Refutation of a Statistical Argument Supporting Coevolution

David (and all)-In cruising for some statistical treatments I came across this gem that obliterates a statistical argument that made a claim I'm quite familiar with you making: "...indicating a (one-tailed) probability of P = 0.00015Â¶ that the organization of the canonical code could result from chance (3)"-http://www.pnas.org/content/97/25/13690.full-For the uninitiated, "Coevolution theory claims that the conserved pathways of amino acid biosynthesis in modern organisms (i.e., those found in all three domains of life) can be used to infer the historical precursor-product relationships between amino acids."-This paper demolishes this line of questioning, showing that chance can account for 23-64% of the amino acid combinations we see today. Of course, as the previous argument I made states that all we do for such statistical arguments is toss out the now offending component--we do not then substitute "chance" as the cause as many of us would like to do. But this paper is a perfect intro for a biochem person to show you how simply by changing assumptions, you can wildly vary a statistical argument. (And, they give you the method to calculate their values!) -You lost an important weapon, David!

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> http://www.pnas.org/content/97/25/13690.full
> 
> For the uninitiated, "Coevolution theory claims that the conserved pathways of amino acid biosynthesis in modern organisms (i.e., those found in all three domains of life) can be used to infer the historical precursor-product relationships between amino acids."
> 
> This paper demolishes this line of questioning, showing that chance can account for 23-64% of the amino acid combinations we see today. > 
> You lost an important weapon, David!-
No way! this article is investigating a previous theory. IT assumes some type of original DNA existed, how they don't say, and then that DNA was enlarged and modified. We still don't know how DNA started and the article itself is filled with presumptions and provisos: copied from the abstract and conclusions:-It has long been conjectured that the canonical genetic code evolved from a simpler primordial form that encoded fewer amino acids [e.g., Crick, F. H. C. (1968) J. Mol. Biol. 38, 367...379].-
A conservative correction for these errors reveals a surprisingly high 23% probability that apparent patterns within the code are caused purely by chance. Finally, even this figure rests on post hoc assumptions about primordial codon assignments, without which the probability rises to 62% that chance alone could explain the precursor-product pairings found within the code. Thus we conclude that coevolution theory cannot adequately explain the structure of the genetic code.-
It is also noteworthy that other patterns of biosynthetic relatedness have been reported within the code (e.g., refs. 40 and 41). Specifically, amino acids from the same biosynthetic pathway tend to be assigned to codons that begin with the same first base. Although the generality of this observation (lacking specific precursor/product pairs) removes problems with unrealistic pathways and lends strong statistical support (20), the pattern cannot be explained in terms of any known biological process. Furthermore, the lack of specific predictions about individual codon assignments appears to require the additional intervention of natural selection (for error minimization) to adequately explain the structure of the genetic code (10, 42). -With such considerations in mind, we word our conclusion with extreme care. Biochemical considerations and statistical reanalysis show that the product-precursor pairings at the heart of code coevolution theory are unreliable markers for a putative evolutionary process of code expansion. Subsequent analyses that used these pairings to predict the intermediate steps of code evolution, and to infer the evolutionary forces at work (27), are therefore speculative at best. It is plausible (if not probable) that the genetic code arose from a simpler form encoding fewer amino acids. However, it remains an open question whether any patterns of biosynthetic relatedness in the modern code can inform us of this process.

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David,-Specifically the article is refuting the p of .00015 (ish) that I know you've referenced before. THAT is the weapon it takes away from you. You can no longer use it. -I'm fully aware that the rest of the paper goes on to say that it doesn't disprove co-evolution (and neither did I). And yes, it makes assumptions, but the assumptions it makes are -1. Based on better evidence than was available when Co-evolution was accepted as theory, and -2. They explicitly state their assumptions. IN statistical arguments, you always have assumptions, you have to or you can't simplify the question to a statistical result. -In either case, my overall point is that we can't trust statistical arguments for systems we don't completely understand.

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David,
> 
> Specifically the article is refuting the p of .00015 (ish) that I know you've referenced before. THAT is the weapon it takes away from you. You can no longer use it. -I don't know where or when I used a p value of any magnitude
> 
> In either case, my overall point is that we can't trust statistical arguments for systems we don't completely understand.-But IF we understand, we can use them. Tell what is not understood.

