Sunday, September 05, 2004

Hunter in Wonderland, Part Two

I will now continue with my response to Cornelius Hunter's response to my earlier essays concerning his work. See my post from this past Tuesday, available here, to find the relevant links to past posts.

The second part of Hunter's essay addresses the universality of the genetic code, and I'm happy to report that his discussion of this topic is far better than his previous writings had led me to believe he was capable of. We pick up the action in the second paragraph:

Taken at face value, Rosenhouse's claim means that common descent is false since the DNA code is not universal. Variations of the code exist in nature. Therefore, will Rosenhouse reject common descent? No, Rosenhouse surely is thinking of more significant variations. How much more significant? We don't know, for Rosenhouse has not defined any criteria. If Rosenhouse wants to claim the universality of the DNA code as a prediction of common descent, he will need to explain why the known variations do not violate this prediction. Specifically, he will need to explain what are the limits of DNA code evolution.

Hunter is referring to this statement I made in my original post:

Actually, the universality of the DNA code, and the universality of the cellular machinery used to translate that code, are evidence for a universal common ancestor. If these universals were not present it would be essentially impossible to argue that any two modern species share a common ancestor somewhere in the past.

And here I will accept a small criticism. I should have been more careful when referring to the universality of the code. It is certainly true that in a very small percentage of species we find that a handful of codons code for proteins different from what the “standard” code predicts. Given that, as Hunter suggests, I should have been more explicit about what the hypothesis of universal common descent leads us to expect about the genetic code.

So let's go about that now. First, to what extent can the code be called universal? Biologist Ken Miller has weighed in three times on this topic here (scroll down to the essay “A Dying Theory Fails Again”). Since I can not improve on his discussion, I will reproduce some choice excerpts below:

All living organisms translate the genetic code using ribosomes, tiny protein building factories, they all translate it with the aid of small molecules called transfer RNA, they all read it in the same direction, and they all read it in the same way, translating the code 3 letters at a time into sequences of amino acids, the building blocks of proteins. It is indeed true that in some organisms, a handful
of these 3-letter “words” have different meanings. Our own cells, for example, contain little structures known as mitochondria in which 4 of the 64 words have different meanings from the “standard” code. In most organisms, these differences are so slight as to be trivial. In common molds, for example, the sequence “UGA” is translated into the amino acid tryptophan. In the standard code, it's a “stop” signal. The other 63 words, however, are identical between humans, elephants, daisies, and molds.

What does all this mean? As evolutionary biologists were quick to realize, slight
differences in the genetic code are similar to differences between the dialects of a single spoken language. The differences in spelling and word meanings between the American, Canadian, and British dialects of English reflect a common origin. Exactly the same is true for the universal language of DNA. 48 of the 64 words are identical in all living organisms, and only 16 are known to vary across the enormous diversity of living things.

Let us consider first the universality of the cellular machinery used to translate the genetic code. It's hard to see how the hypothesis of a universal common ancestor could survive the discovery that living organisms possessed a variety of fundamentally different systems for translating the code. We would then have to hypothesize that some lineage of organisms began with one system for translating the code and later evolved an entirely new system in its place. That may not be strictly impossible, but it seems sufficiently unlikely that the hypothesis of universal common ancestry would be defeated by such a discovery. In light of this, the universality of this cellular machinery is good evidence in favor of common ancestry.

Now, for the code itself. There are a number of known natural mechanisms that can explain how an individual codon comes to code for something other than what the standard code dictates in some species or other. So the mere fact that there are small divergences does not invalidate common descent. The question then becomes just how many divergences the common descent hypothesis can tolerate. It would take someone more knowledgeable about evolutionary genetics than I am to give a good answer to that, but Miller's analogy to dialects of a language is well-taken. People in the Southern United States speak English differently from people in the North, but no one says they speak a different language. On the other hand, English and French are certainly different languages despite having a few words in common. At some point divergences from the standard code could pile up to the point where we would say it is just a different code. I don't know where the line gets drawn, but considering that such variations as are actually known are tiny indeed, I don't think we need to dwell on that point.

