Liberal baloney

OK, this is the kind of thing that just pisses me off: the tendency for some liberals to go off all loopy and credulous. The perfect example is on Salon right now—an article that goes on at ridiculous length about the judgments of a physiognomist, a ditz who derives McCain’s economic policy from the shape of his nostrils, and Obama’s idealism from the breadth of his forehead. This is insane, and irritating, and stupid.

The one thing I dread with a Democratic victory is the ascendancy of navel-gazing crystal-healing New Age loons, without a shred of critical thinking.

Watching every cell of the developing zebrafish

Blogging on Peer-Reviewed Research

How can I respond to a story about zebrafish, development, and new imaging and visualization techniques? Total incoherent nerdgasm is how.

Keller et al. are using a technique called digital scanned laser light sheet fluorescence microscopy (DSLM) to do fast, high-resolution, 3-D scans through developing embryos over time; using a GFP-histone fusion protein marker, they localize the nucleus of every single cell in the embryo. Some of the geeky specs:

  • 1500×1500 pixel 2-D resolution

  • 12 bits per pixel dynamic range

  • Imaging speed of 10 million voxels per second

  • Complete scan of a 1 cubic millimeter volume in 3µm steps in 90 seconds

  • Efficient excitation (5600 times less energy than a confocal, one million times less than a two-photon scope) to minimize bleaching and photodamage

Trust me, this is great stuff — as someone who was trying to do crude imaging of fluorescently labeled cells in the 1980s using a standard fluorescence scope and storing stills on VHS tape, this is all very Buck Rogers. Just load your embryo into the machine, start up the scanner, and it sits there collecting gigabytes of data for you for hours and hours.

But wait! That’s not all! They’ve also got sophisticated analysis tools that go through the collected images and put together data projections for you. For instance, it will color code cells by how fast they are migrating, or will count cell divisions. Similar tools have been available for C. elegans for a while now, but they have an advantage: they’re tiny animals where you might have to follow a thousand cells to get the full story. In zebrafish, you need to track tens of thousands of cells to capture all the details of a developmental event. This gadget can do it.

Here, for instance, are a couple of images to show what it looks like. The right half is the raw embryo, where each bright spot is a single cell nucleus; the left is one where the pattern of cell movement is color-coded, making it easier to spot exactly what domains of cells are doing.

i-a993b2c6d92e3964a73f6707b3cee9ca-dslm.jpg
Cell tracking and detection of cell divisions in the
digital embryo. (A) Microscopy data (right half of embryo:
animal view maximum-projection) and digital embryo (left
half of embryo) with color-encoded migration directions (see
movie S9). Color-code: dorsal migration (green), ventral
migration (cyan), towards/away from body axis (red/yellow),
toward yolk (pink).

I grabbed one of their movies and threw it on YouTube for the bandwidth-challenged. It’s not very pretty, but that’s the fault of reducing it and compressing it with YouTube’s standard tools. This is an example with color-coded migration (blue cells are relatively motionless, orange ones are moving fast), and you can at least get the gist of what you can detect. You can see the early scrambling of cells in the blastula, migration during epiboly and blastopore closure, and convergence in the formation of the body axis fairly easily. Well, you can if you’re familiar with fish embryology, anyway.

This crappy little video doesn’t do it justice, however. Take a look at the Zebrafish Digital Embryo movie repository for much higher resolution images that are crisp and sharp and unmarred by compression artifacts. It contains DivX and Quicktime movies that are somewhat large, 10-40M typically, that represent visualizations of databases that are several hundred megabytes in size.

What can you do with it? They describe observations of early symmetry breaking events; patterns of synchrony and symmetry in cell divisions; direct observations of the formation of specific tissues; and comparisons with mutant embryos that reveal differences in cell assortment. It’s fabulous work, and I think I’m going to be wishing for a bank of big computers and lasers and scopes for Christmas—only about $100,000 cheap! Until then, get a fast internet connection and browse through the movies.


Keller PJ, Schmidt AD, Wittbrodt J, Stelzer EHK (2008) Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy. Science 2008 Oct 9. [Epub ahead of print].

Witch doctors kill

Ignorance leads to evil: albinos are being butchered for their body parts in Burundi. Witch doctors are spreading the claim that their body parts are valuable in attracting gold, so stupid and greedy people are killing them and selling off bits and pieces.

Officials have gathered all the albinos in the country into a walled safehouse to protect them, which seems like a short term solution. I say since their number came up in the genetic lottery as cursed in Burundi, offer them asylum and bring them to Minnesota, where their paleness won’t be at all exceptional.

Say…wasn’t an African witch doctor one of Sarah Palin’s heroes? Let’s be sure not to bring them to Alaska, then.

I wonder who Marty Chalfie is voting for?

Seed and Scientists and Engineers for America are teaming up to promote a youtube challenge — they are collecting videos of scientists stating who they are voting for in the coming election. The first one up is Marty Chalfie, winner of the Nobel in Chemistry this year. Guess who he thinks should be president?

I suspect that the scientific establishment will be showing a profound liberal bias this year, largely because the scientific establishment tends to be pro-reality.

You don’t have to be a Nobelist — if you’re a scientist, record a youtube video of yourself, tag it with “aVoteForScience”, and you too can contribute.

Obama is…Hindu?

Wait until the wingnuts get this: Hindus are presenting Obama with a monkey-god idol.

The idol is being presented to Obama as he is reported to be a Lord Hanuman devotee and carries with him a locket of the monkey god along with other good luck charms. An hour-long prayer meeting to sanctify the idol was earlier organised at Sankat Mochan Dham and by Congress leader Brijmohan Bhama, Balmiki Samaj and the temple’s priests. “Obama has deep faith in Lord Hanuman and that is why we are presenting an idol of Hanuman to him,” said Bhama.

