An encyclopedia of life?

I wish I could be more enthusiastic about the Encyclopedia of Life project. It’s to be an online encyclopedia with a substantive page dedicated each species on the planet, and it’s endorsed by E.O. Wilson, with sponsorship from some of the most prestigious museums around. It’s a fantastic idea that would be incredibly useful.

But then …

The demonstration pages are beautiful, maybe too beautiful. There’s the promise of a colossal amount of information in each one, although at this point all they’ve got are very pretty but nonfunctional images of what the page will look like — but you can see that the content is not trivial and the organization is detailed. I browsed the FAQ to see how they’re going to do it, and it’s awfully vague. “Mashups” of existing databases? Recruiting sources from existing online collections? They were inspired by Wikipedia? (No, please no…if it’s wikified it will be useless as a source of technical information.) I look at the money they’ve got — $12 million — and the number of species they aim to catalog — 1.8 million — and it just doesn’t add up to me. Aren’t they going to burn through that much money in just paying for the emergency room visits for the brawling systematists fighting over the ontological issues?

I don’t mean to sound so negative, since I think it’s an eminently laudable goal, but I get very, very suspicious when I see all the initial efforts loaded towards building a pretty front end while the complicated core of the project is kept out of focus. I’d be more impressed with something like NCBI Entrez, which, while not as attractive as the EOL mockups, at least starts with the complicated business of integrating multiple databases. I want to see unlovely functionality first, before they try to entice me with a pretty face.

(via John Logsdon)

Apocryphal elements

If you’re trying to come up with names for an exotic element with amazing properties for that comic book, fantasy novel, or role-playing game you’re writing, here’s a list of apocryphal elements (there’s also a similar list with more details). These are all genuine false alarms from the world of science, guaranteed to have been generated from the twisted minds of actual chemists and physicists.

We really need elements called Ultimium and Extremium. Neokosmium isn’t bad, either.

We have the brains of worms

Way back in the early 19th century, Geoffroy St. Hilaire argued for a radical idea, that vertebrates and most invertebrates were inverted copies of each other. Vertebrates have a dorsal nerve cord and ventral heart, while an insect has a ventral nerve cord and dorsal heart. Could it be that there was a common plan, and that one difference is simply that one is upside down relative to the other? It was an interesting idea, but it didn’t hold up at the time; critics could just enumerate the multitude of differences observable between arthropods and vertebrates and drown out an apparent similarity in a flood of documented differences. Picking out a few superficial similarities and proposing that something just looks like it ought to be so is not a persuasive argument in science.

Something has changed in the almost 200 years since Geoffroy made his suggestion, though: there has been a new flood of molecular data that shows that Geoffroy was right. We’re finding that all animals seem to use the same early molecular signals to define the orientation of the body axis, and that the dorsal-ventral axis is defined by a molecule in the Bmp (Bone Morphogenetic Protein) family. In vertebrates, Bmp is high in concentration along the ventral side of the embryo, opposite the developing nervous system. In arthropods, Bmp (the homolog in insects is called decapentaplegic, or dpp) is high on the dorsal side, which is still opposite the nervous system. At this point, the question of whether the dorsal-ventral axis of the vertebrate and invertebrate body plans have a common origin and whether one is inverted relative to the other has been settled, and the answer is yes.

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True confessions

Oh, I hate these difficult questions.

If you’re a professor and you want to change the world, what do you do? In 1993–quit and become an activist. In 2007—start a blog.

Or so it seems. PZ Myers blogging at Pharyngula is probably doing more for evolution than PZ Myers publishing papers in scientific journals. Is that true PZ?

No.

Hmmm, I guess it wasn’t so difficult after all!

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Twisty maze of duck oviducts

I’m sure you’ve already heard about it, so I’m a little redundant to bring it up — Carl Zimmer has a spiffy article in the NY Times about duck phalluses. No, that’s not quite right; the most interesting part of the story was the bit about duck oviducts. Female ducks have been evolving increasingly convoluted oviducts to baffle the efforts of duck rapists to inseminate them, and male ducks have been evolving concomitantly long phalluses to thread the maze and deliver sperm to the ovaries.

I’d heard about these huge intromittent organs in ducks before, but this is another fascinating revelation: it took a woman scientist to suggest that maybe, just maybe, they also ought to look at what’s going on in the female ducks, and then the whole wonderful story of coevolution of these structures emerged. It’s actually a rather embarrassing instance of a scientific blind spot, where the biases of the investigators led them to overlook an important component of the story.

Information must be free

My little trip distracted me with the perfect timing to miss the amazing fair-use flare-up — I’m back just in time to catch the happy resolution. I guess I’ll say something anyway, but I’ll be brief.

The general question is whether blogs should be restrained from using figures and data published in scientific journals. My position is that we should use them — scientific information should be freely and widely disseminated, anything else is antithetical to the advancement of science. The only constraints I think are fair is that all material taken from a journal should be acknowledged and formally cited, and that dumping whole articles to the web should not be done. It wouldn’t be appropriate for our audiences anyway; we should be explaining and synthesizing, not blindly replicating.

I’m glad it has blown over for now, at least. Let’s hope journals continue to be sensible about letting blogs excerpt portions of published work—they have a specialized audience, we have a more general audience, and we hope that blogging about science will lead to more scientists, which will increase the market for the science journals. Everyone will be happy!