Are Stereochemical Explanations Causally Sufficient?
by BradfordArthur Hunt posted Signature in the Cell? at his blog The RNA Underworld. Art attempts to refute Meyer by citing a paper (RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol; 69:406–429) authored by Michael Yarus, Jeremy Joseph Widmann and Rob Knight. As Art explains:
Put more plainly, 75% of tested amino acids associate with their anticodon (in some cases, along with their codon) in these studies. This is remarkable, as it is demonstrative of an underlying stereochemical basis for at least some of the genetic code.
Art then proceeds to make a speculative argument based on the study:
Thus, we can discern that the genetic code as we understand it today likely evolved in several steps – a stereochemical era wherein a core set of triplet-amino acid correspondences was first established, followed by subsequent expansion of the assignments of other triplets and recruitment of other amino acids (typified by gutamine and leucine) via other mechanisms.
Let's look at this closely before proceeding. Blogs are not textbooks so we do not expect Art to supply a detailed account of actual protein synthesis but to give you some idea, refresh memories or simply put you on notice that a short one paragraph argument needs some context I'll provide links. First this:
The assembly of biological molecules, including proteins and nucleic acids, requires the generation of appropriate starting materials. We have already considered the assembly of carbohydrates in regard to the Calvin cycle and the pentose phosphate pathway (Chapter 20). The present chapter and the next two examine the assembly of the other important building blocks—namely, amino acids, nucleotides, and lipids.
The availability of appropriate starting materials is a huge point. Protein synthesis depends on the capacity of cells to synthesize basic required biochemicals and make them available as needed. That in turn presumes a cellular state known as homeostasis i.e. a capacity to generate conditions that are hospitable to the realization of cellular functions. Don't presume that such conditions persist in the extra-cellular world of prebiotic earth. If you do so make that assumption clear.
We see Art outline a series of steps describing an evolutionary process: "a core set of triplet-amino acid correspondences was first established." This set will include a variety of amino acids, nucleotides and, at some point, distinct forms of specified RNA. "Recruitment of other amino acids (typified by gutamine and leucine) via other mechanisms" follows. How did these other mechanisms come about and what do the look like? They no doubt evolved but how?
If Art and others wish to dismiss Signature in the Cell with remarks like this:
First, it is true that Yarus’ ideas, and the underlying experiments, are far from a direct and complete demonstration of the origination of the complete RNA decoding system that we see in modern cells. However, the body of work discussed by Yarus et al. constitutes a significant and compelling set of positive experimental support for the hypothesis that the genetic code has an underlying chemical basis. As such, it far outstrips the entire body of positive experimental support (there is none) for Meyer’s claim that there can be no way to explain the genetic code (the Signature in the Cell) in terms of chemistry and physics.
You need to consider the nature of the "significant and compelling set of positive experimental support" and decide for yourselves if it meets this descriptive level.
The level of support necessary is that level needed to establish a viable physical process culminating in a self-replicating cell. More details on biosynthesis follow although it is by no means a comprehensive view of what takes place during protein synthesis. Continuing with the linked source:
In amino acid production, we encounter an important problem in biosynthesis—namely, stereochemical control. Because all amino acids except glycine are chiral, biosynthetic pathways must generate the correct isomer with high fidelity. In each of the 19 pathways for the generation of chiral amino acids, the stereochemistry at the α-carbon atom is established by a transamination reaction that involves pyridoxal phosphate. Almost all the transaminases that catalyze these reactions descend from a common ancestor, illustrating once again that effective solutions to biochemical problems are retained throughout evolution (Figure 24.1).
Don't confuse stereochemical bonding explanations with stereochemical control. The latter entails timely regulatory functions. At this point the precursor cell objection is raised. Bradford, don't you know that protocells were far less complex and did not initially contain these modern cellular features? They subsequently evolved. Fine. Take that as an article of prebiotic faith if you wish but don't confuse it with solid empirical support of the same.
Biosynthetic pathways are often highly regulated such that building blocks are synthesized only when supplies are low. Very often, a high concentration of the final product of a pathway inhibits the activity of enzymes that function early in the pathway. Often present are allosteric enzymes capable of sensing and responding to concentrations of regulatory species. These enzymes are similar in functional properties to aspartate transcarbamylase and its regulators (Section 10.1). Feedback and allosteric mechanisms ensure that all twenty amino acids are maintained in sufficient amounts for protein synthesis and other processes.
Was mention made of enzymes? If anticipated reactions are to proceed we can expect explanations as to how they were catalyzed and where catalytic agents came from. There have been related studies on this and in the comment section you will likely see links to such studies. Bear in mind the conditions required in separate studies and whether complementary outcomes come with mutually exclusive conditions.
In addition to pointing out enormous holes in the much touted positive experimental support, it behooves us to look at a more serious theoretical flaw. A plausible evolutionary process offers a model of a replicating system. Something we can analyze and visualize. More importantly it suggests reasons for supposing that extra-cellular reactions in a prebiotic soup would favor, not only nucleic acids and amino acids of sufficient amount and variety- unencumbered by competing organic chemicals. It requires a natural selection basis consistent with the conditions of that prebiotic world. Significant support? No way.
In his blog piece Art quotes Meyer:
“Polyani argued that, in the case of communications systems, the laws of physics and chemistry do not determine the arrangements of the characters that convey information. The laws of acoustics and the properties of air do not determine which sounds are conveyed by speakers of natural languages. Neither do the chemical properties of ink determine the arrangements of letters on a printed page. Instead, the laws of physics and chemistry allow a vast array of possible sequences of sounds characters, or symbols in any code or language. Which sequence of characters is used to convey a message is not determined by physical law, but by the choice of users of the communications systems in accord with the established conventions of vocabulary and grammar – just as engineers determine the arrangement of the parts of machines in accord with the principles of engineering.
Thus, Polyani concluded, communications systems defy reduction to physics and chemistry for much the same reasons that machines do. Then he took a step that made his work directly relevant to the DNA enigma: he insisted that living things defy reduction to the laws of physics and chemistry because they contain a system of communications – in particular, the DNA molecule and the whole gene-expression system. Polyani argued that, as with other systems of communication, the lower-level laws of physics and chemistry cannot explain the higher-level properties of DNA. DNA base sequencing cannot be explained by lower-level chemical laws or properties any more than the information in a newspaper headline can be explained by the chemical properties of ink.16 Nor can the conventions of the genetic code that determine the assignments between nucleotide triplets and amino acids during translation be explained in this manner. Instead, the genetic code functions as a higher-level constraint distinct from the laws of physics and chemistry, much like a grammatical convention in a human language.”
