Monday, November 16, 2009

Re: Evolution, The Genetic Code, and Message 'Theory'

In May 2009 I published an article entitled, “Evolution, The Genetic Code, and Message ‘Theory’: A Response to Walter ReMine”. Walter ReMine had written a series of articles for that gosh-awful blog “Uncommon Descent” in which he made some outlandish claims, including the claim that Evolution never predicted a universal genetic code, but rather many genetic codes.
Here’s how I argued for common descent: If life evolved from just one original species, then all living things should have inherited the code relatively unchanged because of the severe difficulties in changing the code. Although we do know of mechanisms that can change the code (see my article for details), the real problem with changing it is that if a codon (three letters of the genetic code that represent one amino acid or ‘stop codon’) suddenly begins coding for a different amino acid than it originally did, this will change so many proteins that it will almost certainly kill the organism.
A commenter who went by the name “Walt” (Whom I suspect is ReMine himself) criticized me by saying that Evolution did not predict a universal code, since I admitted that the code could change (if only rarely). And the admission that rare changes are possible means that it is theoretically possible that enough of these rare changes may have occurred so that genetic codes were all completely different from one another. I have email Dr. Douglas Theobald about this, and he has clarified the issue: (My words are in italics and his are not):

Hi Doug,
I just had a question concerning "The 29 Evidences for MacroEvolution": You wrote that the universality of the genetic code was evidence for common descent. But of course scientists have written about how the genetic code can change, and how codons can be reassigned for different use. You're probably aware of this, but if not, I can cite some articles if you need me to.
Anyway, couldn't it have been the case that by the time human beings evolved, the genetic code had undergone so many codon reassignments that there was no longer a universal genetic code?

Of course I have to admit that it is possible -- but for reasons, explained better below, it is unlikely.

On the other hand, Evolution does predict that for some unspecified amount of time the genetic code should have retained statistically signifigant similarity across lineages. It could be that we humans evolved within a time frame to be able to observe organisms before enough time had passed for the code to undergo so many codon reassignments that it was no longer the same in all organisms.
But what if they hadn't evolved within a time frame to observe those signifigant similarities in the code? That wouldn't falsify common descent, we just wouldn't know if common descent were true or not. But I thought that in order to make a scientific prediction, certain possible outcomes were supposed to falsify the prediction. In this case it does not seem that way. Am I making sense? What are your thoughts on this?

I think, for the most part, you are reasoning about it correctly. In evolution everything can change, and if we are all related by a common ancestor, there can be change from the original state. The argument here is that the genetic code is one of the most functionally constrained things in all of biology, and so we expect it to have an extraordinarily low rate of change. Given how similar some products of the genetic code are across all life (e.g., histone proteins), it would be incredibly surprising if the code had changed more. (Boldness added for emphasis)Furthermore, think about how we would react now if we found an organism with a DNA genome and the usual proteins, but with an extremely different genetic code. For a creationist, such a finding would present no problem whatsoever -- God just made this one different. But the scientific community would be at a loss to explain it - it is hard to stress enough how shocking it would be. Why is that?
(This marks the last quote I’ll use from Doug’s email)

Doug’s reasoning about this (which I marked in bold) seems sound to me. I suppose creationists would not have to worry if someone found an organism with a different genetic code. Walter ReMine has written that his theory predicts that all life is meant to look like the product of one designer and is also meant to resist evolutionary explanations. Now, if an organism had a different code (but it was still constructed of DNA) a creationist could still choose to see that fact as evidence of a single designer: Even though there are differences in which codons code for which amino acids, creationists would say, the designer still created all organisms with the same molecule (DNA) to store genetic information.

In fact, if Walt Remine’s Message “Theory” is true, we ought to see different genetic codes because this would falsify common descent, and Remine has stated that (according to his ‘theory’) life was designed to resist evolutionary explanations.

