Archive for Human Genetics

Haldane’s short autobiography

Posted in Books, pictures, Statistics with tags , , , , , , , , , , , , , , , , , , , , , , , , on October 15, 2020 by xi'an

“I was born at Oxford, England, in 1892.  My father was Prof. J.S. Haldane, the physiologist.  I was educated at Eton and New College, Oxford.  I learned much of my science by apprenticeship, assisting my father from the age of eight onwards, and my university degree is in for classics, not science.  I was in a British infantry battalion from 1914 to 1919, and was twice wounded.  I began scientific research in 1910, and became a Fellow of New College, Oxford, in 1919.  I was at Cambridge from 1922-1932 as Reader in Biochemistry, and have been a professor in London University since 1933.  I was visiting professor in the University of Berkeley, Cal., in 1932.  In the same year I was elected a Fellow of the Royal Society of London.

My scientific work has been varied.  In the field of human physiology I am best known for my work on the effects of taking large amounts of ammonium chloride and other salts.  This has had some application in treating lead and radium poisoning.  In the field of genetics I was the first to discover linkage in mammals, to map a human chromosome, and (with Penrose) to measure the mutation rate of a human gene.  I have also made some minor discoveries in mathematics.

Whilst I may have been a credit to my universities, I have been a trial in other ways.  I was dismissed from Cambridge University in 1926 in connexion with a divorce case, but regained my post on appeal to a higher tribunal, which found that the university authorities had decided to dismiss me without hearing my case.  At present I have refused to evacuate University College, London, and, with two assistants am its sole academic occupant.  I am carrying on research there under difficulties.

Besides strictly scientific books I have written a number of popular works including a book of children’s stories.  I consider that a scientist, if he can do so, should help to render science intelligible to ordinary people, and have done my best to popularize it.

Till 1933 I tried to keep out of politics, but the support given by the British Government to Hitler and Mussolini forced me to enter the political field.  In 1936-1938 I spent three months in Republican Spain, first as an adviser on gas protection, and then as an observer of air raid precautions.  I was in the front line during fighting, and in several air raids behind the line.  Since then I have tried, with complete lack of success, to induce the British Government to adopt air raid protection measures which had proved their efficacy in Spain.

Mr. Chamberlain’s policy, and the recent developments in physics and biology, combined to convince me of the truth of the Marxist philosophy.  Though I am a member of no political party, I have of late years supported the communist party on a number of issues.  At present I am engaged on research in genetics, & research intended to save the lives of members of the British armed forces, and writing and public speaking designed to prevent the spreading of the present war, and if possible to bring about peace.  I am a fairly competent public speaker.

It will be seen that my life has been a full one.  I have been married for 14 years, measure 73 inches, weigh 245 pounds, and enjoy swimming and mountain walking.  I am bald and blue-eyed, a moderate drinker and a heavy smoker. I can read 11 languages and make public speeches in three, but am unmusical.”

J.B.S. Haldane, circa 1940

human resource [Nature cover]

Posted in Statistics with tags , , , , , , , , , , on August 7, 2020 by xi'an

Nature tidbits [the Bayesian brain]

Posted in Statistics with tags , , , , , , , , , , , , , , on March 8, 2020 by xi'an

In the latest Nature issue, a long cover of Asimov’s contributions to science and rationality. And a five page article on the dopamine reward in the brain seen as a probability distribution, seen as distributional reinforcement learning by researchers from DeepMind, UCL, and Harvard. Going as far as “testing” for this theory with a p-value of 0.008..! Which could be as well a signal of variability between neurons to dopamine rewards (with a p-value of 10⁻¹⁴, whatever that means). Another article about deep learning about protein (3D) structure prediction. And another one about learning neural networks via specially designed devices called memristors. And yet another one on West Africa population genetics based on four individuals from the Stone to Metal age (8000 and 3000 years ago), SNPs, PCA, and admixtures. With no ABC mentioned (I no longer have access to the journal, having missed renewal time for my subscription!). And the literal plague of a locust invasion in Eastern Africa. Making me wonder anew as to why proteins could not be recovered from the swarms of locust to partly compensate for the damages. (Locusts eat their bodyweight in food every day.) And the latest news from NeurIPS about diversity and inclusion. And ethics, as in checking for responsibility and societal consequences of research papers. Reviewing the maths of a submitted paper or the reproducibility of an experiment is already challenging at times, but evaluating the biases in massive proprietary datasets or the long-term societal impact of a classification algorithm may prove beyond the realistic.

Darwin’s radio [book review]

Posted in Books, Kids, pictures, University life with tags , , , , , , , , , , , , , , , , on September 10, 2016 by xi'an

When in Sacramento two weeks ago I came across the Beers Books Center bookstore, with a large collection of used and (nearly) new cheap books and among other books I bought Greg Bear’s Darwin Radio. I had (rather) enjoyed another book of his’, Hull Zero Three, not to mention one of his first books, Blood Music, I read in the mid 1980’s, and the premises of this novel sounded promising, not mentioning the Nebula award. The theme is of a major biological threat, apparently due to a new virus, and of the scientific unraveling of what the threat really means. (Spoilers alert!) In that respect it sounds rather similar to the (great) Crichton‘s The Andromeda Strain, which is actually mentioned by some characters in this book. As is Ebola, as a sort of contrapoint (since Ebola is a deadly virus, although the epidemic in Western Africa now seems to have vanished). The biological concept exploited here is dormant DNA in non-coding parts of the genome that periodically get awaken and induce massive steps in the evolution. So massive that carriers of those mutations are killed by locals. Until the day it happens in an all-connected World and the mutation can no longer be stopped. The concept is compelling if not completely convincing of course, while the outcome of a new human race, which is to Homo Sapiens what Homo Sapiens was to Neanderthal, is rather disappointing. (How could it be otherwise?!) But I did appreciate the postulate of a massive and immediate change in the genome, even though the details were disputable and the dismissal of Dawkins‘ perspective poorly defended. From a stylistic perspective, the style is at time heavy, while there are too many chance occurrences, like the main character happening to be in Georgia for a business deal (spoilers, spoilers!) at the times of the opening of collective graves, or the second main character coming upon a couple of Neanderthal mummies with a Sapiens baby, or yet this pair of main characters falling in love and delivering a live mutant baby-girl. But I enjoyed reading it between San Francisco and Melbourne, with a few hours of lost sleep and work. It is a page turner, no doubt! I also like the political undercurrents, from riots to emergency measures, to an effective dictatorship controlling pregnancies and detaining newborns and their mothers.

One important thread in the book deals with anthropology digs getting against Native claims to corpses and general opposition to such digs. This reminded me of a very recent article in Nature where a local Indian tribe had claimed rights to several thousand year old skeletons, whose DNA was then showed to be more related with far away groups than the claimants. But where the tribe was still granted the last word, in a rather worrying jurisprudence.

the ultimate argument

Posted in Statistics with tags , , , on February 6, 2015 by xi'an

In a tribune published on February 4 in Le Monde [under the vote-fishing argument that the National Front is not a threat for democracy], the former minister [and convicted member of fascist groups in the 1960’s] Gérard Longuet wrote this unforgettable sentence about the former and current heads of the National Front:

“Sa fille, elle, a compris, et d’ailleurs pourquoi serait-elle son père, alors que deux ou trois générations les séparent.”

[Translation:  His daughter has for her part well understood and in any case why should she be her father when there are two or three generations between them.]