Evolution is all about patterns of differences, so we next ask what can be inferred from the catalog of variants from the standard code that have been discovered. Miller addresses this point as well, reproducing a diagram from a paper by Laura Landweber (et al) of Princeton University. The diagram shows that the deviations from the standard code that are known are themselves related by common descent. Here's Miller again:

Dr. Landweber's comments refer to the phylogenetic “tree” shown in Figure 2 of her paper, which is reproduced below. As she noted, rather than falsifying Darwin's idea of descent from a common ancestor, these “subtle derivatives” of the “standard” code actually provide powerful evidence for the common descent of all organisms from a single ancestor.

Look closely at the figure from this paper, and you'll see something remarkable. The
variations from the standard code occur in regular patterns that can be traced directly back to the standard code, which sits at the center of the diagram. What this means is that these slight variations of the code provide powerful — and unexpected — confirmation of the evolution of the code from a single common ancestor.

So the situation seems pretty good for the hypothesis of common descent. The universality of the cellular machinery used to translate the code and the near universality of the code itself speak well for the hypothesis. Furthermore, the pattern of divergences that are known are also consistent with the idea that they are derived from the standard code via descent with modification. I see nothing in this data that speaks against universal common ancestry. Nor do I know of any rival theory that explains these facts.

From here Hunter continues with:

This would be a daunting task given the limited state of our knowledge. Beyond this, it would also be daunting because evolution routinely considers ad hoc and speculative explanations for what we observe in nature. It would be different if we were testing a more straightforward, more easily modeled hypothesis, such as Kirchhoff's Voltage Law. In that case predictions could be computed mathematically using well-defined equations. But evolution and common descent are broad processes, driven by a wide range of causes and influences. Hence, these processes are capable of explaining a wide range of phenomena, especially given the level of speculation that is often permitted. It is not easy to show why an observable, such as variations in the DNA code, would falsify common descent.

I would certainly dispute the claim that evolution routinely considers ad hoc explanations, and evolution certainly does not permit any more speculation than any other scientific theory, but Hunter's broader point is spot on. It is certainly true that the predictions of evolutionary theory are not as sharp as those of the more mathematical theories we find in physics. That's not a defect in evolutionary theory, it is simply a reflection of the fact that there are many factors that affect the evolutionary trajectories taken by living populations, and the whole process contains an element of chance.

Sadly, Hunter seems to forget this obvious point in framing many of his arguments against evolution. Later in the thread I linked to above, Hunter writes the following:

Complexity is also obvious in the fossils. What do we know? We know that fossil species remain essentially unchanged for long, geological, periods of time. And we do know that complexity appears early and often. For example, the trilobite eye of 400 Myr was said to be “an all-time feat of function optimization.”

The fossil record reveals a history of life that is consistent with evolutionary expectations, and that documents numerous sequences of transitional forms that find no explanation outside of evolutionary theory. Against this Hunter presents the fact that the fossil record also documents long periods of stasis in fossil species. But why is that a problem for evolution? If Gould and Eldredge are right, then the pattern of stasis and relatively rapid change should be viewed as a vindication for modern theories of speciation, not as a problem for evolution. After acknowledging that known evolutionary process can explain a wide range of phenomena, Hunter fails to consider possible explanations for the data he cites.

As for the complexity of the trilobite eye, I'm sure Hunter realizes that the 400 mya date he cites is about 200 million years after multicelleular creatures appear in the fossil record. That's plenty of time for a decent eye to evolve.

He goes on to say:

I cannot prove the independent evolution of features is impossible. But what we do know is that these same designs would have had to have evolved on different continents, over geological time periods. This happens over and over, but evolution is a contingent process. There many ways to solve design problems in biology. The design space is large and multi dimensional in biology, with many different potential solutions. This is why evolutionists maintain that if we were to replay natural history, we would get a different world with different species and designs. There are no pre determined solutions. But these convergences contradict this and call into question Darwin's argument that similarities are strong evidence for evolution.

