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From Barren Planet to Civilization in Four Easy Steps

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In a recent American Spectator article “Evolution—More Certain than Gravity?” I made the point that to not believe in intelligent design, you have to believe that the four fundamental, unintelligent forces of physics alone (the gravitational, electromagnetic and strong and weak nuclear forces) could have rearranged the fundamental particles of physics on our once-barren planet into encyclopedias and science texts and computers and airplanes and Apple iPhones. In a 2017 Physics Essays article “On ‘Compensating’ Entropy Decreases,” I argued that this spectacular increase in order seems to violate the more general statements of the second law of thermodynamics; at least that you cannot dismiss this claim, as is always done, by simply saying, the Earth is an open system and order can increase in an open system.

Whether or not what has happened on Earth technically violates the second law, I can’t imagine anything in all of science that is more clear and more obvious than that unintelligent forces alone cannot produce such things as Apple iPhones. But materialists are not impressed, they believe they can explain how unintelligent forces alone could produce computers and airplanes. There are four steps in the usual materialist explanation of how advanced civilizations can spontaneously arise on barren, Earth-like, planets, without design:

  1. Three or four billion years ago a collection of atoms formed by pure chance that was able to duplicate itself.
  2. These complex collections of atoms were able to preserve their complex structures and pass them on to their descendants, generation after generation.
  3. Over a long period of time, the accumulation of duplication errors resulted in more and more elaborate collections of atoms.
  4. Eventually something called “intelligence” allowed some of these collections of atoms to design computers and airplanes, and write encyclopedias and science texts.

The first step is the origin of life: even most materialists will admit that this is a very difficult problem which has not yet been solved by science. Regarding the fourth step, we may feel that we understand how humans design and build computers and airplanes, because we see it happen all the time. But seeing something happen and understanding how it happens are two very different things, and again I think even most materialists will agree that science cannot yet explain human consciousness or intelligence in terms of unintelligent forces alone.

Darwinists claim that the third step is well understood by science, that natural selection has organized these duplication errors into higher animals and intelligent humans, even though it has never actually been observed to produce anything other than very minor adaptations (see this New York Times article.) As I pointed out in “I Believe in the Evolution of Life and the Evolution of Automobiles,” what we see in the fossil record–large gaps where major new features appear–actually looks more like the way human technology, such as software or automobiles, “evolves,” through testing and improvements. “Gaps among known orders, classes and phyla are systematic and almost always large,” writes Harvard paleontologist George Gaylord Simpson. And new organs and new systems of organs do not appear very gradually, as Darwin had expected, for the same reason that major new technological advances do not appear very gradually: gradual transitions would have to involve puzzling new but not yet useful features. Although he calls evolution “axiomatic,” University of California geologist Joseph Le Conte acknowledges in his 1888 book Evolution that in the fossil record, “species seem to come in suddenly” and that gradual transitions could not be explained by natural selection if they did exist: “An organ must be already useful before natural selection can take hold of it to improve it,” he concedes.

When I point out the similarities between the evolution of life and the evolution of human technology such as the automobile, some people have responded by saying that of course the evolution of life is much easier to explain without design than the evolution of automobiles because cars cannot reproduce, so there are no “variations” for natural selection to work with. Actually the fact that natural selection cannot act on cars is irrelevant to the main point of this comparison, which is simply that similarities between “species” (of cars or animals) do not prove the absence of design.