Art then adds his comment on this:
In other words, Meyer is claiming that the genetic code is arbitrary, that there are no chemical or physical underpinnings to the codon-amino acid correspondence that we see in life. It is because the code is arbitrary, Meyer implies that it must be designed:
I think Art mischaracterizes Meyer's point which is not arbitrariness but rather one of causal adequacy. Meyer had argued that the origin of specified complexity or functionally specified information in DNA must be explained. He also made the point about ink on paper to emphasize that chemical affinity is not the same as a causally adequate chemical pathway to coded systems. Let's stipulate that stereochemical properties describe tRNA. Yes, and…
January 8th, 2010 at 11:27 am
Hi Bradford,
This is just a quick initial reply to one particular point you brought up:
I would suggest more extensive reading on your part before we discuss your post much further. The reason is, you ask questions above that are already either clearly addressed in the paper Art cited, or in its references. Starting by rereading Yarus's 2009 paper cited by Art. Figure 7 outlines the basic model being proposed. The authors comment:
So enzymes are not needed– the catalytic activity required is well within the the chemistry of small RNAs. This was explored in the 2001 paper cited::
Yarus M (2001). On translation by RNAs alone. Cold Spring Harb Symp Quant Biol 66: 207–215
Unfortunately, this paper is not available online, as far as I'm aware. However, an extensive, detailed review encompassing much of how Yarus's group sees the origin of the genetic code can be found here (the 2009 paper elaborates on and summarizes results that further support the ideas in this paper):
Yarus M, JG Caporaso & R Knight (2005). Origins of the genetic code: The Escaped Triplet Theory. Ann. Rev. Biochem. 74: 179-198.
http://arjournals.annualreview...
Comment by KC — January 8, 2010 @ 11:27 am
January 8th, 2010 at 11:44 am
I'm sorry. As I noted in my essay, Meyer hisself stated (on (pp240-1):
Remember, "the information in DNA" = the triplet-amino acid correspondence. (That's Meyer's whole point in drawing upon Polyani.)
Comment by Arthur Hunt — January 8, 2010 @ 11:44 am
January 8th, 2010 at 12:19 pm
The catalytic activity would be supplied by small RNA- that's the belief. The question alluded to in the OP as a theoretical weakness remains unaddressed. What plausible evidence is there for a prebiotic soup giving rise to tRNA, small catalytic RNA and amino acids in a mixture free of other inhibiting organic chemicals? You are suggesting that small RNA would assume the function performed by protein amino acyl synthetases and if we presume all the foregoing what leads you to think this mixture would evolve to produce a cell? IOW what is the natural selection criteria enabling you to predict this with any reasonable certainty?
Comment by Bradford — January 8, 2010 @ 12:19 pm
January 8th, 2010 at 12:33 pm
Adding to the previous comment- Meyer pointed out that enzymes, be they proteins or RNA, are laden with sequence specificity matching function. The sequential fidelity is found in DNA and maintained by mechanisms allowing its transcription. Is the specificity found in a putative RNA world scenario a free lunch outcome i.e one attributable to chance events or is there something more plausible?
Comment by Bradford — January 8, 2010 @ 12:33 pm
January 8th, 2010 at 12:40 pm
Accurately coded for what prebiotic function?
Comment by Bradford — January 8, 2010 @ 12:40 pm
January 8th, 2010 at 12:53 pm
Plausibly selected by intelligent agency with a view of cellular outcomes. What is the plausibility of nature selecting an encoding outcome in an extra-cellular environment?
The assertions of Art and others based on this study are stronger than "can evolve." The question hanging over all this is what is plausible about the belief that initial conditions described arise and if they did why should we expect an evolutionary process in the direction of a cell?
Comment by Bradford — January 8, 2010 @ 12:53 pm
January 8th, 2010 at 1:13 pm
Bradford, you are taking one study on one specific point, and criticizing it for not answering all questions everywhere about every aspect of the origin of life.
Furthermore, you are making a bunch of poor assumptions:
* You are assuming there would need to be cells and membranes at this stage, but the actual model under discussion is about how self-replicating RNAs could start to bind amino acids
* You are assuming that you need 20 amino acids maintained in some nice equilibrium, but all the model is about is about RNA binding the first few amino acids that were used in the code
* You are assuming that the product of RNA grabbing amino acids had to immediately be fully modern, fully chiral proteins, but in fact the earliest function of RNA grabbing amino acids was probably very short amino acid chains, perhaps with no "function" beyond something simple like being hydrophobic. Under such a situation sequence specificity doesn't matter much, chirality doesn't matter such, all of that could evolve later.
Art's point was that Meyer was wrong about one specific point:
Sentence #2 of that passage from Meyer is wrong, as shown by the Yarus paper. That's Art's point. A slightly broader point is that that crack in Meyer's argument actually is a crack that gives us some hints about how the RNA world could have started to become the RNA+protein world.
It's fine, I guess, if you want to insist that miracle is a better explanation for the origin of life until every last detail about a natural origin is understood. It's a free country. But don't pretend that you have a scientific position. Science is about advancing understanding by testing hypotheses. Hypotheses can be confirmed, and general theories can be considered successful and productive and probably on the right track (e.g. the RNA world) long before every last nuance is understood. In fact, in any complex science that is probably the way things will always be. This realistic and practical philosophy of science is another thing that Meyer doesn't get at all.
Comment by nickmatzke — January 8, 2010 @ 1:13 pm
January 8th, 2010 at 1:51 pm
Nick Matzke:
Which brings up the issue of plausibility for an evolutionary process taking off from this point.
But what reason would we have to suspect that this leads anywhere? Maintenance is pertinent to the issue of a robust process.
Nick, how do you presume an evolutionary process in the absence of sequence specificity? That is required even in the initial stages of a process.
Nick: Sentence #2 of that passage from Meyer is wrong, as shown by the Yarus paper. That's Art's point. A slightly broader point is that that crack in Meyer's argument actually is a crack that gives us some hints about how the RNA world could have started to become the RNA+protein world.
