Reproductive history writ in the genome

Blogging on Peer-Reviewed Research

Fossils are cool, but some of us are interested in processes and structures that don’t fossilize well. For instance, if you want to know more about the evolution of mammalian reproduction, you’d best not pin your hopes on the discovery of a series of fossilized placentas, or fossilized mammary glands … and although a few fossilized invertebrate embryos have been discovered, their preservation relied on conditions not found inside the rotting gut cavity of dead pregnant mammals.

You’d think this would mean we’re right out of luck, but as it turns out, we have a place to turn to, a different kind of fossil. These are fossil genes, relics of our ancient past, and they are found by digging in the debris of our genomes. By comparing the sequences of genes of known function in different lineages, we can get a measure of divergence times … and in the case of some genes which have discrete functions, we can even plot the times of origin or loss of those particular functions in the organism’s history.

Here’s one example. We don’t have any fossilized placentas, but we know that there was an important transition in the mammalian lineage: we had to have shifted from producing eggs in which yolk was the primary source of embryonic nutrition to a state where the embryo acquired its nutrition from a direct interface with maternal circulation, the placenta. We modern mammals don’t need yolk at all … but could there be vestiges of yolk proteins still left buried in our genome? The answer, which you already know since I’m writing this, is yes.

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Even in death, he sets an example for us all

For everyone who complained that I didn’t say anything nice about Arthur C. Clarke in yesterday’s very brief note (I can’t help it, I don’t believe in burying my opinions along with the corpse), here’s some information that made my opinion of Clarke shoot up a couple more notches:

The famed science fiction writer, who once denigrated religion as “a necessary evil in the childhood of our particular species,” left written instructions that his funeral be completely secular, according to his aides.

“Absolutely no religious rites of any kind, relating to any religious faith, should be associated with my funeral,” he wrote.

I’d say the same thing about my funeral, with the added stipulation that if anyone tries to preach, at word one I want my friends and family to rise up and carry the jerk bodily out the door, and throw him or her into the street.

Paging Randy Olson

This bad propaganda film for creationism is going to come out soon, so I can sympathize with this call to put together an honest science movie in reply. However, I have huge reservations, particularly with the idea that we need to get people who understand science to write the movie. People who understand science might very well be the worst possible people to write it; the first priority ought to be get people who understand movies to write it. Someone like, for instance, John Rogers or Randy Olson — somebody who knows the movie business and also knows the science.

Then you run into another problem: these guys are professionals. You don’t go up to a pro and tell them that you’ve got a really important idea for a movie, could they please write it for you? For free? And, by the way, we don’t have a budget or any capital lined up, we just think it’s the right thing to do.

I’m afraid the place to start isn’t with soliciting manuscripts from scientists — it ought to be with an idea, something more specific than simply countering some other film that’s going to be a box-office flop, and getting backing so you can do it right, and do it professionally. And that means no amateurs from the ranks of scientists trying to do a job they aren’t trained for.

Can you imagine if Charles Darwin were asked to write the movie of his work? It would be five hours of barnacle anatomy and pigeon breeds.

P.S. I don’t mean to be discouraging, but there really is expertise in the entertainment industry, and it does not help our cause of trying to emphasize the importance of knowledge of science to be so cavalier about other people’s knowledge.

Dicyemid mesozoa

Blogging on Peer-Reviewed Research

You know how people can be going along, minding their own business, and then they see some cute big-eyed puppy and they go “Awwwww,” and their hearts melt, and then it’s all a big sloppy mushfest? I felt that way the other day, as I was meandering down some obscure byways of the developmental biology literature, and discovered the dicyemid mesozoa … an obscure phylum which I vaguely recall hearing about before, but had never seriously examined. After reading a few papers, I have to say that these creatures are much more lovable then mere puppy dogs. Look at this and say “Awwwww!”

i-67abe67694eea42539187c64ab322994-dicyemid.jpg
Light micrograph of Dicyemid japonicaum rhombogen. AX, axial cell; C, calotte; IN, infusorigen; P, peripheral cell.

O dicyemid mesozoan, how do I love thee? Let me count the ways.

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Archbishop flames on

A while back, I posted about the fact that the Archbishop of Canterbury had unambiguously condemned creationism. While I appreciated the sentiment, I had my doubts about his sincerity, and mentioned that I preferred my religious authorities to say “crazy stupid things”. Perhaps the Archbishop reads my blog, because he has obliged.

