PvM posted Entry 2161 on April 17, 2006 05:07 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2156

Recent research on the origins and evolution of the genetic code have shown how “The standard genetic code enhances adaptive evolution of proteins” in a paper by Wen Zhu, Stephen Freeland, Journal of Theoretical Biology 239 (2006) 63–70

Not only is the genetic code ‘optimal’ in the sense that the effects of point mutations or mistranslations on the phenotype are minimized, a property which seems to argue for stasis, but the genetic code also speeds up the rate of adaptive evolution, a property which seems to argue for rapid change.

Again we see how the concept of robustness and evolvability are intricately linked in the genetic code.

The standard genetic code, by which most organisms translate genetic material into protein metabolism, is non-randomly organized. The Error Minimization hypothesis interprets this non-randomness as an adaptation, proposing that natural selection produced a pattern of codon assignments that buffers genomes against the impact of mutations. Indeed, on the average any given point mutation has a lesser effect on the chemical properties of the utilized amino acid than expected by chance. Might it also, however, be the case that the non-random nature of the code effects the rate of adaptive evolution? To investigate this, here we develop population genetic simulations to test the rate of adaptive gene evolution under different genetic codes. We identify two independent properties of a genetic code that profoundly influence the speed of adaptive evolution. Noting that the standard genetic code exhibits both, we offer a new insight into the effects of the ‘‘error minimizing’’ code: such a code enhances the efficacy of adaptive sequence evolution.

Please remind me again how ID explains these observations? Poof…?

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Comment #97052

Posted by PvM on April 17, 2006 10:39 PM (e)

The following paper is also of interest

Roberto Marquez, Sandra Smit and Rob Knight, Do universal codon-usage patterns minimize the effects of mutation and translation error?. Genome Biology 2005, 6:R91

Abstract

Background: Do species use codons that reduce the impact of errors in translation or replication? The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon. However, the extent to which organisms optimize the genetic messages written in this code has been far less studied. We tested whether codon and amino-acid usages from 457 bacteria, 264 eukaryotes, and 33 archaea minimize errors compared to random usages, and whether changes in genome G+C content influence these error values.

Results: We tested the hypotheses that organisms choose their codon usage to minimize errors, and that the large observed variation in G+C content in coding sequences, but the low variation in G+U or G+A content, is due to differences in the effects of variation along these axes on the error value. Surprisingly, the biological distribution of error values has far lower variance than randomized error values, but error values of actual codon and amino-acid usages are actually greater than would be expected by chance

Conclusion: These unexpected findings suggest that selection against translation error has not produced codon or amino-acid usages that minimize the effects of errors, and that even messages with very different nucleotide compositions somehow maintain a relatively constant error value. They raise the question: why do all known organisms use highly error-minimizing genetic codes, but fail to minimize the errors in the mRNA messages they encode?

From the text

Consequently, our hypothesis that genetic messages (as well as genetic codes) are optimized for error minimization was not supported by the data. However, the low variance in codon-usage error values in organisms suggests the intriguing alternative possibility that mRNAs are selected for a specific level of errors, rather than to minimize errors overall.
Because the rate of evolution is limited by mutation, it is possible that the ability to tune the rate of protein sequence evolution by using error-prone codons has provided a selective advantage to modern organisms. Intriguingly, recent research suggests that the canonical genetic code allows target protein sequences to evolve far more rapidly than do the alternative genetic codes [22]. Codon usage may also be tuned for evolvability rather than for error minimization.

22 is the paper of this thread.

Comment #97056

Posted by Bob O'H on April 17, 2006 11:39 PM (e)

“All’s for the best in the best of all possible worlds”

Bob

Comment #97066

Posted by BC on April 18, 2006 3:05 AM (e)

I suppose someone could argue that God designed the DNA->amino acid transcription for best evolvability. Of course, this would undercut arguments that God needs to miraculously insert genes at various points in history (why make a code that favors evolution if everything is just zapped into existence anyway?) I also wonder if perhaps there were a large number of different transcription systems, but the organisms with the bad versions died out (they weren’t capable of keeping up with the faster evolution and error minimizing of the better transcription systems). And, yes, there are some variants on the transcription systems (used by bacteria). It seems unlikely that the transcription system could evolve - since an organism probably had a fair number of genes that would break with any minor change to the transcription system.

