Tuesday, September 21, 2004

Hunter in Wonderland, Part 3

This will be the last post I make in response to Cornelius Hunter's reply (available here) to my comments on his essay from Uncommon Dissent. I will reply to the third part of his essay, which deals with the subject of homology. Barring any especially egregious replies from Hunter, I will end my part of our dispute there.

One of the points I made in my original post on this subject was that Hunter commits the classic fallcy of equating vestigial with non-functional. This simple fact refuted his claim that vestigial structures do not provide strong evidence of common descent. I notice that Hunter has offered no reply to this point.

Instead he begins the third part of his essay by providing a brief explanation of why homologous structures are generally considered strong evidence for common descent. He then argues that there is other anatomical evidence that speaks against common descent. He writes:

Evolution, so the argument goes, is constrained to use what is available. The pentadactyl pattern is a repeated design because it was available. The problem with this argument, however, is that there also exist repeated designs that could not have been inherited from a common ancestor. As I wrote in the essay:

The marsupial-placental convergence is a popular example. Over millions of years and in different corners of the earth the marsupial and placental lineages, supposedly evolving from a mouse-like species, produced a host of similar designs. Everything from sabre-toothed carnivores and wolves to flying squirrels and anteaters were produced independently. Nature is full of lesser-known examples. From salamanders to cacti we find striking similarities that must have arisen independently. If biology is ruled by contingency rather than necessity then why do we find duplicated designs? When similarities are found among allied species they are cited as powerful evidence for evolution. When similarities are found among distant species, they are noted as cases of convergent evolution. Evolution can explain either case but the explanations presuppose evolution. This is not powerful evidence for the theory. [Hunter, 2004, 199-200]

Rosenhouse misses the point. He responds:
Biologists usually make a distinction between homologous characters and analogous characters; the former are the ones that are most plausibly explained via common descent. Hunter is suggesting that biologists are being arbitrary in their determinations about which characters are homologous and which are analogous.

My point was that these homologies are not powerful evidence for the theory, not that the assignments are arbitrary. Rosenhouse then begs the question as he explains how evolutionists judge which characters are homologous and analogous, for this process relies on evolution for their identification. [Hunter, 2001, 27-29]

We should point out that Hunter neglected to include the first sentence from the paragraph in which my quote above appeared. I began that paragraph by writing:

Hunter is fond of the phrase “striking similarities” but it is not clear to me what it actually means.

This makes it clear that I was pointing out that in order to discuss this subject intelligently you can not simply refer to something vague like “striking similarities”. You have to make distinctions between different kinds of similarities. I have made this point in several of my posts, but Hunter has so far refused to address it.

Now take another look at Hunter's self-quote. He writes:

When similarities are found among allied species they are cited as powerful evidence for evolution. When similarities are found among distant species, they are noted as cases of convergent evolution.

That sure sounds to me like he's arguing that biologists are being arbitrary about which similarities are treated as homologies (and are therefore indicative of common descent) and which are analogies (and are therefore indicative of convergence). Elsewhere in the thread linked to above Hunter writes:

Next, Rosenhouse claims that comparative anatomy is strong evidence for evolution. I explained 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.

Actually, the argument is not contradicted by convergences, and the reason the argument is not contradicted is that scientists have reasonable methods for distinguishing between analogies and homologies. Hunter consistently uses the term “similarities” as if it were a well-defined technical term. But it is not “similarities” in some vague sense that biologists are using common descent to explain. Rather, it is certain specific kinds of similarities that are being so explained.

So it is clear that Hunter does believe scientists are being arbitrary in distinguishing homologies from analogies. Consequently my comments on this subject in my original post were entirely appropriate. I also focussed on this point because I think there's a small amount of legitimacy in it, and it is one that is worth addressing. Biologists have good methods for distinguishing analogies from homologies, and these methods work well in most cases. But there are indeed some examples where it is hard to distinguish the two.

But now it seems I gave Hunter too much credit. Rather than focussing on the reasonable, though unconvincing, point that sometimes it is hard to distinguish homologies from analogies, it seems that Hunter wanted us to pay attention to those last two sentences. The ones where he wrote:

Evolution can explain either case but the explanations presuppose evolution. This is not powerful evidence for the theory.

This, sadly, is not a reasonable point. Of course the explanations presuppose evolution! How else do you test a theory except by assuming it to be true and asking what sorts of observations are likely to be made given that assumption?

There are certain patterns of similarities among modern species that are easily explained as the consequences of common descent. There are other sorts of similarities that can not be explained as the result of common descent, but can be explained easily as the result of convergence. There are still other sorts of similarities that we might, hypothetically, have observed which would be easily explained neither by common descent nor by convergence. Happily, we do not make any of those observations.

