Wednesday, July 30, 2008

I'll drink to that

Or maybe staying thirsty would be more appropriate.

My two most recent notebooks were crammed with jottings taken in South Africa, where I had examined, at first hand, certain evidence on the origin of our species. What I learned there - together with what I now knew about the Songlines - seemed to confirm the conjecture I had toyed with for so long: that Natural Selection has designed us - from the structure of our brain-cells to the structure of our big toe - for a career of seasonal journeys on foot through a blistering land of thorn-scrub or desert. If this were so; if the desert were "home"; if our instincts were forged in the desert; to survive the rigors of the desert - then it is easier to understand why greener pastures pail on us; why possessions exhaust us, and why Pascal's imaginary man found his comfortable lodgings a prison.

- Bruce Chatwin, The Songlines

Related:

Even in a palace, it is possible to live well.

- Marcus Aurelius, Meditations


The things you own end up owning you.

- Tyler Durden, Fight Club

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Monday, July 28, 2008

Oh, SNAP!!

I'm going to break with tradition and just blatantly repost in full something that someone else wrote. It's a comment from this post, by someone identifying as George Smiley.

"SYSTEMS" biology is a buzzword, a glib and crass marketing term for a set of approaches that underpin much of modern biology and have for a century. What I find most offensive about it is that this particular piece of bullshit doublespeak is used *overtly* to bury the proud history our field. By pretending that these approaches are new, we imply that our foebears were ignorant of them. That we are smarter than they were. That what they did did not lead to "real" understanding. That what they did does not matter, and that you all need not trouble your pretty little heads with it. (Particularly if you're thinking about donating money to us.) Much of the prattle about "systems" biology is pro-hype, pro-marketing, ahistorical, anti-intellectual, and anti-sholarship.

It's disgusting, and it disappoints me to see some people whom I've known for some time and who really *do* know better spearheading the charge.

ANYONE who tells you that that getting physicists and engineering approaches into biology is new is either abysmally igornant of the field's history, trying to sell you a cartload of warmed-over horseshit, or (most likely) both. The agressive use of mathematical modeling? Go back to the turn of the century. Not the 21st century. The 20th. Morgan, Muller and their intellectual heirs. Look up Kimura. (If you don't know who he is, kindly shut the f-bomb up about "systems biology.") Physics and chemistry? Schroedinger, Pauling, Perutz, Huxley, Hodgkin, Huxley, Crick, Benzer, Boxer, Neher, Sakmann, Hille, Chiu, Ashkin, Berg... The list goes on and on.

What is new is high-throughput biology. Assembly-line biology. Factory biology. This is a function of real advances and it offers real opportunities for framing and testing new hypotheses. But call it what it is, or you're a fool, a charlatan, or worse.

Two final points. The most important advance in basic biology in the last decade is the recognition that RNA-based regulation is central to most eukaryotic biology. The first point is that none of the "systems" approaches led in a meaningful way to the breakthrough (though high-throughput and bioinformatic approaches certainly have been useful subsequently). The second point is that RNA-based regulation had been exhaustively documented in prokaryotic systems for almost two decades before the work of Fire and coworkers. To this day, the eukaryotic folks still generally don't cite that work.

We bury our own history at our peril.
Amen, brother.

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Sunday, July 27, 2008

Another trip to another zoo

I have always loved zoos. Merced has a little zoo, which I visited for the first time today. It's not big--if you weren't inclined to actually stop and look at anything, you could walk all the way around in just a few minutes. But I was inclined to stop and look.


At a coyote...


...some bobcats...


...and some totally badass emus. I'm pretty familiar with emus, having dissected one, and naturally I'm interested in them because they're (a) big extant saurischians, and (b) have inflatable throat-sacs. I've read about the throat-sac, even stuck my hand in one, but I'd never actually gotten to hear an emu using it. Then this emu walked right up to the fence, stared me in the eye, and started burping at me. At least that's what it sounded like: a really deep, internal burp. The bird's mouth didn't open and no sound or stomach gas came out. It was all inside.

