RWP was born in Manchester, in the north of England, in the late 1950s, so he is very old. He really liked the north of England, which by 1965 was hip and had three TV channels, and where he went to a coed school. His parents, for reasons best known to themselves, then yanked him away, to Belfast and then Dublin, which had one TV channel that started up at 6 pm with the Angelus (Catholic call to prayer). He also had to go to an all boys school, where he realized he really missed girls. This probably let him focus on schoolwork, though, and at age 19, after he had finished college, he set off for America, where he still resides. He has a bachelors degree in biochemistry and a Ph.D. from Harvard in biophysics, and has lived also in Mainz, Germany, Setauket NY, and Richland WA. He currently divides his time between Nebraska, Rosslyn VA, and Florida.

Monday, June 22, 2015

We have met the enemy, and it is us: how scientists caused the great amphibian extinction.

Following a remark by Matt Ridley in today's Times, and a little searching, I came across a very disturbing paper about the massive world-wide amphibian extinction currently under way. While some scientists tried first to blame this on the ozone hole (pretty stupid, considering it was also happening in tropical regions which had no ozone hole), and then on climate change, (The Guardian, natch, is still doing this, despite the lack of any significant evidence) there is far more persuasive evidence that it was in fact caused by scientific and medical researchers themselves.

The intermediaries in this tale are a fungus, Batrachochytrium dendrobatidis, and the African Clawed Frog, Xenopus laevis. B. dendrobatidis infects and kills frogs, newts, salamanders, etc.. It has spread from Africa, around the world, in the last 75 years. What spread it was the worldwide trade in a couple of frog species: the African bullfrog, and Xenopus. The bullfrog is a pest spread by people who for some unaccountable reason consider frogs not only edible but a gourmet item, but evidence seems to point to Xenopus as principal culprit.

Who spread Xenopus around the world? Why, it was us (scientists, I mean). Scientists have long used amphibians to study developmental biology -- frog eggs develop into tadpoles in the open, and so can be easily studied -- and since World War II, Xenopus has been the organism of choice. It's featured in every modern textbook of developmental biology. It was also used in the 1950s in medical research and pregnancy testing. Large number of frogs were raised and shipped around the Earth, and the surplus were often sold as pets or released into the wild, where there are now populations spread all over the world. But Xenopus carries B. dendrobatidis, and the die-offs closely follow geographically the adoption of Xenopus as a research animal.

So while all the while we scientists were sanctimoniously lecturing our fellow citizens about how our nasty CO2 was killing amphibians, in fact, we ourselves were responsible. (Well some of us, I personally plead innocence to the sanctimony charge)

Saturday, June 20, 2015

The scientific mystery lurking in Kennewick Man's mitochondrial DNA

The recent Nature paper on the sequencing of parts of Kennewick Man's genome has been widely reported as confirming that he was, despite early reports, related to modern Amerindians, and that is largely correct, from my reading of the paper. (Kennewick Man, you'll recall, is the 9,000 year old skeleton dug out of the banks of the Columbia River in Eastern Washington state, a few miles from my old stomping ground of Richland.) But there's also a largely unreported mystery lurking in his mitochondrial DNA, which is passed down only in the female line. Kennewick's Man's mt-DNA is a perfect match to the X2a haplotype. X2a is a subset of haplogroup X, which is the oddest family of mitochondrial DNA types. It makes up about 5% of Native Americans, but is also found in a second cluster concentrated around the Mediterranean and Near East. Unlike all the other Native American haplotypes, it is not found in eastern or northeastern Asia, as would be predicted by the likely migration route of humans into America via Beringia, the land that now lies under the Bering Straits.

Now that's surprising, but not impossible. It is possible the X haplotype simply died out in Eastern Asia -- it's nowhere particularly common -- or perhaps one woman, or a small population of closely related women, could have traveled from the Near East to America or been brought as captives during the migration. But it is fuel for an alternative and not completely impossible hypothesis that there was a second, parallel migration route into north eastern North America from Europe.

Fascinatingly, Kennewick Man's sequence is perfect basal X2a. What that means is no one with that basal haplotype is living today, but we can infer(and in fact already had inferred) its sequence from the sequences of all its descendants, which have all diverged some distance from it. So it's likely Kennewick Man was reasonably closely related to the ancestress of all current American Indian X2a individuals. A mitochondrial sub-Eve, if you like.

Yet even more fascinating is that, because of this divergence, Kennewick Man's mt-DNA differs by at least 5 - 15 base pairs from all living Native Americans. But it's only 4 base pairs distant from X2a'j, the common ancestress of X2a and X2j. And X2j is found, not in America, but in Tuareg tribesmen in the Western oases of Egypt, and a single Iranian. This could, of course, simply be a recurrence of the same mutation. Further up the mitochondial tree by one branch and one base pair, it connects to a single Druze living in Syria.

What migrations led to this result is a mystery still shrouded in the mists of time, but as of now, the Solutrian hypothesis is still alive, though barely.

Thursday, June 11, 2015

Today in feminism

  1. 'You guys' is now strenglich verboten. Please eradicate it from your vocabulary, or be prepared to publicly abase yourself before the World Internet SJW Tribunal.
  2. Protip: if bested in a debate, complain you were set upon by hordes of Twitter 'mysogynists' (correct spelling is patriarchal). Don't worry if it's not actually true.