August 16, 2006

Three Hundred Year Old Dog?

Carl Zimmer is talking crazy talk:

The scientists propose that several centuries ago, a histiocyte cell in a dog or a wolf turned cancerous. A mutation may have caused the cell to become abnormal--perhaps that LINE-1 element that marks Sticker's sarcoma cells today. But natural selection would have favored other mutations as well that allowed its descendants to become more effective at growing into a tumor. During mating, some of the cancer cells managed to spread to the dog's partner, where they could continue to proliferate.

...

So here's the big question which the authors don't tackle head on: what is this thing? Is it a medieval Chinese dog that has found immortality? If so, then it resembles HeLa cells, a line of cancer cells isolated from a woman named Henrietta Lacks who died in 1951. After her death, scientists have propagated her cells, and in that time they have have adapted to their new ecological niche of Petri dishes, acquiring mutations that make it grow aggressively in the lab. One biologist even suggested that the cells should be consider a new species.

Seriously, read the whole thing.

Posted by todd at 9:00 AM | Comments (0)

May 26, 2006

'Hippocampal Slice' Would Make a Great Rap Name

Here's a neat post at Gene Expression about the roles of three different calcium ion sources in long-term potentiation.

Posted by todd at 8:44 AM | Comments (2)

May 16, 2006

This Odor then Attracts Parasitic Wasps

More good descriptions of parasitic bugs from Zimmer:

If you keep a vegetable garden, there's a fair chance you'll encounter a grisly sight this summer. Some poor catepillar will be clutching a leaf, with the pupae of parasitic wasps sprouting off its back. It has just died in a most grotesque way. A wasp has zeroed in on the catepillar and injected eggs into its body. The eggs hatched, and the larvae devoured their hosts from within, keeping it alive until they were ready to emerge.


What makes this sight all the more grotesque is the fact that the plant the catepillar is sitting on may have been an accomplice to the crime. When catepillars nibble on plants, the plants sometimes respond by releasing a distinctive cocktail of chemicals. This odor then attracts parasitic wasps. The plants are not just releasing a sort of chemical scream. Wasps are very precise in the species of catepillars they choose, and they can tell these odors apart.

The post is really about a new article in PLoS Biology which suggests that the caterpillars also pick up the wasp-attracting chemicals, and cleverly avoid eating the plants at times when they are likely to emit those particular chemical signals.

Someone should let me know if I'm the only one who thinks this weird bug stuff is neat.

Posted by todd at 8:54 AM | Comments (1)

May 11, 2006

This is Why We Need a Subscription to Neuron

Way cool article posted on neurodudes.

If ever there was a paper that would bring tears to one’s eyes, this is it: a previously hidden mental process has now become subject to experimental study. The mental process is the covert movement of attention, the selective focussing of attention to subregions of the visual field, but without eye movement. The movements of covert attention were hypothesized based on psychophysics, but the authors can now follow it using a vector field derived from a population of neurons in the parietal cortex. The monkey has been trained to use covert attentional shifts to solve a maze task. The major finding is that the vector derived from the population of parietal cells follows in time the path through the maze, as the monkey solves the maze.

Posted by todd at 4:46 PM | Comments (1)

February 14, 2006

Scientists on Valentine's Day

Eide Neurolearning Blog has an MRI of love. I'm not an expert, but I think Love has a brain tumor.

Posted by todd at 7:24 AM | Comments (1)

February 12, 2006

Invasion of the Body Snatchers

As will soon become apparent, I spent a hunk of yesterday afternoon setting up a new RSS feed reader. After a bit of searching, I chose a program called BlogBridge, for a couple of reasons. One is that it is written in java, and therefore works on my Windows laptop and my Linux desktop. Another is that it allows me to easily "synchronize" preferences and feed subscriptions between the two, offering the convenience of something like Bloglines or Google Reader with the beefiness of a rich client application.

Anyway, the upshot is that now I can bring you links from blogs other than Pharyngula. Such as this, from Carl Zimmer.