Chemical affinity between nucleotide triplets and amino acids is a prerequisite to but not an explanation for mapping between encoding nucleic acids and encoded end products. The missing piece of Art's argument is the input of genetic information in a process. That requires functional specificity. Art is citing Yarus et al as an answer to Meyer's assignment point but Yarus answers an antecedent question about physical compatibility. Assignment ultimately comes down to proper sequencing to match function. That's an information issue.
Comment by Bradford — January 8, 2010 @ 1:51 pm
January 8th, 2010 at 2:11 pm
Arthur Hunt quoting Meyer:
Art, Yarus has not demonstrated where DNA information originates. It suggests initiation of a process which culminates in a biological coding system based on the plausibility that a stereochemical explanation explains the presence of physical pieces in a translation process. That does not account for the functional specificity encoded in a nucleic acid. To account for that an explanation for the evolution of biological function is needed. There is an inability to see the forest from the trees here.
BTW, your comments are automatically routed to a spam queue from which I must retrieve them. To do that I must continually monitor the spam. Not my idea but I am not sure how to fix this. Bottom line- I'm not intentionally delaying your comments.
Comment by Bradford — January 8, 2010 @ 2:11 pm
January 8th, 2010 at 3:28 pm
Hi everybody,
I read Art's piece at his blog. I think there is some confusion about Meyer's argument. Of course, there is the question of the origin of the genetic code. But then there is the question of once we have the code, how is it that codons are arranged in the proper sequence, so that amino acids will be in the proper sequence in order to become functioning proteins. It is this second problem that Meyer considers to be specified information and spends most of his time discussing.
So even if the origin of codons can be explained stereochemically, it still doesn't answer Meyer's central question of specified information in DNA. This doesn't mean that there isn't a non-design answer. Just that it is a separate question that the origin of the code doesn't explain.
I appreciate Art's comment at the end of his post, pointing out that stereochemical affinity between amino acids and their codons does not necessarily rule out a design explanation.
Comment by Bilbo — January 8, 2010 @ 3:28 pm
January 8th, 2010 at 5:21 pm
Meyer quotes Polanyi. So first, figure out who is saying what.
None of the material quoted in this thread actually written by Meyer seems to be talking about the genetic code itself.
Art:
Remember, "the information in DNA" IS NOT EQUAL TO the triplet-amino acid correspondence.
The code is just that, a code. A convention for the transmission of information.
If someone takes the information written in English on a piece of paper and converts it into morse code, and transmits that code over the airwaves, the morse code is received and translated into a different language, say Chinese, and again written down.
In what sense does the origin of the Morse code suffice as an explanation for either the English or the Chinese text?
Comment by Mung — January 8, 2010 @ 5:21 pm
January 8th, 2010 at 5:50 pm
That is one of Meyer's points, but his other point is that there is (allegedly) no intrinsic physical, stereochemical reason for the binding of a particular codon to a particular amino acid. This second point of Meyer's is wrong.
This thread is about stereochemistry and Art/Yarus/Meyer on codon-amino acid relationships. If you want to talk about the generic origin of "information" in DNA, start a thread about that, and please provide a definition of information specific enough so that we know what would count as an increase in information. I couldn't find such in Meyer's book, but maybe I missed it…
Comment by nickmatzke — January 8, 2010 @ 5:50 pm
January 8th, 2010 at 5:52 pm
Art Hunt:
I keep hearing critics say that this is Meyer's claim, yet no one has ever actually quoted Meyer as saying this.
Anybody got the quote?
Comment by chunkdz — January 8, 2010 @ 5:52 pm
January 8th, 2010 at 6:11 pm
Nick Matzke:
This interpretation is hard to credit. The very fact that we observe bonding between different basic biochemicals within cells infers a physical basis that makes this end result possible. Stereochemical properties may allow for codons and amino acids to bind in specifiable patterns but this fact alone is causally inadequate to account for the binding we observe within the system enabling gene expression. A particular size screw may fit the screwdriver used to screw it in. But that would not explain it being screwed in. The fixing of the screw is the end result of intelligent guidance coupled with the use of the appropriate enabling tools.
You and others are pointing to Meyer's contention that there is no basis in physics and chemistry alone sufficient to generate the outcome of a genetic code as refuted by stereochemical explanations grounded in Yarus and other studies. But what these studies do is point out that the right size screw and screwdriver have been identified. They do not explain the specificity of the screw fastening the functional mechanism in precisely the location required to effect the observed outcome.
Comment by Bradford — January 8, 2010 @ 6:11 pm
January 8th, 2010 at 6:44 pm
Art correctly quoted Meyer stating the following on pages 240-241:
Art then cites studies showing stereochemical reasons detailing the affinity existing between some amino acids and their anticodons. But this is not precisely Meyer's point. Note that Meyer alludes to functional base sequences and whether chemical forces dictated only biologically functional ones and no others. But of course chemistry dictates no such thing. The sequential order of base pairs has nothing to do chemical preferences but everything to do with conferring function to the translated end product. Meyer's critics are shooting at teddy bears and thinking they nailed a Grizzly.
Comment by Bradford — January 8, 2010 @ 6:44 pm
January 8th, 2010 at 6:55 pm
I wouldn't call the genetic code a teddy bear, but it does seem to be a secondary theme for Meyer. One can challenge him on the meaning of specified information, and we can debate how probable functional proteins are…again.
To me, a more interesting question would be asking if a stereochemical code makes more sense from a non-design or a design perspective.
Comment by Bilbo — January 8, 2010 @ 6:55 pm
January 8th, 2010 at 7:00 pm
I don't see how Art's quote of Meyer agrees with Art's, Matzke's, and Falk's characterization of Meyer. Meyer clearly is expressing doubt of a positive, not certainty of a negative.
Comment by chunkdz — January 8, 2010 @ 7:00 pm
January 8th, 2010 at 7:10 pm
Dudes,
Read Art's quote of Meyer again. Pay attention to the bolded bit this time:
This quote is from p. 240 of Meyer.
Re-reading Art's post, I guess I can see that some of his other Meyer quotes deal with the generic question of where the information in the DNA base-pair sequence — of e.g. genes — comes from. I would agree that Yarus by itself doesn't refute those statements. But it is also clear that Art was mostly talking about *the genetic code* (meaning the codon-amino acid correspondence, not the DNA sequence). As Art summarized Meyer:
The Yarus paper demonstrates that various RNAs selected (in in vitro selection experiments, starting from random sequences) to bind amino acids very often end up having the anticodons/codons that are currently observed in biology. Thus the genetic code is not completely arbitrary, rather there is decent evidence that some of it was initially determined by intrinsic chemical attraction between certain short sequences (codons/anticodons) and certain amino acids.
