not true. In the same paper from Axe, he continues at the end of the abstract:

" Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences. " 

A protein domain is a region of the protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. In general, domains vary in length from between about 50 amino acids up to 250 amino acids in length
https://en.wikipedia.org/wiki/Protein_domain

As you know, I use Pelagibacter ubique as the free-living life form with the smallest genome/proteome for origin of life studies and the odds to have such a prokaryote by natural means. As it comes out, and I quote:

The phylogenetic birth-and-death model consistently predicted that the small extant SAR11 ( pelagibacter) genomes (1,300 to 1,500 genes) evolved from a slightly larger common ancestor (~2,000 genes)
https://mbio.asm.org/content/mbio/4/4/e00373-13.full.pdf

In the evolutionary timescale, Pelagibacter is an alphaproteobacterium, and its common ancestor supposedly emerged a bit less than 1,3 billion years ago. The oldest bacteria known however are Cyanobacteria, 

What Was the First Life on Earth?
https://www.livescience.com/57942-what-was-first-life-on-earth.html
Another contender for world's oldest life is a set of rocks in Greenland that may hold the fossils of 3.7-billion-year-old colonies of cyanobacteria, which form layered structures called stromatolites.

Cyanobacteria evolution: Insight from the fossil record
Cyanobacterial fossil record starts unambiguously at 1.89–1.84 Ga and the minimum age for the oxygenic photosynthesis starts with the GOE around 2.4 Ga.

The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009235
Cyanobacteria are among the most successful primary producing aquatic organisms, having populated the Earth for approximately 2.8 billion years. With genome sizes of approximately 3.9 (CS-505), Cylindrospermopsis raciborskii CS-505 and Raphidiopsis brookii D9 and 3.2 (D9) Mb are the smallest genomes described for free-living filamentous cyanobacteria. The strains share a specific set of 2539 genes

So this is the paradox. The oldest known life-forms have a considerably bigger genome, than Pelagibacter, namely 3,2 million base pairs. Which makes their origin far more unlikely from a naturalistic standpoint. 

If the unlikeliness to have just ONE domain-sized fold, (let's take the upper limit ) of 250aa is 1 in 10^77, imagine an entire genome, like of Pelagibacter, which was however based on the scientific data demonstrated above, not the earliest bacteria....

More: Before we even start doing the shuffling, all the following hurdles would have to be overcome, and the following would have to be assumed:

Assume that:
1.  the conditions of the primitive atmosphere were known.
2.  Nitrogen and carbon in fixed form, necessary elements of amino acids, was readily available, and that all of the twenty amino acids used in life did form naturally ( disregarding the lifetime of ammonia which would be short because of its photochemical dissociation)
3.  Organosulfur compounds required in a few amino acids used in life would be readily available, even if in nature sulfur exists only in its most oxidized form (sulfate or SO4), and only some unique groups of prokaryotes mediate the reduction of SO4 to its most reduced state (sulfide or H2S)
4.  Billions of each amino acid would be readily available. ( even if eight proteinogenic amino acids were never abiotically synthesized under prebiotic conditions)
5.  The amino acids would be concentrated all together at one assembly site.
6.  There would be selected twenty, and not more or less amino acids to make proteins.
7.  Only the best suited would have been selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets inside proteins
Nature did somehow "know" that the set of amino acids selected appears to be near ideal and optimal.
8.  The amino acids were only in homochiral, that is the left-handed configuration.
9.  They would be pure, and without contaminating reactants, somehow avoiding the concomitant synthesis of undesired or irrelevant by-products.
10. They would be all bifunctional monomers with amino groups and carboxyl groups. AA's with unifunctional monomers (with only one functional group) would have been sorted out somehow.
11. They would remain stable, and not DEVOLVE to give uselessly complex mixtures, “asphalts”
12. They would be able to bond and polymerize by non-enzymatic means, without the ribosome
13. There are four different ways to bond AA's together by the side chains. if bonded to the wrong side chain, no deal. They would, somehow, bond together at the right place.
14. The polypeptide chain would not hydrolyze to its constituent amino acids.
15. In each trial, the average protein would be  400 amino acid  units in length
16. The rate to form and test each chain would be just one-third of a ten-million-billionth of a second!  This is around 150 thousand trillion times the normal speed in living things.
17. If a usable sequence were obtained, the action would stop so that it would be preserved, and shuffling would restart to obtain all proteins required for life.
18. 1/3 of all proteins once folded require chaperones, other proteins, that help the protein to fold into its proper, functional shape. They were not required for the first protein folds.  
19. The synthesized proteins would be able to merge and interlink into assembly lines and metabolic pathways, ready for working together in a living system.
20. Somehow, nature knew how to transition from prebiotic synthesis to cell synthesis of amino acids occur.  A minimum of 112 enzymes is required to synthesize the 20 (+2) amino acids used in proteins.

Now, even IF, somehow a fully working proteome was formed, it would still have to be interlinked into a functional metabolic network, and an enzymatic system of protein synthesis, using DNA as the information carrier directing the AA synthesis.
How do you think, did THAT happen? 

Uncertainty quantification of a primordial ancestor with a minimal proteome emerging through unguided, natural, random events
https://reasonandscience.catsboard.com/t2508-abiogenesis-uncertainty-quantification-of-a-primordial-ancestor-with-a-minimal-proteome-emerging-through-unguided-natural-random-events

Pelagibacter Ubique is the best candidate to investigate Origin of life scenarios. Here is why
https://reasonandscience.catsboard.com/t3090-pelagibacter-ubique-is-the-best-candidate-to-investigate-origin-of-life-scenarios-here-is-why#8474

Your materialistic case is a lost cause, Mike. You and your crowd laughed yesterday about me, but without foundation.  And your hate against God is unjustified. 

