Thursday, February 04, 2016

Awareness

Today was a day I had not been looking forward to. 11.30 am found me reclined on a hard couch as the dentist pointed a pint-sized hypodermic in the general direction of my lower jaw. During the infusion of vast quantities of anaesthetic, I meditated upon the Trojan levels of destruction he was about to inflict upon my lower left premolar. It's called crown prep.

My sister was right: although tooth demolition is without pleasure, the alginate moulds upon which one bites while they harden (both before and after drilling) are a considerably less aesthetic experience.

---



Fast forward to this afternoon and my attendance at the TTC Speed Awareness Course. There were 23 of us in that bright, modern, anonymous seminar room at the Somer Valley Enterprise Park, 12 women and 11 men. Most of us were quiet, attentive, let's-get-this-over-with types; there were three loudmouths more extravert individuals - thank God - who provided the obligatory degree of audience participation.

The presenters were a genial retirement-age ex-cop (Stan) and a no-nonsense woman of similar age called Kate. To be fair, they were both very professional and often amusing. The general story on these courses is that everyone thinks they're going to be terrible and then ends up being quite impressed; our hosts were clapped at the end of the four hours (this doesn't always happen).

What did we do? It's a coaching exercise. We were told facts about impact injuries at various speeds; we did photo/video based hazard analysis; we group-assessed the consequences and aftermath of car accidents. We were given hints on speed control and some indication that speed limits are not quite so arbitrary as I guess we had all believed. It was manipulation but it was subtle.

---

This was the first outing for my windscreen-mounted radar detector, although I did not mention this during the group activity where we were invited to share what behavioural changes we had made as a consequence of getting a speeding ticket.

Driving to the session I encountered no cameras and the device was quiescent. As I turned into a parking bay (I later observed, at the moment the car was facing the automatic doors of Paulton House), a well-modulated female voice announced, "K-band radar has been detected, please check your speed."

On the way home, as we bounced over some rough road, the radar detector fell off.

Wednesday, February 03, 2016

"Dark Star Safari" - Paul Theroux



Somewhere in "Dark Star Safari" Paul Theroux writes "How nice it would be, I thought, if someone reading the narrative of my African trip felt ... it was the next best thing to being there, or even better - because reading about being shot at and poisoned and insulted was in general less upsetting than the real thing" (p. 406).

Here is what the New York Times had to say back in 2003.
''Dark Star Safari,'' his latest travel book, charts the author's arduous journey through Africa, from Cairo to Cape Town, by truck, bus, ferry, train and bush taxi. Theroux sets out ''hoping for the picturesque,'' and at first finds plenty of it. The pyramids of Sudan leave him feeling humbled and uplifted. In the walled city of Harar, a Maltese nun cooks him a gourmet meal and beguiles him with tales of the lover she left for God. An Ethiopian, once a political prisoner, recounts how in his cell he translated ''Gone With the Wind'' on tiny sheets of cigarette-pack foil -- 3,000 in all -- and later published the translation.

Soon, however, the trip becomes a nightmare. Danger dogs Theroux at every turn, from armed Somali highwaymen in Kenya to land mines in Mozambique. Beggars importune, disease and squalor press in. A man with a runny nose sells oranges, ''handing the snot-smeared fruit to customers.'' Appalled by ''the filth, the dirt, the litter,'' beset by ''fungal infections, petty extortion, mocking lepers, dreary bedrooms, bad food, exploding bowels,'' Theroux narrates a Job-like ordeal during which he is ''abused, terrified, stranded, harassed, cheated, bitten, flooded, insulted, exhausted, robbed, lied to, browbeaten, poisoned, stunk up and starved.''
The NYT review goes on to chastise Theroux for egregious rage at the 'agents of virtue' of the aid bureaucracies and a tendency to 'go light' on the 'crimes of western imperialism'. But that's just their standard dogma; Paul Theroux is much more interesting than that.

I was interested in Paul. He sees so much, so very acutely, yet does not draw conclusions. He is a 'how does it feel?' man, not a 'why is it this way?' analyst. No wonder his sons do so well on TV.

What he feels is an affinity with the rural Africa - the order and stability, in a timeless wilderness, of tribal subsistence farming. His fanciful desire is to end his days in that Africa and lose himself in small good works, teaching and writing.

The hurried West, with its shallow diversions and pointless buzz, has imposed itself as an alien force in Africa - aid & trade - creating slum cities and atomising traditional society. The result is disrespect, endless panhandling, crime, disease and violence. Only Africans can help Africa, Paul feels, but notes that every time Africans are left to their own devices - free of their subsidised and corrupt governments - they relapse to the timeless stability of subsistence farming.

Why is this? Paul doesn't know and more importantly, doesn't care.

---

In the end I had Paul Theroux marked down as an INFP. Not very introverted - he is perfectly happy to meet people and chat with strangers (the writer's obligation) - but equally content to blend in, shabby and unobtrusive, mostly the quietist observer. Also the only way to stay safe.

I had already read his follow-up travelogue, The Last Train to Zona Verde and was convinced that if anyone really wanted to understand the likely future of Africa they need not read the fantasies of The Economist or the optimistic deceptions of politicians, it was sufficient just to absorb Paul's immersive prose.

But I was wrong: as the NYT review showed, liberal prejudice can filter just about anything.

Monday, February 01, 2016

Red Lion Square



In 1974, aged 23, I finished my teacher training course and had already decided that no way was I going to take a job in a secondary school. Two maths teaching practices with the recalcitrant kids of London had seen to that. That summer found me instead working for London Underground at the southern terminus of the Northern Line, cleaning tube trains.

This job was more enjoyable than it sounds. I would turn up around 11 pm and spend some hours dusting and mopping the allotted number of carriages; later I graduated to washing down the outsides of trains, rubber booted in a long protective gown, scraping with a spiky brush dipped in a bucket of acid.

