Monday, September 29, 2014

The Hardy-Weinberg equation

This is either very easy, or very hard. The algebra is easy but the concepts underlying it are a bit slippery. Note that frequency and probability are being used interchangeably here.

Let's start observationally, with an example. Suppose there is a population of 100 individuals: a few are short, most are medium and some are tall. And suppose (contrary to fact) that there is just one gene which controls height, which comes in two alleles, A and a.

The genotype AA is short, Aa is medium and aa is tall.

For the 100 individuals, we'll say that:

  • 16 are short (AA)
  • 48 are medium (Aa)
  • 36 are tall (aa).

So for a random choice of individual in this example:

  • probability (short-genotype) = 0.16 .. call it x
  • probability (medium-genotype) = 0.48 .. call it y
  • probability (tall-genotype) = 0.36 .. call it z

Now we ask the question: how many A alleles are there, and how many a? The answer is obvious:

  • For the A alleles we have: 16 x 2 + 48 = 80
  • for the a alleles we have: 48 + 2 x 36 = 120

Total 200 alleles.

  • frequency of A alleles ( call it p) is 80/200 = 0.4
  • frequency of a alleles (call it q) is 120/200 = 0.6.

What's the connection between between the allele frequencies (p, q) and the genotype frequencies (x, y, z)? This is the famous Hardy-Weinberg equation:

x = p2, y = 2pq, z = q2

p = x + y/2, q = y/2 + z.

Note that the underlying mechanism of a trait determined by two alleles (with frequencies p, q) severely restricts the possible values of x, y, z. It would not have been possible, for example, to have observed these population proportions:

  • 10 are short (AA)
  • 60 are medium (Aa)
  • 30 are tall (aa)

as no consistent values of p and q can generate this outcome. That is, the constraint:

  •  x + y + z = 1 

is considerably weaker than x = p2y = 2pqz = q2. (We're dealing with a special case of a binomial distribution).

The interesting thing about the Hardy-Weinberg equation is that for a population under no selection and with random mating, these proportions are invariant through the generations.

Not so hard once you figure out what the problem being addressed actually is (normally that you're starting with a collection of phenotypes, identifying them with corresponding genotypes and then trying to work out the allele frequency - as in disease management). For more on this see my next post: Using the Hardy-Weinberg equation.

The full story is here (Wikipedia).

Sunday, September 28, 2014

The Blackberry Hunters

Stockhill wood this afternoon to collect blackberries: they are in very short supply. The dry September has led to stunted bushes; what fruits have emerged are small and often covered with fungus ... and spiders and snails.

Sad state of the bushes behind Clare
We'll still get a crumble this evening.

Just add crumble ...


From the current (Catholic) parish newsletter:
"In Luc Besson’s new movie, Lucy, Scarlett Johansson plays a young lady who inadvertently receives a very high dose of a new drug, which unlocks the untapped potential of her brain. As a result her powers become superhuman and knowledge is soaked up in her like a sponge.

"The pursuit of knowledge is a good thing per se. However, it’s what we do with this knowledge which really counts. As Christians, seeking to serve as missionary disciples, knowing Jesus and desiring to enter his mind is what is most important."
Here's a picture of Scarlett Johansson.

Scarlett Johansson in Lucy

Such good advice: my copy of the DVD will be dropping through the letterbox in January.

Meanwhile I feel I understand almost too well* the case of Tory minister Brooks Newmark, who just resigned after a sexual entrapment exercise by the Sunday Mirror. A combination of a male reporter posing as a young, female, activist hottie plus WhatsApp proved his undoing.

More symptomatic is the account of how he "negotiated" with the Syrian leader Assad.
"Newmark first met Syrian president Bashar al-Assad in 2006 and continued "regular" one-on-one meetings until 2011, the start of the civil war"
Picture it. You're smart and photogenic, you've made a pile of money and have expensive houses and property. You're a successful and senior politician. Why shouldn't you be a player? Solve the Syria crisis where your betters and world diplomacy have failed?

The vanity of the B-lister, totally out of his depth and used by the real operators (reminds me of a film I just saw). Why wouldn't he be the exception to the iron law that hot young women do not find men the wrong side of fifty attractive (and the photos he sent - let's not even think of going there).

* Writing a blog - the epitome of vanity - is what I had in mind.

