theory-practice   13

Second Bananas | West Hunter
Still thinking about domestication. Mostly,  the wild ancestors of domesticate animals were social: presumably, such behavioral tendencies were preadaptations that helped the domesticates come to bond with or at least tolerate people.   Social animals can have adaptive personality variation – difference behavioral strategies.  Sometimes those strategies are facultative, sometimes genetic, sometimes a mix.

I would guess that those wild individuals that account for most of the ancestry of f a domesticated species didn’t have a representative mix of personality types. Probably they were more likely to be followers rather than leaders – not the alphas of the pack, not the most aggressive stallions.  Sidekicks.  With dogs, we can probably check this hypothesis fairly easily, since wolves are still around.
A few years ago, I was thinking about genetic male morphs. Turns out that you find qualitatively different forms of males in many species: Barry Sinervos’s lizards, Shuster’s isopods, Lank’s ruffs, jack salmon, etc. Logically, the Y chromosome would be the best place for a such a genetic switch, since that would avoid negative side effects in females. The problem is that the Y carries very few genes.

Alternate strategies don’t have to to be as complicated as they are in ruffs or Uta stansburiana. Different levels of aggressiveness, or different points on the cad/dad axis, would have different selective payoffs in different environments. If a new environment favored lower (or higher) aggressiveness in males , a Y-chromosome that induced lower (or higher) aggressiveness would take off. And since different Y chromosomes do indeed affect the level of aggressiveness in mice [which I just found out], possibly by affecting testosterone production – this mechanism is plausible.

This could explain a funny genetic pattern in the domestication of horses. There’s a fair amount of diversity in horse mtDNA: it looks as if many different mares were domesticated. On the other hand, it looks as if only one stallion was ever domesticated. All living stallions today are his descendants.

Stallions are pretty aggressive, and must have been hard to tame. Maybe one was genetically unusual – wimpier. Tameable.

Fortunately for all concerned, the selective value of aggressiveness, etc. has been the same for all human populations forever and ever, before and after the development of agriculture. Otherwise you might see weirdly rapid expansions of particular Y-chromosome haplogroups – common, yet only a few thousand years old.
A while ago, I wondered if modern stallions are a male morph adapted to domestication, one in which the strategy is mediated via the Y chromosome.

Looks as if I was right*. Check out “Decline of genetic diversity in ancient domestic stallions in Europe”.

Selection favored one particular kind of Y-chromosome. This had to be based on phenotype, not genealogy. Most likely it was favored under the new environment of domestication. Somehow, these stallions performed better, or were easier to get along with (my bet).

We already knew that Y-chromosomes could do things: Haplogroup I increases the risk of heart disease by about 50%, while the particular variant of Y chromosome influences aggression in mice.

Which means you have to re-examine the starburst phylogeny of R1b and R1a: it’s probably biology, rather than history, that drove those expansions. Some kind of selective advantage. Possibly one reason that those particular Y chromosomes far outraced steppe autosomal contributions. Most likely, R1a and R1b induce specific morphs – their carriers are somehow different. Maybe they’re born to be mild, or born to be princes of the universe. Maybe an R1b guy just finds it easier to cooperate with other R1b guys… Or maybe they’re resistant to typhoid.

* correct predictions mean nothing in biology. Ask any biologist.
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september 2017 by nhaliday
All models are wrong - Wikipedia
Box repeated the aphorism in a paper that was published in the proceedings of a 1978 statistics workshop.[2] The paper contains a section entitled "All models are wrong but some are useful". The section is copied below.

Now it would be very remarkable if any system existing in the real world could be exactly represented by any simple model. However, cunningly chosen parsimonious models often do provide remarkably useful approximations. For example, the law PV = RT relating pressure P, volume V and temperature T of an "ideal" gas via a constant R is not exactly true for any real gas, but it frequently provides a useful approximation and furthermore its structure is informative since it springs from a physical view of the behavior of gas molecules.

For such a model there is no need to ask the question "Is the model true?". If "truth" is to be the "whole truth" the answer must be "No". The only question of interest is "Is the model illuminating and useful?".
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august 2017 by nhaliday
Wizard War | West Hunter
Some of his successes were classically thin, as when he correctly analyzed the German two-beam navigation system (Knickebein). He realize that the area of overlap of two beams could be narrow, far narrower than suggested by the Rayleigh criterion.

During the early struggle with the Germans, the “Battle of the Beams”, he personally read all the relevant Enigma messages. They piled up on his desk, but he could almost always pull out the relevant message, since he remembered the date, which typewriter it had been typed on, and the kind of typewriter ribbon or carbon. When asked, he could usually pick out the message in question in seconds. This system was deliberate: Jones believed that the larger the field any one man could cover, the greater the chance of one brain connecting two facts – the classic approach to a ‘thick’ problem, not that anyone seems to know that anymore.

