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.

Friday, January 29, 2016

Preserve us from scienceiness and science fanbois.

This year's SJW disinvitation season got off with a bang this week, as some outfit called NECSS (Northeast Conference on Science and Skepticism) removed Richard Dawkins from their speaker list for the vile heresy of reweeting a link to a video that mocked feminists (and was spot on, IMHO). In the grand scheme of things, no big deal; I expect Dawkins turns down more invitations than he accepts, and it's entirely their loss. Dawkins may well the best expositor of science we have; for example, I still consider The Selfish Gene, which I read nearly 40 years ago, to have laid out the framework of how I look at biology.

Out of curiosity, though, i decided to look up what NECSS is. And, sadly, it appears to be a fanboi conference (what's the gender neutral version of fanboi?), dispensing what I call scienceiness, which bears the same relationship to science that truthiness bears to truth. One clue is that they don't actually have many working scientists as speakers. The two headliners are now Richard Wiseman, a 'psychologist and magician', and Bill Nye, the 'Science Guy' with a bachelor's degree in engineering whose schtick got stale at least a decade ago. As regular speakers, just working alphabetically, we have

  • 'physicist' who's published one paper in 3 years, on protein crystalization of all things
  • a postdoc with an alarmingly sparse record
  • a lawyer
  • a woman with a legit. Ph.D. in physics who calls herself 'The Science Babe' (her appraisal of her own babeliness is a bit off, IMHO) but who seems to work on investment analysis and to have exactly one science paper to her credit.
  • an 'Assistant Professor of Criminal Justice Administration at CSU Dominguez Hills'.
  • some guy with a podcast
  • ...
You get the picture. This is a conference not for scientists, but for posers Who Fucking Love Science; people who want to borrow science's apparently invincible cloak of 'objectivity' to pursue goals that really aren't scientific, and in most cases without the fuss and muss of having to pass second-semester calculus.

And while we're on the subject of the awful I fucking love science, they have an editorial this morning about sexism in astronomy. Now, actually, I have no idea how much sexism there is an astronomy, though there have been a couple of scandals recently, but it really annoys me when astronomy is taken as representative of science as a whole. And the editorial, which calls for 'a reboot of science', whatever that means, is written by an adjunct in sociology at a down-under dump called Swinburne University of Technology (no, I never heard of it either). The crescendo...

Similarly, science cannot reach its full potential without diversity, and diversity cannot flourish in a culture of racism, discrimination and fear. Research excellence cannot happen without rebooting science culture. The rest of us are ready for change. Are you?
That's all very high-minded, but is it actually true? Just the most obvious example: the magnificent intellectual edifice of modern physics was created by a group of almost entirely white, almost entirely male, mostly German (or teutonophone) physicists. A very undiverse bunch indeed. There really isn't much actual evidence 'diversity', by the trendy definition, has increased the rate of scientific progress. And, of course, this woman is a sociologist; she has absolutely no first-hand knowledge of 'science culture'; I bet she doesn't know how to reboot her iPhone. And as for the 'us'; who are 'us', exactly?

Most scientists don't get involved in this sort of thing, because they regard it as a waste of time. I do, because I'm argumentative and easily annoyed. But it's really time we started standing up to this sort of dreck. There are compelling reasons to give everyone equal opportunity in science, and to stamp out some of the most obnoxious behavior of (a few) scientists; but the idea we can't do science without some specified quotas of the appropriate victim groups is pure idiocy.

Friday, January 1, 2016

How, despite the FDA's best efforts, I found out I probably won't get Alzheimer's

Apolipoprotein E (APOE) is a curious protein. It's made in the liver, and transports lipoproteins, fat soluble vitamins like A and D, and cholesterol into the lymph system and thence to the blood. It was implicated in various conditions that cause hypercholesterolemia, but then, surprisingly, was found to be a major predictor of Alzheimer's disease. In brief, people with two copies of the normal APOE gene (APOE-e3) are relatively unlikely to get Alzheimers, but people with one copy of the APOE-e4 variant have somewhere between a 1.5 fold and 3 fold increased risk of the disease, and people with two copies of APOE-e4 have a 20 - 30 fold increased chance. There's also a APOE-e2 variant that actually further reduces one's chances of Alzheimer's. Why, no one knows. APOE-e4 differs from APOE-e3 in a single amino acid (e4(Arg 112 Cys)e3, if you care), and ultimately in a single base-pair difference in the gene, a so called single-nucleotide polymorphism or SNP. While genes undoubtedly have a substantial influence on whether we develop a whole host of diseases, APOE-e4 is, so far, unique, in that a single base switch causes such a huge effect. There are, of course, all sorts of other mutations that cause particular genetic diseases, but APOE-e4 is by far and away the commonest.