Friday, September 26, 2014

"A Most Wanted Man" (film)

Philip Seymour Hoffman waiting to turn someone

From The Telegraph.

"Philip Seymour Hoffman isn’t playing the title character in A Most Wanted Man, but there’s absolutely no doubt who we most want to see,..

"Like so many other Hoffman characters, his Günther Bachmann is a stifled, almost ruinously intelligent and lonely being. He hulks, he shuffles, he measures his words – delivered in a clipped, curious Teutonic accent you believe belongs to one man alone – with a waiting-game precision. Even by the actor’s remarkable standards, Hoffman’s wheezing authority is lavishly mesmerising in this: it’s legitimately one of his three or four greatest performances, and as you start to deduce how great it is, you feel his loss keenly and afresh.

"Lived-in fatigue was the baseline for almost all Hoffman’s best work, and you won’t find many jobs more fatigue-inducing than that of Bachmann, a German spymaster involved in the constant finessing of anti-terror operations without causing any diplomatic meltdowns. As the film starts, he’s licking his wounds in Hamburg, after a mission in Beirut went disastrously wrong – “My network was blown,” he explains to an American attaché called Martha (Robin Wright), but a veil is drawn over the deaths entailed.

"The film is based on John le Carré’s 2008 thriller of the same name, but its personnel have been somewhat reshuffled. You wouldn't necessarily have picked out Bachmann as the prime mover in that story, but Anton Corbijn and his screenwriter, Andrew Bovell, have re-orbited it around him. It becomes a complicated chess game in which Bachmann is the white king, moving stealthily, square by square, while other characters get flashier sallies or long-range bits of business. He’s not always well-guarded, and come the tight and tense end-game, he’s having to watch his back.


"The terrific young Russian actor Grigoriy Dobrygin (How I Ended This Summer) plays Issa Karpov, a Chechen refugee who has entered Hamburg illegally, and is suspected by the Russian authorities of being a dangerous terrorist.

"Bachmann and his team decide they can use him, in a sting operation of which he’ll be entirely unaware, if they can first gain the trust of his immigration lawyer (Rachel McAdams). A fortune is Issa’s by rights, tied up in the inheritance his father entrusted to an international private bank, under the beaky stewardship of Willem Dafoe. But it’s what he does with these funds next that the spooks are gambling on.

"Compared with the spider-web sprawl of machinations in Tinker, Tailor, Soldier, Spy, the story here is contained, pointed and topically very specific: it’s about degrees of allegiance to a notorious cause, and whether having half a foot in the enemy’s camp is grounds to have the whole leg amputated. Le Carré’s novel obliquely criticised the American government’s policy of extraordinary rendition, advancing the softly-softly efforts of these German operatives as simultaneously more humane and more strategically canny. It’s Bachmann who has to explain the pointlessness of biting off one small hydra-head, rather than exploiting the compromised ideologies of Islamist sympathisers to dig right into the extremist mother lode."
And it ends with a bang.

Good film. Over our fish 'n' chips in the local Wetherspoon we debated strategies: operational utility vs. moral compromise in a world where absolutely no-one's hands are clean.

Wednesday, September 24, 2014

"Still Alice" by Lisa Genova

Here's the Amazon description.
"Still Alice is a compelling debut novel about a 50-year-old woman's sudden descent into early onset Alzheimer's disease, written by first-time author Lisa Genova, who holds a Ph. D in neuroscience from Harvard University.

"Alice Howland, happily married with three grown children and a house on the Cape, is a celebrated Harvard professor at the height of her career when she notices a forgetfulness creeping into her life. As confusion starts to cloud her thinking and her memory begins to fail her, she receives a devastating diagnosis: early onset Alzheimer's disease. Fiercely independent, Alice struggles to maintain her lifestyle and live in the moment, even as her sense of self is being stripped away. In turns heartbreaking, inspiring and terrifying, Still Alice captures in remarkable detail what's it's like to literally lose your mind..."

Midway through reading this novel to Clare, I got to the bit where Alice gets a genetic test done for early-onset (or familial) Alzheimer's. The mutated genes in question are APP, PS1 and PS2;
"Familial Alzheimer disease is caused by a mutation in one of at least 3 genes: presenilin 1, presenilin 2 and amyloid precursor protein (APP). Other gene mutations are in study."
Naturally, I scampered across to my 23andMe/Promethease health results to check out my genome. Now, 23andMe don't screen for SNPs on those genes (I can see why!) but they do look at a late-onset Alzheimer genotype - it's the ε4 variant of the APOE gene.
"Although 40-65% of AD patients have at least one copy of the ε4 allele, ApoE4 is not a determinant of the disease - at least a third of patients with AD are ApoE4 negative and some ApoE4 homozygotes never develop the disease. Yet those with two ε4 alleles have up to 20 times the risk of developing AD."
I don't have it.


