Monday, February 25, 2013

We knew it had to work somehow

but we still don't have an agreed-on model for why.

The Cassini spacecraft has spotted MeV (million electron volt) electrons coming from the shock wave around Saturn's magnetic field. These aren't the "ultra-high-energies" the story claims (those probably come from supernova shock fronts), but they are higher energy than the theory predicts.

This observation is of electrons accelerated where the magnetic field points more or less in the same direction as the shock front. (The case where the shock and the field are perpendicular is already known to accelerate electrons, and there are some models for how--but how well they describe Saturn's environment I don't know.) The shock front in question is from the solar wind hitting Saturn's magnetic field. For scale, the solar wind is mostly protons at about 1MeV kinetic energy and electrons with correspondingly smaller (1/2000) energy. This acceleration is able to bounce sling electrons back with energies as much as 2000 times what the incoming electrons have. (Usually smaller energies, though)

Together with the Fermi LAT spotting supernova remnant gamma rays we're starting to converge on some solid data we can use to test models with. Maybe we'll start to understand cosmic rays soon.

Tuesday, February 19, 2013

Rules of thumb and science announcements

Texan99 has a question over at Grim's Hall about how a layman can evaluate claims by scientists. It isn't easy to come up with a simple rule, and I thought maybe I should elaborate on my comments there.

Pronouncements in the press tend to be pretty dramatic. Drama is pretty much the only way to get into the news, so sometimes it is the scientist and sometimes the reporter who gooses the story.

Always remember that what you read is typically what comes out after a reporter has digested the information.

Pronouncements fall into several categories:

  1. Solidly backed by experiment and theory. Sometimes reality is weird (e.g. quantum mechanics) and you need some experience to understand it; and reality is often inconvenient. Look for humility, stable consensus and eagerness to talk about experimental verification, but those aren't perfect guarantees.
  2. Within the bounds of a current consensus that works OK. The consensus might be wrong, but that would be a big deal. Sometimes we know the current theory has holes, but nothing has been better so far. For example, quantum mechanics and theories of gravity don't play well together, so string theory (which is supposed to unify them) has been popular for a couple of decades, despite the fact that it hasn't gotten anywhere. The rest of us muddle along with two inconsistent theories and apply each in the place where it works best.
  3. Badly scrambled: either this is speculative and not really in the consensus or the reporter garbled it. This, for example. The theories about universe bubbles are part of some cosmological theories, but they're quite speculative, they're untestable, and connections to particle physics are even more speculative. The reporter was hunting for something weird enough to print, and I doubt that Hill or Lykken was happy with the story. Look for something that would be hard to test, or which doesn't seem tightly related to the experiment at hand.
  4. Within a current consensus that doesn't work worth beans though we pretend it does (some fads in psychiatry come to mind). AGW is so political that it is hard to have a science discussion about it, although you may have noticed that the "A" (anthropogenic) and "W" (warming) have pretty much disappeared from the media reports. The consensus didn't work so well... If you don't have domain knowledge of the field, about the best you can do is know a little of its history. If the consensus changes frequently, don't trust it. (Don't trust the pronouncements or the consensus.) But the only way to know the history of a field is to either study it (which isn't easy to do) or live long enough and pay attention. Watch for supporters with vested interests.
  5. A wondrous new paradigm shift with new science and new vistas. This is very very rare. I can think of "jumping genes," but not too much else recently. Not something you need to worry about most of the time.
  6. Botched experiment. This is actually rather common, as scientists eager for publication and possible future research grants rush out press releases before the peer review. Hint: is the news about something that has been accepted for publication? If not, be cautious; and even if it has been accepted, know that there are some vanity science publications out there...
  7. Hollow. We've no shortage of "theories" about healing energies or ways to disprove Einstein or allow perpetual motion. In the physical sciences these are usually easy to spot if you have the habit of trying to be precise about meanings of words or of looking for what a theory predicts mathematically. I'm not so sure how to spot them in linguistics or neurology or psychology. A rule of thumb: if the speaker explains how he is overthrowing current paradigms or going against an intrenched establishment, he's usually full of it. But not always. Sometimes the intrenched establishment is full of it (see above), and sometimes they both are.
  8. "What a noble mind is here o'erthrown." Doing important work in one field doesn't mean you're going to be right at whatever your hand finds to do. Linus Pauling was a genius, but got a bee in his bonnet about vitamin C and lost track of his own disciplines. Look for simple solutions to hard problems; chances are they're too simple and the visiting expert has left some things out.