Dimiter Claim: To make a perfect recognition of the 3 prime wobble base, there is a specific mechanism in the Ribosome, a protein called EF-Tu. It interacts with the tRNA and positions the tRNA inside the A site, and also catches, it catches in a way that interacts with the one loop of the large subunit. It's like a spring, and this spring is only released if it recognizes completely well, there is some mechanism involved from the small subunit when it recognized perfectly well the 3prime nucleotide, then the spring releases by hydrolyzing GTP, and now the actual amino acid goes inside and continues. If it's not recognized well, the spring mechanism will not release it. Now you can make it directly, every single trinucleotide be recognized very well immediately without needing the extra mechanism. however that is not the case. Again, lack of foresight. it's a perfect mechanism. It works very well, thanks to the EF-Tu, the fidelity of the translation process is enormous, it's huge, however, it is obvious you have a lack of foresight, you can make it perfectly recognizing the trinucleotide.

Reply:  This is actually evidence of design, rather than non-design. 

The Organization of mRNAs and the Initiation of Translation
https://www.ncbi.nlm.nih.gov/books/NBK9849/

The requirement for hydrolysis of GTP before EF-Tu or eEF-1α is released from the ribosome is the rate-limiting step in elongation and provides a time interval during which an incorrect aminoacyl tRNA, which would bind less strongly to the mRNA codon, can dissociate from the ribosome rather than being used for protein synthesis. Thus, the expenditure of a high-energy GTP at this step is an important contribution to accurate protein synthesis; it allows time for proofreading of the codon-anticodon pairing before the peptide bond forms.

B.Alberts: Molecular biology of the Cell, 7th ed. 
Under some conditions in vitro, ribosomes can be forced to synthesize proteins without the aid of these elongation factors and GTP hydrolysis, but this synthesis is very slow, inefficient, and inaccurate. Coupling the GTP hydrolysis-driven changes in the elongation factors to transitions between different states of the ribosome speeds up protein synthesis enormously. The cycles of elongation factor association, GTP hydrolysis, and dissociation also ensure that all such changes occur in the “forward” direction, helping translation to proceed efficiently

Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection
https://www.pnas.org/content/117/7/3610
EF-Tu’s presence on the ribosome after GTP hydrolysis is expected to increase fidelity during early aspects of the proofreading mechanism

The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis
https://www.frontiersin.org/articles/10.3389/fmicb.2019.02351/full
EF-Tu has evolved the capacity to execute diverse functions on the extracellular surface of both eukaryote and prokaryote cells. EF-Tu can traffic to, and is retained on, cell surfaces where can interact with membrane receptors and with extracellular matrix on the surface of plant and animal cells. Our structural studies indicate that short linear motifs (SLiMs) in surface exposed, non-conserved regions of the molecule may play a key role in the moonlighting functions ascribed to this ancient, highly abundant protein.

Dimiter claim:1) In the case for EF-Tu you have a clutch mechanism which works well to recognize two of the codon-anticodon bases without need of EF-Tu. Why didn't all 3 nucleotides be able to recognize directly, but needs to spend EF-Tu-GTP mechanism to do so? It is a simple proof of NO PLANNING and second of EVOLUTIONARY STEPS.
Reply: You claim that EF-Tu has a clutch mechanism which works well to recognize two of the codon-anticodon bases without need of EF-Tu. But according to following paper, that's not its function:

In the elongation cycle of protein biosynthesis in bacteria and eukaryotic organelles, one of the most essential steps is the formation of an active ternary complex between elongation factor Tu (EF-Tu), aminoacyl-tRNA (aa-tRNA) and GTP, after which the aa-tRNA is delivered to the ribosomal A-site 1

In both prokaryotes and eukaryotes, the growth of the polypeptide chain requires additional protein factors called elongation factors. 2

My comment: How can you say then that the ET-Fu's are superfluous?

Two proofreading steps amplify the accuracy of genetic code translation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137768/

Our work highlights the essential role of elongation factor Tu for accurate genetic code translation in both initial codon selection and proofreading. First, aa-tRNAs in ternary complex with EF-Tu·GDP are selected in a step where the accuracy increases linearly with increasing aa-tRNA affinity to EF-Tu. Then, following dissociation of EF-Tu·GDP from the ribosome, the accuracy is further increased in a second and apparently EF-Tu−independent step. Our findings identify the molecular basis of proofreading in bacteria, highlight the pivotal role of EF-Tu for fast and accurate protein synthesis, and illustrate the importance of multistep substrate selection in intracellular processing of genetic information.

My comment: EF-Tu plays a PIVOTAL role for fast and accurate protein synthesis. There is nothing over-engineered here. So what is the problem ?


How is it that you and others are not capable of understanding ( i exclude for now the possibility of lack of will based on a priori commitment to naturalism) the powerlessness of non-intelligent mechanisms and limited to come up with the arrangement of matter to produce semantophoretic molecules, capable to store a huge quantity of information stored in the smallest possible space, using technology not accessible to man, and things where there is a relationship of information directing the assembly of multi-subunit machines as we see in the machinery of DNA replication, and the ribosome?

For example, fidelity of genetic information transfer relies heavily on discrimination between complementary, Watson-Crick base pairing, and in translation in codon-anticodon recognition. If we consider that random chemical reactions have no goal nor purpose, why would they produce that state of affairs of mutual recognition - unless there is a higher goal to be achieved, that is, to make life possible?

1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1188084/
2. http://oregonstate.edu/instruction/bb331/lecture13/lecture13.html

Dimiter: O Boy, nothing of what you say changing the fact why EF-Tu exists. Do not look for problems in my statements, but try to understand what I'm saying. Of course, there are so many details and interactions that are subject to lecture/course, but even so, what I'm saying is the main point. It seems that you are not looking for answers, but changing the point and try to create a conundrum of facts to escape from the main idea.

Lets recapitulate what Dimiter said in the stream: You can make it directly, every single trinucleotide be recognized very well immediately without needing the extra mechanism. however that is not the case. Again, lack of foresight. it's a perfect mechanism. It works very well, thanks to the EF-Tu, the fidelity of the translation process is enormous, it's huge, however, it is obvious you have a lack of foresight, you can make it perfectly recognizing the trinucleotide.