Also — although it is true that the Yarus paper does not directly address the general question of where functional sequence ("information") in general comes from, it *does* address the specific question of where the "information" came from in the specific case of RNA sequences that bind amino acids. Namely, the information was produced by selection of those sequences with an intrinsic physical attraction to the amino acid in question.
(The implications of this are actually pretty big, since pretty much all "function" at the molecular level is about binding affinity, and if mutation/selection can in general find the sequences with improved functional binding affinity, then Meyer's question about where functional sequence "information" comes from is basically answered, ID is sunk, those who didn't think of this perfectly obvious and well-known explanation before critics pointed it out look pretty silly, etc.)
Comment by nickmatzke — January 8, 2010 @ 7:10 pm
January 8th, 2010 at 7:14 pm
I don't think so. From Ch 11 (IIRC):
It is precisely Meyer's point.
Everyone here is alluding to a separate argument Meyer makes – that protein functionality cannot be produced without intelligence. Meyer relies extensively on Axe to support his case, but, as readers of my blog and PT know, Axe's work does no such thing. This fact, as well as a wealth of other experimental work, refutes this other of Meyer's point in no uncertain terms.
But, as Nick says, that's for another discussion. I'm not seeing anything here that tells me that I have gotten Meyer wrong, or that my point is not a good one.
Comment by Arthur Hunt — January 8, 2010 @ 7:14 pm
January 8th, 2010 at 8:56 pm
If we strip away all the scientific mumbo-jumbo, isn't this argument really about whether or not God created life? The positions set forth here reflect the underlying beliefs of the posters; with the believers supporting that view, the atheists rejecting it, and the agnostics undecided.
I predict that the discussion will continue in this vein until all the parties tire of it. Nothing will ever be resolved. This is why it's silly for believers to try to argue materialist science. Why not rather acknowledge that ID IS all about God and get about the business of learning all we can about Him from His creation?
Just a thought.
Comment by Daniel Smith — January 8, 2010 @ 8:56 pm
January 8th, 2010 at 9:07 pm
Hi Nick Meyer's argument depends depends upon contingency primarily between order of nucleotides binding and secondarily in the genetic code. But even if there is no contingency in the genetic code, this doesn't affect the question of contingency between nucleotide binding. Nor does this affect the question of selection for protein binding. There is already chemical necessity between amino acids and their codons due to the aminoacyl-tRNA synthetases.
Comment by Bilbo — January 8, 2010 @ 9:07 pm
January 8th, 2010 at 9:17 pm
I am starting to wonder why this blog is called Telic Thoughts, since there seems not much thinking in the posts. A nice piece of research is critiqued because it doesn't answer all questions. What alternative is offered? An intelligent agent did it. No details. No definitions of this agent. No predictions.
Comment by IrynaB — January 8, 2010 @ 9:17 pm
January 8th, 2010 at 9:47 pm
IrynaB:
There is not much thought in that comment. The research was put into its proper perspective. The possibility of an intelligent source is indicated by the nature of DNA. Sorry if that offends you.
Comment by Bradford — January 8, 2010 @ 9:47 pm
January 8th, 2010 at 9:54 pm
Nick:
The absurdity of this is easily demonstrated by a sequence of a dozen amino acids in a protein binding site coded for by a corresponding sequence of codons. The sequential order of translation is essential to function. Scramble the order and you no longer find a functional binding site even as the identity and amount of amino acids remain the same. The chemical bonding attractions have not changed. Their expression order has and that is the difference between function and junk.
Comment by Bradford — January 8, 2010 @ 9:54 pm
January 9th, 2010 at 1:27 am
nick:
Dude. That's Art quoting Meyer quoting Polanyi. Pay attention to the quotes.
We're asking where Meyer makes a claim regarding the genetic code. It's clear from the following quote that he made no such claim wrt the genetic code.
nick:
Art's constructed a fine straw man. Can we deal with Meyer's actual argument? Hint: It has nothing to do with the genetic code per se. This is why you're seeing this resistance to Art's "argument." Because it has nothing to do with what Meyer actually argues.
We want a quote or cite of Meyer where it is Meyer saying something specific about the genetic code, and more importantly, where he says something relevant to Art's supposed refutation.
Comment by Mung — January 9, 2010 @ 1:27 am
January 9th, 2010 at 1:31 am
This does bring up an interesting question. Is there any "information content" to the genetic code itself?
If not, why would such a thing ever evolve?
Comment by Mung — January 9, 2010 @ 1:31 am
January 9th, 2010 at 1:46 am
Art:
No, Art, wer'e not. What we are doing is pointing out that what you have provided is something written by Polanyi, not something written by Meyer, but only quoted by him.
And then, when Meyer does write about what he took from Polanyi's quote, he doesn't say anything about the genetic code, it's all about the base sequences in DNA.
Art:
Exactly. Nothing at all whatsoever about the genetic code. And you agree with Meyer:
But then you go on to argue that, there are chemical preferences, and cite a paper about the genetic code. But clearly, that's irrelevant to Meyer's actual argument.
Perhaps you should have your posts peer reviewed before you stick them on the web.
Comment by Mung — January 9, 2010 @ 1:46 am
January 9th, 2010 at 1:51 am
Mung:
You nailed it.
I agree. Meyer's actual arguments are only tangentially touched on by the Yarus paper. Yarus therefore does not refute Meyer.
Comment by Bradford — January 9, 2010 @ 1:51 am
January 9th, 2010 at 1:55 am
The code maps codon sequences to specific amino acids or stop messages. It's a convention enabling the storage and expression of genetic information.
I see no reason to suppose it would based on what we know about nature. An a priori philosophical commitment drives the chemical evolution belief.
Comment by Bradford — January 9, 2010 @ 1:55 am
January 9th, 2010 at 1:56 am
IrynaB:
Wow. Just, wow.
Here we have all sorts of people from both sides of the debate (those why deny that thoughts are telic and those who affirm that thoughts are telic) arguing about whether sufficient thought has been put into the making of an argument for or against the purpose of the argument being put forth, and someone questions why the blog is called Telic Thoughts.
I'm stunned.
ok, so it's a nice piece of research. It's irrelevant to Meyer's claim. But it takes thought to identify why and purpose to post that on a blog.
