Friday, October 17, 2014

Shirley Porter's funeral

Clare and myself attended Shirley Porter's funeral this morning at the South Bristol Crematorium. Details of the service and some pictures in this updated post.

Wednesday, October 15, 2014

Any chance of stopping this Ebola thing?

An aside: you might think that an airliner must be an ideal Petri dish - recirculating air and a captive audience. It is claimed that cabin air filters have a virus removal efficiency of greater than 99.999% but that manufacturer's guarantee shouldn't be relevant as the Ebola virus currently doesn't transmit via the air, only by personal contact; so we hope for the best. (See here for an informed contrary view).

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Ebola is not going to be stopped in Central Africa: too many cases, too-porous borders, high population densities, poor infrastructure and incompetent authorities, rubbish disease-incidence reporting. Ghana won't be safe for too much longer.

From GhanaWeb

Projection data for the likely spread of Ebola is modelled here - click on charts.

The media (the BBC is a typical offender) talks about 'irrational fears' and the shocking humiliation caused to those on the wrong-end of screening. Very comforting - God help that we should over-react or anything.

What is scary with exponentially-increasing and highly-lethal epidemics is the way things can turn from a background somebody else's problem to something directly, immediately threatening on a time frame of less than a month. (Although here in Europe we'll probably get the Ebola experience quarter one of next year via North Africa).

We're in a situation far too reminiscent of the mediaeval Black Death. The thing which we know works is draconian quarantine. People will be shot (or quarantine will fail). I expect there are contingency plans to set up quarantine zones in the UK right now - if not, someone isn't doing their job right.

The other thing which might work is a treatment or vaccine.  The development schedule is not encouraging.

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The Wikipedia article notes:
"Ebolavirus is classified as a biosafety level 4 agent, as well as a Category A bioterrorism agent by the Centers for Disease Control and Prevention. It has the potential to be weaponized for use in biological warfare, and was investigated by the Biopreparat for such use, but might be difficult to prepare as a weapon of mass destruction because the virus becomes ineffective quickly in open air."
I have this vision of sections of the Nigerian military collecting the corpses of Ebola victims, dressing them in soldiers' uniforms and dropping them by parachute into areas know to be occupied by Boko Haram - they'd be sure to investigate. The equivalent to the mediaeval practice of catapulting the bodies of plague victims into besieged castles. Could anyone, do you think, be so stupid?

Sunday, October 12, 2014

Ebola nuclear strike: a really poor idea

Sierra Leone topography (Wikipedia)
It might have occurred to you that rapid sterilization of the current Ebola outbreak could paradoxically be the most humane course of action in the long run. So we read statements like this *:
"Under the circumstances, we must assume the worst-case scenario,” Weurfuqd’naowe concluded at the close of his press conference.  “The evidence we have indicates that this is a new and extremely contagious strain of filoviridae Ebola, posing a health threat worse than any previously-known epidemic.  If the virus succeeds in migrating out of Guinea, it could very well sweep the planet more rapidly than any medical intervention would be possible.”

“We will monitor conditions in Guinea’s urban centers closely over the next twenty-four to thirty-six hours.  If the disease spreads as rapidly as we fear, it will be imperative that the outbreak be contained and exterminated at any cost.  Regretfully, it is the recommendation of the World Health Organization that members of the United Nations must consider the use of a nuclear weapon, if necessary, in hopes of stopping the lethal virus before it spreads across the world.”
Here are some reasons why this is a poor idea.
  1. The last thing anyone wants is kilotons of wind-borne radioactive fall-out dusting Central Africa. This might suggest using high-altitude radiation-enhanced weapons (aka neutron bombs). Unfortunately, while gamma rays are good at killing people, viruses are remarkably tough. So in practice we would need to ensure detonation of the thermonuclear fireball pretty close to ground level. Unfortunate.

  2. Sierra Leone is big - see the map above. So are Guinea and Liberia. There are big cities where the epidemic concentrates, but also networks of far-flung villages where infection ebbs and flows. Nuclear bombs are not good area-denial weapons: the fireball radius goes only as the cube root of the weapon yield. To sterilize a country the size of any of the three affected would require hundreds of high-mega-tonnage systems, with no guarantee of complete success.

