10 October 2005

Dog Bites Man

I was going to title this post something like, "Casey Luskin totally misunderstands and misrepresents something related to biology," but the title I settled on seems to sum up the news level involved much more concisely. In this instance, Casey attempts to explain away some of the evidence for human-chimp common descent that was presented by Ken Miller during his testimony last week in the Dover case.

I'd like to be able to quote the entire relevant portion of Dr. Miller's testimony here, both because it establishes the context for Luskin's ill-founded critique, and because it is a beautifully elegant and simple explanation of a powerful piece of evidence that supports the common ancestry of apes and humans. However, it is too long for that to be convenient. If you want to read the whole thing for yourself - and I encourage you to - you will find it starting on page 22 of the pdf file linked above.

Luskin starts off by taking some gratituitous digs at the status of evolution, deliberately misunderstanding the reasons for Miller's testimony, and with some other inanities. He then moves on to his main complaints with Miller's testimony:
Miller made his prediction that there was a fusion event simply by counting chromosomes in apes and humans—not by analyzing the chromosomes themselves.

Miller started off his "prediction" by simply observing that humans have 23 pairs of chromosomes and apes have 24 pairs; therefore two ape chromosomes were fused into one human chromosome. Miller claims that this simple chromosome-counting requires a fusion event if common ancestry is true.

Actually, Dr. Miller did more than "chromosome counting". This is fairly obvious after just a cursory reading of the testimony.
Miller:
Now, what that means, Mr. Walczak, is that you and I, in a sense, are missing a chromosome, we're missing a pair of chromosomes. And the question is, if evolution is right about this common ancestry idea, where did the chromosome go?

Now, there's no possibility that that common ancestry which would have had 48 chromosomes because the other three species have 48, there's no possibility the chromosome could have just got lost or thrown away. Chromosome has so much genetic information on it that the loss of a whole chromosome would probably be fatal. So that's not a hypothesis.

Therefore, evolution makes a testable prediction, and that is, somewhere in the human genome we've got to be able to find a human chromosome that actually shows the point at which two of these common ancestors were pasted together.
As you can see, the reason for Miller's prediction goes a bit beyond the, "apes have 48, we have 46, so we must have had 48 once, too" line that Luskin presents. The prediction is trivially obvious - if you understand the slightest thing about common descent. If humans and apes are closely related, then their genomes will, we expect, be very similar. This means that if we are short a chromosome pair in comparison to apes, then that genetic material needs to be somewhere.

Mr. Luskin, however, has some ideas about other things that could be responsible for the chromosomal patterns that we see:
Why couldn't it be the case that the common ancestor had 23 distinct chromosomes, and one chromosome underwent duplication in the line that led to apes? Or maybe the common ancestor had 20 distinct chromosomes and there have been 4 duplications events in the ape line, and 3 in the human line?
The short answer to Luskin's question is that the different chromosomes are, well, different. We have looked at them. We have sequenced them. They are not obvious duplicates. They have different genes. That would, to me, seem to argue strongly against the pattern that we see being the result of a series of recent duplication events. Of course, I'm kind of strange when it comes to formulating opinions about stuff like that. I think that evidence actually means something.

Casey continues:
or maybe the ancestor had 30 distinct chromosomes and there have been 6 fusion events for ape-line but 7 fusion events for the human-line.

Do you see my point? Simple chromosome-counting or comparisons of numbers of chromosomes does not lead common ancestry to make any hard predictions about how many chromosomes our alleged ape-human common ancestor had. So, under Miller's logic, there is no reason why a chromosomal fusion event is a necessary prediction of common ancestry for all upper primates.
Casey might actually have a point here, if his representation of Miller's argument had even the faintest resemblance to reality. However, the argument is nowhere near as simplistic as Luskin makes out. (Shocking, that.)

Not content with mere error, however, Luskin descends into sheer inanity:
In fact, if we find evidence that humans have two distinct chromosomes that have evidence of fusion (i.e., let's say human chromosome #2 has fusion evidence, and then, hypothetically, we also find evidence for fusion on human chromosome #9), then under Miller's logic, if apes lack any evidence for a fused chromosome, then this should count against common ancestry. Thus, at the present time, absent a full analysis of fusion evidence in our chromosomes, we cannot necessarily say that the presence of one fused chromosome in humans is a prediction of common ancestry. Much more research still needs to be done.
Wow. Now there is an argument that lacks honesty, integrity, reason, intelligence, and logic. And all at once, too. Where to start...
First, Casey's so-called argument is based on the assumption that unless we know everything, we know nothing. That's a rather pitiful attempt to dodge actually looking at any evidence ever. Second, Casey somehow or another manages to assume that we actually don't know about the other chromosomes. The fact is, we have a pretty good idea about human and chimp chromosomes. It's one of the things that you pick up after years of study - particularly when you do little things like sequence the entire genomes of humans and chimps.

Luskin decides not to quit while he's behind:
So I am more than willing to acknowledge and affirm that Miller did provide some very good direct empirical evidence for a chromosomal fusion event which created human chromosome #2. But I'm more interested in two other questions: if we accept Miller's chromosomal fusion evidence as accurate, then (1) is his chromosome fusion story good evidence for Neo-Darwinian common ancestry between humans and apes? Or (2) does it perhaps pose great problems for a Neo-Darwinian account?

The answer to question (1) is "NO" and the answer to question (2) is "YES!"
This should be good.

