James Watson and the Insidiousness of Scientific Racism
▻https://www.wired.com/story/james-watson-and-scientific-racism
“How does it feel to be a black scientist who owes much to James Watson in general, and in my case, is linked to his specific pedigree?”
Les parts d’ombre du génome humain
▻https://www.lemonde.fr/sciences/article/2018/09/26/les-parts-d-ombre-du-genome-humain_5360331_1650684.html
Nos 21 000 gènes ne représentent que 2 % du génome humain. Mais le reste n’est pas que de l’ADN poubelle. Une grande partie semble vouée à contrôler l’expression de nos gènes.
Le dévoilement du génome humain est un chemin pavé de surprises. Un immense pas a été franchi en 1943 quand l’Américain Oswald Avery (1877-1955) a découvert que le support biologique de notre hérédité était l’ADN. En 1953, James Watson (né en 1928), Francis Crick (1916-2004) et la trop souvent oubliée Rosalind Franklin (1920-1958) révèlent sa structure – deux brins enroulés en une double hélice – qui lui permet d’être dédoublé, copié et transmis lors de la division cellulaire.
Reste à lire cet ADN pour y trouver les gènes supports de notre hérédité. Il est constitué d’une succession de molécules, les nucléotides (ou bases), elles-mêmes composées d’une partie fixe (un phosphate et un sucre) et d’une partie variable, une base azotée. Il en existe quatre notées A, C, G et T, qui s’assemblent deux par deux (A-T ou G-C) sur le double brin.
Décoder un gène revient à déterminer un enchaînement particulier de ces bases, une séquence capable d’être copiée en une molécule, l’ARN messager, afin de produire une protéine. Pour cela, il a fallu séquencer le génome. Comme le génome humain comprend 3,2 milliards de paires de base – dont 2,9 milliards sont lisibles – le travail s’annonçait titanesque. Il ira finalement assez vite. En 2003, 99 % du génome humain est séquencé. Surprise, il ne comporte qu’environ 20 000 gènes (le chiffre exact varie encore selon les auteurs) au lieu des 100 000 attendus, ce qui représente (seulement) 2 % de notre ADN.
Le reste ne serait-il que de l’ADN inutile, souvent qualifié de « poubelle » ? Ou bien les clés de notre complexité se trouveraient-elles dans la partie non codante ? En 2012, le programme de recherche international Encode penche en faveur de la seconde hypothèse. Il annonce que 80 % du génome humain est doté d’une fonction biochimique. « En fait, 50 % du génome humain est constitué de séquences amorphes répétitives, de pseudogènes inactifs, de transposons, qui a priori ne sont pas fonctionnels. Encode n’a donc étudié que 80 % de l’autre partie, donc c’est 40 % du génome humain qui aurait des fonctions actives », précise Stanislas Lyonnet, directeur de l’Institut Imagine. Reste à savoir lesquelles.
Séquences régulatrices
D’une part, à côté des gènes qui codent les protéines, des gènes régulateurs traduits en ARN non codant contrôlent l’expression des gènes. Il y en a pratiquement autant que des gènes codants : 1700 micro-ARN, 8000 mini et 12000 grands. « Mais l’utilité de ces ARN synthétisés fait encore débat. Il faut prouver qu’ils ont tous un rôle, ce qui n’est pas encore fait », souligne le biologiste et historien Michel Morange. Une équipe américaine vient de décrire dans Nature Genetics un algorithme permettant de mieux appréhender les fonctions des grands ARN non codants.
D’autre part, des parties de l’ADN non transcrites en ARN semblent aussi utiles. Ces séquences régulatrices souvent très courtes, 10 à 20 nucléotides, peuvent amplifier (« enhancer ») ou inhiber (« silencer ») la transcription d’un gène tout en étant assez éloignées de lui. « Nous avons montré qu’une anomalie congénitale, une fente dans le palais, était liée à l’anomalie d’un enhancer très éloigné du gène concerné, relate Stanislas Lyonnet. Souvent, pour trouver ces séquences, on regarde si elles existent chez d’autres espèces possédant la même caractéristique, donc si elles ont été conservées au cours de l’évolution. » Très nombreux, les enhancers formeraient près de 13 % du génome humain.
