Tuesday, October 18, 2005

Plesiosaur poop!

As Chris Clarke told me, "They were big ducks!" Two newly discovered elasmosaurid plesiosaur specimens from the Cretaceous contained a surprise that told us a little more about their diet.

What was found were specimens with their stomach contents preserved, and what they contained were gastroliths, or gizzard stones (no surprise there; plesiosaur remains have long been associated with gastroliths) and gastropods and crinoids. The gastroliths in this case were identified to have come from a site over 300km away, so the plesiosaurs were certainly doing some traveling over their lifetimes.

Here's a new word for me, too: bromalite. You've probably heard of coprolites before, fossilized feces. A bromalite is basically fossilized colon contents, all the stuff that has worked its way through the gut but hasn't been excreted yet…so this poor beastie was killed before it could void its bowels one last time. Here's a picture of that terminal lump of intestinal blockage:

This changes our view of their feeding habits a bit—they were ducking their heads down under water to scoop up benthic (bottom dwelling organisms) like clams and gulping them down. I've always had this image of long-necked plesiosaurs darting after fish, but they may have used those necks more to reach down and snaffle up less mobile prey.

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McHenry CR, Cook AG, Wroe S (2005) Bottom-feeding plesiosaurs. Science 310(5745):75.

Disquieting facts about evolution

Jody Wheeler finds a jewel of a quote from Barbara Forrest:

We have established scientifically some disquieting facts: (1) human beings have evolved from nonhuman life forms, meaning that (2) at one time we did not exist, and that (3) according to paleontological and astronomical evidence, at some time in the future we shall cease to exist.

Furthermore, from a scientific standpoint, there is no discernible reason that we had to evolve in the first place, and there is no guarantee that we shall continue to evolve successfully; more hominid species have become extinct than have survived. The price of such knowledge has been the gnawing question of whether human existence has genuine meaning if it was constructed with cranes rather than supported by skyhooks, as Daniel Dennett says.

The problem of meaning is easily resolved for those who embrace a preconstructed system of meaning such as religion. However, religion cannot help us find meaning in any honest sense unless it can assimilate the truth about where human beings have come from, and the only real knowledge we have about where we came from we have acquired through science.

I can see where many would find that first paragraph disturbing. You'd think the concept of personal mortality would make a similar idea about the species as a whole familiar, if uncomfortable to contemplate, but fundamentalist Christianity seems to be an exercise in the denial of death.

Now if only she hadn't cited the awful Dennett…

Monday, October 17, 2005

Science and non-science

Yesterday's San Francisco Chronicle had an interesting op-ed: Creation and the limits of science.

The requirement that science stick to material observation means that the scientist can state that the world acts as if it were created 14 billion years ago. It does not mean the scientist can legitimately claim that science shows that the world actually was created 14 billion years ago.

Indeed, it is not inconsistent with science to assert that the world was created 6,000 years ago or 10 minutes ago.

This point was elegantly articulated decades ago by the British Nobel Prize-winning philosopher and logician Bertrand Russell. Russell observed that it was entirely possible that the world was created 10 minutes ago and that he, Bertrand Russell, was created simultaneously, wrinkles and memory included.

Since this hypothesis could in no way be tested, it held little interest for Russell.

When I raise Russell's line of reasoning with scientists, they're surprised and dubious, but once they've thought it through, they agree with the logic.

I'm neither surprised nor dubious—I thought it was conventional wisdom. Creationists have a specific set of beliefs that are actually very easily justified. Just declare a miracle. They have this god-being who can do anything and everything, so why not use him? Poof, the universe exists. Poof, it's populated. Zap, he kills everyone with a magical flood. And of course, abracadabra, he conceals all the evidence for these amazing events beneath a mirage of old age. There aren't any arguments science can bring to bear against any of that. As Russel noted, the sin of Last Thursdayism is that it's simply uninteresting.