Just a few possibilities ... You can also win a little by looking for poison citations. Someone who cites Fort, or has research that cites only his own work (Noam Chomsky)--dubious. Each field has its own usual suspects. Perpetual motion or disproving special relativity are obvious ones in physics, but I don't know what their counterparts are in archaeology or embryology. Maybe somebody should make a list.

Sunday, February 17, 2013

Bloodlands by Timothy Snyder

Bloodlands is about the lands of eastern Europe alternately occupied by forces of National Socialism and International Socialism. Using the more detailed information now available, he estimates that 14 million people were murdered, only a fraction of them in Nazi death sites. The death sites were not really death camps; people were typically killed on arrival so the place didn't have to have much in the way of residences. Camps were usually more for slave labor.

The executive summary is that the Soviets murdered more in peacetime and the Nazis more in wartime; and both mostly murdered by deliberate starvation or by rounding up people and shooting them. The people of (e.g.) Poland or Belarus were caught in a vise: what you needed to do to survive under one would get you killed under the other. And slave labor, killing, and forced migrations didn't end when the war did.

Because the ideology was supreme (though Stalin was perfectly happy to use nationalism when it suited him), peasants didn't matter as much as industrialization, so they could starve--and should. And on the other side, Hitler claimed that international Jewery was the cause of the failure delay of the Russian campaign, so the best way to win was a massive campaign to kill all available Jews.

I'd never realized how devastated Poland was.

If you want the details, read the book. If not, you'll probably sleep better if you don't read it.

I'm given to understand that the Soviets were pretty brutal when they incorporated the Chechens and other Muslim groups into the Soviet empire, but they aren't the subject of this study.

Tribes invading other tribes looking for loot and land and slaves is an old story, as is the plight of those caught in the seesaw. I don't know if it is the sheer scale, the methodical care, the fact that this is within living memory, or the insanity of the ideologies that makes this seem more horrible.

Meteors and coincidences

It seems as though everybody was watching the 150' asteroid, and nobody paying attention to the smaller boomer. One report claimed that the Russians had a little forewarning of it, but apparently not much. Or maybe they were surprised too; I can't read Russian and so there's no point in trying to track the sources.

Given that one came up from the south and the Russian one more or less down from the north, there doesn't seem to be any connection between the two. But there were a couple of other meteors streaking over California and Cuba. Such things aren't that uncommon: I've seen a fairly big one and I don't spend a lot of time watching the sky at night. I gather car-sized ones (the California one) hit us about once a week or so. Two in a night should happen at about the .5%-1% level, maybe better than that if the Cuba one was smaller.

But I'd really like to know where the other two radiated from. Eyeballing the California meteor suggests that it went more or less north--like the big one that missed. (I haven't located any direction for Cuba's.)

Over time small differences in position turn into big differences in orbit, so random chunks of asteroid, even if blasted off the same big one, will flail randomly around the sky in more or less in the same plane as the planets. But who else remembers Shoemaker-Levy?

The image gets clipped in Blogger. You may have to "View Image".

It broke up, and the fragments didn't have time to disperse widely, so Jupiter got a cosmic rat-a-tat-tat across its surface. They're still arguing whether the Silverpit crater was one of a set of impacts from a similar breakup hitting the Earth.

Maybe the new pair are related to the big boy that missed.

Or should I be suspicious? "Once is happenstance, Twice is coincidence, Three times is enemy action. -- Auric Goldfinger" Maybe the Martians want to collect on overdue parking tickets...

Friday, February 15, 2013

Supernova remnants

The Fermi Large Area Telescope (LAT) looks at gamma rays. A lot of them come from radiation produced when high energy electrons move in strong magnetic fields, but some come from the decays of pi-zero mesons. The latter tend to have a "minimum energy" and so their spectrum has some characteristic features that differ from the former.

