SOTU prognostications

Well, Kevin Drum’s prediction about the State of the Union address is a bit vague and general:

Bush’s theme may well be that he’s right and his critics are wrong; and his vision may well be of a year of partisan trench warfare with congressional Democrats.

But Chris Mooney gets specific:

A while back I blogged about an idea floated by Morton Kondracke: That George W. Bush should try to become the “science” president by emphasizing, in his State of the Union speech, themes of global scientific competitiveness and the need to ensure that the good old USA is leading the pack. Well, it now seems official: According to the Boston Globe, in his speech tonight Bush plans to highlight Norman Augustine, a former Lockheed Martin CEO who “last year led a congressionally mandated National Academies team that issued a report warning that America is ‘on a losing path’ in the global marketplace.” Why are we falling behind? If you believe the NAS, it’s because of inadequate scientific and mathematical training for our high school students, not enough funding of basic scientific research, etc etc.

I won’t be watching it—I have a Cafe Scientifique to attend tonight, and if I want to watch an evil buffoon on TV, I have some Blackadder DVDs—but if Bush tries to claim he’s going to be the Science President, I’m going to laugh and remind everyone that Bush endorses Intelligent Design creationism. I’m also going to remember that he called himself the Education President, and what we got from that was an unfunded demand that everyone teach to the test.

Bad business at the Burke

Chris Clarke sent me some unfortunate news about my alma mater, the University of Washington. There’s a scandal brewing at the Burke Museum, involving a retired curator of vertebrate paleontology, John M. Rensberger. The Seattle Weekly has published a series on the troubles, with a professional evaluation of the collection. Basically, the Burke has a beautiful assemblage of vertebrate fossils, but their collection was very poorly documented (scribbled notes on scraps of brown paper bags?), and there are also allegations that many of the collecting trips were made without permits or permission—so ownership of at least some of the specimens is up in the air. It’s not a pretty story.

I have to hammer on a theme I’ve pounded on here before. Science is not a collection of facts. Science is not a fossil in a display case. Science is a process—it is the meticulous documentation of observation and experiment, with full transparency about how conclusions were derived, so others can evaluate them independently. This is just as true in a largely historical science like paleontology as it is for an experimental science like molecular genetics.

If the allegations against Rensberger are valid, then I do deplore the ethical lapses they represent, and also the administrative incompetence that has allowed the problem to build despite complaints over decades. Even worse to me, though, is the fact that he betrayed fundamental scientific principles, and 30 years worth of work on that collection has been undermined. Without a solid, replicable methodology and documented provenance for each specimen, it wasn’t science.

Life is chemistry

Sometimes creationists say things like, “Evolution doesn’t explain the origins of life!” The common reply is that that’s the domain of abiogenesis, not evolution, with the implied suggestion that the creationist should go away and quit bugging us.

That’s a cop-out.

I’m going to be somewhat heretical, and suggest that abiogenesis as the study of chemical evolution is a natural subset of evolutionary theory, and that we should own up to it. It’s natural processes all the way back, baby, no miracles required. Life is chemistry, vitalism has evaporated and is one with phlogiston, and scientists legitimately and respectably study physical processes that were the potential instigators of life. Someday we’re going to be able to create living cells from scratch, and those mechanisms will be taken for granted afterwards, just as Wöhler’s synthesis of urea is nowadays.

What prompts this assertion of uncompromising naturalism is a reminder from two publications. Natural History has published a nice review of The Origins of Life, and The Scientist has an article on the work to create a synthetic cell, Is This Life?. They’re both good, light summaries that don’t stint on pointing out the problems in these fields—but the main point is that there has been great progress as well, and that these are productive lines of inquiry.

Giant octopus attacks!

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Here’s a nifty video (mpg) of an octopus confronting an ROV working off Vancouver Island. The poor thing was just trying to crush and eat an interloper (or perhaps disassemble it for spare parts to use in its high-tech scheme to take over the world), and the ROV operator uses its thrusters to fling debris at it and drive it away.

It’s quite a battle, and the octopus holds on for a surprisingly long time in the face of an extremely obnoxious machine.

Paedocypris

I saw on Muton, and several readers have mentioned it to me, this article about the world’s smallest vertebrate, fish of the genus Paedocypris. It’s a gorgeous translucent cyprinid, so is somewhat related to my favorite fish, Danio rerio. They live in cool, slow moving water in peat swamp forests of Southeast Asia. One female, only 7.9mm long, contained about 50 eggs, so they know it was sexually mature.