Note: how do two SNPs determine three APOE variants? (From 23andMe).

Variant:  rs429358  + rs7412 (these are the two SNPs within the APOE gene)

ε2 = T + T

ε3 = T + C

ε4 = C + C

I'm ε3/ε3 - on the  chromosome 19 pair (TT + CC). It's surprising how blasé one can be about all this once it's clear that you don't have the 'bad' allele ...

Saturday, September 20, 2014

Robert Conquest’s Three Laws of Politics

From here and here.
  1. Everyone is conservative about what he knows best.
  2. Any organization not explicitly right-wing sooner or later becomes left-wing.
  3. The simplest way to explain the behavior of any bureaucratic organization is to assume that it is controlled by a cabal of its enemies.
Why might these be true?
  1. Head over heart where it's important.
  2. Eventual capture by the many idealists with a retributive agenda.
  3. Regulatory capture.
Good though, aren't they.

Digit ratios

Dr James Thompson writes about digit ratios and feminists, a recent news story.

The statistic in question is the length of your second digit (index finger) divided by the length of your fourth digit (ring finger). This is normally less than one, indicating you have a longer ring finger (digit 4). Here are scans of the author's right hand - palm up - and his wife's, with all relevant data points indicated.

The idea is this:
"It has been suggested by some scientists that the ratio of two digits in particular, the 2nd (index finger) and 4th (ring finger), is affected by exposure to androgens e.g. testosterone while in the uterus ..."
A low ratio (e.g. 0.94) suggests you are more likely to be high in testosterone, male and black. A high ratio (e.g. 0.98) suggests lower testosterone levels, female and caucasian or east asian. See here for details.

The article Thompson discusses looks, however, at how all this might illuminate the paradox of feminism:
"The feminist movement purports to improve conditions for women, and yet only a minority of women in modern societies self-identify as feminists. This is known as the feminist paradox."
Why might this be?
"Evolutionary psychology observes that the basic pattern of psychological differences between the sexes can be explained by their having essentially different innate adaptations associated with, most importantly, women investing considerably more resources into offspring through pregnancy and breast-feeding (e.g., Buss, 2012). Males are more aggressive and risk-taking on average, because these traits have paid off historically in terms of increased fitness, given that male-male aggression and risk-taking in the pursuit of resource acquisition have led to more offspring. This would thus explain why males tend to dominate professions where these traits are necessary for success, such as in the military, business, politics and even crime, where competition is high. Females are on average more sociable and empathic than males, because caring for offspring and negotiating social relations that promote their survival until they reach reproductive age ensured that the mother’s genes live on. Hence women dominate professions where these traits are maximally valued, such as teaching, social work, and in human and veterinary medicine (Lippa, 2010). ...

"Another possible explanation of why feminism represents a minority position amongst women is therefore that the activists who shape feminist attitudes and beliefs are themselves generally more physiologically and psychologically masculinized than is typical for women (Wilson, 2010). This might for example explain their belief in sex-role interchangeability, as they may perceive the behaviors and interests of sex-typical women as incomprehensible and at variance with their own more masculinized preferences in terms of child-rearing and status-seeking. This might then lead them to infer that women in general have been manipulated to become different from themselves by external forces, as embodied by notions of social constructions or gender systems ..."
And so they did the 2D: 4D finger length ratio test at a feminist activists' conference. Their account is quite amusing.
"We therefore recruited our sample directly from the operational definition, that is, attendees at a feminist conference in Sweden. This public one-day event was advertised through posters, flyers, and social internet media, and featured some 20 talks and lectures in several parallel sessions, presented by political and other interest organizations. In the conference hall we set up a table and a sign saying (translated from Swedish) “Answer a few questions and image your hands in exchange for fruit or candy. Your participation is anonymous.” We surmised that any mention of feminism, and the possible connection between feminism and biomarkers in particular, would have deterred attendees from contributing. In order to maximize participation, therefore, we did not ask them if they self-defined as feminists, and did not disclose the purpose of the study.

