Spiral cleavage

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Developmental biologists are acutely interested in asymmetries in development: they are visible cues to some underlying regional differences. For instance, we’d like to know the molecules and interactions involved in taking a seemingly featureless sphere, the egg, and specifying one side to go on to form a head, and the the opposite side to form a tail. We’d like to understand why our back (or dorsal) side looks different from our belly (or ventral) side. One particularly intriguing distinction, though, is the left-right axis. For the most part, left and right are nearly identical, mirror-images of one another, but there are also key asymmetries. Your heart, for instance, is larger on the left side than the right, your liver lies mostly on the right side of your abdomen while the stomach arcs to the left, and these arrangements are essential for normal function. Left-right asymmetries are more subtle than anterior-posterior or dorsal-ventral differences, and that makes them especially fascinating.

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Tiktaalik makes another gap

Paleontologists have uncovered yet another specimen in the lineage leading to modern tetrapods, creating more gaps that will need to be filled. It’s a Sisyphean job, working as an evolutionist.

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This creature is called Tiktaalik roseae, and it was discovered in a project that was specifically launched to find a predicted intermediate form between a distinctly fish-like organism, Panderichthys, and the distinctly tetrapod-like organisms, Acanthostega and Ichthyostega. From the review article by Ahlberg and Clack, we get this summary of Tiktaalik‘s importance:

First, it demonstrates the predictive capacity of palaeontology. The Nunavut field project had the express aim of finding an intermediate between Panderichthys and tetrapods, by searching in sediments from the most probable environment (rivers) and time (early Late Devonian). Second, Tiktaalik adds enormously to our understanding of the fish-tetrapod transition because of its position on the tree and the combination of characters it displays.

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The swiftboating of Eric Pianka

Pianka speaks out. Nick Matzke has a good post on Pianka at the Thumb, addressing the smear campaign against him*. He links to an interview with the good Dr—what he’s saying is simple sense, common in the biological community, and he’s not endorsing mass murder…he’s talking about conservation and planning ahead. Mims is a “crazy kook” who distorted the story and turned it into screaming match.

Get used to it. This is part of the right-wing strategy to attack the academy: when scientists honestly state bad news (and there is much bad news, and it’s growing), they are going to be rabidly accused of all kinds of outrageous crimes. It’s the new McCarthyism. The majority of us do not support short-sighted policy, we don’t endorse jingoism, we are going to urge people to think before acting, we are going to predict the consequences of bad policy, and we are generally going to be critical of demagogues and fools…and that is being treated as a crime.

*Quite unlike the situation with Paul Mirecki; I can’t help but interpret this to mean you’re going to be left twisting in the wind if the right-wing mobs try to lynch you, and you admit you’re godless.

Taphonomy of fossilized embryos

There are these fossilized embryos from the Ediacaran, approximately 570 million years ago, that have been uncovered in the Doushantuo formation in China. I’ve mentioned them before, and as you can see below, they are genuinely spectacular.

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Parapandorina raphospissa

But, you know, I work with comparable fresh embryos all the time, and I can tell you that they are incredibly fragile—it’s easy to damage them and watch them pop (that’s a 2.3MB Quicktime movie), and dead embryos die and decay with amazing speed, minutes to hours. Dead cells release enzymes that trigger a process called autolysis that digests the embryo from within, and any bacteria in the neighborhood—and there are always bacteria around—descend on the tasty corpse and can turn it into a puddle of goo in almost no time at all. It makes a fellow wonder how these fossils could have formed, and what kind of conditions protect the cells from complete destruction before they were mineralized. Another concern is what kinds of embryos are favored by whatever the process is—is there a bias in the preservation?

Now Raff et al. have done a study in experimental taphonomy, the study of the conditions and processes by which organisms are fossilized, and have come up with a couple of answers for me. Short version: the conditions for rapid preservation are fairly easy to generate, but there is a bias in which stages can be reliably preserved.

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gen•e•sis

Some fields of science are so wide open, such virgin swamps of unexplored territory, that it takes some radically divergent approaches to make any headway. There will always be opinionated, strong-minded investigators who charge in deeply and narrowly, committed to their pet theories, and there will also be others who consolidate information and try to synthesize the variety of approaches taken. There are dead ends and areas of solid progress, and there is much flailing about until the promising leads are discovered.

Origins of life research is such an unsettled frontier. I wouldn’t want to work there, but the uncertainty and the confusion and the various small victories and the romance of the work do make for a very good story. And now you can read that story in Robert Hazen’s Gen•e•sis: The Scientific Quest for Life’s Origins (amzn/b&n/abe/pwll).

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I wish we’d had the internets when I was a kid

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The New England Journal of Medicine sometimes provides great stuff to read over breakfast, like this story of a man who returned from a trip to Hungary with his guts infested with worms, Enterobius vermicularis. OK, so it’s not much of a story…but the cool thing is that they provide a movie clip of his colonoscopy, and you can watch the worms writhe.

(via Over My Med Body)

Cloning as solace

You all may recall the memorable, late Tito the wonder dog. Hank Fox has done something thought-provoking: he has frozen away some of Tito’s cells, on the chance of cloning him.

At 325 degrees below zero, the essence of Tito sleeps.

I got a call today from Genetic Savings & Clone, the company that stores tissue samples of pets, and they told me the culturing of the samples I’d sent them was successful. I now have about 10 million cells waiting for the future moment — if ever — when the technology and the money coincide to allow me to clone him.

This is a personal decision, and I wouldn’t argue one way or the other about what Hank should do; it sounds like he’s wrestled over the issues already. All I can say is what I would do if I were in his sorrowful position.

I wouldn’t even try cloning.

I disagree with his first sentence up there: the essence of Tito isn’t reducible to a few million cells or a few billion nucleotides. While the genome is an influence and a constraint—a kind of broadly defined bottle to hold the essence of a dog—the stuff we care about, that makes an animal unique and special, is a product of its history. It’s the accumulation of events and experience and memory that generates the essentials of a personality and makes each of us unique.

Even if cloning were reliable and cheap, I wouldn’t go for it. It would produce an animal that looks like Tito, and would be good and worthy as an individual in its own right, but it wouldn’t be Tito.

Hank mentions that “Even we atheists grapple with mortality, and entertain hopes.” That’s true. But I think that what we have to do, the honest part of being an atheist, is to recognize that mortality is inevitable and that things end. Grief and loss are the terrible prices we pay for living in a world that changes, and that has produced us, so briefly. The dead are gone forever, never to return, and all we can do is fight as hard as we can to delay it, rage at our inevitable failures, and eventually, reconcile ourselves to the reality.

I think Hank is still fighting when the battle has already been lost. That’s a noble effort, I suppose, but Tito is not in that dewar of liquid nitrogen, I’m sorry to say.

Another Tuesday, another Café Scientifique

We’re having another Café Scientifique here in Morris this evening—come on down! Nic McPhee of the Computer Science discipline (who also has a weblog, Unhindered by Talent) will be discussing “Privacy, security, and cryptography: What happens to your credit card number on-line, and is that e-mail really from your boss?“. It is open to everyone, of course, and is being held at the local coffeeshop, the Common Cup, from 6:00 to 8:00 this evening.