Friday, August 13, 2004

They just keep yammering away at it

A wingnut starts babbling in my "Flying while brown" thread, and Annie Jacobsen is still whining about "Terror in the Skies". She's delusional and paranoid. It's hard to believe these people still think their racist stance is justifiable.

I can't stand it. Just read Pandagon—Jesse mocks it well, as it deserves.

In defense of monsters

The other day, I posted a picture of the skeleton of a cephalothoracopagus infant. Here's another interesting one, a case of derodymus, or conjoined twins with two heads and a single body.

These are a bit disturbing to most people, and I can appreciate the personal tragedies that lie behind these relics. But I've got to tell you that I also find them beautiful and fascinating, and actually, the emotion I feel most strongly on seeing instances of such extreme developmental plasticity is wonder. One of the things I do in my research is intentionally make monsters (not human, of course; fish), and I'm a practitioner of a formal field of study with a long, distinguished history, called teratology...the study of monsters or wonders. I'm not at all unusual in this—whether you call it experimental embryology or Entwicklungsmechanik or developmental genetics, the bulk of what developmental biologists do is introduce errors into embryos, and analyze the outcomes.

Even a casual examination of oddities like the derodymus or cephalothoracopagus tells us something about the nature of development.

One message is that there is no designer, no overarching governor who oversees the process, no central plan. This is a lesson that applies not just to the religious who imagine some supernatural being overseeing the developing organism, but also to the naive scientific view that there is a central genetic plan encoded in the DNA for the overall form. There is nothing in the organism that says, "Thou shalt form one head at one end of the body." Development is local. Cells, like minute independent automata, make general fate decisions on the basis of regional information; there is no overseer who reviews the overall progress of construction and detects egregious errors.

There is no authority, whether gene or angel, that lays down a blueprint for the organism…so where does the normal, consistent pattern come from? The clear explanation from these strange forms is that it is a product of both the genetic instructions within the organism and interactions with the environment outside it. (Another significant consideration is that the environment is also shaped by the organism, so there are also some intensely recursive feedback loops going on here…but that's something for a different day.) The developing organism tries to compensate for radical changes in its environment, but it's also capable of incorporating those changes to produce surprising variations in its own form.

Another important lesson is that development is remarkably plastic. Cells persevere—put them in a novel situation, in a chunk of anatomy that simply doesn't exist in the canon of normal development, and they compromise and form the best intermediate they can. Vertebrae are never supposed to be found side-by-side and paralleling one another, a situation that hasn't ever occurred as a normal outcome in hundreds of millions of years of chordate history, and the cells that lie between them are in an acutely anomalous situation, but they resolve it. They form muscles and fused ribs that represent a reasonable adjustment to the condition.

One utterly amazing observation is that development, even in these extreme situations, manages to assemble an integrated, functional organism. This is not a healthy condition, of course. Development is difficult when it takes its normal path, and compounding aberrations increases the likelihood of lethal error; many of these conjoined twins are doomed to die in utero or shortly after birth. But some manage to live into adulthood, even in cases like derodymus. Think about that. Look inside a normal person, and the complexity is overwhelming. Just putting together the tangle of plumbing is bewildering. Yet here we have a dumb organism that has an unusual situation—Two heads! We need twice as many carotids! And they have to hook up to a functioning aorta!—and it just happens. Everything works.

This is, I think, one of the key concepts in the evolution of development. While some of the forces in evolution are trying to fix stable outcomes, locking in specific patterns, some of the most interesting stuff going on in the evolving organism is the formation of robust mechanisms that respond to change in an adaptive manner. We have to couple instructions that say, "build an arm" with capabilities that say, "interact and negotiate with your neighbors and cooperate". The latter are perhaps far more significant in evolution than the former, and are responsible for the automatic coordination of parts that we see in even the most aberrant embryos.