However, even though it is irrelevant to the main point of that comparison, let’s look at the argument that evolution is easier to explain if there is reproduction, because that brings us to the second step of the materialists’ explanation. That the third step seems even superficially plausible (until we look at it in more detail) depends completely on the second step, the fact that living things are able to reproduce, that “these complex collections of atoms are able to preserve their complex structures and pass them on to their descendants, generation after generation.” Reproduction is the most fundamental characteristic of life, we see it happen everywhere, so we may feel there is no mystery to reproduction. But again, seeing something happen and explaining how it happens naturally are two very different things. Is it really true that if cars were able to give birth to other cars—that is, if they were able to reproduce themselves almost perfectly, with occasional minor duplication errors—that would make the evolution of cars easier to explain without design? Although it is far beyond our current technology, imagine that it were possible to construct a fleet of cars that contained completely automated car-building factories inside, with the ability to construct new cars—and not just normal new cars, but new cars containing automated car-building factories inside. If we left these cars alone and let them reproduce themselves for many generations, is there any chance we would eventually see major advances arise through natural selection of the resulting duplication errors? Of course not, the whole process would grind to a halt after a few generations without intelligent humans there to fix the mechanical problems that would arise. We are so used to seeing animals make nearly perfect copies of themselves that we dismiss this as just another “natural” process; but if we actually saw cars with fully automated car factories inside, making new cars with car factories inside them, maybe we would realize what an astonishing process reproduction really is. (“How do these instruction sets not make mistakes as they build what is us?” mathematician Alexander Tsiaras asks in the video “Conception to Birth—Visualized.” How indeed?) And we might conclude that reproduction actually makes evolution even more difficult to explain without design.

Mathematicians are trained to value simplicity: when we have a clear, simple, proof of a theorem, and a long, complicated counterargument, involving controversial and unproven assertions, we accept the clear, simple, proof, and we know there must be errors in the counterargument even before we find them. The argument for intelligent design here could not be simpler or clearer: unintelligent forces of physics alone cannot rearrange atoms into computers and airplanes and Apple iPhones. And the counterargument consists of four steps, each of which–to put it very generously—is based on dubious and unproven assertions. QED.

