(Yet) A(nother) Defense of Darwinian Evolution

Leave it to Mr. McLatchie of Crossexamined.org to fly right under just about every point on that list I just made....yeesh. Alright, where do I begin? First:

Since the body plan of organisms is established right at the beginning of development, the types of changes which are required to evolve a novel body plan are the very kind which are least likely to be tolerated by organisms.

I don't know why he's saying this again. He actually said this in the first article, which I took pains to re-acknowledge in my latest response. Here is what I said (or, if you don't believe me, you can go read it yourself again, here):

...with regard to the change in "body types" being unlikely: yes, in a single generation, or in even several successive generations, a population is very, very, very unlikely to exhibit any major changes to its morphological arrangement --- limb placement, the addition or subtraction of major features (such as a tail, limb, eye, or fin), and so on --- but that is not what happens. The "mutations" which Mr. McLatchie refers to as "unlikely to be beneficial" during embryonic development are, of course, generally not responsible for the major morphological changes observed in evolution! There is very little, if any, real "body plan mutation" -- in fact, there is much debate over whether such a scaled mutation is even possible.

So now that we've cleared that up (again, and hopefully for the last time), let me say it loudly and clearly once more: embryonic mutation is *not* considered a primary vehicle for natural selection under Darwinian evolutionary theory. Anyone who tells you it is, is talking about a different school of thought within the evolution debate than the one I am defending here. Within the school of which I consider myself a part (the "Darwinist" school), there is debate over whether this is even possible to the extent that a beneficial mutation(s) is even likely to occur with enough frequency to account for any degree of major --- or minor --- evolutionary change.

If Mr. McLatchie raises this point against me again, as if I had not just made it myself for a third time, I will simply point to this quotation here and not explain it any further. I hate wasting my energy more than anything.

Second, Mr. McLatchie scolds me for not having read his back-catalogue of arguments from his other blog:

Tim gives us three pieces of evidence for neo-Darwinian evolution that I am allegedly “wholly unaware of”. This is a curious claim, since his third example I have already explicitly discussed in my writings (towards the end of this post).

 I would like to extend a hearty public (albeit somewhat snide) apology to Mr. McLatchie for not having read his blog. I don't follow it (in fact, I didn't even know it existed until a few months ago), and I certainly haven't had all the time I'd like to have properly browsed it. But for the sake of this particular discussion, it's safe to assume here on out that, if you haven't written it up in one of these articles, I probably haven't read it. So if you refrain from assuming my familiarity with all of your previous writings, and take pains to make your individual points as they apply, then this will go a lot more smoothly in the future.

Third: Mr. McLatchie criticizes the Nguyen et al paper (or rather, my interpretation --- or better, his misrepresentation of my interpretation --- of it), saying that:

On the bacterial flagellum, amazingly, Tim cites a paper (Nguyen et al., 2000) which demonstrates the very opposite from the line of argument he wishes to take! The paper suggests “that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems.” So that research is not much use to Tim’s case (which requires that the flagellum evolved from the Type-III secretion system).

 ....with regard to the bold-faced segment, well, I don't know any nicer way to phrase it than to say that Mr. McLatchie is just plain flat-out wrong here. And I'm not sure why or how he became so wrong. Because I took great pains to state my *actual* case clearly in my last response. Here is what I said (again, click my earlier link to go read it for yourself in context):

What the consensus tells us is that the flagellum and the T3SS probably each had an early precursor from which they diverged, which shared many (but not all) of the necessary genes to express the complete flagellum.

 That is actually quite different from Mr. McLatchie's presentation of what I said. According to him, I'm claiming that the T3SS came first and later evolved into the flagellum. What I actually said was that, regardless of the order in which the two specifically evolved, and based solely on the written conclusion of the study I quoted (i.e. their words, not mine), the T3SS and flagellum evolved not from one another but from a similar construct with many (but not all) genes homologous to parts of both the T3SS and flagellum. In this particular case, there would actually be less evolutionary change necessary to go from the simple homologous ancestor construct to the T3SS and/or flagellum, because a percentage of the necessary genes were already in place in either case. The Matzke model, whether or not it describes an actual account of the history of the T3SS/flagellum relationship, shows that it is at the very least possible, in principle, for such change to occur. Therefore, a smaller degree of change would be mathematically more probable anyway. That was my point.

If Mr. McLatchie would prefer to respond to what I actually said, instead, then that would be fine of course. I don't have much time to waste on straw men, however.

Next point; I won't go into the much larger debate of Lamarckism vs. Mutationism vs. Darwinism vs. etc. so on and so forth; in this paragraph, Mr. McLatchie sums up the current scene of this debate pretty well:

What Tim is describing as “mutationism” here is probably closer to some forms of neo-Lamarckism which maintain that mutations arise not randomly, but in response to environmental pressures. One classic study (Luria and Delbruck 1943) is traditionally cited in these discussions in support of the traditional view that mutations occur irrespective of environmental concerns. This study involved the exposure of a strain of E. coli to bacteriophages and demonstrated that the probability distribution for the number of mutants exhibited the characteristics expected only if random mutations had been present prior to exposure to the phage, apparently ruling out the proposition that the mutations occurred as a result of the phage. That being said, there have been a number of interesting papers that have been published in recent years which report regulation of mutation rates and localised variation in response to stress (see, for instance, Galhardo et al., 2007 and Rando and Verstrepen, 2007).