By 2.30 am we had done enough and then we kipped on the trains before clocking off at dawn. With all day free, a complimentary bus & tube pass, and real money I was delighted. My workmates were also interesting: the dispossessed of the world washed up in Morden. I remember a Nigerian teacher - unable to work as such due to unrecognised qualifications – with whom I shared many erudite conversations in our small tea-room at night.

So it was as a proletarian that I participated in the infamous Red Lion Square demonstration of Saturday 15 June 1974. Here is how Wikipedia describes it:
"The British far-right organisation, the National Front booked Conway Hall in Red Lion Square for a meeting to take place on 15 June 1974. A counter-demonstration was called by the London Area Council of Liberation (formerly the Movement for Colonial Freedom). This counter-demonstration attracted support from groups not directly under the control of Liberation, including the International Marxist Group (IMG), the Communist Party of England (Marxist-Leninist) and the International Socialists (later the Socialist Workers Party).
...
"The front of the Liberation march came westwards along Theobald's Road and entered Red Lion Square by Old North Street before turning right where a platform was set up for the meeting. A police cordon blocked the square to the left of Old North Street.
...
"The cordon was then charged by the larger contingent from the IMG who were closely followed by the smaller CPE(M-L) contingent . Several minutes of pushing and scuffling followed. There were several charges and countercharges. The police cordon was reinforced by members of the Special Patrol Group and by mounted police who eventually succeeded in forcing the demonstrators back.

"Photos show the use of truncheons by some police officers. At least one demonstrator reported being knocked to the ground and trampled by a police horse.
...
"A large number of demonstrators were arrested. Photos show that many who were arrested had their hair pulled or were otherwise treated with what appeared to be excessive force by police."
Picture us as we marched into the square. The IMG was a large contingent, marching in order about eight abreast. IMG stewards including myself, walked outside the crocodile moving up and down the ranks giving directions. Outside of us the police also marched, but as we came towards Conway Hall the side roads and the hall itself were blocked by cordons of police reinforced with horses.

The IMG intended to stop the National Front from using Conway Hall and charged the police cordon. I was close to the action but was rapidly ejected from the mêlée and found myself fifty yards away, wondering what to do next. As I could see my comrades struggling with the police, some being arrested, I figured I needed to return to the fray and had soon locked arms with the front line, pushing and shoving with the police not twenty yards from the hall entrance itself.

In my opinion, the police did not abide by middle-class demo-etiquette. I was grabbed by the hair and ‘private parts’ and dragged to the ground, where I was immobilised by a couple of extremely large constables. The IMG surged back and I was dragged into a police van with other, equally disoriented demonstrators.

As we were driven off, the supervising policeman in the back revealed he was from Norfolk, drafted in as extra manpower. He seemed genuinely baffled to be dealing with us: “”What are people like you doing mixed up in all this?” – We were far from his staple diet of low-lifes.

I gave a stock answer, “Those who ignored fascism in the past were overrun by it,” which even at the time seem less than totally compelling as a narrative about the rather marginalised National Front. The real answer was that most Saturdays I was doing a demo, it was one of the main ways the IMG recruited, so I was there as part of the road to revolution. But that argument seemed too cynically utilitarian to use.

Things were busy at the police station where I was banged up in a narrow cell which looked like a toilet, white porcelain tiles and a single bench. I was bailed by one of the ‘red lawyers’ who always attend demos.

My trial came a few months later. I was charged with assault on the police, a stock indictment. Several officers stood up in court and gave bored recitals about how I had stood there, punching them until they had managed to restrain me and lead me away. My lawyer carefully cross-examined them to ensure their version of events was minutely described. I was looking at six months.

During the police evidence I remember shouting in exasperation that none of this was true – I was genuinely shocked at the idea that policemen might calmly stand up in a court of law and just lie – but was shushed by my lawyer for my naivety. Only later did I understand that everyone knew this was a tedious charade and they all just wanted to get through the script.

We had a secret. I am now embarrassed to talk about it, but at the time I had an intense attachment to what can only be described as thick, woollen, diamond-patterned, Rupert Bear trousers. These were exceptionally distinctive. I had steered a bee-line to where the action was, but so had half the press and their photographers. My defence team had their pictures, many of which featured a young man in Rupert Bear trousers being wrestled to the floor and then squashed by burly cops.

Press photographers hate to be subpoenaed in these circumstances for all the obvious reasons. Nevertheless we had the guy there and the photographs were duly shown to the magistrate. Let us say there was plainly discordance between the official version of events and what the photographic record actually showed: with great reluctance, the magistrate acquitted me.

I was very lucky; most of the arrested had no such compelling defence and went down.

---

While I was having my mini-drama of being arrested, a student in our contingent from my old university (Warwick), Kevin Gately, was actually killed. The IMG view was that he had been hit over the head by a police baton from the Special Patrol Group but this was never definitively proved.

My story merited a few column inches in the papers: “London tube worker acquitted of police assault”.

My parents were mortified.

---

IMG-related:  Occupying the Embassy and A Mission to Prague.

How Much Do Our Genes Influence Our Political Beliefs?

This is the title of a New York Times piece in July, 2014, which had an illuminating thesis. Click on the table below to make it larger.
"Identical twins are more likely than fraternal twins to share traditional values with their twin siblings, suggesting a biological link on cultural outlook.

"In this table, 0 represents no correlation in outlook; 1 represents identical outlooks. In reality, the numbers fall in between, but identical twins are much more culturally alike (higher numbers) than fraternal twins.


"In an email, Ludeke explained how to interpret this information: “These correlations represent the extent to which members of a given type of twin pair resemble each other for the trait in question,” he wrote. “Low correlations, like those we found for fraternal twins, indicate that knowing the scores of one twin won’t give you much, if any, clue for figuring out the scores of the other. On the other hand, based on the correlations presented here, knowing the scores of one identical twin gives you a pretty good indication of the scores of the other.”