Doh!
Comment by Mung — January 9, 2010 @ 1:56 am
January 9th, 2010 at 5:32 am
Bradford quotes me:
Arrgh!!!! This shouldn't be so hard to understand! In this passage, I am talking about the information involved in an RNA sequence binding to a single, free-floating amino acid — e.g. what a tRNA does. We are talking about how things like tRNAs (which determine the genetic code, i.e. what each of the 64 codons code for) originated, *not* about the origin of *specific sequences* of amino acids. There is no point in continuing this discussion unless you can get these two things separate in your head, Bradford!
Mung claims about Art:
Wrong. We have quoted the following passage from Meyer again and again in this thread:
It's right there, Meyers says the words "genetic code" and talks about the codon-amino acid correspondence, and asserts (wrongly, as Art/Yarus show) that stereochemistry can't explain it.
Comment by nickmatzke — January 9, 2010 @ 5:32 am
January 9th, 2010 at 10:48 am
Mung:
I realize that my essay may have been a bit confusing on this, but as Nick has stated, the money quotes in my essay and in this thread about the genetic code were Meyer's own words. (It shouldn't be that hard to actually pick the book up and check it out yourselves …)
Bilbo said (somewhere up there …):
10^150 quatloos for Bilbo for reading the whole essay. Thanks.
I'll make the point here – even in an ID framework, Meyer is wrong. Yarus' work argues that, whenever the point of intelligent intervention, it wasn't when the triplet-amino acid assignments were made.
Somewhere else up there, Bilbo noted:
Yarus' work explains the genesis of this chemical necessity. As such, it helps to frame (by providing one end of the pathway) a whole lot of new and interesting hypotheses.
Comment by Arthur Hunt — January 9, 2010 @ 10:48 am
January 9th, 2010 at 12:23 pm
Art notes:
Since aminoacyl-tRNA synthetases are proteins, that necessity suffers from the chicken-and-egg problem when trying to explain the origin of translation. However, Yarus, in his 2001 paper shows that there are self-aminoactylating RNAs which perform the same function, and in fact, do it more efficiently than the proteins. Thus, in an RNA world, there is not necessarily a chicken-and-egg problem.
Comment by KC — January 9, 2010 @ 12:23 pm
January 9th, 2010 at 1:04 pm
The question of the origin of genetic information, which begins with the assignment of codons to specific tRNAs and amino acids— the very functional specificity of translation itself—is not irrelevant to Meyer’s argument. Without that specific, functional association, proteins cannot be translated from a DNA or RNA template. So, if Meyer is concerned with it, then he has to consider Yarus’s work—at the very least by rebutting it. If he is not concerned, then his book has started off by ignoring the essential first question: how that informational association began.
Comment by KC — January 9, 2010 @ 1:04 pm
January 9th, 2010 at 1:34 pm
Nick Matzke:
Nick, tRNAs do not determine the code. They are physical elements connected with the translation of it. You may not be talking about the origin of specific sequences of amino acids but Meyer is and this OP is about Meyer, not you. Can you get that in your head?
Comment by Bradford — January 9, 2010 @ 1:34 pm
January 9th, 2010 at 1:40 pm
Art:
Yarus explains chemical affinity much the same as a chemist could who wishes to explain why ink adheres to paper. The issues Meyer is focused on are much more substantial than this. He is seeking a causal source for the sequence specificity found in nucleic acids and proteins. That is not explained by Yarus.
Comment by Bradford — January 9, 2010 @ 1:40 pm
January 9th, 2010 at 1:43 pm
This back-and-forth reminds me of this great joke with the punchline No, no, no. You go get your own dirt!
Nick, it's a pointless exercise. Every missing link creates two new gaps, dontcha know!
Comment by olegt — January 9, 2010 @ 1:43 pm
January 9th, 2010 at 1:46 pm
What about the 'purpose' or 'goal-directedness' of biological processes?
Can anyone deny that every biological process – every step in a metabolic cycle, every catalytic event – proceeds as if directed towards the achievement of an end; a purpose, a goal. This cannot be denied. The materialist/atheist attempts to explain every single instance by pointing to the goal of 'survival'. (But survival doesn't explain music, art, etc. – in fact there's an awful lot that survival doesn't explain).
The origin of DNA proceeded as if directed towards the goal of information storage, retrieval and dissemination. No matter whether it evolved by purely naturalistic means or if it was created intact, it cannot be disputed that the process cannot be explained apart from goal-directedness.
Comment by Daniel Smith — January 9, 2010 @ 1:46 pm
January 9th, 2010 at 1:57 pm
Awww how cute, the atheists reassure themselves that they got it right.
Comment by Jean — January 9, 2010 @ 1:57 pm
January 9th, 2010 at 1:59 pm
Daniel,
Aristotle was convinced that heavy objects fell down because it was their ultimate goal to be as close to the center of the Earth as possible. Did that perspective turn out to be useful for anything? Not much, I am afraid. It was ultimately replaced with Newtonian mechanics, which was not interested in teleological categories but instead dealt with observations on a quantitative level.
You can argue till you are blue in the face whether or not a rock has the center of the Earth as its goal, but ultimately that question is (a) unresolvable and (b) inconsequential.
Comment by olegt — January 9, 2010 @ 1:59 pm
January 9th, 2010 at 2:06 pm
Meyer's argument is on another level and cannot be refuted or confirmed by the hypothesis investigated by Yarus.
You need not rebut a concept that does not refute your position.
Again and again throughout the book Meyer emphasizes the search for a causally adequate explanation for functional specificity. In the previous sentence I used two phrases taken directly from Meyer's book in an effort to stick as close as possible to what he is saying rather than erect straw men. The information association you allude to is not sufficient to answer the questions posed by Meyer. There is information conveyed in this comment. The arrangement of letters confers functional specificity much the same way that specific sequences of codons confers functional specificity to genes. A knowledgable computer technician could explain in detail the physical basis allowing for the appearance of the letters you see- analogous to Yarus explaining the chemical affinity involving amino acids and anti-codons. What neither the computer technician nor Yarus do is explain either the causal trail that led to the coding covention or the causal reason which distinguishes the very great specificity observed from a random arrangement of letters or codons. Since sequence specificity is at the heart of any causal explanation for coding conventions, separate explanations, distinct from causes related to the physical medium i.e. computer hardware or biochemical elements, must be forthcoming to deal with the larger issues raised by Meyer.