Comment #97075

Posted by Konrad Crist on April 18, 2006 6:28 AM (e)

“Poof?…” [insert mutation] “Proof!…”
ID wins. Isn’t it supposed to be that easy?

Comment #97077

Posted by Ron Okimoto on April 18, 2006 7:01 AM (e)

It should also be mentioned that the genetic code has signs that it evolved and isn’t just optimally designed. Just look at Asn-Asp and Gln-Glu tRNAs and their codon sequence with an understanding of charging proteins and the likely-hood of evolving similar shaped active sites and similar anti-codons. The code looks like a lot of things were tried, but we have the results of what eventually emerged.

Comment #97085

Posted by Joe G on April 18, 2006 8:33 AM (e)

How do random, blind and purpose-less processes explain these observations?

I would say that ID explains this as “built-in responses to environmental cues”.

Comment #97088

Posted by Jim Wynne on April 18, 2006 9:41 AM (e)

Joe G wrote:

How do random, blind and purpose-less processes explain these observations?

Why do you characterize something that happens for a reason (adaptation) as “purpose-less” {sic}?

Joe G wrote:

I would say that ID explains this as “built-in responses to environmental cues”.

And I would say that it happens because that’s the way the His Noodliness wants it to happen. How is your explanation any better than mine?

Comment #97089

Posted by Jon Fleming on April 18, 2006 9:43 AM (e)

How do random, blind and purpose-less processes explain these observations?

By the observed power of the combination of variation and selection.

I would say that ID explains this as “built-in responses to environmental cues”.

And you would be trivially and obviously wrong. But that’s standard for IDists.

Comment #97090

Posted by Bruce Thompson GQ on April 18, 2006 9:55 AM (e)

Title: Do universal codon-usage patterns minimize the effects of mutation and translation error?

Observation: The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon.

Question: Do species use codons that reduce the impact of errors in translation or replication?

We tested the hypotheses that organisms choose their codon usage to minimize errors, and that the large observed variation in G+C content in coding sequences, but the low variation in G+U or G+A content, is due to differences in the effects of variation along these axes on the error value.

Conclusion: Consequently, our hypothesis that genetic messages (as well as genetic codes) are optimized for error minimization was not supported by the data.

I love the smell of science in the morning.

Delta Pi Gamma (Scientia et Fermentum)

Comment #97095

Posted by Rich on April 18, 2006 10:49 AM (e)

“Not only is the genetic code ‘optimal’”

A gem from the qoute mine!

Comment #97096

Posted by PvM on April 18, 2006 10:52 AM (e)

How do random, blind and purpose-less processes explain these observations?

I am glad you ask:

First of all let’s explore the evolution of the genetic code to answer these questions.
The following websites have many of the relevant references to this

Freeland Lab

Knight’s homepage
See especially Knight’s thesis although additional findings have supported some of his hypotheses.

There are several ‘competing’ explanations

1. Selection (is the code optimal in some sense)
2. Stereochemistry (Did chemical interactions shape the code)
3. History (Does the code contain traces of its past)
4. Frozen accident

Knight Freeland and Landweber in a 1999 paper argue that these explanations need to be mutually exclusive

Knight, R. D., S. J. Freeland, and L. F. Landweber (1999). “Selection, history and chemistry: the three faces of the genetic code.” Trends Biochem Sci 24(6):241-7.

The conclusion is that there is strong evidence of selection and stereochemistry.

Stereochemical evidence shows that there is an association between triplets in the binding sites of aptamers for amino acids and the genetic code.

Association between Arg (arganine) codons and binding sites is strongly supported by the data and the same holds for Tyr (tyrosine), Lle (isoleucine), Gln (glutamine), Leu (leucine) and Phe (phenylalanine). This suggests that at least some of the codons and anticodons survived from the RNA world.