"The significance of the different correlations for identical and fraternal twins, Ludeke added, is that “when we see identical twins who are this similar, while fraternal twins are much less similar, we have a good indication that genes account for some of the difference between people for the trait in question.”
High heritability for political outlook doesn't mean you are destined to share your parents' views; after all, you are neither a clone nor an average mixing of your parents. It does mean that your unique genome is providing you with temperament/personality settings which inform your political outlook.

In my previous post, I quoted Scott Alexander's figures that elite US universities, like Harvard or Yale, sort something like 90:10 liberal vs. conservative. That academics - particularly in the social sciences - are bleeding-heart lefties is a truth universally acknowledged. In business, to the contrary, I have rarely found the ranks of management thus populated. Occupations are a great sorter, not just for intelligence but also for temperament and personality type.

In Keirsey/Myers-Briggs terms I suggest:
  • Liberal-leftists tend to be NF-Idealists
  • Libertarians (of left and right) are NT-Rationals
  • Conservatives (of left and right) are ST-Guardians
  • Populist insurgents are often SP-Artisans.
So some examples.
  • The emotion-driven, fuzzy-thinking, heart-on-sleeve, leftist BBC/Guardianista is the classic Idealist-NF. My favourites include Lyse Doucet and Shami Chakrabarti.

  • Left-wing Rationals include Jeremy Corbyn and Bernie Sanders; on the Right you have US neocons such as Paul Wolfowitz, John Bolton, Richard Perle - and Michael Gove.

  • You find small-c conservative Guardians in all political parties. David Cameron is one, and so is Tom Watson, deputy leader of the Labour Party. Also Hillary Clinton.

  • My favourite Artisan is the leader of the Italian Five Star movement, Beppe Grillo, ... and then there's Trump.

We're all puppets of our own temperaments. Rod Liddle (a working-class Rational) rages at bien-pensant liberals; they rage at heartless and utilitarian dessicated intellectuals ... so it goes.

Trump is the liberal antichrist .. and he knows it

Scott Alexander (Slate Star Codex) has an interesting piece which you should read from which the following is excerpted:



"Donald Trump appeals to a lot of people because despite his immense wealth he practically glows with signs of being Labor class. This isn’t surprising; his grandfather was a barber and his father clawed his way up to the top by getting his hands dirty. He himself went to a medium-tier college and is probably closer in spirit to the small-business owners of the upper Labor class than to the Stanford MBA-holding executives of the Elite.

"Trump loves and participates in professional wrestling and reality television; those definitely aren’t Gentry or Elites pastimes! When liberals shake their heads wondering why Joe Sixpack feels like Trump is a kindred soul even though Trump’s been a billionaire his whole life, they’re falling into the liberal habit of sorting people by wealth instead of by class. To Joe Sixpack, Trump is “local boy made good”.
Listening to bien-pensant liberals in the media (TV Channel 4 comes to mind) smugly opining that Trump is crazy, mad, beneath contempt, dangerous, (soon to come: the H-word), it is clear that with Trump we are in the presence of a liberal value-atrocity.

(British liberals are ideological soulmates of their American co-thinkers while the Republican base doesn't find a ready echo here .. this gives the UK media a free run.)

Trump understands the US culture wars better than his critics. He knows what he has to do to rally the "Red Tribe", the Republican base. Trump in a presidential election or as President? For good or ill, that's an entirely differently-badged animal.

We could debate (nobody does) whether Trump's personality and character would make him a good or terrible candidate for the Presidency, but I'm more interested in what motivates liberals to be so aghast about it.

So back to Scott Alexander on why liberals appear to support every group except putatively their own, which they take to be the root of all evil.
"We have a lot of people [...] boasting of being able to tolerate everyone from every outgroup they can imagine, loving the outgroup, writing long paeans to how great the outgroup is, staying up at night fretting that somebody else might not like the outgroup enough.

"And we have those same people absolutely ripping into their in-groups – straight, white, male, hetero, cis, American, whatever – talking day in and day out to anyone who will listen about how terrible their in-group is, how it is responsible for all evils, how something needs to be done about it, how they’re ashamed to be associated with it at all.

"This is really surprising. It’s a total reversal of everything we know about human psychology up to this point. No one did any genetic engineering. No one passed out weird glowing pills in the public schools. And yet suddenly we get an entire group of people who conspicuously love their outgroups, the outer the better, and gain status by talking about how terrible their own groups are.

"What is going on here?"
His answer is this (rather long) essay which you will find unfailingly interesting.

Sunday, January 31, 2016

Do it for fun, but not for profit

Just a couple of choice selections from the cornucopia which is Jess Riedel's blog.

---

American drone for covert underwater warfare

Trident will be obsolete before the next-generation hits the water
"For half a century, big missile submarines, known as boomers, have been arguably the most decisive weapon systems in modern warfare – the queen on the strategic chessboard – because of their capacity to remain unseen until the critical moment, unleashing enormous destructive force without warning.

"Now that dominant position is under threat. A submarine can hide from a few noisily obvious ships and planes, but it is harder to hide from a swarm of small, virtually undetectable drones. The robots being developed here can potentially be made cheap and expendable, and capable of being deployed in large numbers to cover vast expanses of sea. Once fully developed, they could tilt the balance of power beneath the waves – much as airborne drones are already doing in the sky.

"It is unclear how far other countries have got with underwater drone technology; it is known that the Russian navy is working on it intensively."
I foresee an arms race where the ballistic missile submarine deploys a screen of 'drone fighters' to take out the enemies underwater surveillance drones. Good luck with that.

