Biography

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 had really liked 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.

Thursday, May 21, 2015

The Apple Watch

If you know me, you know I'm what the Register calls a fanboi. I bought my first Apple IIfx in 1991. I own more Macs than I can count, including a relatively rare Apple XServe cluster. iPhone, iPad, you name it, I have it. So, of course, I was going to buy an Apple Watch; I ordered it on April 10, and it came last week. I bought the big one, with the 42 mm face. Not the gold one, of course. And I've been using it for a week, so here's my review.

First, the bullets, pro and con

Pro

  • The battery life is way better than reported. I charge it on getting up in the morning. It takes about 1.5 hours, via an inductive coil that sticks magnetically to the back of the watch. It doesn't need to be charged again until the next day. People who claim 5 hour battery lives are nuts; I suspect they're simply playing constantly with it. Under normal use, I find it has about 20% left at 6 a.m.
  • It's not complicated to use. It took me about an hour to get the hang of 90% of the functions, and maybe a couple of days to get the rest.
  • It's surprisingly useful. It reminds me to walk around every hour, to get exercise; it shows me my grocery list, lets me access Twitter, tracks my exercise and airplane flights, wakes me at 5:30 a.m., and of course tells me the time. It does all the notifications an iPhone does, except it jogs your wrist to tell you to look at them. There are enough of them to keep you up to date, but not enough to be annoying. And there's a 'do not disturb' button.
  • Apple Pay is great. Since I'm a chronic loser of credit cards, I expect over a year it will save me twice or three times the hassle of reporting one missing. I haven't yet dared to go into a store without a wallet yet, but it's fun not to have to take it out.
Cons
  • There aren't enough 3rd party apps yet. I have Microsoft Notes, United, Twitter, eTrade, and TripAdvisor.
  • Not enough stores accept Apple Pay. Notice to merchants: I shop at Walgreens now, because CVS won't accept Apple Pay. I was actually the first person use use an Apple Watch to buy something at the Apple Store in Clarendon Square. I had to show the "Genius" how to do it. :-)
  • There is a significant bug in the Activity software (more below).
I've actually been wearing an activity tracker watch for the last 15 months, partly because of the recommendation of Dr. David Agus. Humans can do amazing things if they're given feedback of the right type; a surgeon, for example, can operate on things he can barely see, if he's given a microscope that lets him see what his scalpel is doing with micron precision. Activity watches track your heart-rate, steps and calories; mine, the Basis Carbon, will even analyze your sleep, and sets all sort of goals for activity, with little 'self-esteem' messages when you meat them and slightly naggy messages when your in danger of missing one. It really has increased the number, level and regularity of my workouts. And the Apple Watch does all that too, although their software is nowhere near as good as the Basis software yet. (Their heart rate sensor seems to be better, though)

More importantly, I've calibrated the Basis watch over the last year. If you count calories, you can see if your intake equals your output; over an extended period, if the two match, you should remain the same weight, and with the Basis watch's calorie figures, that is correct. I've been wearing the Basis watch and the Apple Watch for a week, and the Apple Watch's numbers are significantly off.

The Apple Watch is reading way too high. Basically, it gives me 2802 resting calories a day for doing nothing (far too much for my height, weight and age) and then too few calories for exercise (about 24% too few). The net result is that it estimates 250 - 450 too many calories, depending on whether I've been active or a slug.

Thousands of people have been complaining about this, and Apple is supposedly promising there will be a fix, though it wasn't in the 1.0.1 update. In the meantime, it's not hard to simply use the regression equation in the chart to adjust their number. But it's surprising they got this so wrong, given that health/activity monitors were supposed to be the device's strongest points.

Anyhoo, it's a toy, but a quite entertaining toy, and if you have an iPhone (it's needs an iPhone to talk to) I'd recommend it.

Thursday, March 19, 2015

I'm not a True Husker. That is, my IQ is above room temperature (Celsius)