"In total, 35 attendees participated in data collection over the course of the whole conference day, mostly when moving between rooms, in exchange for items of fruit or candy. To ensure anonymity no biographical information was collected, and sex and age were assessed visually (20–45 years). The total number of attendants was estimated at ∼100 over the day and the female-to-male ratio to ∼2/3. Twenty-five of the respondents were female and hence were eligible for inclusion in the analyses, which means that our sample included ∼35% of the female attendees."
And after all the fruit and candy had been distributed, what were the results? Their diagram below shows: the reference female population, the reference male population and the sample from the feminist conference. The mean 2D:4D figures, read off the chart are as follows: mean female = 0.992, mean male = 0.969, mean feminist = 0.95. Yep, the feminist women scored more masculine than the average Swedish man. This may explain something about Sweden.

The x-axis increment is 0.0135

It's hard to obtain large population studies which are tightly controlled for ethnicity, at least via Google, so I don't know where Clare and myself lie on the British/Caucasian spectrum. However, lower ratios predispose males at least to higher risks of prostate cancer and autism spectrum disorders, as you can see from this table. I think this is compatible with what my 23andMe results already suggested.

Friday, September 19, 2014

Under the Skin (film)

We just watched the DVD of "Under the Skin" featuring Scarlett Johansson as Isserley, the alien which predates Scottish hitchhikers. (I struggle with a link to yesterday's referendum.)

Scarlett Johansson as 'the alien'

Michel Faber's book is really excellent, expertly charting Isserley's psychological transition from resentful corporate hunter-gatherer to terminally-rebellious renegade. The film (apparently due to lack of funds) dispenses with the meat-processing backroom cast and the posh-boy from corporate HQ, replacing plot and setting with dreamy Scottish imagery and Ms Johansson.

The Director and Producer wanted this to come across as art-house, but cinematic staging can't substitute for plot, motive, dialogue and character development. I won't say we wasted 104 minutes of our lives, but the longueurs were exasperating and the overall treatment just didn't work.

Read the book instead.

Be as stupid as possible

"All animals are under stringent selection pressure to be as stupid as they can get away with." (Echopraxia, p. 23).

Obviously - intelligence costs.

Echopraxia (and prequel Blindsight)  present ordinary, baseline humans dealing with entities far smarter than they are. It's a hard call for the author: are his super-intelligent beings smarter than the author himself, his readers? How then can they possibly be imagined?

Try another question first. What possible utility could super-intelligence have in evolutionary terms? After all houseflies, not known as paragons of smartness, seem to have had no problem colonising the planet. The answer has been known for a long time: in a predictable environment (aka ecological niche) the organism can get away with hard-wired reflexes - instincts - and that's the way to go. Intelligence is the way animals deal with problem-solving in variable, somewhat unpredictable environments, often when they are social creatures and have to compete with equally-complex and hard-to-fathom conspecifics.

Still, we are where we are and there's not much sign of super-intelligence in the myriad species inhabiting this globe. So what are the fictional super-smarts actually doing?

In Blindsight/Echopraxia they are capable of maintaining and manipulating multiple highly-abstract models applied to extrapolating from the current situation. They understand what they perceive at a much deeper level and can predict and direct consequences far better than we can. This assumes of course that these deep levels of abstraction are actually relevant: a quantum physicist understand the dynamics of the world far more profoundly than any lay person but in everyday life it makes no difference - and even gets in the way.

To be super-intelligent in a way which pays off you have to be in a situation where complex phenomena are directly causally present, and you must possess super-senses and super-tools to act effectively on your superior understanding. In Echopraxia for example, most of the super-smarts are able to perceive and affect human brain states directly, and manipulate effective theories of human brain functioning in real-time. No wonder they run rings round us. They have a similar relationship to advanced technologies, which makes them pretty effective in dealing with power and transportation platforms and weapon systems - always useful in an SF novel!

The moral is that being as stupid as possible (but not stupider) is the right answer - but the ratchet of that minimal level keeps cranking up, as science and technology complexify our environment.

So how does Peter Watts convey to us, his readers, the super-intelligence of his protagonists? By making his stories intricate puzzles where we're never quite sure who's doing what to whom, and why. After the novel is finished, you reflect, try to make some sense out of the hints, the apparently purposeless or perverse actions. And then it starts to come together: being slow-witted is sometimes homologous to cranking down the clock speed of the very smart.