---

Propensity to exercise and increased lifespan are correlated but not causal
"Observational studies report a strong inverse relationship between leisure-time physical activity and all-cause mortality. Despite suggestive evidence from population-based associations, scientists have not been able to show a beneficial effect of physical activity on the risk of death in controlled intervention studies among individuals who have been healthy at baseline. On the other hand, high cardiorespiratory fitness is known to be a strong predictor of reduced mortality, even more robust than physical activity level itself.

"Here, in both animals and/or human twins, we show that the same genetic factors influence physical activity levels, cardiorespiratory fitness, and risk of death. Previous observational follow-up studies in humans suggest that increasing fitness through physical activity levels could prolong life; however, our controlled interventional study with laboratory rats bred for low and high intrinsic fitness contrast with these findings.

"Also, we find no evidence for the suggested association using pairwise analysis among monozygotic twin pairs who are discordant in their physical activity levels. Based on both our animal and human findings, we propose that genetic pleiotropy might partly explain the frequently observed associations between high baseline physical activity and later reduced mortality in humans."
What this is saying is that the same set of good genes are both encouraging higher physical activity levels and giving you a longer life. If you happen to have the good genes and for some reason you're not physically active ('monozygotic twin pairs who are discordant in their physical activity levels') you still get the long life.

This is not genetic determinism. Your genes give you a set point: a certain lifespan, body-plan, weight; your choices of diet and exercise will have a varying effect, but only around that set point - not arbitrarily.

Riedel comments, "Stunning if true. Think this will slowdown our culture’s obsession with exercise for health? Me neither."

Saturday, January 30, 2016

SSC SNP picks


er, ... no ... .

I mentioned in my previous post that you could link a SNP (eg rs4570625) to your own 23andMe results using a link like this:
https://www.23andme.com/you/explorer/snp/?snp_name=rs4570625
Scott Alexander at the almost-always-reliable* Slate Star Codex wrote (November 2014) this amusing post "How To Use 23andMe Irresponsibly" describing his favourite SNPs.

Well, now they're my favourites too and I copy his (lightly edited) thoughts below, but with the SNP references switched from his choice - SNPedia - to my choice, 23andMe.

Quick reminder: most traits in life are quantitative, they come in degree, not kind. In the human genome they are polygenic - many SNPs are involved (and other genetic mechanisms too) .. so one SNP is hardly going to be decisive. In most cases.

--- How To Use 23andMe Irresponsibly - (from SSC)  ---
"rs909525 is linked to the so-called “warrior gene” which I blogged about in the last links roundup. People with the normal four or five repeat version of these gene are less violent than people with the three-repeat version, and people with the two-repeat version are massively overrepresented among violent criminals. ... Although this SNP isn’t the warrior gene itself, it’s linked to it closely enough to be a good predictor.

"This is on the X chromosome, so men will only have one copy (I wonder how much of the increased propensity to violence in men this explains). It’s also one of the minus strand ones, so it’ll be the reverse of what SNPedia is telling you. If you’ve got T, you’re normal. If you’ve got C, you’re a “warrior”. I’ve got C, which gives a pretty good upper limit on how much you should trust these SNPs, since I’m about the least violent person you’ll ever meet. But who knows? Maybe I’m just waiting to snap. Post something dumb about race or gender in the open thread one more time, I dare you…"

I'm T and my mother, Beryl Seel was (T;T), both .. normally unwarlike.

"rs53576 in the OXTR gene is related to the oxytocin receptor, which frequently gets good press as “the cuddle hormone” and “the trust hormone”. Unsurprisingly, the polymorphism is related to emotional warmth, gregariousness versus loneliness, and (intriguingly) ability to pick out conversations in noisy areas.

"23andMe reads this one off the plus strand, so your results should directly correspond to SNPedia’s – (G;G) means more empathy and sociability and is present in 50% of the population, anything else means less. I’m (A;G), which I guess explains my generally hateful and misanthropic outlook on life, plus why I can never hear anyone in crowded bars."

We're both (G;G) which makes us kind and empathic ... .

"rs4680 is in the COMT gene, which codes for catechol-o-methyltransferase, an enzyme that degrades various chemicals including dopamine. Riffing on the more famous “warrior gene”, somebody with a terrible sense of humor named this one the “worrier gene”.

"One version seems to produce more anxiety but slightly better memory and attention; the other version seems to produce calm and resiliency but with a little bit worse memory and attention. (A;A) is smart and anxious, (G;G) is dumb and calm, (A;G) is in between. if you check the SNPedia page, you can also find ten zillion studies on which drugs you are slightly more likely to become addicted to. ..."

Both of us are (A;G) which makes us average and average.

"rs7632287, also in the oxytocin receptor, has been completely proportionally and without any hype declared by the media to be “the divorce gene”. To be fair, this is based on some pretty good Swedish studies finding that women with a certain allele were more often to have reported “marital crisis with the threat of divorce” in the past year (p = 0.003, but the absolute numbers were only 11% of women with one allele vs. 16% of women with the other). This actually sort of checks out, since oxytocin is related to pair bonding. If I’m reading the article right (G;G) is lower divorce risk, (A;A) and (A;G) are higher – but this may only apply to women."

Both my mother and I are (A;G) which makes her a bit .. flighty?

"rs11174811 is in the AVPR1A gene, part of a receptor for a chemical called vasopressin which is very similar to oxytocin. In case you expected men to get away without a divorce gene, this site has been associated with spousal satisfaction in men. Although the paper is extremely cryptic, I think (A;A) or (A;C) means higher spousal satisfaction than (C;C). But if I’m wrong, no problem – another study got the opposite results."

I'm (C;C) as was my mother, Beryl Seel, which means .. probably nothing.

