Sunday, July 22, 2012

Why All the Fuss About Chromosomes?

I've been following the latest kerfluffle on the fusion of two chromosome into one during human evolution. I understand the superficial dispute involving Carl Zimmer. He had the audacity to ask for evidence to back up a claim being made by the IDiots on their Facebook page and they responded by going nuclear [The Mystery of the Missing Chromosomes, Continued: An Update From Your Preening Blogger].

Typical.

Let's step back a bit and ask why the IDiots are so upset. Carl Zimmer posted a really nice summary of the evidence that two smallish chimp chromosomes fused to produce human chromosome 2 [The Mystery of the Missing Chromosome]. That evidence is based on an analysis of the chimp, human, and gorilla genomes and it allows scientists to reconstruct the events that led up to the fusion. All of the DNA sequence around the fusion point are consistent with what we might expect, especially the presence of defective telomeres (sequences at the ends of chromosomes).

Why are the IDiots so bothered by this evidence? It's not as if it's new—the essential evidence has been around for decades. There must be something else going on that causes the IDiots to circle the wagons at this time.

It think it's all about their latest book Science & Human Origins by Ann Gauger, Douglas Axe, and Casey Luskin.1 The book is published by the Discovery Institute Press. In that book, two of the authors (Gauger and Luskin), apparently argue that science cannot rule out a recent origin of humans descended from Adam and Eve. The chromosome fusion data threatens that bizarre claim and perhaps that's why they are reacting so strongly.

I think I understand this. The IDiots have made bold claims about some of their recent books (e.g. Signature in the Cell: DNA and the Evidence for Intelligent Design , The Myth of Junk DNA) but those books have been met by yawning indifference from the general public and devastating criticism from real scientists. Two of the authors on this latest book (Gauger and Axe) have substantial scientific credentials so the Discovery Institute must have expected that the book would stand up to criticism by other scientists.

Instead, a "mere" graduate student (Paul McBride) has dimantled the book chapter by chapter [Science & Human Origins: Review] and a "mere" science writer, Carl Zimmer, has challenged the integrity of two "scientists" (and a lawyer). No wonder they're upset. All of their wonderful books are scientific embarrassments.

On what grounds do the IDiots want to deny the chromosomal evidence that humans and chimps share a common ancestor? Carl Zimmer supplies a partial answer when he quotes one of the chief IDiot defenders, David Klinhoffer, who says ...
The evidence from chromosomal fusion, for one, is strikingly ambiguous. In the Darwinian presentation, the fact that humans possess 23 chromosome pairs and great apes 24 clearly points to an event in which human chromosome 2 formed from a fusion, leaving in its wake the telltale sign of telomeric DNA — normally appearing as a protective cap at the end of the chromosome — in the middle where it doesn’t belong. Ergo, common descent.

But Casey [Luskin, of the Discovery Institute and co-author of the book] explains, there’s a lot wrong with this inference. Even if there was such an event and humans once had 24 chromosome pairs, it doesn’t at all follow that this happened in some prehuman past. Nothing stands in the way of picturing a human population bottleneck accomplishing the spread of a fused chromosome 2 from part of an early human community to all of it.

But the idea of such an event having occurred at all is itself far from sure. The telomeric DNA parked in the middle of chromosome 2 is not a unique phenomenon. Other mammals have it too, across their own genomes. Even if it were unique, there’s much less of it than you would expect from the amalgamation of two telomeres. Finally, it appears in a “degenerate,” “highly diverged” form that should not be the case if the joining happened in the recent past, circa 6 million years ago, as the Darwinian interpretation holds.
That's it? The fusion event could have happened relatively recently in human evolution so it's no big deal? And if you don't buy that, then maybe it didn't happen at all because the junction sequence isn't exactly what a typical IDiot might expect if evolution were true?

(Carl asked for the evidence that that the junction sequence isn't what one might expect and that's what caused the latest problem.)

I think that even the most stupid IDiots realize that they are in a very weak position on this one. They have been painted into a corner where the only way out is to admit that chromosome fusions happens&mdashbut only in the past 10,000 years—or that solid scientific evidence is wrong and there was no fusion. Neither option is appealing.

That's why you see people like Cornelius Hunter desperately looking for another way out [Carl Zimmer Doubles Down on Chromosome Two Lies and Misdemeanors] and why the people at Uncommon Descent have picked up on a non-scientific way to defend Intelligent Design Creationism [Why no one can confute Darwinism and, consequently, no one should believe it].

My question for Intelligent Design Creationists is, "why all the fuss?" What is there about the figure at the top of the page that really upsets you? Aren't most of you supporters of common descent in some form or another? Are all of you really going to defend the idea that humans have no evolutionary history with the other apes?


