Monthly Archive for November, 2008

Further adventures in gayness

Published
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on November 23, 2008
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Fabulous... and adaptive, too.
I guess the whole depressing California-Prop-8 thing has everyone talking about gay sex and how natural it is. There was a great post up at Pleiotropy about how common homosexuality is in other species, much better informed than my earlier post on the subject. He’s also got a follow up post quoting from a short Hufington Post piece. (Did you follow all that?) The Huffington Post piece disputes the common religious argument that God will punish a society that allows gay marriage. The article argues that the contrary is true, more secular societies have higher incomes and are better places to raise a family. It doesn’t look like much of a scientific study, but the broad contours seem like they might be true. More tolerant societies may be more successful in general, however I’m sure you could find some counter-examples. Saudi Arabia vs. India, South Africa vs. Botswana, things like that (though being a dumb American I’m not sure how good my examples are)

Also relevant to my earlier discussion of the prevalence of homosexuality in animals is Bjørn Østman of Pleiotropy’s quote of the following very cute story of the religious right’s favorite movie stars.

Roy and Silo, two male chinstrap penguins at New York’s Central Park Zoo have been inseparable for six years now. They display classic pair-bonding behavior—entwining of necks, mutual preening, flipper flapping, and the rest. They also have sex, while ignoring potential female mates.

This reminds me of the many species previously thought to form high-fidelity pair bonds for life. I picture the paternity-testing-scientists looking confusedly at the labels on their tubes, wondering if they had accidentally mislabeled them or something. I wonder if Roy and Silo ever cheat on each other, and whether it’s with male or female penguins. We need to fund some really patient ethologists with stamina and video cameras to see what’s really going on. Inquiring minds want to know.

One Gene, One Protein?

Published
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gillt
on November 20, 2008
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We’re enlightened–continually–by Carl Zimmer, this time writing in the New York Times, describing the hope-filled birth of a word, long-since burdened to a life of heavy lifting.
[Gene] was coined by the Danish geneticist Wilhelm Johanssen in 1909, to describe whatever it was that parents passed down to their offspring so that they developed the same traits. Johanssen, like other biologists of his generation, had no idea what that invisible factor was. But he thought it would be useful to have a way to describe it.
Many people will assume the “invisible factor” to be DNA. Technically, this is correct, it’s all nucleotides after all, but to think of a gene–all the information needed for protein design–as a single sequence of DNA is incorrect. For example, every cell has the coding sequence of every gene and therefore the ability to manufacture any protein in our body. When a cell makes a protein, that protein’s nucleotide correlate must first, to paraphrase Madonna, express itself. (Happily, genes are much less prolifigate than the Queen of Pop, save for those big genetic blunders under which teratomas arise.)
What’s this about censoring expression? Zimmer has this to say,
But it turns out that the genome is also organized in another way, one that brings into question how important genes are in heredity. Our DNA is studded with millions of proteins and other molecules, which determine which genes can produce transcripts and which cannot. New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel.
These “millions of proteins and other molecules” are themselves no more than the expression of proximal and distal DNA sequences. But as Zimmer points out, a second-channel mechanism above the level of DNA is at work. Fighting the urge to invoke strange loops, lets take a closer look at some of the ways these proteins and molecules regulate gene expression.
Take chromatin for instance; it’s of those “millions of proteins and molecules.” If DNA were spaghetti, then chromatin would be the twirling tines of a fork that wrap it up (three times) during expression. This looped-up DNA–otherwise known as an altered spatial organization–is under specific and temporal expression control. A master regulator of body segmentation in the Drosophila, the Bithorax complex, falls into this category of expression regulation via spatial organization of DNA.
What’s fascinating is when something upsets the setup. In humans, disruption of chromatin complexes can lead to overexpression and ill-timed expression of genes, which yields to both undifferentiated and unchecked cell growth–in a word, cancer. Fruitful then would be the study of the mechanism and regulation of chromatin complex function so as to better understand how higher order chromatin structure influences the intricately orchestrated expression programs needed for proper development and differentiation. And if not in humans then zebrarfish, and if not zebrafish, Drosophila.
Not suprisingly, the best studied chromatin domain to date happens to be Drosophila’s gypsy chromatin insulator. It’s a big complex of DNA wound around three proteins. There’s some evidence to suggest that these DNA binding proteins bridge distant DNA sequences, which are then trascribed in toto. Aggregates of these complexes can form even higher order scaffolds of looped DNA–groups of genes in effect working as a whole. What’s interesting is how these mighty architectures can be undone by a simple structure: RNA.
Scientists think RNA indirectly interacts with DNA binding proteins. Deactivating the RNA–RNA silencing–regulates expression of DNA at the protein level. Researchers at Harvard Medical School† studying the gypsy chromatin insulator found evidence for this when they biochemically silenced RNA, and again when they found mutations in Drosophila genes encoding RNA silencing components. Now they want to express the gypsy chromatin insulator in vitro–in cell culture–then induce double-strand RNA knockdowns to find what new and exciting factors are involved.
Let’s review: DNA->RNA->(protein<-RNA)->DNA->RNA… Or something like that.
†
1. Gerasimova TI, Lei EP, Bushey AM, Corces VG Coordinated Control of dCTCF and gypsy Chromatin Insulators in Drosophila. Mol Cell (28): 761-72, 2007.
2. Caretti G, Lei EP, Sartorelli V The DEAD-Box p68/p72 Proteins and the Noncoding RNA Steroid Receptor Activator SRA: Eclectic Regulators of Disparate Biological Functions. Cell Cycle (6), 2007.
3. Lei EP, Corces VG  A long-distance relationship between RNAi and Polycomb.  Cell (124): 886-8, 2006.
4. Lei EP, Corces VG  RNA interference machinery influences the nuclear organization of a chromatin insulator.  Nat Genet (38): 936-41, 2006.
5. Pai CY, Lei EP, Ghosh D, Corces VG  The centrosomal protein CP190 is a component of the gypsy chromatin insulator.  Mol Cell (16): 737-48, 2004.