Laura F. Landweber Testing ancient RNA-protein interactions, PNAS Vol. 96, Issue 20, 11067-11068, September 28, 1999

Statistical Evidence for Triplet/Binding Site Associations

Michael Yarus,1­J. Gregory Caporaso and ­Rob Knight ORIGINS OF THE GENETIC CODE: The Escaped Triplet Theory Annual Review of Biochemistry Vol. 74: 179-198

I would say that ID explains this as “built-in responses to environmental cues”.

In other words selection? Well well…

Comment #97098

Posted by chunkdz on April 18, 2006 10:55 AM (e)

Please remind me again how a built-in error correction algorithm explains it’s own origin by NS?

Comment #97100

Posted by Anton Mates on April 18, 2006 11:01 AM (e)

chunkdz wrote:

Please remind me again how a built-in error correction algorithm explains it’s own origin by NS?

A transcription system with a superior built-in error correction algorithm outperforms a transcription system with a crappy one. Organisms with the former therefore outcompete those with the latter. Next!

Comment #97101

Posted by PvM on April 18, 2006 11:08 AM (e)

Please remind me again how a built-in error correction algorithm explains it’s own origin by NS?

Could you give more details? This posting is about discussing the genetic code. If the code evolved under adaptive pressures such as minimizing the translation error, then we should be able to find evidence for such ‘optimality’ in the code itself.
For this, the genetic code must be able to vary (it does) and there must be some identifiable selective pressure.

The organization of the SGC (standard genetic code) is highly non-random. In the four decades since the discovery of the SGC a large spectrum of hypotheses have been conceived to explain how its organization came about. These include a variety of load minimizing hypotheses, the frozen accident hypothesis, the ambiguity reduction hypothesis, the stereochemical hypothesis, and the metabolic coevolutionary hypothesis. None of these hypotheses has laid down a theory that is fully edged in the sense that it (i) begins from biological or biochemical considerations, (ii) derives the evolutionary mechanisms that follow from such considerations, and (iii) shows how these mechanism can reproduce the patterns in the organization of the SGC. Here we present the first fully fledged theory for the evolution of the SGC. The theory derives from two fundamental observations: first, there are patterns in the SGC that strongly suggest that systematic errors in replication and translation played a causal role in its evolution; and second, the evolution of a genetic code is mediated through the protein-coding genes, where selection acts upon the proteins which are the product of translating these genes with the genetic code. We derive the evolutionary mechanisms of code formation that follow from these observations, and show how these mechanisms reproduce two of the salient organizational patterns of the SGC.

Guy Sella and David H. Ardell The Coevolution of Genes and the Genetic Code February 19, 2001

and

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.

David H. Ardell and Guy Sella No accident: genetic codes freeze in error-correcting patterns of the standard genetic code Phil. Trans. R. Soc. Lond. B 2002

Comment #97107

Posted by harold on April 18, 2006 11:38 AM (e)

Joe G wrote -

“I would say that ID explains this as “built-in responses to environmental cues”.”

This isn’t ID.

You’re saying that organisms were “designed to evolve” at some very early stage of life. I don’t agree with that, because it’s a needless magical explanation for things that don’t necessarily need magical explanations, but it isn’t ID either.

ID doesn’t say that organisms evolved because God made them very good at evolving. It says that certain major features of organisms, like the flagella of bacteria, couldn’t possibly have evolved and were magically “designed”, and that certain features of living cells show the same kind of obvious “evidence of design” that Mt Rushmore does. That’s what ID says. That’s what they said in Dover. They used so many pictures of bacterial flagella that the crowd in the courtroom started laughing.

The obvious question is, why design organisms to change with the environment? Why not design the environment too? And if you’re going to say that God set things off from some starting point with the intention that humans would evolve, a view which is not in conflict with science, why not just say that? Why argue against the evidence that God pins flagella on bacteria?

Comment #97114

Posted by Tyrannosaurus on April 18, 2006 12:21 PM (e)

Joe G stated;
I would say that ID explains this as “built-in responses to environmental cues”.

