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Author
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Topic: Evolution of genetic code
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Pim van Meurs
Member
Member # 541
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posted 12. July 2003 17:07
In another thread Mike and I discussed the genetic code and in particular the issue of "frozen accident" and cytosine deamination. I would like to discuss in more detail the ideas of the genetic code and "frozen accident"
Knight, R. D. and L. F. Landweber (1999). "Is the genetic code really a frozen accident? New evidence from in vitro selection." Ann N Y Acad Sci 870: 408-10
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The textbook view of the origin of the genetic code is that no explanation is required for the present set of codon assignments: rather, the form and content of the genetic code are a frozen accident [1].
Knight Landweber et al argue a different perspective namely
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However, the genetic code actually does assign similar amino acids to similar codons [2-5]. If this relationship is not accidental, it could be due to such factors as selection to minimize the effect of mutations [6], of concession of codons from metabolic precursors to derivatives [1, 7], or because similar amino acids bind most strongly to similar RNA sequences [2]. If codon assignments arose from specific binding between amino acids and short RNA motifs, then evolution in vitro may be able to recapitulate such interactions.
An interesting example where non-teleological thinking seems to be able to shake the 'frozen accident' scenario. Of course I am sure that a teleological viewpoint may have led to similar findings which would only serve to strenghten my argument that any particular assumption is not relevant for observing patterns in biology. Of course when the assumptions are based on observable patterns and mechanisms which can be used to construct simulations and do 'experimental' analyses one might argue that there may be some advantage to non-teleology or at most that non-teleology and teleological presumptions are irrelevant and that neither one can be said to be supported by the observations which follow from the presumptions. Thus how do we support non-teleological viewpoints? Well, at least where it overlaps with Mike's viewpoints is that from the initial condition onwards, the two are indistinguishable and in fact no intelligent design intervention is argued to take place, thus from the initial condition onward methodological naturalism seems to be valid. The question now remains why going back in time there should be a disruption in this? Surely the suggestion based on observations that methodological naturalism works quite well going back in time requires any suggestion that there is a discontinuity to provide some evidence for this "extraordinary" (out of the ordinary, not necessarily logically following from what we observe) claim.
The origins and evolution of the genetic code is a fascinating area. Methodological naturalism and non-teleological viewpoints seem to be helpful in proposing workable and perhaps even testable hypotheses. I wonder if front loading "ID" can be as scientifically fruitful.
Surprisingly my research led me to the following interesting papers
"Asymmetric directional mutation pressures in bacteria Jean R. Lobry and Noboru Sueoka in Genome Biol. 2002; 3 (10)"
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The effect of asymmetric mutation pressure on the amino-acid content of proteins has been reported [27,28,29]. In terms of amino-acid composition, the diversifying selection on integral membrane proteins (enriched in hydrophobic amino acids) and on cytoplasmic proteins (enriched in hydrophilic amino acids) is generally the most important factor in within-proteome variability [30]. In Borrelia burgdorferi, however, the effects of this selective pressure are quantitatively less important than those resulting from asymmetric mutation pressure [31], stressing again that mutation pressure is far from being a negligible phenomenon.
Seems to me that Mike's observations may have been observed by others without necessarily teleogogical presumptions. Fascinating.
See also "Frank AC, Lobry JR: Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 1999, 238:65-77 " as well as Lobry's thesis work "J.R. LOBRY THE BLACK HOLE OF SYMMETRIC
MOLECULAR EVOLUTION"
Another interesting work is "On the Evolution of Redundancy in Genetic Codes David H. Ardell, and Guy Sella in J Mol Evol (2001) 53:269–281"
Instead of taking the frozen coding stage as a start, they perform coevolution calculations that lead to a frozen state.
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Abstract. We simulate a deterministic population genetic model for the coevolution of genetic codes and protein-coding genes. We use very simple assumptions about translation, mutation, and protein fitness to calculate mutation-selection equilibria of codon frequencies and fitness in a large asexual population with a given
genetic code. We then compute the fitnesses of altered genetic codes that compete to invade the population by translating its genes with higher fitness. Codes and genes coevolve in a succession of stages, alternating between genetic equilibration and code invasion, from an initial wholly ambiguous coding state to a diversified frozen coding state.
