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Darwin at 200

Firsties!

One impression of the NHGRI sponsored seminar: has the once mighty Drosophila become so blase as to not even get a tip of the hat at a genetics seminar? I would expect as much from a bunch of paleontologists or ecologists, but shame on you geneticists. I wouldn’t interpret this as model bashing, because Mus and Danio had bit rolls in a few of the talks. I think the message is that genomics has moved on. We are now at a stage where researchers are becoming intrepid Victorian specimen collectors, chasing down rare and exotic flora and fauna for their private collection. I thought the smartest point made was that now even humans are a model system, or, rather, everything is a model!

Second: Genetic drift got short shrift. Mutation and random fluctuations in the frequencies of alleles or haplotypes seem like a worthwhile topic when discussing Darwin’s legacy. I would have liked to see more on theory incorporated into the discussion. On a related note, one of the speakers stated that negative mutations were the most common form of mutation. I’ll give him the benefit of the doubt that he either mispoke or I misheard him.

David Kingsley talked about skeletal genes. He made the point that changes in regulatory regions rather than coding regions allow for dramatic phenotypic variation, while keeping it confined to specific tissues. For example, the same genes involved in embryonic development in sticklebacks also regulate armor plating and melanin. Mutations in the corresponding genes in mice and humans are often lethal. Sticklebacks are probably not a lab animal: being anadromous I doubt they can breed them in the lab yet, so all the work is done in hotel bathrooms in Alaska.

There was a bit of junk DNA bashing from Elaine Ostrander, but that’s what makes these events fun. I’m sure if Larry Moran was there, he’d show her what snarkyness really is:

Total Essential (so far) 4.5%
Total Junk (so far) 54%

David Haussler was the third of six speakers at the Darwin @ 200 seminar. Since I saw at least one phlogenetic twig during the presentation, I would hope that the arborist would tackle Haussler’s talk.

A quick note though, either one of the two Davids or Ajit Varki speculated that humans as a species may be immunizing ourselves against the tooth and claw logic of natural selection. I’m not suggesting that natural selection is a tautology, but by what means they have reason to suspect that “natural” selective forces are quantitatively decreasing across the species from Bangor to Bangladesh is a mystery to me. I imagine that what is being put forward is a semantic rather than a real argument.

Apoclyptastic

What is it with humans and our existential insecurities? Rapture this global warming that. Apparently, the price of an oversized cortex is a steep one. It means we make movies, Mad Max, Night of the Living Dead, Day After Tomorrow and Idiocracy and write books, Left Behind, The Stand, Oryx and Crake, and The Road , slapping ourselves on the wrist over our transgressions to god and mother Earth: one-size fits all diatribes. Even behind the cheap laughs of Idiocracy and bravado of Mad Max stands akimbo a stern-looking Miss Wormwood telling us to sit-up straight, take notice and recycle, say our prayers, and stop being such greedy little bastards. (Shawn of the Dead being an obvious exception.)

Adding to the pantheon is a movie (The Age of Stupid) due in spring, and a TV series (Remnants) with no release date. If the movie is anything like its trailer below, it’ll be an uninspiring hour and a half of non-sequiturs backdropped against post-production cgi. If the series is anything like its trailer, it’ll be the Office post global pandemic. Though these two genre vehicles have similar subject matter, they are somewhat opposite in their approach to that material.


The Remnants (preview) from John August on Vimeo.


The Age of Stupid: final trailer Feb 2009 from Age of Stupid on Vimeo.

Tempest Prognosticator

Everyone’s favorite Leech Blog, BdellaNea, discusses a leach-powered storm-stracking system on display at the Great Exhibition at London’s Crystal Palace in 1851. “The device required a leech in each of 12 jars. The glass was to be transparent so that the leeches could “see each other” and so agree amongst themselves as to their prognostication. If any leech climbed up and into the escape tube, its weight would dislodge a piece of whalebone, releasing a hammer that would ring the bell thus announcing the onset of inclement weather.”

Proper Darwin

Eugene C. Scott & Glenn Branch writing in the journal Evolution: Education and Outreach have a wonderful article addressing a common misconception. Their title says it all: Don’t Call it “Darwinism”

ABSTRACT: Evolutionary biology owes much to Charles Darwin, whose discussions of common descent and natural selection provide the foundations of the discipline. But evolutionary biology has expanded well beyond its foundations to encompass many theories and concepts unknown in the 19th century. The term “Darwinism” is, therefore, ambiguous and misleading. Compounding the problem of “Darwinism” is the hijacking of the term by creationists to portray evolution as a dangerous ideology—an “ism”—that has no place in the science classroom. When scientists and teachers use “Darwinism” as synonymous with evolutionary biology, it reinforces such a misleading portrayal and hinders efforts to present the scientific standing of evolution accurately. Accordingly, the term “Darwinism” should be abandoned as a synonym for evolutionary biology.

When we see someone in the MSM getting things horribly wrong we howl in savage delight. Like a pack of African Wild Dogs, we’ll zero in on the lame creature, separating it from the false safety of the herd–all the while yipping for others to join in the hunt–tire the hapless prey and run it to ground, then bite and tear off large dripping chunks as it thrashes instinctively, helplessly. Those of use who don’t partake in the slaughter revel in watching the macabre unfold.