I of course take no issue with that paragraph. However, as a commenter helpfully pointed out to me in another posting, Mr. McLatchie seems to have (once again) completely missed my point with this criticism:

A further confusion on Tim’s part pertains to his assertion that “An example of [speciation] would be if a particular population of a certain species had mutated sex cells that prevented them from forming offspring with members of other populations of that species; we would then say that this population was ’speciated’ from all other populations.” Mutations in the germ cells which negatively affect an organism’s capacity to reproduce are not going to become fixed in any population because a key part of this process is the ability to reproduce. Does Tim really think this is a serious argument? In any case, Tim seems to think that I somehow have doubts about the occurrence of speciation; but such skepticism is harboured nowhere in my writings.

I was referring to the speciation of populations, not of individual organisms. My argument here pertains to the speciation of entire groups (i.e. populations) of organisms which, while able to reproduce amongst themselves, cannot reproduce with other populations of the same "species." Hence, the differentiation --- or "speciation." Mr. McLatchie's argument that "mutations...which negatively affect an organism's capacity to reproduce are not going to become fixed in any population" only applies here if we're talking about individual organisms. As long as each organism is capable of reproducing within a select population, it doesn't matter what its reproductive compatability is with regard to other populations from which it is genetically isolated (as it has no means of contacting them in the first place, much less breeding with them). So this point is lost on Mr. McLatchie as well.

Skipping ahead a little, to the manatees. I had pointed out the various land-mammalian features of these sea-dwelling features, paired with their apparent lack of need for said features as a mild form of suggestive evidence for the idea that they may be related to land mammals (as, if they are not, then it becomes even more important to explain why they have these features; if they used to be land mammals, and are not anymore, as Mr. McLatchie suggests below, then that would make for a prime example of large-scale evolution, would it not? A land mammal evolving into a completely sea-dwelling mammal with vestigial limbs and parts as evidence of its alteration). Mr. McLatchie writes:

Indeed, it is true that these sea cows possess elephant toenails on their flippers. But this only succeeds in bringing us back to the old “common features = common ancestry” argument. It is also by no means implausible that these organisms were once able to walk on land.

 Again, as mentioned above, this is indeed part of my original argument --- that manatees are in some way related to land mammals! If a manatee used to be a land mammal, then that would make it the evolutionary successor of a land mammal, would it not? Hence, Mr. McLatchie makes my point for me.

With regard to ape chromosome fusion, Mr. McLatchie writes:

To make much of the 2q13 interstitial telomeric sequence and portray it as typical of what is observed in chimp and human genomes may be considered careful cherry-picking of data.

To "make much" of it...."may" be "considered" careful cherry-picking of data. Notice the careful use of these terms so as not to imply a definite conclusion? Mr. McLatchie commits the fallacy of assuming that I offered this evidence as, in itself, conclusive. It is simply suggestive. He doesn't do much to negate my point here other than to point out that, in itself, it is not 100% conclusive. Well, I could have told you that! The closest thing to any single fact about evolution that can be construed as anything close to "100% conclusive" is the classically-cited lack of, say, rabbits in the Cambrian layer. Find one rabbit in the Cambrian and you ruin the entire theory of evolution. And yet to this day, no rabbits in the Cambrian. That in itself is rather convicting evidence....but again, only in context with the rest of the theory! For without the rest of the theory, we wouldn't know *why* the lack of rabbits in the Cambrian is proof.

No, Tim, this is a retrospective analysis based on sequence homologies. At the very best, it would demonstrate common ancestry of the globin protein family (but even that conclusion is suspect).

...I would ask Mr. McLatchie if he even read what I said in any detail. "At the very best, it would demonstrate common ancestry of the globin protein family." That is exactly what I said! My original quote, which (oddly) Mr. McLatchie cites in his response:

there is evidence that the four protein chains in current human adult globins actually originated from an ancestor genome which “split” around 500,000,000 years ago into two parts; each part then later mutated separately and became a different cluster. This happened again around 400,000,000 years ago, and the alpha gene mutated again, following a similar path and giving us the zeta chain. This much is actually supported by contemporary phylogenetic analysis, as well — other animals descended from those who existed around the time of the genome split (and which were associated with our ancestral line) also demonstrate this same split, and the same chromosomal arrangement of these genomes.

