It’s Springtime for Molly on Pharyngula

I noticed that, in this recent thread asking why you were all here, that many of you said it was for the community and for the smart commenters here. Nobody said it was for my irresistible physical beauty and scintillating and delicate charm…in fact, I got the distinct impression I could drop dead and you’d all keep chatting away happily. Well, then, I guess it’s time to update the Molly awards, since you all love each other so much. <sniffle>

The people have spoken, and they have selected the lovely and diplomatic raconteur, Sven DeMilo, as the recipient of the Molly for the month of February. Kudos! Speech! No, never mind, sit down again. You’re old news now.

Now you have to look back to the past month and pick another worthy recipient for the month of March — simply leave a comment here saying who was your recent favorite, and why. Special note: I’m going to have to specifically exclude the recent outcasts from Survivor: Pharyngula! from eligibility, because I happen to know most of you are incorrigible smart-asses who would love to prank the voting with a certain name.

Guiyu oneiros

i-e88a953e59c2ce6c5e2ac4568c7f0c36-rb.png

A fish is a fish, right? They’re just a blur of aquatic beasties that most people distinguish by flavor, rather than morphology or descent. But fish are incredibly diverse, far more diverse than terrestrial vertebrates, and there are significant divisions within the group. Most people know of one big distinction, between the Chondrichthyes (fish with cartilaginous skeletons, like sharks and rays) and the Osteichthyes (fish with bony skeletons), but there’s another particularly interesting split within the Osteichthyes: the distinction between Sarcopterygians (the word means “fleshy fins”, and we call them lobe-finned fishes colloquially) and the Actinopterygians, the ray-finned fishes. The lobe-finned fishes most distinctive feature is the muscular and bony central core of their fins — extant forms are the coelacanth and lungfish. It is this lineage that led to us terrestrial tetrapods, but other than that successful invasion of the land, the sarcops were something of an aquatic failure, with only a few genera surviving. The ray-finned fishes, on the other hand, are a major success story, with more than 28,000 species today. To put that in context, there are only about 5,500 species of mammals.

The Sarcopterygii and the Actinopterygii must have begun diverging a long time ago, and a couple of questions of interest are a) when did the last common ancestor of both groups live, and b) what did it look like? We don’t have a good and specific answer yet, because Osteichthyes origins are lost far, far back in time, over 400 million years ago, but every new discovery edges us a little closer. What we now have is a well-preserved fossil of a fish that has been determined to be an early sarcopterygian, and it tells us that a) the last common ancestor had to have lived over 419 million years ago, the age of this fossil, and the divergence probably occurred deep in the Silurian, and b) this animal has a mosaic of primitive Osteichthyan features, which tells us that that last common ancestor may well have shared some of these elements. It is another transitional fossil that reveals much about the gradual separation of two great vertebrate groups.

And here it is:

i-ba4ab7bcea24c3417d69b43fa74705c5-guiyu.jpeg
(Click for larger image)
a, b, A near-complete fish in part and counterpart. c, Close-up view of the anterior portion of the trunk shield in dorsal view, showing MD1 and MD2 flanked by rhomboid scales. d, Close-up view of the dorsal fin spine. MD1, first median dorsal plate; MD2, second median dorsal plate. Scale bar, 1 cm.

That may be a bit disappointing at first — it looks like Silurian road-kill — but really, that’s a remarkable good and useful specimen. The animal was covered with thick bony scales, and the skull was built of thick bony plates, and so while it was squashed flat by pitiless geology, the pieces are all there, and it can be reassembled into a much more fishy state. This drawing may be more satisfying:

i-79484c5905eacb406749c6e61d25ddb4-guiyu_resto.jpeg
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a, Restoration of the entire fish in lateral view. b, Interpretive drawing of the holotype V15541. Areas shaded in grey are unknown, and are reconstructed from other early osteichthyans. ano, anterior nostril; br, branchiostegal ray; cla, clavicle; cle, cleithrum; drs, dorsal ridge scale; dsp, dorsal fin spine; et, extratemporal; eta, accessory extratemporal; f.add, adductor fossa; f.gl, glenoid fossa; gu, gular; ju, jugal; l.ext, lateral extrascapular; lj, lower jaw; m.ext, median extrascapular; mx, maxillary; n.sp., spiracular notch; op, opercular; pa, parietal shield; pcl, postcleithrum; pop, preopercular; ppa, postparietal shield; psc, presupracleithrum; pt, post-temporal; scl, supracleithrum; sop, subopercular; sp., pectoral spine; tr, lepidotrichia; vrs, ventral ridge scale.