Another article by Ardell et al "No accident: genetic codes freeze in error-correcting
patterns of the standard genetic code"
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The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or ‘frozen’ by, the protein-coding genes that they translate, and so cannot easily change by natural selection. Yet the
standard code has a significantly non-random pattern that corrects common errors in the transmission of information in protein-coding genes. Because of the freezing effect and for other reasons, this pattern has been proposed not to be due to selection but rather to be incidental to other evolutionary forces or even
entirely accidental. We present results from a deterministic population genetic model of code-message coevolution. We explicitly represent the freezing effect of genes on genetic codes and the perturbative effect of changes in genetic codes on genes. We incorporate characteristic patterns of mutation and translational error, namely,
transition bias and positional asymmetry, respectively. Repeated selection over small successive changes produces genetic codes that are substantially, but not optimally, error correcting. In particular, our model reproduces the error-correcting patterns of the standard genetic code. Aspects of our model and results
may be applicable to the general problem of adaptation to error in other natural information-processing systems.
Wildman in "Evaluating the Teleological Argument for Divine Action." seems to raise an interesting question about teleology, namely that given that complex systems are open ended, can a particular goal be achieved by an intelligent designer. Wildman seems to conclude that 'The failure of the teleological argument is located in its underlying metaphysical ambiguity'. I will see if I can get a hold on the full paper.
And although some have suggested that "Materialists have only one hope: to quickly find a way to teach and study life without ID concepts and language." it seems clear to me that front loading is (so far) no enemy of materialism of methodological naturalism.
Mike may also be interested in the work by Rosenberg
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One of the few authors arguing that biological approaches in teleological terms are not only useful for molecular biology, but in fact have superior explanatory power than physico-chemical approaches, is Al. Rosenberg (1985). According to him, some phenomena on molecular level can be well explained in two different ways, from both biological and physico-chemical points of view, but only the biological explanations in teleological terms take into account certain important aspects of these phenomena. To justify this idea, Rosenberg analyses the way one of the recent discoveries in molecular biology has been obtained - the discovery of the reason for the difference in the chemical structures of DNA and RNA (more precisely, the fact that DNA always contains thymine and RNA uracil). The explanation of this fact was first obtained in strictly biological way using teleological language, i.e. proceeding from the effects to the causes of the phenomenon. The same phenomenon can also be explained in purely chemical way, by describing the causal chain of chemical reactions that underlie it. These two explanations are different not only in their formal structures, but mainly in their explanatory powers. Especially, from physico-chemical point of view, the universal character of the explained phenomenon is purely accidental (chemically, both DNA and RNA molecules can contain thymine or uracil), while for the biological understanding it is essential. This universal character has precise biological reasons which are central to biological explanations. Thus, Rosenberg has shown that the development of molecular biology has given to the problem of teleology even more strength than before.
And finally talk.origins has an interesting article on teleology and biology
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Or is it? Teleology, too, is making a minor comeback. In science, teleology is a way of modelling a system's behaviour by referring to its end-state, or goal. It is an answer to a question about function and purpose. Why do vertebrates have hearts? In order to pump blood around the body to distribute oxygen and nutrients, etc. This is a functional explanation. The function of hearts is to pump blood. In evolution, the question 'why do organisms exhibit adaptation?' is not answered teleologically with 'in order to survive', but historically - 'because those that were less adaptive didn't survive'. However, some forms of teleology are still used, on the understanding that they reduce to historical explanations.
they end up concluding that
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Many criticisms of Darwinism rest on a misunderstanding of the nature of teleology. Systems of biology that are end-seeking are thought to be end-directed, something that Darwinism makes no use of in its models. Outside biology - indeed, outside science - you can use external teleology all you like, but it does not work as an explanation of any phenomena other than those that are in fact the outcomes of agents like stock brokers. And even there, teleology is not always useful, for which stock brokers (or cabal of stockbrokers) desired the goal of the 1987 crash, or the 1930 depression? External teleology is useless in science, and any science that attempts to be teleological will shortly become mysticism
[ 12. July 2003, 22:19: Message edited by: Pim van Meurs ]
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Mike Gene
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Member # 149
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posted 13. July 2003 22:06
Pim,
I was under the impression that this particular sub-forum was devoted to discussions of particular journal articles. Your posting brings up several articles, including a talk.origins web page, all in some apparent effort to score some point against my views. I don’t want to get in a point-by-point response that will ultimately lead us back to your main complaint (front-loading fails to prove that “methodological naturalism” is impossible), given that it would seem to violate the intent of this sub-forum. Nevertheless, I think two general points of response should suffice.