Thursday, September 18, 2014

No, NO, NO! Yes, YES, YES!

They both wanted a ‘Yes’ vote. She was a Celtic romantic, starry-eyed for the noble Caledonians, advancing to their own drumbeat, building their own future. He was a cool realist, anticipating Schadenfreude as the Scots finally ran into the car-crash of their statist-socialist utopia.

They snuck downstairs at 4 am, holding hands on the couch to watch the BBC. More in hope than expectation it has to be said: they had seen the final polls. Results dribbled in: the Highlanders, more distrustful of Edinburgh than of London, were plumping for ‘No’; as dawn approached, the socialist masses huddled in the tenements of Glasgow were redressing the balance towards ‘Yes’.

Alas, it was not to be: a fifth column of public sector jobs and MOD contracts had sucked the vitals of Nationalist support. The disastrous result began to assemble itself on screen.

First light caressed the blinds. “Make the Saltire,” he commanded, pressing her onto the couch. Their act of union formed, grew, overwhelmed her. She barely heard the announcer, reviewing final returns from the Highlands, the Centre and the Scottish Borders:  “It looks like ‘No, No, No’.”

Her only possible response ... her cry rang out:

“Yes, YES, YES!”

Wednesday, September 17, 2014

Tree alert! Incursion detected!

How do I look?

I would say the tree has no chance ..

"Biological" science-fiction

I spent the morning learning about mitosis, meiosis and recombination from YouTube: absorbing the differences between chromatids and chromatin, and figuring out tetrads.

I have a longer-term mission to get my head around genetics, and specifically population genetics, not least to interpret my own genome in its historical context, as these things gradually unveil. However, a proximate driver was reading Echopraxia by Peter Watts.

I was rather taken by the first installment of Watts' alien-contact saga, Blindsight. We're familiar with the exciting extrapolations of the physics/engineering-oriented community: Clarke, Asimov and Heinlein through Greg Bear (Eon, Eternity) and Greg Egan (Quarantine, etc etc); quantum mechanics, relativity, cosmology interlaced with artificial intelligence. But Peter Watts is a biologist and his extrapolation-settings include resurrection of extinct species, brain-re-engineering via retroviruses, biohacked-plagues, genetic enhancement and machine-human hybrids.

I'm quite excited by this future!

Watts has a short linking text - almost a story - to get us to Echopraxia, which was good. So far I'm about half way through the novel .. but disappointment is fluttering just under my consciousness. It's like Watts assembled all the components (he particularly likes super-intelligent Hive Minds) but somehow the engine is misfiring. All that authorial-energy searching for a plot worthy of it!

That's it for now; let me read on - it may all come together.

Update: Finished. Rating upgraded as I get it now. Not a 'there and back again' chase saga as I first surmised, rather an exploration of transcendence and evolutionary replacement of us baseline humans. Wow!

I'd star it (**, ****). Two stars if you're not interested in Watts's preoccupations (intelligence, consciousness, the future of both in the universe); four stars if, like me, you are.

Saturday, September 13, 2014

Can martial artists actually fight?

Tricia Sullivan - SF author and fighter

Tricia Sullivan thinks not.
"Most people think of martial arts and fighting as being more or less synonymous. I see them as a Venn diagram of two sets that overlap by a tiny margin. This is because most martial artists don't fight and their training isn't directly based on what happens in a fight.

There are reasons for this. The problem of training for a fight is a tricky one. If an instructor puts students in an actual fight (as opposed to highly controlled drills with restricted moves), they might get seriously hurt. But if instructors can't create an accurate representation of a fight in the gym, trainees will never really be tested. To make up for the lack of fighting, martial arts typically focus on displays of fake combat that illustrate the combative moves that have been passed down through history. They may have non-contact or light contact fighting, but this only tests your ability to touch the other person with the techniques you have been taught--not your ability to hurt them for real much less take a beating yourself.

Most people who study martial arts study a system. Whether the system is historical (like kung fu and karate) or modern (like Systema and Krav Maga) the techniques are taught formally, with ranks, with semi-compliant drilling between members of the same school, and with a heavy dose of hierarchy that keeps everybody in their place. With a few exceptions (Gracie Barra jiu-jitsu is one system that grades predominantly through hard competition) the idea of all-out fighting is a theoretical one, kept well in the background.

