Humans evolving to escape from bacterial iron piracy
arstechnica.com
arstechnica.com
> Alice Liddell first encounters the Red Queen in Chapter 2 of Through the Looking Glass. Alice tries to catch her, but although they each run faster and faster, neither of them ever gets anywhere.
Although the writer of the article specifically references chapter 2, they obviously did not read it, nor even glance at the illustrations.
1. The character in the book is only ever named as “Alice”. The real person which the author knew, and on which the character “Alice” is based, was indeed named “Alice Liddell”, but they are not one and the same.
2. Alice does not try to “catch” the Red Queen. In fact, Alice and the Queen are running hand in hand, and it is the Red Queen which urges Alice to go “Faster! Faster!”. The accompanying illustration shows the Red Queen running and holding Alice’s hand, dragging her behind her since Alice has trouble keeping up.
Besides the old middlebrow dismissal question you should be asking yourself before posting ("is that the most interesting thing one can say about this article?"[1]), let me ask you this: is the distinction you're making here at all material to the article?
Did you consider the possibility that the author hasn't read Through the Looking-Glass in a while (a "Ph.D. in Cell Biology and Genetics" means you have to put off a good bit of recreational reading for a number of years) and thought that the explanation was close enough as background information about why a 40-year-old, fairly famous evolutionary theory is named the way it was?
And again I'll ask: do either of the author's two mortal sins you've pointed out in any way change the aptness of the metaphor or give the audience an incorrect impression of why it was named the way it was? Because I'm pretty sure they don't.
Sorry if I'm a little heated, but you might say it annoys me when people try to look intelligent by dismissing interesting things by nitpicking irrelevant details. Or maybe we shouldn't assume people's motives ("try to look intelligent"? seriously?), grant a little principle of charity, leave a correction for the author, and then engage in actually interesting conversation.
For example, if I were to use a sour grapes analogy to explain how compression optimizations beyond a certain point are not worth the effort, because the gains decrease as the difficulty increases exponentially, that would ignore the point of the fable, which doesn't tell a story of a fox that realizes the grapes higher up are not as good as the ones lower on the tree; rather, he decides the grapes he can't reach must be sour.
Misremembering the story you are using to help explain a concept can serve to confuse people who use that association as a 'hook' to remember how that concept works later.
Nor is it being used to explain a concept. Not only is the entire rest of article being used to explain this particular instance of the concept, the very next sentence gives a simplified explanation of the Red Queen hypothesis without analogy. The "literary reference" is not a literary reference at all. It's pointing out that Van Valen was making a literary reference by choosing that name.
And it's still not misleading. The difference between "Alice Liddell" vs "Alice" and "catch" vs not caching might be correct vs incorrect, but it still has nothing to do with the reason the hypothesis is named as it is. "They must run and run just to stay where they are." is right in there.
Finally, on a meta note, this is exactly the kind of thread asking oneself "is that the most interesting thing one can say about this article?" can avoid, because it isn't. Luckily there are some biologists in the article's comments on Ars to save the day (though you have to wade through some noise first), if anyone's interested in more.
[1] http://en.wikipedia.org/wiki/Red_Queen_hypothesis
[2] http://ebme.marine.rutgers.edu/HistoryEarthSystems/HistEarth...
Namely, the author characterizes the relationship between the two as competitive, or predator-prey. In other words, the two entities described herein (the bacterial and human genomes) are competing just to maintain the same relationship with one another. While this is an accurate description, the actual Carroll story is characteristic of a cooperative relationship; Alice and the Queen are holding hands and running, only to stay in the same place.
I realize this is a very minor gripe, and the author of this article is in fact misstating the story in a way that is really truer to the Red Queen hypothesis than it is to the story after which that hypothesis is named. While perhaps not the most interesting discussion point of this article, I do think it was an interesting enough distinction that it was worth pointing out.
(The “try to look intelligent” bit was not meant as a snark, it seemed like a reasonable assumption on my part. I’d remove it if I could, since it does not change any point I was trying to make.)
Let me know when you start writing only bug-free code (if someone has had a bug in their code, how can we trust anything else they have written? Getting the details right is important, after all)
> [...] that transferrin has undergone positive evolutionary selection in a manner often seen in molecular arms races between mammals and viruses.
but all the discussion is about bacteria. Bacteria and virus are very different, so the strategies against them are very different too. (I'm not a biologist, but this strategy to sequester iron while in transit looks like unuseful against virus, because the virus is only active inside the infected cells. IANAB.)
The one bit of actual research I was able to do (in the late '70s) was in a lab that had serendipitously discovered a new iron scavenging mechanism in E. Coli. If you put it in a sufficiently iron poor environment (e.g. all the glassware was treated with HCL and then bathed for days in deionized water) it would synthesize a previously unknown iron binding protein and grab what it could.
So we shouldn't assume this is the only way many bacteria can get iron, but it's perhaps worth checking out. And a focus on iron in general might be a fruitful approach.