As an adult, Ampulex compressa seems like your normal wasp, buzzing about and mating. But things get weird when it's time for a female to lay an egg. She finds a cockroach to make her egg's host, and proceeds to deliver two precise stings. The first she delivers to the roach's mid-section, causing its front legs buckle. The brief paralysis caused by the first sting gives the wasp the luxury of time to deliver a more precise sting to the head.

The wasp slips her stinger through the roach's exoskeleton and directly into its brain. She apparently use ssensors along the sides of the stinger to guide it through the brain, a bit like a surgeon snaking his way to an appendix with a laparoscope. She continues to probe the roach's brain until she reaches one particular spot that appears to control the escape reflex. She injects a second venom that influences these neurons in such a way that the escape reflex disappears.

From the outside, the effect is surreal. The wasp does not paralyze the cockroach. In fact, the roach is able to lift up its front legs again and walk. But now it cannot move of its own accord. The wasp takes hold of one of the roach's antennae and leads it--in the words of Israeli scientists who study Ampulex--like a dog on a leash.

As I believe the kids these days say, read the whole thing.

Posted by todd at 1:01 PM | Comments (0)

February 11, 2006

Neuroscience Reading List

A reading course in computational neuroscience at Berkeley has a webpage up with a really handy reading list of neuroscience and AI papers, for the most part complete with links. Of course, a lot of the links will be useless from non-campus networks, but many of the papers are probably available from professors' websites nonetheless.

I, for one, will start with the paper that has the best title: Churchland, Ramachandran, and Sejnowski* A Critique of Pure Vision.

[*] Screw you, UCSD, and your "standards."

Posted by todd at 5:19 PM | Comments (0)

January 29, 2006

Beautiful Forms, Uninspired Wars

When Christmas rolled around last month, and my family wanted to know what to get me, I emailed them links to PZ Myers' Updated Book List for Evolutionists. As a result, I came home with copies of Sean Carroll's Endless Forms Most Beautifu and Andrew Brown's The Darwin Wars.

Myers describes The Darwin Wars as "a study of the sociology of evolutionary biology." In reality, it is little more than a blow-by-blow account of the 'war' between Richard Lewontin and Steven Jay Gould on the one hand, and E. O. Wilson, Richard Dawkins, and Dan Dennett on the other. It is, here and there, a lot of fun. He describes the birth of Richard Dawkins as having been attended by a pair of fairies.

The good fairy gave him good looks, intelligence, charm, and a chair at Oxford specially endowed for him. The bad fairy studied him for a while and said: `Give him a gift for metaphor.'
Elsewhere, he quotes biologist John Maynard Smith descirbing a theory as "Absolute fucking crap," and the footnote attributes this to "Personal communication, walking back from the pub."

However, I was disappointed, because I expected to learn more about evolution from the book. The fact that he focuses on a relatively small subset of the researchers working to advance evolutionary understanding would be ok, if I felt that he did a particularly good job of explaining the views of the two camps. Unfortunately, I don't. He makes it clear that Gould believed that "natural selection 'is not the exclusive means of [genetic] modification.'" But he never says what else Gould thought was going on. He makes it clear that Gould objected strongly to Wilson's program of sociobiology, without ever explaining why anyone would believe in Wilson's argument.

And, because he has elected to focus only on this corner of the subject, he is forced to leave out much of interest. The rise in the last twenty five years of evolutionary developmental biology is left out entirely, while no less than two whole chapters are devoted to memes, which amount to a throwaway thought experiment in a book by Dawkins that was subsequently taken too far.

By contrast, I was surprised by how much I learned from Sean Carroll's slim volume. Endless Forms Most Beautiful describes the basic ideas and some of the history of evolutionary developmental biology. Dr. Carroll, a pioneer in the field, spends a good deal of time describing the effects of specific genes and proteins on the process of a fertilized egg growing into an organism. In a way that is refreshing for a popular science book, Carroll never skimps on the biology. At times when another author might have resorted to a metaphor, he buckles down and teaches a course on the logic of genetic switches.

In one of the most frustrating passages in The Darwin Wars, Brown quotes a full half of a page from an important paper on kin selection. The original author, William Hamilton, has just drawn the reader in when Brown breaks out of the quotation and ended the passage with "- and so on for two paragraphs of mathematics, after which he surfaced to say...." Brown seems to feel the need to shield the reader from the meat of this important work, as though he assumes the reader is either not interested or incapable of understanding.

