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For Darwin Day: False Facts & Dawkins’ Whopper

Darwin Day, February 12, is coming up tomorrow, and we want to do our part to mark the occasion. Much of what Charles Darwin said makes perfect sense to us and is worth celebrating.
Seriously. Take this famous quote, for instance, from Darwin’s Descent of Man (1871, p. 385):

False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for everyone takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened.

Meet A False Fact: What Would Darwin Do (WWDD)?
Now, in the spirit of challenging false facts and views, as Darwin encourages us to do, we have a particular “false fact” in mind, used to support a false view. Both are widely promoted by Richard Dawkins, who should know better. (More about that, below.) We’ll call this false fact Dawkins’ Whopper.
You can listen to the Whopper here, as Dawkins answers this question:

Out of all the evidence used to support the theory of evolution, what would you say is the stongest [sic], most irrefutable single piece of evidence in support of the theory?

Or you can read a transcript of what Dawkins says in the video:

There’s an enormous amount of evidence, from all sorts of places, and it’s hard to pick one strand which is more important than any other. There’s fossils, there’s the evidence from geographical distribution, there’s the evidence from vestigial organs. I think to me perhaps the most compelling evidence is comparative evidence, from modern animals — particularly biochemical comparative evidence, genetic, molecular evidence.
If you take any set of animals, and identify the same gene in different animals, and you really can do that, because the letters of the DNA code — that is, the same code in all animals — and you really can find a gene which is the same — in, say, all mammals. For example, there’s a gene called FOXP2, which is a couple of thousand letters long, and most of the letters are the same in any mammal, so you know it’s the same gene. And then you go through, and you literally count the number of letters that are different.
So, in the case of FOXP2, if you count the number of letters that are different between humans and chimpanzees, it’s only about 9. If you count the number of letters that are different in humans and mice, it’s, I don’t know, 30 or something like that. Actually, frogs have them as well, you find a couple of hundred that are different.
So, you can take any pair of animals you like — kangaroo and lion, horse and cat, human and rat — any pair of animals you like, and count the number of differences in the letters of a particular gene, and you plot it out, and you find that it forms a perfect branching hierarchy.
It’s a tree, and what else could that tree be, but a family tree. And then you do the same thing for another gene. Having got the family tree for FOXP2, you then do the same thing for another gene, and another, and another. You get the same family tree.
You also get the same family tree if you take genes that are no longer functioning, that are just vestigial, that are not doing anything. It’s like fragments of a document on your hard disk, which are no longer being used, they’re no longer on the directory, so you no longer see them. Again, you get the same family tree.
This is overwhelmingly strong evidence. The only way you could get out of saying that that proves evolution is true is by saying that the intelligent designer, God, deliberately set out to lie to us, deliberately set out to deceive us.

Understanding the Whopper
Okay, so why is this a whopper? By “whopper,” we mean a falsehood: something that Richard Dawkins should not be telling the public, because it simply isn’t true.
First, here’s a graphical representation of what Dawkins is claiming:
Let’s say we sample the genomes of species A, B, and C, and find that each species has a copy of the genes X, Y, and Z. As Dawkins notes, these genes share such a high degree of similarity that they are functionally the same genetic “word.” We align the gene sequences, count the differences, and in each case, the genes give the same branching pattern: C is the most deeply branching group, with A and B more closely related to each other than either is to C.
If you find this too abstract, think (as an analogy) of the branching order describing the children of a human family: Alan, Bill, and Claire.
Claire was born first, whereas Alan and Bill were born later, as twins. Keep this pattern in mind, and remember that if this history (i.e., pattern of relationships) is true, it necessarily excludes other possible histories, such as Alan and Claire being twins.
Dawkins claims that, using genetic comparisons, biologists always find the same evolutionary “family tree” and never observe a pattern such as the following:
Here, gene X yields one history, whereas genes Y and Z yield contradictory histories, as indicated by the “?” sign. Only one of these branching patterns can be true. (Actually, they might all be false, but if one is true, the others must be false.) Again, as a helpful analogy, think of Alan, Bill, and Claire:
If Alan and Bill really are twins, younger than Claire, then the other patterns cannot be the case. Think about your own family. Is there any doubt about who is the oldest sibling, versus the youngest, or in the middle, or (if it’s the case) who are the twins?
Yet we never see such contradictions in real genetic data, Dawkins claims. We always find the same tree.
Well…baloney. That’s a Whopper, and Dawkins, the former Professor of the Public Understanding of Science at Oxford University, should not be telling audiences this, or writing it. The claim is a falsehood. If you happen to attend one of Dawkins’ public appearances, and are able to ask him about this — we’re fairly certain he reads this site — please bring the problem to his attention, in front of the audience.
Genes contradict each other all the time. Click on this figure, for instance, from the second paper cited below, to see an example (B, at bottom in the figure) that exactly parallels the Alan, Bill, Claire confusion illustrated above. Churakov and colleagues found that five genes supported the first pattern, where human and armadillo are most closely related; nine genes supported a contradictory history, where human and elephant are most closely related; whereas eight genes supported a third, mutually contradictory history, where elephant and armadillo were closest relatives.
If you want to explore this further, here are four papers dealing with various aspects of the problem, although we could cite hundreds of others:
Gene tree discordance
Mosaic retroposon insertion
Large-scale taxonomic profiling of eukaryotes
Conflicting phylogenetic signals
The problem of discordant genetic phylogenies now represents an entire field of study within comparative biology. If Dawkins doesn’t know this, he should not be talking about the subject. If he does know, well…let’s just say he’s telling Whoppers.
What About the False View?
You know what it is: all the evidence supports the Darwinian picture of the history of life, as interpreted by Richard Dawkins and friends.

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