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David,
> > 
> > Specifically the article is refuting the p of .00015 (ish) that I know you've referenced before. THAT is the weapon it takes away from you. You can no longer use it. 
> 
> I don't know where or when I used a p value of any magnitude-I remember a number that was 1.5 x 10 ^ -some number which is what made me think of this one. -> > 
> > In either case, my overall point is that we can't trust statistical arguments for systems we don't completely understand.
> 
> But IF we understand, we can use them. Tell what is not understood.-I've discussed this before--without a mechanism or a pathway leading from nonlife to life, we cannot begin to calculate a p for the process, because kinda like physics, we have a chemistry for organic and biochem, but the distinctions between them belie their specialized scope: organic is simply carbon molecules, and biochem is LIFE chemistry. We have a bridge to neither and even if we were designed, the designer had only these (missing) tools to work with. -The probabilities as I've seen them are based ONLY on what we know now, and the most important key to the puzzle--our Rosetta stone--is finding a path from nonlife to life. If we have an A, and a Z, but can only find A->G, with a bunch of stuff missing with a known W->Z, the best you can do is discuss the results at present, which is we're missing H->V. Adler is very fond of making these types of "snapshot" judgments (such as in Difference), but what I see you doing is making an early judgment. I'll discuss that in the more related thread...

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> > http://www.pnas.org/content/97/25/13690.full
> > 
> > For the uninitiated, "Coevolution theory claims that the conserved pathways of amino acid biosynthesis in modern organisms (i.e., those found in all three domains of life) can be used to infer the historical precursor-product relationships between amino acids."
> > 
> > This paper demolishes this line of questioning, showing that chance can account for 23-64% of the amino acid combinations we see today. > 
> > You lost an important weapon, David!
> 
> 
> No way! -Matt: You wil hate this fascinating article by materialist scientists, some really top of the line types. There is a long review discussion and at the end a computation that states probability odds for replication and translation development by chance are 10^-1018, and life requires an infinity of multiverses, certainly not the 10^500 predicted by string theory.-Eugene Koonin's article and commentaries:-
http://www.biology-direct.com/content/2/1/15

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Right off the bat, the paper starts discussing multiverses, a concept that at present is purely hypothesis itself. (And you would need to tell me which versions of String Theory--there are several!) -"In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse)."-This line from the hypothesis is similar to my previous claim that life was inevitable for our universe. So far, this seems like observing that the sun radiates light. I still need to dive into the meat of the paper. Which I promise to do first day of spring break (next saturday) and give a more detailed response.

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Ah hell, there's alot here. I'll break it up.-" There is, e.g., an infinite number of (macroscopically) exact copies of the earth with everything that exists on it, although the probability that a given observable region of the universe (hereinafter O-region) carries one of such copies is vanishingly tiny. This picture seems counterintuitive in the extreme but it is a direct consequence of eternal inflation, the dominant model of the evolution of the universe in modern cosmology [3-5]."-In other words, statistically, all permutations and combinations will eventually be tried, or possibly even have been tried already. -"Thus, although the model of eternal inflation cannot be considered proved,"-Means that the entire paper is raw speculation following from the assumption that "eternal inflation" correct. (They are specific about which kind, at least.)-"How such a system could evolve, is a puzzle that defeats conventional evolutionary thinking."-And the earth is round? Still waiting...-" The MWO model dramatically expands the interval on the axis of organizational complexity where the threshold can belong by making emergence of complexity attainable by chance (Fig. 1). In this framework, the possibility that the breakthrough stage for the onset of biological evolution was a high-complexity state, i.e., that the core of the coupled system of translation-replication emerged by chance, cannot be dismissed, however unlikely (i.e., extremely rare in the multiverse)."-Sounds like the writer is about to simply formally state what I had said myself last spring...-"Prior to the onset of biological evolution, there could be no function, just complexity, and the emergence of any level of complexity is guaranteed by the MWO model."-Yup. This paper up to this point is basically saying that the many-universes scenario guarantees that life will be created by chance in at least one of the universes in consideration. -What this paper says, is that (knowing what we know now) chance only has an automatic win if an MWO scenario is correct. -I don't hate this article at all, it simply verifies what I said back when I first came to this thread. There is no evidence of MWO, and we lack a method of abiogenesis--so therefore the question is far from solved. IF MWO is somehow proved it simply means that irreducible complexity is an invalid argument. A good paper, but very, very, very, speculative.

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> I don't hate this article at all, it simply verifies what I said back when I first came to this thread. There is no evidence of MWO, and we lack a method of abiogenesis--so therefore the question is far from solved. IF MWO is somehow proved it simply means that irreducible complexity is an invalid argument. A good paper, but very, very, very, speculative.-Agreed. Did you want to comment about the calculation in the commentaries? That replication and translation mechanisms are unlikely to the extent of 10^-1080. I'm back to my chance odds. It is in the final comment.

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Refutation of a Statistical Argument Supporting Coevolution (Origins)