Monday, September 03, 2007

A Couple Of Vehement Pro-Darwinist Arguments Shot Down

Richard Dawkins "blows away" Michael Behe's latest book in the New York Times, by referring to dog breeding. A blogger named ERV finds a "fatal mistake" in the book. The Darwinists all party like it's 1999, doing a victory dance in the endzone, not noticing the flags on the field.

Post Darwinist
has an excellent post illustrating that dog breeding proves quite the opposite of what Dawkins thinks. The way I've summed up the erroneous reasoning of Dawkins is that, while you can get a Chihuahua from an Arctic wolf, you will never get an Arctic wolf from breeding Chihuahuas. The complete information necessary to build an Arctic wolf is missing from Chihuahuas. It has been bred out. Domestic breeding is not "evolution". Dawkins leaves that inconvenient truth out of his diatribe. Another inconvenient truth is that domestic breeding is an intelligent process. Breeders impose huge selection coefficients on particular characteristics that nature never could. You could wait in vain for millions of years, and nature would not yield a Jack Russell terrier, a Pekingese, or a St. Bernard. And yet the Darwinists jump up and down with glee over Dawkins and his "argument".

ERV's challenge is given here. Upon seeing it, the Darwinsts declared, "GAME, SET AND MATCH!!!"

Not so fast, kids. This post opened up a heated discussion, which included ERV for a time, until she was given the boot (unfairly in my opinion). The discussion carried on elsewhere. This comment, I think, summarizes where things stand:

I’ve been over at ERV’s blog trying to discuss her ‘challenge’. ERV has been, for the most part, AWOL. (In her defense, she’s a student. OTOH, she’s started up a thread or two in the meantime).

In any event, it seems to me that there’s several issues involved here.

ERV’s basic challenge–although it wasn’t formally accepted as such on her blog–is that, contrary to what a.) Behe says in EoE, and contrary to what he should clearly have been aware of, b.) HIV presents an example of multiple protein-to-protein binding sites (4) in c.) much less the number of replications in a CCC (10^20), thus d.) falsigying Behe’s claims.

I’ll start with d.) and work backwards.

The argument Behe makes in EoE deals exclusively, and consistently, with eukaryotic cells. Viruses aren’t even classified as “life”. We’re not even dealing with prokaryotic life. So, to take what Behe claims about “cells” (meaning eukaryotic cells) and then to turn that around and claim that this is falsified by what is found in a virus, is, I believe, to completely miss the point of the book. Behe wants to compare the number of replications (progeny) that eukaryotes need simply to come up with a two a.a. change to its genome (in the case of the malarial parasite) to the number of mammals that have ever arisen. If an argument is to be attacked, that’s where one should start.

I think this is so self-evident, that I won’t comment any further.

As to c.)—where it is being claimed that novel complexity is seen occurring in far less replications than a CCC (10^20)—I think we have to step back and remember point d.), that Behe claims a CCC limit in eukaryotic cells—not in any kind of virus; and then we need to try and remember how Behe arrived at his CCC in the first place.

His CCC is based on a review written by Nicholas White. In that review, quoting EoE, White “[multiplied]the number of parasites in a person who is very ill with malaria times the number of people who get malaria per year times the number of years since the introduction of chloroquine, then you can estimate that the odds of a parasite developing resistance to chlorquine is roughly one in a hundred billion billion. In shorthand scientific notation, that’s one in 10^20.” (p. 57)

Now, to get an idea of Behe’s thinking on this, here’s what he wrote on p. 59:
“The odds [of achieving atovoquone resistance and of chloroquine resistance] are, respectively, one in a trillion (10^12) and one in a hundred billion billion (10^20). The ratio of the two numbers shows that the malarial parasite is a hundred million times (10^8) less likely to develop resistance to chloroquine than to atovaquone. This is reasonable since the genome size of the malarial parasite is in the neighborhood of a hundred million nucleotides. The implication is that if two amino acids in a protein have to be changed instead of just one, that decreases the likelihood of resistance by a factor of about a hundred million.”

