Flee at Once ! All is Discovered !

In the last few years, law enforcement has begun to cash in on modern genetic technology in a new and more powerful way, one that works on perps that have been careful enough to avoid being genotyped.

The perp’s DNA sample is matched against a large database of genome sequences, and if a moderately long subsequence is identical-by-descent, it’s clear that the perp and the matching person in the database share fairly recent common ancestry. The degree of sharing shows, approximately, how recent that common ancestry is.

This has been done for some time with close relatives, which share up to 50% of their DNA. But by now, enough people have been genotyped that there’s a pretty good chance that the typical perp ( of European ancestry) has some moderately distant match in the database: say, a 3rd cousin. We can now detect those matches. A few such matches tells us that the unknown perp is one of the descendants of an ancestor a few generations back – so we now only have to examine a very limited pool of potential perps, perhaps a few hundred instead of tens of millions! After excluding individuals of the wrong sex, impossible ages, deceased, etc finding the real killer often becomes quite practical.

In particular, enough people have been genotyped and have uploaded their info to a genetic genealogy site to allow this. I said of European descent: genotyping and interest in genealogy have not as yet been widespread enough among African-Americans to allow this approach , but that will come, probably fairly soon.

What this means, to a pretty good approximation, is that law enforcement is soon going be able to identify the perp in all cases where DNA evidence is available. Decades of unsolved rapes, assaults, and murders will be cleared up – in as little as a couple of years, if we make a serious effort.

Exceptions? DNA from your evil twin, and DNA from truly obscure groups with no representatives in the US. People will write murder mysteries featuring Andaman Islanders -they’ll have to.

We will not find that all or most prominent people have a criminal past ( I think) – but quite a few will, undoubtedly including people you would never have guessed. It will even include people that I never suspected. Successful guys that rarely think about that perfectly understandable mistake that happened ever so many years ago will suddenly find themselves wearing orange jumpsuits. They’ll wish they had converted their holdings into Krugerrands or bitcoin, vamoosed to Chad or Yemen, but it will be too late.

Unless they act now.

Kurgan

If we combine genetic genealogy and the new method of determining identity-by-descent in ancient DNA, we could, and should,

search for immortals.

Calling a deer a deer

We all know that most people are pretty good at calling a deer a horse – pretending that the Emperor really is wearing uncommonly fine clothes that are only invisible to stupid or unfit people, etc.

Most of the time, the penalty for calling a deer a deer is not as drastic as that exacted by Zhao Gao. Most of the people saying instantly falsifiable things about current issues are not doing it because someone is holding a gun to their head. Sometimes negative career consequences are a possibility, more often social penalties, but it seems to me that most people want to go along – outside threats are not the biggest drivers.

Now we all know that going along with horseshit can be a bad thing for society as a whole, sometimes even at the individual level. It is good for society to avoid marching off a cliff, and that is also good at the individual level, even if everyone else is doing so.

But being right when nearly everyone else is wrong does not necessarily confer a net benefit.

Sure, you avoid walking on air – but the penalty for conformity is not always that dramatic, while the penalties for _nonconformity_ are almost always there. They happen even if you’re proved right – maybe especially if you’re proved right.

Still, there are some people that prefer the truth to the trend and have enough mental horsepower to get there fairly often.

The question is, is this a bug or a feature? Is it bad for fitness, or is it some kind of minority genetic strategy? Sure, it has some social utility, but that doesn’t pay the genetic bills.

Kolmogorov’s options

A while ago, Scott Aaronson wrote about Kolmogorov’s way of dealing with life in a Stalinist paradise. He mentions how Kolmogorov testified against his former mentor Luzin. It is suggested that Kolmogorov was blackmailed into doing this by the secret police, who threatened to reveal Kolmogorov’s homosexuality.

But that’s silly. It is based on the assumption that Stalin’s agents needed a reason to put you in the jug, send you to Siberia, or kill you. If you kept your nose clean, obeyed the written and unwritten rules, nothing bad could happen to you! Because that would be wrong !

