Some of those critics who see neo-Darwinism as grossly insufficient assert that lots of adaptations result not from mutations that arise within a species, as evolutionary biology posits, but from “lateral gene transfer” (LGT) the capture of genes from one species by a different one.  This transfer can occur by either hybridization (mating with a different species) or assimilation (eating or absorbing foreign DNA).

This attack on neo-Darwinism is misguided on two counts.  First, neo-Darwinism doesn’t really require that genetic variation originate by mutation in the species in which that variation is selected.  The dynamics of natural selection will work on adaptive genetic variation no matter what its source. Second, while bacteria often acquire genes from different species (much of antibiotic resistance, for example, is carried on plasmids—small circular pieces of DNA—that one species acquires from another), there are only a handful of cases in which nonbacterial “eukaryotes” (animals, plants, and fungi) get genes from a different species (Wikipedia has a nice summary of these cases).

One reason we think that LGT is fairly rare in eukaryotes is because we’d detect it by making DNA based phylogenies.  Genes captured from a different species, especially one that is quite different, would stick out of these phylogenies like sore thumbs.

Indeed, that is the method used by two researchers in a really nice demonstration of LGT between fungi and aphids, reported by Nancy Moran and Tyler Jarvik in this week’s Science.

Moran and Jarvik were studying a color polymorphism in the pea aphid (Acyrthrosiphon pisum): some individuals are red, and others are green (Fig. 1).  This polymorphism behaves as if it were controlled by a single gene, with red color dominant to green.  Assays of differently colored aphids showed that they contain different kinds of the pigment carotene: green aphids have three types of carotenes, while red ones have those three and two additional ones.

Fig. 1.  Clones of red and green aphids (from Moran and Jarvik).

Further, the polymorphism is thought to be maintained by natural selection: ladybugs preferentially pick off the red aphids, while green aphids are more often destroyed by parasitoid wasps.  This may cause frequency-dependent selection, in which the color morphs are kept polymorphic because the rarer forms are eaten/parasitized less frequently.  This kind of selection can, theoretically, maintain both genes—and colors—in the population.

This puzzled Moran and Jarvik, because all carotenes in animals have been thought to come solely from diet, since no animal species is known to make the pigments with its own metabolic machinery. (In WEIT, I discuss how male house finches become more attractive mates if they have redder feathers; the red pigment derives from carotenoids in the seeds that the finches eat, and is a sign to a female of a healthy, well-fed male who would be a better father [see photos below].)  But it’s unlikely that aphids get carotenoids from plant sap (the aphids’ food), because those pigments are not soluble in sap, and the carotenoid polymorphism appears, as I said, to act as if it were produced by genes in the aphids themselves.  Indeed, DNA sequencing—the aphid genome was just sequenced completely—revealed that aphids do indeed carry carotenoid-synthesizing genes in their genome.  There were seven of them, coding for both carotenois desaturases and carotenoid synthases.

This led Moran and Jarvik to hypothesize that somehow the aphids acquired genes for making carotenoids from another species, presumably bacteria. They thus compared the aphid carotenoid genes to those from other species in the genome databank.  And they got a surprise.  Yes, the aphid genes did come from another species, but not a bacterial one.  They were closely related, instead, to genes from fungi.

Figure 2 gives a phylogenetic tree of the carotenoid desaturases, and shows clearly that the aphid genes nest within the group of desaturases from fungi.  This tree (and the tree for synthases as well) also show that all seven of the aphid genes were acquired from fungi in a single capture event between 80 and 30 million years ago.  We don’t know how this happened, but it’s possible that an ancestral aphid infected with a fungal disease captured some of the fungus DNA.

Fig. 2.  Phylogeny of carotenoid desaturase genes from various species.  Bacteria in black, plants in green, fungi in red, and aphids in blue.  Aphid genes cluster within fungus genes.

Moran and Jarvik also showed that the red-versus-green polymorphism is based on a mutation that presumably happened after the genes were captured:  green aphids derive from a “mutation” in one of the carotenoid desaturase genes, a mutation that deleted about 30,000 base pairs of the DNA.  Presumably the red color was ancestral, and the green resulted from an error in DNA replication.  (Moran and Jarvik also studied a mutation from red to green that spontaneously arose in the lab, and found that the new green form was based on a single amino-acid change, from glutamic acid to lysine, in the same carotenoid desaturase gene.)