People sometimes refer to the 'miracle of birth'. I resent that. There is no miracle here: the frequent errors, and the remarkable efforts at recovery, tell us that development is the product of strenuous work, complex exertions, and a billion years of practice. To imply that it is some effortless bit of offscreen, supernatural magic diminishes its beauty.

Stop that man! He's got a 20-sided die and a book of spells!

Here's yet another example of fear and insecurity being used as an excuse to intrude on personal liberty: searches being used as an excuse to judge the 'appropriateness' of books.

This morning, they're doing bag searches again to get on the ferry. And the guy doing the searches pulls me aside and says, "Sir, I feel that I need to confiscate this book."

I pause and say, in that tone of voice that most people would recognize as meaning, "have you lost your grip completely, chuckles?": "You need to confiscate... a book."

"Yes. I feel it's inappropriate for the other people on the ferry to be exposed to it."

Read the rest. It's got a happy ending and a good message: we need to stand up for our rights before these petty, sanctimonious pests, puffed up with their own sense of authority.

(via The Pagan Prattle)

Rural abominations

It's county fair time out here in Western Minnesota, and this afternoon my daughter and I had to make a brief stop at the fairgrounds to drop off a poster she'd made for the humane society. There I saw a sight that chilled me. Something I had not thought possible.

It was in the food court.

Deep-fried twinkies. Onna stick.

The horror. The horror.

And Skatje insists that she's going to try one when we return to the fair on Sunday. Is this a good thing? Am I committing child abuse by omission by allowing her to poison herself this way?

Thursday, August 12, 2004

Evolution of the whale ear

John Lynch has already mentioned this paper on how the evolution of whale hearing unfolds in fossil record over on The Panda's Thumb, but it's fun stuff and I thought I'd discuss some of the data in a little more detail. In particular, take a look at this diagram of the structure of the ear to see how the changes occurred.

Start with the top left diagram. This is the ear of a typical modern land mammal. The horn shaped structure angling down towards 8 o'clock is the external auditory meatus (EAM), your ear hole, which leads to the dark gray oval, the tympanic membrane (TyMe), better known as the ear drum. Sound in air travels down the EAM to the TyMe, which vibrates. The vibrations are amplified the the chain of inner ear bones, the malleus (Mal), incus (Inc), and stapes (Sta), or hammer, anvil, and stirrup (I know—the terminology gets a little dense). Finally, the amplified vibrations are transmitted to the cochlea, where they are transduced into localized deflections of hair cells that trigger pitch-specific nerve impulses.

That's the path that works well in the air, but it doesn't work so well in water. Try immersing your head in the bathtub or swimming pool, though, and sounds are immediately dampened; the EAM fills with water that puts pressure on the eardrum, reducing the amplitude. Instead, the vibrations are transmitted through the bones and tissues of the head, vibrating the tympanic bone (TyBo) and by that path the inner ear bones.

The next three diagrams show the progression of changes in the whale lineage. The top right picture (b) is a pakicetid from about 50 million years ago. It's not much different from the generic land mammal, with an EAM, eardrum, etc., but note the one special feature: the tympanic bone isn't connected to the periotic bone (Per), and it's actually thickened into a structure called the involucrum. Basically, the bony structure of the ear is less tightly attached to the skull, and is more free to vibrate in response to sound transmitted through the tissue of the head.

The next step is seen in a group of whales called the remingtonocetid/protocetids, from 43-46 million years ago (c). The ear capsule is even less strongly attached to the skull, and the involucrum is more robust and even more remote from the skull—the whole thing is better at moving freely. The ear drum is reduced and conical in shape, and the malleus is fused to the bone, so although the pieces are all there, it's not going to be particularly effective at capturing sound waves in air. Another feature is a deep groove in the mandible that indicates that these animals had a fat pad (FaPa) in the jaw that would better transmit vibrations from the jaw bone to the ear capsule.