Naturally I stepped up to the fence and burped back. You know how you can make a loud burp in your throat, even though your mouth is closed? That's what I did. So we stood there burping at each other for a few minutes. No lie.

Good thing the zoo was not heavily attended at the time...


My favorite critters today were the mountain lions. I went in the morning, before it got hot, and they were all outside and active, padding around.


Man, are they gorgeous animals, or what?



Also checked out this momma bear...


...and her playful cub. And he was playful, too, bouncing between the pool, a nice perch up in a dead tree, this hammock, and his mom for reassurance. It's behavior I've seen before in a certain diminutive primate of my acquaintance.


These raccoons cracked me up. A bunch of them were asleep on a branch, monorail-cat style, the first time I walked by, but the second time they were running all over the place, checking people out. From the intensity of their scrutiny, I was uncertain whether they were in the zoo for my edification and enjoyment, or I was in for theirs.

I almost hate to post pictures from the zoo because all you see is fencing. Most of the animals in the Merced Zoo are rescued critters; if they weren't in the zoo, they'd be dead. And I'm pretty pro-zoo anyway. First, because I really like going to the zoo. Always have. Second, because of the conservation work they do in terms of animal breeding and so on. Finally and most importantly, because I really believe that they do a vital service in letting us see endangered wildlife. I'm not crazy about the fact that almost no zoo animals have as much space as they actually need, but if we never get to see the critters then their extermination is a hypothetical problem. When I was a kid, seeing a tiger in a zoo made me about 100 times more concerned about the fate of its wild relatives. Heck, when I was a kid there were a lot of animals that I wouldn't have known existed if I hadn't seen them in zoos (Himalayan tahr, I'm lookin' at you). I doubt if I was or am alone.

At the same time, it hardly ever occurs to me to go to the zoo. Witness the fact that I've lived in Merced for more than a year, and only got to the zoo a month before moving away. I did make it to the San Francisco Zoo about three times and the Oakland Zoo once when we lived in Santa Cruz and then Berkeley, but that's four zoo trips in six years. Not impressive. (I'm not counting the visit to the San Diego Zoo last summer; that was a planned part of a vacation, not just some time I got a wild hair to go to the zoo.)

But heck, there are very few things I do as often as I'd like--I've only been to one real arena-style concert since moving to Cali, for example. And too many things I do too often. Like staying up too late blogging. Which I've now done again.

G'night.

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Friday, July 25, 2008

Vary. Vary. Good.


I just read Darren's post on the living and fossil species of Tursiops. (The skeleton above is that of Lagenorhynchus, stolen from here.) Was surprised by this:

The large, offshore dolphins are now called T. truncatus Montagu, 1821, and the smaller, nearshore ones are T. aduncus Ehrenberg, 1832. T. truncatus is longer-bodied (with 62-67 vertebrae, as opposed to 59-62 in T. aduncus) and has a proportionally shorter rostrum.

That's a range of 8 vertebral positions with the genus (whatever that is), and 5 just within T. truncatus. That's a lot. In most tetrapods, it's not unusual to find individuals that vary by one or two positions from their conspecifics. Humans usually have 7 cervicals, 12 thoracics, 5 lumbars, 5 sacrals, and four coccygeals (caudals), for a total of 33, but according to White and Folkens (2000) as many as 1 in 10 people may vary from that norm. Most of the people who do vary do so at the lumbo-sacral junction; for example, having 4 lumbars and 6 sacrals or vice versa. But that wouldn't change the total count 33. My guess is that of the people who actually have a different total number of vertebrae, the difference is in the coccyx. It's tempting to write that off as a consequence of our caudal vertebrae being vestigial, but I immediately wonder if caudal vertebrae are not inherently more variable in number (than other kinds of vertebrae) in other tetrapods. I mean, having a tail that is one vert longer or shorter is probably going entail a lot fewer changes in the rest of the body than having a different count in the neck, thorax, or sacrum.