The Science Policy Insiders

Published
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gillt
on November 18, 2008
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Last week I attended a panel discussion for scientists who are interested in science policy. AAAS and NAS applicant reviewers comprised the panel and provided us with their backgrounds and some useful tips on applying to fellowships. Mostly, it was a droll list of do’s and don’t’s when filling out an application, and what to expect from a fellowship. For example, don’t think you can come to Capital Hill wanting to make a difference. If you desire a long successful career as a policy-maker, you’d better play the game–their game. Do understand that politicians have short attention spans, so don’t use any big words, such as fruit fly, lest you mire them in jargon. Don’t harbor any illusions that facts matter in politics. Policy is all about the manipulation of perception. Do fashion yourself a science svengali. In short, I found the attitude and views of the speakers just short of appalling.

Also, I have serious reservations over a few points made about “spinning” and “framing” science. The way it was described, dumbing-down and giving equal weight to every other guy with a stake in the issue, is wrong. Our politicians need to be slapped out of their ignorant stupor with some urgent facts on Global Warming, Stem Cell research, medical woo, and the dismal state of science education in America. Then, hopefully, they’ll go back to their constituents armed with a clear picture of reality and of what will happen if you continue to ignore it. The problem the entire panel failed to recognize-as they appear to be perfectly adapted to life on the Hill-is a Washington culture that politicizes science for its own ends, often screwing around with the data for reasons of greed and ignorance. Every wannabe policy wonk should have a copy of The Republican War on Science, so at least they can recognize what it looks like when a politician ignores or misrepresents science.

Right now, science is not sitting at the grown-ups table. And for this, it is forced to fight for small scraps of legislation with which it must use to continually justify its own relevancy amid the noise and chatter of every other special interest group crowding Congress. Here’s a crazy idea, why aren’t AAAS fellowships also playing a role as watchdogs on the Hill, educated people providing sound science judgment, then holding politicians to the fire when they ignore it. The fourth estate can facilitate this last bit.

Money walks in Washington, just as it does everywhere else. As a community of scientists we cannot win the spin game, simply because our adversaries are far better funded. Honestly, besides the burden of truth, what chance does a former bench scientist, turned policy-maker, have against a glad-handing tobacco and coal lobbyist armed with deep pockets and great hair? If it’s nothing more than framing and spinning your issues, science will lose. And this is exactly what we stood by and let happen over the past eight years in Washington.

