The standard genetic code enhances adaptive evolution of proteins

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?

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.

"All's for the best in the best of all possible worlds"

Bob

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.

"Poof?..." [insert mutation] "Proof!..."
ID wins. Isn't it supposed to be that easy?

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.

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".

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

— Joe G

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

— Joe G

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".

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.

"Not only is the genetic code 'optimal'"

A gem from the qoute mine!

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".

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

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

— chunkdz

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

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.

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.

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?

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 :)

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

— harold

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

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...))

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)

Couple of steps missing here

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

— William E Emba

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.

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

— BlastfromthePast

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.

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.

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?

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