And in other news, we have a lovely brass statue of the Buddha at our house, which I guess makes me a Buddhist, and we also have a stuffed cobra, which makes us Satanists. And we have a Bible or two, and a copy of the Koran, and somewhere I have a copy of some very pretty and colorful book the Hare Krishnas handed to me in an airport once. Since I also own a complete set of DVDs for both Buffy and Firefly, I must also be a devout Whedonist. I guess Obama and I have a plurality of gods to go up against the blinkered and benighted monotheists, then.

Ruse vs. Fuller

The latest issue of Science has a deservedly cruel review of Steve Fuller’s dreary philosophical assault on evolution, Dissent over Descent: Intelligent Design’s Challenge to Darwinism. I could tell from the title alone that the book was going to be worthless—Intelligent Design creationism provides no coherent “challenge” to evolution other than the purblind relabeling of it as “Darwinism”—but poor Michael Ruse had to actually read the whole book. Here’s his quick summary of the contents:

More amused than cross, let me go to the heart of Fuller’s case against Darwinian evolutionary theory and for IDT—for his is as much a negative critique of the opposition as a positive defense of his own beliefs. Fuller feels that Charles Darwin failed to make the case for his mechanism of natural selection. Darwin did not give a cause for evolution. He certainly did not unify the field. At most he gave lists of facts. Moreover, today if we feel that advance has been made, it is primarily in the molecular field, and this owes little or nothing to traditional evolutionary thought. At best Darwinism is a kind of tarted-up natural theology and, this being so, why not IDT?

Well. If that is an accurate description, and I have no reason to think otherwise since I have read some of Fuller’s pronouncements on these topics and they are entirely in line with the summary, then Fuller is an even bigger fool than I thought. Those statements are wrong in every case. Not just wrong, but transparently wrong, since even a non-philosopher like myself can read The Origin and see that his accusations against Darwin’s argument are false, and as someone who follows the field of molecular evolution somewhat closely, I think his claims about the state of the modern biological sciences are utterly silly.

Fortunately, Ruse has concisely skewered Fuller’s arguments for us.

The important thing is that all of this is completely wrong and is backed by no sound scholarship whatsoever. In at least one case, Fuller makes his case by an egregious misreading—of something I wrote about the role of genetic drift in Sewall Wright’s shifting balance theory. For the record, Charles Darwin set out to provide a cause, what he called—following his mentors like William Whewell (who in turn referred back to Newton)—a true cause or vera causa. Darwin felt, and historians and philosophers of science as well as practicing evolutionary biologists still feel, that he succeeded, for two reasons. First, he showed how organisms can be changed by human picking or selecting. Although Fuller repeatedly claims that Darwin intended no analogy here, that is simply not true. In the face of virtually everybody—including Alfred Russel Wallace, who (in the manuscript he sent to Darwin in 1858) explicitly denied a link between artificial and natural selection—Darwin insisted that we can gain confidence about selection in nature from what happens when humans are active. Second, Darwin brought everything together in a “consilience of inductions.” He argued that if you take selection as the causal mechanism, then you can explain instinct, the fossil record, geographical distributions of organisms, anatomy, systematics, and embryology. In turn, the success of these explanations feeds back to support the belief in selection. About as unifying a setup as it is possible to imagine.

One can go on to look at things today. It is ludicrous to claim that modern evolutionary biology is not integrated with molecular biology. Motoo Kimura’s neutral theory depends crucially on the claim that selection has little or no effect on processes down at the molecular level. Genetic fingerprinting has proved absolutely vital for observational and experimental studies of evolution. Someone like British ornithologist Nicholas Davies, working out the relationships among individual dunnocks (Prunella modularis), would have been powerless without the technique. And in evolutionary developmental biology (evo-devo), currently the hottest area of evolutionary research, how does one speak of genetic homologies between fruitflies and humans without talking about molecules?

Somehow, Fuller has been granted the status of an authority by Intelligent Design creationists. I don’t know how or why, but I hope they keep picking buffoons to represent their cause.


Ruse M (2008) A Challenge Standing on Shaky Clay. Science 322(5898):47-48.

Pray for a poll to turn out the way they want it

How can I resist this poll? It’s on a site called Pray for McCain-Palin, which is hilarious in itself, and here’s the poll on that page:

Senator McCain’s Pick of Sarah Palin as Vice Presidential Running Mate

Solidified my vote for him: 66%
Didn’t change my vote for him: 5%
Made me less likely to vote for him: 4%
Didn’t change my vote against him: 1%
Solidified my vote against him: 25%

Prayer won’t help you now, Jebusites. The Pharynguloid hordes are coming.

Physics is important to us biologists, too

The Canadian Undergraduate Physics Conference is in trouble — government support has been flat, and corporate support has been declining. They are really in trouble: here’s what I got from one of the people working on it:

The CUPC is the largest conference in North America organized entirely by undergraduate students. It brings together students from across Canada and the world studying a vast array of subject areas from mathematical and theoretical physics to medical biophysics to engineering and applied physics. This important event gives many students their first experience with academics outside of the classroom, and helps to cultivate an interest in research and higher study. I, and every one else working on the organization of this event, would therefore be extremely grateful if you would be willing to post a link to your blog for the conference (http://cupc.ca/) and ask for donations (which are accepted on the site). The conference is in only a few short days and we are desperate for funds. If the we cannot find adequate support, this will be the 44th and final CUPC, which will be a tremendous shame for science education.

If you can, donate. If you know any potential sponsors who care about undergraduate physics research, pass the word on.