And Finally the Hounding Duck Can Rest

[Note: This is the last of a four-part series:

For the past five days, I’ve been trying to get an answer from creationists. Today, I finally got it. And it’s an instructive lesson in how creationism makes itself irrelevant to the progress of science. Plus, it’s a good opportunity to look at the delightfully sloppy way our chromosomes evolve.

I’ve been blogging this experience along the way, so I won’t go back over it all again. Consider this the final chapter in a strange saga.

I do have to recap a little, though, so that this post makes sense.

As I blogged on Thursday, there’s a growing pile of evidence for how one of our chromosomes (chromosome 2) evolved through a fusion of two other chromosomes. I focused in particular on a paper that came out in the journal Genome Research last month from Evan Eichler at the University of Washington and his colleagues. Among many other pieces of evidence are telomeres, bunches of repeating DNA that typically form caps at the ends of chromosomes. There is telomeric DNA right in the middle of chromosome two.

On July 6, a site that promotes intelligent design (a k a the progeny of creationism) published an article by David Klinghoffer, the site’s editor, questioning whether this actually happened. Klinghoffer stated that the telomeric DNA at the fusion site “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.”

This passage stuck out for several reasons. Who was he quoting? Why was he calling six million years ago the recent past? Who ever said that if the fusion happened six million years ago, the DNA there should not be degenerate or diverged?

Unable to ask Klinghoffer directly at his site (no comments allowed), I did the next best thing and wrote my question on a Facebook page that’s also linked to the same outfit, and which posted his article. What, I asked, was the evidence for this particular claim?

I was told to read a book that expresses doubts about human evolution. I asked for scientific papers. I got silence, invitations to debate, and more distraction.

After five days of repeatedly asking my question–and of being accused of lies, misdemeanors, and being some kind of duck–I discovered this morning that Klinghoffer has at last provided the evidence for his claim.

Did he direct me to a passage from Eichler’s new 2012 paper?

No.

Did he point me to some other recent paper, such as the one unveiling the chimpanzee genome in 2005, which also provided additional evidence of chromosome fusion?

No.

Instead, he typed out a few paragraphs from the book in question, Science and Human Origins, recently published by the Discovery Institute Press, and written by three Discovery Institute-related people, Douglas Axe, Ann Gauger, and Casey Luskin. (Although the book is written by three people, Klinghoffer only refers to Luskin having written the fusion stuff. I have no idea why. Luskin himself has done no research on chromosomes, and is not a scientist.)

Here’s what it’s taken so long for Klinghoffer to divulge:

I repeat my contention that reasoned discussion of a book isn’t possible unless you grapple with the argument the book makes, as opposed to obsessively flogging one small point because you figure you may have an advantage there. Zimmer simply will not consider the larger case for skepticism about evolutionary explanations of human origins. He’ll only lecture us about human chromosome 2.

It would seem to be reasonable at this point to give up on Carl Zimmer. For readers who want to know what Casey said in his chapter, and what I had in mind when I wrote my own post, here are several paragraphs I highlighted in my copy of SHO [Science and Human Origins-cz]:

…[T]he evidence for chromosomal fusion isn’t nearly as clear-cut as evolutionists like [Kenneth] Miller claim.

Telomeric DNA at the ends of our chromosomes normally consists of thousands of repeats of the 6-base-pair sequence TTAGGG. But the alleged fusion point in human chromosome 2 contains far less telomeric DNA than it should if two chromosome were fused end-to-end: As evolutionary biologist Daniel Fairbanks admits, the location only has 158 repeats, and only “44 are perfect copies” of the sequence.46

Additionally, a paper in Genome Research found that the alleged telomeric sequences we do have are “degenerated significantly” and “highly diverged from the prototypic telomeric repeats.” The paper is surprised at this finding, because the fusion event supposedly happened recently — much too recent for such dramatic divergence of sequence. Thus the paper asks: “If the fusion occurred within the telomeric repeat arrays less than ∼6 mya [million years ago], why are the arrays at the fusion site so degenerate?”47 The conclusion is this: If two chromosomes were fused end-to-end in humans, then a huge amount of alleged telomeric DNA is missing or garbled.

Finally, the presence of telomeric DNA within a mammalian chromosome isn’t highly unusual, and does not necessarily indicate some ancient point of fusion of two chromosomes. Evolutionary biologist Richard Sternberg points out that interstitial telomeric sequences (ITSs) are commonly found throughout mammalian genomes, but the telomeric sequences within human chromosome 2 are cherry-picked by evolutionists and cited as evidence for a fusion event….