Enfin, une nouvelle piste – l’approche topologique par régions du génome – est explorée, car, au-delà des séquences, l’organisation tridimensionnelle de l’ADN jouerait aussi un rôle dans la régulation. Bref, quand notre génome aura révélé toutes ses fonctions régulatrices, il nous livrera peut-être enfin la clé de notre complexité. Sans compter qu’un dixième de nos 21 000 gènes sont vraiment étudiés, la plupart des travaux se concentrant sur les mêmes 2 000 gènes, comme le dénonce une étude récente dans PLOS Biology.
Opinion | How Genetics Is Changing Our Understanding of ‘Race’ - The New York Times
▻https://mobile.nytimes.com/2018/03/23/opinion/sunday/genetics-race.html
In 1942, the anthropologist Ashley Montagu published “Man’s Most Dangerous Myth: The Fallacy of Race,” an influential book that argued that race is a social concept with no genetic basis. A classic example often cited is the inconsistent definition of “black.” In the United States, historically, a person is “black” if he has any sub-Saharan African ancestry; in Brazil, a person is not “black” if he is known to have any European ancestry. If “black” refers to different people in different contexts, how can there be any genetic basis to it?
Beginning in 1972, genetic findings began to be incorporated into this argument. That year, the geneticist Richard Lewontin published an important study of variation in protein types in blood. He grouped the human populations he analyzed into seven “races” — West Eurasians, Africans, East Asians, South Asians, Native Americans, Oceanians and Australians — and found that around 85 percent of variation in the protein types could be accounted for by variation within populations and “races,” and only 15 percent by variation across them. To the extent that there was variation among humans, he concluded, most of it was because of “differences between individuals.”
In this way, a consensus was established that among human populations there are no differences large enough to support the concept of “biological race.” Instead, it was argued, race is a “social construct,” a way of categorizing people that changes over time and across countries.
It is true that race is a social construct. It is also true, as Dr. Lewontin wrote, that human populations “are remarkably similar to each other” from a genetic point of view.
But over the years this consensus has morphed, seemingly without questioning, into an orthodoxy. The orthodoxy maintains that the average genetic differences among people grouped according to today’s racial terms are so trivial when it comes to any meaningful biological traits that those differences can be ignored.
The orthodoxy goes further, holding that we should be anxious about any research into genetic differences among populations. The concern is that such research, no matter how well-intentioned, is located on a slippery slope that leads to the kinds of pseudoscientific arguments about biological difference that were used in the past to try to justify the slave trade, the eugenics movement and the Nazis’ murder of six million Jews.
I have deep sympathy for the concern that genetic discoveries could be misused to justify racism. But as a geneticist I also know that it is simply no longer possible to ignore average genetic differences among “races.”
Groundbreaking advances in DNA sequencing technology have been made over the last two decades. These advances enable us to measure with exquisite accuracy what fraction of an individual’s genetic ancestry traces back to, say, West Africa 500 years ago — before the mixing in the Americas of the West African and European gene pools that were almost completely isolated for the last 70,000 years. With the help of these tools, we are learning that while race may be a social construct, differences in genetic ancestry that happen to correlate to many of today’s racial constructs are real.
Recent genetic studies have demonstrated differences across populations not just in the genetic determinants of simple traits such as skin color, but also in more complex traits like bodily dimensions and susceptibility to diseases. For example, we now know that genetic factors help explain why northern Europeans are taller on average than southern Europeans, why multiple sclerosis is more common in European-Americans than in African-Americans, and why the reverse is true for end-stage kidney disease.
I am worried that well-meaning people who deny the possibility of substantial biological differences among human populations are digging themselves into an indefensible position, one that will not survive the onslaught of science. I am also worried that whatever discoveries are made — and we truly have no idea yet what they will be — will be cited as “scientific proof” that racist prejudices and agendas have been correct all along, and that those well-meaning people will not understand the science well enough to push back against these claims.
This is why it is important, even urgent, that we develop a candid and scientifically up-to-date way of discussing any such differences, instead of sticking our heads in the sand and being caught unprepared when they are found.