Last (d) is the ear structure of a modern whale. All of the trends of the previous organisms are accentuated: the ear capsule is specialized to receive sounds transmitted through the fat pad, and has completely given up on sounds transmitted through air—the external auditory meatus is closed off and gone, and while the eardrum is present, it's not connected to the external world.

The virtue of this paper is that it illustrates yet another unambiguous transitional serious, showing how over the course of less than seven million years we have a functional transformation of a specialized structure unique to an identifiable lineage.

---

Nummela S, Thewissen JGM, Bajpal S, Hussain ST, Kumar K (2004) Eocene evolution of whale hearing. Nature 430:776-778.

Hollywood Science

The 12 August 2004 issue of Nature has an article in it titled "Hollywood or Bust", about a class that tried to bring together scientists and screenwriters to correct a few problems...like bad science in movies. It's a bit of a hoot.

In the 1997 disaster movie Volcano,whole sections of Los Angeles are demolished by lava. For advice on the film, the production crew turned to Christopher Vogler,one of Hollywood's top story consultants. "Lava actually makes a tinkling sound like glass as it cools," Vogler says, "but they wanted it to roar like a freight train. Any volcanologist who saw the movie probably thought it was a comedy."
On a bright summer morning in mid-July, Vogler recounted this anecdote to a group of 15 scientists. They had come to Hollywood from all over the United States and from various scientific disciplines for a weekend workshop on screenwriting. Their goal was to learn how they could help improve the image of science and scientists in the movies. "You face an uphill battle with this stuff," Vogler continued. "But it's a good fight."

More of the article is about the perception of scientists in films than about the absurdities of movie science, though.

But it is the issue of how scientists themselves are portrayed that brought many of the participants to the workshop. Diandra Leslie-Pelecky,a materials scientist at the University of Nebraska in Lincoln, fears that media stereotypes are turning generations of children off any thought of a career in research. In film and television, scientists are often quirky, nerdy, obsessed, reclusive, self-important and not infrequently mad. These are not character traits that appeal to kids, she says.

Ya think?

Although I don't think we necessarily want to try and change all of those stereotypical portrayals—"mad" should definitely go, but the reality is that scientists are often quirky and nerdy—the traits that are desirable in a rapper, for instance, aren't going to be an advantage to a career in science (MC Hawking is just the exception that proves the rule.)

Let's not try and portray scientists as something they aren't, but let's also try and correct this little problem:

Leslie-Pelecky has had numerous conversations with children about their views on scientists. She is leading a project funded by the National Science Foundation that is investigating the impact of the media on children's attitudes. She has encountered many children who believe that the researchers who have visited their elementary schools aren't the real McCoy. "They might say the person was too 'normal' or too good-looking to be a scientist," Leslie-Pelecky told Nature. "The most heart-breaking thing is when they say, 'I didn't think he was real because he seemed to care about us'."

The funniest bit, though, was a paragraph that confirmed a stereotype:

The challenge, then, is how to bring science into a script that is driven by the story of its protagonist. "I read things in Science and Nature every week that are absolutely fascinating," said Tom Katsouleas, a plasma physicist at the University of Southern California, citing a Nature News Feature published in February about the last universal common ancestor, the theoretical first cell that gave rise to all cellular life on Earth (see Nature 427, 674-676; 2004). He asked the instructors: "How do we put something like that into a script about character?" Frank Spotnitz, who for four years was executive producer of the TV drama The X-Files, suggested that the protagonist might have to recreate this creature to save the planet. "If it were for The X-Files, I'd think about how it could start killing people," he added.

Yeah, television producers are freaking brain-dead morons. And they're completely lacking in imagination.

Spotnitz told the group he toyed with the idea ofshowing the details ofan experiment on The X-Files. The crew filmed a half-hour segment of Agent Scully working in the laboratory, but killed it and rewrote the script after everyone agreed it was far too boring. Singer concurred: "Most scientific work is unfilmable."

True. But the same could be said of police work and cattle ranching, yet somehow there have been a lot of cop and cowboy movies made.