  3. Not all Ebola-carriers would be vapourised in any conceivable strike. Inevitably refugees would flee into neighbouring countries: Senegal, Mali, Ivory Coast, there to become the seeds of a subsequent round of infection. There is a limit to the number of African countries which can be nuked. And in the aftermath of the sterilization event, do-gooders from a hundred countries would flock in for 'disaster relief'. Can you imagine a more effective method of then spreading Ebola around the globe?
And radiation-induced viral mutation; we so don't want to go there. No, nuking the epidemic is a poor response and I would advise policy makers not to go down that route.

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* Check the date, by the way, on that report.

Saturday, October 11, 2014

Ebola: should you be worried?

Just to the end of October 2014
That's the trouble with exponentials: they burble around beneath the noise floor - 1, 2, 4, 8, 16 - and then sixteen iterations later it's one million, two million, four million .. and you're overwhelmed.

Scientific American writes:
"In a worst-case scenario the CDC projected that by mid-January, Sierra Leone and Liberia alone could have up to 1.4 million cases."
Yes, mid-January .. and 1.4 million.

Dr James Thompson at UCL has been posting about this, the latest being his satirical "Ebola IQ test"
"Given a viral disease which is transmitted by contact with the contaminated bodily fluids of infected dying and dead people such that each case can lead to 2 new cases, and for which there is no known cure, though rehydration and basic nursing improve outcomes somewhat, which of the following is the best strategy to save the most lives?

"In each case, chose either A or B."

(continue reading)
The NHS could presumably handle what eluded the Spanish, the prompt isolation of a carrier followed by quarantine of all contacts. But this is highly labour-intensive (dozens of at-risk contacts); it's hard to see it working if we had a hundred belatedly-identified carriers. The UK, along with the rest of Western Europe, is densely populated and highly-interconnected by busy transport links. City-wide or regional quarantine would be difficult in the extreme, even if the political will could be found for the necessary military enforcement

If the Ebola exponential wildfire sweeps across Sub-Saharan African early next year, then the UK isn't just subject to the  threat of incoming air flights. Most likely the virus will burst out to the more adjacent Middle-Eastern or North African regions, and thence into Europe by a thousand routes.

At the moment, due to West African poverty and lack of development, the virus is moving slowly. Incursions into Europe have mostly been self-inflicted through the repatriation of infected health workers. However, if incursions become more organic and massive then all those complacent "We're protected," bets are off.

Time for that trip to town, to stock up on soups, bottled water and Campingaz cartridges. A shotgun would be handy too as you hunker down.

Friday, October 10, 2014

Evolutionary roots of homophobia

From The Economist: legality of homosexuality
The Economist this week has a main feature on Gay Rights. Some countries are moving forwards, while others move backwards. The map above, showing where homosexuality is permitted in law (shades of blue-green) and where it is illegal (orange and red), cries out for explanation: it is very far from random.

There is a hint, perhaps, in the language used by red-zone politicians. The Economist writes
"IN THE argot of human rights, LGBT means lesbian, gay, bisexual, transgender—a catch-all term for sexual minorities. But Yahya Jammeh, president of Gambia for 20 years, has a different reading. “As far as I am concerned,” he thundered during a televised speech in February, “LGBT can only stand for leprosy, gonorrhoea, bacteria and tuberculosis.” He compared gay people to vermin, and said his government would fight them as it does malaria-bearing mosquitoes, “if not more aggressively”."
The Economist also notes that:
"Revulsion against homosexuals is ancient, deep and, in its way, sincere,"
Why?

Homophobia clearly draws on ancient, powerful emotions - chiefly disgust. Some of us oldies will remembers literary dialogues of the mid-twentieth century, where a refined woman gets to drawl in genuine puzzlement: "But what exactly do homosexuals actually do?"

Sex is inherently a mucky and disease-prone activity; we've all heard of sexually-transmitted diseases. Arguably, certain homosexual practices are more disease-prone. Some people find the whole idea of sexual activity frankly disgusting: homo- or heterosexual. However, any male or female who believes this sufficiently strongly is not going to leave any descendants - so genes coding for that emotional reaction are unlikely to spread widely in the population.