The Omphalos hypothesis is just the most extreme version of an uninteresting explanation. Unfortunately, as comic book fans know and mock, the omnipotent superhero who can do anything without any struggle also makes for an awfully boring narrative. The old gods at least engaged in a little carnal boinking or got drunk and brawled, but this new monotheism is awfully tedious and sterile that way. And it's increasingly hard to take credit for natural events like rain and grain sprouting with those scientists explaining everything. And when people are looking for real miracles, they turn away from the priests and look to the much more reliable doctors.

The 'scientific' creationists and Intelligent Design creationists know this, and they've been scrabbling to grab a piece of science's credibility for years. They've contrived feasibility studies of Noah's Ark, used computer models (poorly) to argue for vapor canopies, and fudged physics to claim the speed of light has been decreasing. This is where our beef with creationism lies—their desperate abuse and corruption of science to rationalize their beliefs. They do bad science. It's the same with the Intelligent Designers—it's not that that kind of intervention is declared impossible a priori, but that they don't have the evidence to support their contention. If they just said "God (or Designer) did it," we'd be done with the argument…although then, of course, they'd have abdicated any attempt to smuggle their religion into our public school science classrooms.

I do have a few gripes with Craig's article. This comment—"it is not inconsistent with science to assert that the world was created 6,000 years ago or 10 minutes ago"—is not correct. As I say over and over again, science is a process, not a body of conclusions, and any competing process that relies on assertion and revealed knowledge is inconsistent with science. When someone tries to replace the hard work of observation and testing and logic with clerical fiat, they are being anti-scientific in a very profound and fundamental way.

I also think he is splitting rhetorical hairs.

In the present contentious environment, the scientific community needs to cease making the indefensible claim that science shows the world was not created 6,000 years ago.

To say that science shows the world was not created 6000 years ago is a perfectly reasonable statement, unless one mistakenly treats science as an oracle and interprets it as meaning that science has uncovered an absolute truth about the world. When it is treated appropriately as a collection of evidence and tools and procedures, then it is clearly true: the scientific evidence is incompatible with a young earth. You have to use non-scientific ideas to show otherwise.

Creeping crinoids

They move. They look like immobile plants, squatting there on their stalks, but it turns out they can take off and scuttle slowly around.

How to euthanize a fish

Idyllopus asks a good question: how do you humanely euthanize a fish? As a fish biologist, I get this question fairly often.

Another question I get is, "Fish can't feel pain, right?" It's usually phrased exactly that way, too—they aren't looking for an accurate answer, they're looking for a reassurance that casual brutality towards cold and slimy creatures is acceptable. The actual answer, though, is "Of course they can feel pain, you clueless boob! Mind if I put this barbed hook through your lip?"^* The fish cutaneous sensory network is intricate and exquisite, and they react vigorously to noxious stimuli. We often don't recognize their responses because fish faces are rather expressionless, but if you're in the know you learn to notice the signs. Zebrafish, for instance, blanch noticeably when they're stressed or fearful or in pain.

So how should one kill a fish? People recommend some incredibly brutal methods. Throw them in a blender, they say, it's quick—yeah, and I imagine that throwing cats in a woodchipper would be quick, too, but no one suggests that humane societies should adopt it. There's also the 'club them over the head' method, or 'pick them up by the tail and whack them hard against a table edge'. Those work, if the executioner is swift and sure, which most people aren't. In most cases you end up with a fish frantically flopping on the table, or a bleeding mess of an animal that's feebly twitching, so you have to whack it a few times. (This is how my father and I used to kill salmon, though: we had a heavily weighted club, and we were also very quick and confident.) I think plucking an aquatic animal out of its environment and swinging it through a hostile atmosphere also counts as inhumane.

Less nasty techniques are the freezer and alcohol strategies. I don't think putting a fish in a freezer is humane: they don't seem to react strongly to slowly freezing to death, but then they can't—their metabolism is shutting down. Fish tend to be very sensitive to cold, though, and seek out optimal temperatures and avoid the cold, and can respond to changes of a few degrees with shock, so I have my doubts that this is a good way for them to go. Putting them in water with a few percent alcohol might be OK; they do get drunk, pass out, and die, just like people can.