"rs25531 is on the serotonin transporter. It's Overhyped Media Name is “the orchid gene”, on the basis of a theory that children with one allele have higher variance – that is, if they have nice, happy childhoods with plenty of care and support they will bloom to become beautiful orchids, but if they have bad childhoods they will be completely screwed up. The other allele will do moderately well regardless. (T;T) is orchid, (C;C) is moderately fine no matter what. There are rumors going around that 23andMe screwed this one up and nearly everybody is listed as (C;C)."

For my mother and myself, 23andMe did not report on this one.

"rs1800955 is in DRD4, a dopamine receptor gene. It's overhyped media name is The Adventure Gene, and supposedly one allele means you’re much more attracted to novelty and adventure. And by “novelty and adventure”, they mean lots and lots of recreational drugs. This one has survived a meta-analytic review. (T;T) is normal, (C;C) is slightly more novelty seeking and prone to drug addiction."

I was not genotyped at this location and my mother, Beryl Seel was (C;T) which made her a little bit adventurous with lots of use of recreational sherry.

"rs2760118, in a gene producing an obscure enzyme called succinate semialdehyde dehydrogenase, is a nice polymorphism to have. According to this article, it makes you smarter and can be associated with up to fifteen years longer life (warning: impressive result means almost certain failure to replicate). (C;C) or (C;T) means you’re smarter and can expect to live longer; (T;T) better start looking at coffins sooner rather than later."

I'm (T;T) and my mother, Beryl Seel was (C;T) which makes me resigned to an early grave. She lived to 92.

"rs6311 is not going to let me blame the media for its particular form of hype. The official published scientific paper on it is called “The Secret Ingredient for Social Success of Young Males: A Functional Polymorphism in the 5HT2A Serotonin Receptor Gene”.

"Boys with (A;A) are less popular than those with (G;G), with (A;G) in between – the effect seems to be partly mediated by rule-breaking behavior, aggression, and number of female friends. Now it kind of looks to me like they’re just taking proxies for popularity here, but maybe that’s just what an (A;A) nerd like me would say. Anyway, at least I have some compensation – the popular (G;G) guys are 3.6x more likely to experience sexual side effects when taking SSRI antidepressants."

I'm (G;G) and my mother, Beryl Seel was (G;A) which makes me out to be some kind of bad boy!? I must remember to keep off those SSRI tablets.

"rs6265, known as Val66Met to its friends, is part of the important depression-linked BDNF system. It’s a bit depressing itself, in that it is linked to an ability not to become depressed when subjected to “persistent social defeat”. The majority of whites have (G;G) – the minority with (A;A) or (A;G) are harder to depress, but more introverted and worse at motor skills."

I predicted I would be (A;A) based on poor motor skills and in fact I'm (A;G). My mother, Beryl Seel was the normal (G;G) which is consistent with her not-bad motor skills (except at driving).

"rs41310927 is so cutting-edge it’s not even in SNPedia yet. But these people noticed that a certain version was heavily selected for in certain ethnic groups, especially Chinese, and tried to figure out what those ethnic groups had in common.

"The answer they came up with was “tonal languages”, so they tested to see if the gene improved ability to detect tones, and sure enough they claimed that in experiments people with a certain allele were better able to distinguish and understand them. Usual caveats apply, but if you want to believe, (G;G) is highest ability to differentiate tones, (A;A) is lowest ability to differentiate tones. (A;G) is in between.

Sure enough, I’m (A;A). All you people who tried to teach me Chinese tonology, I FRICKIN’ TOLD YOU ALL OF THE WORDS YOU WERE TELLING ME SOUNDED ALIKE."

Both of us test (A;G) so I'm sure we would have struggled with Mandarin, a daily requirement in Bristol.
So, just to reiterate, if you have a 23andMe account, click on the rs... links and see how you scored.

---

* If you care, I don't share his worries about the existential threat of the 'new AI'.

Friday, January 29, 2016

Linking a SNP (rs1234567) to your own 23andMe variant

You read about a new genetic discovery - some allele has some effect - and you wonder about yourself. Your genome (or at least the subset they sequenced) is catalogued in the 23andMe database and some sites let you check your own allele variant (SNP - 'snip') in just one click. How do they do that?

They use a link like this.
https://www.23andme.com/you/explorer/snp/?snp_name=rs4570625
Gene variants for schizophrenia are just in the news. Now in the current report the relevant risk factor is number of copies of the C4 gene, something which is not assessed by 23andMe at present. But SNPs do have some predictive power for schizophrenia and other mental conditions - for example this (at Genetic Lifehacks):
rs4570625T is the minor allele and has been studied in reference to a number of psychiatric conditions. A recent study found that those carrying the T allele were more susceptible to major depression even when not exposed to “high-negative life events”.  A Chinese study in 2014 found that those with the T allele were more susceptible to paranoid schizophrenia.
When you click on the rs4570625 link above, you're taken to the 23andMe login page. After logging in, this is what you see (click on image to make larger):



I seem to be OK as regards that particular allele (one SNP is not going to make that much difference in what is a polygenic condition) - here's what SNPedia has to say about rs4570625 (for what it's worth).

Incidentally, I'm GG and my mother was GT. What can we say about my father? Well, I received one of those Gs from my mother, so I must have got the other from my father, so he was either GG or GT. Now, I didn't actually need my mother's sequence to deduce my father's options, but knowing she was GT means that the odds favour my father being GG.

---

In case you're wondering: what's with these rs1234567 things ...?
"A reference SNP ID number, or “rs” ID, is an identification tag assigned by NCBI to a group (or cluster) of SNPs that map to an identical location."

Thursday, January 28, 2016

Notebook



A year ago I promised myself that I would continue chipping away at decoherence. During the last couple of days I reviewed "Demystifying decoherence and the master equation of quantum Brownian motion" by John King Gamble and John F. Lindner .. and I finally get the drift. My February resolution is to take up pen and paper and work through the details seriously rather than just superficially reading around it.