1. I haven't read the book. It's on order but it still hasn't been released in Canada (see Amazon.ca).

19 comments:

  1. Don't forget that ID is a big tent. A few of them, like Behe, accept pretty much the entire history of life, just with occasional tweaks from the Finger of God. Others are YECs, or OECs, or hold internally inconsistent mashups of all the above. And to make matters worse, it can be hard to tell just where an individual stands on all that. Maintenance of the big tent takes precedence over transparency. But I'm guessing that Casey Luskin and Ann Gauger may be at least progressive creationists. Doug Axe is a more ambiguous case.

    The importance of chromosome 2 isn't that it shows a relationship between humans and chimps but that it destroys a supposed objection to that relationship. It's an autapomorphy and so is uninformative about phylogeny. But why should humans have the same primitive state as (other) primates? As long as there's no way to transform 24 into 23, there's an argument for human uniqueness. Not a good argument, but you use what you have.

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  2. The fact that humans have 46 and not 48 chromosomes has the potential to falsify common ancestry among humans and apes if it is shown that humans have one less chromosomal pair. The fusion event prevents any falsification, but it does not verify common ancestry.

    There is no evidence that this fusion event happened 6 million years ago. It could have happened 2 million years ago or 1 million years ago (i.e when Homo erectus was around). However, most experts believe that the fusion event was critical in the formation of the human lineage by acting as a reproductive barrier.

    Why does Larry have such a problem understanding this basic point?

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    1. I don't have a problem undrstanding the basic points.

      1. No evolutionary biologist believes that the chromosomal event, by itself, is responsible for the possible (unproven) reproductive isolation of humans and chimps. But even if it was (were), so what? Why does this make the IDiots so worried today when they've known about this for almost three decades?

      2. The degeneration of the telomere fusion region suggests that the fusion event took place millions of years ago. It has to be at least long enough ago for the rearrangement to have become fixed in the human population by random genetic drift. This suggests that it happened at least one million years ago. Why is this important to the IDiots? Biologists don't care whether it happened one million years ago or six million years ago. Why should IDiots? (Many of them think that the universe was only created 6000 years ago so the whole discussion about the evidence for chromosome rearrangements is pointless.)

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    2. Who are these "most experts"? Most experts I know of agree that acrocentric fusions are not a significant barrier to reproduction.

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    3. 1. It is only unproven because nobody is mad enough to try and breed chimp-human hybrids! Of course, if such a thing were possible, it would severely dent the arguments of creationists who believe in the specialness of humans. But chromosomal variation, like it or not, is a major cause for reproductive isolation leading to speciation.

      2. Degeneration at any sequence rendered functionally useless can be a very rapid process indeed. I agree the fusion event is unlikely to have happened 6000 years, but it is far from established if it happened 6 million years ago.

      3. As I have pointed out to you ad nauseam, Larry, a speciation event due to reproductive isolation involves a break with the larger population - similar to the founder effect. It need not have taken 1 million years just to become fixed in our lineage by neutral means! You had better get your buddy Joe Felsenstein to explain this to you.

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    4. You understand, I hope, that there are species other than H. sapiens and Pan troglodytes. And that we could test the reproductive cost of acrocentric fusions in these other species. And that we have indeed done such things, and they don't affect interbreeding very much. Oddly enough, Carl Zimmer mentions some of these cases in his post, but I suppose you just unaccountably overlooked that.

      Degeneration in any nonfunctional sequence happens at the rate of neutral evolution. Are you suggesting some sort of active mechanism to make it happen faster?

      What evidence do you have for speciation due to founder effect in the human lineage, or evidence that founder effect speciation is the sole mechanism of speciation?

      Are you entirely sure you're a grad student in bioinformatics?

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    5. If a rearrangement were an effective isolating agent, it would be at the extreme of founder effects - the bearer would be unable to perform a successful meiosis; a founder group of 1. Hard to see how a population of 1, producing infertile offspring if at all, can be a founder. But translocations are routinely observed to have no effect on phenotype and no or a limited effect on fitness.

      There is a balance between the negative effects of a break/fusion (unbalanced gametes in heterozygotes reduces fitness) and an effect, through drag or drive, of avoiding the polar body fate in meiosis. The polarity of mammal meiosis seems capable of reversal with no obvious preference either way, but a consequential shift in the balance of chromosomes favoured - acrocentric or metacentric. Within genera, chromosomes are either 'mostly acrocentric' or 'mostly metacentric', with very little representation in the middle - the favoured type scuttles after the optimum polarity in meiosis like passengers shifting from side to side in a ship. If 'founder effect infertility' were the rule, there would be no such pattern.

