Molecular machines!

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If you’ve ever wondered what the heck Behe was smoking when he claims there are literal trucks trundling about on literal highways with literal traffic signals inside of cells, well, I don’t have an answer for you…but there is a wonderful Flash movie that will show you the Inner Life of a Cell so you can see what “molecular machines” look like, more or less. It’s a spectacular show. What you’ll see is the series of events that transpire when a lymphocyte encounters a cell surface signal that triggers emigration out of a capillary and into other tissues; it zooms rather abruptly from a cellular view to the molecules on the surface interacting with one another, then into the interior of the cell to see the response. All kinds of cool stuff fly by: actin and microtubule assembly and disassembly, kinesin-mediated vesicle transport, protein synthesis on ribosomes, ER processing, vesicle fusion, etc.

I do have a couple of gripes, though. One is an understandable shortcut: the cell is far too uncluttered, and events proceed in too directed a manner—there ought to be much more stochastic noise at the molecular level. We’re seeing chemistry in action, after all. Another is that there is no explanation at all for anything we’re seeing, it’s simply a weird and trippy voyage into a subcellular world. This clip was created under the auspices of Harvard scientists, so I hope there is a viewing guide somewhere, otherwise it’s only going to be appreciated by people who have already read Molecular Biology of the Cell(amzn/b&n/abe/pwll). I think it also needed a disclaimer somewhere that this video too is a visual metaphor for cellular activity.

But I’m being picky. Otherwise, it’s an excellent introduction to the profound weirdness of the processes going on inside a cell.

And really, Buffy’s biology is wonderful!

Physicists get all the fun. Jennifer Ouellette has announced a book I’ll definitely be buying: The Physics of the Buffyverse(amzn/b&n/abe/pwll). How could I not? It will go on the shelf next to my copy of The Physics of Superheroes(amzn/b&n/abe/pwll).

So, where’s The Biology of Superheroes? The creators of superheroes trample all over the principles of physiology and genetics as thoroughly as they do those of physics, so there’s got to be a story in there somewhere.

Generating right-left asymmetries

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We’re only sorta bilaterally symmetric: superficially, our left and right halves are very similar, but dig down a little deeper, and all kinds of interesting differences appear. Our hearts are larger on the left than the right, our appendix is on the right side, even our brains have significant differences, with the speech centers typically on the left side. That there is asymmetry isn’t entirely surprising—if you’ve got this long coil of guts with a little appendix near one end, it’s got to flop to one side or the other—but what has puzzled scientists for a long time is how things so consistently flop over in the same direction in individual after individual. There has to be some deep-seated mechanism that biases developmental events to favor one direction over the other. We know many of the genes involved in asymmetry, but what is the first step that skews development to make consistent asymmetrical choices?

In mammals, we’re getting close to the answer. And it looks to be beautifully elegant—it’s a simple trick to convert an anterior-posterior difference into a left-right one.

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Symmetry breaking and genetic assimilation

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How do evolutionary novelties arise? The conventional explanation is that the first step is the chance formation of a genetic mutation, which results in a new phenotype, which, if it is favored by selection, may be fixed in a population. No one sensible can seriously argue with this idea—it happens. I’m not going to argue with it at all.

However, there are also additional mechanisms for generating novelties, mechanisms that extend the power of evolutionary biology without contradicting our conventional understanding of it. A paper by A. Richard Palmer in Science describes the evidence for an alternative mode of evolution, genetic assimilation, that can be easily read as a radical, non-Darwinian, and even Lamarckian pattern of evolution (Sennoma at Malice Aforethought has expressed concern about this), but it is nothing of the kind; there is no hocus-pocus, no violation of the Weissmann barrier, no sudden, unexplained leaps of cause-and-effect. Comprehending it only requires a proper appreciation of the importance of environmental influences on development and an understanding that the genome does not constitute a descriptive program of the organism.

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Michael Gerson and the new Republican alibi for crippling stem cell research

This Newsweek article on the latest innovation in stem cell research is infuriating. The author, Michael Gerson, is a Republican hack with no competence in biology, which seems to qualify him to be a serious judge of science to this administration.