Here's the way I euthanize fish, though, and since I've killed many thousands, I can say it's the cleanest, least painful way to do it, for both me and the fish. It's an anesthetic used for frogs and fish that goes by various names: ms222, MESAB, 3-aminobenzoic acid ethyl ester, tricaine methanesulfonate, or, as most of the pet and aquaculture supply houses call it, Finquel. For routine anesthesia, I use a 0.2% solution of the stuff—let a fish swim in it for a few minutes, they lose consciousness, you can do various surgeries on them, and then put them in clean fresh water, and a few minutes later, they're awake and swimming around again. If I need to euthanize them, I use a 0.4% solution (or more crudely, I use my 0.2% stock and sprinkle a few extra crystals of the ms222 powder in the beaker), put the fish in it, they fall asleep…and after 3-5 minutes, their heart stops. It will kill them at lower doses, but simply takes longer.

I get my stuff from Sigma, catalog number a-5040, for those of you who can purchase through academic suppliers. Otherwise, here are a few commercial places that will sell it to you: Doctors Foster & Smith, PondRX, and Argent Labs. It's about $15-20 for a 5 gram bottle, which sounds expensive, but a little goes a very long ways. I bought a 25 gram bottle 8 years ago, and I've still got lots left…and I euthanize fish far more often than your usual pet fish owner.

It's good to be prepared, too. Several years ago, my colony was suddenly struck with hemorrhagic septicemia, a bacterial infection that causes blood vessels to rupture and fish to die slowly and unpleasantly and messily, and after spending days trying to treat it with antibiotics and water changes and new tanks and hoses and so forth, I had to spend a sad afternoon putting about 400 fish out of their misery. Using an anesthetic in bulk was the only reasonable way to do it.

^*While I am fully aware that fish can feel pain, I still enjoy fishing and eating fish. I just don't delude myself into thinking the fish are enjoying themselves in a friendly tussle out there on the end of the line.

Saturday, October 15, 2005

Tourette's and SLITRK1

Our brains are complicated structures in a delicate balance, and there are many ways that their function can go wrong. Tourette's Syndrome, for instance, is a strange disorder where the afflicted have motor and vocal tics of varying severity—the most dramatic cases have socially debilitating outbursts of grunting, barking, or shouting, but most cases involve only minor twitches. They are driven by unusual behavioral compulsions beyond their control (I think many of our behaviors are driven by deep biological imperatives that we take for granted and don't notice because everyone else is doing the same thing…Tourette's is a situation where the drives generate behaviors that do stand out). A new paper in Science describes one gene that may play a role in Tourette's, and I thought the most interesting thing about it was the multiple, subtle ways the gene can be modified to affect the behavior.

The gene of interest is SLITRK1. This gene gets its name from its similarity to Slit, a well-known gene that is secreted and can repel growing neurons, and Trk, a family of tyrosine protein kinase receptors—it's a protein that can bind extracellular signaling molecules, and can also affect the growth of neuronal processes. SLITRK1 is also expressed in specific regions of the brain that are known to be affected in Tourette's Syndrome. That's a suggestive combination.

Just being suggestive isn't enough, though: you need to find evidence of a link. Here's an example of such evidence, a teenaged boy with an easily detected chromosomal change.

The pedigree shows that the affected individual (the dark square) has no family history of Tourette's Syndrome; he's a brand new case, likely the product of a novel mutation. Examining his chromosomes revealed a change in chromosome 13, with a region (q11 to q33) inverted, which was not shared with any of his other family members. There are 3 genes in this region that might be affected, but only SLITRK1 has the association with the brain to make it a likely candidate.

