We need a thousand Sagans

I’m joining in on the Carl Sagan Memorial blog-a-thon, but I can’t offer unstinting praise. Sagan wrote about biology now and then, and every time he irritated me; I always felt like arguing with him about some detail that bugged me, and I think that was actually among his virtues—he was a scientist you cared enough about to want to criticize, and he also addressed questions wide and deep enough that we all felt like this curious astronomer was touching on our part of the universe.

Here’s one example, a short excerpt from my favorite Sagan book, The Demon-Haunted World: Science as a Candle in the Dark(amzn/b&n/abe/pwll).

The blueprints, detailed instructions, and job orders for building you from scratch would fill about 1,000 encyclopedia volumes if written out in English. Yet every cell in your body has a set of these encyclopedias. A quasar is so far away that the light we see from it began its intergalactic voyage before the Earth was formed. Every person on Earth is descended from the same not-quite-human ancestors in East Africa a few million years ago, making us all cousins.

Whenever I think about any of these discoveries, I feel a tingle of exhilaration. My heart races. I can’t help it. Science is an astonishment and a delight. Every time a spacecraft flies by a new world, I find myself amazed. Planetary scientists ask themselves: “Oh, is that the way it is? Why didn’t we think of that?” But nature is always more subtle, more intricate, more elegant than what we are able to imagine. Given our manifest limitations, what is surprising is that we have been able to penetrate so far into the secrets of Nature.

At the same time that I want to tear apart his annoying analogy of the genome to a set of encyclopedias, while I deplore the incessant focus on human evolution rather than, say, the beauty of a sponge or a beetle, there’s one thing he did well: he represented the joy we can find in the natural world. That’s something we don’t communicate enough, I think, that science is this wonderful, powerful, far-reaching enterprise that reaches farther into the glories of the universe than any other idea that has ever occurred to humanity. That’s something he made explicit in the title of his book, too — the way we will beat back the darkness is to illuminate it with science.

Evolution of vascular systems

Once upon a time, in Paris in 1830, Etienne Geoffroy St. Hilaire debated Georges Léopole Chrétien Frédéric Dagobert,
Baron Cuvier on the subject of the unity of organismal form. Geoffroy favored the idea of a deep homology, that all animals shared a common archetype: invertebrates with their ventral nerve cord and dorsal hearts were inverted vertebrates, which have a dorsal nerve cord and ventral hearts, and that both were built around or within an idealized vertebra. While a thought-provoking idea, Geoffroy lacked the substantial evidence to make a persuasive case—he had to rely on fairly superficial similarities to argue for something that, to those familiar with the details, appeared contrary to reason and was therefore unconvincing. Evolutionary biology has changed that — the identification of relationships and the theory of common descent has made it unreasonable to argue against origins in a common ancestor — but that difficult problem of homology remains. How does one argue that particular structures in organisms divided by 600 million years of change are, in some way, based on the same ancient organ?

One way is sheer brute force. Characterize every single element of the structures, right down to the molecules of which they are made, and make a quantitative argument that the weight of the evidence makes the conclusion that they are not related highly improbable. I’ll summarize here a recent paper that strongly supports the idea of homology of the vertebrate and arthropod heart and vascular systems.

[Read more…]

Last gasp of my development course

Today, I gave my final lecture in developmental biology this term. We have one more class session which will be a final discussion, but I’m done yapping at them. Since I can’t possibly teach them everything, I offered some suggestions on what to read next, if they’re really interested in developmental biology. They’ve gotten the fundamentals of the dominant way of looking at development now, that good ol’ molecular genetics centered modern field of evo-devo, but I specifically wanted to suggest a few titles to shake them up a little bit and start thinking differently.

  • For the student who is interested in the field, but doesn’t feel that development is necessarily their discipline, I recommended Richard Lewontin’s The Triple Helix: Gene, Organism, and Environment(amzn/b&n/abe/pwll). It’s short, it’s easy, and it’s a good counterweight to the usual gene-happy approach we see in developmental biology.

  • Since we are a liberal arts university, and we value a philosophical approach in addition to the usual bluntly pragmatic tactics we follow in the sciences, I also recommended one work of philosophy: The Ontogeny of Information: Developmental Systems and Evolution(amzn/b&n/abe/pwll), by Susan Oyama. That one is not an easy read, except maybe to the more academically minded. I mentioned that Developmental Systems Theory does not have the powerful research program that is making evo-devo so successful, but it’s still a usefully different way of thinking about the world.

  • If any of my students wanted to go on to grad school in developmental biology, and hoped to make it a profession, I had to tell them that they are required to read D’Arcy Wentworth Thompson’s On Growth and Form(amzn/b&n/abe/pwll). It’s old, it’s a little bit weird, but it’s still a major touchstone in the discipline.

  • Lastly, I told them that there was one more book they had to read if they wanted to consider a career in development: Developmental Plasticity and Evolution(amzn/b&n/abe/pwll), by Mary Jane West-Eberhard. If I were a young graduate student in the field right now, I think I could just open that book to a random page and find an interesting and challenging research problem right there. I might have to flip through a few dozen pages before I found one that wasn’t impossibly hard, but hey, it’s one of those books that fills you in on the array of issues that people are worrying over at the edge of the science.