As I pointed out at ERV’s blog, it’s quite obvious that Behe sees a connection between genome size and the level of improbability of getting particular point mutations in that same genome. But why, then, isn’t the CCC one in 10^16 (i.e., 10^8 for the first mutation, times, 10^8 for the second), and not, as Behe presents, one in 10^20? Well, it’s because Behe is using actual in vivo numbers. The fact is that the in vitro (what is seen in the lab) resistance to atovaquone is one in 10^10 or lower, but because of some kind of in vivo (the more life-like scenario) effect (for some of the reasons that White points out in his paper, and especially host immunity) inerfering with the development of resistance to atovaquone. So we end up with one in 10^20. But Behe’s remark about one in 10^8, linked as it is to genome size, makes it legitimate (in my view, at least) to sort of guess how Behe would approach the case of the virus. In EoE, he tells us that the mutation rate of the HIV virus is 10,000 greater than eukaryotes (which ought to be a warning about comparing the two). The figure, per Wikipedia, is in the area of 3×10^-5. The actual genome of HIV is roughly the inverse of this number. For two mutations, then, a simple calculation would be (3 x 10^-5) x (3 x 10^-5)= 9 x 10^-10=approx. 10^-9. Well, this 10^-9 number is the very number that Ian Musgrave (I believe it was he who made the calculation) gives for HIV-1 and the changes it has undergone. I hope this makes clear that it would be wrong to simply carry over the one in 10^20 CCC number that Behe uses for eukaryotes and apply it to the case of HIV.

Let’s now discuss b.): HIV presents an example of multiple protein-to-protein binding sites. Again, the starting point has to be EoE. It is very clear that Behe was talking about protein-to-protein interactions arising within the eukaryotic cell. If you look at his book, and the language that he uses, he’s always talking about the “cell”. Well, HIV isn’t a cell. For most scientists, it doesn’t even represent “life”. But what one also finds is that Behe is preoccupied with the development of novel cellular structures. In the case of P. falciparum, the malarial parasite, the a.a. changes happened to IT. The PARASITE changed. Two transporters have changed, allowing IT to survive. In the case of HIV, the vpu protein has changed, protecting it from the human immune system, in fact debilitating it. But the effect is exogenous, not endogenous, as in the case of P. falciparum.

Now this could be misconstrued as being too nitpicky: what does it matter if the changes are inside or outside? Well, to be consistent with Behe’s argument, it should technically consider only internal changes. When Behe addresses HIV, he says he see no novelty in it, meaning, I’m rather sure, that you have the same complement of genes now as you did 50 years ago; and, if you look at HIV microscopically, it doesn’t appear to be any different than before. This, pretty much, is what a.) is all about: simply understanding what Behe meant in his comments about HIV.

But, for the sake of the argument, let’s leave this solid understanding of Behe’s argument to the one side, and simply begin to examine just how many a.a. substitutions are involved in the changed function of vpu in HIV-1 versus, let’s say, vpu in SIVcpz. The first thing we have to consider is just how highly variable HIV is, as Behe rightly points out. Wikipedia says this: “HIV differs from many other viruses as it has very high genetic variability. This diversity is a result of its fast replication cycle, with the generation of 109 to 1010 virions every day, coupled with a high mutation rate of approximately 3 x 10-5 per nucleotide base per cycle of replication and recombinogenic properties of reverse transcriptase.”

HIV’s genome size is in the tens of thousands of nucleotides—very small. So, at 10^9 to 10^10 virions per day, and with the high error rate associated with reverse transcriptase (HIV’s genome is basically RNA, which is then “transcribed” [in reverse fashion] to DNA) all kinds of things can happen to HIV in very short order. So why should we be surprised that vpu in HIV is different from that of SIVcpz? There are all kinds of possibilities that can be explored mutationally in any of HIV’s gene complement. But, again, what about genetic, biochemcial novelty? Do we see it? Well, no. What we do see, though, are changes in the effects its gene’s products have on its hosts; and, thus, its survivibility. Yes, it’s NS at work. And so it would be no surprise at all that different “types” (subtypes) of HIV could co-exist. And they do. Again, no surprise here. Well, what about these changes, what’s involved? How complex are they? My brief literature search suggests to me that in some of the changed interactions between host and HIV that ERV mentions, that the “essential” changes (remember, there can be lots of so-called “neutral” substitutions) involve two a.a.s. Rather ho-hum, don’t you think?