Hunter's confusion on this point becomes even more evident in his response to this quote from Simon Conway Morris:

During my time in the libraries I have been particularly struck by the adjectives that accompany descriptions of evolutionary convergence. Words like, 'remarkable', 'striking', 'extraordinary', or even 'astonishing' and 'uncanny' are common place. It is well appreciated that seldom are the similarities precise, and this in itself is as concrete a piece of evidence for the reality of evolution as can be provided.

This was part of a longer quote from Morris offered by commenter Salvador Cordova in response to some of Hunter's earlier comments. Hunter responds to that last sentence by asking if the line had been quoted accurately. He then states:

If so, now I've heard everything. Not only are similarities evidence for evolution, differences are too. Does he elaborate on how he comes to this strange conclusion?

Of course, Morris' comment makes perfect sense. Natural selection will craft similar adaptations to similar situations, but on probabilistic grounds it is unlikely that two species will converge on identical adaptations to similar situations. As I mentioned in an earlier post, nearly identical, highly complex adaptations in species would be hard to explain via convergence.

We should also point out that only someone determined to reject common descent would write something as silly as “Not only are similarities evidence for evolution, differences are too.” I disagree with many of the things Morris has written, but his arguments deserve better treatment than Hunter gives them here. “Differences” is no more of a technical term than “similarities”.

Moving on, Hunter next provides a quote from biologist Brian Hall to the effect that homologous structures are often seen to form from different processes of embryonic development. Alas, I don't have easy access to the paper Hunter cites. Happily, what Hunter writes next is easily responded to regardless:

In my essay I gave an example of two closely related frog species with similar eye lenses that develop differently. Rather than acknowledge that this is a legitimate issue, Rosenhouse complains that I did not provide sufficient details of the case: “Hunter's argument here is far too vague to be replied to.” In science, it is important to consider all the evidence and test a theory rather than protect it from evidential problems.

Hunter accuses me of trying to protect evolution from evidential problems. But the whole point is that Hunter did not provide enough details in his original essay to determine whether the frog species he cites are a problem for common descent or merely an interesting anomaly. This is something we have seen over and over again from Hunter. He points to observation X and asserts, without any further argument, that it challenges the conclusion of common descent. That obervation X does no such thing does not seem to trouble him.

To determine if Hunter's frog example is something to worry about we would need to know, among other things, the precise manner in which the eye lenses in question develop, how similar the final products are and how different their development is, and the various natural mechanisms that might lead two structures related by common descent to follow different patterns of development. To turn his vague assertion into an actual argument Hunter would need to provide a lot more detail than he provided, exactly as I said in the first place. The problem is not that I am trying to protect evolution from evidential problems, it is that Hunter is trying to argue on the cheap.

Of course, the relationship between evolution and development is a popular area of research these days, and new results are being produced far too quickly for amateurs like me (or Hunter) to keep track of. I will simply observe that the biologists actually engaged in this research do not seem to have arrived at the same conclusion as Hunter. For example, have a look at Brain Hall's home page. His description of his research begins as follows:

As a developmental biologist, I study how embryos of fish, frogs and chicks form from the much more simple structure of the egg. We are particularly interested in how the skeleton develops, especially the embryonic origins of the cells that form the cartilages of the head, the fins in bony fish, and the tooth-like scales in the skin of skates. We are also interested in how the mechanisms that control embryonic development have changed during the evolution of the various classes of vertebrates, especially fishes, amphibians and birds. This bringing together of developmental and evolutionary biology is a rapidly growing field known as evolutionary developmental biology (“evo-devo”).

This doesn't sound like someone who thinks common descent is on its way out.

Sadly, Hunter loses it completely in the next paragraph:

Problems with the homology evidence also appear at the molecular level. Rosenhouse quotes my first paragraph on this topic and again complains that my explanation is “too vague to be responded to.” He wants to know what functional reasons there might be for molecular differences between different species. He agrees such reasons are conceivable, but writes that “it is safe to say that no one has a plausible suggestion for what that functional reason might be.” Actually, I gave six such suggestions in the next paragraph. [Hunter, 2004, 201]

Golly! Six? How'd I overlook that?

Of course, I overlooked no such thing. What Hunter actually does is throw out six bits of biology jargon that have no connection to the question I asked in my reply. In my initial response to Hunter's essay I wrote:

Again, this is too vague to be responded to. Consider the structure of hemoglobin in different animal species. Hemoglobin is the molecule responsible for transporting oxygen to the various tissues of the body. That is it's function wherever it is found. It's precise structure varies from species to species, and the pattern of these differences is entirely consistent with the patterns of descent inferred from morphology and paleontology. Thus, human hemoglobin is far more similar to chimpanzee and gorilla hemoglobin than it is to dog hemoglobin, for example. Is Hunter suggetsing that the differences between human and dog hemoglobin are the necessary consequences of the differences in the morphology of humans and dogs? If that is his suggestion, then I'd appreciate it if he'd tell us what that functional necessity is.