According to a paper accepted by Science magazine (I can't link to it, but I saw an early copy), the Fermi LAT team was able to

  1. Tell where a gamma ray came from
  2. Tell what energy it had
  3. Accumulate enough statistics in their sky map to be able to tell that
    • Nearby supernova remnants are bright in the gamma ray spectrum
    • Their spectrum of gamma rays is consistent with having a lot of gamma rays from pi-zero decays

The MAGIC and VERITAS experiments showed that the supernova remnants produce pretty high energy (TeV) gamma rays, but couldn't tell the difference between "bremstrahlung" radiation and pi-zero decays. LAT can, and so we have proof for the first time that supernova remnants generate high energy cosmic rays. That's not a huge surprise, but nobody has a good model for how it works yet--there's always some detail that doesn't fit. Notice that this is the remnant, not the initial explosion. Therefore the high energy particles are coming from something else, likely the shock fronts colliding.

Pi-zero's come from interactions of protons and neutrons (not so much from electrons), and tell of high energy cosmic rays (mostly protons) coming from the area. Where you have pi-zero's you also have pi-plus and pi-minus, and therefore you also have neutrinos.

So, does IceCube see neutrinos coming from supernova remnants? Neither gamma rays nor neutrinos are bent by galactic magnetic fields...

Well, Naoko was just allowed(*) to unblind part of her analysis yesterday (certain important details are left out until we're sure the analysis isn't biased to look for whatever happened to pop up first). The results haven't been approved for publication yet. But I can say that our statistics are far lower than LAT's. Like less than 3 dozen events. True, a couple of them are doozies--PeV level energies--but you just can't do anywhere nearly as clean a sky map with that few events. But it is interesting, and results should be public shortly.

Disclaimer: I had nothing to do with either of the analyses. Congratulations to both.

(*) That conference call discussion was long. Someone else had a not-quite-mature analysis that overlapped, and which would be much less valuable if the whole of Naoko's analysis was unblinded. The discussions with the mute button on were much franker than those with it live.

Wednesday, February 13, 2013

Ancient languages

I've wondered about the mechanism of Grimm's Law. If there is a trend away from certain sounds, how did they appear in the first place? (I hope I may be forgiven for doubting that Indo-European was the language of Eden.)

You could perhaps explain it if the shifts appear because of interactions with other languages, but not so easily if they are supposed to be spontaneous or universal.

At any rate, the BBC reported on a new computer model for reconstructing ancient languages. Unfortunately the original paper assumes extensive knowledge of the literature, and about all I came away with is that they have a giant optimization problem and that they used Monte Carlo techniques to solve it rather than futilely trying an analytical approach or even a simplex method. They had too many language variables, and in cases like that the systematic approaches require impractical amounts of computer memory and take roughly forever, so you often get a better answer by randomly throwing sets of values through the "phase space" of the variables.

To be specific, suppose you have a million parameters in your problem. You can generate ten thousand sets of the million parameters with random values, calculate whatever you're trying to optimize for each of those ten thousand sets, and look for the minimum. Then do it again in a neighborhood of that minimum. And again in a tighter neighborhood, and after a while you'll be pretty close. Unless the function is pathological.

OK, fine. The optimization is only as reliable as the assumptions that go into it, of course, and I'm not able to judge those.

They looked at Proto-Austronesian (Polynesian et al).

Eldest Son asked "Why didn't they try it on the Romance languages and see if they could reconstruct Latin?" Good question. That sort of exercise has been done by hand, but it would be a nice calibration tool for the automated system. Assuming the algorithm could work smoothly with only a handful of dialects in each language...

Monday, February 11, 2013


I never met Benedict 16, and probably never will this side of eternity. I'm not Catholic either. But I read a little of what he wrote over the years, and he seemed a kindred spirit. His disciplines were quite different from mine, and I gather he is far better in his than I in mine, but something about his approach seemed familiar, though exactly how is hard to make explicit.

I haven't read the stories yet, but headlines were depressingly familiar: "Abuse survivors give their views on the resignation." I wonder if the writer justified his maliciousness or was unaware of it.

I expect lots of speculation on why he's resigning--and I'll join that crowd and guess that he was feeling too tired and fuzzy mentally, and didn't believe he could be a good pastor or administrator if he wasn't thinking straight. That's what would make me give up if I were in his shoes.