The issue of stem cells was the first test of the infant Bush administration, pitting the promise of medical discovery against the protection of developing life and prompting the president’s first speech to the nation. His solution–funding research on existing stem-cell lines, but not the destruction of embryos to create new ones–was seen as a smart political compromise. In fact, the president was drawing a bright ethical line. He argued that no human life should be risked or destroyed for the medical benefit of another. This was an intentional rejection of the chilly creed of utilitarianism–the greatest good for the greatest number–because the greatest number would gain the unrestricted right to extend their lives by ending or exploiting the lives of the weak.

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Terrorism works!

A neurobiologist at UCLA, Dario Ringach, has stopped doing research on primates. The reason?

Colleagues suggested that Ringach, who did not return e-mails seeking comment, was spooked by an attack on a colleague. In June, the Animal Liberation Front took credit for trying to put a Molotov cocktail on the doorstep of Lynn Fairbanks, another UCLA researcher who does experimentation on animals. The explosive was accidentally placed on the doorstep of Fairbanks’s elderly neighbor’s house, and did not detonate.

Whoa. Incompetence and thuggish violence—what a combination. I love animals and think they needed to be treated with care and respect (although, if our cat pees on the furniture one more time…), and I can sympathize with people who are concerned about animal research. I would suggest, though, that they spend less time firebombing people and more time working for their local humane society. It’s penny wise and pound foolish to harrass scientists when all you have to do is visit your local grocery store’s dumpster to find malnourished, diseased, and injured cats scavenging for something to eat. Or look into animal hoarding—it’s more common than you might think.

Whatever you do, though, don’t throw away your moral compass as some fanatics do.

Jerry Vlasak, a practicing physician, a spokesman for the Animal Liberation Press Office, and a former animal researcher, said that “obviously the roughly 30 non-human primates [Ringach] was killing every year would be ecstatic” with his decision to halt his work. Vlasak said that when he was an animal researcher, he published papers on his work, but didn’t feel that he contributed anything important to society. As to the Molotov cocktail, Vlasak said that “force is a poor second choice, but if that’s the only thing that will work … there’s certainly moral justification for that.”

Why, no. No there isn’t.

It’s really that simple.

There is no excuse for bombing people. There is especially no excuse for being so stupid that you try to bomb random people. What this is is terrorism, plain and simple, and Dario Ringach is a victim of domestic terrorism.

(via Virtually Shocking)

The Politically Incorrect Guide to Darwinism and Intelligent Design: Chapter 3: Simply incorrect embryology

This article is part of a series of critiques of Jonathan Wells’ The Politically Incorrect Guide to Darwinism and Intelligent Design that will be appearing at the Panda’s Thumb over the course of the next week or so. Previously, I’d dissected the summary of chapter 3. This is a longer criticism of the whole of the chapter, which is purportedly a critique of evo-devo.

Jonathan Wells is a titular developmental biologist, so you’d expect he’d at least get something right in his chapter on development and evolution in The Politically Incorrect Guide to Darwinism and Intelligent Design, but no: he instead uses his nominal knowledge of a complex field to muddle up the issues and misuse the data to generate a spurious impression of a science that is unaware of basic issues. He ping-pongs back and forth in a remarkably incoherent fashion, but that incoherence is central to his argument: he wants to leave the reader so baffled about the facts of embryology that they’ll throw up their hands and decide development is all wrong.

Do not be misled. The state of Jonathan Wells’ brain is in no way the state of the modern fields of molecular genetics, developmental biology, and evo-devo.

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The Republican War on Science

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Chris Mooney is trying to kill me.

It’s true. He sent me this book, The Republican War on Science(amzn/b&n/abe/pwll) (now available in a new paperback edition!), that he knew would send my blood pressure skyrocketing, give me apoplexy, and cause me to stroke out and die, gasping, clawing in futile spasms at the floor. Fortunately, I’ve been inoculating myself for the past few years by reading his weblog (now also in a new edition!), so I managed to survive, although there were a few chest-clutching moments and one or two life-flashing-past-my-eyes experiences, which will be handy if I ever write a memoir.

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