Well, well let’s see this statement more closely. Could you please tell me the difference between your “built-in responses to environmental cues” and adaptation and selection?
Just in case go back and for once read about a subject that obviously you know nothing about. On the other hand keep on opening your mouth and inserting your foot in it, is so much fun :)

Comment #97145

Posted by William E Emba on April 18, 2006 3:51 PM (e)

harold wrote:

The obvious question is, why design organisms to change with the environment? Why not design the environment too?

In the early/mid-90s, there were several papers on optimality of DNA repair rate. Too accurate reproduction and a species would be unable to evolve quick enough, so its “ultimate fitness”, that is, as measured over thousands of generations, was quite poor. Too inaccurate reproduction, and its “immediate fitness”, the next generation, was quite poor. Theoretical and experimental papers found support for the notion of an optimal mutation rate.

So the same question arose: why design DNA to optimally evolve?

Comment #97153

Posted by Steviepinhead on April 18, 2006 4:14 PM (e)

This is a taut thread: not only do most of the commentators back up their assertions with links to data but, along the way, we receive free entertainment.

It’s like a front row ticket to batting practice before the All-Star Home Run Hitting Contest:

Joe G? Blam! Out of the park!

chunkdz? KaPow! It’s going, going, gone, over the wall in deep centerfield!

(…and all without that annoying, insulting, and off-putting sarcastic tone that occasionally mars the efforts of certain lesser commentators (like, well, yours truly…))

Comment #97174

Posted by Bruce Thompson GQ on April 18, 2006 5:20 PM (e)

Title: Do universal codon-usage patterns minimize the effects of mutation and translation error?

Observation: The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon.

Question: How do random, blind and purpose-less processes explain these observations?

Hypothesis:

Experiment:

Conclusion: Joe G on ID: I would say that ID explains this as “built-in responses to environmental cues”.

Couple of steps missing here, something doesn’t smell right this afternoon.

Delta Pi Gamma (Scientia et Fermentum)

Comment #97189

Posted by 'Rev Dr' Lenny Flank on April 18, 2006 6:31 PM (e)

Couple of steps missing here

*ahem*

“And here, a miracle occurs.”

Comment #97224

Posted by BlastfromthePast on April 18, 2006 10:35 PM (e)

William E Emba wrote:

So the same question arose: why design DNA to optimally evolve?

The correct formulation of the question should be: “Why design DNA to optimally adapt?” Then the answer is obvious: so that organisms can survive when environments change.

Comment #97229

Posted by PvM on April 18, 2006 11:02 PM (e)

The correct formulation of the question should be: “Why design DNA to optimally adapt?” Then the answer is obvious: so that organisms can survive when environments change.

Cool but the same would be the outcome of selection, so why the extra requirement of an intelligent designer when it can be shown that regularity and chance cannot be excluded? After all that is the ID inference, that which remains once chance and regularity have been excluded.

Why are you assuming that the goal of the designer to have organisms adapt to changing environments? After all, there is no reason why to make this assumption without resorting to some additional premise.
Note that the sufficiency of regularity and chance does not disprove an Intelligent Designer either, science cannot really address the question of the supernatural.
Seems ID becomes a rather vacuous concept if it fully embraces regularity and chance and cannot even present logical reasons why one would expect the designer(s) to be interested in the survival of organisms in a changing environment.

Stereochemistry and selection seem to be very reasonable explanations for the origin and evolution of the genetic code. How does ID explain these observations in a non begging the question manner?
See why people insist that ID has no content.

Comment #97234

Posted by Anton Mates on April 19, 2006 12:15 AM (e)

BlastfromthePast wrote:

So the same question arose: why design DNA to optimally evolve?

The correct formulation of the question should be: “Why design DNA to optimally adapt?” Then the answer is obvious: so that organisms can survive when environments change.

No, that’s not correct; the paper is not just about DNA enabling its owners to adapt, but to adapt through evolutionary mechanisms–exploitation of random mutations. As opposed to, say, adaptation through unpacking of pre-existing “front-loaded” genetic information.