To get a sense of what modern genetic research into average biological differences across populations looks like, consider an example from my own work. Beginning around 2003, I began exploring whether the population mixture that has occurred in the last few hundred years in the Americas could be leveraged to find risk factors for prostate cancer, a disease that occurs 1.7 times more often in self-identified African-Americans than in self-identified European-Americans. This disparity had not been possible to explain based on dietary and environmental differences, suggesting that genetic factors might play a role.
Self-identified African-Americans turn out to derive, on average, about 80 percent of their genetic ancestry from enslaved Africans brought to America between the 16th and 19th centuries. My colleagues and I searched, in 1,597 African-American men with prostate cancer, for locations in the genome where the fraction of genes contributed by West African ancestors was larger than it was elsewhere in the genome. In 2006, we found exactly what we were looking for: a location in the genome with about 2.8 percent more African ancestry than the average.
When we looked in more detail, we found that this region contained at least seven independent risk factors for prostate cancer, all more common in West Africans. Our findings could fully account for the higher rate of prostate cancer in African-Americans than in European-Americans. We could conclude this because African-Americans who happen to have entirely European ancestry in this small section of their genomes had about the same risk for prostate cancer as random Europeans.
Did this research rely on terms like “African-American” and “European-American” that are socially constructed, and did it label segments of the genome as being probably “West African” or “European” in origin? Yes. Did this research identify real risk factors for disease that differ in frequency across those populations, leading to discoveries with the potential to improve health and save lives? Yes.
While most people will agree that finding a genetic explanation for an elevated rate of disease is important, they often draw the line there. Finding genetic influences on a propensity for disease is one thing, they argue, but looking for such influences on behavior and cognition is another.
But whether we like it or not, that line has already been crossed. A recent study led by the economist Daniel Benjamin compiled information on the number of years of education from more than 400,000 people, almost all of whom were of European ancestry. After controlling for differences in socioeconomic background, he and his colleagues identified 74 genetic variations that are over-represented in genes known to be important in neurological development, each of which is incontrovertibly more common in Europeans with more years of education than in Europeans with fewer years of education.
It is not yet clear how these genetic variations operate. A follow-up study of Icelanders led by the geneticist Augustine Kong showed that these genetic variations also nudge people who carry them to delay having children. So these variations may be explaining longer times at school by affecting a behavior that has nothing to do with intelligence.
This study has been joined by others finding genetic predictors of behavior. One of these, led by the geneticist Danielle Posthuma, studied more than 70,000 people and found genetic variations in more than 20 genes that were predictive of performance on intelligence tests.
Is performance on an intelligence test or the number of years of school a person attends shaped by the way a person is brought up? Of course. But does it measure something having to do with some aspect of behavior or cognition? Almost certainly. And since all traits influenced by genetics are expected to differ across populations (because the frequencies of genetic variations are rarely exactly the same across populations), the genetic influences on behavior and cognition will differ across populations, too.
You will sometimes hear that any biological differences among populations are likely to be small, because humans have diverged too recently from common ancestors for substantial differences to have arisen under the pressure of natural selection. This is not true. The ancestors of East Asians, Europeans, West Africans and Australians were, until recently, almost completely isolated from one another for 40,000 years or longer, which is more than sufficient time for the forces of evolution to work. Indeed, the study led by Dr. Kong showed that in Iceland, there has been measurable genetic selection against the genetic variations that predict more years of education in that population just within the last century.
To understand why it is so dangerous for geneticists and anthropologists to simply repeat the old consensus about human population differences, consider what kinds of voices are filling the void that our silence is creating. Nicholas Wade, a longtime science journalist for The New York Times, rightly notes in his 2014 book, “A Troublesome Inheritance: Genes, Race and Human History,” that modern research is challenging our thinking about the nature of human population differences. But he goes on to make the unfounded and irresponsible claim that this research is suggesting that genetic factors explain traditional stereotypes.
One of Mr. Wade’s key sources, for example, is the anthropologist Henry Harpending, who has asserted that people of sub-Saharan African ancestry have no propensity to work when they don’t have to because, he claims, they did not go through the type of natural selection for hard work in the last thousands of years that some Eurasians did. There is simply no scientific evidence to support this statement. Indeed, as 139 geneticists (including myself) pointed out in a letter to The New York Times about Mr. Wade’s book, there is no genetic evidence to back up any of the racist stereotypes he promotes.