Which brings me back to the dolphins. I am curious about how much of that 8-vertebra spread is accounted for by varying numbers of caudal vertebrae.

One question that might come to mind is how one would tell. In most tetrapods it's easy: start counting at the end of the sacrum, and keep going until you run out of vertebrae to count. But extant cetaceans--even those with pelvic elements, like most baleen whales--don't have sacral vertebrae. So figuring out where the tail starts is a bit of a pain. I read a paper on it once, which I don't have to hand and am not going to dig up, and the upshot is that even though the sacral ribs that define the bony sacrum are gone, you can still identify the base of the tail based on patterns of blood vessels and nerves. Which is fine when you're dissecting a dolphin (I'd love to but never have), but not much use when you're just looking at a skeleton. If it's a complete articulated skeleton, you could use the haemal arches to get you in the right neighborhood, but the haemal arches are probably variable themselves, and might not be present anyway.

If I was a more dedicated blogger I'd be citing more refs and getting your more answers and fewer guesses. But I've got other fish to fry.

I know that the argument from personal incredulity is weak, but I just can't believe that it's wrong all the time. And, despite my near-total ignorance of vertebral variation in most tetrapods and in cetaceans specifically, a 5-vertebra range of variation strikes me as too much for one species. And since Darren's post touches on variation, cryptic species, and the splitting of Tursiops anyway, it made me wonder if some of that range of variation in T. truncatus isn't actually parceled out among multiple species.

But that's not the actual thought that went through my head. The thought that went through my head was "How do you tell individual variation from biodiversity?"

And the answer, of course, is that you can't. Individual variation IS biodiversity. I've just been teaching my intro bio students about Darwin's views on variation and the origin of species. For Darwin it's all one big continuum, from individual variation to incipient varieties to varieties to subspecies to species to genera and so on up to the entire tree of life. People sometimes rag on Darwin for writing On the Origin of Species without actually addressing speciation. But I think that's because we think species are special (well, not all of us), and must come into existence through some process that is not just business-as-usual. But Darwin didn't think species were special. He worked out the logic of natural selection and showed that it worked. And he argued that organisms struggle most fiercely with those to which they are most similar, usually their closest relatives. Natural selection gives you a mechanism for change, and struggle among the similar gives you a mechanism for diversification (if the struggle is most intense against those to whom you are most similar, it has to be less intense elsewhere). And that's all you need (according to Darwin [according to my reading]). As things diversify they pick up different mate recognition signals or lose the ability to interbreed or do whatever it is that defines them as species to us, but those are effects of diversification that is already in motion, that starts with variation among individuals.

Not everyone agrees. For all the stuff they disagreed about, Ernst Mayr and Stephen Jay Gould were both convinced that species are special. And even if Darwin was right, that doesn't mean that speciation isn't interesting and worth studying. Only maybe we should call it lineage divergence rather than speciation so we can stop pretending that we know what a species is. But my point is that it is all connected, all the way up--from individual variation up to the whole tree of life--and back down again--because there is no tree of life, not as a Ding an sich (thank you, Great Books Discussion Group). There are only individuals. There is only variation.


White, T.D., and Folkens, P.A. 2000. Human Osteology, Second Edition. Academic Press, New York.

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Thursday, July 10, 2008

Storm Hawks


Imagine Sky Knights whose motorcycles transform into x-winged jet fighters and who use energy swords for sky-fu battles against flying sharks, sentient dinosaurs, and the transforming-jet-fighter-borne legions of a dark queen, in a world where verdant mountaintop kingdoms rear above lava-monster-infested wastelands, steampunk technology runs on energy crystals and, er, actual steam, and life is constantly punctuated by dogfights and wisecracks, all rendered in anime-style 3D.

That's Storm Hawks.


It's like someone took a seine haul through my subconscious when I was 10, looked at the resulting mess, and said, "What the heck, this might be good TV. Let's dump it in a nuclear reactor and turn it up to 11!" I don't care that the target audience is a small fraction of my age. This show flat-out rocks, and I love it. And so does my three-year old.

