The science is in: the Tripoli Six are innocent

Go read Effect Measure on the recent events in the case of the Tripoli Six. This is the story of a team of health care workers who were blamed for an outbreak of HIV among young patients at a Libyan hospital—they’ve been tried in a kangaroo court and face very unpleasant prospects.

Now, in a powerful reply to the Libyan accusations, Nature has published the results of a detailed analysis of the viruses afflicting the children, and the story is clear: the cause of the outbreak was the poor hygiene present at the hospital before the six workers arrived. Here are the major conclusions of the paper:

In 1998, outbreaks of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) infection were reported in children attending Al-Fateh Hospital in Benghazi, Libya. Here we use molecular phylogenetic techniques to analyse new virus sequences from these outbreaks. We find that the HIV-1 and HCV strains were already circulating and prevalent in this hospital and its environs before the arrival in March 1998 of the foreign medical staff (five Bulgarian nurses and a Palestinian doctor) who stand accused of transmitting the HIV strain to the children.

The strains present were also traceable to North Africa and at least one was prevalent in Egypt. They also found that the timing was off: the outbreak had begun before the workers had arrived.

We found that, irrespective of which model was used, the estimated date of the most common recent ancestor for each cluster pre-dated March 1998, sometimes by many years. In most analyses, the probability that the clusters from the Al-Fateh Hospital originated after that time was almost zero. For the three HCV clusters, the percentage of lineages already present before March 1998 was about 70%; the equivalent percentage for the HIV-1 cluster was estimated at about 40%.

Apparently, the scientific evidence which would have exonerated the accused was not allowed in the court. The Gaddafi government continues to live up to its reputation.

Notch

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One of my favorite signal transduction pathways (what? You didn’t know that true nerds had favorite molecular pathways?) is the one mediated by the receptor Notch. Notch is one of those genes in the metazoan toolkit that keeps popping up in all kinds of different contexts—it’s the adjustable wrench of the toolbox, something that handles a general problem very well and therefore gets reused over and over again, and the list of places where it is expressed in Drosophila is impressive.

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Animations of urogenital development

I found these on youtube, a couple of nice cartoony animations of the development of the urogenital system. This is one of the weirder modules in organogenesis, I think; many strange things go on that are relics of ancestral states. We actually build three pairs of kidneys—pronephros, mesonephros, and metanephros—and throw each one away in succession, except the last. Both sexes form paramesonephric (or Müllerian) ducts, in blue in the animation, and these form the core of the female plumbing, but again, males basically throw it away and use a more primitive duct (the mesonephric or Wolffian ducts, in green). It’s a bizarre way to construct an organ, but what’s going on is that we have two systems, excretion and reproduction, tied together in ways that constrain the other’s development, and each is building on elements of the other.

It’s in French, but that shouldn’t slow anyone down. It’s easy to figure out what “paramesonephrique” must refer to, for instance.

Males:

Females:

Neil deGrasse Tyson on ID

Since Nick Matzke has become a fanboy, and Larry Moran has never heard of him, I thought I’d mention that I’ve liked Neil deGrasse Tyson’s column (titled “Universe”) in Natural History for a long time. It is generally on astronomy/astrophysics/cosmology, so it’s far afield from my usual comfort zone, but I don’t mind stretching my brain now and then. I’ve put a few excerpts from one column below the fold here that I thought was particularly good, from the November 2005 issue. It’s titled “The perimeter of ignorance”, and subtitled “a boundary where scientists face a choice: invoke a deity or continue the quest for knowledge.”

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Lobster vs. Sea Hare

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Ah, Aplysia. Also known as the sea hare, Aplysia is a common preparation used in neurobiology labs; it’s a good sized beastie with the interesting defense mechanism of spewing out clouds of mucusy slime and purple ink when agitated. I well remember coming into the physiology lab in the morning to find a big bucket full of squirming muscular slugs in a pool of vivid purple goo. And then I’d reach in to grab one, and they were all velvety soft and undulating and engulfing my whole arm in this thick, slick, wet, slippery knot of rippling smooth muscle…

Ahem. Well. Let me compose myself for a moment. I will say that I always thought handling Aplysia is an amazingly sensuous experience.

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What’s up, NSTA?

This is a troubling development, and perhaps some members of the National Science Teachers Association in the readership here know something about it. They seem to be in the pocket of the oil industry.

In tomorrow’s Washington Post, global warming activist Laurie David writes about her effort to donate 50,000 free DVD copies of An Inconvenient Truth (which she co-produced) to the National Science Teachers Association. The Association refused to accept the DVDs:

In their e-mail rejection, they expressed concern that other “special interests” might ask to distribute materials, too; they said they didn’t want to offer “political” endorsement of the film; and they saw “little, if any, benefit to NSTA or its members” in accepting the free DVDs. …

[T]here was one more curious argument in the e-mail: Accepting the DVDs, they wrote, would place “unnecessary risk upon the [NSTA] capital campaign, especially certain targeted supporters.”

As it turns out, those supporters already include “special interests,” including Exxon-Mobil, Shell Oil, and the American Petroleum Institute, which have given millions in funding to the NSTA.

This is not merely an attempt to avoid entanglement in a “controversial” (not that global warming is actually controversial among scientists), since the article mentions that the NSTA has distributed PR for the oil companies. I like the NSTA and I read their newsletter…but this sounds like they’ve been bought and paid for by Exxon-Mobil, and it casts an unfortunate shadow on their reputation. Can we please have a science advocacy group we can trust?


I like the way Sara Robinson’s mind works.

Memo to the Christian Coalition: The NSTA is for sale. For a mere million bucks a year, I’ll bet you could get them on board with Intelligent Design, too.

Memo to parents: It might be time to find out if your kids’ science teachers are members of this group, and have a word with them about it. If you — or the teachers — want to complain directly to the NSTA, the complaint form is here. They need to hear from everyone who still thinks that scientific truth shouldn’t be auctioned off to the highest donor.

The Cambrian as an evolutionary exemplar

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I’ve been reading Valentine’s On the Origin of Phyla(amzn/b&n/abe/pwll) lately, and I have to tell you, it’s a hard slog. This is one of those extremely information-dense science texts that rather gracelessly hammers you with the data and difficult concepts on page after page. I am convinced that James W. Valentine is ten times smarter than I am and knows ten thousand times as much, and it’s a struggle to squeeze that volume of knowledge into my miniscule brain pan.

One thing I would like to greatly condense and simplify is his discussion of the Cambrian ‘explosion’. Misinterpretation of the Cambrian is one of the many prongs of the creationist assault on science; both old school Biblical creationists and the new stealth creationists of the ID movement have seized upon it as evidence of an abrupt creation—that a Designer poofed the precursors to all modern forms into existence suddenly, and without precursors, and that this observation contradicts evolutionary theory.

It doesn’t. Valentine has an excellent diagram that shows how wrong the creationists are.

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