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.

Vertebral variation, Hox genes, development, and cancer

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First, a tiny bit of quantitative morphological data you can find in just about any comparative anatomy text:

mammal number of vertebrae
cervical thoracic lumbar sacral caudal
horse 7 18 6 5 15-21
cow 7 13 6 5 18-20
sheep 7 13 6-7 4 16-18
pig 7 14-15 6-7 4 20-23
dog 7 13 7 3 20-23
human 7 12 5 5 3-4

The number of thoracic vertebrae varies quite a bit, from 9 in a species
of whale to 25 in sloths. The numbers of lumbar, sacral, and more caudal vertebrae also show considerable variation. At the same time, there is a surprising amount of invariance in the number of cervical vertebrae in mammals — as every schoolkid knows, even giraffes have exactly the same number of vertebrae in their necks as we do. What makes this particularly striking is that other vertebrates have much more freedom in their number of cervical vertebrae; swans can have 22-25. I was idly wondering why mammals were so limited, and stumbled onto a couple of papers that addressed exactly that question (Galis & Metz, 2003; Galis, 1999). Galis’s explanation is that it is a developmental constraint that may have something to do with the incidence of cancer.

Development is an intricately choreographed process that treads a dangerous line. On one side is stability; but development is in many ways a destabilizing process, in which cells have to change their path and form new tissues, and stability is not compatible with it. On the other side is chaos, unregulated proliferation — cancer. During development, the organism has to foster proliferation and change to a greater degree than it can tolerate later, and that loosening of constraints represents a danger. Galis suggests that one reason we mammals may always have 7 cervical vertebrae is that the regulatory genes that specify the number of vertebrae are coupled to processes that otherwise regulate cell fates, and that modifications to those genes that would cause variation in vertebra number would also lead to unacceptable increases in the frequency of embryonal cancers.

This isn’t at all an improbable idea. Genes exhibit bewilderingly complex patterns of expression, and pleiotropy (the regulation of multiple phenotypic characters by a single gene) is the rule, not the exception. The Hox genes, the particular genes that control the identity of regions along the length of the animal, are known to switch on and off in proliferating mammalian cell lines in culture. Perhaps the Hox genes involved in defining cervical vertebrae are somehow also involved in controlling cell proliferation, making them dangerous targets for evolution to tinker with?

Galis provides several lines of evidence that this is the case. To see whether variation in cervical vertebra number leads to increased incidence of cancer, we need to look for instances of variation in mammalian vertebrae.

There isn’t much variation in cervical vertebra number, though. There is an exception: sometimes, the 7th cervical vertebra is found to undergo a partial homeotic transformation and forms a pair of ribs, which are normally found only on thoracic vertebrae. Humans develop cervical ribs with a frequency of about 0.2%; do they also develop cancers? The answer is yes, with a frequency 125 times greater than the general population.

Another place to look would be in phylogenetic variation — between groups rather than within a population. It turns out that there are two groups of mammals that do have a non-canonical number of cervical vertebrae: one manatee genus and two genera of sloths. No data is available on frequencies of embryonal cancers in either, and Galis reports that manatees at least seem to have a low incidence of cancer. One explanation is that both sloths and manatees have exceptionally slow metabolic rates, which in itself will reduce the frequency of cancer, since it will reduce the rate of oxidation damage; the idea is that this low cancer rate may have made these organisms more tolerant of variation in these genes.

An open question is how birds can have greater variability in the number of cervical vertebrae — they certainly don’t have low metabolic rates. One suggestion is that the coupling between these particular Hox genes and a predilection for cancer is unique to mammals. Another possibility is that birds possess other, unidentified mechanisms that reduce free radical production, reduces oxidative damage, and makes them relatively cancer-free. Galis cites several studies that show that birds do seem to be less severely afflicted with cancers than us mammals.