I don’t think any of these would be a good foundation for an undergraduate course (either Thompson or West-Eberhard or Oyama would probably have a lethal effect on the brain of any unprepared student trying to plow through them), but they’d be great mind-stretchers for any student planning to move on.

So all my lecturing is done for the term, and all that’s left are monstrous piles of grading that will grow ominously in the next week and a half even as I struggle to keep up, and then I can try to polish it all off by Cephalopodmas.

Look out, Phoenix!

In a few weeks, on January 3-7, I’m going to be attending the 2007 Annual Meeting of the Society for Integrative and Comparative Biology in Phoenix. I’m going to be part of a panel in a Media Workshop, along with a few other names you might recognize:

Blogs are online “diaries” that are growing in popularity. Popular political and social commentary blogs are making the news, but is there more out there than chatty gossip and collections of links? How about some science? Can this trendy technology be useful for scientists? Come to the Media Workshop and find out! Experienced science bloggers P.Z. Myers (Pharyngula; http://scienceblogs.com/pharyngula/), Grrl Scientist (Living the Scientific Life; http://scienceblogs.com/grrlscientist/), and John Lynch (Stranger Fruit; http://scienceblogs.com/strangerfruit/) answer your questions about how blogging works, setting one up, finding things to write about, and using the medium for your classes, for research, or for educating the public.

Cool, hey? Even better, afterwards there will be a ten-round boxing match between me and John, with GrrlScientist doing the honors as the card girl (nah, not really…all three of us will probably just buy each other beers and get embarrassingly sloppy.)

The real coolness, though, is in the schedule: there are some great talks and posters going on at this meeting, and once I get the panel out of the way, I am going to thoroughly enjoy myself, learning new stuff. And yes, of course, I will be blogging the SICB meeting.

That’s some tongue

Behold the spectacularly long-tongued glossophagine nectar bat, Anoura fistulata:

i-637ca2695ab40ca81df624a2b3792d1c-anoura.jpg
Anoura fistulata feeding from a test tube filled with sugared water; its tongue (pink) can extend to 150% of body length.

This length of tongue is unusual for the genus, and there is an explanation for how it can fit all of that into its mouth: it doesn’t. The base of the tongue has been carried back deep into the chest in a pocket of epithelium, and is actually rooted in the animal’s chest.

i-2b61d1fb1ab14963a2732fab0816bd67-anoura_anatomy.jpg
Ventral view of A. fistulata, showing tongue (pink), glossal tube and tongue retractor muscle (blue), and skeletal elements (white).

Across the glossophagine nectar bats, maximum tongue extension is tightly correlated with the length of their rostral components, such as the palate and mandible. Although the correlation holds for A. caudifer and A. geoffroyi, A. fistulata falls far outside the 95% confidence interval. Close examination of tongue morphology reveals the basis for this pattern. In other nectar bats, the base of the tongue coincides with the base of the oral cavity (the typical condition for mammals), but in A. fistulata the tongue passes back through the neck and into the thoracic cavity. This portion is surrounded by a sleeve of tissue, or glossal tube, which follows the ventral surface of the trachea back and positions the base of the tongue between the heart and the sternum.

Unsurprisingly, this adaptation co-evolved with the lengthening corolla of a tropical flower, Centropogon nigricans—observations suggest that this bat is the only pollinator of this particular flower.

I’m sure Gene Simmons would be jealous.

Muchhala N (2006) Nectar bat stows huge tongue in its rib cage. Nature 444:701-702.

The science is in: the Tripoli Six are innocent

Go read Effect Measure on the recent events in the case of the Tripoli Six. This is the story of a team of health care workers who were blamed for an outbreak of HIV among young patients at a Libyan hospital—they’ve been tried in a kangaroo court and face very unpleasant prospects.

Now, in a powerful reply to the Libyan accusations, Nature has published the results of a detailed analysis of the viruses afflicting the children, and the story is clear: the cause of the outbreak was the poor hygiene present at the hospital before the six workers arrived. Here are the major conclusions of the paper:

In 1998, outbreaks of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection were reported in children attending Al-Fateh Hospital in Benghazi, Libya. Here we use molecular phylogenetic techniques to analyse new virus sequences from these outbreaks. We find that the HIV-1 and HCV strains were already circulating and prevalent in this hospital and its environs before the arrival in March 1998 of the foreign medical staff (five Bulgarian nurses and a Palestinian doctor) who stand accused of transmitting the HIV strain to the children.

The strains present were also traceable to North Africa and at least one was prevalent in Egypt. They also found that the timing was off: the outbreak had begun before the workers had arrived.

We found that, irrespective of which model was used, the estimated date of the most common recent ancestor for each cluster pre-dated March 1998, sometimes by many years. In most analyses, the probability that the clusters from the Al-Fateh Hospital originated after that time was almost zero. For the three HCV clusters, the percentage of lineages already present before March 1998 was about 70%; the equivalent percentage for the HIV-1 cluster was estimated at about 40%.

Apparently, the scientific evidence which would have exonerated the accused was not allowed in the court. The Gaddafi government continues to live up to its reputation.