Reply: How are error check and correction mechanisms not evidence of intelligent design? 

The Ribosome: Perfectionist Protein-maker Trashes Errors
The enzyme machine that translates a cell’s DNA code 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 their 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 that Green says is “shocking” and reveals just how much of a stickler (insisting) the ribosome is about high-fidelity protein synthesis. 
https://www.sciencedaily.com/releases/2009/01/090107134529.htm

B.Alberts, Molecular Biology of the Cell, 6th edition:
EF-Tu provides opportunities for proofreading of the codon-anticodon match. In this way, incorrectly paired tRNAs are selectively rejected, and the accuracy of translation is improved.

How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome 31 October 2016
https://www.nature.com/articles/ncomms13314
We probe the role of EF-Tu during aa-tRNA accommodation (the proofreading step) through the use of energy landscape principles, molecular dynamics simulations and kinetic models. We find that the steric composition of EF-Tu can reduce the free-energy barrier associated with the first step of accommodation: elbow accommodation. We interpret this effect within an extended kinetic model of accommodation and show how EF-Tu can contribute to efficient and accurate proofreading.

Discussion:
The most striking result is that a balance between the rates of EF-Tu dissociation and aa-tRNA accommodation can heavily influence the level and efficiency of proofreading. Multiple free-energy barriers are introduced by steric features that impede aa-tRNA motion. Here, we have shown how EF-Tu can help aa-tRNA overcome one such steric obstacle. 

What would happen without EF-tu proofreading the ribosome? 
https://en.wikipedia.org/wiki/Kinetic_proofreading
In protein synthesis, the error rate is on the order of 1 in 10,000. This means that when a ribosome is matching anticodons of tRNA to the codons of mRNA, it matches complementary sequences correctly nearly all the time. 
A one-shot machine which tests whether the codons match or not by examining whether the codon and anticodon are bound will not be able to tell the difference between wrong and right codon unless the free energy difference is at least 10kT, which is much larger than the free energy difference for single codon binding. This can be overcome by kinetic proofreading, which introduces an irreversible step through the input of energy.

Recognition and selection of tRNA in translation 7 February 2005
https://www.sciencedirect.com/science/article/pii/S0014579304014310
The ribosome is a large ribonucleoprotein complex that catalyzes the translation of a messenger RNA (mRNA) into protein. During elongation of the growing polypeptide, the mRNA codons are displayed one after another and aminoacyl-tRNAs (aa-tRNA) with complementary anticodons are selected. Elongation factor Tu (EF-Tu) delivers aa-tRNA to the ribosomal aa-tRNA binding site (A site) where tRNA recognition and selection takes place. Biochemical and kinetic studies have shown that the movement of aa-tRNA into the A site proceeds through a number of intermediate states. 




Kinetic mechanism of EF-Tu-dependent aa-tRNA binding to the A site. 
Kinetically resolved steps are indicated by rate constants k1 − k7, k−1, k−2 and the two chemical steps that are rate-limited by the preceding step are designated kGTP and kpep. 

Recognition of Cognate Transfer RNA by the 30S Ribosomal Subunit
https://sci-hub.st/https://science.sciencemag.org/content/292/5518/897
The ribosome recognizes the geometry of codon anticodon base pairing in a way that would discriminate against near-cognate tRNAs. The minor groove of the first and second base pairs between the codon and anticodon is closely monitored by a set of interactions that are induced by the binding of cognate tRNA. These interactions would be disrupted by mismatches, so that the induced structural changes would no longer be energetically favorable. The third or “wobble” position has less stringent constraints, and therefore can allow a broader range of base-pairing geometries, consistent with the requirements of the genetic code. 

My comment: Monitoring and taking action when something is wrong requires "knowledge" of the correct state, "knowledge" of the wrong state, and know how to correct the wrong state. Knowledge, monitoring, error recognition and repair are actions only known to be performed by intelligence. 

Ribosomes are optimized for autocatalytic production 
https://www.nature.com/articles/nature22998
Many fine-scale features of ribosomes have been explained in terms of function, revealing a molecular machine that is optimized for error-correction, speed and control.

The  Elongation Factor Tu
https://reasonandscience.catsboard.com/t1661p25-translation-through-ribosomes-amazing-nano-machines#8442

Error check and repair mechanisms require foresight
https://reasonandscience.catsboard.com/t3105-error-check-and-repair-mechanisms-require-foresight

Molecules don't care if they are assembled in a way to bear a specific function. And if they do and the function is damaged and breaks down , those molecules neither "care" that they cease bearing that function.  The very concepts of proofreading and repair implies goal-orientation and "know-how" to keep something working and going.  In cells, in a variety of biochemical processes, when something goes havoc for some reason,  there is readily an armada of different error check and repair mechanisms with their "antenna" out to detect errors, and correct them, preventing lethal consequences . How is this not evidence of intended implementation by intelligence to achieve the specific purpose to maintain the complex cell machinery intact and operating properly?  In some cases, very complex multi-part machines are involved performing efficient action to keep other complex molecular machinery and systems  outside their own structural needs functional. They operate like fire-men that are called to cease a fire and rebuild the damaged part of the house ( photosystem II). Or a computer technician is called to repair a hard disk ( DNA ) Or a mechanic that is called to repair a 3D printer ( ribosome). But in contrast to human intervention, this biomolecular machinery is preprogrammed to know beforehand exactly when something is not working properly, and is able to work like a roboter and with the precision similar to a surgeon.  

The process of gene expression is critical to all life-forms. No life-form could/would survive without these advanced mechanisms in place right from the beginning, when life started.   In the pathway from Genes to proteins, and even post-translation, there are many sources of errors - and they must be fixed. Erroneous protein synthesis is due to any disruption in the conversion of the informational nucleotide sequence stored in DNA into a functioning protein. Besides amino-acid misincorporations, sources of errors are transcription errors, aberrant splicing, premature termination, faulty posttranslational modifications, and kinetic missteps during folding. This definition explicitly includes correctly synthesized polypeptides that fail to fold into a functional protein.Translation is the most error-prone step of protein synthesis.