Comment by Bradford — January 9, 2010 @ 2:06 pm
January 9th, 2010 at 2:17 pm
It is pointless to exchange views with those determined to believe that mindless forces of nature of necessity must generate codes not known to be sourced from human minds. You have your own gap fillers made to suit your preferences.
Comment by Bradford — January 9, 2010 @ 2:17 pm
January 9th, 2010 at 2:42 pm
Daniel Smith:
An anti-telician will contend that functional DNA resulted from an undirected physical process. That is why emphasis is placed on chemical affinity between elements involved in the translation of DNA. But the presence of elements needed to translate DNA do nothing to explain the origin of DNA itself or more significantly the reason why nature would generate a nucleic acid containing sequences that code for functional enzymes and structural end products prior to a point in time when message sending mechanisms are in place. This is an analytical point where irreducible complexity becomes relevant. All objections to IC are based on the assumption of a viable self-replicating system.
Comment by Bradford — January 9, 2010 @ 2:42 pm
January 9th, 2010 at 3:01 pm
Bradford wrote:
That's where you go off the rails, Bradford. Science limits itself to answering the how question. The why question belongs in philosophy and theology.
Comment by olegt — January 9, 2010 @ 3:01 pm
January 9th, 2010 at 3:31 pm
That's exactly what Yarus does. The associations between amino acids and codons are significantly beyond what we would expect from chance alone, and are explained by stereochemical affinity. I'm truly beginning to enjoy the Herculean efforts to divorce Meyer from his own clearly-stated, fatally-flawed argument (my emphasis):
Comment by KC — January 9, 2010 @ 3:31 pm
January 9th, 2010 at 5:54 pm
It seems that Meyer has achieved status of prophet. Nothing he says can be wrong, not matter how strong evidence against it. O well.
In other thread I have tried explained how information from environment leaks into gene pool from natural selection, by example of camouflage. But no answers. So, are IDists ready to answer this now?
Comment by IrynaB — January 9, 2010 @ 5:54 pm
January 9th, 2010 at 8:01 pm
Even Yarus does not claim to explain the entire canonical 20 by stereochemical references. Affinity is not akin to an historical film of an event which is why I went to the trouble of pointing out numerous other problems with the soup concept. The bigger issue of the codes's origin is not explained by affinity between aa's and anticodons even if we presume a viable soup and stereochemical explanations for all 20.
Comment by Bradford — January 9, 2010 @ 8:01 pm
January 9th, 2010 at 8:13 pm
IrynaB:
This has been answered before at TT. You need to study a basic primer explaining the difference between natural selection acting on a living robust replicating cell, replete with an information storage system, expression mechanisms and error detection mechanisms, as compared to the matter at hand in this thread which would be natural seelection acting on a putative prebiotic soup mixture.
Since you are new to the forum may I suggest that you get together with fellow critic and atheist Olegt. You might find some chemistry between the two of you. The cultural affinity resulting from shared values (he is a fine young Russian man) may lead to bonding and the subsequent generation of a love code. If nothing else Olegt can tutor you on the fine art of distinguishing between evolutionary conundrums and origin of life fantasies. The latter are the stuff of moist atheistic dreams.
Comment by Bradford — January 9, 2010 @ 8:13 pm
January 9th, 2010 at 8:37 pm
Hi KC,
I am only seeing your last comment here and wonder if you are claiming that the anti-codon itself, say, GCC, is what determines the association with the particular amino acid. Are you saying that the anti-codon itself chemically interacts with the AA?
If so, what is the point of the remainder of the tRNA, its 3-D shape, its chemical make-up or the synthetases themselves?
Comment by Pez — January 9, 2010 @ 8:37 pm
January 9th, 2010 at 10:54 pm
Pez,
No. I suggest you read the paper by Yarus that Art discusses and especially the ones I mentioned as well.
Comment by KC — January 9, 2010 @ 10:54 pm
January 9th, 2010 at 11:07 pm
Bradford,
The trouble you took was more avoiding addressing the actual issue discussed in Art's original essay. The issue is the origin of the association between codon and amino acid– the genetic code. If you want to regress to discussing the plausibility of the origin of nucleotides themselves, or hell, the Big Bang for that matter, that's fine, but it should be clear that those issues, while important in and of themselves, shed very little light on Art's point, and thus are unnecessary distractions. .
Comment by KC — January 9, 2010 @ 11:07 pm
January 10th, 2010 at 12:22 am
I agree with Art that Yarus's work opens the pathway to all sorts of new hypotheses for both non-teleologists and teleologists.
Comment by Bilbo — January 10, 2010 @ 12:22 am
January 10th, 2010 at 1:22 am
On that score you cite a study showing stereochemical affinity. Your next inference is a jump. You may think it reasonable but strictly speaking, to show an origin entails connecting the dots- all of them. Associations between codons and amino acids are not genetic codes. You can argue that this is how the code formed. It started with associations in a prebiotic soup and then… well I'm sure your imagination is up to the task. As for Art's original essay, quoting from the OP (Art):
No matter how you try and slice this turkey it is an attempted refutation of Meyer based on speculative and vague add ons to Yarus. And I should add an attempted refutation of a single issue in a long book discussing many issues.
BTW, from your prior quote of Meyer (what page?):
Meyer may be mistaken on this point but (and its a big but), you and Art may be as well. For the stereochemical point be meaningful the associations cited by Yarus would have to be part of a series of steps (as Art correctly surmised) culminating in a genetic code which somehow was used by life's first organisms through some very undefined steps. This is Meyer's speculation up against the speculation of others.
Comment by Bradford — January 10, 2010 @ 1:22 am
January 10th, 2010 at 9:33 am
Bradford wrote:
O really, Bradford? Let's ask a few competent sources.
Try again.
Comment by olegt — January 10, 2010 @ 9:33 am
January 10th, 2010 at 1:41 pm
Rocks fall towards the center of the earth because they are directed there by something. This we know to be true. Indeed everything we see seems to operate as if directed towards a purpose, (Man being the only thing that wanders aimlessly searching for a purpose). Everything else acts as if it knows what to do and just does it. That's not to say that everything is consciously directing itself. On the contrary, it only says that something has set this plan in motion. What this something is is neither unresolvable nor inconsequential.