But fighting is chaotic. It's often unpredictable. It doesn't systemize well and it's difficult to pass on as a body of knowledge. What people don't realize is that no matter how effective the founder of a discipline may have been in his (or in the case of Wing Chun, her) day, unless the practices of that system involve rigorous testing in realistic fighting conditions against non-compliant opponents from outside your system, you can never really know whether you can make their moves work for you.

..."      (continue reading)
The many comments are pretty insightful too.

Tricia is a prolific science-fiction writer as well as martial artist, the reason she's writing this post on Charles Stross's blog. I haven't read any of her stuff and I guess her reviews are mixed although her novel "Dreaming in Smoke" won the 1999 Arthur C. Clarke award.

She has follow-up posts here and here.

Sadly for those who devote their lives to the perfection of Karate, Aikido or Taekwondo, skilled practitioners often come off very badly in fights with drunken idiots. Despite lack of formal training, being large, aggressive and fearless takes you a long way in a fight as does the use of improvised weapons such as bottles, drinking glasses and ash-trays. The sensei complains that his or her victorious opponent wasn't following the rules.

Tricia has most time for Judo and Wrestling - at least you really get to grapple with opponents - but even MMA has to outlaw those injurious or  lethal moves which are decisive in real fights.

One of the videos Tricia embedded in her second post was this one, of a real street fight in Turkey where a gang set upon a guy who happens to be a boxer ...

... looks like boxing really works.

Friday, September 12, 2014

Tech Support

We were in Stroud yesterday advising my first cousin once removed's (my mother's cousin's) husband on how to get on-net. I arrived loaded with large laptop, tablet, router, Kindle plus assorted extension cables and power bars - two bags worth of tech support. In the event Derrick was most impressed with my Galaxy S3 smartphone; Wendy has the most wonderful gardens front and rear of their house.

Here's a nice pic from when we were in the states back in 2002.

Alex and Clare at our house in Fairfax County, VA.

Wednesday, September 10, 2014

The vampire in serious science-fiction: Peter Watts

I think Adrian was with me when I explained that the story started with 65,536 iron meteors simultaneously hitting the atmosphere in grid alignment: a kind of global flashbulb. The plot-line is alien first-contact, although that hardly does "Blindsight" justice. It was when I mentioned that the leader of the expedition is a vampire that I lost him.

Peter Watts was (is?) a researcher, a frighteningly-erudite marine biologist, so these are not your stereotypical vampires of teen-fiction:
"Homo sapiens vampiris was a short-lived human subspecies which diverged from the ancestral line between 800,000 and 500,000 year BP. More gracile than either neandertal or sapiens, gross physical divergence from sapiens included slight elongation of canines, mandibles, and long bones in service of an increasingly predatory lifestyle. Due to the relatively brief lifespan of this lineage, these changes were not extensive and overlapped considerably with conspecific allometries; differences become diagnostically significant only at large sample sizes (N>130).

However, while virtually identical to modern humans in terms of gross physical morphology, vampiris was radically divergent from sapiens on the biochemical, neurological, and soft-tissue levels. The GI tract was foreshortened and secreted a distinct range of enzymes more suited to a carnivorous diet. Since cannibalism carries with it a high risk of prionic infection, the vampire immune system displayed great resistance to prion diseases, as well as to a variety of helminth and anasakid parasites.

Vampiris hearing and vision were superior to that of sapiens; vampire retinas were quadro-chromatic (containing four types of cones, compared to only three among baseline humans); the fourth cone type, common to nocturnal predators ranging from cats to snakes, was tuned to near-infrared. Vampire grey matter was "under-connected" compared to human norms due to a relative lack of interstitial white matter; this forced isolated cortical modules to become self-contained and hypereffective, leading to omni-savantic pattern-matching and analytical skills.

Virtually all of these adaptations are cascade effects that— while resulting from a variety of proximate causes— can ultimately be traced back to a paracentric inversion mutation on the Xq21.3 block of the X-chromosome. This resulted in functional changes to genes coding for protocadherins (proteins that play a critical role in brain and central nervous system development). While this provoked radical neurological and behavioral changes, significant physical changes were limited to soft tissue and microstructures that do not fossilise. This, coupled with extremely low numbers of vampire even at peak population levels (existing as they did at the tip of the trophic pyramid) explains their virtual absence from the fossil record.