About 6 months ago, I received an email from a close relative, telling me they had done a 23andme analysis, in the UK, and found they had a single copy of e4. I was able to reassure my relative that a single copy of e4 isn't that dangerous, and that one could easily reduce the chances of Alzheimer's back to average with some lifestyle changes. So it's useful information to have. I was however worried; both my mother and her mother died after prolonged and agonizing (for the family) dementia, and I could conceivably have double-e4. So I decided to get tested. And found out -- nothing.

This is because two years ago the Food and Drug Administration, an agency that is supposed to protect us from noxious foods and drugs, but in practice protects us from access to health information and cheap pharmaceuticals, told 23andme they couldn't give out health information without approval by the agency. So now 23andme will tell you if you carry genes for various rare conditions, but they aren't allowed to tell you if you have APOE-e4. Fortunately, I have a Ph.D. in biophysics, considered doing my Ph.D. with Wally Gilbert, who invented gene sequencing, and have taught courses on molecular phylogenetics. It wasn't hard to look up the chromosomal location of the APOE gene and simply read the sequence. And, after about 20 minutes of tedium, I found out what 23andme were forbidden to tell me; that I have two copies of APOE-e3 and thus have a pretty low risk of Alzheimer's. Good news, no? In fact, a friend then told me I could simply send the raw DNA sequence information to a site called promethease.com, and for $5 they'd deliver a report about a large number of polymorphisms that affect human health, though none as directly as APOE-e3. So I've found out I probably have a somewhat elevated risk of heart disease and cancer (no surprise, given my personal and family history) and a low risk of diabetes. Most of this I evaluated by doing a great deal of reading about the significance of these various SNPs. 23andme could have told me the same things, and saved me a lot of effort.

Morals? First, in the information age, the FDA is standing squarely in the path of progress, yelling 'STOP'. How can it be justified that the government can prevent a person from contracting with a company to find out information about their own genome? Second, it's pointless, because (as we used to say back at the dawn of the 'net) information interprets censorship as damage, and routes around it. A cumbersome bureaucracy like the FDA is simply not nimble enough to prevent small enterprising companies from selling interpretation of genomic information (or for that matter, from selling nootropics). All they can do is be an expensive nuisance.

Burgeoning access to information is likely to be the doom of the Mommy State, but in the interim, more and more people are going to be finding out government is usually not your friend. It's the friend of the companies who want to sell you drugs at 100 times their cost in other countries, and doctors who want to maintain their monopoly on health care.

Back from the dead.

I'm going to try to blog more frequently in 2016, and focus on the nexus between science and politics. But we shall see!

Thursday, July 16, 2015

Deborah Nucatola and the moral sense.

Humans have an innate moral sense, that transcends religion, or culture, or education. We (most of us) are born with it. This is not up for debate; it's the conclusion of thousands of scientifc studies. Deny it, and you're equivalent to a creationist or denier of global warming.

Two very important parts of the moral sense are protectiveness towards babies and children, and a sense of disgust and fear of contamination. (There is an actual scientific debate about whether the latter two are separate.) Our protectiveness towards children is very much an evolutionary product of our being social animals. It's triggered by big eyes, big heads, small bodies, etc.. For example, in contrast to us, male lions slaughter the offspring of other male lions. As any biologist will tell you, there's little difference between a 22-week fetus and a newborn anyway; a breathing reflex, perhaps, and a change in blood flow that happens on birth. But, more innately, when we look at a 22-week gestational age human being in a preemie nursery, our brains see it as a baby, and our protective instinct is triggered. Light-hearted chatter about crushing the bodies of late term fetuses disturbs us, and it should. It's completely natural we feel that way. Blather all you want about it not being a baby; your brain knows better.

Now compound this protectiveness with disgust and fear of contamination, which exists, among other things, to protect us from eating bad food. There's a reason why we say 'not while I'm eating lunch' in response to disgusting stories. Watching conversation about dismembering babies, while the speaker is eating lunch, sets off two alarms. If it doesn't disturb you, you're probably a sociopath. And we don't like sociopaths, because we rtightly fear and shun people who don't have instincts that allow them to live peaceably with others.