Some small percentage of the population (c. 3-4%) is significantly into homosexual practices. As this kind of sexual activity can't lead to descendants how can such people exist? Greg Cochran thinks the culprit is some kind of infectious agent priming an underlying heritability of 0.3 - 0.4; we know that sexuality is on a hormonal continuum so perhaps LGBT people are simply 'on the spectrum'?

Still, like all practitioners of sex, homosexual people historically engage in a potentially disease-spreading activity. And there is no genetic come-back from disgust in the heterosexual community, as so graphically articulated by Yahya Jammeh, President of Gambia above.

In the West, our standards of hygiene are higher and perhaps we're rather more self-controlled and empathic. We've become 'tolerant' (there's a word!) and of course we should be - LGBT people are what they are - and in the last decades we've agreed not to use the power of the state against them.

But let's not pretend - in some blank slate fashion - that those underlying, ancestral, selected-for emotions have somehow been edited out, because they plainly haven't.

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Sparse pickings on the Internet for this topic. A Scientific American article makes a brave attempt but looks to paedophilia and xenophobia for explanations - disconfirmed both by common sense and the evidence. The whole area is stymied by liberal hand-wringing.

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In case it wasn't obvious, let me summarise the speculative thesis of this post.

The reason for an evolved heterosexual disgust towards homosexuals (mislabelled as 'homophobia') is that in the environment of evolutionary adaptedness (EEA) homosexuals were more likely to be disease vectors.

Wednesday, October 08, 2014

Best introduction to human genomics

Puzzled by your 23andMe/Promethease results? Having trouble figuring out what SNPs are and what they're good, or bad for? Time to learn some human genetics and genomics.



"Human Genetics and Genomics" (4th Edition) by Bruce R. Korf and Mira B. Irons is a bird's eye view of the basics of molecular biology through to the technologies of genome analysis to the medical implications of DNA and chromosome variation. It's aimed at medical students, so there are case studies to keep it real.

Chapter 1 starts us off with a tour round human DNA. We look at how it's structured, how it's replicated in cells and how DNA is transcribed into proteins. We take a quick look at epigenetics (the way some genes can be chemically silenced - switched off).

Chapter 2 looks at genetic variation. This covers single nucleotide polymorphisms (SNPs), DNA repair mechanisms, gene duplication and its role in evolution. PCR (Polymerase Chain Reaction) as used for forensic analysis of DNA samples amongst other things is also described.

Chapter 3 is 'Patterns of Inheritance'. Here you'll learn how to take a family history looking for dominant or recessive patterns of Mendelian inheritance. We also look at sex-linked inheritance (X or Y chromosome location of the gene in question), mosaicism and genomic imprinting.

Chapter 4 describes the Human Genome Project and the history of attempts to find out where on the human chromosome set a gene of interest (often disease-causing) actually resides. You'll meet some common terms such as linkage disequilibrium, which is carefully explained. The working example in this chapter is cystic fibrosis.

Chapter 5 discusses 'Multifactorial Inheritance'. Most 'quantitative traits' such as height, personality and intelligence are under the control of hundreds or thousands of alleles of small effect. The same is true of many diseases. So in this chapter we learn about heritability, additive and threshold models of multi-allele effects and that very latest thing: genome-wide association studies (GWAS) which are shedding light on .. almost everything.

Chapter 6 raises its gaze to the organisation of genes into chromosomes. Sadly, this is another level where errors can occur (e.g. chromosome 21 trisomy leading to Down Syndrome) and there are plenty of more subtle things which can go wrong (deletions, duplications, inversions, rings, translocations). Characteristic diseases and syndromes duly follow.

Chapter 7 looks at Population Genetics. We learn about the Hardy-Weinberg equation (very clear explanation) and how it is used to work out the carrier frequency of a recessive disease in various populations. The working example here is Sickle Cell Anaemia.

Chapter 8 focuses on Cancer Genetics. Cancer is a genetic disease, emerging from a cascade of errors in those genes which regulate cell development and division. We now have a causal narrative of the mechanisms behind many cancers, as this chapter explains in good detail.