This is how Gamble and Lindner introduce their paper:
"The details of decoherence theory are sufficiently complicated to discourage students and physicists from other fields to pursue a basic understanding of decoherence. The available literature is aimed at an advanced audience and contains significant gaps for most physicists.

"In this paper we attempt to rectify this situation by making the underlying concepts associated with decoherence accessible to a more general audience. We begin in Sec. II by introducing the concept of a state operator, an object of central importance to quantum decoherence theory, through a simple example first developed by Bernstein. We consider a rudimentary universe consisting of quantum particles and an “environment” randomized by a roulette wheel, and show that this randomization leads to diagonalization of the state operator and the emergence of classical behavior."
Now that I have immersed myself in outer products, projection operators, density matrices and expected values, the wood is finally emerging from the trees.

---

My other resolution for February is to revisit "The Vital Question: Why is life the way it is?" by Nick Lane. Universally acclaimed as groundbreaking and brilliant (which it is), this book is not an easy read and has defied concise summarization.



Nick Lane explains how the first cell might have got going from inorganic precursors. This involves a detailed review of the most elementary mechanisms of cellular operation: membrane metabolism, protein synthesis, bioenergetics and cell-replication. In computer terms, it's like microprocessor analysis at the sub-gate level.

I am determined to internalise it sufficiently to write a proper review.

---


Clare and myself walked to Wookey Hole this morning under bright sunshine and a pure blue sky, accompanied by a chilly wind. On arrival at an empty Wookey Hole Inn we asked for hot chocolate. In my case this is always more in hope than expectation: the drink almost invariably arrives lukewarm.

And so it was to be. The young woman who made the drinks was interesting: Barbie looks - very slim; tight trousers with tucked-in top; an over-made-up, rather pinched face. She made an art form of failing to meet my eye, studiously talking in a peremptory fashion to points adjacent to my head. I said to Clare afterwards, "I doubt she'll last."

---

The Amazon elves have done their work and a big parcel arrived this morning. After the Xylitol chewing gum, perhaps the smallest entity in the box was this.



Julian Barnes' new novel recounts how Shostakovich survived Stalin (review). The book is for Clare, who studied the composer during her OU arts unit.



By far the heaviest constituent was the package of six large jars of sauerkraut you see above. I had watched one of those cute medical programmes featuring that doctor who is a twin and who has that beard and who tries stuff out .. and sauerkraut is apparently a superfood for your gut biome. Well, we here just love our gut biomes and so I decided they needed a treat.

I am waiting for Clare's smile of delight once she gets in from the garden and has had a chance to absorb (sic) this addition to our already rather over-stuffed pantry. A side-dish of sauerkraut, anybody?

---

This Zika virus never used to be so bad; it might have mutated. I was all doom and gloom over Ebola and yet, thankfully, the epidemic burned itself out before it hit Europe. Let's hope we get lucky again.

Tuesday, January 26, 2016

The Inquisition and Galileo (redux)

1633 – Galileo Galilei arrives in Rome for trial before the Inquisition

Just a couple of depressing stories for you today.

Professor Jonathan Anomaly (from Duke University) writes: (h/t Razib Khan)
"In the first half of the twentieth century, many public intellectuals made odious claims about the moral or intellectual superiority of men over women and of some races over others. Those claims—which were often couched in pseudo-scientific jargon—helped justify colonialism, discriminatory laws, and even the Holocaust (though the primary group targeted in the Holocaust, Ashkenazi Jews, were killed because of their “domination” of the sciences, medicine, and business, not because of their intellectual inferiority).

"As the twentieth century made clear, beliefs have consequences. So after the Second World War, many academics had an understandable fear of allowing themselves (or others) to believe that different groups have different average abilities or aptitudes.

"Although the fear is easy to explain, and in some cases justifiable, it has led to a widely shared and religiously held dogma in academic circles: that people are, in all relevant ways, biologically identical. Those who deny this dogma should be “educated” about their implicit biases, and made to recant their views, regardless of the evidence.

"After reading some recent work on the biology of group differences last summer, it occurred to me that as an ethics professor, I should write something about the moral upshot: if there are such differences, what are the consequences for how we should treat one another? Should we support policies that attempt to equalize opportunities only if they produce equal outcomes?

"My conclusion was modest: if there are biological differences between groups, and if, as Lee Jussim has argued, some stereotypes turn out to be accurate in part because of correct generalizations about biological differences, these facts should not undermine our commitment to treating one another as moral equals, or to increasing opportunity for all, regardless of group membership.

"But I had committed a sin in the eyes of the two referees who read and commented on my paper. I simply acknowledged the possibility of group differences while arguing that whether or not they exist, they should not matter. For having done that, the two journal referees used expletives and exclamation points to give the most venomous and dismissive feedback I have ever encountered. (Needless to say, the paper was not accepted for publication after such hostile comments.) "
Well, one swallow doth not a summer make .. but wait, what's this (from Henry Harpending)?
"Over a year ago Mike Weight (an undergraduate) and I posted a draft of a manuscript about using quantitative genetic theory to evaluate changes over time in traits. We had in mind a technology useful for distinguishing cultural from genetic transmission. Many readers of our blog made helpful comments and, to our shame, found a large number of typos.  I shudder when I reread that old post.  It was written shortly after I had my temporal lobe bleed and the whole part of my brain that was capable of proofreading seems to have been knocked out.

"We thought we should submit it somewhere where social scientists would read it.  We got back, from a succession of three journals, a stunning set of ignorant and irrelevant reviews.  For example the first sentence of the first one we read said “this is really about race and it ought to be made clear”.  Another said “they are trying to push genetics where it has no place”.  The tone of all of them was like this, angry and scornful.  One reviewer told us that our views were outdated and discredited since epigenetics had swept the field!