Now it looks like a kind of armored, spiky salmon with a thick muscular body (and yes, I too wonder about flavor, and would like to taste a slab of that). It’s definitely not a salmon, though — the bony structure is a curious set of compromises where some features are distinctly sarcopterygian, some look like they belong on a primitive actinopterygian, and others are unique or show affinities to characters of ancient extinct fishes, like rhipidistians. This is very cool. What we see here are relics of an ancient common osteichthyan ancestor, which are being honed into the specific characteristics of the Sarcopterygii. The analysis of the totality of the animal’s features, though, place it more in the lobe-finned than the ray-finned clade. That places it on a branch of the line leading to us…a very, very old branch, making this your many-times-great grand uncle, or cousin only a few million times removed. Now my curiosity about a taste-test is making me feel mildly cannibalistic.

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The topology is the most parsimonious tree arising from a matrix of 23 taxa coded for 153 morphological characters (tree length = 292, consistency index = 0.572, retention index = 0.737, rescaled consistency index = 0.421). The numbers at nodes indicate bootstrap support (where the value is greater than 50%) and Bremer decay index (bottom and top numbers, respectively). Eif., Eifelian; Ems., Emsian; Fam., Famennian; Fras., Frasnian; Giv., Givetian; Gor., Gorstian; Loch., Lochkovian; Lud., Ludfordian; Prag., Pragian.

When you look at that diagram, what should jump out at you is all the diversity in the Devonian, the so-called Age of Fishes, and the paucity of representative fossils from the Silurian…which is exactly where all the interesting branch points in the fish family tree are located. Once again, paleontology is a predictive science, and this tells us where to look for the next batch of exciting and informative fossils.

Zhu M, Zhao W, Jia L, Lu J, Qiao T, Qu Q (2009) The oldest articulated osteichthyan reveals mosaic gnathostome characters. Nature 458:469-474.

“The Pope is either stupid, ignorant or dim”

Richard Dawkins did it again, clearly stating his opinion of the Pope’s policy on birth control and AIDS prevention. One problem: he left out another possibility. The Pope could be evil.

I tend to favor a combination of all of the above.

I have received a communique from Richard Dawkins in which he protests that he was misquoted in the Telegraph. What he actually said was,

The Pope is either stupid, ignorant or wicked.

Much better.

Why I hate April 1st

You just can’t trust anything posted to the web today. Take, for instance, this story about Howard Ahmanson. In case you don’t know who he is, he is an extremely wealthy Californian who also happens to be one of those Christian Reconstructionists — a follower of R.J. Rushdoony, who thinks we ought to have a literal Christian theocracy — and is a major contributor to the Discovery Institute and other evangelical/fundamentalist causes. So I have to read this with a bit of skepticism.

WHY I REGISTERED DEMOCRAT>
By Howard Ahmanson

About six weeks ago, I, a known leader of the Religious Right in California, decided to reregister in the Democratic Party. Why did I do this?

Well, I think I was reading about the budget struggles and threatened purges in the Legislature, and I was getting more and more tired and disgusted of it, and I realized that, had I been a Republican assemblyman, I could have hardly escaped being purged myself. The Republican Party of the State of California seems to have decided to narrow itself down to one article of faith, which may be described as NTESEBREE: No Tax Shall Ever Be Raised Ever Ever. Now, I’m concerned about this constant tax ratcheting, but I don’t think this is the answer. The Democratic Party in California, however, is now so big and diverse and all-inclusive that it has ABSOLUTELY NO PRINCIPLES WHATSOEVER. The Hollywood and San Francisco establishments within the Party may hold to some pretty detestable principles, but the party as a whole? I have not changed any of my opinions. There is not a single right-wing opinion I hold that some section of the Democratic Party doesn’t support it. Opposed to “marriage equality” and freewheeling abortion rights? A lot of Democrats of color will agree. And also many of them will agree on the importance and social justice of vouchers and tax credits for non-government schools. Opposed to fiscal irresponsibility? A lot of Silicon Valley Democrats will probably agree. Opposed to “urban redevelopment” schemes that run small business and residents out of the way for the benefit of the politically important? Got a high view of property rights? Lots of Democrats, including Robert Cruickshank and Senate President Darrell Steinberg, agree with me to a considerable degree.