Another high-profile example is James Watson, the scientist who in 1953 co-discovered the structure of DNA, and who was forced to retire as head of the Cold Spring Harbor Laboratories in 2007 after he stated in an interview — without any scientific evidence — that research has suggested that genetic factors contribute to lower intelligence in Africans than in Europeans.
At a meeting a few years later, Dr. Watson said to me and my fellow geneticist Beth Shapiro something to the effect of “When are you guys going to figure out why it is that you Jews are so much smarter than everyone else?” He asserted that Jews were high achievers because of genetic advantages conferred by thousands of years of natural selection to be scholars, and that East Asian students tended to be conformist because of selection for conformity in ancient Chinese society. (Contacted recently, Dr. Watson denied having made these statements, maintaining that they do not represent his views; Dr. Shapiro said that her recollection matched mine.)
What makes Dr. Watson’s and Mr. Wade’s statements so insidious is that they start with the accurate observation that many academics are implausibly denying the possibility of average genetic differences among human populations, and then end with a claim — backed by no evidence — that they know what those differences are and that they correspond to racist stereotypes. They use the reluctance of the academic community to openly discuss these fraught issues to provide rhetorical cover for hateful ideas and old racist canards.
This is why knowledgeable scientists must speak out. If we abstain from laying out a rational framework for discussing differences among populations, we risk losing the trust of the public and we actively contribute to the distrust of expertise that is now so prevalent. We leave a vacuum that gets filled by pseudoscience, an outcome that is far worse than anything we could achieve by talking openly.
If scientists can be confident of anything, it is that whatever we currently believe about the genetic nature of differences among populations is most likely wrong. For example, my laboratory discovered in 2016, based on our sequencing of ancient human genomes, that “whites” are not derived from a population that existed from time immemorial, as some people believe. Instead, “whites” represent a mixture of four ancient populations that lived 10,000 years ago and were each as different from one another as Europeans and East Asians are today.
So how should we prepare for the likelihood that in the coming years, genetic studies will show that many traits are influenced by genetic variations, and that these traits will differ on average across human populations? It will be impossible — indeed, anti-scientific, foolish and absurd — to deny those differences.
For me, a natural response to the challenge is to learn from the example of the biological differences that exist between males and females. The differences between the sexes are far more profound than those that exist among human populations, reflecting more than 100 million years of evolution and adaptation. Males and females differ by huge tracts of genetic material — a Y chromosome that males have and that females don’t, and a second X chromosome that females have and males don’t.
Most everyone accepts that the biological differences between males and females are profound. In addition to anatomical differences, men and women exhibit average differences in size and physical strength. (There are also average differences in temperament and behavior, though there are important unresolved questions about the extent to which these differences are influenced by social expectations and upbringing.)
How do we accommodate the biological differences between men and women? I think the answer is obvious: We should both recognize that genetic differences between males and females exist and we should accord each sex the same freedoms and opportunities regardless of those differences.
It is clear from the inequities that persist between women and men in our society that fulfilling these aspirations in practice is a challenge. Yet conceptually it is straightforward. And if this is the case with men and women, then it is surely the case with whatever differences we may find among human populations, the great majority of which will be far less profound.
An abiding challenge for our civilization is to treat each human being as an individual and to empower all people, regardless of what hand they are dealt from the deck of life. Compared with the enormous differences that exist among individuals, differences among populations are on average many times smaller, so it should be only a modest challenge to accommodate a reality in which the average genetic contributions to human traits differ.
It is important to face whatever science will reveal without prejudging the outcome and with the confidence that we can be mature enough to handle any findings. Arguing that no substantial differences among human populations are possible will only invite the racist misuse of genetics that we wish to avoid.
David Reich is a professor of genetics at Harvard and the author of the forthcoming book “Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past,” from which this article is adapted.