Chapter 9 looks at chromosome translocation with specific application to Down Syndrome.

The remaining chapters (10-17) are shorter and look in detail at:
  • Molecular diagnosis of conditions based on genetic testing
  • Newborn screening (e.g. for PKU) 
  • Developmental genetics (CHARGE syndrome is the example) 
  • Carrier screening (Tay-Sachs in an Ashkenazi context is the example in this chapter)
  • Genetic risk assessment (companies like 23andMe are discussed in some detail)
  • Genetic testing for risks of cancer (BRCA1 and 2 is the example)
  • The genetics of drug response - Pharmacogenetics (example: malignant hyperthermia)
  • Emerging treatment for genetic disorders such as gene therapy.

This book was published in 2013 so it's pretty much up-to-date. If you're not a medical student with good recall, have Google/Wikipedia next to you as you read it: most terms are explained - and then you come to something like Epistasis!

Shirley Porter

My aunt, Shirley Porter, died in the early hours of this morning. I remember her as a very attractive and pleasant woman, married to my mother's brother Gordon who pre-deceased her by a number of years.

Shirley and Gordon Porter


Shirley Porter in the 1960s

Shirley with my mother, and (L to R) myself, Elaine and Adrian (early-sixties)
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Shirley Grace Porter (née Brown): b. 26th July 1935, d. 8th October 2014 aged 79.

Husband: Gordon Alexander Porter: b. 30th October 1925, d. April 30th 1990 (lung cancer) aged 65.

Update (Friday October 17th):

Clare and myself attended Shirley's funeral today at South Bristol Crematorium. There were 30 mourners, mostly her family. The presiding Minister noted that Shirley had trained as a shorthand typist and had worked at the firm John Hall & Sons in Bristol as a secretary and later PA. It was said that anyone she PAed for ended up as a Director, testifying to her competence and, I suppose, her shrewdness in choosing good bosses.

It was there that she met her husband-to-be Gordon Porter (my uncle) who was working as an electrician. They were married in March 1958.

Here are some pictures from today.

Our bouquet

The dedication

The author and his wife preparing to attend the funeral

Order of Service: cover - click to enlarge

Order of Service  - click to enlarge

Tuesday, October 07, 2014

The web of deceit

Did I mention that I'm surrounded by electronic devices which do whatever they want and have minds of their own? Sick of living in their autistic machine-world, I can now preview an X-Lab development which will transform our lives.

Initially running on a chromecast-like device plugging into a USB slot, the new module will have speech capabilities ('you can converse with it') and will communicate with its attached device using CTP (Communication Things Protocol).

Version 1.0 will be painfully honest, as in this sample dialogue.
You (to Sky Box): "Why have you gone into automated standby?"

Module: "I'm doing a software upgrade."

You: "But my favourite programme's just about to come on, can't you delay?"

Module: "No."
This is clearly not going to go down too well.

Subsequent versions will model the user and simulate emotion.
You (to Sky Box): "Why have you gone into automated standby?"

Module: "I'm feeling terrible."

You: "But my favourite programme's just about to come on, can't you delay?"

Module: "You know, I would if I could but honestly, I'm so sick I'm about to faint. I will do the best I can when I feel better to search down your programme and record it for you."

(It won't of course).
Same useless outcome, but you feel guilty rather than incandescent.

Naturally, CTP is a crude protocol: the module doesn't really know what the attached device is actually doing, especially if it's malfunctioning. The X-lab module will spend most of its time justifying and lying to you, to overcome its own confusion.

Strange to think that biology addressed the self-same problem a hundred thousand years ago.

Monday, October 06, 2014

Idiocracy has already arrived

Tonight my Sky+ HD box decided to autonomously place itself on standby without any explanation. It then refused to allow itself to be turned back on. We switched over to Freeview and decided to google 'Sky TV outage'.

Then the router fell over depriving us of Internet access.

My brother phoned from my mother's house where he's been visiting. The Sky box there,  of ancient lineage, had decided to lose most of the terrestrial channels - after behaving itself for years. My mother's iPad won't download the ITV player app as her IOS version is so old it won't even auto-update while her laptop mysteriously lost Internet access - perhaps a problem with the Wifi link though it was hard to tell over the phone.