Comparative anatomy reveals many patterns of similarities that strongly suggest common descent (the identical bone structure of the forelimb in humans, whales and cats is a famous example). Against this, Hunter presents the fact of convergent evolution. He is fond of citing things like the converged upon saber teeth of certain marsupial and placental mammals. But why is convergence a problem for evolution? If the various genetic modifications required to produce saber teeth occur with reasonably high probability, and if there is selection pressure in favor of such teeth, then the convergence of these structures is easy to explain in terms of standard mechanisms. In fact, under such circumstances, a lack of convergence would be puzzling. In this sense, many known convergences can be viewed as vindications for evolutionary theory. Hunter routinely gives examples of convergences and asserts that they bode ill for evolution. But he never explains why known mechanisms are incapable of explaining the examples he cites.

Now, back to his main essay. Hunter changes gears in his next paragraph:

This is, however, not the main problem presented by the DNA code. I pointed out in the essay that the DNA code and associated machinery are highly complex. Evolution lacks a detailed explanation of how it evolved. Rosenhouse complains that this is a topic for the origin of life, not evolution: “Evolutionary theory has nothing to say one way or the other about the origin of the code. The code is simply taken as a given.”

Hunter writes that evolution lacks a detailed explanation for the evolution of the genetic code. Well, so does Einstein's theory of relativity, a fact that is about as relevant as Hunter's statement. It is a simple fact, not a complaint, that evolution is a separate subject from the origin of life. Darwin was explicit about this in The Origin of Species, as have most scientists since then.

Our entire understanding of how evolution happens is based on understanding the mechanisms that lead to changes in gene frequencies from one generation to the next. The universal common ancestor possessed a genetic code, and that is the point from which evolution is considered to begin. To even discuss anything like a Darwinian evolutionary process, you need a collection of imperfect replicators competing for resources. The first replicators were likely far simpler than the first thing that was unambiguously alive, but the fact remains that evolutionary theory takes for granted a certain minimal level of complexity. The distinction between the origin of life, and the subsequent development of life once it appeared, is not complicated.

Hunter continues:

Actually, evolutionary theory has plenty to say about the origin of the code, it just isn't very specific. The problem is not that the origin of the code has nothing to do with evolution, the problem is that evolution is unable to explain, beyond handwaving, how protein synthesis arose. Nonetheless, my point does not hinge on categorical definitions. Rosenhouse can draw the line between evolution and the origin of life problem however he likes. Evolutionists such as Mark Ridley still rely on the argument that homologies such as the DNA code would not exist "if the species had independent origins." [Ridley, 49]

At the risk of repeating myself, I'm sorry, but evolutionary theory has nothing to say about the origin of the code. Certainly there has been a lot of research into the origin of protein synthesis, and many theories have been proposed as a result of this research. But those ideas should be regarded as separate from evolutionary theory. Hunter discusses some of these theories in a later post. Without passing judgment on the worth of these theories, I would simply point out that none of them were proposed by evolutionary biologists. And to the extent that evolutionary biologists do write about the origin of life, the ideas their writings are based on come from other branches of science.

Of course, I did not say that the origin of the code has nothing to do with evolution. If we had a good understanding of how the code evolved we would also gain a better understanding of the earliest stages of evolution. But the fact remains that the origin of the code will almost certainly not be discovered by evolutionary biologists.

Findings in one branch of science often have relevance for people in other branches, but the lines between the branches are no less real for that.

And, sorry again, but Hunter's point does hinge on categorical definitions. If the origin of life is a discipline separate from evolutionary biology, then it is hardly proper to use difficulties in origin of life research to indict evolutionary biology. The quote from Ridley does nothing to alter that assessment. He is assuming only that it is asking too much of chance to argue that precisely the same genetic code and translation apparatus evolved more than once. You don't need a detailed theory of how the code originated to justify that assumption.

After writing this essay, Hunter posted some further thoughts on this subject later in the same thread. Since this later addition mostly just repeats his claims about the difficulty of explaining the origin of the code, I don't think it merits a separate response.


At 2:51 AM, Anonymous Anonymous said...

My response is at the ISCID site:


At 2:54 AM, Anonymous Anonymous said...

Note that my response is down at the bottom (the 15th post on that page). --CGH


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