The Archbishop hit out against the "two extremes" in the range of theories of how the world began in his Holy Week lecture on Faith and Science last night. He said "Science has more to do than is simply covered by these theories."

Creationists believe in the literal version of creation as told in Genesis, and argue that man walked the earth at the same time as the dinosaurs. Neo Darwinists argue that culture is subject to evolutionary forces which will eventually weed out religion.

Dr Williams admitted that Neo Darwinism, a theory supported by Atheist Professor Richard Dawkins, is "most problematic" to theology, but he called it "a pseudo science" and "deeply vulnerable to intellectual challenge because it is trying to be a theology."

In a sideswipe at evolutionary scientists such as Professor Dawkins, Williams warned "Science can be seduced into making exaggerated claims."  He added "Neo Darwinism of Dawkins’ kind carries with it a rather subjective agenda…It is as vulnerable as Christianity". Both Neo Darwinism and Christianity are telling stories, the Archbishop continued, Christianity acknowledges that fact, Neo Darwinism doesn’t.

Thattaboy, Archbishop. I appreciate the help in exposing the inanity of religion.

For those following along, Rowan Williams clearly has no idea what the neo-Darwinian synthesis says, because nowhere does it claim that evolution will weed out religion; even I, brutal opponent of all things godly, can see reasonable arguments for the adaptiveness of religion, or the absence of selection against religion, or that there are acceptable rationales for religion as an exaptation. But otherwise, the admission that science is a problem for theology, and the ignorant claim that evolution is a pseudo-science, are useful tools for the atheist conspiracy.

In which I concede that some scientists are evil and stupid

The name Satoshi Kanazawa wasn’t familiar to me until I read Cosma Shalizi’s lovely needlework on the guy, but then I remembered … I have his book, Why Beautiful People Have More Daughters, on my shelf. It has a wonderfully provocative title, so I even skimmed a couple of chapters, which sent multiple wtf signals bouncing around in my brain — the premise of the title is the product of statistical shenanigans, and I don’t think the authors would recognize a mechanism if it advanced menacingly on them and threatened them with physical dismantlement — so I set it aside and allowed it gather dust.

Now I learn that Kanazawa has a blog, like everyone does nowadays, and he calls himself the “Scientific Fundamentalist”. I wish I could say that finally we have a target for all those people who complain about fundamentalist atheists and fundamentalist scientism and fundamentalist whatever-they-hateists, but no, Kanazawa does as much violence to the word “fundamentalism” as he does to biology. He’s more like an amoral, principle-free, unconscious reactionary, which isn’t really a fundamentalist mindset. How bad is he? Well, he argues that Americans need to hate a little more.

Here’s a little thought experiment. Imagine that, on September 11, 2001, when the Twin Towers came down, the President of the United States was not George W. Bush, but Ann Coulter. What would have happened then? On September 12, President Coulter would have ordered the US military forces to drop 35 nuclear bombs throughout the Middle East, killing all of our actual and potential enemy combatants, and their wives and children. On September 13, the war would have been over and won, without a single American life lost.

Yes, we need a woman in the White House, but not the one who’s running.

Whoa.

That’s an argument that carries reductionism well past over-simplification, beyond stupid, and deep into the territory of bug-eyed crazy. That’s not a thought experiment, it’s a right-wing masturbation fantasy. Kanazawa must be looking for a gig writing for WingNutDaily.

I have to go take a shower right now, so I’ll leave you with this most excellent rebuttal.

The above, to be sure, is somewhat ambiguous. It could be that what he’s saying is that, were Coulter president, she would have hated her new-found enemies appropriately, nuked the Middle East and thus “won” the war on terror in a day. But it could be that Kanazawa doesn’t think that would have been a good idea, it could be that he’s simply arguing hypothetically without endorsing that course of action. And yet… it really doesn’t read that way. The tone, the context, and the register all suggest to me that Kanazawa would have approved of a nuclear response to 9/11. And this, I submit, is a little extreme. Forget for the moment that killing millions of innocent people is a Bad Thing, forget that the Middle East contains a good proportion of the world’s oil, forget that America’s democratic ally Israel is in the Middle East, forget that the fall-out would do extensive damage to other parts of the world, forget that there are tens of thousands of Americans (and far more other foreigners) living in the area, forget that the environmental damage would be enormous, forget that the Middle East contains innumerable priceless cultural artifacts, forget that there are hundreds of millions of Muslims living outside the Middle East (India, Pakistan, Indonesia, etc.), and forget that 9/11 was planned from Afghanistan, outside the Middle East. Have you forgotten all of these factors (and any others you came up with for yourself)? Good. Now it’s a good idea to nuke the entire Middle East. Now only does it make any sense whatsoever to call the hypothetical nuclear destruction of the entire Middle East a “victory” for America.

