UPDATE: Sept. 8, 4:20 pm:
I corrected some typos and made small changes in the phrasing in certain parts of this entry.
When I began to respond to Cornelius Hunter's thoughts from this thread
over at ISCID, I said I would not respond to any further posts he made on this topic. I said that because these sorts of internet debates can easily go on forever, and I wanted to cut-off the discussion at a point where failure to respond would not be interpreted as admission of defeat.
However, Hunter has now responded to my second entry in this series (my essay is available here
, Hunter's reply is available here
(scroll down to the bottom of the page)). I'm afraid that Hunter's reply is so wide of the mark, that I have to weigh in one more time to try to make my argument clear. But I definitely will not be replying directly to any reply he makes to this post. And this time I really mean it!
One of the main points of contention is whether the universality of the genetic code can be considered strong evidence for evolution. I say it is. He says it isn't.
To be precise, I argued that the complete universality of the cellular machinery used to translate the code across all known species speaks well for common descent, since it would be very difficult to defend common descent in the face of multiple, different sets of cellular machinery. I then argued (basing myself on Miller, who was basing himself on Landweber) that the small variations in the code that are known occur in patterns that also are suggestive of common descent.
Finally, I addressed the question of how many changes from the standard code could be tolerated before we would have to discard the idea of universal common descent. I commented that it would require far more knowledge of evolutionary genetics than I possess to answer that question. It would depend on things like how sensitive an organism is to changes in the code, and what sorts of natural mechanisms could be produced to explain how a codon that originally coded for one amino acid (or a stop) later comes to code for something different.
After providing a brief quote of my thoughts on the matter, Hunter writes this:
Rosenhouse is not alone here, as this is a difficult question. What is clear, however, is that it would be difficult, as I earlier pointed out, to place a tight limit on the evolution of the code without presupposing evolution. Amino acids tyically have multiple codons so single codon reassignment does not mean a complete absence of the corresponding amino acid. Furthermore, many amino acids are similar, so conservative code changes are conceivable. And finally, proteins are quite robust to amino acid substitutions. Perhaps someday we'll find evidence for the code's rigidity, but at this point we have only speculation.
So this invalidates Rosenhouse's claim that the near universality of the code is strong evidence for common descent. Greater differences in the code, at this point anyway, could be explained by evolution and common descent.
Hunter does not address my point that the universality of the cellular apparatus speaks well for common descent. Common descent would be out the window without this universality, and there is no rival theory that also accounts for this universality. Chalk it up to common design if you want to, but then you will have to explain why it amused the designer to make trivial changes in the code in a handful of species.
And while it is true that common descent could account for greater changes than we actually find, it is equally true that there are good reasons to believe that there are limits to how far you can change the code before sacrificing the viablility of the organism. For that reason, the fact that the code varies very little across species speaks well for common descent.
To put it another way, the more universal the genetic code the easier it is to accept common descent. To bring variant codes under the tent of common descent, we need to invoke other mechanisms to explain how the divergence happened. As things stand, geneticists have provided a number of possible mechanisms for how one codon could change what it codes for in a given species, and these mechanisms are adequate to explain the variations we actually encounter. These mechanisms have their limits, however.
But where Hunter really starts to go wrong is in his next paragraph. He says I was too uncritical in my acceptance of Miller's claim that the pattern of divergences from the standard code is itself suggestive of common descent. Hunter writes:
Actually, there is no such evidence. Miller's powerful confirmation is, in reality, scattered across various types of organisms. For example, the UAR codon is observed to switch from &lduqo;stop” to “Gln” in green algae, various ciliates, and some diplomonads. Likewise, the UGA codon is observed to switch from “stop” to “Trp” in other various ciliates and two firmicutes. There is no powerful, unexpected confirmation of evolution here. 
Unfortunately Rosenhouse accepts Miller's tale unequivocally, concluding that “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.”
The citation at the end of the first paragraph is to the paper “Rewiring the Keyboard: Evolvability of the Genetic Code” by Knight, Freeland, and Landweber (though for some reason Hunter only mentions Knight). Landweber was the senior author on the paper. It appeared in Nature Reviews: Genetics
in 2001. This is the same paper Miller was citing in his work.
Miller was basing his statement about the pattern of differences from the standard code on a similar statement made by Dr. Landweber herself. So if Miller is confused on this point, then so is the senior author on the paper in question.
Happily, Miller and Landweber are right, and Hunter is wrong. Landweber et al are quite explicit in the paper that in certain cases, the same codon shift occurred in unrelated species. Nothing Miller wrote (or by extension me in quoting him) contradicts that. That was not the issue. The question is whether the patterns of divergences that we find across species is consistent with common descent. For example, once a shift occurs in some lineage, does the change persist in the evolutionary cousins of that species? Or are the variations from the standard code effectively random with respect to the phylogenies we have inferred from other means? The elaborate diagram reproduced by Miller in his essay shows that these patterns are indeed consistent with common descent.