This is a remarkable use of an acquired gene in an adaptive way, for the captured fungus DNA is the basis for the color polymorphism presumably maintained by natural selection.  It’s clear, then, that evolution in one species can be based on the acquisition of genetic information from a distantly related species.  Now that different species’ genomes can be sequenced quickly and reasonably cheaply, we’re bound to find more cases like this.  I don’t think they’ll be that common, simply because we don’t see evidence of LGT from existing gene trees in animals and plants. Nevertheless, Moran and Jarvik have shown that nature still has the capacity to surprise us.  And a good thing, too, because it makes our jobs as evolutionary biologists even more interesting.

Fig. 3.  Male house finches (Carpodacus mexicanus) showing color variation due to diet. Finch at bottom has had a lot more carotenoids. Photos from Project FeederWatch.

_______

Moran, N. A. and T. Jarvik.  2010. Lateral transfer of genes from fungi underlies carotenoid production in aphids.  Science 328:624-627

“In Finland we are back in sauna with cats.  Hot cats.”

The baby Sumatran tiger at the Sacramento Zoo has arrived at the stage of maximum cuteness.  She’s now six weeks old; here’s a video from day 30:

EXTRA:  South Carolina housecat adopts baby bobcats.

Biological offspring of foster mom Zöe (Felis catus) and adopted bobkittens (Lynx rufus)

Lately the Guardian is into nature photographs, and some lovely snaps they are.  First is their presentation of the ten greatest nature photographs of all time.  I can’t get on board with all of their selections, but there are some undeniably great pictures.  Here are two:

Fig. 1. Galápagos tortoises (Geochelone nigra) having a dip at dawn on Isabela island.  Photograph by Frans Lanting.

Fig. 2: A swimming polar bear (Ursus maritimus)—and its reflection—off Baffin Island.  Photograph by Paul Nicklen.

And, at another site, the Guardian has 21 nice photos of microscopic marine life. Here’s one:

Figure 3:  A larval spider crab (family Majidae, species unknown). Photograph by Cheryl Clarke-Hopcroft.

h/t: Matthew Cobb

by Matthew Cobb

In the letters page of this week’s issue of the Times Literary Supplement, Fodor and Piatelli-Palmarini reply to the trashing of their book by Samir Okasha. Surprise, surprise, Okasha didn’t understand what they were saying – “an egregious misreading”. For most of us, if someone doesn’t understand the point we’re making, it’s because we haven’t expressed ourselves in the right way… Some philosophers seem to think that any misunderstandings are inevitably the fault of the reader. Who finds their riposte convincing? I hope Okasha comes out fighting.

Sir, – Samir Okasha’s review of What Darwin Got Wrong (March 26) contains a number of serious criticisms of a line of argument the conclusion of which is that there is something radically wrong with Darwin’s Theory of Natural Selection (TNS). Since we do think that there is something radically wrong with TNS, this would worry us a lot if the argument that Okasha deconstructs were even remotely like the one to which our book is committed. But it’s not. Okasha’s review is a really egregious misreading of the book; we don’t hold (and didn’t publish) the views that Okasha says we do. In fact, we explicitly don’t hold these views, and we devote a lot of the book to explaining why no one should. We know from experience that reviewing is hard work and that it conduces to fast reading. But still.