Egnor gives away the store

Michael Egnor has made a blatant tactical error, and Larry Moran catches him on it. Note what Egnor says about evolution, that it is “obviously true”.

Dr. Wells pointed out that research on antibiotic resistance wasn’t guided by Darwinian evolutionary theory. That evolution occurred — that is, that the population of bacteria changed over time — is obviously true, and obviously was relevant to the antibiotic resistance research. Dr. Wells made the observation that the research owed little to Darwin’s theory that all biological complexity arose by natural selection without teleology.

Larry challenges the IDiots to ‘fess up and agree that they’ve conceded on the facts of evolution and are reduced to rhetorical sophistry, squabbling against this “Darwinism” thing of their own invention. I don’t expect they will; they’ll either pretend it was never said, or begin a little evasive dance, which will at least be entertaining.

I’d like to see the creationists do something else. Egnor’s redefinition shows that their objection is to the absence of teleology in evolutionary explanations, so let’s see them counter it with evidence for teleology. In those bacteria that evolved antibiotic resistance, for instance — show me the hand of a god reaching in and tweaking those genes.

An end to war?

That John Horgan fellow — he’s always going on and on about the end of something or other. This time, it’s about the end of war. There’s a little bit of “duh” about it — modern science can end war, all it has to do is end scarcity, or as it says, “Given adequate food, fuel, and gender equality, mass conflict just might disappear” — but also a good question. Are people intrinsically warlike by nature, or will they favor peace if given the opportunity?

I’m inclined to agree that people would rather avoid war, and that ending resource scarcity (which I’m not convinced that science can do) would reduce the incidence of war, but I think the article ignores one central source of conflict: ideology. Baboons and bonobos don’t seem to have it, but we do, and it can trigger wars for that other resource, human minds. We want people on our side. The Thirty Years War, the American Civil War, the Cold War … were those fought because one side wanted the other side’s food or land or minerals? Or over the spread of ideas that weren’t satisfied by science?

I have a suspicion that if we had a world of peace and plenty, where everyone was brought up to abhor war, and in which there was no biological imperative for conflict, we’d still have people coming up with ideas they’d be willing to die for … and we’d conjure up new tribes out of the contented hordes and set them to battling with one another.

Two wrongs don’t make a right

A far right wing wanker is suing Ohio State University for discrimination. I hate to say it, but if this account is at all accurate, he might have a case.

In 2006, Savage agreed to serve on a committee to determine required reading for incoming freshmen at the Mansfield campus.

Savage said the books considered by the committee were too liberal and suggested The Marketing of Evil by David Kupelian.

Professors James F. Buckley and Norman W. Jones filed a sexual-harassment complaint against Savage, saying he was homophobic for suggesting the book. The complaint was dismissed as unfounded.

Because he continued to be harassed, Savage said, he was forced to resign.

Kupelian is a vile, dishonest hack, and his book, which is the usual tripe about a gay conspiracy to force college students to become atheist abortionists and communists, is unadulterated garbage of the sort peddled by Wing Nut Daily. To even suggest such a bad book reveals that Scott Savage is an incompetent ideologue, and that yes, he most certainly is a homophobe. I’d be socially snubbing such a person at my workplace, just as I would if he were to show up wearing KKK robes.

But being a homophobe isn’t a crime, and suggesting a rotten book (a suggestion that I’m sure was shot down without hesitation by the other members of the committee) isn’t sufficient grounds for a lawsuit. Unless there’s an awful lot more to Savage’s actions than are revealed in this story, it sounds like people did try to drive him out of his job.

Of course, my sympathy for the clown has limits. This exceeds them:

The suit says he is a devout Christian, married for 18 years and the father of eight. It says he has struggled to find library work since leaving OSU.

Lots of people at universities are Christian, many of them have been married for a long time (my 28th wedding anniversary was just yesterday), and although 8 children may be a little excessive, you’ll also find lots of people who love kids at universities — and you’ll also find gay communist atheists who love children and have long term relationships. That claim is irrelevant to his lawsuit and is the protest of a close-minded bigot who likes to toss out these nice testimonials to his purported goodness while denying that the people he demonizes might have very similar values.

So no sympathy for the ugly little hater from me, but I have to concede that at least one of the actions against him also crossed the line.