Further Comments on ReMine’s So-Called Theory

Here are some miscellaneous comments that I have on Remine’s So-Called Theory, some of which I published to the comments section of

1. Walt claims that Evolutionary theory could explain everything and its opposite because it is theoretically possible that there might have been enough time for new genetic codes to evolve. Point taken. But he misses the fact that even if a designer created organisms to be unified at the biochemical level, it is also theoretically possible that they may have evolved new genetic codes since the original creation. So Evolution doesn’t predict a universal genetic code and neither does Message “Theory”. And if Message “Theory” does predict a universal code, then Mr. Remine needs to explain why we find organisms with slightly different codes. Is that a falsification of his theory?

2. I brought up the fact that whales swim by moving their tails up-and-down while fish swim by moving their tails from side to side. This makes perfect sense in light of evolution because land mammals (like otters) swim the same way as whales do. Whales swim that way because they are descended from land mammals. On the other hand, there’s no reason a designer couldn’t have designed whales to swim the same way as fish. Indeed, if he’s so fond of uniting organisms on the biochemical level (for some reason) then the same reason that caused him to design animals alike on the molecular level ought to cause him to design animals as similarly as is reasonably possible on the macro-level. What flaw is there in that reasoning, Walter?

3. As I see things, Message “Theory” and all forms of the “Common Design” argument are falsified at the macro-level. However, that may not preclude the hypothesis that a designer made the very first forms of microscopic life and designed their genetic codes all the same way (He, She, it or they, if they were limited beings, might have used the same code again and again as a matter of convenience). Of course, that would be the same thing as common descent, since those microbes would have been able to exchange genetic material and would have represented a single gene pool, which is compatible with the current definition of common descent. But here is the point that I want to make: Scientists have methods of finding out the characteristics of the (hypothetical, not actual) common ancestor of practically any group of similar organisms. When scientists use their techniques to figure out what the hypothetical common ancestor of all life would have been like, they find that it would have been rich in amino acids thought to be most common on the early earth[i]. This is surely to be expected if life arose naturally from the chemicals on the early Earth. Later organisms could’ve evolved ways to synthesize amino acids which were not readily available in the environment. Yet the very first organisms would not have had the ability to synthesize just any amino acid. They would have had to use what was readily available – the simple amino acids generated by Miller-type experiments. The fact that the LUCA predominantly used these simple amino acids means it likely evolved from an organism which used these simple amino acids exclusively (or almost exclusively). This is what we would expect if this form of life originated naturally. And exactly what we would not expect to see if life was designed. If life was designed, then the hypothetical common ancestor of all living things might have been a highly advanced organism that retained no vestige of an earlier evolutionary history.

Further comments from Dr. Douglas Theobald

Dr. Theobald wanted me to share these further comments he made:

[I]t might be a bit clearer if I emphasized the three different (though related) arguments that have been made for expecting a universal (or nearly universal) genetic code based on common ancestry:

1) The genetic code is extremely functionally constrained, hence should have an extraordinarily low rate of evolution, and thus we expect genetic codes from different species to be highly similar(if common descent is true).

2) All known life carries genetic information in nucleic acids, and all known life performs metabolic functions with proteins. All known life thus must have a genetic code to relate the two. If all known life is also united by common descent, it must also be united by a universal genetic code.

3) Given the fact that we now know that all organisms studied to date have a very similar genetic code, we can use common descent (and argument 1 above) to predict that all undiscovered or unexamined organisms will also have a similar genetic code -- even though this prediction is not functionally necessary, as there are many other functionally equivalent genetic codes (an astronomical number of them).The first two arguments were used by scientists before the genetic code was cracked, and before it was known that it was highly similar in all organisms. The third argument is an extremely strong argument based on additional information gained since then.


[i] Brooks DJ, Fresco JR, Lesk AM, Singh M. “Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code.” Mol Biol Evol. 2002 Oct;19(10):1645-55.
Accessed 11/14/09 at:

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