The act of anticipation — foresight — is not a characteristic of blind material processes. It is an act of intelligence, of a mind.

DNA and RNA error checking and  repair, amazing evidence of design
https://reasonandscience.catsboard.com/t2043-dna-and-rna-error-checking-and-repair-amazing-evidence-of-design

Error detection and repair during the biogenesis & maturation of the ribosome, tRNA's, Aminoacyl-tRNA synthetases, and translation: by chance, or design?
https://reasonandscience.catsboard.com/t2984-error-check-and-repair-during-messengerrna-translation-in-the-ribosome-by-chance-or-design

Dimiter: Otangelo, you are looking at the phenomenon "life" only from one single model and you do not allow any other models to be correct. Your model assumes that we have fully developed systems/organisms/cells all the time without changes and from that perspective it seems you are correct. The problem is that there is so much evidence that this model is NOT correct, therefore your arguments are false. In detail to say what actually is wrong with your model: your model assumes that EVERYTHING in the cell should work in "max" "perfect" in order life to exist which is FALSE. 
Reply: What does "max" "perfect" even mean in context of biology ?

How Structure Arose in the Primordial Soup
About 4 billion years ago, molecules began to make copies of themselves, an event that marked the beginning of life on Earth. A few hundred million years later, primitive organisms began to split into the different branches that make up the tree of life. In between those two seminal events, some of the greatest innovations in existence emerged: the cell, the genetic code and an energy system to fuel it all. ALL THREE of these are ESSENTIAL to life as we know it, yet scientists know disappointingly little about how any of these remarkable biological innovations came about.
https://www.scientificamerican.com/article/how-structure-arose-in-the-primordial-soup/

There is no working model of how the building blocks, the genetic code, nor energy could have emerged independently on the prebiotic earth. And much less, how to interconnect everything into the interactome:

The interactome, and the origin of life
https://reasonandscience.catsboard.com/t3120-the-interactome-and-the-origin-of-life

considering that everything needs everything in order for the individual systems, and the cell to work:

The cell is irreducibly complex
https://reasonandscience.catsboard.com/t1299-abiogenesis-the-cell-is-irreducibly-complex

Open questions in prebiotic chemistry to explain the origin of the four basic building blocks of life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-mathematically-impossible#7759

There is no working model of how the information systems could have emerged prebiotically ( The RNA world )

The problem of the origin of the hardware and software in the cell is far greater than commonly appreciated
https://reasonandscience.catsboard.com/t2997-the-problem-of-the-origin-of-the-hardware-and-software-in-the-cell-is-far-greater-than-commonly-appreciated

The genetic code, insurmountable problem for non-intelligent origin
https://reasonandscience.catsboard.com/t2363-the-genetic-code-insurmountable-problem-for-non-intelligent-origin

There is no working model of how metabolism could have emerged prebiotically ( The RNA world )

The origin of metabolism is a major gap in our understanding of the emergence of life
https://reasonandscience.catsboard.com/t2074-the-origin-of-metabolism-is-a-major-gap-in-our-understanding-of-the-emergence-of-life

Major metabolic pathways and their inadequacy for origin of life proposals
https://reasonandscience.catsboard.com/t2004-major-metabolic-pathways-and-their-inadequacy-for-origin-of-life-proposals

There is no working model of how the generation of energy could have emerged prebiotically:

ATP: The  Energy  Currency for the Cell
https://reasonandscience.catsboard.com/t2137-atp-the-energy-currency-for-the-cell

Where did Glucose come from in a prebiotic world ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world

Dimiter: Your model assumes also that the selection forces are the same all the time which is also SUPER WRONG.
Reply: In my previous email, I exposed why there was no evolution, and consequently, no selection on the prebiotic earth. It seems you missed it.

There was no prebiotic selection to get life originating
https://reasonandscience.catsboard.com/t3121-there-was-no-prebiotic-selection-to-get-life-originating

1. Life requires the use of a limited set of complex biomolecules, a universal convention, and unity which is composed of the four basic building blocks of life ( RNA and DNA's, amino acids, phospholipids, and carbohydrates). They are of a very specific complex functional composition and made by cells in extremely sophisticated orchestrated metabolic pathways, which were not extant on the early earth. If abiogenesis were true, these biomolecules had to be prebiotically available and naturally occurring ( in non-enzyme-catalyzed ways by natural means ) and then somehow join in an organized way and form the first living cells. They had to be available in big quantities and concentrated at one specific building site. 
2. Making things for a specific purpose, for a distant goal, requires goal-directedness. And that's a big problem for naturalistic explanations of the origin of life. There was a potentially unlimited variety of molecules on the prebiotic earth. Competition and selection among them would never have occurred at all, to promote a separation of those molecules that are used in life, from those that are useless. Selection is a scope and powerless mechanism to explain all of the living order, and even the ability to maintain order in the short term and to explain the emergence, overall organization, and long-term persistence of life from non-living precursors. It is an error of false conceptual reduction to suppose that competition and selection will thereby be the source of explanation for all relevant forms of the living order.
3. We know that a) unguided random purposeless events are unlikely to the extreme to make specific purposeful elementary components to build large integrated macromolecular systems, and b) intelligence has goal-directedness. Bricks do not form from clay by themselves, and then line up to make walls. Someone made them. Phospholipids do not form from glycerol, a phosphate group, and two fatty acid chains by themselves, and line up to make cell membranes. Someone made them. That is God.