So people who shake their heads at the 'ick' factor here are simply blind and ignorant; they are denying who we are.

Interestingly, research -- a lot of it done here are UNL -- shows conservatives tend to react more intensely to disgust (and conversely, disgust tends to make people more conservative). And liberals tend to be more protective, which is why they hate fetal pictures. This tape manages to trigger all of us.

Libertarians and liberals tend to argue we can transcend our innate moral sense, where it doesn't squae with our rationally based ethics. Peter Singer, for example, argues that if newborns and late term fetuses are essentially the same (and they are) we should be able to kill newborns just as we perform late-term abortions. Libertarians sometimes argue our incest taboo (another part of the moral sense, linked to disgust) makes no sense applied to sex between consenting adults who can't conceive deformed children, such as same-sex and infertile siblings. They're pissing into the wind.

Conservatives, on the other hand, argue that the moral sense is incredibly important. We humans are simply not smart enough to do complex ethical calculus on the fly. We need a moral instinct, just as we need an instict that lets us figure out the flight of a baseball, and can't just integrate Newton's equations of motion, as a computer would.

We trifle with this stuff at our peril. There's no evidence our moral sense is a cafeteria from which we can pick and choose.

Saturday, July 4, 2015

The great social inversion

Reading Jacob Sullum's column about the PA governor's veto of a law that would free up private liquor sales in that state, I reflected on the fact that 40 years ago, liquor sales were still quite restricted in Nebraska. It's all changed. Nowadays, you can buy anything you want in a supermarket, any day of the week. The range of beers is fantastic. Although it's probably formally illegal, I've had cases of wine shipped in from Washington State and from France, without hassle. Since last Friday, you can get married to someone of the same sex here, with the usual restrictions (no underage, no close relatives, and neither of you should already be married). We repealed our sodomy laws way back in 1977.

That's not saying we're an oasis of libertarianism. Unlike most of the states bordering us, you still have to wear a helmet when operating a motorcycle. You can smoke tobacco pretty much nowhere in public. Unlike neighbor Colorado, you can't smoke dope (although cannabis grows wild all over the state). The police seem to be mostly interested in marijuana prohibition so we can intercept pot and money on I-80, but I still wouldn't light up in front of one.

I have no doubt the liquor restrictions in Pennsylvania (and New Hampshire, and in a dozen or so other states) are largely corrupt arrangements between the state and various private interests. Still, moralistic arguments have been offered in their defense. If you're a college student in California and New York, the state now places incredible restrictions on your sexual behavior. If you're at an institution of higher education in those states, your speech is heavily policed for political correctness. Heck, if you're in any sort of public position, even private monetary contributions towards unorthodix causes will lose you your job. You can't buy sugary soda. Even getting a job at a university requires a background check to make sure you're not a pervert.

Meanwhile, drive any interstate through the south, and you're bombarded with billboard ads for X-rated videos and sex shops. Most places don't prosecute prostitution except when it's out on the streeet and creating a public nuisance. Lincoln's own decidedly liberal police chief seems to have given up on Craigslist hooker stings.

My point is this; the places that were once socially conservative are now socially liberal, and the places that were once liberal are now becoming puritan. You don't need a notarized affidavit to have sex with a classmate in most of the red-states; in New York and California, it's safest to be accompanied on a date by a constitutional lawyer.

Anthony Burgess (Clockwork Orange) wrote a book about this once, called The Wanting Seed. It was written, presciently, in the early 60s, and predicted how the swing towards libertinism would bring about, much later, a reaction. So as liberals once preached free love, now, they're ring-fencing love with a barricade of rules. As they preached access to drugs; now they want to ban everything you might ingest that could conceivably do you harm; as they once championed the "Filthy Speech" movement; now, where they reign, speech requires walking on eggshells, lest you offend one of a myriad of hypersensitive identity groups.

Just as in the past, religious nonconformism led to puritanism, and the fight for women's rights led to prohibition; now the 60's revolution has led to the nanny state. Liberal thought is a giant oscillation between libertinism and prudishness. Meanwhile, conservatism follows along sheepishly, out of phase by a quarter cycle. As puritanism becomes orthodoxy, conservatives will adopt it, and then become angry as liberals suddenly decide libertinism is once again for them.

Right now, the liberal puritan wave is still building, and conservatives are about as libertarian as they'll ever be. All this will change.

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.