From where I sit, you continue to misunderstand the very basic nature of my arguments.
A. First, let’s deal with my observations related to cytosine deamination that were introducedhere.
You cite the Lobry and Sueoka paper and assert:
quote:
Seems to me that Mike's observations may have been observed by others without necessarily teleogogical presumptions. Fascinating.
Yet this is not the case. Neither the Lobry and Sueoka paper, nor the references they cite, make the same observation I did. I noted that cytosine deamination is channeled, by the genetic code, to produce mutations that
1) swap from a pool that appears randomly distributed (in terms of hydrophobicity) to one that clusters around the most hydrophobic amino acids (the IHE):
2) swap from a pool that is largely indifferent to secondary structure replacing it with a pool that is often involved in alpha-helix and beta-strand formation
The pattern then deepens when both strands are considered.
The various papers you bring up come close to making these connections, but they don’t actually make them. For example, papers will argue that mutational bias exists and some draw attention to cytosine deamination. Other papers will argue that the amino acid content is influenced by nucleotide content. All of this supports my hypothesis and adds to the plausibility of its biological relevancy. But the arguments don’t make the same connections as one complete synthesis. What allowed me to make the connections was the attempt to explain cytosine deamination in teleological terms (after a teleological cause was rejected in favor of a non-teleological explanation) and use my thesis of front-loading as a guide.
B. Your second basic misunderstanding is even more generic and it continues to revolve around this notion that a teleological explanation must find something that only a teleological perspective can explain. That is, we are supposed to assume what you call “methodological naturalism” unless we are forced to abandon it. Yet you continue to miss the whole thrust of my approach. As I explained to you before, I already strongly suspect that life itself was designed as a consequence of several clues. My front-loading thesis is not the cause behind these suspicions. The front-loading thesis is a hypothesis that is derived from these suspicions. The front-loading approach is a positive attempt to construct a testable design scenario that can shed light on biotic reality. That you can’t point to any data that would have me abandon it, but can only appeal to the standard non-teleological perspective that cannot be distinguished from my views (according to you and others), means that the light remains ‘green’ and teleological explanation expands. The only reason given for me to abandon my teleological approach (that continues to generate payoffs) is that it violates game rules. Yet it is ironic that the game rules themselves are front-loaded to exclude teleological causes and force us into a mindset where teleological explanations are required to generate “extraordinary evidence.”
What is interesting is that you expend much energy and effort trying to convince me my approach is doomed unless it eventually delivers something that would force you to invoke design. Yet if my approach is indeed doomed, why spend so much effort trying to push me off the track?
Anyway, thanks for the references. They should allow me to expand my argument later on.
[ 14. July 2003, 01:23: Message edited by: Mike Gene ]
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Pim van Meurs
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Member # 541
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posted 13. July 2003 23:36
I am glad that I have been able to provide some useful references to Mike's argument. Of course while I do encourage Mike's usage of teleological thinking in proposing hypotheses I do believe that I have addressed sufficiently the lack of a logical link between a teleological viewpoint and the necessity of such a viewpoint. In fact, given the existence of purely natural pathways one may argue, as I have, that Mike's position of a discontinuity requires some supporting evidence since as I understand Mike's argument his claims are not dissimilar from methodological naturalism other than his attempt to infer from the success of his hypothesis a validity to his viewpoint of teleology. But as I have shown, teleology has not been shown to be a requirement for cytosine deamination and in fact cytosine deamination may be understood quite well in fully natural terms without the need for intelligent design. Or alternatively we may accept the intelligent design inference but conclude that Mike's approach suffers from the same limitation as Dembski's namely that such an inference cannot exclude natural selection as the intelligent designer.
What I am hoping for is some independent evidence that would help explain why such a discontinuity is needed. After all methodological naturalism was doing fine all the way to the initial condition and there is no apriori reason to suspect why it would fail during the initial condition. Of course there is nothing preventing an intelligent designer from intervening at any time or place but the question is how we establish the validity of such an extraordinary event. Extraordinary even in the viewpoint of Mike's front loading I would argue.