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


Dimiter: In actual science (that means NO DISCOVERY INSTITUTE) the models are seeking for evidence(s), and THE SCIENCE HAVE TONS OF EVIDENCE TO SUPPORT THE EVOLUTION. Your so called "evidence" are only two major types: COMPLICATED BIOLOGY=irreducible complexity and INFORMATION=ID. Both of those types of arguments are BASED ON WRONG MODELS as I explained above.
Reply: Your colleagues disagree with you. So what is it? Is the Cell irreducible or not? If not, how is it that several science papers attempt to elucidate what a minimal first ( or last ) universal common ancestor eventually looked like? ( And evidently, requiring a minimal number of parts? )

The whole is more than the sum of the parts. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system.  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?  Never do we see blind, unguided processes leading to complex functional systems with integrated parts contributing to the overarching design goal.

The principle of evolutionary continuity, succinctly formulated by Albert Lehninger in his Biochemistry textbook. An adaptation that does not increase the fitness is no longer selected for and eventually gets lost in the evolution (in the current view, only those adaptations that effectively decrease the fitness end up getting lost). Hence, any evolutionary scenario has to invoke – at each and every step – only such intermediate states that are functionally useful (or at least not harmful).
https://onlinelibrary.wiley.com/doi/abs/10.1002/cbdv.200790167

What might be a Cell’s minimal requirement of parts?  
https://reasonandscience.catsboard.com/t2110-what-might-be-a-protocells-minimal-requirement-of-parts

LUCA—The Last Universal Common Ancestor 
https://reasonandscience.catsboard.com/t2176-lucathe-last-universal-common-ancestor

The cell is the ultimate example of irreducible complexity. My book Evolution Shot Full of Holes with co-author Frank Sherwin, contains a chapter on the topic of the origin of life. The cell is an interdependent functional city. We state, “The cell is the most detailed and concentrated organizational structure known to humanity. It is a lively microcosmic city, with factories for making building supplies, packaging centers for transporting the supplies, trucks that move the materials along highways, communication devices, hospitals for repairing injuries, a massive library of information, power stations providing usable energy, garbage removal, walls for protection and city gates for allowing certain materials to come and go from the cell.” The notion of the theoretical first cell arising by natural causes is a perfect example of irreducibly complexity. Life cannot exist without many numerous interdependent complex systems, each irreducibly complex on their own, working together to bring about a grand pageant for life to exist.

The cell is the irreducible, minimal unit of life 5
https://sci-hub.st/https://link.springer.com/chapter/10.1007/978-3-319-56372-5_8

Chemistry and the Missing Era of Evolution: A. Graham Cairns-Smith
We can see that at the time of the common ancestor, this system must already have been fixed in its essentials, probably through a critical interdependence of subsystems. (Roughly speaking in a domain in which everything has come to depend on everything else nothing can be easily changed, and our central biochemistry is very much like that.
https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/18260066

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

So do you claim that the fact that life depends on complex information storage and transmission systems is not a relevant abiogenesis problem? If not, where is your working model, that instructional assembly information stored in genes can emerge without invoking intelligence? 

Coded information comes always from a mind
https://reasonandscience.catsboard.com/t1312-coded-information-comes-always-from-a-mind

Tan, Change; Stadler, Rob. The Stairway To Life:
In DNA and RNA, no chemical or physical forces impose a preferred sequence or pattern upon the chain of nucleotides. In other words, each base can be followed or preceded by any other base without bias, just as the bits and bytes of information on a computer are free to represent any sequence without bias. This characteristic of DNA and RNA is critical—in fact, essential—for DNA and RNA to serve as unconstrained information carriers. However, this property also obscures any natural explanation for the information content of life—the molecules themselves provide no explanation for the highly specific sequence of nucleotides required to code for specific biologic functions. Only two materialistic explanations have been proposed for the information content of life: fortuitous random arrangements that happen to be functional or the combination of replication, random mutations, and natural selection to improve existing functionality over time.

Dimiter:  Now pay attention to the next sentence: YOU CANNOT ARGUE WITH WRONG MODEL TO DISPROVE CORRECT MODEL. 
Reply: Eugene Koonin The Logic of Chance: page 351:" 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. 

Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Persistent lack of progress on a scientific problem is exactly what one should expect when a causal puzzle has been fundamentally misconceived, or when the toolkit employed in causal explanation is too limited. ( Contrast this with Popperian falsification, where propositions are corroborated to the degree that they successfully withstand attempts to falsify them ) When the available option forms a dichotomy, just to option, A, or not A, they form a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. As Sherlock Holmes's famous dictum says: when you have eliminated the impossible, whatever remains, however improbable, must be the truth. In this case, eliminative inductions, in fact, become deductions.

Dimiter:How do we know which model is correct? IT IS EVIDENCE BASED. 
Reply:  Agreed. Here is the evidence:


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

Cells are factories in a literal sense:
https://reasonandscience.catsboard.com/t2245-abiogenesis-the-factory-maker-argument#6959

1. Living Cells store very complex genetic and epigenetic information through the genetic code, and over forty epigenetic languages, translation systems, and signaling networks. These information systems prescribe and instruct the making and operation of cells and multicellular organisms. The operation of cells is close to thermodynamic perfection, and its operation occurs analogously to computers. Cells ARE computers in a literal sense, using boolean logic. Each cell hosts millions of interconnected molecular machines, production lines and factories analogous to factories made by man. They are of unparalleled gigantic complexity, able to process constantly a stream of data from the outside world through signaling networks. Cells operate robot-like,  autonomously. They adapt the production and recycle molecules on demand. The process of self-replication is the epitome of manufacturing advance and sophistication.

2. The origin of blueprints containing the instructional complex information, and the fabrication of complex machines and interlinked factories based on these instructions, which produce goods for specific purposes, are both always the result of intelligent setup.

3. Therefore, the origin of biological information and self-replicating cell factories is best explained by the action of an intelligent designer, who 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.”

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

Michael Denton’s 1985 Evolution: A Theory in Crisis:
The inference to design is a purely a posteriori induction based on a ruthlessly consistent application of the logic of analogy.