To explain why this is such a massive evidence fail, I need to talk a bit about telomeres.

The ends of chromosomes are very vulnerable places. If they simply dangle loosely, DNA-cutting enzymes can nibble away at them, destroying the genes they encounter. The dangling end of one chromosome can also get attached to the dangling end of another, fusing chromosomes together. We are mostly protected from such changes thanks to special proteins called telomerases. They tack on little repeating bits of DNA, which form a loop–a telomere–so that chromosomes end as a hairpin curve, rather than dangling ends.

When cells divide, however, telomeres tend to get chewed up. To keep telomeres big enough to protect their chromosomes, telomerases keep adding more DNA to them. In a 1997 paper, Nobel-prize-winning biologist Carol Greider and her colleagues illustrated just how important this addition is by creating mutant mice that couldn’t produce telomerase–and could therefore not add extra DNA to their telomeres.

The mice were healthy enough to grow up and have babies. But from one generation to the next, their telomeres got shorter until they disappeared. After just four generations, the mice suffered an explosion of chromosome fusion. Their dangling DNA then began to get chewed away, damaging their genes until they became sterile.

This experiment and other studies indicate that defective telomeres with few repeats are vulnerable to chromosome fusion. So it would be no surprise to find that a fusion between two chromosome had a low number of repeating bits of DNA.

And once the chromosomes did fuse, the telomeres would now be stuck in the middle of the chromosomes, where telomerases would not be adding any extra DNA. You’d expect that over time, bits of the telomeres would get deleted and not replaced.

So the small quantity of telomere DNA does not, in fact, raise grievous doubts about the evolution of fused chromosomes. Nor does the fact that the repeating DNA in the fused chromsome has mutations in it. Telomere DNA is just prone to mutation. In fact, if you look at the telomere on a chromosome, you’ll typically find that the newest pieces of repeating DNA are correct, but the older segments further from the loop’s end are slightly garbled. These errors arise in your own body. If a chromosome’s telomeres are damaged, you might well expect the new ones to be gone, and the garbled ones remain.

You’d also expect that after the chromosomes fused, the telomere DNA would continue to mutate. Which brings us to Daniel Fairbanks, the geneticist quoted by Luskin and Klinghoffer. Quoted isn’t the right word: cherry-picked is. They select just four words out of a sentence, so as to distort Fairbanks’s words.

You can see for yourself. Luskin quotes Fairbanks from Relics of Eden, a very good popular book in which Fairbanks outlines the genetic evidence of human evolution. Here’s the page in Google Books where the quote comes from. Fairbanks is talking about the chromsome fusion. I’m going to quote the passage in full, italicizing the cherry-picked bit that Klinghoffer and Luskin pulled out.

Of the 158 repeats, 44 are perfect copies of TTAGG or CCTAA. In most cases, the remaining repeats differ from the standard sequence by no more than one or two base pairs.

This is precisely what we expect if the fusion happened long ago in the remote ancestry of humans. After the fusion event, the repeats no longer functioned as telomeres, so mutations (changes in the DNA sequence) in them had no harmful or beneficial effect. The ancient telomere at the fusion site is now a nonfunctioning relic of evolution embedded in the middle of the chromosome. The more generations humans are separated from the fusion event, the more mutations we expect to accumulate in the sequence. Because the majority of the repeated segments have mutations in them, the chromosomes must have fused a long time ago, probably tens of thousands of generations deep into our ancestry. Thus, the evidence clearly eliminates chromosome fission and independent origins as reasonable alternatives to fusion.

To push the idea that this telomere DNA is way too divergent to have evolved through fusion, Luskin quotes from this 2002 paper, which you can read for free. This research was carried out back before scientists had the chimpanzee genome at hand, and when the human genome was still only roughly mapped out. (Repeating chunks of DNA are particularly tough to sequence and map to their location in the human genome.)

Barbara Trask of the Fred Hutchinson Cancer Research Center and her colleagues had to do the best they could, sequencing the region around the fusion site in humans and around chimpanzees. They found that all of the chunks around the fusion site in human chromosome two mapped to corresponding parts at the ends of two chimpanzee chromosomes. Again–this is exactly what you’d expect if fusion occurred in our distant ancestors. “When observed at the sequence level, the ancestral chromosomes appear to have undergone a straightforward fusion,” Trask and her co-authors write. (Funny that this is not the quote that Luskin or Klinghoffer choose to pull out.)