Significant deleterious effects also resulted from this cascade. For example, vampires lost the ability to code for -Protocadherin Y, whose genes are found exclusively on the hominid Y chromosome. Unable to synthesise this vital protein themselves, vampires had to obtain it from their food. Human prey thus comprised an essential component of their diet, but a relatively slow-breeding one (a unique situation, since prey usually outproduce their predators by at least an order of magnitude). Normally this dynamic would be utterly unsustainable: vampires would predate humans to extinction, and then die off themselves for lack of essential nutrients.

Extended periods of lungfish-like dormancy (the so-called "undead" state)—and the consequent drastic reduction in vampire energetic needs— developed as a means of redressing this imbalance. To this end vampires produced elevated levels of endogenous Ala-(D) Leuenkephalin (a mammalian hibernation-inducing peptide) and dobutamine, which strengthens the heart muscle during periods on inactivity.

Another deleterious cascade effect was the so-called "Crucifix Glitch"— a cross-wiring of normally-distinct receptor arrays in the visual cortex, resulting in grand mal-like feedback seizures whenever the arrays processing vertical and horizontal stimuli fired simultaneously across a sufficiently large arc of the visual field. Since intersecting right angles are virtually nonexistent in nature, natural selection did not weed out the Glitch until H. sapiens sapiens developed Euclidean architecture; by then, the trait had become fixed across H. sapiens vampiris via genetic drift, and—suddenly denied access to its prey—the entire subspecies went extinct shortly after the dawn of recorded history."
Why does Watts need a highly-intelligent, empathy-free sociopath as a central character? Because his book is an extended examination of consciousness: what is it, what is it good for (or not) and how sure are we that it even widely exists? His alien protagonists are also not overly-burdened with consciousness but it doesn't seem to slow them down any. And bringing back your species' top predator - even on a leash - might not be the smartest option.

Watts' authorial persona is super-smart aggressive: he writes like Richard Morgan (Takeshi Kovacs) or Greg Cochran (the non-fictional West Hunter). The aggression seems to reflect the real-life person - a criminal record locks him out of the USA.

The case for the prosecution in "Blindsight" doesn't really work, as I think the author concedes. But what a case! You will understand the sheer depth and ingenuity of his thinking when you truly understand this passage.
"Now you get it," Sascha said.

I shook my head, trying to wrap it around that insane, impossible conclusion. "They're not even hostile." Not even capable of hostility. Just so profoundly alien that they couldn't help but treat human language itself as a form of combat.

How do you say We come in peace when the very words are an act of war?

"That's why they won't talk to us," I realized.
"Blindsight" is available for free on the author's website but as he has to eat, it might be better to buy it and the popular sequel Echopraxia on Amazon. Or both together, bound for Kindle as Firefall.

Tour of Britain - Bristol

We were at the Downs, Bristol today to watch the finish of this stage of the Tour of Britain.

Leading riders finishing --- exhausted

The author relaxing at coffee

A fan bangs those blow-up things

The Team Sky Bus awaits Bradley et al.

They're coming when you see the helicopter ..

The Peloton struggles along the Portway

The pros are just soooo fast!

Monday, September 08, 2014

Beheading as strategy and history

Perseus with the beheaded Medusa

A little overlong as always, War Nerd writes an essay about beheading, putting it into some kind of context.
"Well, here we are: Another American journalist beheaded by the Islamic State (IS). First it was James Foley, a wild-child freelancer, who was shown kneeling on the sand in an orange jumpsuit—a little visual revenge on Guantanamo dress code—while a Brit jihadi scolded America for daring to interfere with the Islamic State’s blitzkrieg-lite campaign to overrun Northern Iraq.

Foley’s beheading video was released on August 19, 2014. Two weeks later, IS killed a second American hostage, Steven Sotloff, using the same jihadi mise-en-scene: Sotloff in an orange jumpsuit, kneeling in the sand, while the same London-raised war tourist stands next to him with a short combat knife, gesturing with the blade while complaining again about the sheer unfairness of airstrikes taking out IS comrades.

..."    (continue reading).


We're off to collect blackberrys now (the fruit, that is).

