Disappearing Genes

Four-leaf clover

We’re not actually talking about four-leaf clovers today.

Gah, some real writers block on this one. Sometimes I get halfway through a post and I know what I want to say, but I can’t wrestle it into my usual style. It tends to happen when the topic is generally fairly boring, yet at the same time intensely interesting to me personally in a way that I can’t show to anyone else. I want to go down all kinds of rabbit holes, but this isn’t terrible conducive to producing a coherent and informative blog post. So I’ve stopped writing and opened a text document, and I’m going to try give you a tour of the more interesting bits.

First: the Brian Thomas article is “Clever Clover: Evidence for Evolution?“; the paper is “Adaptive gains through repeated gene loss: parallel evolution of cyanogenesis polymorphisms in the genus Trifolium (Fabaceae),” (press release, pdf). Some clover plants produce cyanide, some don’t, the pattern isn’t what you might expect – you see both forms in the same species, and the versions that lack cyanide (having it is the default) seem to have evolved independently via the same pattern of gene deletion. You get the idea, I hope.

The first interesting thing is this paragraph from Thomas’ article:

We commonly think of mutations as mistakes that damage genes. Just one DNA copying error in the instructions for manufacturing a complicated protein can yield a tiny but critical change to its shape, and it quickly becomes a useless mess. But that’s not what researchers found in clovers.

You’ll note that this is very similar to a paragraph from the press release:

This [gene deletion] is not the “normal” way we think of adaptive variation occurring, [lead author Ken] Olsen said. Most of the time, random mutational changes affect one or a few nucleotides within one gene, which might convert one amino acid to another, which might alter a protein’s function. So the changes are random and incremental. Instead, in this case, the entire gene disappears.

The similarities are less interesting than the differences, however – I’ll let you examine for yourself how Thomas’ changed it to say something more convenient for his cause.

Another Thomas paragraph reads:

The plants use an ingenious system to deploy this poison, only when needed, while protecting their own tissues. Under ordinary conditions, cyanide is safely bonded to sugar molecules that are sequestered in secure pockets inside each plant cell. The enzyme that separates the cyanide from its sugar lies outside that pocket. When an insect chews the clover leaves, the cyanide-sugars and enzymes mix—like bending and shaking a plastic glow stick—and this releases the poisonous cyanide concoction.

If you take a look at the source paper and press release you’ll find that the “secure pockets” are actually normal plant cell vacuoles. To my eye this is an example of a creationist using a mechanical metaphor to subtly influence how you view a biological process.

The thrust of Thomas’ article is based on this:

Washington University professor Ken Olsen told Washington University news that something other than random mutations must be deleting the whole gene over and over, independently.

That’s not actually what he said, which might be why Thomas uses italics rather than, say, quote marks.

The press release – the only thing Thomas actually cites; he doesn’t seem to have read the paper – is pushing the view that the findings it reports favour the “evolution is repeatable” side of that old philosophical argument. The paper hypothesises, but doesn’t demonstrate, that repetitive sequences surrounding two of the important genes are responsible for making it more likely for them to be deleted (and also presumably for them to be duplicated, as they found that happened also). This increased probability means that over time it becomes inevitable that the mutation will happen eventually, and considering an equilibrium between cyanide possessing and lacking plants appears favourable that scenario will also be inevitable and occur repeatedly. Unhelpfully, the press release talks about this meaning that “chance played little part,” but this is like saying that chance plays little chance in the fact that if you roll a six sided dice 50 times you will almost certainly get at least the one 4. Chance plays all the parts, it’s just a very high chance that it approaches the point of certainty.

Thomas says:

The Washington University news describing these clovers could easily lead readers to believe that “evolution” can happen the same way multiple times, but there is good reason to reject calling these changes “evolution.”

Changes within a kind—like the clover plant kind—and especially specific trait changes within that kind operate on an entirely different functional plane than evolution’s broad-scale changes that supposedly morphed a cell into a plant. Just because a Microsoft software program can deploy one or another subroutine does not mean that it can morph itself into a program that runs on a different operating system.

Yeah, yeah, creationists will never accept “broad-scale” evolution – though that’s a novel way of putting it, at least. What I found more interesting was his analogy.

Have you ever heard of OS/2? Back in the day (around 1990, which may not be so long ago for some of you) Microsoft and IBM were cooperating on an operating system to succeed MS-DOS, but an ugly breakup lead to IBM having custody of what would eventually become OS/2 Warp. Warp had compatibility with Windows programs, and was supposedly “a better DOS than DOS and a better Windows than Windows.” This is, ironically, credited as its downfall, as why bother writing software for Warp when you could just make it for Windows? And if everything is on Windows, why buy Warp?

That’s not a terribly relevant tangent, but then neither is Thomas’ analogy. He concludes:

Big-picture evolution needs a way to invent new traits, their genes, and integrate those additions into new body plans. Deleting a cyanide gene is not the way to make these comprehensive changes. The precisely repeated means by which clovers delete their cyanide genes point toward the fact that a clever Creator crafted the clover.

We may come back to this topic if and when somebody actually investigates the mechanism – and provided the result can be spun to Thomas’ satisfaction. In the meantime you’ll have to excuse me while I go hunt for a synonym for “interesting.” It’s getting embarrassing…

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4 thoughts on “Disappearing Genes

  1. So findings show that there is a lot of activity happening around this gene. Sometimes it is being duplicated to other places and sometimes it is being deleted altogether.

    My first thought (before reading the paper’s hypothesis) was that this gene could be situated on the end of a chromosome and lie distal to some unstable DNA (full of repeating sequences).

    This is very similar what we have seen happen with the great ape chromosomes 2A and 2B, which is detailed in the link below (we see evidence of this in gorillas, chimpanzees, bonobos and humans):

    http://blogs.discovermagazine.com/loom/2012/07/19/the-mystery-of-the-missing-chromosome-with-a-special-guest-appearance-from-facebook-creationists/

  2. “Big-picture evolution needs a way to invent new traits, their genes, and integrate those additions into new body plans. Deleting a cyanide gene is not the way to make these comprehensive changes.”Who would imagine that it is?

    The cyanide loss mutation seems to be facile, which is why it has occurred several times independently in different species. If it conveys a disadvantage, the varieties that have lost the relevant enzyme will tend to disappear, but may be replaced by lines in which the same mutation has happened again. Much the same presumably applies to human haemophilia (the fact that the allele is a sex linked recessive will slow down loss but won’t change the logic. And we know that haemophilia can emerge de novo from a single mustation.- as in the Russian royal famly.)

  3. http://www.icr.org/article/8214/

    This does no seem to disprove evolution, merely highlight that to produce new proteins/functions something very improbable must have occurred in the past. Behe of course believes God guided what happened and thus does NOT appear to be saying evolution is disproven but merely unguided ‘Darwinian’ evolution. Another example (though the relevant link is supplied) of a YEC trying to make others say what the science rejecting YECs think, rather than what the other people actually think.
    Thomas having a laugh – except that many arrogant creationists appear to lack much of a sense of humour.

  4. Hello is all right. Mr. Ashley Haworth-Roberts and the others here, ridicule is not refutation. Denial is not refutation. Uneducated children are not able to offer refutation.

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