Comments
OLV, Noticed all those posts in response to my comment @192. Thanks. However, probably it was not expressed clearly, but what I meant is that it would be interesting if someone could dissect the papers that JVL cited @181 and tell us how do they relate to what JVL stated. Do they support his statements? Yes, no, maybe? Also, what about the other papers you referenced, in addition to JVL's citations? Do they shed light on the topic JVL raised @181? Any conclusions? Thanks.PeterA
October 24, 2018
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jawa: Yes, I must confess that I expected something more, too. Maybe we are too optimistic, my friend! :)gpuccio
October 24, 2018
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jawa, The discussion could be interesting even if the knowledge levels are different. What matters is the motivation level. If all sides are very interested in finding the truth, the discussion will definitely be interesting, assuming all involved have enough time and communicate in a common language or have good translation.PeterA
October 24, 2018
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Incorrectly expected this discussion would turn more interesting, but the enormous difference of scientific knowledge between gpuccio and his interlocutor soon surfaced. If more sciscientifically qualified interlocutors like the university of Kentucky professor AH or the professor JF couldn’t hold a serious discussion with gpuccio, how can we expect less scientifically qualified interlocutors to have serious discussions with gpuccio?jawa
October 23, 2018
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Antonin: I wish you the best. :)gpuccio
October 23, 2018
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I respect your decisions and don’t tell you what you should do. Could you be kind enough to do the same?
Apologies. We should all be masters of our own destiny.
The point is that I come here to defend what I think is true.
The fact it is not much of a challenge has been the point I have been suggesting. But of course it is your choice.
I always consider others’criticisms. And, if they are interesting, I answer them in detail. It’s all in that long history.
Sure. I wonder if you haven't already written enough to compile into a book. I'm sure there's a niche market.
I don’t want you to change your opinion. I change my opinions all the time. But there must be reasons for that.
Do you? I find it hard to adapt to new information that challenges a long-held view. But there's no choice, really. Reality or delusion? I have to, in the end, choose reality.
If you have facts or ideas that can make me change my opinions, I am ready to consider them. For me, you are not nobody. Nobody is.
Well, I'm not a scientist so my opinions on genetics and molecular biology aren't worth much. But Joe Felsenstein seems like a reasonable interlocutor. It might be interesting to venture out into a venue where you could communicate more directly. Anyway, I've enjoyed our exchange. I'll look out for another article from you, should you decide to write one. Stay well and vai con dio :)Antonin
October 23, 2018
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Antonin: I respect your decisions and don't tell you what you should do. Could you be kind enough to do the same? The point is that I come here to defend what I think is true. I always consider others'criticisms. And, if they are interesting, I answer them in detail. It's all in that long history. I don't want you to change your opinion. I change my opinions all the time. But there must be reasons for that. If you have facts or ideas that can make me change my opinions, I am ready to consider them. For me, you are not nobody. Nobody is.gpuccio
October 23, 2018
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If you are not convinced by ideas...
Ideas are just the start. They can be worth pursuing or not It's really up to you to decide. Is your idea something worth pursuing? Is it worth listening to feedback? Not from me, I'm nobody. But there has been feedback from career scientists. You seem, it's just my impression, to wave it away. Fine, but you're not going to impress the scientific community if you don't at least consider their criticisms.
...you will not be convinced by formal papers.
But scientists may take you seriously if you present your idea more formally. Otherwise, what's the point?
If there is any criticism that you agree with, I am available to discuss it here in detail, as I have done with the criticisms you have already expressed.
I don't agree that you have taken on board Felsenstein's points and I don't think you have really considered the points raised by DNA_Jock.There may be much we agree on if we were to compare notes but that would be boring and no help at all in avoiding the onset of dementia!
So, the history will become longer.
I have this hypothesis. Let me tell you about it...
Of course, you can just stick with your opinion.
You want me to change my opinion? How easy do you find to change yours? When did you last change your opinion about something? I'm going to think hard and see if I can come up with an example where I was able to change my opinion on the presentation of new facts. I'll race you! :)Antonin
October 23, 2018
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Antonin: If you are not convinced by ideas, you will not be convinced by formal papers. If there is any criticism that you agree with, I am available to discuss it here in detail, as I have done with the criticisms you have alredy expressed. So, the history will become longer. Of course, you can just stick with your opinion.gpuccio
October 23, 2018
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@ dionisio
Aren’t gpuccio’s explanations based on overwhelming empirical evidences?
Well, Gpuccio is developing an idea from data that have been collected and published and thus available for anyone to analyse.
What other test do you need?
To test a hypothesis, you need predictions that can be either found or not found. I don't think gpuccio's idea predicts anything testable.
Isn’t it easy to falsify?
Isn't what easy to falsify? Gpuccio claims to falsify the theory of evolution, unless I'm mistaken. I think the best that can be said is his model fails. His model, in my opinion, is not an accurate model.
Just present one example where functional complexity originates from unguided processes, hence it’s not intelligently designed.
Assuming the consequent. I'm not claiming that processes are unguided. Of course evolution is guided. Where did you get the idea that I thought otherwise?
That simple.
Ants! Sidewalk! :)Antonin
October 23, 2018
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Antonin, Aren’t gpuccio’s explanations based on overwhelming empirical evidences? What other test do you need? Isn’t it easy to falsify? Just present one example where functional complexity originates from unguided processes, hence it’s not intelligently designed. That simple.jawa
October 23, 2018
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@ gpuccio There seems quite a history here. I'm back to 2012 with threads that follow on from other threads, and a back-and-forth with the TSZ site. Had you not thought of writing a more formal paper, perhaps taking on board some of the criticism?Antonin
October 23, 2018
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Can this argument be settled once for all?
I think gpuccio is presenting the germ of an idea. I don't think this is the ideal venue for discussion about that idea. Gpuccio, I believe, thinks his idea is scientific. But scientific ideas are subject to testing. If the idea fits observation and/or experiment, then it is worthy of further consideration. I'm not convinced gpuccio has presented an idea that can be tested.Antonin
October 23, 2018
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Do we all realize the enormous functional complexity of what we’re observing, which is (partially) the object of the discussion? Maybe we should start from that? Couldn’t we lose the right perspective otherwise? Just questions popping up in my mind when I read this discussion.jawa
October 23, 2018
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Antonin: My point, quoted by PeterA: “finding the simple solution will not get you any nearer to any of the complex solutions. Having a randomly assembled basic hourglass is no pathway to a clock, in an unguided system, as anyone should easily understand.” is well explained in my mental experiment of the thief and the safes, which is summed up in my comment #65 in the Defending Intelligent Design Theory thread: https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/#comment-656385 The simple solution for the thief is to find by a few attempts the simple keys to each of the 150 small safes. Each time he opens one of them, he gets 1/150 of the whole sum (so, each simple solution found gives a fitness advantage). In a short time, he will open the 150 small keys. The thief could well try to open the big safe, which has a 150 digit key, to get the whole sum immediately. But finding the 150 digit key by repeated attempts is simply empirically not possible. The important points are: a) The sum of 150 individual simpler functions is completely different from one complex function b) Finding one of the simpler functions, or even all of them, is no help at all to finding the complex function. I think this mental experiment is simple and clear.gpuccio