All this with a double episode of 'Coronation Street' imminent!

Apart from turning stuff off and then back on again the humble consumer is powerless in the face of these provocations. When did these smart-stupid machines take over our lives?

Update: at least at this end the Sky box appears to have undergone an unadvertised software upgrade and has come back to life, while Internet access has been opaquely restored. I have no news at present from my mother's.

Smart genes from stupid people?

Intelligence, as measured by IQ, is largely - but not completely - under genetic control. For example, this from Wikipedia:
"There are some family effects on the IQ of children, accounting for up to a quarter of the variance. However, adoption studies show that by adulthood adoptive siblings aren't more similar in IQ than strangers, while adult full siblings show an IQ correlation of 0.6.

"Conventional twin studies reinforce this pattern: monozygotic (identical) twins raised separately are highly similar in IQ (0.86), more so than dizygotic (fraternal) twins raised together (0.6) and much more than adoptive siblings (~0.0)."
This means that when you meet someone smart they're likely to have the benefit of a good set of genes (for IQ) and some lucky environmental input. Apart from basic stuff like good nutrition, lack of serious diseases and a non-traumatic upbringing, no-one is too clear what a 'lucky environment' actually is. However, only the genes-part makes it through to the next generation so without the luck the kids are likely (but not certain) to be a little less bright than their luckier parent.

Equally, someone a little bit dim is likely to have been dealt a poor hand in the genes-for-high-IQ department, but also to have had ill-luck environmentally speaking. Their kids will not inherit the bad luck, on average, and will therefore tend to be brighter.

This phenomenon is called regression towards the mean.

We can put some numbers behind all this, as Steve Hsu explains. Recall that IQ is conventionally standardised (for European Caucasians) as mean = 100 and standard deviation (SD) = 15 IQ points.
"Assuming parental midpoint of n SD above the population average, the kids' IQ will be normally distributed about a mean which is around +0.6n with residual SD of about 12 points. (The .6 could actually be anywhere in the range (.5, .7), but the SD doesn't vary much from choice of empirical inputs.)

"So, e.g., for n = 4 (parental midpoint of 4 x 15 = 160 -- very smart parents!), the mean for the kids would be 100 + 0.6 x 4 x 15 = 136 with only a few percent chance of any kid to surpass 160 (requires +2 SD fluctuation). For n = 3 (parental midpoint of 145) the mean for the kids would be 127 and the probability of exceeding 145 less than 10 percent.

"No wonder so many physicist's kids end up as doctors and lawyers. Regression indeed! ;-)"
This gives us a chance to revisit Cinderella.

Prince Charming is, frankly, not the sharpest tool in the box. More a lover than a fighter, his IQ is around 105 - below average for someone of his royal socio-economic status.

Cinders, naturally, lives amongst the dregs of society. She is part of half the population with below average IQ. In fact, when she was tested, her IQ was only 90. However, she is known as the pretty-but-dim one of the family so there is hope that she just got unlucky: perhaps those evil step-sisters deprived her of essential nutrients as a child.

So, prince and poor-girl get together. What can we say about the likely IQ of their kids?

Their parental midpoint IQ is (105 + 90)/2 = 97.5 which is 2.5/15 = 1/6 of a standard deviation below population average: this is the 'n' in the formula above. The mean IQ for their kids is therefore predicted to be 100 - 0.6 x (1/6) x 15 = 98.5 with a standard deviation of 12 IQ points. There is a 45% chance that a child of this fairytale marriage will have an IQ of 100+.

Reasonable odds of not being a dreg .. even a royal dreg!

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Table of IQ requirements for various jobs (not including royalty).


Sunday, October 05, 2014

Tyntesfield

Arts and crafts at Tyntesfield (National Trust) today.

A tower of chairs: Nov 5th beckons

The cider press is a bit of a pull

The author fronting Tyntesfield House

The band does a popular medley of Beatle songs
This following a family get together at The Fox.