The sticker for me during the discussion was when the speakers smirked at us and one another as they mocked past applicants who were naive enough to think one could march upon Capitol Hill, facts and figures in hand, and demand politicians start doing things differently.

What gall, what cynicism.

I still remember the discussants eyes a-twinkle in delight as they spoke of their proximity to the levers of control and power this job of theirs provides. If their line of work is to act in the interest of science in Washington, then they fail…and have failed for an approximate decade. Why anyone would still listen to them is what I want to know.

biolog 2008-11-06 22:44:31

Published
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gillt
on November 6, 2008
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As they flipped the switch on the Large Hadron Collider, the results dropped, from 20-1 odds to 33-1 odds of measuring the “God particle.”

*

Isabella Rossellini does bees

Published
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on November 3, 2008
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This is awesome! With this video you have the bees down. Now I just have to find one about the birds. This is how educational videos should be done.

In Time for Winter Solstice

Published
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gillt
on November 2, 2008
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George R.R. Martin, most prolific in the ’70s, wrote a fascinating short story back then about life on a planet orbiting a smoldering sun. In the House of the Worm, the refugees lived below the surface in ancient winding tunnels built from an earlier race. Society, at this late stage in their existence, comprised a largely inbred aristocracy and an oppressed labor force of a separate race–somewhat resembling the situation in Shakespeare’s The Tempest, from Prospero down through Caliban.

The Caliban of this story is an exceedingly deceitful brute, who, despite succumbing to the protagonist’s blade, ultimately prevails the way Mel Gibson’s William Wallace does in Braveheart, by sharing a little of himself with a fair lady. It’s not entirely accurate to call the protagonists in Martin’s stories anti-heroes; they are by no means immune to all the injustices of a cruel and indifferent world(s), often more susceptible than most. The failure to meet whatever challenge Martin throws their way is at once personal and tragic but also epic, with reverberations felt across the cosmos–it’s science fiction after all.

Danny Boyle’s distant future sci-fi flick, Sunshine, also involves the fate of a species tied to a dying sun. Unlike Martin’s worm-people–it’s unclear whether they are descendants of humans evolved to subterranean life or an alien race on a distant planet–Boyle’s characters are not only human but overtly American. Their can-do additude over a mission to the sun in the hope of reigniting it via nukes constrasts the worm-people’s fatalism (For the worm-people must adapt, even if it means out-crossing with an inferior race, or go the way of the dodo). Even without knowing that the payload of nukes hurling toward the sun is only the size of a large city when a typical solar flare exceeds nine earths, it’s easy to see how Sunshine’s plot is plain irrational: you don’t get warm by throwing a match on a pile of cinders; you find more fuel or another fire (this is usually the point in a movie like this where I tell myself how much Hollywood needs my name in the credits under the title Disbelief Consultant).

Plot logic aside, the director of The Beach, Trainspotting, and 28 Days Later, uses dialogue to great effect in his films. Movies such as The Abyss, Event Horizon, Star Trek, Serenity, and Sunshine, which spend much of their time moving about the cramped innards of a ship, can quickly become tedious without engaging conversations and clever banter. Sunshine even manages to do without sex.

Unfortunately, things unravel into complete incoherence toward the end of the movie. Remember Boyle’s  forgettable The Beach? Of the two themes in Sunshine–sacrifcing a few to save the many and immortality–only the first gets properly explored throughout the course of the movie. Immortality, admittedly a tough topic, is left to trite materialistic references to the fact that we’re all stardust and the lunatic sunburn victim quickening the rapture by killing everyone. Actually, since this walking carcinoma immolates himself in solar radiation perhaps this is sublte commentary on America’s two popular pastimes, religion and sunbathing.

Science and scientists play a centrol role in the film, and I’ve never seen it and them represented more accurately on celluloid. Too often, directors feel the need to humanize both in their movies. The first is an excuse to skip over any actual explanation of the science and the second becomes a quest for the scientist as Tinman in search of a heart.

On a final note, in light of creeping climate changes on the scale of solar winters and global warming, how much hubris is it that we are capable of organizing the resources in time to affect change, or is it more likely we’ll go the way of the worm-people and learn to adapt or slowly die-off?