Dimiter: The mechanisms of mutations and gene amplification is enormously well studied, the selection forces are well studied as well, the predictions for LACK OF FORESIGHT, same protein motifs in different proteins making phylogeny possible, fossils and SO ON........all predicted by evolution.  First you need to explain the origin of RNA, DNA, and Genes. Where is your working model? I explained to you a million times so far that in evolution a more simple system does not require the advantages of a more complicated system which will appear later in time. FOR EXAMPLE a complex from few peptides and few short RNAs capable of Darwinian evolution does not need modern helicases or polymerases or ribosomes or repair error prone correction: those are useless in such a simple system.
Reply:  Peptides and RNA's would SIMPLY DEVOLVE into asphalt.

Paradoxes in the Origin of Life
https://reasonandscience.catsboard.com/t1279p75-abiogenesis-is-virtually-impossible#7309

Steven A. Benner

https://www.ncbi.nlm.nih.gov/pubmed/25608919

Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken together) suggest that the “origins problem” cannot be solved.

The Asphalt Paradox 
Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  the literature reports (to our knowledge) exactly  ZERO CONFIRMED OBSERVATIONS where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. it is IMPOSSIBLE for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. 

Decomposition of Monomers, Polymers and Molecular Systems: An Unresolved Problem 2017 Jan 17
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5370405/
It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.

CAIRNS-SMITH genetic takeover, page 70
Suppose that by chance some particular coacervate droplet in a primordial ocean happened to have a set of catalysts, etc. that could convert carbon dioxide into D-glucose. Would this have been a major step forward
towards life? Probably not. Sooner or later the droplet would have sunk to the bottom of the ocean and never have been heard of again. It would not have mattered how ingenious or life-like some early system was; if it
lacked the ability to pass on to offspring the secret of its success then it might as well never have existed. So I do not see life as emerging as a matter of course from the general evolution of the cosmos, via chemical evolution, in one grand gradual process of complexification. Instead, following Muller (1929) and others, I would take a genetic View and see the origin of life as hinging on a rather precise technical puzzle. What would have been the easiest way that hereditary machinery could have formed on the primitive Earth?

Intractable Mixtures and the Origin of Life 2007
Whatever the exact nature of an RNA precursor which may have become the first selfreplicating molecule, how could the chemical homogeneity which seems necessary to permit this kind of mechanism to even come into existence have been achieved? What mechanism would have selected for the incorporation of only threose, or ribose, or any particular building block, into short oligomers which might later have undergone chemically selective oligomerization? Virtually all model prebiotic syntheses produce mixtures. 6

OPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH February 2014
Attempts to obtain copolymers, for instance by a random polymerization of monomer mixtures, yield a difficult to characterize mixture of all different products. To the best of our knowledge, there is no clear approach to the question of the prebiotic synthesis of macromolecules with an ordered sequence of residues.
https://www.sciencedirect.com/science/article/pii/S2001037014600076

Dimiter: Final notes: Otangelo, instead of looking at your READYMADE answers, please sit down and think from the perspective of different models.
Reply: I have done so, as you can see in this reply. When will you think about Intelligent Design as a superior model seriously? What else do you need to understand that naturalistic models are bankrupt and implausible to the extreme?!! How strong are the bonds of materialism withholding you to start thinking about ID as a serious and more logical, plausible, and probable alternative ?  

Paradoxes in the origin of life. 2015 Jan 22 Benner SA1.
http://sci-hub.ren/https://www.ncbi.nlm.nih.gov/pubmed/25608919
 We are now 60 years into the modern era of prebiotic chemistry. That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology” …. For the most part, these papers report “success” in the sense that those papers define the term…. And yet, the problem remains unsolved

Andrew: This thing is complex. We don't know how it happened. there must be a designer. This is an argument from absurdity.


Dimiter:  so what? You are wrong again. everywhere and everything in biology has only one explanation: EVOLUTION.
Reply:   We will see one day who was right.
Dimiter: Otangelo, I know exactly what you mean by "one day". I know about Christianity more than you can guess. A wish you everything nice and happy life. Thrust me, I mean it.
Reply: I trust you, and believe that you mean it. I also do, whatever I do, wishing the best for my fellow human beings, including you.
What you might not consider, however, is the consequence in a broader sense of a naturalistic worldview, with evolution as one of its main tenets.

Yu Fei: there is no such thing as a inherently "higher level" concept in evolution.
Reply:  Complexity, Natural Selection and the Evolution of Life and Humans
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4427860/
I suggest the process of evolution to be illustrated by means of a schematic diagram of complexity versus time, interpreted as a form of the Tree of Life. The suggested model implies that complexity is cumulatively increasing, giving evolution a direction, an arrow of time, thus also implying that the latest emerging species will be the one with the highest level of complexity.
...... This means an increase of the number of parts and of the amount of differentiation among these parts of the heart, in other words an increasing level of complexity.
With his classical book What is Life? physicist Schrödinger (1955) was maybe the first to call attention to the problem of how the process of life can proceed in increasing its level of complexity, while obviously violating the second law of thermodynamics.
Gould means that in an analogous way, living organisms are drifting toward higher complexity at random, because there is a limit of minimal complexity.
I maintain that the natural variation of the functional capability of many features by natural selection is driven to successively higher levels of complexity.