Mike suggests that "The front-loading thesis is a hypothesis that is derived from these suspicions." but that seems to be in contradiction with his approaches as I understand them. That Mike may feel that there are other, so far unspecified clues led him to the hypothesis of front loading is not very helpful since such front loading does not preclude for instance evolutionary mechanisms to be the 'cause' of this front loading, or initial condition.
My point is that going back in time we see an unbroken chain of natural events and Mike argues that at some instance, somewhere somehow, some unspecified intelligent designer did something to make something happen.
Mike suggests that front loading is an attempt to create a testable design scenario but so far I believe such attempts fail at its origin. No attempt to test the design part of the scenario all that is 'testable' is the hypothesis which may or may not be linked to the presumptions of teleology. In fact no reason has been given why we should accept such an ad hoc teleology.
Surely Mike may take strength in the fact that his thesis cannot be tested in any workable manner and/or differentiated from methodological naturalism but in the mean time we do observe how methodological naturalism is succesful in explaining what happened since the front loading and I doubt that Mike's approach could disagree with this. The question now remains if there is any reason to prefer a teleological explanation which fails to provide for any testable scenario over a natural explanation which seems to at least be testable (for instance the attemtps to establish and/or disprove the hypothesis of a frozen accident for the genetic code0
Mike may suggest erroneously that the game rules preclude teleological causes, its just that when such causes remain untestable that one wonders about the use of such teleology of the gaps argument. The game rules however do not preclude Mike from presenting evidence to support his claims about the necessity of teleology when at most we can assume "we don't really know" and Mike does not seem to be expecting to be adding to our understanding in this aspect either.
Mike wonders why I spend so much time addressing his arguments, suggesting in some way that there must be something to them or I would not spend the effort. And yet the explanation may be so simple that one may have overlooked it, namely that while I do accept that front loading is only way to succesfully introduce a concept of intelligent design into nature, especially when moving the instance to before the Planck time, conveniently hiding the front loading from scientific observation, I also believe that arguments from front loading, for obvious reasons will fail to provide for a scientifically sound frame work for intelligent design. Thus simply the fact that I have considered these matters and have been spending much time and effort exploring them should not be taken as giving any support to the validity of Mike's claims, on the contrary I would say.
So far Mike has not given me much reason to revise my viewpoints here. Certainly Mike has failed to show that methodological naturalism is untenable, in fact he seems to strongly rely on methodological naturalism nor has Mike given any reason why our ignorance of the initial condition is in any form or manner helpful to intelligent design.
I do thank Mike for his efforts in clarifying some of his thoughts in this matter.
Also Mike may not fully appreciate the function of this forum.
[ 13. July 2003, 23:38: Message edited by: Pim van Meurs ]
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Mike Gene
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Member # 149
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posted 14. July 2003 00:31
Pim,
I see nothing in your response that indicates you understand the points I was trying to make in A and B, so I feel no need to rehash old arguments. And, as I mentioned, it always seems to come back to your opinion that I must provide something you require:
quote:
lack of a logical link between a teleological viewpoint and the necessity
such a viewpoint….. Mike's position of a discontinuity requires ….. teleology has not been shown to be a requirement …… without the needfor intelligent design…. an inference cannot exclude natural selection….. why such a discontinuity is needed……
For some reason, you think I’m supposed to be showing that intelligent design is supposed to be required to explain the chemistry of cytosine deamination. Oh well.
As one metaphor might say, you are trying to force new wine in old wineskins.
Anyway, thanks for your concern about people deriving “a scientifically sound frame work for intelligent design.” It’s always been so obvious. ![[Wink]](wink.gif)
[ 14. July 2003, 00:31: Message edited by: Mike Gene ]
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Pim van Meurs
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Member # 541
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posted 14. July 2003 12:04
Mike,
I am glad to see that you realize that scientific claims come with certain requirements. If all you are trying to do is showing that 'intelligent design' is always a possibility, then we may agree but in order for this idea to have a scientific merrit more is needed.
Perhaps I was expecting too much and should have known better that with the failure of CSI and IC as reliable markers of intelligent design, such issues are likely to remain unresolved. As far as a "scientifically sound frame work" for Intelligent Design. Perhaps my pipedream but we should all be allowed at least one dream. You seem to have yours, I seem to have mine. :-)
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