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Saturday, July 05, 2008

Impact factors, copyright law, and other science publishing buzzwords

One of my former labmates just sent around the latest list of journal impact factors. I'd repost 'em here, except that I don't want to perpetuate the perception that they are important (although I was grateful to have seen the last version, in a checkout-stand-tabloid-curiosity sense). Here's why:

People seem prone to forgetting that journals have impact factors because individuals papers are cited widely, or not. It's not like every paper that Nature (IF = 28.something) publishes is widely cited, or every paper that Canadian Journal of Earth Sciences (IF = 0.955) publishes is not. In a field as small as sauropod paleobiology, everyone is going to read all of the literature no matter where it is published (the last remaining exception being obscure foreign journals that are not easily available as PDFs; and I mean foreign here as in "outside any researcher's country", not just "outside the US"; getting hold of un-PDFed papers from Oklahoma Geology Notes is probably a cast iron bitch if you're in a local museum in China). The only real advantage of a high-profile journal is to possibly bring the paper to the attention of non-sauropod workers. Whether Nature does that any better than CJES is probably up for discussion (at least in the small world of sauropod paleobiology). Unless some avian physiologist or human bone biomech person is going to have their world rocked by what I write, that 'crossover' appeal is probably not worth stressing over too much.

And there is an entirely different form of impact that we need to be thinking about, which is: how easy is it for people who are interested in your research area to find out about your work and acquire it? I'll bet that my effective impact is much greater than it would be otherwise simply because all of my papers are freely available online (thank you, Mike!). Although individual researchers are doing this more and more--see the badly-in-need-of-updating list here.

And there's a third kind of impact that is arguably more important than either of other two, which is: how big is the intellectual footprint of a given paper? For example, I'd argue that Kristi Curry-Rogers's paper on Apatosaurus ontogeny in JVP has been far more important and influential than her paper on Rapetosaurus in Nature (feel free to argue otherwise, I'm just shooting from the hip here).

Seems to me that what matters for Impact(3) is quality and timeliness of ideas (and timeliness often trumps quality), and publication venue is almost completely irrelevant (although I'd be interested in seeing a counterargument). What matters for Impact(2) is availability of work, which is better for papers that came out in open access journals but easily remedied for papers that didn't (at least until publishers crack down on free distribution of PDFs, if ever*). And Impact(1) is not unimportant, but it's also not nearly as important as people think it is; indeed, Impact(2) and Impact(3) actively erode the importance of Impact(1).

The main thing propping up Impact(1) as something we all have to at least pretend to care about is that the perceived prestige of having published in a high-IF journal really does matter to bean-counters in universities and funding agencies who can't be bothered to assess the actual quality of someone's work and for whom a nice convenient number is a godsend, even if it is horribly flawed. Therefore it also matters to many of us, who can't get ahead without having the approbation of those faceless but immensely powerful entities. See also: student teaching evaluations.

If we're going to be stuck with one number to evaluate something like the impact of a scientific paper, how about the number of citations that pop up on Google scholar? It's fast, free, and doesn't pretend to be anything other than what it is: the number of papers indexed by Google Scholar that cite the paper in question. Tragically, I suspect that ISI impact factors are popular in bureaucracies specifically because they are slow, inaccurate, and not transparently available to all.

* Recently there was a post on the Vert Paleo listserv about how copyright is a barrier to making the existing backlog of literature easily available electronically. My feeling is that those of us needing to get work done will scan what we need ourselves, circulate it through private channels, and keep plowing on. Those who try to stop us with be publicly humiliated at worst (when they come down on us and we all collectively vow never to use their stuff again) or marginalized at best (when we just stop using their stuff because it's harder to get hold of).

Finally, if you haven't been following the blogosphere brush fire (or brush war?) that sprung up in the wake of Nature's pathetically transparent slam of PLoS, Greg Laden has kindly assembled about a million relevant links here.

Discuss.

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