This is another example of Hunter being too enamored of the idea that convergence is some sort of problem for evolution. He seems to think that the mere fact that same codon shift was converged upon in separate lineages condemns common descent. He consistently fails to consider what sorts of natural mechanisms can account for such convergences.
From here Hunter turns back to fossils. Sadly, he also turns back to some of the truly dopey arguments I criticized so strongly in my initial posting in this discussion (avialable here
Regarding the fossils, Rosenhouse mistakenly thinks that “The fossil record reveals a history of life that is consistent with evolutionary expectations.” Actually, evolution does not expect for phenomenal complexity to appear abruptly. In fact, it does not expect phenomenal complexity at all. Also, if the earth was full of nothing but bacteria that could just as easily be described as being consistent with evolutionary expectations.
Hunter made a similar remark in responding to criticisms of Richard Wein. After describing the complexity of the echolocation system in bats, he writes:
Evolution does not predict this complexity, nor does it have a scientific explanation for how it arose. Therefore, this is not consistent with evolution and is evidence against it.
Alas, this is total nonsense.
Hunter seems to think that “phenomenal complexity” is some sort of precisely defined technical term. Like maybe evolution could explain mere complexity, or perhaps extreme complexity, but not phenomenal complexity.
What could it possibly mean to say that “evolution does not expect phenomenal complexity”? A process in which random variations are sifted through a non-random selection process can lead to outcomes far more complex than what you started with. That's simply a fact about such processes. On the other hand, since there is also an element of chance involved in the process, there is no guarantee that complexity will increase (Hunter is, at least, right on that point). So complexity by itself is not evidence one way or another for evolution.
Curiously, ID proponents like Michael Behe and William Dembski understand this very well. That is why both of them attempted to identify special kinds of complexity (irreducible complexity in Behe's case, complex specified information in Dembski's) that were outside of what natural selection could produce. As it happens, neither was successful, but we won't rehash that debate here.
To determine if a particular system could have been crafted by natural selection it is not enough to diagnose it as being complex. Furthermore, there is no shortage of complex systems whose origins have been largely revealed. No doubt Hunter would sweep this work under the rug as being unscientific, but he would simply be wrong to do so.
Hunter continues to deteriorate with his next paragraph:
Regarding comparative anatomy, a few posts back Rosenhouse agreed that massive convergence would be a problem for evolution, now he finds it to be vindication:
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.
Evolutionists generally do not acknowledge evidential problems. Hence, massive convergence becomes a vindication for evolution. Rosenhouse denies evolution invokes ad hoc explanations, but this is ad hoc.
The interior quote is from me. Hunter begins his reply to this with a slur against the intellectual integrity of evolutionists. He then attributes to me the idea that massive convergence becomes a vindication for evolution, which is not what I said. (And let me also point out that “massive” like “phenomenal” and “striking” is not a technical term). He then says that my brief description of the conditions under which we might expect convergence to happen is ad hoc. It is not. I am simply pointing out that the prolonged action of natural selection can lead to similar solutions to similar problems. Again, that's simply a fact about natural selection. It is not a kluge meant to get around inconvenient data.
Although he agreed that massive convergence is a problem for evolution, Rosenhouse now asks why evolution is incapable of explaining convergences. That is a convenient way of framing the problem, but it misses the point. Above, Rosenhouse claimed the pentadactyl pattern strongly suggests common descent. They are obvious similarities right? So they strongly suggest common descent because they must have come from a common ancestor.
Of course, I did not say that massive convergence is a problem for evolution. Here's what I actually said:
Rampant convergent evolution would be a problem if we found several lineages evolving major, complex morphological innovations in parallel.
I thought my point here was obvious, but for Hunter's sake I guess I better spell it out. First, at the risk of being repetitive, we note that “convergent evolution” is not a precisely defined term. Generally we have in mind certain similarities in design that did not arise as a result of common descent. By itself, this is not a problem. The end result of prolonged natural selection is that organisms end up better adapted to their environment than they were at the start. Sometimes that means crafting similar adaptations to solve similar problems. The streamlined shape of fish and dolphins is a good example of this. So there is nothing in the mere fact of convergence that calls evolutionary theory into doubt.
However, though evolution will often craft similar solutions to similar problems, it is asking too much of chance for evolution to produce identical complex systems in unrelated lineages. That's what I was holding out as troubling for common descent.
Hunter's statement that I have framed the problem conveniently is yet another example of his unwillingeness to take seriously just what it is that evolutionists have been saying all these years. The problem isn't that I have framed the problem in some convenient way, it is that Hunter thinks he can make bold assertions about what evolution does and does not predict without fully considering all of the available resources evolution has at its disposal.