Comment #97263

Posted by W. Kevin Vicklund on April 19, 2006 5:28 AM (e)

Couldn’t even make it a month before coming back, eh blast? That’s all right, there’s still a seat at the table for you over at the Mutation thread (go to the Archives, look for February 13). As I recall, you left the insinuation that the Chlorella in question might be a misclassified Scenedemus(sp?) on the way out the door.

Comment #97281

Posted by harold on April 19, 2006 8:09 AM (e)

William Emba -

“So the same question arose: why design DNA to optimally evolve?”

Although I am something of a theistic evolution proponent, very broadly defined, I really oppose invoking magic for natural phenomenae. The more logical conclusion is that the features in question themselves evolved through variation and natural selection, at a very early stage of life. As Anton Mates said above “A transcription system with a superior built-in error correction algorithm outperforms a transcription system with a crappy one. Organisms with the former therefore outcompete those with the latter. Next!” I would substitute more neutral terms for “superior” or “crappy”.

And there is evidence to support this. Forgive me for not giving a reference (someone will come up with one, I’m sure), but there are species of lake fish which live in extremely unstable environments. In these environments, conditions change so fast that having more variable offspring increases the odds of offspring living to reproduce. Hence, a slightly higher rate of germline mutation than would be ideal in more stable situations has been selected for.

Blastfromthepast

I am glad to see that you have abandoned ID (I refer to flawed science and/or philosophy, not your religion, of course).

You say “The correct formulation of the question should be: “Why design DNA to optimally adapt?” Then the answer is obvious: so that organisms can survive when environments change.”

This is a strong denial of ID.

You’re saying that organisms were “designed to evolve” at some very early stage of life. I don’t agree with that, because it’s a needless magical explanation for things that don’t necessarily need magical explanations, but it isn’t ID either. In fact, the whole concept of ID is useless if you acknowledge that major features of organisms can evolve, and that’s true even if they were “meant to” evolve by a higher power.

ID doesn’t say that organisms evolved because God made them very good at evolving. It says that certain major features of organisms, like the flagella of bacteria, couldn’t possibly have evolved and were magically “designed”, and that certain features of living cells show the same kind of obvious “evidence of design” that Mt Rushmore does. That’s what ID says. That’s what they said in Dover. They used so many pictures of bacterial flagella that the crowd in the courtroom started laughing.

The obvious question is, why design organisms to change with the environment? Why not design the environment too? And if you’re going to say that God set things off from some starting point with the intention that humans would evolve, a view which is not in conflict with science, why not just say that?

Comment #98683

Posted by Kon on April 26, 2006 6:21 AM (e)

DEATH OF A STAR
A star died millions of years ago. Only today did the explosion register on our telescopes. Yesterday we thought that it was alive. Today, in awe, we witness its end, which in reality occurred millions of years ago.
What we believe to be real may not always be so. Real in relevance to time and space. Pinch yourself. You say this is real. You can feel it. You can prove it (the painful reminder). So what? It’s a momentary reality.
The awakening of man is a slow mundane process. Significantly so. What we see, what we understand, what we accept are fallacies.
BIG BANG, BIG BOOM
BBa Big Bang, beginning
é Earth and its time
BBo Big Boom, end

BBa-é-BBo1 BBa-é-BBo2 BBa-é-BBo3
BBa-é-BBo4 BBa-é-BBo5 BBa-é-BBo6
BBa-é-BBo7 BBa-é-BBo8 BBa-é-BBo9
BBa-é-BBo10 BBa-é-BBo11 BBa-é-BBo∞(infinity)
In the year 2001 I wan an incarnate of Kon Athanasiou in the specific BBa-é-BBo2. In BBa-é-BBo5 I might be the incarnate of a well- known movie star; in BBa-é-BBo7 of a politician; in another a street cleaner and so forth. Each BBa-é-BBo has a year 2001. this is what a parallel world is. The entire system is immaculate. No aspect of it is ever threatened. Considering that a molecule, lets call it molecule X, is in my fingernail, 5 billions years ago it was star dust, and this same molecule, molecule X, 5 billion year from now will once again be star dust, I am immortal. With or without a God, this is what Immortality is. kongrp@hotmail.com