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Living Paedocypris progenetica, CMK 18496, (a, b) male, ca 9 mm; (c) female, ca 8.8 mm.

That size isn’t at all shocking—my zebrafish larvae at about that size are active hunters with functioning visual systems, capable of coordinated bouts of swimming, and they’re also very impressive animals…but they don’t have sex. It takes about 6 months for zebrafish to reach sexual maturity, and they are several centimeters long at that point. I would love to know how old these fertile Paedocypris were, but they were captured in the wild and virtually nothing is reported about their behavior or lifecycle. Ah, to have a fish colony that could be raised in a set of beakers, and could produce a couple of generations of crosses in a single semester…

One other clue that these are fully functioning, sexually mature adults are the presence of some pelvic specializations. Males have a hook and flange widget on their pelvic fins, and an odd prepelvic knob. Again, though, without knowing anything about their behavior, we don’t know how these are used in mating and courtship. Wouldn’t it be cool to put a pair under my Wild M3 scope and watch courtship and mating?

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(a) Paedocypris micromegethes, paratype male, ZRC 49869, 10.4 mm; pelvic fins, anteroventral view, showing hook and flange on anterior ray. (b) Paedocypris micromegethes, paratype, male, BMNH 2004.11.16.1-40, 10.9 mm, ventrolateral view on hypertrophied pelvic arrector and abductor muscles marked by asterisk symbols. (c) Paedocypris progenetica, paratype male, ZRC 43199, 8.5 mm, scanning electronic micrograph of pelvic region in ventrolateral view, arrow points to keratinized prepelvic knob.

Of course, in addition to not knowing their generation time yet, these fish have another drawback relative to zebrafish: tiny eggs. They extracted a range of sizes from the ovaries, but assuming the smallest are immature, they max out at around 0.3mm diameter. That’s respectable, but Danio eggs are about 1mm in diameter.

Can you tell I’d love to get my hands on a bunch of these little fish? Unfortunately, I’ve heard from fish importers that it is agonizingly expensive and time consuming to bring wild tropical fish into the country, and for good reason: to block invasive species, to prevent the spread of new fish diseases, and also to discourage the plundering of native populations. I may not ever see one of these animals, short of making a trip to Malaysia, and even then I won’t be bringing any home.

Ambergris!

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Majikthise reports that an Australian couple has found a $295,000 lump of ambergris on a beach. Ambergris is cool stuff, so let me add to it’s splendor by bringing up two scientific views of it.

First, let’s hear from the chemists:

Since ancient times, ambergris has been one of the most highly valued perfumery materials. It is secreted in the stomach or intestinal tract of the sperm whale and released into the sea in the form of a grey to black stone-like mass. When exposed to sunlight, air and sea water, the material gradually fades to a light grey or creamy yellow colour and, at the same time, the main component, the odourless triterpene alcohol ambrein, is oxidatively degraded. Some of the products resulting from this chemical process are responsible for the organoleptic properties of ambergris.

We know the chemical structure of many of the active components of ambergris—it’s a beautifully complex collection of compounds.

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Two ambergris odorants and their natural precursor, ambrein (1).
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Examples of non-trans-decalin ambergris odorants.

And what about us biologists?

The effect of ambrein, a major constituent of ambergris, was studied on the sexual behavior of male rats. The rats were administered ambrein in doses of 100 and 300 mg/kg body weight. Male sexual activities were assessed by recording the erectile responses (penile erection) and homosexual mountings in the absence of female. The copulatory studies were carried out by caging males with receptive females brought into estrus with subcutaneous injections of estradiol benzoate and progesterone. The copulatory pattern of treated male rats (mountings, intromissions, ejaculations and refractory period), the pendiculations (yawns/stretches) and orientation activities towards females, the environment and themselves, were recorded. Ambrein produced recurrent episodes of penile erection, a dose-dependent, vigorous and repetitive increase in intromissions and an increased anogenital investigatory behavior, identifying the drug used in the present study as a sexual stimulant. It is conceivable from the present results that the ambrein-modified masculine sexual behavior in male rats supports the folk use of this drug as an aphrodisiac.

Mmm-mmmm. Good stuff, that ambergris.

Gorbachov M.Yu., Rossiter K.J. (1999) A New Electronic-Topological Investigation of the Relationship between Chemical Structure and Ambergris Odour. Chem. Senses 24:171-178.

Taha SA, Islam MW, Ageel AM (1995) Effect of ambrein, a major constituent of ambergris, on masculine sexual behavior in rats. Arch Int Pharmacodyn Ther 329(2):283-94.