The identical forelimb design of humans, cats, whales and bats is an example of having the identical bones in the same relative positions to one another in a situation where there is no functional explanation for the similarity (indeed, the design seems rather ill-suited for many of the purposes it is put to). The level of morphological similarity here is far greater than in any of the examples of convergence Hunter is so fond of. The lack of a functional explanation for the structure makes it hard to view it as the outcome of natural selection crafting similar solutions to similar problems. That all suggests common descent as the most likely explanation. In my opening post of this series, I discussed the various methods scientists use to distinguish homologies from analogies. Hunter asserted that I missed his point (and more on that in part three). But here Hunter plainly needs to give more thought to how homologies and analogies can be distnguished.
But now, with similarities that could not conceivably have been inherited from a common ancestor, this too is a vindication because it must have been caused by similar mechanisms responding to similar selective pressures. This is ad hoc. If a similarity can conceivably be ascribed to a common ancestor then it is viewed as a homology and strong evidence. If it cannot be, then it is viewed as an analogy, and again strong evidence.
This is just a repetition of his earlier pargraph, but it does make explicit his refusal to consider the possibility that homologies can be distinguished from analogies. Hunter is plainly descending into cartoon arguments here. As I've already explained, there is nothing ad hoc in explaining convergence as the end result of known evolutionary mechanisms.
The point is that if similar designs are present in distant species, where common descent cannot be used to explain those similarities, then common descent need not be invoked to explain similarities in species that are not so distant. Homologies, such as the pentadactyl pattern, were a key argument for Darwin. He viewed them as a mandate for common descent. But this argument is contradicted by the convergences. It is not scientific to say that the pentadactyl similarity mandates common descent when there are other such similarities that do not mandate common descent. The argument is arbitrary. It is not a question of whether the theory allows for similar adaptations to evolve, it is question of whether or not evolution is supported by the evidence.
But there aren't “other such similarities” that do not mandate common descent. That's the whole point! “Similarity” is not a technical term. The pentadactyl pattern of various mammalian forelimbs shows a fundamentally different sort of similarity from the saber-like teeth of certain marsupial and placental mammals, or the streamlined shape of fish and dolphins. Hunter's failure to recognize this point is fatal is to his argument here.
Hunter concludes his essay with a cartoon discussion of my thoughts about the distinction between origin of life research and evolutionary biology. He writes:
Regarding the question of origin of life (OOL) Rosenhouse continues to maintain that the creation of the DNA code is outside of evolution and an OOL problem. But he avoided answering my question. Does he think the creation of the DNA code is a serious problem for OOL? If not then this is merely a rhetorical dodge since he would believe the code evolved (somehow).
The answer to Hunter's question here will depend on what he means by the phrase “serious problem”. The origin of the DNA code is the central question in OOL research. Currently I agree that there is no really persuasive explanation for how it formed. In that sense, it is a serious problem for OOL research.
There are a lot of possible explanations, however, and that is enough to dismiss any claims that we must resort to the supernatural in explaining its origin. If Hunter means that our failue so far to come up with a fully plausible explanation for the code is good reason to think that the problem is fundamentally insoluble then I would not agree with his description. OOL is an infant science, and it seems to me that progress is being made.
Also, I'm not comfortable with saying that the code evolved. I would say that it formed by some naturalistic process that probably shared certain characteritics with evolution by natural selection.
Furthermore, Rosenhouse fails to understand that DNA code evolution falls into the category of Darwinian evolution, even according to his own definition:
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.
We can agree with all this, and it means the DNA code evolution falls into the Darwinian evolutionary process. The code had to have evolved from simpler codes. How strange that the first cells to appear with the extant code constitute “a collection of imperfect replicators” but in going back just one step in the code's evolution we no longer have “a collection of imperfect replicators.”
Here I thought I was writing in English, but perhaps not. I asserted that anytime you have a collection of imperfect replicators competing for resources, you have something “like a Darwinian evolutionary process”. Indeed. But the fact remains that when we talk about evolutionary biology we are thinking of the development of life from the universal common ancestor onward. Learning what happened before the universal common ancestor is certainly of interest to evolutionary biologists, but studying that question requires different tools and different ideas from those evolutoinary biologists rely on.
Probably the modern code did form through a process that shares certain attributes with natural selection. OOL researchers often use the term “chemical selection” to capture this similarity, while also making it clear that they are talking about something different from natural selection as that term is usually used.
Hunter is eager to lump evolutionary biology together with OOL because the latter is not nearly as well developed a science as the former. He accuses me of resorting to various rhetorical tricks, but here we find him trying to bring down evolution by associating it with a branch of science with some large unresolved questions.
The remaining paragraphs of Hunter's essay contribute nothing new to the discussion. Since I'm sure my regular readers must be getting tired of these very long posts, I will stop here for now. I will write one more long post addressing the third part of Hunter's original essay.