I must confess, though, that what was not so ho-hum, and which actually startled me at first about ERV’s claims was that vpu (she writes Vpu; BTW, this stands for viral protein U) HIV’s vpu, that is, could now form an “ion-channel”, and that it did so by forming a viroporin (a composite structure). Well, this deserved some examining. And upon a very brief examination (you can look here and here, for example) interestingly, vpu is found to be structurally similar to the M2 gene of Type A influenza, and, in turn, M2 proteins, more or less, spontaneously form “ion-channels”. This then brings up the whole question as to whether what makes HIV the unique virus it is (different, that is, from the vpu in SIVcpz), is that somewhere along the line, whether in a human or a simian, it replaced its original vpu gene with this M2 gene. HIV is known to form hybrid viruses. M2 is also known to interact with CD4+T-cells. So, are we dealing with a case here where two viruses swapped genes? In all honesty, I can’t say (and I have no desire to spend all the time and effort that would be needed to run this down); but what little I have looked at is very suggestive. In Dembski’s terms, maybe all we’re seeing is the Law of Conservation of Information at work, where the information of the M2 gene is simply being “added” to that of SIV/HIV (really, replacing the previous information with this different information). I’m sure our Darwinian friends would strenously disagree with this view. But I don’t think it unreasonable in the least. I think the burden of proof is on them to demonstrate unequivocally that vpu does not have its origins in M2.

To summarize, then, the probability of a CCC occuring in a eukaryotic cell is far different from that of HIV. The challenges that ERV makes to Behe and EoE, fall outside the import of what Behe was saying about HIV in his book. The supposed novelty(ies) in HIV-1 may not, in some cases, be real novelties at all, but may in some way be linked to the phylogenetic history of the vpu gene itself. And, in those instances where some kind of novel interactions with the host are involved, in those changed interactions between host and HIV, what is seen represents, at least preliminarily, no more than an equivalent viral CCC; i.e., a two a.a. change within 10^9 replications of HIV.

[[As a kind of addendum to all of this, let me make a point here that I briefly alluded to at ERV’s blog. The current cry of OOL Darwinists is that DNA didn’t get everything started; that life began as a RNA-world. And they would argue that all that would be needed is for replication to start happening. Well, are those ingredients found in retroviruses, where you have RNA replicating itself at will? And don’t you have even much more than that, given that the replication takes place in an eukaryotic host which has an abundance of RNA and DNA among its constituents? Think of the speed of replication. Think of its high error rate (mutation rate). Think of its high recombinant rate. And what do we have after millenia of interactions between viruses and their hosts? Viruses and their hosts. And, viruses haven’t even made it to the starting gate: they’re still not considered “life”.]]

It is as I have witnessed it, again, and again, and again over the last ten years. "Devastating" pro-Darwinist arguments are always reasonably rebutted. But this will not prevent us from endlessly hearing from now on that Behe has been consigned to the outer darkness by Dawkins and ERV, and that there's "nothing to see here". When reasonable folks who have been following the debate disagree, they will be branded as IDiots, theocrats, creationists, and morons.

Ah, well.

The world can be a very confusing place to those blinded by their metaphysical commitments.


Hermagoras said...

That comment at UD didn't even characterize ERV's challenge correctly. It set up a strawman. So, not really.

Matteo said...

But of course. If there is a difference of opinion with a Darwinist about evidence, or how an argument has proceeded, the Darwinist is always, ALWAYS right. So I stand corrected.

Hermagoras said...

It's not quite that simple. Whatever the merits of PaV's argument -- and we can disagree about that -- it did not address ERV's central point. As I put it in a comment to PaV at ERV (sorry for the second person),

If "basic challenge" refers to ERV's first post on the subject, then No. That was not her "basic challenge." As you point out, she didn't even say that on her blog. It was not her point. Her point was addressed to a specific moment in an interview where Behe repeats something that is easily shown to be wrong. This moment in the interview leads ERV back to the same claim in the book (that HIV's "basic genetics have changed little in the last decades," Figure 7.3). It is that claim which she shows to be wrong.

She's not showing that the whole book is wrong (though her findings have implications for the whole). She is showing that, where Behe's claims interact with her area of expertise, Behe is wrong.

This is, of course, highly amusing, as Behe's the expert, and ERV is "just" a graduate student. It makes one wonder what other broad and unsupported claims are in the book.

Now, I appreciate PaV's tone, which is rare at UD. But PaV simply gets the main point of ERV's critique wrong. The point was about a specific claim with respect to HIV.