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    6. Let's get a few things straight:

      1. The time taken for neutral changes to fix depends on the population size. In a small population it would a matter of a few hundred generations. Hence, any degeneration could be rapid.

      2. A chromosomal fusion would not itself set up a complete reproductive barrier, but it would over time. If the event was accompanied by migration, or population isolation, then this would easily lead to speciation.

      3. Indeed, it is widely accepted that chromosomal arrangements are major causes of reproductive isolation. I have already informed you about horses and donkeys producing infertile mules because one has a fused chromosome. I suggest you read this paper as well:

      http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2601666/

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    7. 1. The time taken for neutral changes to fix depends on the population size. In a small population it would a matter of a few hundred generations. Hence, any degeneration could be rapid.

      Not according to that nice Mr Kimura. You are omitting the role of mutation rate. Each degradative mutation fixes in a population-dependent time, true. But there are proportionately fewer in a small population. Therefore - assuming degradation involves more than a single change - population size is cancelled out of the 'rate of degradation' equation.

      If the event was accompanied by migration, or population isolation, then this would easily lead to speciation.

      If the event was accompanied by other events that can result in speciation on their own, it's hardly 'speciation by chromosome rearrangement', is it? It is not impossible that chromosome rearrangement can be a primary cause of sympatric speciation, but you seem to be pushing it as some kind of general correlation.

      3. Indeed, it is widely accepted that chromosomal arrangements are major causes of reproductive isolation. I have already informed you about horses and donkeys producing infertile mules because one has a fused chromosome. I suggest you read this paper as well:

      Infertile mules don't go on to produce species. You don't get much more reproductively isolated than that.

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    8. Re Atheistoclast

      Actually, as I stated on another thread on this blog, there have been experiments to produce chimp/human hybrids. These were conducted in the former Soviet Union and possibly in Nazi Germany and were failures. However, it could be argued that they were failures not because of reproductive isolation but because the artificial insemination techniques available at the time were too crude (in-vitro fertilization did not exist at the time). I would agree with Mr. Atheistoclast that such experiments are immoral and will not be performed in western countries. So, unless some mad scientist in a third world country makes the attempt using modern artificial insemination techniques, the controversy will continue.

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    9. I am happy to donate my sperm towards such an experiment. If there is a resulting offspring, I will treat it as my own and love it as such. But it would shatter my views on origins.

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  3. It could be interesting to try and estimate the timing of the fusion vs. other events. Larry's central point stands, it doesn't matter vs. evolutionary theory if it is 1 or 6 million years old. The simplest conceivable test I doubt would work (looking at Neanderthal DNA) I'd guess that on average it is too degraded to reliably determine it's chromosome structure, particularly when you start to talk about repetitive elements like telomeres.
    The other strategy would be to use existing sequence data to try and estimate coalescence times for the different chromosomes and see if that is illuminating. Though it wouldn't have to be as any population level event acting on chromosome 2 would also be influencing the other chromosomes making the signal more difficult to detect, unless you had a lot more specific model than this very crude one.

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    1. Put it this way: Let us just accept that the Biblical account of human origins is true for a moment, and suppose that Adam had chromosomal pair whereas Noah had 23 pairs. The bottleneck resulting from the catastrophic global flood would have effectively selected Noah and his chromosomes against those of the original progenitor of mankind. This is what Luskin and other creationists appear to be suggesting.

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  4. Yes and then all land animal genealogies would coalesce to the same number of generations (with the appropriate distribution of error). This is not even remotely in the ballpark of what happens.

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  5. I normally skip over reading any quotes from the IDiots, as they are embarrassingly dumb, but I happened to read the yellow box and I'm sorry I did. Embarrassingly dumb animals they are. I can't really even wrap my head around what Klinhoffer is trying to say...

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  6. When creationists (e.g. IDiots) say that they accept the hypothesis and evidence of common descent, they're either lying and/or they're thinking only of non-human organisms. To them, humans are exceptional, superior, and "specially created in the image of God". They see apes and all other non-human organisms as lower life forms that were created (but not specially in "God's image") only to serve humans.

    Creationists (IDiots) will not accept or tolerate an hypothesis or evidence that links them to organisms that they see as inferior, not special, and not exceptional.

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  7. If you think there's trouble convincing IDiots of the common ancestor, just think how much fun it will be convincing them WE are the FREAKS and the great apes are the normal ones....(c;]
    None of this matters. The freaks will destroy life on the planet before much longer. The cockroaches who survive won't care, one way or the other.

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