The stem cell/abortion conflict

Kevin Drum is criticizing Saletan's "religion of stem-cell research" article, and he makes a point I've also made before:

As for the moral arguments, let's insist on a full and complete discussion of those too—without the usual shilly shallying and prevaricating. The idea that a 1-week old embryo is a human being has always struck me as depressing: a nihilistically mechanical view of humanity in which DNA + miscellaneous chemicals = human life. Still, it's a fact that some people feel this way. But if they do, then they have to accept the logical consequences of this view in their public speech too: a complete ban on all abortion, all fertility treatments that utilize multiple eggs, and all embryonic stem cell research. Not just a ban on federal funding, but a complete ban. Put that on the table and I think we'd find out pretty quickly how many people really believe that humanity begins at conception.

This is one of those curious reversals that bothers me: I'm the biologist, the materialist, the atheist, and my gripe with the anti-abortionists who insist that human life begins at conception is that these typically religious, spiritual, oh-so-concerned people are cheapening human life. They assign the full value of a human life to an imaginary, invisible component they call a "soul", and they equate the richness of life and mind we can see in a toddler with a pinpoint cluster of cells. Their whole argument rests on ignorance, misattribution, and fantasies.

Wednesday, August 11, 2004

Psychiatrist, heal thyself

I've been slumming. Read some right wing garbage. That lunatic Krauthammer jerk.

Scared myself.

Syria is weak and deterred by Israel. North Korea, having gone nuclear, is untouchable. That leaves Iran. What to do? There are only two things that will stop the Iranian nuclear program: revolution from below or an attack on its nuclear facilities.
The country should be ripe for revolution. The regime is detested. But the mullahs are very good at police-state tactics. The long-awaited revolution is not happening.
Which makes the question of preemptive attack all the more urgent. Iran will go nuclear during the next presidential term.

There may be no deus ex machina. If nothing is done, a fanatical terrorist regime openly dedicated to the destruction of the "Great Satan" will have both nuclear weapons and the terrorists and missiles to deliver them. All that stands between us and that is either revolution or preemptive strike. Both of which, by the way, are far more likely to succeed with 146,000 American troops and highly sophisticated aircraft standing by just a few miles away -- in Iraq.

This. Is. Insane.

We botched Afghanistan, we got mired in a bloody mess in Iraq on false pretenses, and now the deranged neo-con dingleberries are inventing rationalizations to invade another country? We're hearing the same accusations of WMD and promise of a populace ripe to welcome our aid? And the unjustified presence of our troops, who are already dying in dribs and drabs , in adjacent Iraq is an asset and excuse to attack?

The second four years of a Bush administration looks a bit predictable, I think…a good reason not to give them to him.

I want my Frankencoffee!

Brazil has decoded the coffee genome.

Suddenly, scientists know an awful lot about coffee in Brazil.
Having studied 200,000 strands of DNA, they have identified 35,000 coffee genes, a combination of which gives the drink its aroma and flavour.
"We are going to create a super-coffee that everyone can benefit from eventually," Mr Rodrigues told reporters in Brasilia.
He said this would be achieved naturally through cross-pollination of coffee plants and not through genetic modifications in a laboratory.
If that boast rings true, Brazil will move even further ahead of its competitors.
Already, the country accounts for a third of the world's coffee production.
The government will not make these findings available internationally for at least two years.

It's a long way to go from the genome to better coffee (especially if they aren't going to use the information directly, a claim I don't believe for a minute but which is probably politically expedient), but as a dedicated coffee addict, this is a lovely sentiment. I'd be much more impressed, though, if the data were made widely available.

(via Mirabilis)

Democratic snark

This comment by James Carville, about the congressman Rodney Alexander who made a last-minute switch from Democrat to Republican, just made my day:

Alexander was known as the stupidest Democrat in Louisiana, which would probably make him the smartest Republican in Washington.

Pharyngula

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