Sorry for the lengthy quotes, but I think it's important to point out just how selective Hunter has been in quoting me. He provided my line about his assertion being too vague to respond to, but does not give his readers any clear indication of what I actually said.

I did not ask for suggestions for why there might be molecular differences between different species. As my quote above shows, I didn't ask for anything close to that. What I asked is how the specific patterns in hemoglobin differences (to choose just one example) that we find across species is explained functionally.

This from a man who accuses me of attacking strawmen.

My point was that we can use similarities in molecules like hemoglobin to infer phylogenetic relationships and when we do so we obtain results consistent with the phylogenies obtained from other sources. Common descent is one explanation for that fact. If Hunter wants to suggest a functional explanation for these patterns he is free to do so.

Back to the six suggestions. Here they are:

In fact, the claim that molecular comparisons constitute powerful evidence for evolution essentially amounts to circular reasoning. Contingency is assumed to dominate, and so the similarities must have no functional explanation; therefore evolution is the only alternative. But the amino acid sequences of proteins, for example, have many functional implications. These include quaternary interactions, free-energy tuning, transport interactions, mRNA destabilization, positioning interactions, and amino acid storage and transport. It is logical to conclude that differences between species are found at all levles simply because all levels contribute to function in one way or another. (P. 100-101) (Emphasis in original)

There is a lot to respond to in this paragraph, but in the present context it will suffice to point out that there isn't the ghost of a suggestion here for how the patterns of differences in hemoglobin reflect functional necessities. There is only a lot of jargon thrown around for no good purpose. This essay was included in a volume intended primarily for non-scientists. Do you really think Hunter was trying to bring clarity to scientific issues here?

This essay has gone on long enough, so I won't reply to Hunter's next set of comments about similarities between species in non-coding regions of the genome. Suffice it to say that it is more of the same: Hunter offers an idle bit of data (in this case certain similarities in the non-coding regions of human and mouse genomes) and simply asserts, without justification, that it poses a challenge to common descent.

Hunter, like many critics of evolution, like to present himself as part of a beleagured minority suffering the outrage and ad hominems of a dogmatic scientific elite. But as he shows in his closing remarks, he's perfectly happy to use ad hominems himself:

While the biological evidence raises questions and doubts about evolution, evolutionists claim their theory is a fact. For them, evolution is not an idea that just might be wrong, though they don't think so. No, it must be true. And anyone who doesn't agree must be up to no good. Rosenhouse spells this out in his mission statement:

For more than a century Darwin's theory of evolution has been the cornerstone of biological research. This status was hard-won through countless successes in the field and the laboratory. Today it remains one of the most vibrant and productive areas of scientific research.

Some people, motivated almost entirely by religious conviction, are unimpressed by this track record. They believe that evolution poses a threat to morality and decency and sundry other forms of goodness. As a result, they avail themselves of every opportunity to denigrate the accomplishments of Darwin and the scientists who succeeded him. This denigration takes the form of fallacious scientific arguments, ad hominem attacks against scientists, and an endless stream of propaganda designed to fire the passions of scientificaly ignorant people.

These folks, who call themselves things like “creationists” or “intelligent design theorists”, have the ear of numerous politicians at all levels of government. Their main goal is not to produce new science or learn new things about nature. Rather, they want to inject their bad arguments in to science classrooms, with the intention of changing what they perceive as the atheistic inclinations of modern society.

Presenting creationist ideas in science classes as if they have any scientific merit would be a terrible disservice to our students. It is tantamount to telling them lies. For this reason, creationism in all its forms must be opposed.

It is little wonder that Rosenhouse is not particularly interested in exploring the nuances and difficulties of the evidence. After all, these are merely propaganda brought about by people who want to denigrate the work of scientists. Unfortunately, these ad hominem attacks are not unusual. Rosenhouse's sentiment is, in fact, quite typical and it sets up an atmosphere in which rational debate is impossible.

My mission statement is available here.

Of course, nothing in that statement says that anyone who doesn't agree with the conclusions of evolutionary theory is up to no good. I assert simply and clearly that some people who criticize evolution are up to no good. I think that is obvious from the behavior of many proponents of creationism and ID. If Hunter believes that the actions and writings of, for example, the Institute for Creation Research and Answers in Genesis are honorable and above board, then he ought to say so. Otherwise, he must agree with my statement.