The firmament of the Soviet Union during the Great Purge was studded with dead stars. No one was safe, no one was innocent. Old Bolshies, creative artists, four-star generals, farmers with a cow, ex-heads of the Cheka, personal friends of Stalin serving in the Politburo – nothing made you immune.

Supreme talent in a profession with military applications gave better-than-average protection: there were some scientists that, as far as we know, never informed on anyone. I’ve never heard that Kapitsa did.

That was probably more the case after the Bomb, when the survival and success of the state hinged on nuclear physics, and they really had to put up with people like Sakharov.

Kolmogorov was a hell of a mathematician, but not a particularly admirable man.

Henry’s Buffalo

Probably most of our readers don’t have personal experience with old-fashioned, Pleistocene-style big game hunting.  The only place in which it is still possible – not for much longer, at that – is Africa, where the big game had a chance to adapt as mankind gradually became formidable hunters and thus managed to survive until today. Without that experience, it’s hard to realize how remarkable Neanderthals were, how difficult hunting bison and elk with thrusting spears must have been.  It’s not easy to appreciate the risks stone-age hunters had to take when they went after mammoths, rhinos, or Cape buffalo: it’s not exactly safe today, even with modern weapons.  One of us, however (Henry Harpending) does have that experience, and the following note gives a flavor of what it’s like – particularly when you don’t have the faintest idea what you’re doing.

Encounter with a Buffalo

When I (HCH) was a graduate student in the 1960’s I spent a year and a half in the northern Kalahari desert doing fieldwork with !Kung Bushmen, foragers who lived by foraging wild foodstuffs and hunting game animals.  With several other graduate students we had a base camp near the border with Southwest Africa (now Namibia) about 100 miles south of the Caprivi Strip on the northern border of Botswana.  The nearest source of supplies was a two-day trip from their camp by four wheel drive truck.

Several weeks after the rainy season ended there were reports in the neighborhood of a cape buffalo that was harassing people and animals.  Often older males lose rank and leave herd to wander by themselves, angry and uncomfortable.  They are a threat to people and stock, especially horses. 

We were out of meat in our camp, and so with the confidence and foolishness of youth we decided to hunt down the buffalo.  We had visions of steaks and chops as well as many pounds of dried meat for travel rations and dog food.  At that time permits for Buffalo were only a few dollars from the Botswana game department, and we had several.  Although there were stories of Buffalo being aggressive and dangerous to hunt, to my eye they were simply large cattle. Bushmen never hunted them with their poison arrow and spear technology, but they too were naïve and had great faith in our high-powered rifle. 

One morning we set off to where the animal had last been reported.  The party was a colleague, several young Bushman males, and myself.  We soon picked up its tracks and for several hours followed its wanderings through the low thorny scrub.  To me the tracks looked exactly like those of a cow but the Bushmen never hesitated.  When it was apparent at one point that there were no tracks at all in view I asked, and the Bushmen told me that there was no point in following the tracks since they knew exactly where it was going.  We often saw this hunting with Bushmen­–they used actual tracks as a guide but knew the habits of animals so well that they often proceeded on their own to pick up actual tracks later on. 

This went on for hours until, suddenly, a young man grabbed my shoulder and said “there it is.”  I looked long and hard until I saw it, well camouflaged behind several yards of thick brush, sideways, staring hard at us with its bright pig eyes.  It was about forty yards away. 

As I brought the rifle up I was dismayed to realize that it still had a powerful telescopic sight.  I should have removed it and use open iron sights in thick bush but I had forgotten.  With the magnification of the scope I saw a black mass surrounded by brush.  It took a moment to locate the front legs, then the chest.  Oriented, I aimed and fired.  “Bang-whump”, the bang from the rifle and the whump as the bullet struck the buffalo.  He jerked a little, then simply stood there staring at me.  “Bang-whump, bang-whump” as I fired two more rounds.