#dna is Worth Billions. How #blockchain Helps to Securely Store Medical Data
▻https://hackernoon.com/dna-is-worth-billions-how-blockchain-helps-to-securely-store-medical-dat
Biological and medical science experienced a real breakthrough when the DNA structure was decoded in 1953.DNA is a macromolecule that stores and transfers essential information about living beings, i.e. the genetic code. Francis Crick and James Watson, the scientists who described the double helix of this biopolymer, received the 1962 Nobel Prize, nine years after the discovery.Could they know at that time that their achievement would be the object of cyber-theft after half a century?Genetic passportSimply put, DNA is a sequence of molecules (nucleotides) where the genome information is stored in the form of a certain code.DNA is a carrier and transmitter of heredity from skin color and eye shape to specific diseases that were transferred from parents. The unique code contained in the (...)
We Need to Save Ignorance From AI - Issue 61: Coordinates
▻http://nautil.us/issue/61/coordinates/we-need-to-save-ignorance-from-ai
After the fall of the Berlin Wall, East German citizens were offered the chance to read the files kept on them by the Stasi, the much-feared Communist-era secret police service. To date, it is estimated that only 10 percent have taken the opportunity. In 2007, James Watson, the co-discoverer of the structure of DNA, asked that he not be given any information about his APOE gene, one allele of which is a known risk factor for Alzheimer’s disease. Most people tell pollsters that, given the choice, they would prefer not to know the date of their own death—or even the future dates of happy events.Each of these is an example of willful ignorance. Socrates may have made the case that the unexamined life is not worth living, and Hobbes may have argued that curiosity is mankind’s primary (...)
Des chercheurs découvrent une nouvelle forme de notre ADN
▻http://www.gurumed.org/2018/04/24/des-chercheurs-dcouvrent-une-nouvelle-forme-de-notre-adn
Une équipe de chercheurs australiens de l’Institut de recherche médicale Garvan de Sydney a identifié une version à “nœud” de l’ADN, connue sous le nom de I-motif, qui apparaît à l’intérieur de l’ADN lorsqu’il est lu.
Selon John Mattick, le directeur de l’institut Garvan :
Cela montre un autre niveau de régulation dynamique de l’ADN. Ce n’est pas seulement une voie ferrée tordue ; il y a des panneaux de signalisation et des bifurcations en cours de route.
Tout comme les 1 et les 0 dans le code informatique/ binaire, les généticiens pensent depuis 1953, l’année où James Watson et Francis Crick ont découvert la double hélice, que l’information dans l’ADN était strictement linéaire.
Mais au cours des deux dernières décennies, des scientifiques curieux (pléonasme…) ont réussi à montrer que des structures d’ADN autres que l’élégante hélice apparaissent au microscope. En tout, il y en a 5 autres qui diffère de la forme « standard », connue sous le nom d’ADN B : ADN A, ADN Z, ADN triplex, G-quadruplex, et l’ADN I-motif.
En vingt ans, la Terre a perdu un dixième de ses espaces sauvages
▻http://www.lemonde.fr/biodiversite/article/2016/09/08/en-vingt-ans-la-terre-a-perdu-un-dixieme-de-ses-espaces-sauvages_4994780_165
Toutes les régions du monde ne sont pas égales face au déclin de ces milieux. En Amazonie et en Afrique centrale, la situation vire à la catastrophe. Avec des pertes respectives de 30 % et 14 %, la dégradation des territoires sauvages s’y est accélérée significativement ces deux dernières décennies. « L’exploitation forestière et l’agriculture sont plus importantes dans ces zones, explique James Watson. Et la mise en place des espaces protégés prend du temps. »
Certes, les chercheurs australiens ont réussi à observer une augmentation des zones de protection dans le monde – leur surface a presque doublé depuis le Sommet de la Terre de Rio de Janeiro en 1992. Mais, malgré cette progression, les efforts ne suffisent pas à pallier les pertes : en vingt ans, 2,5 millions de km2 ont été déclarés zones protégées pendant que 3,3 millions de km2 disparaissaient. « Aujourd’hui, les milieux sauvages se dégradent à une vitesse supérieure à celle de leur protection, prévient James Allan. Si on continue à ce rythme, il ne restera aucune parcelle de #nature vierge d’ici à la fin du siècle. »
[...] Autre menace qui pèse sur ces régions, la fragmentation des espaces est de plus en plus importante. Ce phénomène est notable car, sous le seuil de 10 000 km2, les aires de nature sauvage ne peuvent plus être considérées comme « milieu naturel significatif ».