I describe myself as a “social conservative, an economic moderate,” and to a considerable extent a property libertarian. By “economic moderate” I mean that the philosophy of “starve the beast” has failed. The beast will feed welfare and pork and starve infrastructure. If we want to confront irresponsible spending, we have to confront it directly. We have to confront directly the issue of the role of government and what we want it to do and not do. And when we do want government to do something, we want it to have enough money to be able to do what it does pretty well (at least considering it’s a government), but we have to fight the mentality of entitlement. The whole mentality entitlement is dangerous. The nearest thing we have to entitlements are property rights, and they are to defined things that actually exist. And all other rights, in the end, depend on property rights; freedom of speech, religion, and press is freedom in a place, or it is nothing. I am not one to radically abolish all welfare programs, as I was in my wild youth – and Social Security and Medicare are welfare, whether you like it or not – but the attitude of entitlement, especially to resources that may not even clearly exist, makes it impossible to pursue any kind of a rational fiscal policy.

I may have made a rash move, in that it will be hard for me to find Democrats that I can actually support – there probably are some, though; social conservatives in the inner city, Democrats with an open mind to vouchers and tax credits and in other ways willing to confront the public sector union beast (I don’t consider private-sector unions, for the most part, a serious enemy nowadays), Democrats open to fiscal sanity, Democrats open to property rights rather than “urban redevelopment” social engineering schemes out of City Hall. And by the grace of God, there probably are some!

It’s not impossible that this is accurate — the Rev. Phelps was once a Democrat, too, and the Democratic Party does seem to have become rather amorphous — but jebus, this really ruins my morning.

I think the best thing for my sanity is that I should retire to my remote stronghold, Chateau L’Pieuvre, and disconnect from the net until 2 April. Or perhaps I shall simply torture a few students with an evil genetics exam instead. I know I am not going to read The Panda’s Thumb, that’s for sure.

Yeah, the Catholic church has a real problem with gay priests. Sure.

One of the Vatican’s “solutions” for their perennial sex scandals is to start testing and screening candidates for the priesthood. Australia is even considering doing it: unfortunately, the targets are all wrong.

Melbourne’s Catholic Church has embraced a Vatican suggestion to test potential priests for sexual orientation. Those who “appear” gay will be banned.

The head of the Vatican committee that made the recommendations has made it clear celibate gays should also be banned because homosexuality is ”a type of deviation”.

I really want to know details about how these tests are going to be done. Do they hook the candidate up to a plethysmograph and then show them pictures of varying degrees of titillation to various sexual orientations? That sounds fun — they might get a flood of new prospects who are really just there for the test. Heck, if I was sufficiently bored, I might sign up … especially if the testing is done by hot novices in sexy wimples.

But, still, it’s all incredibly wrong-headed. Priests are people who are supposed to be celibate…it should hardly matter whether they are turned on by women or men or turnips, for that matter. There might even be a significant number of church leaders who are radical perverts deep down, but are in the priesthood specifically and sincerely for the whole denial of the flesh aspect. Why single out gays? Shouldn’t we be more worried about priests with uncontrollable urges towards children, or even heterosexual priests who are unable to resist the women who look up to them as authority figures?

This isn’t about correcting the problems of the church at all. It’s more about finding another opportunity to discriminate against gays.

Empedoclean evolution

I must echo Huxley and say, “How stupid of me not to have thought of that!” in response to the discovery of a new mode of evolution. This changes everything!

In an entirely relevant mode of logic, I have noticed that we are suffering with a surprising and rather nasty blizzard today, which was clearly intended for tomorrow. Its appearance today only makes sense if it is Australian, and therefore John Wilkins is responsible for flying over here and shoveling my driveway.

Best pointless poll ever!

I must thank io9 for taking the spirit of the pointless poll to the next level. They have an article on the term “nerd” and are asking whether it’s a useful label or not. Here are the results so far.

Should we retire the term “nerd”?

You’re dead wrong man, keep the faith! Cool stuff is still happening! Nerd4Life! 10% (169 votes)

You’re way late guy; it was all over by The Phantom Menace, or maybe that Hackers film with Angelina Jolie. 19% (327 votes)

Let’s keep it alive anyway for what’s still valuable. Future generations of misfits will thank us. 26% (449 votes)

Answer 4 19% (323 votes)

Answer 5 27% (476 votes)

“Answer 4”? “Answer 5”? What’s this? The poll software insisted on 5 possible answers, but the pollsters only had 3 choices in mind, so these empty placeholders made it into the listing…and they’re doing quite well.

Personally, I had to vote for Answer 5. After all, 5 is a term in the Fibonacci sequence, while 4 is not.