Now he tossed his head and snorted, then started running toward us.  Buffalo charge with their nose high, only lowering their head to use their horns on contact.  I fired one more round at the charging animal, head on, simply pointing at him because he was so close, then turned and ran.  We discovered later that the bullet had struck his shoulder, ricocheted off his scapula, and exited through the skin on his side.  It certainly didn’t slow him down at all: I might as well have been shooting at a railroad locomotive.

There were three of us running away now from the charging animal: my colleague, our camp dog, and myself.  Perhaps fortunately for us the buffalo went after the dog, which handily outran it.  After its charge the buffalo wandered off several dozen yards and collapsed in a thicket. 

My colleague and I got together after the charge, brushed each other off, then noticed that none of the Bushmen with us was near.  We looked around and called but got no response.  Then, out of the corner of my eye, I saw a fellow about fifteen feet up a tree frantically signaling me to be quiet, then pointing at the (apparently) dead buffalo.  I laughed and told him to come down, the animal was dead, it was getting dark and we needed to get started butchering it.  He shook his head, silent, and frantically waved us back in the direction opposite the carcass.  All the Bushmen were up in trees, all waving at us to get away, no one making any noise.

My rifle was empty, slung over my shoulder, as I honed a belt knife for the job ahead.  I urged everyone to get out of the trees and get to work but everyone refused.  I said “all right, we will just make sure”, then loaded my rifle and sat in a stable shooting position.  The buffalo’s carcass was about forty yards away with its back to us.  I took careful aim at the center of the neck, exhaled, and fired.  “Bang-thump”.

Immediately the “dead” buffalo got to its feet, glared at us, and walked away.  I told my Bushman friends that I was sorry that I had mocked them and that I was grateful they had not let me start to skin a live buffalo.  They looked at me in disgust and told me that they understood that Europeans were very bright about certain things but that they could see that we could also be capable of heroic stupidity.

Evening was close by this time, and we had a mile or so walk to our truck, so we left off the chase and returned to our camp for the night.  Fortunately the area where our encounter had occurred was far away from any settlement or any route between settlements so we were not concerned about the animal assaulting any humans that night.

We didn’t sleep very well that night.  We were up late around the fire as all the participants took turns telling the story of the day.  Of course everyone told the same story, since there was only one, but somehow we were all attentive to each new version.

The next morning we were up very early.  Some trace of sanity came to us as we decided to drive down to the local headman’s hamlet and borrow his dog, renowned for his hunting and tracking abilities.  We also wanted to borrow another rifle from him, a Martini-Henry rolling block antique left over from the Boer war.  When we arrived he came out and gave us a warm welcome and a windy speech congratulating us for doing something for the community, ridding it of the dangerous buffalo.

Several months before I was sitting in camp reading a science fiction novel on a Sunday afternoon when a large group of armed men on horseback came storming into our camp in a scene straight out of a 1950’s western movie.  They had one saddled horse with no rider which, it turned out, was to be mine.  There was a lion or lions in the area that had been killing cattle, it was time to go out and hunt them down, and they were sure I would want to participate.

These were Herero, the local Bantu-speaking tribe.  They are pastoralists living off herds of cattle, sheep, and goats.  Lions are a major threat to their herds, and these group hunts are in part simply farmers protecting their stock but they are also macho male rituals demonstrating bravery.  I pointed out that I had never been on a horse in my life and that I was as scared of horses as I was of lions.  Galloping around in a mass of heavily armed men waving a high powered rifle in one hand was not my idea of how to learn to ride a horse, I said.  I also cheerfully admitted to my cowardice.

I was hardly reassured when my Herero interpreter explained that it was great fun, not really very dangerous, and that it was the duty of all men.  As he said this he gestured with a hand missing three fingers that had been bitten off by a lion in the course of one of the hunts years before.  They were all polite and cheerful and did their best to hide their disgust with me.