The fusion-evidence implies that some of our ancestors likely had 48 chromosomes. But Miller has not provided any evidence that the individual with 48 chromosomes was historically related to modern apes. (I grant that our chromosome #2 has banding patterns similar to two ape chromosomes, but given that our chromosome structure is generally similar to that of apes anyways, it is not a stretch to assume that any 48 chromosome ancestor of you and me had a chromosome structure similar to apes, regardless of whether or not that individual was related to apes. Claiming that banding pattern similarities is evidence of common ancestry with apes simply invokes the “similarity = ancestry” argument, and thus begs the question.) It is entirely possible that our genus Homo underwent a chromosomal fusion event within its own separate history.

OK. First, we expect, based on common ancestry, to find that our chromosome structure is similar to that of apes. The Intelligent Design folks, on the other hand, expect that... well, actually, this is another case where ID predicts absolutely nothing.

Second, we do not claim that the chromosome banding patterns are evidence for common ancestry because they "look similar". Chromosome banding patterns are yet another area that we have been researching for decades. We know that they are heritable characters. In fact, they are heritable characters that are shared between humans and apes. That is evidence for common descent.

As far as the third point is concerned, the chromosome fusion certainly could have taken place any time after the human-ape split. Nobody I know of is claiming that the chromosome fusion is the reason that we are different from apes. It is evidence that we share a common ancestor with them, and it may have played a role in the divergence, but it may also have played no role whatsoever.

Luskin, however, fails to grasp this:
All that evolutionists have claimed is that this fusion event occurred after the split that led to humans, so it occurs only in the human lineage. Evidence of a chromosomal fusion event is not evidence that our line leads all the way back to apes.

Given that we had a 48-chromosome ancestor, we don't know if our 48-chromosome ancestor was an ape or not. For all we know, our 48-chromosome ancestor was a part of a separately designed species, as fully human as anyone you meet on the street today. There is no good reason to think that going from a 46-chromosome individual to a 48-chromosome individual would make our species more ape-like.

Common descent could not have been falsified if there was no evidence for a fusion event, but common descent certainly is not refuted by the presence of a fusion event. The question now stands, does this fusion event provide any evidence for common ancestry between humans and apes? The answer to that question is no.
That last paragraph is a bit confusing, and I'm not entirely sure what he's trying to get at. Let me try to make the reality-based view a bit more clear. Based on everything that we know about our relationship with apes, we could quite firmly predict that there would be a chromosome fusion, and we could predict which chromosomes would be involved. The prediction turned out to be correct. Had it not turned out to be correct, that would have been a very, very large problem. It would, in fact, have refuted our common descent-based expectations. Personally, I think that the fact that the predictions of common descent were so clearly met is powerful evidence in favor of common descent. But again, that's just my own reality-based view.

Luskin, after presenting a fancy (but meaningless and misleading) animated gif, moves on to his next line of misunderstanding:
Under Neo-Darwinism, genetic mutation events (including chromosomal aberrations) are generally assumed to be random and unguided. Miller's Cold-Fusion tale becomes more suspicious when one starts to ask harder questions like "how could a natural, unguided chromosomal fusion event get fixed into a population, much less how could it result in viable offspring?"
That is actually a relatively reasonable question, and the concepts involved can be confusing. I'll try to explain them as clearly as possible, as I respond to each of Casey's points.
Casey:
(1) In most of our experience, individuals with the randomly-fused chromosome can be normal, but it is very likely that their offspring will ultimately have a genetic disease. A classic example of such is a cause of Down syndrome.
This is actually not quite true. Down syndrome is caused by duplication of chromosome 21, resulting in the victim having not the normal two, but rather three copies of the chromosome. A chromosome fusion is not a duplication. A chromosomal fusion occurs when two different chromosomes get stuck together, forming one larger chromosome. Someone with a chromosome fusion has no more, and no fewer, copies of any particular gene than someone without that fusion. They are likely to be genetically normal.
Casey:
(2) One way around the problem in (1) is to find a mate that also had an identical chromosomal fusion event.
Actually, all that is necessary for successful reproduction is for the chromosomes in one individual be able to line up with the other individual's chromosomes. This is entirely possible in the case of a recent fusion, particularly since the same chromosome sequences are present in both individuals.

In some cases, differences in chromosome number can result in the offspring being sterile. This is, in fact, what happens in mules. However, that type of thing doesn't happen right after a fusion. It happens once enough changes have occurred in the fused chromosomes that they can no longer line up with their unfused counterparts.

There are actually some populations of Drosophila species that are polymorphic in their number of chromosomes. That means that, within the species, some individuals will have the chromosome fusion, and others will not. The two types interbreed freely.

Luskin concludes:
Miller may have found good empirical evidence for a chromosomal fusion event. But all of our experience with mammalian genetics tells us that such a chromosomal aberration should have resulted in a non-viable mutant, or non-viable offspring. Thus, Neo-Darwinism has a hard time explaining why such a random fusion event was somehow advantageous.

If it were to turn out that the fusion of two chromosomes can only result in a viable individual if the fusion event takes place in a highly unlikely and highly specified manner, then we may actually be looking at a case for a non-Darwinian intelligent design event in the history of the human genus.
Actually, none of our experience with mammalian genetics tells us that a chromosome fusion should have resulted in either a non-viable or a non-fertile offspring. In fact, our knowledge of Drosophila genetics - coupled with our evolutionarily-informed understanding that fly genetics are not all that different from mammalian genetics - tells us that these sort of fusions don't usually have any impact on the viability or fertility of the offspring.

Mr. Luskin's criticisms are, as always, poorly informed. Dr. Miller, unlike Casey, understands biology and evolution. His choice of the chromosome differences between humans and apes was a very good example of evidence for common descent.
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