Run for the hills! It’s the Framingstein monster again!

The criticisms must have stung, because Matt Nisbet has put up short replies on Russell Blackford’s and Jerry Coyne’s blogs. Unfortunately, in response to the substantial criticisms of the idea of compatibility between faith and science, Nisbet only offers a feeble and wrong correction to a minor point.

A correction is in order on Blackford’s post. Contrary to his framing, market research was not used to decide the position of the NAS, nor the 20 professional scientific organizations in the editorial at FASEB that endorsed the themes in the booklet. These organizations have had a long standing position on science and religion that has emphasized compatibility. The audience research indicated that emphasizing this long standing position was an effective way to communicate about evolution.

I suggest taking a look at what NAS staffers wrote in an article at Life Sciences Education about how they used public opinion data and evidence-actually listening to their audience-before trying to communicate with them about a complex and sometimes controversial area of science.

The most severe insult offered in this comment is the part where he accuses Blackford of framing. Is that actionable, I wonder? Did Russell weep hot wet salty tears of shame when he was lanced with that horrific rhetorical thrust?

The serious issue he’s addressing is the National Academy of Sciences useful little booklet, Science, Evolution, and Creationism. When it came out, I said good things about it — it’s a handy short introduction to evolution for the layman. However, it also contained a rather objectionable section that perfectly represents the problem that Larry Moran and I have been complaining about for years, and that Jerry Coyne has recently torn into: it also pukes up a thick wad of partially digested, slimy religious pablum claiming that “Science and Religion Offer Different Ways of Understanding the World”.

You know how much I detest that phrase.

It’s not true, and it’s also unrepresentative — there is a significant (and growing) strain of scientific thought that finds the claim objectionable. That argument is completely omitted from the NAS booklet. As I wrote in my original comment,

Do science and religion offer different ways of understanding the world? Sure. One is verifiable, testable, and has a demonstrated track record of success; the other is a concoction of myths that actually leads to invalid conclusions. Perhaps it ought to be rephrased: science provides one way to understand the world, while religion provides millions of ways to misunderstand it.

What the NAS published contained an intentionally one-sided version of the state of affairs in science — it emphasized only the accommodationist view that religion and science are compatible, soliciting comments on the subject from the usual subjects, people like Collins and Miller and Ayala. These are good people and good scientists, but dear dog, they are a poor reflection of the attitudes of the scientific community. If the only people these organizations ever put up as the face of science were Richard Dawkins and Sam Harris, everyone would see the problem immediately…but Collins and Miller have become the reassuring tranquilizing narcotic that scientists fire into the faces of the public, to fool them into thinking that science really doesn’t offer any world-changing perspectives on comfortable old myths.

It’s a lie. Science will make you uncomfortable. It will change your ideas about the universe. It will force you to confront awkward facts and difficult consequences. It is not a balm to reinforce the status quo, and if you try to present it as if it is, you’re doing it wrong.

What does Nisbet offer in his brief reply? His defense is that the NAS did not use market research to define their message. They used institutional tradition (which, I would argue, ought to be more accurately called institutional inertia, and give the strength of creationism in the US, ought to be rejected as a failure), and gives us a link that shows…the NAS used market research in composing the booklet!

It’s not like you have to read between the lines to figure that out. It says it plainly.

…this new edition was shaped to a large extent by a careful program of audience research.

There’s a section entitled “Listening to intended audiences” even. They come right out and say that whole sections were rewritten: they cut out any emphasis on the Dover decision, because, they say, “the public does not readily understand the role of the courts in such matters”. They admit that they expanded the section on science and religion, and solicited statements from various religious denominations and religious scientists. And it repeats something that many people, atheists and theists alike, have been saying is a lie.

It makes clear that acceptance of the overwhelming and continually growing body of evidence for evolution need not be in conflict with religious beliefs for many people.

It “need not”? But it is. This head-in-the-sand approach of pretending that all those fervently-held religions that make anti-evolutionism a central part of their creed is precisely the kind of befuddled and condescending obliviousness that has put us in the situation we’re in right now. Face it. Reality erodes faith-based belief, and science is all about dredging up reality and rubbing your faces in it. Nothing in science supports religious beliefs, and all those acclaimed scientists who are trotted out to issue their homilies about the importance of their faith are operating in defiance of reason.

I would also argue that market research, which is all about tailoring the message to what the audience wants to hear, is antithetical to science, which should be about telling people what they need to know, no matter how uncomfortable it makes them.