Comment by Daniel Smith — January 10, 2010 @ 1:41 pm
January 11th, 2010 at 1:23 am
Olegt:
Yes, let's look at the first source you supplied.
The first thing to notice is the phrase "set of rules." Compare that to the much more vague word associations. Art and KC are right in noting that the Yarus study yields associations. To go from there to a set of rules would require the type of speculation about subsequent events which Art indulged in and of which I quoted him. So associations are the first phase and not the realization of a set of rules.
Note also the phrase "by which information encoded in genetic material (DNA or RNA sequences) is translated." Encoded DNA is not comprehended within the core of Art's argument. It is speculated to have happened later but is a speculative inference from Yarus. The translation to proteins very much exceeds what the Yarus study will solidly support. What we see Olegt, is you jumping from an association of some amino acids and anticodons to a definition which cites protein translation according to a set of rules.
My statement stands. There is more to a genetic code than mere associations involving a partial set of amino acids. The support for that lies with your own source.
Comment by Bradford — January 11, 2010 @ 1:23 am
January 11th, 2010 at 9:25 am
Bradford,
Hunt did not set out to present a detailed explanation of the genetic code's origin. That wasn't his goal. He only pointed out that Meyer had made a strong negative claim:
Hunt need not provide a point-by-point account of the origin of the genetic code, he just needs to establish the plausibility of its natural origin. WHich he does:
This is a typical situation with creationists. They make a strong negative claim based on nothing but personal incredulity. A scientist points out a loophole in the creationist's argument. The creationist says "but you don't have a full-fledged theory so my bullshit argument stands!"
Comment by olegt — January 11, 2010 @ 9:25 am
January 11th, 2010 at 10:04 am
Olegt, you are sounding more and more like a shrill atheist troll. What is plausible to you may not seem so "plausible" to others. Those with a materialist mindset seem quite comfortable in loosening up their evidential thresholds whenever it suits them.
Comment by Jean — January 11, 2010 @ 10:04 am
January 11th, 2010 at 10:16 am
Not quite.
The "information in DNA" also refers to the regulatory sequences and other sequences that do not have a codon-amino acid correspondence.
Comment by ID guy — January 11, 2010 @ 10:16 am
January 11th, 2010 at 10:45 am
Bradford, you know every well that the "rule" of codon-amino acid specification is the association between the two. You are now attempting to make a distinction without a difference in order to rescue Meyer from his argument.
Comment by KC — January 11, 2010 @ 10:45 am
January 11th, 2010 at 2:15 pm
For those interested, Michael Yarus will be publishing a book summarizing his work in April, 2010: Life from an RNA World: The Ancestor Within, apparently geared towards nonscientists (yay).
http://www.hup.harvard.edu/cat...
Comment by KC — January 11, 2010 @ 2:15 pm
January 11th, 2010 at 5:42 pm
And you know that the link supplied by Olegt had more to it than the rule.
I'm trying to call attention to those who use Yarus to explain the origin of the genetic code. They do this in order to debunk an entire book. If the codon amino acid association is all sufficient then let us know the rest of the story. How did DNA acquire those sequenced codons uniquely suited to code or functional proteins? Did Yarus answer that too? This is not a separate issue because what you need to do is is explain why an association would become a pemanently fixed outcome continually replicated countless times. To do this you need to reference two concepts that extend beyond mere association- a viable self-replicator and natural selection. These issues are inextricably linked to the fixation of a genetic code.
Comment by Bradford — January 11, 2010 @ 5:42 pm
January 11th, 2010 at 5:52 pm
Olegt:
and later:
Jean was on target when he observed that "What is plausible to you may not seem so "plausible" to others." You cite my dissatisfaction with a chemical affinity argument for a partial set of amino acids as personal incredulity. My response to that is that faith in a physical process outcome is not required when empirical results establish a claim without a need for speculation and promissory notes.
Comment by Bradford — January 11, 2010 @ 5:52 pm
January 11th, 2010 at 6:01 pm
ID guy nails it. The matter of information storage in DNA is not explained by a chemical association existing among a subset of amino acids. A "chemical rule" does not explain the functional sequencing. The scramble argument is a strong refutation of a chemically based explanation. Take the same codons and reverse their order. Codon content and bonding explanations remain unaffected but function is gone.
Comment by Bradford — January 11, 2010 @ 6:01 pm
January 11th, 2010 at 8:04 pm
Bradford wrote:
Once again, Bradford, Meyer's argument is a strong negative claim: as a matter of principle, no natural process can explain the origin of the genetic code. He uses the analogy with written and oral language:
Yarus's work shows that the language analogy fails: chemistry does seem to determine the mapping from codons to amino acids. Yes, much further work is needed in this direction, but Meyer's argument from analogy fails.
Umm, this is not even wrong. An encoded message is not necessarily functional. You can write gibberish and read it by following the rules of pronunciation. That does not guarantee that the sounds coming out of your mouth will make sense, as feedback from your friends and family will indicate.
Likewise, when a genetic sequence is scrambled by a mutation, natural selection will correct it if the resulting product is less viable and reward it if it is more effective.
Comment by olegt — January 11, 2010 @ 8:04 pm
January 11th, 2010 at 8:09 pm
Bradford,
Thank you for trying to set me up with delicious Russian hunk Olegt. I will invite you to our wedding, if we achieve that.
You wrote
When one gap is filled, you just call attention to other gap. Poor you, what will you do when you run out of gaps? There is always the big bank I suppose.
Comment by IrynaB — January 11, 2010 @ 8:09 pm
January 11th, 2010 at 9:00 pm
Poor you, what will you do when you run out of promissory notes?
See, I can play that game too. As always, the atheist fundamentalists are a funny bunch.
Comment by Jean — January 11, 2010 @ 9:00 pm
January 11th, 2010 at 10:53 pm
Olegt:
Chemistry indicates an affinity involving a partial set. Amino acids alone are not analogous to much more than letters in an alphabet; certainly not a language. A sequence of amino acids can signify nonsense (gyeinfksiir) or function for a particular species (Im Himmel es gibt kein Bier) but not in another species which uses virtually the very same letters but has a differently structured functional end product (There's no beer in paradise). Function is context sensitive. What works with species x may not work with y. Function is also connected to meaning. Staples sells orange babies is perfect English but is nonsense. The parallels to language are strong.
Chemistry makes mappings possible. So does ink in my pen or strokes of my keyboard. Chemistry does not generate meaningful sequences of amino acids. That's the function of intelligent design. Keyboards do not generate helpful messages. That's the function of enlightened IDists.