Something called University of Nebraska-Lincoln’s Character Council is launching a sort of loyalty oath thingy called the 'True Husker' campaign, wherein we're all (students, faculty, staff and alumni) supposed to sign an awful pledge to mush-headed contemporary platitudes about 'diversity'. It's not even original; it's borrowed from Oklahoma, where they, natch, call the pledgers 'Real Sooners' Needless to say, I'm not signing. Here's why you shouldn't.
A true Husker shows open-mindedness. They are eager to learn and accept other’s ideas even when they are different from their own.
  • I'm more-or-less inured to the use of they as a gender-neutral alternative to he or she, which is awkward if used repeatedly. But they is still plural number, and using it as a singular pronoun is jarring. An even-slightly-competent editor would have written.
    True Huskers show open-mindedness. They are eager to learn and accept other’s ideas even when they are different from their own.
  • but, of course, the editor would have substituted others' for other's
  • More substantively, it's codswollop. They don't really want you to remain open, for example, to ISIS's ideas. I hope. What they want is for you to be open to their ideas, and closed to contrary ideas. For example, I bet they hate my ideas.
They do not discriminate based off of race, ethnicity, nationality, gender identity, sexual orientation, religious affiliation, disability, military or veteran status, age or other characteristics.
Off of? OFF OF?! Gag. How to sound both illiterate and hick in two tiny pronouns?

And their little list, by pure coincidence, is simply filched from the University's anti-discrimination policy. Just substitute "I will do as my masters desire". "Gee, this person is a convicted pedophile, but that's an other characteristic, so it wouldn't be fair to exclude them from this childcare job."

A true Husker shows respect. They show deference to their peers, and to the community.
ok but...
They do not stand for the disrespect of their peers and others.
...sounds a bit disrespectful of disrespect. And then...
They are faithful to their morals, and encourage others to become involved and engaged.
...unless, of course, your morals include, say, considering homosexuality sinful, in which case, see the non-discrimination boilerplate. "I really respect you, and am truly torn up you're going to burn in Hell because of the people you have sex with."

Etc. etc. etc. I can't stand any more of this tripe.

Sunday, March 8, 2015

Sex parties

Thanks to this morning's Sunday Times, I now know how to run a sex party. I have to admit, running a sex party is still not on my bucket list, but you never know when a skill might be useful. One could be on the organizing committee of an academic conference, say, and having successfully evaded all the really arduous responsibilities, have some officious chairperson say "OK, the last item is organizing the sex party. RWP, you don't seem to have anything else assigned. How about you take that on?" So there you are, stuck with it. And let's face it, if you put on a disaster of a sex party, you'll be branded as an incompetent for life, and never get to be on any other Really Important Committees.

Apparently the keys to a successful sex party are (1) candlelight and (2) not letting the men talk to anyone. See, when a man turns up at a sex party he says to himself. "Right, I'm at a sex party. Better go get some sex". And so the three or four vaguely attractive women at the party find themselves surrounded by men, while the other women, who are probably even more interested in sex, get ignored. Therefore the rule is, you can't initiate a conversation with her; you have to wait for her to initiate conversation with you. It's a bit much, but I have a feeling most men, although deeply wounded by the inequity of it all, put up with it, because sex.

If this all sounds horribly matriarchal, I expect that's because it is. Basically, the general tenor of life for a modern heterosexual white men is that if something is fun, or could be fun, they will screw with it until it becomes just vaguely unpleasant, but not unpleasant enough to make one put one's foot down and flat out refuse to participate(e.g. the opera). So, they're making American football safe by making all the really hard hits illegal; pretty soon you'll watch it because you remember it used to be fun, but can't quite recollect why. And I gather Sarbanes-Oxley has done the same to Wall Street.

It's gone way too far, my brothers. Time to reconstitute the Patriarchy (assuming it's OK with the wife)!

Lynxes in Britain

A phrase in today's Sunday Times

"Wild lynx, extinct in Britain for more than 1300 years..."

Hmm, I thought, 1300 years would place the extinction at 715 CE. How could they possibly know that? There are very few records for that particular period in British history (the Dark Ages, remember?). If we aren't even clear if King Arthur existed, how the heck do we know about lynx extinction? Internet searches give you the usual series of hops between unattributed links.

The answer is, we don't. It was originally assumed lynxes became extinct in Britain at the end of the ice age. But a 2005 paper carbon-dated a couple of lynx skulls; the younger dated to 455 +/- 20 CE (1560 years ago). And apparently a lynx might have been described in the Cumbric poem Pais Dinogad, though the translation is disputed. Pais Dinogad, which may date to 500 CE, originally was written in that long-extinct language, but survived because it was translated into the closely related medieval Welsh. 'Lewirn' in Cumbric means a medium-sized wild cat. Could be a lynx.

So the actual truth is there were almost certainly lynxes in Britain in 500 CE. And there aren't now. And there weren't in historical times for which we can trust the records, say after 1000 CE. That is what we know.

And this is what skepticism looks like.

Monday, February 23, 2015

Outrage number 1: Irish Car-Bomb Stout.