Subsequent research has supported this conclusion. Eichler’s 2012 paper, for example, shows how the genes across the entire fused chromosome still retain much of their original order in their unfused predecessors. See my post for pictures that illustrate this.
See my post for pictures that illustrate this.
Again, Luskin doesn’t even try to address the large-scale similarity of these chromosomes.

One particularly neat piece of evidence for fusion has to do with the centers of chromosomes, called centromeres. Centromeres have a distinctive structure, and they play a crucial part in the replication of chromosomes. If human chromosome two had indeed evolved from the fusion of two older chromosomes, then it must have acquired two centromeres. As Trask and her colleagues note in their 2002 paper, human chromosome two does, indeed, have two centromeres. One is still working, while the other has been inactivated by mutations.

But you’d never know about this evidence from the Discovery Institute.

Being good scientists, however, Trask and her colleagues pointed out some intriguing results in their 2002 study. For example, the repeating DNA they sequence is very divergent. This is the sentence that Luskin quotes. But he then fails to mention the explanations that Trask and her colleagues start to consider in the very next sentence. By 2002, for example, scientists already knew that telomere DNA has a high mutation rate. And in 2005, when Trask got a chance to compare the human and chimpanzee genomes, she confirmed that, indeed, telomeres and nearby DNA undergo lots of mutations. In other words, you’d expect this kind of DNA to be divergent and degenerate.

The third piece of evidence Klinghoffer and Luskin offer comes, unquoted, from Richard Sternberg. There’s no footnote, so this is presumably just Sternberg telling Luskin this information. Sternberg, incidentally, is a fellow at the Discovery Institute–something Luskin fails to note. Sternberg claims that there’s telomere DNA in the middle of lots of mammal DNA, and so scientists must be cherry-picking the stuff in chromosome two to indoctrinate people about evolution.

As I hope is now clear, there is an overwhelming amount of evidence that the telomere DNA in the middle of chromosome 2 is the result of fusion–evidence both from the fusion site, and across the entire chromosome. So this is the opposite of cherry-picking. It is true that there are hundreds of chunks of telomere DNA wedge in mammal chromosomes. But this fact in no way undermines the evidence for the fusion of human chromosome two.

To see why, check out this 2008 paper, “Telomeric repeats far from the ends: mechanisms of origin and role in evolution,”  which three Italian scientists published in the journal Cytogenetic and Genome Research. These scientists carefully examine telomeric repeats located in the interior of chromosomes in a number of mammal species. Lo and behold, they found evidence that these chunks of telomere DNA got moved from the ends of chromosomes to their interior, too. Their research shows that there are a number of ways that this has happened. Some of these moves started with a chromosome fusion. Later, these chromosomes broke, and one of the resulting chunks got swapped with a chunk of another chromosome. As a result, the telomere DNA was able to spread far from the ends of chromosomes.

Another opportunity to spread telomere DNA occurs when DNA breaks. To fix broken DNA, specialized proteins zoom in to stitch the loose ends back together. But these proteins can also grab onto the telomeres at the end of chromosomes. Thanks to this glitch in the repair system, cells will sometimes accidentally insert a bit of telomere DNA at a spot where they’re trying to repair a break. The Italian researchers support this hypothesis with comparisons of mammal genomes, which reveal the footprints of these events.

In other words, the presence of other pieces of telomere DNA away from the ends of chromosomes does not bring the fusion of chromosome two into question. Instead, they arose through other fusions and other mutations. In other words, more evolution.

And that’s it.

After five days of stonewalling and name-calling, Klinghoffer points us to a passage from a book published by his employer, the Discovery Institute, written by someone else at the Discovery Institute. The passage he points us to cherry-picks another book and a 2002 paper. Reading the original sources quickly reveals that Luskin’s interpretation of those quotes is wrong. Luskin also nods to another Discovery Institute fellow, who makes a comment that is clearly contradicted by peer-reviewed research. Luskin has nothing to say about any of the research that has come out in the past ten years. Klinghoffer has nothing to say, either.

For Klinghoffer to say that you have to read the entire book to appreciate the weight of the evidence about human chromosome two is absurd. Klinghoffer himself made a specific claim, and the evidence he offers actually shows that he’s wrong. Unless the rest of the book provides better evidence concerning human chromosome two, it’s irrelevant to my question.

And if the rest of the book is as wrong as this passage, then I hardly see why it’s worth reading.

And that is why I ask for evidence.

[Update: Fixed Fairbanks’s first name. Daniel, not Douglas. Must be a swashbuckling oversight!]