Not so. Natural selection perhaps will destroy the entire medium used for messaging but it is the design within DNA i.e. error detection and correction mechanisms, coded for by DNA sequences, which actually correct a large proportion of genetic mistakes.
Comment by Bradford — January 11, 2010 @ 10:53 pm
January 12th, 2010 at 8:09 am
Sorry, Bradford, but you're attempting to move the goal posts. Meyer says unequivocally:
That last sentence is W-R-O-N-G. Admit it and move on.
Comment by olegt — January 12, 2010 @ 8:09 am
January 12th, 2010 at 8:40 am
You obviously have explained the assignments by reference to chemical properties and I do not deny Yarus but what I have been pointing out is essential to a determination of the larger issue i.e. design. Two points. Yarus is partial in its applicability to the canonical 20. Secondly, there is a process implied by Yarus invoking a natural selection dynamic and the sufficiency of initial conditions. The conditions recall the intial point about chemical propoerties. Chemical affinity and selection are related issues but existence of the former does not compel the latter in the absence of both suitable conditions and plausible selection over time. If you acknowledge the foregoing and wish to claim a chemical property basis for the realization of protein translation I'll not object as long as you make it clear the affinity encompasses a subset of amino acids.
Comment by Bradford — January 12, 2010 @ 8:40 am
January 12th, 2010 at 8:57 am
I don't have to acknowledge anything, Bradford. Meyer said plainly that chemistry can't explain the genetic code, understood specifically as the mapping from codons to amino acids. It clearly can. Period. Full stop.
Now, if you want to argue his other point,
it's a straw man. It's like saying that phase transformations, e.g. the melting of ice, cannot be explained by low-level laws of classical mechanics. Of course it can't! Reductionism only takes you so far. In this context it can explain certain properties of gases, but not the irreversibility inherent to the work of a thermal engine. For that people had to develop a new branch of physics called statistical mechanics, which deals with macroscopically large systems. More is different.
Likewise, it's naive to think that chemistry alone can explain the structure and function of proteins. You have to take into account the feedback provided by natural selection in reproducing organisms. That's not chemistry's domain, Bradford, it's biology's.
Comment by olegt — January 12, 2010 @ 8:57 am
January 12th, 2010 at 9:36 am
Olegt:
I am surprised by your philosophical tenacity. Naval gazing is provocative indeed.
I'll leave the pertinent biological points aside for the moment and make this simple. The assumption of chemical adequacy is embeeded within a Yarus based process. Where? It is front loaded at the outset in the chemical sufficiency of prebiotic soup. Not just any mix of amino acids and codons will do. Nature is seldom so cooperative in keeping complicating chemical impurities out of mixtures.
The second chemical property point is the partiality of Yarus. To get from Yarus to a genetic code, utilized by life as we know it, unsubstantiated speculation is required. Game, set, match to Meyer.
Comment by Bradford — January 12, 2010 @ 9:36 am
January 12th, 2010 at 9:56 am
Bradford,
You're making a fool of yourself by defending the indefensible.
Meyer made himself vulnerable by making a sweeping negative claim: chemistry cannot explain the genetic code. Yarus's work indicates that it clearly can. We don't need to present a full-blown theory of that at the moment to prove Meyer wrong, we just need to point out a loophole in his argument. That's what Arthur Hunt did.
On a larger point, this is a great illustration of how ID works (or doesn't). All of it consists of either sweeping negative claims about evolution or straw-men fallacies along the lines of a hurricane and the Boeing 747. The former are easily rebutted, the latter are plain silly. I am amazed that some apparently intelligent people buy that crap.
On a smaller point, it's navel, not naval gazing.
Comment by olegt — January 12, 2010 @ 9:56 am
January 12th, 2010 at 10:01 am
Olegt:
You are making a fool out of yourself by pretending that a partial mapping of codons to amino acids is a biologically relevant code. It's a conceptual code contingent on further research results to establish a biological reality. What organism uses the partial amino acid availability suggested by Yarus?
Comment by Bradford — January 12, 2010 @ 10:01 am
January 12th, 2010 at 10:17 am
Bradford,
You're grasping at straws. The point is not that chemistry at the moment does explain everything about the genetic code, the point is that it can. Go back to Hunt's post and reread it. Here is his main point:
Try to argue with that.
The lesson is that IDers set themselves up for nasty surprises. Meyer wasn't the first. Remember Behe's concession?
One instead of zero.
Comment by olegt — January 12, 2010 @ 10:17 am
January 12th, 2010 at 10:36 am
Why would I argue points I have made myself? Art says that a clear stereochemical basis for at least part of the genetic code is suggested by Yarus. I have said the same but my emphasis has been on the incompleteness of the mapping both to show its current conceptual rather than biological relevance and as a matter of emphsizing that subsequent speculation based on Yarus may not pan out as anticipated.
The genetic code referred to by Meyers is not the genetic code you keep on citing which might more properly be dubbed Olegt's genetic code to distinguish it from anything observed in the biological realm.
Comment by Bradford — January 12, 2010 @ 10:36 am
January 12th, 2010 at 10:40 am
I wrote:
I take that back. Sorry, Bradford, for that snarky (and incorrect) reply. If you read the Yarus paper I suggested that more fully explains the escaped triplet idea, you'll find the answer. It's called a ribocyte
Comment by KC — January 12, 2010 @ 10:40 am
January 15th, 2010 at 10:31 am
I read the paper. Yarus et al., don't do what olegt and Arthur Hunt are claiming.
Did Yarus et al., show that the RNAs required can be formed via blind, non-goal oriented processes? No.
Did Yarus et al., show that all the amino acids can form via blind, non-goal oriented processes? Again No.
Yarus et al., made some observations on how RNAs act in living organisms today.
Then, thinking/ assuming that these actions can be reduced to chemistry and physics, they proposed a pathway that led to it.
They didn't show the pathway could work.
They assumed the pathway based on the overall assumption that living organisms are so reducible.
Comment by ID guy — January 15, 2010 @ 10:31 am
January 17th, 2010 at 11:39 am
David Berlinski weighs in on "the RNA World":
Responding to Stephen Fletcher's Views in the Times Literary Supplement on the RNA World
I post it because he supports what I said in the above post…
Comment by ID guy — January 17, 2010 @ 11:39 am