So the Blue Blood Brewing Company, a usually reliable producer of drinkable beer, have decided to honor the feast day of our holy St. Patrick with a substance abhorrently named Irish Car Bomb Stout. You bastards. Do you know how many of my fellow countrymen were killed or maimed by car bombs in my lifetime? I myself was close enough to one to be knocked over -- I was a minute away from being killed -- and saw bodies lying in the street after the explosion. Why don't you, for February, concoct a Slavery Stout, or for May, a Drug-cartel Jalapeno Weizen?

Heck, if you love terrorism so much, how about a Tsarnaev Brothers' Boston Ale? I have a slogan for you. "The Dzhokhar's wild!" Hilarious, huh?

Because you wouldn't dare, that's why! But sure, let's make fun of other people's misfortune. You rotten bastards.

Announcing the 2015 St. Patrick's Day whinefest

It's just a fact of American life that every ethnic, racial and other identity group whines incessantly, even about stuff that is entirely unoffensive and well-intentioned. For example, African Americans at Wright State just got all bent out of shape by a Black History Month menu that featured fried chicken, collard greens, cornbread and mashed potatoes. Meanwhile, a black frat at UNL just put on a similar menu. The hypersensitivity is such there is no way of predicting whether any well-intentioned action will cause delight or offense.

And in this case we won't be discussing well-intentioned actions. St. Patrick's Day in the US paints the Irish as a bunch of drunken, crud-eating aggressive louts. It's an excuse for binge-drinking foul fluorescent-green-colored American faux-beer, Budweiser or worse, while singing cretinous Irish American ditties like Toora-loora-loora, consuming stinking overcooked corned beef and cabbage, assuming fake 'brogues' (the word means 'shoe', morons) and generally associating my fair native land of mists with the most brutish of behavior.

On my first St. Patrick's Day in America, I naively travelled to South Boston, the Irish area of the city, with a pal from Ireland and a Yank hanger-on, in the expectation that when they heard we hailed from the old sod (or ⅔ of us did), we wouldn't have to buy a beer for ourselves the whole night. So we all ordered pints and settled down at what looked like one of the cleaner bars. About halfway through the first round, the bartender sidled over to us and asked where we were from.

"I'm from Dublin, John's from Wicklow, and this guy's from some place called Vermont." I said beaming, expecting the next phrase would be "Drinks on the house lads!"

"Well, I hate to do this, but I think it would be better if you would leave. It's St Paddy's Day (grrrrr) and there's a bunch of local guys who'll be down here later on, and they won't want anyone who isn't Irish at the bar"

"But we are Irish. We're from Ireland"

"No, you're not Irish. You're not from South Boston."

So I was thrown out of a bar in the most Irish precinct in America, on St. Patrick's Day, for being Irish. So fuck the Yanks and drink their wives, I say.

On this blog, for the next three weeks or so, I will be collecting miscellaneous offense, grievance and obnoxiousness associated with the locals' befouling of St. Patrick's Day, which after all, is a religious holiday and holy day of obligation in Ireland. You sacriligious bastards.

Saturday, February 7, 2015

Unwarranted faith in science

I'm as happy to bash antivaxers as the next guy. But we should not promote childhood vaccination by urging the public to have Faith in Science. Science screws up, often, and the public should know that. Scientists working in biomedical fields, where often they don't have a research Ph.D., and scientists working for the government, are particularly prone to screw up. The Federal Government is a cumbersome bureaucracy within which no one really excels.

Latest instance; the flu vaccine people my age are urged to get doesn't work against the major strains of influenza around this winter. I've heard numbers of 30% effectiveness in the US, though I'm not sure I believe them. In the UK, it's more like 3%. The BBC says, with classic understatement:

This is a poor result
No shit, Sherlock.

The vaccine mix used for the current season was based on a recommendation made by the World Health Organization last February, based on the breakdown of strains in the population of each country even earlier than that. It's a guess at the current flu season, in other words. The FDA appreoved the mix on February 28, 2014. Dozens of generations of flu viruses have lived, multiplied, died, and been subject to natural selection since then. Six companies make the vaccines March through August, before switching to the Southern Hemisphere.

In actual fact, it really only takes a few days to make the vaccine by the conventional route, and less using a recently approved cell-free system. The rest of the delay is regulatory; each batch has to be approved by the FDA. Shipping of some lots began in July.

It is not clear how long the FDA lot approval process takes, but it's clear the entire process is taking too long.