All that information churning in his head produced results, enough so that his bureaucratic rivals concluded that he had some special unshared source of information. They made at least three attempts to infiltrate his Section to locate this great undisclosed source. An officer from Bletchley Park was offered on a part-time basis with that secret objective. After a month or so he was called back, and assured his superiors that there was no trace of anything other than what they already knew. When someone asked ‘Then how does Jones do it? ‘ he replied ‘Well, I suppose, Sir, he thinks!’
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november 2016 by nhaliday
Not Final! | West Hunter
In mathematics we often prove that some proposition is true by showing that  the alternative is false.  The principle can sometimes work in other disciplines, but it’s tricky.  You have to have a very good understanding  to know that some things are impossible (or close enough to impossible).   You can do it fairly often in physics, less often in biology.
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november 2016 by nhaliday
Thick and thin | West Hunter
There is a spectrum of problem-solving, ranging from, at one extreme, simplicity and clear chains of logical reasoning (sometimes long chains) and, at the other, building a picture by sifting through a vast mass of evidence of varying quality. I will give some examples. Just the other day, when I was conferring, conversing and otherwise hobnobbing with my fellow physicists, I mentioned high-altitude lighting, sprites and elves and blue jets. I said that you could think of a thundercloud as a vertical dipole, with an electric field that decreased as the cube of altitude, while the breakdown voltage varied with air pressure, which declines exponentially with altitude. At which point the prof I was talking to said ” and so the curves must cross!”. That’s how physicists think, and it can be very effective. The amount of information required to solve the problem is not very large. I call this a ‘thin’ problem’.


In another example at the messy end of the spectrum, Joe Rochefort, running Hypo in the spring of 1942, needed to figure out Japanese plans. He had an an ever-growing mass of Japanese radio intercepts, some of which were partially decrypted – say, one word of five, with luck. He had data from radio direction-finding; his people were beginning to be able to recognize particular Japanese radio operators by their ‘fist’. He’d studied in Japan, knew the Japanese well. He had plenty of Navy experience – knew what was possible. I would call this a classic ‘thick’ problem, one in which an analyst needs to deal with an enormous amount of data of varying quality. Being smart is necessary but not sufficient: you also need to know lots of stuff.


Nimitz believed Rochefort – who was correct. Because of that, we managed to prevail at Midway, losing one carrier and one destroyer while the the Japanese lost four carriers and a heavy cruiser*. As so often happens, OP-20-G won the bureaucratic war: Rochefort embarrassed them by proving them wrong, and they kicked him out of Hawaii, assigning him to a floating drydock.

The usual explanation of Joe Rochefort’s fall argues that John Redman’s ( head of OP-20-G, the Navy’s main signals intelligence and cryptanalysis group) geographical proximity to Navy headquarters was a key factor in winning the bureaucratic struggle, along with his brother’s influence (Rear Admiral Joseph Redman). That and being a shameless liar.

Personally, I wonder if part of the problem is the great difficulty of explaining the analysis of a thick problem to someone without a similar depth of knowledge. At best, they believe you because you’ve been right in the past. Or, sometimes, once you have developed the answer, there is a ‘thin’ way of confirming your answer – as when Rochefort took Jasper Holmes’s suggestion and had Midway broadcast an uncoded complaint about the failure of their distillation system – soon followed by a Japanese report that ‘AF’ was short of water.

Most problems in the social sciences are ‘thick’, and unfortunately, almost all of the researchers are as well. There are a lot more Redmans than Rocheforts.
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november 2016 by nhaliday
Son of low-hanging fruit | West Hunter
You see, you can think of the thunderstorm, after a ground discharge, as a vertical dipole. Its electrical field drops as the cube of altitude. The threshold voltage for atmospheric breakdown is proportional to pressure, while pressure drops exponentially with altitude: and as everyone knows, a negative exponential drops faster than any power.

The curves must cross. Electrical breakdown occurs. Weird lightning, way above the clouds.

As I said, people reported sprites at least a hundred years ago, and they have probably been observed occasionally since the dawn of time. However, they’re far easier to see if you’re above the clouds – pilots often do.

Pilots also learned not to talk about it, because nobody listened. Military and commercial pilots have to pass periodic medical exams known as ‘flight physicals’, and there was a suspicion that reporting glowing red cephalopods in the sky might interfere with that. Generally, you had to see the things that were officially real (whether they were really real or not), and only those things.

Sprites became real when someone recorded one by accident on a fast camera in 1989. Since then it’s turned into a real subject, full of strangeness: turns out that thunderstorms sometimes generate gamma-rays and even antimatter.
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november 2016 by nhaliday

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