This boy has a perfectly normal SLITRK1 gene, though. It's within the inverted region, but has not been damaged in any way by the flip—it has only changed its position within the chromosome. The investigators suspect a position effect. Gene activity can be modulated by the location within a chromosome, by the level of activity of neighboring genes. For instance, cellular mechanisms to inactivate genes, such as methylation or the binding of proteins, are not perfectly precise, so a gene that is located near a region that is strongly inactivated is at risk that it will be 'accidentally' silenced with a high frequency. They suspect that this boy's SLITRK1 gene has been downregulated in its new location.

With SLITRK1 as a new suspect as one causal agent in Tourette's Syndrome, the investigators began screening known Tourette's sufferers for more anomalies in this particular gene. Most were negative. This is not a surprise; complex behavioral syndromes are not going to be easily pinned down to precisely one cause. However, they did find another individual with the pedigree to the right; he was affected with Tourette's, and his mother (the half-shaded circle) had a related syndrome, trichotillomania.

When their SLITRK1 genes were screened, mother and son were found to have something unique, that was not shared with other, unaffected members of the family. Their gene had a truncating frameshift mutation. This is not a subtle change at all, but an abrupt break in the gene product. One of their copies of the SLITRK1 gene is completely nonfunctional.

They found other cases of a changed SLITRK1 gene in individuals with Tourette's, but this one is the most subtle of them all. In this case, the coding sequence of the gene is unchanged, but one nucleotide of the untranslated region of the gene is changed from a G to an A. This a portion of the DNA that gets transcribed into the RNA string, but is clipped out of the sequence that will make the actual protein—you'd think it wasn't particularly significant. In this case, however, the change helps the SLITRK1 RNA bind better with a specific micro-RNA, miR-189. Micro RNAs are tiny pieces of RNA that bind to transcripts and modulate their translation into protein, in this case to reduce the production of SLITRK1 in the cells.

So, in a minority of Tourette's cases, they've discovered three kinds of changes to SLITRK1 that are correlated with the syndrome: a change in gene position within the chromosome, a truncation of the gene product, and an increased sensitivity to micro RNA binding. What exactly does SLITRK1 do to neurons?

You can't poke around in Tourette's brains, and you can't go around tweaking their genes to see what happens either, but you can do a cool experiment: introduce human SLITRK1 genes into mouse cells.

On the left are a quartet of mouse neurons in the control group at 6 days in vitro. They had a construct introduce that consisted of only GFP, green fluorescent protein, as a marker.

In the middle are a quartet of neurons containg GFP and human wildtype SLITRK1. These were significantly bushier than the controls.

On the right are mouse cells with the truncated mutant form of SLITRK1; they are significantly less branchy than the cells with wildtype SLITRK1. The presence of the gene is clearly associated with more complex arbors in these cells.

So changes in this gene are associated with changes in behavior, and gene expression affects growth and morphology of neurons. I'm comfortable with the case made that this gene affects processes that are responsible for some cases of Tourette's Syndrome. I want to emphasize, though, that this is not a Tourette's Syndrome gene—it is one among many genes that modulate complex interactions in brain development, and contributes to the molecular machinery that assembles the brain. We have to be very careful about statements that a particular gene is for something. We wouldn't say that cadmium red pigments are responsible for an artist's painting of a sunset, after all, even if they are helpful in generating brilliant color. A good artist can make a great painting with only ochre in his spectrum of reds, and all the cadmiums and chromiums in the world won't turn a duffer at the easel into a Matisse. It's the same with genes like this that affect the brain; a broken SLITRK1 does not make for a broken brain, just as an unmutated form doesn't guarantee a healthy one—it just means the individual is working with a different palette.

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Abelson JF, Kwan KY, O'roak BJ, Baek DY, Stillman AA, Morgan TM, Mathews CA, Pauls DL, Rasin MR, Gunel M, Davis NR, Ercan-Sencicek AG, Guez DH, Spertus JA, Leckman JF, Dure LS 4th, Kurlan R, Singer HS, Gilbert DL, Farhi A, Louvi A, Lifton RP, Sestan N, State MW (2005) Sequence Variants in SLITRK1 Are Associated with Tourette's Syndrome. Science 310(5746):317-20.