The fact that this same sequence split is manifest across species lines (and in species which other evidence suggests to be distantly related) is evidence of evolutionary speciation on a large scale. And the further fact that these analyses match up with our other evidence indicating the approximate time of speciation between those species is yet another point of interest. If Mr. McLatchie had read the Dawkins article I linked to, he would've read this passage:

Here’s the fascinating point. Careful letter-by-letter analysis shows that these different kinds of globin genes are literally cousins of each other, literally members of a family. But these distant cousins still coexist inside our own genome, and that of all vertebrates. On the scale of a whole organism, the vertebrates are our cousins too. The tree of vertebrate evolution is the family tree we are all familiar with, its branch-points representing speciation events — the splitting of species into pairs of daughter species. But there is another family tree occupying the same timescale, whose branches represent not speciation events but gene duplication events within genomes.

The dozen or so different globins inside you are descended from an ancient globin gene which, in a remote ancestor who lived about half a billion years ago, duplicated, after which both copies stayed in the genome. There were then two copies of it, in different parts of the genome of all descendant animals. One copy was destined to give rise to the alpha cluster (on what would eventually become Chromosome 11 in our genome), the other to the beta cluster (on Chromosome 16). As the aeons passed, there were further duplications (and doubtless some deletions as well). Around 400 million years ago the ancestral alpha gene duplicated again, but this time the two copies remained near neighbours of each other, in a cluster on the same chromosome. One of them was destined to become the zeta of our embryos, the other became the alpha globin genes of adult humans (other branches gave rise to the nonfunctional pseudogenes I mentioned). It was a similar story along the beta branch of the family, but with duplications at other moments in geological history.

Now here’s an equally fascinating point. Given that the split between the alpha cluster and the beta cluster took place 500 million years ago, it will of course not be just our human genomes that show the split — possess alpha genes in a different part of the genome from beta genes. We should see the same within-genome split if we look at any other mammals, at birds, reptiles, amphibians and bony fish, for our common ancestor with all of them lived less than 500 million years ago. Wherever it has been investigated, this expectation has proved correct. Our greatest hope of finding a vertebrate that does not share with us the ancient alpha/beta split would be a jawless fish like a lamprey, for they are our most remote cousins among surviving vertebrates; they are the only surviving vertebrates whose common ancestor with the rest of the vertebrates is sufficiently ancient that it could have predated the alpha/beta split. Sure enough, these jawless fishes are the only known vertebrates that lack the alpha/beta divide.

That is a very, very interesting coincidence, given Mr. McLatchie's assertion that these speciation events never took place! I hold here that divergent evolutionary speciation is a much better, much more concise, and much more roundly-supported explanation for this convergence of otherwise very mysterious "coincidences." So how does Mr. McLatchie account for this interesting coincidence, given a complete lack of mass-scale speciation as he has hypothesized? Or can he, even? I wonder. He seems to be a proponent of Intelligent Design Creationism; do they hold this as a great mystery of life? Or do they have some explanation for it? You may not be able to tell through my somewhat snarky tone at the moment, but I'm genuinely interested to hear of it if they do.

I mean, he talks of globins as if I'm saying they just evolved willy-nilly overnight. Each of these events is believed to have happened over 100 million years apart! And the degree to which he attributes them to a single chance mutation is reminiscent of the "what use is half an eye?" argument that creationists used to use before common sense gave us the answer: "crude function out-competes no function at all," i.e., it's better to see badly than not see anything. But that's another debate altogether, and I don't want to get TOO much farther off topic in this posting.

Speaking of Intelligent Design Creationism....McLatchie writes:

[C]ommon ancestry is not, in and of itself, a causal process. Common descent could be correct but the neo-Darwinian mutation/selection mechanism totally wrong. Since ID — in its purest sense — only claims to be able to detect patterns in nature which are best explained as the product of an intelligent cause, the theory is silent on the issue of common ancestry.What ID does challenge is the materialistic view of evolution which envisions the origins and development of life on earth as being the product of the mindless and impersonal forces of nature.

For my closing, I would like to ask two questions....

(1) So you admit, then, that IDC cannot explain why we see common descent?
(2) If evolution happened, it happened; it doesn't matter whether god did it or whether it happened because of some hidden inevitability given the laws of physics, enough time, and enough opportunity. Even if we say "someone" (i.e. god) created life, or that this "someone" somehow engineered the process of evolution, that's completely irrelevant information unless we can say HOW they did it. Science is not a question of, "who did it? Nature or god?" That's a false dichotomy painted by IDC proponents and perhaps some overly fierce atheists. No, the central question of any explanatory theory is, "how?"

That is my biggest problem with IDC, is that its proponents find themselves almost completely unconcerned with the methodology of "how," only with the ideological ramifications of accepting the existing theory of evolution. In fact, it's as if the entire IDC movement exists solely as a counterpoint to the perceived moral and ideological ramifications of the existing evolutionary theory. Look, I really really hope the Christian god isn't real, but if he was, I would have to accept that, regardless of the ideological ramifications it would bring to my current worldview. To oppose the materialistic theory of evolution because of some ideological ramification is just, well, dishonest. Dishonest, and stupid. It's like saying, "guns don't work because if you shoot someone in the face, that's wrong."

Ideology has nothing to do with it, at least for me.

--Tim D.