Is DNA the Language of the Book of Life? - Facts So Romantic
▻http://nautil.us/blog/is-dna-the-language-of-the-book-of-life
Thinking of nucleobases as a long sequence of letters may contribute to the illusion that DNA is a language.Neil Palmer / CIAT via FlickrWhen we talk about genes, we often use expressions inherited from a few influential geneticists and evolutionary biologists, including Francis Crick, James Watson, and Richard Dawkins. These expressions depict DNA as a kind of code telling bodies how to form. We speak about genes similarly to how we speak about language, as symbolic and imbued with meaning. There is “gene-editing,” and there are “translation tables” for decoding sequences of nucleic acid. When DNA replicates, it is said to “transcribe” itself. We speak about a message—such as, build a tiger! or construct a female!—being communicated between microscopic materials. But this view of DNA has (...)
Les dix plus belles prises des milliardaires russes | Russia Beyond the Headlines
▻http://fr.rbth.com/art/2014/12/17/les_dix_plus_belles_prises_des_milliardaires_russes_32047.html
Ce n’est pas la crise pour tout le monde.
Le 4 décembre, lors d’une vente aux enchères organisée par Christie’s à New York, l’homme d’affaires russe Alicher Ousmanov a déboursé 4,76 millions de dollars pour la médaille du prix Nobel remise en 1962 au biologiste James Watson pour avoir déchiffré la structure de l’ADN. L’homme d’affaires souhaite la restituer au scientifique, jugeant « inacceptable qu’un chercheur éminent soit contraint de vendre son prix ».
« Le Carré noir » de Kazimir Malevitch
Actualité > Un second code caché dans l’ADN !
▻http://www.futura-sciences.com/magazines/sante/infos/actu/d/biologie-second-code-cache-adn-50992
Certaines recherches font plus de bruit que d’autres. La découverte de la structure de l’ADN (acide désoxyribonucléique) par James Watson et Francis Crick en 1953 en fait partie. Récompensée par le prix Nobel de médecine en 1962, elle a en effet complètement révolutionné les connaissances dans le domaine de la biologie.
La molécule d’ADN est en réalité connue depuis le début des années 1950. À cette époque, les biologistes savaient qu’elle était constituée de quatre types de molécules plus petites, appelées nucléotides, se distinguant par leur base azotée : A (adénine), T (thymine), C (cytosine) et G (guanine). Ce qu’ils ignoraient en revanche c’est comment l’ADN était structuré. James Watson et Francis Crick ont brillamment éclairci le mystère et ont montré que la molécule d’ADN possédait une structure en forme de double hélice au sein de laquelle les bases s’appariaient de façon spécifique, les A avec les T et les C avec les G.
L’ADN est constitué de quatre nucléotides différents, notés A (adénine), T (thymine), C (cytosine) et G (guanine), du nom des bases azotées correspondantes. Ces nucléotides se regroupent par paires spéciales : A avec T ; T avec A, C avec G et G avec C. © Dosto, Wikimedia Commons, cc by sa 2.5
Grâce à ces données fondamentales, les scientifiques ont pu comprendre comment se transmettait l’information génétique dans la cellule. Les chercheurs ont démontré que les nucléotides présents dans l’ADN étaient alignés de façon spécifique, formant un code permettant la production des acides aminés et des protéines. Trois nucléotides accolés constituent une sorte de mot, appelé codon, qui est lu puis traduit en un des 20 acides aminés de la cellule. Les acides aminés sont alors ficelés les uns aux autres puis sont assemblés pour former une protéine. Dans certaines conditions, des mutations peuvent apparaître et modifier le code. La protéine mutée résultante peut perdre sa fonction, ce qui peut conduire au développement d’une pathologie...
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DNA pioneer James Watson takes aim at cancer establishments | Reuters
►http://www.reuters.com/article/2013/01/09/us-usa-cancer-watson-idUSBRE90805N20130109
current approaches are not yielding the progress they promised. Much of the decline in cancer mortality in the United States, for instance, reflects the fact that fewer people are smoking, not the benefits of clever new therapies.
[DNA therapy:] (...) almost none of the resulting treatments cures cancer. “These new therapies work for just a few months,” Watson told Reuters in a rare interview. “And we have nothing for major cancers such as the lung, colon and breast that have become metastatic.”