ERNST MAYR SPECIATION AND MACROEVOLUTION March 15, 1982
https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1558-5646.1982.tb05483.x
Darwin, the champion of gradualism, declared that it was a purely quantitative problem. If one would simply pile enough small differences on top of each other, one would eventually get something that is qualitatively different, that is, a higher taxon or an evolutionary novelty. . It was simply thinking in terms of phyletic lines that gradually and inexorably moved upward to ever-better adaptations or ever greater specializations. s. If we define evolution as changes in adaptation and diversity, then the students of adaptation deal with what we might call the vertical dimension of evolution, while the students of diversity deal with the horizontal dimension, that is with the changes
of populations in latitude and longitude. Paleontologists, when studying macroevolution, traditionally never come to grips with the problem of the origin of the taxa or types that evolved "higher" or experienced adaptive
radiations

Yu Fei:  Next, how does evolution equals to "anything goes"? Is that how evolutionary biologist describe evolution regarding morality?
Reply:   “Where no guiding ideals are left to point the way, the scale of values disappears and with it the meaning of our deeds and sufferings, and at the end can lie only negation and despair. Religion is therefore the foundation of ethics, and ethics the presupposition of life.”
[Heisenberg, Werner. 1973. “Naturwissenschaftliche und religioese Wahrheit.” Frankfurter Allgemeine Zeitung, 24 Maerz, pp. 7-8. (Speech before the Catholic Academy of Bavaria, on acceptance of the Guardini Prize, 23 March 1974)]

If there is no God, there are no objective moral values, since they are prescribed " ought to be's". If there is no God, then moral values are just a matter of personal opinion, and as such, no objectively or universally valid at all.
https://reasonandscience.catsboard.com/t1369-moral-argument-for-gods-existence


1. The problem with using epoxy resin is that it will turn the price of the boat considerably more expensive. Epoxy resin is up to 10x more expensive here in Brazil. The price difference for a 36 foot is about 10th us$ With Ester vinyl price difference is about 5000 us$   
2. Epoxy resin is not a resin to make molded boats with Gelcoat as a finish. They, afterward, are made with painting PU. Dolphin uses the best gel coats, which gives durability over 10 years. That Gelcoat does not adhere to epoxy resin, so it cannot be put into the mold. The entire envelope of the boat has to be made with ester vinyl. The hull, the platform, and the deck. It can be done with epoxy, but it will turn the 36-foot boat about us$ 20 thousand more expensive. ( not included the tooling )

The Dolphin line so far has been made with polyester, besides a few in carbon. But with epoxy, or ester vinyl it can be made according to the wish of the client. 

The majority of today's boat builders make their boats today using Polyester resin with Gelcoat polyester, and vinylester below the waterline. It is used an epoxy radical, with polyester ( ester vinyl)

Dimiter,

thanks for your reply. 

in order to start a plausible narrative of how life could have emerged from nonlife, one has to start from the beginning. You have not answered in regards to the ( in my opinion ) unbridgeable problem to synthesize RNA prebiotically, without enzymes. The papers which you quoted, did not provide a solution to the problems exposed. But we can go even a bit further.

One major problem is that there was NO prebiotic selection process of the functional nucleobases for Watson-Crick basepairing amongst myriads of possible configurations. THIS ALONE is a check-mate situation for the unguided abiotic origin of life hypotheses. 

https://reasonandscience.catsboard.com/t2865-rna-dna-it-s-prebiotic-synthesis-impossible#7700

As following paper reports:

Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides May 18, 2020
https://sci-hub.st/https://pubs.acs.org/doi/10.1021/acs.chemrev.0c00069

Even if the noncanonical nucleotides present on the prebiotic Earth were not able to achieve the functions that would have allowed for the action of evolution to push these molecules along the path to the extant nucleotides, the work reviewed earlier on possible prebiotic syntheses of the canonical nucleotides, primarily by the groups of Carell, Sutherland, and Powner, also raises the possibility that the prebiotic importance of noncanonical nucleosides was simply their mechanistic intermediacy en route to canonical nucleosides. 

Question: Why should that be the case? Did noncanonical nucleosides have the anthropomorphic "urge" or goal to become complex semantophoretic macromolecules that carry genetic information ? 

An enormous amount of effort has been put into finding the prebiotic origins of the extant nucleotides and our opinion that the journey is not yet complete.

My comment: And upon my understanding, the simple fact that there was no SELECTION MECHANISM of the dearly needed basic building blocks of life, and the fact that Systems, given energy and left to themselves, DEVOLVE to give uselessly complex mixtures, “asphalts”.  ( Steven A. Benner  https://sci-hub.st/https://www.ncbi.nlm.nih.gov/pubmed/25608919 ) makes ANY unguided abiogenesis hypothesis untenable and unlikely to the extreme. Using my pharising, i keep saying, impossible !! 

The trajectory from a prebiotic synthesis of the basic building blocks of life, to the sophisticated synthesis by cell factories: an unsolved riddle
https://reasonandscience.catsboard.com/t2894-prevital-unguided-origin-of-the-four-basic-building-blocks-of-life-impossible#7650

Nucleotides are building blocks for DNA and RNA. Three Pyrimidines and Two Purines Are Commonly Found in Cells.
The pyrimidine synthesis pathway requires six regulated steps, seven enzymes, and energy in the form of ATP.
The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the highly complex pentose phosphate pathway, which uses 12 enzymes. 1 
De novo purine synthesis pathway requires ten regulated steps, eleven enzymes, and energy in the form of ATP. 

Question:  How would you go from a prebiotic synthesis of RNA, to enzymatic synthesis, required all the enzymes mentioned above?

The DNA double helix, evidence of design
https://reasonandscience.catsboard.com/t2028-biosynthesis-of-the-dna-double-helix-evidence-of-design

Enzyme expert Dr Richard Wolfenden, of the University of North Carolina, showed in 1998 that a reaction ‘“absolutely essential” in creating the building blocks of DNA and RNA would take 78 million years in water’, but was speeded up 10^18 times by an enzyme.1 This was orotidine 5′-monophosphate decarboxylase, responsible for de novo synthesis of uridine 5′-phosphate, an essential precursor of RNA and DNA, by decarboxylating orotidine 5′-monophosphate (OMP).

Wolfenden said,
‘Without catalysts, there would be no life at all, from microbes to humans. It makes you wonder how natural selection operated in such a way as to produce a protein that got off the ground as a primitive catalyst for such an extraordinarily slow reaction.’

Question:  In order to make RNA and DNA, prebiotic earth without this enzyme would have needed to wait 78 million years to yield Uridine monophosphate to make RNA. by natural processes......