Carroll, on the other hand, fills his work with detailed explanations and colorful photographs. As a good teacher must, he assumes his readers are both interested and capable, and is willing to hold our hands until we've made it through to the next chapter.

Another nice thing about Carroll is that, unlike Dawkins and Gould, he does not indulge in many just-so stories. There is much to be said for these, and I recommend that everyone read The Blind Watchmaker, which amounts to a collection of them. But there is precious little science to them. In Watchmaker. Dawkins discusses mimicry in butterflies, and attempts to come up with a plausible story for explaining how natural selection could take an organism which looks 5% like a dangerous cousin or 5% like a twig and, in a series of small steps, make the resemblance nearly perfect. Carroll, on the other hand, admits that this is a "mystery," but discusses the research avenues which may lead to clues, and the specific protein groups which probably play important roles in butterfly wing construction.

Carroll was not visited by the bad fairy at birth. He uses metaphor sparingly, and at times I wished that he had let himself go a bit more, that he had explained an idea a second or third time, with a bit more flourish. He is without other writers’ willingness to paint in bold strokes, and as a consequence Andrew Brown will probably never write a book about him. But he is full of ideas, and you will finish his book feeling smarter.

All in all, The Darwin Wars is worth picking up if you already understand both Gould and Dawkins, and you're interested in learning more about the characters themselves. Endless Forms Most Beautiful, on the otherhand, should be enjoyed by any lay person interested in biology.

Posted by todd at 11:33 AM | Comments (0)

August 2, 2005

Dr. Myers is so Predictable

Since we don't get cable, Ruth and I don't watch a lot of television. Many days, the only time we do so is while eating breakfast before work. Even then, it's mostly just something noisy to fill up the room while we wait for our coffee to sink in.

However, this morning a bit rolled past the ticker on the bottom of the screen and caught my eye. Apparently the president held a press conference and spoke out in support of teaching intelligent design alongside evolution.

I thought to myself, "My oatmeal needs more raisins." And then, "I can't wait to hear what P. Z. Myers is going to have to say about that."

He seems a bit more incensed than usual, which is saying something.

On Monday the president said he favors [equal time in the classroom] for intelligent design "so people can understand what the debate is about."
Here's what the debate is about.

Scientists have established the fact of evolution with thousands of lines of evidence and the work of hundreds of thousands of researchers. This idea is based on material evidence and repeated experiment, extensively documented in the scientific literature.

This evidence flatly contradicts literal religious accounts. Religious conservatives have mounted a long running social and political campaign to get their falsified dogma treated as the truth, despite the absence of any material or logical support for their position.

This debate is not about assessing the evidence, but about getting faith-based bullshit taught as science.

And that is what should be taught: teachers, we need to get in front of our students and expose them to both sides. We need to stand up and plainly state that creationism is a lie and any attempt to incorporate faith and the supernatural into science is as destructive to the enterprise as would be requiring religion to provide concrete, repeatable tests of their beliefs.

Word.

I wish I understood why religious politicians feel the need to prescribe the course of study for high school biology. There are only two possible outcomes: they create a populace with a stunted understanding of biology and the nature of the scientific endeavor, or they are revealed as single-minded baffoons.

All of this may sound like the hubris of the establishment, and you may wonder why all of the revolutions of science in the past haven't taught us anything. The point is that intelligent design is not science, has nothing to do with science, and cannot be understood as a scientific theory. Even if an alternative understanding of speciation were to be developed (it's not clear to me that such a thing is possible, but I'm not an evolutionary biologist) it would not be a victory for the Discovery Institute.

If they really want to protect their notion of the creation of man, they should be rounding their children up for Sunday school and spoon-feeding them some kind of gobbledy-gook about God setting evolution in motion and leaving fossil evidence to test our faith. Then we would have to pity their children, but at least ours would be safe.

Posted by todd at 11:19 AM | Comments (1)

June 24, 2005

PZ on Friday

Two posts from P.Z. Myers for those of us waiting for test-runs of web-crawling scripts to complete on a Friday morning:

Posted by todd at 11:49 AM