October 23, 2018
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these statements: "the existence of digital clocks does not make the existence of a classic watch any more likely as the result of unguided forces." "finding the simple solution will not get you any nearer to any of the complex solutions. Having a randomly assembled basic hourglass is no pathway to a clock, in an unguided system, as anyone should easily understand." are obviously true... why does it take so much sweating for some folks to get it? really mysterious.PeterA
October 22, 2018
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Can this argument be settled once for all?PeterA
October 22, 2018
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Antonin: OK, your answer is simple and clear. So, I suppose that we infer design for the watch because it is complex enough. Being a human product is not necessarily a requisite. If we found on a distant planet an object that clearly works like a watch, even if a little different in the general build, we would still infer that it is designed, because it is complex enough. Few would doubt that, and I hope you are not among those few. But then, we are considering the complexity of the object big enough to infer design. And yet, we know that there are many alternative solutions to measure time, many of them implemented by humans, others certainly possible. So, let's reflect a moment. We cannot really compute with absolute precision the functional complexity of the object because, even if we can compute it for the object we are observing (with a difficult, but perfectly possible in principle, computation of the analogic target space and of the analogic search space), still someone could object that we should know the target space of all possible unrelated alternatives, and add it to the target space of our watch. And that is technically true. And yet, we are ready to make the design inference. How is that? The reason is simple enough. We know quite well that adding to the target space of our watch the possible target spaces of digital watches, and of other alternatives, would not significantly change the computation of our functional complexity. Why? Because the functional complexity of the watch is big enough to ensure that even a very big number of possible complex solutions, if added, would not change the result in any empirically relevant way. So, the existence of digital clocks does not make the existence of a classic watch any more likely as the result of unguided forces. But what about simple solutions? We can imagine, for example, that some very basic form of hourglass could be simple enough that it could be found as a non designed object, maybe in the desert, shaped by lucky natural forces, like the wind and rain acting on rocks. I don't think that is likely, but let's assume it as a possibility. So, of course if we add this simple solution to our target space, the whole target space of course comes into the range of what an unguided system can do. But in that case, what do you expect you will find in your desert? The basic hourglass or the watch? The answer is simple enough. You give it. IOWs, if I have a target space that is made as follows: 0.9999999999999999999999999 of it corresponds to one simple solution 1E-25 of it corresponds to 100 complex solutions what do you think you can reasonably observe? The simple solution or one of the 100 complex solutions? And the important point is: finding the simple solution will not get you any nearer to any of the complex solutions. Having a randomly assembled basic hourglass is no pathway to a clock, in an unguided system, as anyone should easily understand. So, if these things are true, how is it that people forget them as soon as we speak of biological objects? Because indeed there is no difference. There is absolutely no evidence, none at all, that functional complexity is different in biological objects. The existence of many possible unrelated complex solutions is no more relevant for complex biological objects than it is for watches. And there is no rationale at all and no evidence at all that supports the weird idea that simple solutions are pathways to complex solutions in the biological world. None at all. And yet, those weird ideas are believed as dogmas by most people, and offered as absolute truth in the scientific literature.gpuccio
October 22, 2018
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Glad to see this interesting discussion between gpuccio and Antonin. Thanks guys!jawa
October 22, 2018
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Would you argue that a watch is not designed only because there are certainly many possible different ways to build a tool that measures time?
No. Humans have indeed devised many ways to measure time, observational, mechanical, electronic.
A simple answer, please.
Questions are easy to ask but often hard to answer, especially simply! :)Antonin
October 22, 2018
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Antonin: regarding your old objection that there are alternative solutions, and therefore sequence and function are two different things (and I agree with both statements), let's keep it simple. Just answer this question: Would you argue that a watch is not designed only because there are certainly many possible different ways to build a tool that measures time? A simple answer, please.gpuccio
October 22, 2018
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Antonin: In brief, just to give you a clue, Joe Felsestein's biggest mistake is that he seems to believe that complex functional information can originate in the genome as the sum of many simpler events, even in different parts of the genome, that give some fitness advantage. That is completely wrong, as I have tried to explain with my example of the thief and the safes. I am not aware that he has ever addressed that point.gpuccio
October 22, 2018
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Antonin: Yes, I have addressed Joe Felsestein's criticism, as far as I have been aware of it. I cannot go on following TSZ forever. Yes, the link you give at #243 is correct. From #394 on I am addressing Joe Felsestein specifically. But I had already done that previously. For example, look at my comment #65 in the thread you linked, and you will see that I am quoting many previous answers to Joe Felsestein from a previous thread in my Ubiquitin OP. I would like to specially recommend that you consider my example of the thief and the safe, because it expresses well a key point about functional complexity that, IMO, Joe Felsestein has never answered. That said, Joe Felsestein is certainly an intelligent and competent interlocutor, but sometimes the discussion with him stops because he seems not to really answer the important points. Also, he does not enter, usually, into the molecular biology details, because that's not his expertize. He is however one of the best at TSZ.gpuccio
October 22, 2018
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I guess this is the parallel thread!Antonin
October 22, 2018
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There are genotypes (say DNA sequences) and we have a biological function that we have defined. If we know, quantitatively, how well a given genotype carries out that function, we can associate that number with the genotype.
I see Professor Felsenstein has already made a similar point to me, that function and sequence, while connected, are not the same thing.Antonin
October 22, 2018
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Just had some time to reread some comments upthread. Gpuccio refers to a parallel discussion taking place at TSZ - googling I find there is a site, The Skeptical Zone, where there have been long threads regarding gpuccio's ideas. There was one intriguing post by Joe Felsestein, who is a well-known professor of genetics which garnered nearly 2,000 comments. I suspect I will be reinventing the wheel when others have made such an effort to understand and criticise gpuccio's (can I call it an) hypothesis. It'll take a while to read and absorb Professor Felsenstein's critique. Has gpuccio addressed his points in a previous post or comment?Antonin
October 22, 2018
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PeterA (192), Here’s more on the same topic JVL raised in #181: On universal coding events in protein biogenesis  
The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by matching with the acceptor units of their cognate tRNAs (“operational RNA code”) and ribosomal codon-anticodon pairing of messenger RNA (“triplet code”). However, this codon-anticodon matching is possible only when protein translation machinery (translation factors, ribosome) accepts an esterified amino acid. This capacity (“charge code”) correlates mainly with the amino acid nature and the identity elements in the tRNA 3D structure. A fourth potential “folding code” (also referred as “stereochemical code”) between the translation dynamics, sequence composition and folding of the resulting protein can also be defined in the frame of the ‘Anfinsen dogma’ followed by post-translational modifications. All these coding events as well as the basic chemistry of life are deemed invariant across biological taxa due to the horizontal gene transfer (HGT) making the ‘universal genetic code’ the ‘lingua franca’ of life of earth.
 