Here is the most flagrant example: “. . . Fodor and Piattelli-Palmarini insist that . . . there is no basis on which to distinguish the selected-for traits from the free-riders. This distinction could only be drawn, they argue, by invoking an intelligent designer . . .”. If words were the kinds of things that can be false, every one of those would qualify. In particular, we think (as does Okasha) that the selected-for traits are the ones that causally contribute to fitness. We take this to be common ground for everybody involved in the present conversation, Darwin included. For present purposes, it’s OK with us if you take that to be true by definition. (This does not, of course, commit us to accepting that any traits are selected-for; only that, if any are, then they are causes, not just correlates, of fitness.) Nor do we think that the distinction between causes and correlates can only be made by invoking an intelligent designer. To the contrary, we devote a whole chapter (Chapter Seven) to discussing some of the ways in which causes and correlates are routinely deconfounded, both in science and in everyday life. Running control experiments, formal or informal, is the standard technique; and there are many, many others. But (so we argue) only things with minds can run experiments; and since it is also common ground that Natural Selection hasn’t got a mind, distinguishing causes from confounds by running experiments isn’t among its options. Likewise for all the other ways of distinguishing among confounded variables that we could think of. If we’re right about that, then the conclusion isn’t that there is an intelligent designer; it’s that there is something wrong with TNS. So, then, our view is not that it is impossible to deconfound causes of fitness from freeriders. Still less is it that there is no such distinction. What we do think (and what we do think our book shows) is that Darwin’s theory can’t specify a mechanism by which selection could reliably distinguish causes of fitness from correlates of causes of fitness. This is not, to repeat, because there is no such distinction; it’s because TNS recognizes only exogenous variables as selectors, and the only (relevant) fact to which such variables are sensitive, according to TNS, is the strength of the correlations between phenotypic changes and changes of fitness. And, of course, correlation doesn’t imply causation. It patently doesn’t in the kind of cases we discuss, where phenotypic traits are linked, so that the correlation with fitness is identical for both of the candidate causes.

Our difficulty with Darwin is very like our difficulty with our stockbroker. He says the way to succeed on the market is to buy low and sell high, and we believe him. But since he won’t tell us how to buy low and sell high, his advice does us no good. Likewise, Darwin thinks that the traits that are selected-for are the ones that cause fitness; but he doesn’t say how the kinds of variables that his theory envisages as selectors could interact with phenotypes in ways that distinguish causes of fitness from their confounds. This problem can’t be solved by just stipulating that the traits that are selected for are the fitness-enhancing traits; that, as one said in the 1960s, isn’t the solution; it’s the problem.

We have other complaints as well. Three examples: we do not hold a “covering law” view of scientific theories; we are explicit that we don’t. What we hold is that if there were laws of selection, that would solve the problem of reconciling TNS with the intensionality of “select-for”. But we don’t think there are such laws in biology, and Okasha doesn’t either. Also: we disapprove of Okasha’s appealing to the “paradigm” explanatory power of mathematical models of natural selection to rebut our objections to TNS. Models don’t even purport to reveal the mechanisms that underlie the phenomena they’re models of; and our claim is that no mechanism could do what TNS says natural selection does. Also: Okasha summarizes several recent discoveries in biology that our book recounts. He sets them aside saying (correctly) that “they simply concern aspects of biology about which traditional neo-Darwinism didn’t have much to say”. But our point about these discoveries is not that neo-Darwinists ignore them; it’s the marginalization of TNS that they imply; it seems the action is mostly in a different part of town.

There is, however, one place where we admit to a fair cop. Samir Okasha chides us for not telling our readers about the distinction between “random” variation and “undirected” variation. Guilty as charged. But that isn’t because, as Okasha graciously suggests, we don’t understand the difference; it’s because we try not to make readers attend to distinctions which, though perfectly valid, aren’t germane to the topic being discussed. Insisting that readers should is just the sort of thing that gives pedantry a bad name.

JERRY FODOR
Department of Philosophy, Rutgers University, New Jersey 08903.

MASSIMO PIATTELLI-PALMARINI
Cognitive Science Program, University of Arizona, Arizona 85701.

nb: Yes, I know it’s a joke.

In the past I often said that the importance of evolutionary biology is not measurable in the hard currency of human welfare—that evolution’s value was not in making us richer or healthier, but in giving us the true story of how we got here and when, and who we’re related to.  I’ve tempered that opinion over the years as I’ve become aware of the real contributions evolutionary biology has made to medicine (see for example my exchange with David Hillis).

In today’s New York Times, Carl Zimmer gives further evidence of how evolution is advancing medicine.  Zimmer tells the story of Ed Marcotte at the University of Texas, and how his work on yeast, combined with the concept of deep homology between yeast and human genes, has enormous promise for medicine—everything from cancer to genetic defects.   It involves going back and forth between species, with the iterations finding ever more genes that might be involved in human diseases; and it all rests on the proposition that genes in humans that do one thing might be evolutionarily related to genes in other species that do different things. (This, of course, is one of the observations that has been used to refute Intelligent Design’s notion of “irreducible complexity.”)