I also think there are many critics of evolution who are merely mistaken, as opposed to dishonorable. I used to include Hunter in this category, but now that I've read more of his comments I think that assessment was too generous.

And for sheer, unmitigated, totally-divorced-from-reality-gall it's hard to top Hunter's statement that I am “not particularly interested in exploring the nuances and difficulties of the evidence.”

Excuse me? I'm the one whose not interested in exploring nuances and difficulties? In nearly every case I've responded to Hunter's arguments by pointing out that he fails to consider nuances and subtleties that show that what he offers as difficulties are, in reality, not difficulties. And he has responded not by providing more nuance to his original arguments, but merely by ignoring what I actually said and restating precisely the same bad arguments.

It was Hunter who claimed that patterns of stasis in the fossil record challenge common descent without giving any consideration to punctuated equilibrium or the mechanics of speciation and fossilization. It was Hunter who claimed that convergence challenges common descent without giving any consideration to the mechanics of natural selection or the means by which biologists distinguish homologies from analogies. It was Hunter who, after acknowledging that natural selection can craft complex structures, asserted without justification that certain structures nonetheless defy the explanatory power of evolutionary theory.

In each case it is Hunter who refuses to consider the nuances of the points he is making. From this I conclude that he is more interested in scoring cheap rhetorical points than he is in seriously discussing evolutionary theory.


At 5:33 AM, Anonymous Anonymous said...

I pointed out that highly-conserved, non functional regions of the human and mouse genome weaken the case for common descent. Professor Rosenhouse says that this is all meaningless. "Suffice it to say," he explains, "that it is more of the same: Hunter offers an idle bit of data (in this case certain similarities in the non-coding regions of human and mouse genomes) and simply asserts, without justification, that it poses a challenge to common descent."

Sorry, but this is science, and science does use data. And this is hardly "an idle bit of data." In fact, though I provided the reference, it doesn't require an expert to see that highly conserved functionless regions in fairly distant species is not what evolution predicted. In fact, before such findings evolutionists used to say that this sort of thing would falsify evolution

See the rest of my response at ISCID Brainstorms:

http://www.iscid.org/ubbcgi/ultimatebb.cgi?ubb=get_topic&f=6&t=000540&p=5#000064 (bottom of page 5)

At 11:41 AM, Blogger Jason said...

In response to my claim that you asserted, without justification, that the data on mouse genomes you mention is a challenge to common descent, you simply repeat, still without justification, the same assertion.

And, as is obvious to anyone who read what I actually wrote, I did not say the data was meaningless. I said simply that I would not respond to it beyond noting that your style of argument here is the same as your style elsewhere.

At 2:09 PM, Anonymous Anonymous said...

Similarities in different species are supposed to be powerful evidence for evolution. Contingency, rather than necessity, is supposed to have caused these similarities, and this is supposed to be a sure sign of evolution. As I've described at the ISCID Brainstorms, there are several problems with this evidence. For instance, there are similarities in distant species, which cannot be ascribed to common descent. Evolutionists tell us that in this case, these must be caused by necessity, not contingency. But there is no evidence for this. All kinds of other designs could have arisen. Why are we compelled to think these designs are caused by necessity?

There is also the problem that the similarities that are supposed to be a sure sign of evolution often do not arise from the same development pattern. As I described in the frog example, in Rana fusca the lens develops from the epidermis on the optic cup. It is the optic cup that induces the epidermis to differentiate into the lense which ends up perfectly fitting. It makes sense that the lens perfectly fits in the optic cup since it is developing from the epidermis. In Rana esculents, however, the lens develops without the presence of the optic cup. As Sir Gavin de Beer put it, the lenses in these two closely related species "differ completely in the mechanism by which determination and differentiation are brought about. This is no isolated example."

Is this an anomaly? No, there are many more examples (as Pere Alberch put it, they are "the rule rather than the exception."). How similar are the lenses? Well, put it this way: they were considered to be homologous. How different is their development? Completely different (as de Beer put it). In one case the optic cup is the inducer, in the other case the optic cup is irrelevant. It can be completely cut out. How could evolution explain these examples? One can construct such explanations. For instance, neutral mutations caused a switch in the development path that, nonetheless, left the final design intact and functional. Those mutations eventually became fixed in the gene pool. Of course, this is a just-so story. There is no evidence that such a thing ever did, or even could, happen. These observations are not easily explained by common descent or by convergence. But then again, there's also no evidence that the frogs themselves could have evolved in the first place.

But there is yet another problem. Evolutionists used to say that if similarities were found in distant species that are not caused by necessity, then this would contradict evolution. But in the mouse and human genomes, highly conserved functionless segments are found. In this case, the just-so story that the similarity must have been caused by necessity is not available.

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