Life is a process, which requires transmission, modification and interpretation of information. It is easy to assume that this information is simply encoded in genes, because there is a simple and universal set of rules how this information from the abstract form of four letters gets translated to the more complex 20(+2) letter set of the executive machinery, proteins. Though, as any process, translation occurs in time and requires its chemical implementation if the form of a complex molecular machinery, thus having several levels of control (or sub-coding). Moreover, this machinery has developed from a simpler to more sophisticated form in the course of evolution, thus it contains rudiments of an evolutionary development. As a result, there is a complex picture for how a gene would be accurately translated into an amino acid sequence, or how would amino acid land into a ready protein. Engineering of this process requires understanding of the; 1) Individual interacting components (discussed here as coding levels); 2) Driving forces behind them (e.g., HGT provides a source of innovations); 3) Interactions between them (e.g., correlation of the translation and protein folding velocities).; 4) Biological context (e.g., how the change in code can be fixed by different mechanisms like gain or loss of novel functions under specific selective pressures) The interacting components during the translation process are amino acids, aaRSs, tRNAs, translational factors, mRNAs and ribosomes, which are composed of dozens of proteins and ribosomal RNAs. In addition, folding features are encoded in mRNAs and primary amino acid sequences. The understanding of the interacting components in protein biogenesis along with its experimental engineering both will help us to articulate the chemical boundaries of life, i.e., how the chemical environment influences the size and contents of genetically encoded information.
 OLV
October 20, 2018
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PeterA (192), Here’s more on the same topic JVL raised in #181: Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm
Many biological systems are typically examined from the point of view of adaptation to certain conditions or requirements. One such system is the standard genetic code (SGC), which generally minimizes the cost of amino acid replacements resulting from mutations or mistranslations. However, no full consensus has been reached on the factors that caused the evolution of this feature. ...the optimality of SGC could be a by-product of other processes.
 