Pedantry and dead-pan sarcasm

It's something those Brits do so well.

Friday, October 14, 2005

I know what I want for Christmas…

I've been browsing the catalog for Skulls Unlimited. Mmmmm. So many pretty things.

Thursday, October 13, 2005

The ghost of Popper

Those darn creationists are awfully fond of Karl Popper—they think they've got a rock-solid refutation of evolution in Popper's claims about refutation. John Wilkins shoots 'em down. I like having a short explanation of what Popperism is and isn't handy.

I have to add, though, that the pronouncements of a philosopher like Popper (or Hume or Hull or Wilkins or Plantinga or Flew) just don't have much practical impact on science, which is another reason the frequent Popper citations just make us roll our eyes. Scientists are a pragmatic bunch who are more likely to poke something with a stick than wonder if they should poke something with a stick. We are Bold Men and Women of Action! Very few have much training in the philosophy of science, and the usual experience in grad school is to get dissuaded from taking any courses at all (and sometimes, from thinking at all), and instead get right to work with a sharp knife or a PCR machine or whatever. Philosophy, if anything, is the exercise we do after the fact to rationalize what we just did.

Although…the older I get and the more philosophy I read, the more I think some exposure to philosophy would be a useful requirement for biology graduate students. Questioning assumptions is a good first step towards learning something new, and that's exactly what philosophy can train people to do.

Get crackin'—the Tangled Bank wants YOU!

You've got less than a week to get your submissions in for the Tangled Bank, due to arrive at The Questionable Authority next Wednesday. Write and send those links to me or host@tangledbank.net by Tuesday evening!

Wednesday, October 12, 2005

I and the Bird #8

Birders, take a look at I and the Bird #8 at Science and Sarcasm. And if you are inspired, send in links for the next one at Living the Scientific Life.

Educated and medicated

It's a new Carnival of Education, and Grand Rounds, Vol. 2 Issue 3. That'll keep all you educated nerds occupied for a while.

Tuesday, October 11, 2005

Little Charlie Darwin, God bless him

McSweeney's has a short summary of exactly how ol' Chuck Darwin got that berth on the Beagle. It's fairly accurate, although the comments about how Darwin was feeling about the ups and downs of his career are, well, speculative. Funny speculative.

Chris Mooney in the flesh

The Chris Mooney book signing was a blast, although we were all greatly disappointed that none of the wingnuts who huffed and puffed about it showed up (follow that link; the guy whines that it's so unfair, the U would never sponsor a conservative speaker, and the commenters proceed to point out past conservatives who have spoken there—such as Ken Starr, and just about everything the MacLaurin Institute books). Aside from the cowardly lack of confrontation, though, Chris gave a fine talk, a rapid-fire overview of the major themes of his book. It was well received by an audience of about 60 people.

Among the crowd were myself, Kele Cable, Kristine Harley, Scott Lohman, Mike Mosedale, Greg Peterson, and David Wilford. It's getting to be the case that every time I go to some event in Minneapolis, I recognize a growing group of people. I think we need to form a cabal.

And look! Evidence that Myers and Mooney do exist in the same universe! (In case you can't tell, I'm the grizzled one with the grimace and the squint; Chris is the photogenic one.)

Monday, October 10, 2005

Incentivize an illustrator today!

So that's what Chris Clarke looks like—man, he really needs to trim his nails.

That's one of many paintings done by Carl Dennis Buell, illustrator of the ancient world extraordinaire. Carl has been promising us a website for some time, and Chris is pushing him to do it. Get over there and add your words of encouragement—the work Carl does is inspiring and imaginative, and is just the kind of stimulus the public needs to appreciate evolutionary biology more.

(By the way, over half the pictures in my random rotating Pharyngula logos were done by Carl, so if you're a regular here, you've seen his work.)

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