The headman made reference to this incident in his speech that morning. He said he was delighted to see that I was finally overcoming my unmanly cowardice.  He would be happy for us to use his dog, his rifle, and he also sent one of his sons to help out.  We then drove to the place where the charge that ended the hunt the day before had happened, looked around for the tracks of the departed buffalo, and set off to hunt it down.

We followed it for hours through nasty low thorn brush.  We saw where it had circled onto high ground and watched our approach.  Everyone was on high alert, men at the rear of our party constantly looking backward, expecting an ambush at any time.  My colleague and I had started the day thinking that we each were some combination of John Wayne and Ernest Hemingway but after hours of high tension slogging through Kalahari sand we were hot, thirsty, tired, and feeling quite burned out.

Suddenly, in early afternoon, we heard the dogs baying, then loud snorting and crashing noises about fifty yards in front of us.  The dogs had come upon the wounded buffalo.  My colleague and I turned, looked at each other, and without a word being spoken simultaneously dropped our guns on the ground and frantically scrambled up the nearest tree.  We were no more than five or six feet off the ground, but all the trees here were small and covered with thorns as our cut up hands and legs showed.  Wayne and Hemingway indeed!

Soon several Bushmen came strolling up to our tree chatting casually even while the awful chorus of snarls, barks, and snorts was going on nearby.  They saw us, stopped, looked at us, looked at our guns in the dirt, and burst out laughing. One said “would you please come down, clean up your guns, and shoot the buffalo?” 

Our shame at this point overcame our abject terror.  We climbed down, cleaned our guns, and moved up to try to get a (safe) shot at the buffalo.  It was in thick cover and we were very reluctant to plunge in after it.  Finally my colleague realized that there was a large Cape Fig tree that he could climb.  He could shoot from a high vantage point and we would not need to go into the thick stuff.  He climbed the tree, found a comfortable position on a limb, took careful aim, and shot.

Unfortunately there was a sapling in the path of the bullet.  The round ricocheted off the sapling and eviscerated the headman’s dog.  Meanwhile my colleague was clinging to his branch with the rifle swinging by it sling and hitting him in the leg.  He had forgotten about the effect of the recoil on him and his springy branch.  He then got back into position, shot several times, and the buffalo dropped.

This time our approach to the body was not as cavalier as it had been the day before.  We spend many minutes hitting it with thrown sticks and rocks to assure ourselves that it really was dead.

Several of us walked back to fetch the truck while the rest of us worked for hours skinning and dismembering the animal.  It took four of us to life a hindquarter into our truck.  We ever took the head back to be given to old people who would cook it and patiently get as much meat off it as could be gotten.

Finally we had some meat in camp.  Unfortunately it turned out to be completely inedible.  There was hardly a trace of fat anywhere in the animal, and like everyone in the Kalahari we craved and dreamed about fat.  We boiled the tongue all the next afternoon, hours and hours, and at the end we could hardly cut it with a knife.

________________________________________________________________________

Feynman

What Feynman says in this video is false.

Scientists Against Time

Back in WWII, air defense was difficult. You were shooting at high altitude, fast-moving targets. Missing was the most natural thing in the world. One out of thousands of anti-aircraft shells hit. So, there was a need for better methods.

The solution was the proximity shell – a shell with a tiny radar inside that would make the shell explode when it got _close_ to a target. This was technically challenging: it’s not easy to cram a radar into an artillery shell, not easy to build one that still works after experiencing accelerations of thousands of gravities. Moreover, people needed an answer _soon_.

The British had made some progress, but lacked sufficient resources. The US picked up the project, starting a lab that eventually became APL (Applied Physics Lab, associated with Johns Hopkins, which still exists today) . Its leader was Merle Tuve, who understood what the wartime priorities were:

” I don’t want any damn fool in this laboratory to save money. I only want him to save time.”