It’s an interesting idea, but the evidence so far is a collection of correlations. I’d be interested in seeing some direct analyses of the role of patterning genes on carcinogenesis. Still, it’s the first answer I’ve seen to explain why such a peculiar restriction in morphology should be nearly universal within a whole class of animals, when other classes allow so much more diversity.

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Galis, F and JAJ Metz (2003) Anti-cancer selection as a source of developmental and evolutionary constraints. BioEssays 25:1035-1039.

Galis, F (1999) Why do almost all mammals have seven cervical vertebrae? Developmental constraints, Hox genes, and cancer. J Exp Zool (Mol Dev Evol) 285:19-26.

Castrating trematodes!

Since I mentioned yesterday that penis size mattered, upon stumbling on this article about the horrific effects of a trematode infestation, I thought everyone might enjoy a grim and vivid picture of what trematodes can do to a poor, innocent mollusc.

This is a photo of a trematode, or fluke. Trematodes are parasitic flatworms with very complex life cycles; this particular one is a cercaria, or tailed larva. They swim about and infest various hosts at various stages, proliferating and spreading through tissues, before moving on to infect the next host in their cycle.

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[Read more…]

Male enhancement works!

I hate those commercials on cable TV for Enz*te, that fake “male enhancement” product that promises a “boost of confidence” for all the guys who take their little pill. I don’t believe it, of course—it’s probably a concoction of sawdust and rat droppings. But the phenomenon of male confidence as a function of the size of their physical attributes might just have some validity.

AL Basolo, who did some well-known work on mate preference in swordtails a few years ago (short answer: lady swordtails prefer males with longer swords), has a couple of new papers on the subject. She has looked at competition between males—the fishy equivalent of checking out the other guy’s equipment in the lockerroom—and found that the length of the sword makes a big difference in the struggle between males, even with no females involved.

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Xiphophorus helleri is a common aquarium fish with a distinctive feature: that long sword on its tail. The males have competitive interactions with each other that are fairly easy to assess: dominant males chase away inferiors, and inferiors avoid the winners, so you just have to record who is chasing who to sort out who thinks they are in charge. Usually, it’s the fish that is bigger overall that wins. The investigators suspected that the size of the sword might also be a deciding factor. Observations of pairs of fish matched for body size, but with natural differences in sword length, did not bear this out, however, showing little correlation. That suggests, as one might expect, that there are multiple factors that influence competitions.

To simplify those factors, they carried out what sounds to me like a very cruel experiment. Pairs of fish matched for body size were anesthetized, their swords chopped off, and replaced with transparent plastic swords of identical size. The difference, though, was that different length swords were painted on the transparent plastic—one lucky fish got a new painted sword roughly the same length as the old one, while the other got a sword half the length.

After recovering from their implant surgery, they were put together in a tank…and the truncated male consistently lost all competitions. I guess size matters, after all.

Without the gross surgical modifications, however, size wasn’t such a clear indicator of victory, so other factors must also play a role. A companion paper looked at stripes on the sword, and how they affected female interests. This work modified the tails digitally; a video recording of a hunky male was made, and then edited to either remove the stripes from its entire length, to remove them from the proximal half or the distal half, or left intact. The video was played back to a female, and the length of time she paid attention to it measured (longer is better).

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Female response to the four male video stimuli (pictured above each bar from left to right: complete sword, distal stripes, proximal stripes, no stripes). Bars with the same colour pattern did not differ significantly.

The lessons are clear. Having a long sword will help you intimidate and beat up your competition, and painting stripes along its length (or at least at the tip) will win you the admiration of females.

If you’re a fish, that is.

There is no necessary expectation that it will help at all if you’re a hairless ape, but if anyone tries it, let me know how it turns out.

Benson KE, Basolo AL (2006) Male–male competition and the sword in male swordtails, Xiphophorus helleri. Animal Behaviour 71(1):129-134.

Trainor BC, Basolo AL (2006) Location, location, location: stripe position effects on female sword preference. Animal Behaviour 71(1):135-140.