Saturday, September 06, 2014

The Personal Genome Project

The Economist this week (in Technology Quarterly) covered - in a profile of Harvard's Prof. George Church - the global Personal Genome Project. Here is what Wikipedia has to say.
"The Personal Genome Project (PGP) is a long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personal genomics and personalized medicine. It was initiated by Harvard University's George M. Church and announced in 2005. As of August 1, 2014, more than 3,500 volunteers have joined the project. Volunteers are currently accepted if they are permanent residents of the US, Canada or the UK, and are able to submit tissue and/or genetic samples. The Project is planned to launch for Europe and in development for South America and Asia.

The project will publish the genotype (the full DNA sequence of all 46 chromosomes) of the volunteers, along with extensive information about their phenotype: medical records, various measurements, MRI images, etc. All data will be placed within the public domain and made available over the Internet so that researchers can test various hypotheses about the relationships among genotype, environment and phenotype.

An important part of the project will be the exploration of the resulting risks to the participants, such as possible discrimination by insurers and employers if the genome shows a predisposition for certain diseases.

The Harvard Medical School Institutional Review Board requested that the first set of volunteers include the principal investigator George Church and other diverse stakeholders in the scientific, medical, and social implications of personal genomes, because they are well positioned to give highly informed consent. As sequencing technology becomes cheaper, and the societal issues mentioned above are worked out, it is hoped that a large number of volunteers from all walks of life will participate. The long-term goal is that every person have access to his or her genotype to be used for personalized medical decisions.

The first ten volunteers are referred to as the "PGP-10". These volunteers are:

Misha Angrist, Duke Institute for Genome Sciences and Policy
Keith Batchelder, Genomic Healthcare Strategies
George M. Church, Harvard
Esther Dyson, EDventure Holdings
Rosalynn Gill-Garrison, Sciona
John Halamka, Harvard Medical School
Stan Lapidus, Helicos BioSciences
Kirk Maxey, Cayman Chemical
James Sherley, Boston stem cell researcher.
Steven Pinker, Harvard

In order to enroll each participant must pass a series of short online tests to ensure that they are providing informed consent. By the end of 2012, more than 2000 participants had enrolled in the Harvard PGP. As of August 1, 2014, more than 3,500 volunteers have joined the project."
I'm naturally very keen to get my entire genome sequenced and interpreted, and relaxed about the privacy issues. The PGP disclaimer document you have to sign is pretty lurid - here are some of the dangers you're warned against.
"(ii) Anyone with sufficient knowledge and resources could take your DNA sequence data and/or posted trait information and use that data, with or without changes, to:

(A) accurately or inaccurately reveal to you or a member of your family the possibility of a disease or other trait or propensity for a disease or other trait;

(B) claim statistical evidence, including with respect to your genetic predisposition to certain diseases or other traits, that could affect the ability of you and/or your family to obtain or maintain employment, insurance or financial services;

(C) claim relatedness to criminals or other notorious figures or groups on the part of you and/or your family;

(D) correctly or incorrectly associate you and/or your relatives with ongoing or unsolved criminal investigations on the basis of your publicly available genetic data; or

(E) make synthetic DNA and plant it at a crime scene, or otherwise use it to falsely identify or implicate you and/or your family."
and, a little later,
"More nefarious uses are also possible, if unlikely. DNA is commonly used to identify individuals in criminal investigations. Someone could plant samples of DNA, created from genome data or cell lines, to falsely implicate you in a crime. It’s currently science fiction -- but it’s possible that someone could use your DNA or cells for in vitro fertilization to create children without your knowledge or permission, or to create human clones."
In any event, my attempts to sign up were met with this response.

"Dear PGP-UK Volunteer,

The response to our recent request for enrolment has been fantastic and the first available 1,000 slots have now all been assigned. To help us establish a smooth running of the entire process, we have temporarily paused the enrolment to focus our limited resources on the first 1000 volunteers.

We will open the enrolment again as soon as we can. In the meantime, you can follow our progress on the PGP-UK web site ( and social media ( of the international PGP Community.

Thank you for your patience and continued support,

PGP-UK Team"
So I'll just have to wait my turn. Watch this space.

Friday, September 05, 2014

Weston super Mare

A visit yesterday to the Somerset Riviera ,,

Beryl Seel - we're to the right of the pier (at the paddling pool)

Clare fronting Steep Holm in the mist

The author in Weston's watery sunlight

For the briefest of moments we thought the promised 'nice day' was at hand; then the clouds reformed and a mist descended. We ate our picnic to a strutting, mewling audience of gulls on the concrete ledge and did not donate (recalling 'The Birds').