It’s way cool.

Okay, we all know that Blag Hag (Jen McCreight) had the bright idea of “Boobquake,” a way to make fun of a Muslim cleric’s accusation that immodestly dressed females cause earthquakes.  Jen jokingly suggested a “scientific” experiment in which women would test this hypothesis by showing their breasts today on the internet and looking for an increase in seismic activity. (Actually, this isn’t really a test of the cleric’s idea, since he blamed earthquakes on the adultery attendant on display of boobage):

“Many women who do not dress modestly … lead young men astray, corrupt their chastity and spread adultery in society, which (consequently) increases earthquakes,” Hojatoleslam Kazem Sedighi was quoted as saying by Iranian media.

Regardless, the idea has been taken up with approbation by some of my favorite bloggers, including P.Z., erv, and Russell Blackford.  How do I feel?

I can’t get behind it.

Call me humorless, call me a militant pro-feminist, call me a prude—call me what you want, but somehow the idea of women mocking religion by showing their breasts comes perilously close to making points through sexuality instead of through good arguments and brains. (Just imagine how tepid the response would be if, in the same cause, all of us male bloggers decided to show ourselves in jockstraps).  The predictably leering response of men, who of course have tendered enthusiastic thanks for the mammaries, just confirms this suspicion.

What’s worse is that some women who don’t want to participate in this affair have been derided as anti-sex.  Even Russell Blackford took this tack:

Unfortunately, there was a lot of 1980s pseudo-feminism that took a similar attitude to that of Christianity and Islam, problematising displays of female beauty and even expressing disgust with heterosexuality itself. The worst offender was the egregious Andrea Dworkin – who died relatively young back in 2005. In her case, good riddance. These pseudo-feminists merely use feminist-sounding language to rationalise the religion-based anti-sex morality into which they were socialised. But they lack the self-insight to understand that it’s what they’re doing.

Look, Russell, if you really think that male and female bodies are both beautiful, why do you suppose that this event is getting much more publicity than would a similar display of male skin? Do you think CNN would be all over the event if it was men who were showing their junk? Of course not—and you know why.

And do you really want to tar women who object to selling ideas with sex as acolytes of Andrea Dworkin?  That’s simply unfair.  Some women don’t want to bare their mammae, and NOT because they have a “religion based anti-sex morality”; they simply have good reason to think that in the long run such stunts will hinder women being taken seriously as thinkers and colleagues.

I have to agree with the take of Miranda Hale at Exquisite With Love,  who is an atheist and a feminist, but won’t be doffing her duds today:

The idea is fantastic and well-intentioned. It points out both the ridiculousness of the cleric’s claim and the despicable and harmful practice of blaming all sorts of horrible things (including sexual assault) on women.

However, the great majority of the responses to this effort have been anything but fantastic. Instead, it has inspired, primarily at its Facebook event page, many comments of the “show us your tits!” or “Dude, awesome, I’ll get to see some boob photos on Monday” variety. And, for some reason, women are complying. They’re posting photos of their cleavage and men are responding with “awesome boobs!”, etc. The Facebook event page has almost 200,000 “attendees” and the effort has received a great deal of media coverage. And that’s all well and good, but how many of these individuals are actually concerned with raising awareness of this issue? Very, very few, I’d say.

Sure, one can assert that the event has been unfairly “hijacked” by the men who are reacting in this way, but this response wasn’t hard to predict. And although the men making these types of comments are solely responsible for the attitudes expressed in them, why provide them with fodder? I understand that this is intended to be a lighthearted attempt to point out the ridiculousness and stupidity of the assertions made by the cleric, but that intention has been completely buried under a constant stream of “show us your tits” comments. . .

. . . Let’s dress however we want to, let’s be as modest or as immodest as we choose, and let’s use our sexuality however we see fit. It’s all about choice. If Boobquake is your kind of thing, then, by all means, enjoy it. But don’t stop there. Write about these issues. Raise consciousness about them. Speak out against the “show us your tits” reactions. And please don’t pretend that merely showing as much cleavage as possible is somehow making any kind of difference. It’s not.

If it doesn’t make a difference in promoting atheism and mocking faith, what good is it? It’s just Playboy on the internet.

UPDATE:  Ceiling Cat weighs in.