The intelligence sweet spot


In an otherwise NA-specific article Steve Sailer makes the following observation about advertisers, that they prefer those:
"who have been to college, because they have more money, but who are not all that bright because (cf. The Bell Curve) there aren’t many people out at the right edge of the bell curve. The spending sweetspot is a little to the right of the median IQ."
This has the ring of truth about it, also accounting for the general dumbness of much TV and the broader media. And Mr Sailer has more: there is a class of irritating intellectual emanating from this part of the distribution which Sailer amusingly labels the Lumpenintelligentsia, characterised by 'self-absorption ,..., wounded amour propre, dimwittedness, and general cluelessness'. You will have heard their opinions in the broadcast media (Radio 4 in the UK is a particular offender) and TV news and current affairs programmes; also in the opinion pages of way too many newspapers.

Further on the subject of the immediate right-hand side of the IQ bell curve, Steve Hsu notes the results of an impressive Swedish Study.
"Match Made at Birth? What Traits of a Million Swedes Tell Us about CEOs

"Abstract: This paper analyzes the role three personal traits — cognitive and non-cognitive ability, and height — play in the market for CEOs. We merge data on the traits of more than one million Swedish males, measured at age 18 in a mandatory military enlistment test, with comprehensive data on their income, education, profession, and service as a CEO of any Swedish company."
Since the standard deviation of the IQ distribution is set at 15 points, the study tells us that the CEOs of large (Swedish) companies have IQs averaging around 115. This is not that high by academic standards. How puzzled should we be?

Steve Hsu observes: (bold = my emphasis)
"Performance beyond a certain level in the vast majority of fields (and business is certainly one of them) is principally a function of having no cognitive and personal qualities which fall below a (high, but not insanely high) hygene threshold -- and then multiplied by determination, of course.

"Conscientiousness, in fact, is the best single stable predictor of job success for complex jobs (well established in personality psychometrics).

"Very high intelligence actually negatively correlates with career success (Kotter), probably because smart people enjoy solving problems, rather than making money selling things -- which outside of quant trading, show business and sport is really the only way of being really successful.

"There are some extremely intelligent people in business (by which I mean high IQ, not just wise or experienced), but you tend to find them in the corners of the business landscape with the richest intellectual pastures: some areas of law, venture capital, some cutting edge technology fields."
Yep, seen this in telecoms. The toilers at the base of the organisation think the senior execs must be incredibly smart. Those I've seen mostly not so much.

Saturday, October 04, 2014

'Political Order and Political Decay' by Francis Fukuyama

The second volume of Francis Fukuyama's magnum opus, 'Political Order and Political Decay', is 548 pages and I therefore subcontract its review to the Wall Street Journal (I reviewed the first volume here).
" ... to the extent that he has an overarching narrative, it is this: Human beings are possessed of certain biologically rooted imperatives to favor kith and kin over others—what he calls patrimonialism. Successful political order entails the establishment of institutions that check and redirect these impulses in productive and publicly beneficial ways.

"Since the Industrial Revolution and the spread of market capitalism (i.e., globalization), the institutions that most successfully accomplish this feat have been the modern state coupled with the rule of law and some degree of democratic accountability. What we call corruption is really the imperfect realization (or absence) of such institutions.

"Political decay, to which the final section of this work is devoted, is the condition where public institutions, grown sclerotic over time, prove increasingly unable to manage the natural reassertion of patrimonial impulses."
In a close-to-home example of political decay, Dr Fukuyama sees the 'checks and balances' system in the US as having been latterly captured by special interest groups and lobbyists, constituting a 'vetocracy'. He is not an optimist as regards future governance prospects there. Interestingly, he's more a fan of the UK's 'elective dictatorship' which, he believes, gets things done and is much more resistant to special interest group capture.

'Political Order and Political Decay' is crammed full of insights and allows the re-framing of many contemporary hot-spots such as Ukraine and the Middle-East. The question of transition to advanced development status as in 'getting to Denmark' is a central preoccupation of the book. But talking in the abstract about institutions and social capital doesn't quite hack it given the biologically rooted diversity of both humans and human groups across the planet as regards pro-social and cognitive competences. Fukuyama appears somewhat aware of the literature on the subject but this is one hot potato he's (perhaps understandably) not prepared to engage with, to the detriment of his conclusions. Perhaps not everywhere, sadly, has an unaided route to 'Denmark'.