"We had two and one half mildly sensible reviews, one about technical aspects of quantitative genetic theory and another by a reviewer unhappy with the level of detail and statistical aspects of the treatment of Amish test results.  Since we regarded the Amish data as a toy set of data, we made no changes. The other reviewers were all hostile and angry at what we had written, several convinced that the paper must be racist but they didn’t quite understand how or why.  We could only laugh at the collection of reviews because none of them had any idea what they were talking about.  None  made it so far as to read and understand the central point of the paper.  With the exceptions mentioned above, they were pig ignorant and proud of it."
I remember watching the Brecht play, the Life of Galileo:
"The Inquisitor represents the geocentric view of the church authorities: “They (the laity) have been assured that God’s eye is always on them – probingly, even anxiously – that the whole drama of the world is constructed around them so that they, the performers, may prove themselves in their greater or lesser roles. What would my people say if I told them they happen to be on a small knob of stone twisting endlessly through the void round a second-rate star?.. I can see how betrayed and deceived they will feel. so nobody’s eye is on us, they’ll say.”

"The authorities  are annoyed that Galileo writes his theories of astronomy in the “idiom of fishwives and merchants”.  They believe that if the peasants start talking about the “phases of Venus” they may even start to question the work of God.  They may not see God as responsible for all miracles. Their world view could change. “Have we got to look after ourselves, old, uneducated, and worn out as we are? Our poverty has no meaning: hunger is no trial of strength, it’s merely not having eaten: effort is no virtue, it’s just bending and carrying”.

"Ludovico explains the perspective of the landowners and farmers. They do not want the peasants talking about the change to the universe. They believe that it would disrupt their livelihood and the status quo. ..."
A commentator Dale wrote the following about Harpending and Weight's experience:
"My observation is that a sudden flash of incoherent rage in your interlocutor is a sign that you’ve violated a taboo. The wise person tries to discern exactly what the taboo is.

"You write, “We had in mind a technology useful for distinguishing cultural from genetic transmission.” But of course that violates the anti-racist taboo because it considers possible that there is a cultural trait in humans that is genetically transmitted. And the core principle of anti-racism is to deny anything that has ever been used by racists in their arguments.

"The significance of all this requires analysis that has not yet been done. Of course, the human brain is an organ for survival and reproduction, not for discerning the truth, and in reality, academic disciplines are at best devices for the propagation of the cultures that nurture them, not for the discernment of the truth per se. With physics, discerning the facts helps our culture prosper (and out-compete others) by enlarging practical technologies … but also, our culture has gone through a lot of agonizing adjustments so that its activities aren’t discomfited by inconvenient physical facts. A few hundred years ago, those adjustments hadn’t been made and physics inquiry could threaten the social order.

"The social sciences are worse off. Partly because discovered facts can be used directly to argue for political positions, and those arguments may be directly harmful to our culture’s competitiveness by messing up the agreements, compromises, and distributions of power that make the culture run smoothly. And partly because the practical technology to be obtained from social science fact seems to be fairly limited."
It's been forty years since E. O. Wilson's "Sociobiology" proposed the reconstruction of social science on biological/Darwinian foundations. The social-sciences have since maintained their invincible, fortress-like ignorance .. but that could be about to change.

As Dale perceptively observed, it's technologies that make ideas matter in the real world, create options for societies to advance and remake the social-order.

Genomics and genetic engineering are the technologies that will empower the future Biotech Galileans against the Inquisition.

Let's hope they're more successful.

No more radar lock-on

The road from Wells to Dorchester undulates through rolling countryside and the occasional village. The speed limit flicks irregularly from 30 to 40 to 50 to 60 and back again. I might have been doing 35 through a 30 mile per hour zone when Clare said worryingly, "You just passed a speed camera."

Do they still flash? Was this one of the ones they turned off to save money (but they make money, don't they)?

How does anyone drive around in the UK today without rapidly incurring 12 points and losing their licence (not to mention c. £400 in fines)? After my recent problem (Speed Awareness Course next week) I am determined not to go down that route .. and as always, I look to technology to help me out.

Most camera detectors have very mixed reviews: many seem to break (yes, as in stop working), to not actually detect the cameras (although they seem to do a good job on supermarket automatic doors), or to require complex configuration. This one seemed the best of the bunch.

Aguri Skyway GPS/radar/laser speed trap detector

It's not cheap, but saving one speeding ticket basically pays for it. It's legal in the UK to use a device which directly detects the radar (or laser light) from a speed camera, as well as using a camera GPS location database. People complain that it's a charter for speeding idiots, but I doubt that. Impulsive risk-takers are unlikely to be conscientious enough to go to the trouble of acquiring and regularly using such a detector - they'll be more than outweighed by the rest of us who just need regular hints to be more cautious against these modern automated predators.

I'll let you know how it performs once it arrives.

If I can get it to work.

---

Update: Wednesday 27th January 2016. The Aguri Skyway arrived promptly this morning and it's now in the car as shown. Handy that I have a cigar socket doubler.

The Aguri Radar Detector joins the Sat Nav - click on image to make larger

It was not immediately obvious how to attach it to the windscreen - I was googling images to find an example - and configuration is as hard as it always is with multi-mode push buttons.

My advice to Aguri, as to all other vendors of small, configurable electronic devices, would be to add a configuration tool - basically an e-form - to be used when the device is plugged into the PC. It would make all the difference.

I did manage to update the speed camera database. The documentation said that this was unnecessary as the device ships up-to-date but (a) I never believe that, and (b) I wanted to know how it worked.

Whether the device works in the real world I have yet to find out. I guess I'll be doing a drive soon enough which takes me past a speed camera.