Every so often, though, we must admire our quarries vim and vigor, paying respect to a spirit of vitality. Take a moment to read this strong editorial in the Guardian on “the greatest Englishman since Newton.”

In a democracy, citizens should respect each other’s beliefs; and citizens have a right to express their beliefs. But in a democracy, a newspaper has an obligation to what is right. The truth is that Darwin’s reasoning has in the last 150 years been supported overwhelmingly by discoveries in biology, geology, medicine and space science. The details will keep scientists arguing for another 200 years, but the big picture has not changed. All life is linked by common ancestry, including human life. The shameful lesson of this 200th anniversary of his birth is that Darwin’s contemporaries understood more clearly than many modern Britons.

We sit and file our teeth. For now.

Update: That didn’t take long. Prime cut, highest quality and marbled with flagrant ignorance. Carcass ready for abattoir.

MC Natural Selection

Charles Darwin

I couldn’t resist posting this track by Baba Brinkman. It apparently was created as part of the Darwin Bicentennial celebrations. As a warning, it’s both anti-creationist and anti-theistic to some degree. It’s very rare for an academically themed song to be any good. I’m impressed.

Download Natural Selection

Hat tip The Rough Guide to Evolution

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Graphical Woo

The National Endowment for the Arts [pdf] plotted a curve based on percentage of 18 to 24 year old’s who read “literature.” Their idea of “literature” must be quantitative, because I’m pretty sure the release of Harry Potter accounts for the 2002 uptick.

When I was in undergrad fulfilling the requirements for a Biology and English Literature degree, there were, to put it nicely, a few bureaucratic brambles along the way. For instance, I had two advisers from different planets. My biology adviser only knew, and was only interested in knowing, the requirements for a biology degree. He thought the “Poetics of Dynamic Text” was a chapter on blood formation. The same gaping knowledge hole afflicted my English Lit adviser as well. This Confederacy of Dunces said I needed a statistics course, one especially geared toward my degree program. That meant two semesters of redundancy on a rather dry subject. As you can imagine, the Humanities stat. requirement was orders of magnitude more basic than the one for biology. Anyway, I had to take both, and so I resented both. I didn’t do so hot, but I learned enough to spot when someone is blatantly manipulating data in a graph. Dear reader(s), can you flush out the egregious, almost laughable, attempt to skew the data in the following graph from the National Endowment for the Arts?

http://www.motherjones.com/kevin-drum/Blog_NEA_Reading_2008.gif

Poor old National Endowment. They’re always the first, followed by education, to have their funding slashed when we feel the need drop bombs or bail out some captain of industry. Can you really blame them for propagandizing such benevolent government initiatives as increasing literacy? You betcha!

Revised Graph

I made a new graph that righted two fibs. First, the spacing on the x-axis from 1982-85 is almost the same distance as it is from 2002-08. One is a three year gap and the other a six year gap. The NEA can judge what constitutes literature but they can’t count. By shortening the 2002-08 gap, they skew the percent increase in their favor. They even admit as much: “this dramatic turnaround shows that the many programs now focused on reading, including our own Big Read, are working [!]” I fixed that.

Second, unless you have a good reason it’s usually a good idea to have percentages start at zero. Not doing so may make the graph prettier, but also less accurate. I fixed that, too.

Graphs act as visual aids to a list of numbers, teasing out otherwise hard to detect trends. They are supposed to represent the data, not your interpretation of the data. If the NEA is lying by graph, what’s to stop them from fudging the data their fudged graph is based on?

I plotted their graph correctly, but am having problems importing it. (Was that a C or B I got in CS 101?) C’est la vie.

Japan in 6 Minutes

Speakers on


Japan from Eric Testroete on Vimeo.

Onion does New Scientist

I wouldn’t expect the sensation retailers on the editorial board at New Scientist to get this.

Genetic Experiment Goes Horribly Right

PASADENA, CA—A grotesque and unsettling genetic experiment in which human corneal tissue was grown on the backs of naked mole rats has gone horribly, horribly right, sickened Caltech scientists announced Monday. “Never in our worst nightmares could we have foreseen the appalling success of this advantageous abomination,” head researcher Dr. Trevor Keller said of the phenomenal medical breakthrough, which could potentially treat those suffering from congenital blindness. “Oh the humanity! The benefit to humanity!” Keller said that mankind’s only hope is for his team to continue their research.

The abomination in question.

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Larry Moran , suggested this pithless headline, “More evidence that Charles Darwin didn’t know everything there is to be known about evolution when he published his book in 1859.”

Black Stacey called it yellow journalism and even had problems with the relatively more sensible (to biologists at least) editorial inside. Something about how when a distinguished but old scientist says something is possible he’s usually right, and when he says something is impossible he’s usually wrong.

Pre-Med Student Accidentally Cures Cancer

From the Science Creative Quarterly, this reminds me of undergrad.

“Pat’s research results were mind-blowing. I didn’t even know this level of antioxidant activity was possible. But there’s an Excel chart to prove it.”

Pre-Med Student Accidentally Cures Cancer

Tim Minchin, Everyone

“To gild refined gold, to paint the lily, to throw perfume on the violet, is just fucking silly.”