John Paul II was noted for his pastoral skills, but apparently was a lousy administrator. Benedict XVI is noted for his scholarship and insight, but apparently is a lousy administrator. Are you seeing a pattern here? Pastor is not the same as Teacher is not the same as Administrator, and the offices are all supposed to be filled by the same man: the same problem so many Protestant churches have, but with a "congregation" and bureaucracy several orders of magnitude larger. Perhaps a different approach might be in order?

I don't believe Dante was right: popes ought to be able to retire. I wish him all the best.

I've been poking around the New Testament and early church history a bit, and haven't some up with any really solid evidence that Peter was supposed to be numero uno in the church. Jesus re-commissioned him as pastor, but pastoring who? He isn't the head of the church in Acts, and the "this rock" was early on taken to mean the gospel Peter announced. The most convincing argument so far is my own (I think): all the gospels agree that Peter denied Christ. Repenting from that would be good training for being the chief. A ruler, by virtue of the "secular" obligations and distractions of office, will often find himself bogging down and denying the spirit he serves. Peter in the courtyard is the archetype of much of church leadership.

And no, I'm not trying to be cynical: power is dangerous, Pournelle's Iron Law of Bureaucracy is unavoidable and humiliation can be good training.

Be that as it may, there's a shortage of proof that Peter's successor was supposed to be numero uno after him.

Sunday, February 10, 2013

Note to self:

Do not drive a pickup in southern California. I don't have a pickup, but a minivan is classed as a light truck, so I need to be careful.

The Whydah

The vessel got its name from the port where it picked up slaves: Ouidah. We hear all the time about how terrible the middle passage was, but it hadn't occurred to me that the economics of the situation demanded that the slave transport ships be large and fast, and moderately well-armed.

In order to make best use of overwhelming force, pirates liked to use ships that were large and fast. So pirates liked to capture these slave transport ships. (Presumably the cargo could be fenced somewhere for a little extra cash.)

And so the Whydah became a pirate ship, as detailed in the traveling exhibit on pirates currently at Milwaukee Public Museum. The ship's bell was found, making this the (so far) only fully verified pirate wreck excavated. (They're pretty sure of some others, but don't have 100% proof.)

A fellow named Bellamy decided to seek his fortune salvaging a foundered pirate wreck (contra the introductory movie!), and then switched to piracy himself when that turned out to have already been salvaged by the time his team arrived.

He racked up quite a list of hits, captured and outfitted the Whydah for his personal use, and when he felt he had a sufficient haul headed his small fleet back to New England to cash in.

The description quoted on this site adds a few details the traveling exhibit omitted:

About the latter end of April, there came upon the Coast a Ship called, The Whido, whereof one Bellamy was Commander: A Pirate Ship, of about 130 Men and 23 Guns. These Pirates, after many other Depraedations, took a Vessel which had Wines aboard; and put Seven of their Crew on Board, with Orders to Steer after the Whido. The seven Pirates being pretty free with the Liquor, got so Drunk, that the Captive who had the Steering of the Vessel, took the opportunity of the Night, now to run her ashore, on the backside of Eastham.

A Storm was now raised and raging; and the Whido ignorantly following the Light of her Stranded Prize, perished in a Shipwreck, and the whole Crew were every on of them drowned, except only one Englishman, and one Indian, that were cast on Shore alive.

They slew their prisoners once they reached shore so these victims would not testify against them. The pirates didn’t elude capture, though, and were tried in Boston by a Special Court of Admiralty. Six were found guilty and sentenced to death: John Brown of Jamaica, Thomas Baker and Hendrick Quintor of the Netherlands; Peter Cornelius Hoof of Sweden; John Shaun of France; and Simon Van Vorst of New York. Carpenters Thomas South and Thomas Davis, who was tried separately, were deemed not guilty because they had been forced to join the pirates. John Julian, a sixteen-year-old Miskito Indian, wasn’t brought to trial, but was sold into slavery.


During the prayer that followed, the minister included a “Supplication” for seafarers.

That they may more generally Turn and Live unto GOD; That they may not fall into the hands of Pirates; That such as are fallen into their Hands, may not fall into their Wayes; That the poor Captives may with Cries to GOD that shall pierce the Heavens, procure His Good Providence to work for their Deliverance; And That the Pirates now infesting the Seas, may have a Remarkable Blast from Heaven following of them; the Sea-monsters, of all the most cruel, be Extinguished; and that the Methods now taking by the British Crown for the Suppression of these Mischiefs may be prospered.