Monday, January 25, 2016

Visiting Durnovaria

A quick visit to Durnovaria (aka Casterbridge - modern Dorchester) by way of Sherborne. While the latter is well-heeled and full of mediaeval sandstone wonders, Dorchester has been painfully 'modernised'. Not to say that there aren't plenty of Roman relics scattered around the town.

The signposting is erratic. Trying to find the Roman Town House I was initially super-impressed by Google's ability to map a four minute walk from where we happened to be standing. Yet on arrival, the Town House was nowhere to be seen: it took a local to direct us to the entrance three hundred metres away.

The problem is that the Roman remains are off the road, just behind the Council Buildings. Google has the GPS for the ruins plus the street map; what it doesn't know is where the entrance is. It's a small but decisive failure at this release.

Just around the corner from our hotel was the ancient neolithic henge of Maumbury Rings, subsequently repurposed by the Romans. I tend to be underwhelmed by amphitheatres as they all look the same (pictured below); it's hard to imagine the ancient blood and gore. I anxiously await the first tourist release of Google Glass with augmented reality so I can enjoy the same authentic spectacle as a civis romanus in good standing.

We arrive (eventually) at the Roman Town House

Most of the rooms have mosaic flooring

Clare at the Roman Town House

The Amphitheatre (Maumbury Rings) at Dorchester

Sherborne Abbey
Trivia: Sherborne School, next to the Abbey, boasts as old boys Alan Turing, Jeremy Irons, Chris Martin and John le Carré.

The proximate reason for our visit was to view the Tutankhamun Exhibition, lavishly endowed with precision replicas of artefacts and mummies from the fabled tomb in the Valley of the Kings. Always good to see a God-King from an archaic state, but no photos allowed, I'm afraid.

Saturday, January 23, 2016

Occupying the Embassy


The Chilean Embassy in London

In the early 1970s, the International Marxist Group had a serious crush on our cousins across the channel, the Ligue communiste révolutionnaire (French Section of the Fourth International). Initially just another French groupuscule, the Ligue had surfed les événements de mai 1968 to become a formidable Trotskyist force in left-wing politics, with perhaps 10,000 members.

The IMG had around 450.

The Ligue did serious stuff. It allegedly smuggled guns to the FLN in Algeria and occupied Embassies. Wanting a piece of the action, the IMG restructured its prosaic demo stewarding organisation to form the ‘Red Defence Force’ (RDF), and I was asked to head it.

Soon afterwards I'm enjoying a pint in a pub at King’s Cross, near the IMG headquarters in Pentonville Road. What's that I hear? It's the veteran working-class activist and IMG leader Bob Pennington referring to me derisively as the IMG’s Che Guevara.

In an uncharacteristic moment of moral courage I walk across to his table and confront him:
“It was the IMG leadership’s idea to set up the RDF, not mine. If you think it’s so stupid, take it up with them, not me.”
I like to think that’s when he first took a shine to me.

---

In 1973 the Chilean military overthrew the socialist government of Salvador Allende, which was then in the process of wrecking the Chilean economy. What was probably in hindsight the least bad option was nevertheless a messy and thoroughly cruel and repressive event. Naturally the IMG was signed up to all the London demonstrations against the Chilean coup.

So we have this enormous demo coming up on Chile, and an IMG leader takes me aside (was it Peter Gowan? I think it might have been) and tells me it has been decided we should occupy the Chilean Embassy on the morning of the demonstration. The demo will pass the Embassy and the IMG contingent will break through the police cordon and rescue us.

I have never heard of a more unlikely proposal in all my life: the police are quite used to our demos and we never manage to break their cordons.

Nevertheless, I have my instructions. Clearly someone has to reconnoitre the Embassy, to plan our incursion, and that person has to be me. At this time I'm a teacher-training student at Furzedown College in south-west London. I therefore concoct a story that I'm doing a project on education in Latin America, and specifically Chile. I call the Embassy and make an appointment.

I turn up - dishevelled clothes and long hair - and a security-goon escorts me up wide curving stairs into the sumptuous office of the junta's cultural attaché. We discuss Chilean secondary education, and somehow in the conversation it comes up that the whole Embassy is Chilean territory, that the guards possess guns and that they're authorised to use them.

I file this useful information away.

On the Saturday I brief my RDF team, carefully explaining about the guns, and we arrange to meet at a location about half a mile away from the Embassy at 8.30 the following morning. We all experience a rather troubled night’s sleep.

Sunday morning arrives, as it is wont to do, and I turn up a little early to check out the Embassy. I don’t get too close, just stroll in its general direction from the tube station until I have it in view. To my gathering unease there are way too many vans of the Special Patrol Group cruising the otherwise deserted streets while a large body of burly policemen block the Embassy entrance.

Returning to the rendezvous point, I gather my team together and tell them the operation is cancelled as we have no chance of getting in. We retire to the students union at UCL to debrief. I share my opinion that the police must have been forewarned about our mission; probably by an informer. Strangely, no-one seems that disappointed. I say that with one exception: when I inform Peter Gowan later that morning, he clearly expresses his view that I have messed up big-time.

We join the rest of the IMG contingent for the demo that afternoon. As we approach the Chilean Embassy we see phalanxes of police and mounted officers guarding it. Not in a million years would the IMG have got through that.

So I save the bacon of my fellow RDF comrades and myself - at the cost of showing yet again that we can't play in the league of the Ligue.

---

I once said to a senior comrade, “I don’t understand why they put me in charge of the RDF. I have no combat skills and I’m not at all aggressive. In fact I’m much more of a thinker than a doer.” The comrade smiled and replied, “Did you ever consider that that might actually have been the reason?”

The RDF didn't last long and performed adequately in its comfort zone of marshalling street processions and the odd agitprop street theatre. No more direct confrontations with the forces of the state!

---

IMG-related: A Mission to Prague and Red Lion Square.