The problems do not end here. In order to make nucleobases, carbon and nitrogen

DK: RNA-peptide hypothesis for the origin of life is based on well-known facts like Watson/Crick base pair interactions
Reply: As previously elucidated, Watson-Crick base-pairing depends on the very specific isomeric arrangement of nucleobases, in special carbon and nitrogen.

But carbon and nitrogen were not ready available on early earth. That is another huge, unsolved problem. 

Availability of nitrogen and ammonia on early earth
https://reasonandscience.catsboard.com/t2689-availability-of-nitrogen-and-ammonia-on-early-earth

Where did Glucose come from in a prebiotic world ?
https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#8116

DK: Let me give you an example of fantasy: Assembly of the complicated organism “out of blue” due to some unknown force of intelligent designer. No previous scientific data, no physico-chemical interaction no laws allowing this. The explanation that comes from irreducible complexity or  “I believe so” is not a scientific explanation, therefore we are talking about fantasy.  
Having this in mind to criticize that something IS JUST HYPOTHESIS is unfair, especially if you have an alternative fantasy.
Reply: Chance of intelligence to set up life: 
100% We KNOW by repeated experience that intelligence produces all the things, as follows:
factory portals  ( membrane proteins ) factory compartments ( organelles ) a library index ( chromosomes, and the gene regulatory network ) molecular computers, hardware ( DNA ) software, a language using signs and codes like the alphabet, an instructional blueprint, ( the genetic and over a dozen epigenetic codes ) information retrieval ( RNA polymerase ) transmission ( messenger RNA ) translation ( Ribosome ) signaling ( hormones ) complex machines ( proteins ) taxis ( dynein, kinesin, transport vesicles ) molecular highways ( tubulins ) tagging programs ( each protein has a tag, which is an amino acid sequence  informing other molecular transport machines were to transport them.) factory assembly lines ( fatty acid synthase ) error check and repair systems  ( exonucleolytic proofreading ) recycling methods ( endocytic recycling ) waste grinders and management  ( Proteasome Garbage Grinders )   power generating plants ( mitochondria ) power turbines ( ATP synthase ) electric circuits ( the metabolic network ) computers ( neurons ) computer networks ( brain ) all with specific purposes.

Chance of unguided random natural events producing just a minimal functional proteome, not considering all other essential things to get a first living self-replicating cell,is:

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

The simplest free-living bacteria is Pelagibacter ubique. 13 It is known to be one of the smallest and simplest, self-replicating, and free-living cells.  It has complete biosynthetic pathways for all 20 amino acids.  These organisms get by with about 1,300 genes and 1,308,759 base pairs and code for 1,354 proteins.  14  That would be the size of a book with 400 pages, each page with 3000 characters.  They survive without any dependence on other life forms. Incidentally, these are also the most “successful” organisms on Earth. They make up about 25% of all microbial cells.   If a chain could link up, what is the probability that the code letters might by chance be in some order which would be a usable gene, usable somewhere—anywhere—in some potentially living thing? If we take a model size of 1,200,000 base pairs, the chance to get the sequence randomly would be 4^1,200,000 or 10^722,000. This probability is hard to imagine but an illustration may help.  

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

DK: evolution of proto-aaRS is based on aaRS phylogenetic DATA.
Reply:  How can there be a phylogenetic tree about proteins that must be there all at once, and on top of that, prebiotically,  in order for the translation machinery to work? There is NO evidence that a smaller genetic code, as for example using two, rather three nucleotides, and a smaller set of amino acids would/could confer functional proteins. Also, how do you explain the selection of an optimal amino acid set?

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids
https://www.nature.com/articles/srep09414
Additional factors beyond selection for the three properties principally considered in our test contributed to the adaptability of the coded set as a LUCA organism colonized habitable spaces on Earth. Given that each additional criterion greatly reduces the number of better sets, it would seem that adding functional criteria would only make the coded set even more unusual, and possibly reflect the truly limited set of possibilities that life has to choose from.

Not considering, that proteins by their own have no use, and no function, unless embedded and working in a joint venture with other proteins, as in metabolic pathways, productionline-like arrangements to make complex macromolecules, to generate energy etc.

Homology: A Concept in Crisis
https://reasonandscience.catsboard.com/t1454-homology-a-concept-in-crisis
Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. This constitutes an important methodologic dimension not often taken into account.

Structural similarities among automobiles, even similarities between older and newer models are due to construction according to pre-existing patterns, i.e., to design. Ironically, even striking similarities are not sufficient to exclude design-based explanations. In order to demonstrate naturalistic evolution, it is necessary to show that the mechanism by which organisms are constructed (unlike the mechanism by which automobiles are constructed) does not involve design.

DK: PREBIOTICALLY nothing complicated can come to be. The complication comes AFTER the formation of Darwinian evolution. There is an initial function of short peptides (not fully formed aaRS) to stabilized RNA-peptide complex (experimentally proven fact). After that, the short peptides EVOLVED into longer peptides accepting step by step more functions in a step by step more complicated life system until you have a fully developed translation system.
Reply: You keep ASSERTING that. Please give me good reasons why I should take your claim at face value. 

Proteins and Protein synthesis
https://reasonandscience.catsboard.com/t2706-main-topics-on-proteins-and-protein-synthesis

How Did Protein Synthesis Evolve?
The molecular processes underlying protein synthesis in present-day cells seem inextricably complex. Although we understand most of them, they do not make conceptual sense in the way that DNA transcription, DNA repair, and DNA replication do. It is especially difficult to imagine how protein synthesis evolved because it is now performed by a complex interlocking system of protein and RNA molecules; obviously the proteins could not have existed until an early version of the translation apparatus was already in place. As attractive as the RNA world idea is for envisioning early life, it does not explain how the modern-day system of protein synthesis arose.
Molecular biology of the cell, 6th ed. pg. 365

Kind regards

Otangelo