The standard genetic code (SGC) is one of the most intriguing products of evolution. Its origin and uniqueness remain mysterious, especially if we take into account the extremely large number of possible alternatives built from 61 codons encoding 20 amino acids and three stop translation codons. This figure is around 1.51?1084 [1], which substantially exceeds the number of hydrogen atoms in our observable universe.
 
...the SGC was not directly optimized to minimize the consequences of mutations and mistranslations and its optimization properties can be a by-product of other mechanisms.
On the efficiency of the genetic code after frameshift mutations  
Statistical and biochemical studies of the standard genetic code (SGC) have found evidence that the impact of mistranslations is minimized in a way that erroneous codes are either synonymous or code for an amino acid with similar polarity as the originally coded amino acid. It could be quantified that the SGC is optimized to protect this specific chemical property as good as possible. In recent work, it has been speculated that the multilevel optimization of the genetic code stands in the wider context of overlapping codes.
 
...the SGC is not only very efficient in minimizing the consequences of mistranslations, but rather optimized in amino acid polarity conservation for all three effects of code alteration, namely translational errors, point and frameshift mutations. In other words, our result demonstrates that the SGC appears to be much more than just “one in a million”.
 
...the SGC is most efficient in minimizing the effect of translational errors. It outperforms more than 99.99% of one million randomly generated codes.
 
the consequent next step will be to take a closer look at biological relevant data and compare how competitive the SGC will be on real data scenarios.
Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics  
Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved.
 
When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility
   OLV
October 19, 2018
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Long-term evolution on complex fitness landscapes when mutation is weak  
Understanding evolution on complex fitness landscapes is difficult both because of the large dimensionality of sequence space and the stochasticity inherent to population-genetic processes. Understanding evolutionary dynamics on general fitness landscapes remains an important project for theoretical population genetics
 
we still lack a general theory that would apply to finite polymorphic populations on complex fitness landscapes, making it difficult to address the types of questions we have considered here in that more realistic context.
 OLV
October 19, 2018
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Antonin: Please, take your time. There is no need to rush. :) And, of course, I do agree that the biological designer(s) was not human. Humans were not there, when design happened. I still believe that a cause must chronologically precede its effect. I just meant that, when you are observing a designed thing, and someone asks you: "What design takes place there?", you simply ask describing the design you are observing. That has nothing to do with the identity of the designer, the when, the how and the why. So, if you observe a house, you just answer: "The design here is the design of a house", whether it is a human house on our planet, or an alien house on some distant planet. That has nothing to do with "assuming the consequent".gpuccio
October 19, 2018
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