Cotton Mather ended his account with the words, “Behold, Reader! The End of Piracy!”

The item in red above is a rather interesting sidelight: I wonder why it was omitted?

Another item makes me a little angry; quoting from the the Field Museum's page again:

All six men repented in the presence of Mather, but they still hanged, the tide lapping at their feet and the skyline of old Boston rising in the distance. Mather published their story and confession in a pamphlet called "The End of Piracy"—a prophetic title soon to be realized.

Note the illiterate interpretation of Mather's phrase. Perhaps this comes from the general allergy to teleology, or perhaps both the writer and editor were ill-read (and enamored of the slave theme of the exhibit).

On a happier note, the exhibit had a life-sized mockup of the ship we toured. It showed artifacts and described how they worked (lots of details about cannon I'd never heard before), had actors representing pirates fielding questions. The exhibit was quite interesting and worth seeing.

But they didn't go into what privateers were and what they were used for, which left sort of a large gap in understanding why piracy would be attractive/acceptable to so many people.

A somewhat more detailed analysis goes into the political use of pirates, and also how they organized themselves, in quite a bit more detail than (and sometimes contradicting) the exhibit.

Most piracy historians agree that 25-30% of pirate crews were African.

These Anglophonic men were usually picked up on the Sierra Leone coast, or were Angolans and Coromantee taken from the cargo holds of merchant slavers. While some historians like Ken Kinkor have made an expansive case for pirates as a race-blind workforce, my research finds a mixed record. While it is clear that certain pirate crews would accept Africans as highly motivated crewmates, others had few Africans who signed the articles. Nearly all made a sharp distinction between Anglophone Africans and “outlandish” people, whom they suspected of cannibalism. Evidence suggests that they would go to great lengths to ransom crewmates from West African communities and crewmen reported that no one could blame them for not deserting on the coast of Sierra Leone because they were scared of the Negroes “who did live in that place.” Others pled that they could not escape because “there was always a report that the Negroes would kill them.”

Men frankly admitted that they were more scared of the Africans of Sierra Leone than they were of pirates; clearly, they expected the Admiralty court to sympathize and forgive them for not running away to prove their reluctance to be pirates.

With such a low opinion of outlandish Africans (and a clear understanding that Africans could be readily commodified as slaves), it strains credulity to imagine a racially egalitarian workplace.

Moreover, African men captured aboard pirate ships never made it to trial in Admiralty courts; one assumes that they were consigned to slavery or summary execution on capture, though more investigation is called for into the fate of these men.

The exhibit repeatedly claimed that black men made up large fractions of the crew, suggesting that this was probably an attractive alternative to becoming slaves. It also suggested that the pirates coveting slave ships and interrupting slave trade was the main reason the British mounted a major campaign against them (no mention of looting of India-bound ships?). That makes for a nice tight "narrative" but misses a lot of what was going on.

One poster described two female pirates, who appear to have been perfectly representative of all (2) female pirates of the era.

Eldest Son burst into song during the tour. The actors professed not to have heard of the opera.

Worth seeing, but do your own research first. I didn't pick the audio tour, and have no comments on that.

Saturday, February 02, 2013

School shooting solutions

Don't just stand there, do something! Never mind whether it makes sense or not.

The mass school shootings, tragic and frightening though they are, are rare and have been getting more rare. (Not so the gang shootings in Chicago.)

So politicians posture and pundits clamor, and as the dust settles I see two clusters of suggestions: restrictions on guns and having armed people in the schools. (Nothing much about dealing with gangs, though.)

I will take it as understood that the media misrepresent both the risks and the benefits, and take it as given that many people don't trust the governments with a monopoly of force (and I know of no reason why they should).

But that doesn't mean I'm in favor of arming teachers or bringing in security guards (as a rule. There are exceptions, such as when some children are special targets like the President's kids would be, or when the community is awash with violent gangs).

Suppose the school is "gun free." There will always be some small probability Pr that some student will kill some other student--but those kinds of fights are usually limited (except for gang fights, but we'll not consider those here). In addition, there is the very small probability that somebody will come in and start shooting up the place, call that Pv, and the number of deaths resulting Nv. So the number of deaths with a "gun free" school will be of the order of the number of schools times Pv*Nv plus the number of students times Pr. There are well over 100,000 schools in the US, and about 75 million students (some adult).