The New York Times, written & edited by orcs, for orcs, is criticizing Emergent Biosolutions for screwing up covid vaccine production – and those criticisms may well be valid. But they are also criticizing the original decision to throw money at Emergent Biosolutions for vaccine production – and I doubt if that is valid. The right thing to do, which by some odd chance we actually did, was ( besides getting rid of procedural obstacles) to try several vaccine approaches, several manufacturers, and use whatever was shown to work and could be produced rapidly. We didn’t know which companies would succeed ( Merck didn’t), so a shotgun approach was the logical way forwards.

The cost of the whole vaccine effort was nothing compared to the other costs of covid, while an effective vaccine was by far the most likely way of getting us out of this crappy situation.

The Silly Season

Inside a Battle Over Race, Class and Power at Smith College

In midsummer of 2018, Oumou Kanoute, a Black student at Smith College, recounted a distressing American tale:
She was eating lunch in a dorm lounge when a janitor and a campus police officer walked over and asked her what she was doing there.

The officer, who could have been carrying a “lethal weapon,” left her near “meltdown,” Ms. Kanoute wrote on Facebook, saying that this encounter continued a yearlong pattern of harassment at Smith.

Ms. Kanoute was determined to have eaten in a deserted dorm that had been closed for the summer; the janitor had been encouraged to notify security if he saw unauthorized people there. The officer, like all campus police, was unarmed. ”

Here, in what is likely the sign of some internal power struggle, the NYTimes is actually dissing some young moron who thinks that all the janitors of the world are out to get her, rather than honoring her lived experience

But there is a deeper significance: this must be the most boring story ever told. When I was bitten by a spider in my back yard and alternated between agony and a strange crisp energy, that was more interesting. When ants came over the wall from next door (where the lady lived who once worked on the Manhattan Project) and kidnapped our ants, that was more interesting.  When my youngest boy tried to crawl through the fence to the condo behind us and got his punkin head stuck, _that_ was more interesting.

When my Dad’s sister won the golf tournament at the country club but was denied the prize because she wasn’t a guy,  followed by my uncle Dean’s protest (crapping in every hole in the golf course just before he went off to the Army)  – that too was more interesting.

I would imagine that many of my readers have had experiences  ( possibly in the last half hour) even more worthy of coverage in the Paper of Record than Ms. Kanoute’s.

 

 

 

 

 

 

 

Black Doctors, Black Babies

There’s a paper out claiming that black infant infant mortality is much higher when they’re treated by white doctors, rather than black doctors.

Could it be that MCAT scores have negative predictive value?

No, there’s a simpler explanation: the report is nonsense.  A metaphorical cee-gar to the first person to explain why.

And the next question is: why do the pinheads that authored this paper have jobs?

A Random Walk on Scientists

A number of  epidemiologists and virologists  did not expect to see significant adaptive evolution for increased transmission in covid-19, and continue to argue against that hypothesis.  Vincent Racaniello, well-known virologist, takes this position.  So does  David Dowd, an infectious disease epidemiologist at Johns Hopkins.

They think that chance can drive a new variant with no transmission advantage to high frequency, even when there are many cases ( tens of thousands or more) .  The B.1.1.7 variant went from ~1% to a big majority of cases in England.

I’ve just run some sims ( with the sort of transmission dispersion observed in cov-19).  R (fitness)  = 1, in both cases.  I propagate 100 times in each run. Variant A starts out with 5,000 cases, B with 2000.  How often did B catch up with A? 6 out of 100 runs.

How often did B catch up with A when A started out with 50,000 cases and B with 20,000 cases? zero, out of 100 runs.

Start out with 2000 B and 50,000 A, same fitness: how often did B catch up? zero out of 100 runs.

Start out with 2000 B ( with a fitness of 1.05) and 50,000 A with a fitness of 1: How often did B catch up? 100 out of 100 runs.

 

The top curve shows the relative frequency of B.1.1.7 as a function of time in Denmark.  Dowd can look at that and believe it is a random fluctuation. Wow.