Pr isn't big: in 1992-1993 34 K-12 children were murdered at school (or a bus, etc), and in 2009-2010 this was 17, suggesting Pr of .2E-6. Pv is also very small: I get about 6 in 7 years from the Wikipedia article (counting "subdued" as meaning the culprit would have done more if he could), for something less that 1E-5, with an average of about 12 dead per attack. So Pv*Nv is about 1E-4, which times 100,000 schools gives about 12 deaths per year. Add that to the 17 per year, and you get about 29 dead per year (though some of that 17 is gang-related).

Suppose the school includes armed teachers or security guards (who may not be much better than armed teachers). Pv (the intruder) is likely to be smaller, though the murderer may just look for easier targets. Nv (the number killed on average) will be smaller, because the murderer will be stopped more often and sooner. Let me pull wild numbers out of the air (I know of no better ones) and guess that the number killed would be cut by a third and the number of incidents would drop by half. So we'd get of order 2 deaths per year from intruders trying to kill students.

But there's a new factor. Pr may not be so small anymore.

The problem is that now it is easier for a student, or disgruntled teacher, or other staff member, to get ahold of an inadequately secured weapon. Most of the time nothing will happen. It takes continual training to keep attentive when there are no problems; otherwise you slack off. If there are five armed guards or teachers in school, what would you guess are the odds that one of them will be careless with the weapon during a school year? Cynical sort that I am, I'd guess the probability is nearly 1. So now the question is "What are the chances that a disgruntled teacher or bullied student will be around to notice?" 0.1% maybe? OK, be optimistic and say 0.001% That's Pr=1E-5, which we multiply by the number of students (about 75 million). That gives about 750 deaths per year.

The numbers are guesses, so I could easily be off by an order of magnitude or more. My point is that the cure may be deadlier than the disease. (And are you sure you can rely on the security guards?)

Banning "assault rifles" will not change the numbers at all, of course; I doubt that it would be meant to.

Autism "spectrum"

I saw this story "revealing" a link between gut bacteria and autism, and so of course I looked it up. I'd heard the anecdotes about "My son was fine until he got that horrible stomach bug and was never the same afterwards."

Naturally, the real report doesn't "reveal" any such link; though it strongly suggests one: propionic acid (PPA).

Executive Summary: autistic children have mitochondrial disease or some biomarkers compatible with it at a rate higher than the general population. Something like autism can be induced in rats infused with PPA. Surveys of autistic and neurotypical youngsters showed fatty acid concentrations that were abnormal, somewhat (not entirely!--their figure 1 has a logarithmic concentration scale and symmetric error bars? and isn't easy to compare) like that in the rats.

Autistic youth typically seem to have a different mix of gut flora than normal, more of which produce PPA, some of which will presumably go into the bloodstream and help disrupt mitochondrial activity. (BTW, antibiotics change the gut flora mix, apparently increasing the proportion of PPA-makers.)

So, since O(17%) of children with ASD apparently had abnormal mitochondrial fatty-acid metabolism (like those rats with pseudo-autism), and some of them showed no genetic abnormalities to account for it, some subset of autism is possibly due to (internal) environmental disruption of mitochondrial activity.

End Executive Summary.

It isn't clear that this is fixable after the fact, though it would be wonderful if it were (assuming this is actually the issue).

But notice the number 17%. We use the term "autism spectrum" but apparently there are quite a few different genes involved: 15 according to the notes in this paper.

That second paper is worth a look too. The authors looked at copper and zinc levels (copper levels are high in autism spectrum children relative to neurotypical children, zinc levels low in autism and PDD (but not Aspergers). They applied a B6 and zinc supplement therapy, and found changes to more normal levels in autistic and PDD children, and apparent improvement in behavior--but not in Aspergers children. (I didn't see where there was any medium-term follow-through to see if there really was improvement.)

I call this sort of thing evidence that the phrase "autism spectrum" is a misnomer. "Autism constellation" would be a better term, since it looks as though there are multiple causes with similar effects.

Which is kind of discouraging when you want to know "What should I do for my kid?"