Showing posts with label genetics. Show all posts
Showing posts with label genetics. Show all posts

Sunday, January 1, 2017

Future world of Genetic Inheritance

Let me call it the GI-world. Humanity is leaving an era in which the letters “G.I.” generally evoked soldiers of the United States Army and airmen of the United States Army Air Forces. We are now moving slowly but surely into a new era in which those same two letters are likely to be used to designate Genetic Inheritance: that’s to say, the part of human behavior that is derived more from Nature than from Nurture. The stuff that happened to be written already on the slate when we were born.

Observers often think it would be nice to believe that our slates are blank at the moment of our birth, and that children then meet up with countless real-world experiences enabling them to extend and enrich the writing on their personal slates. This blank-slate vision might be partly valid, but researchers discovered cases of identical twins, brought up in worlds apart, who adopted highly similar behaviors, suggesting that fragments of their DNA code were apparently duplicated.

Commonsense often makes us imagine that such afflictions as alcoholism or insanity might indeed be present “in the family”, meaning that the offspring of afflicted ancestors might indeed have an inherited tendency to fall into drinking or madness. While it’s extremely difficult to prove that this might be true, many observers feel that human behavior can be the outcome of a subtle mixture of Nature and Nurture. It’s possibly what a French humorist referred to as Nightingale Pastry. The stuffing is obtained by mixing together nightingale meat and horse meat in equal proportions: the flesh of one nightingale mixed with the flesh of one horse. In the Nature versus Nurture context, it’s still hard to determine whether the code already present on the slate was a huge horse or rather a tiny nightingale. No doubt a bit of both.

I believe personally that, in the future GI-world, a new class of investigators will examine simultaneously both the horse and the nightingale. For example, if both a mother and her daughter manifest symptoms of the kind designated as bipolar disease, then they might envisage the possibility that the daughter inherited this disorder from her mother. In order to form an opinion on this question, other individuals on the patient’s genealogical tree might be brought into the picture. Have comparable behavioral characteristics been observed at several places on the family tree ?

DNA-based investigations have revolutionized many aspects of our existence. At the modest level of my family-history research, a couple of trivial Y-chromosome tests enabled me to confirm the identity of one of my paternal great-grandfathers: Chromosomes reveal the truth.

Ernest Skyvington [1891-1985] between his parents in London. My grandfather could never tell me what had happened to his father.

Sooner or later, in tomorrow’s GI-world, whenever we’re confronted with striking cases of weird behavior inside the family, observers will not be unduly surprised if observers decide to browse through both genealogical and biological data of all kinds. Pluridisciplinary research of that kid will appear to observers as no less unusual than, say, conventional psychoanalysis or psychotherapeutics.

Thursday, January 28, 2016

Genetic light starts to shine upon schizophrenia

For the very first time in the history of psychiatry, US researchers in genetics and neurology feel that recent studies might reveal the causes of schizophrenia, which has always been a widespread but mysterious affliction in our modern societies. In the USA, there are over two million victims of this psychiatric disorder, giving rise to delusions, emotional withdrawal, hallucinations and a decline in cognitive abilities. Their troubles can be attenuated slightly by medical substances, but cannot yet be cured. Well, promising research has been carried out recently by scientists from the Harvard Medical School, Boston Children’s Hospital and a research institute linked to Harvard and the Massachusetts Institute of Technology, and their results have been published in the journal Nature. But it is still far too early to, in the immediate future, to envisage any revolutionary methods of treatment.

Human synapses between brain neurons, with C4 proteins marked in green.

Researchers examined the ways in which genes can increase a person’s risk of developing schizophrenia. They examined a gene in our immune system called complement component 4, referred to as C4, whose structure varies considerably between individuals. It was found that certain people with specific forms of the C4 gene stand a higher chance of developing schizophrenia.

That risk is tied to a natural process called synaptic pruning, in which the maturing brain discards weak or redundant connections between neurons. And individuals whose C4 genes increase that pruning effect appear to have a greater chance of developing schizophrenia.

Thursday, January 21, 2016

Illegal to patent natural genes in France

France's higher house of parliament, the senate, adopted yesterday an amendment that prohibits the patenting of "products that are the outcome of purely biological procedures".

In the immediate future, this legislation aims to protect open research in the domain, not of animals, but of ordinary plants and crops. For example, imagine that a corporation were to be granted the right to patent a certain gene that was found, most often, in broccoli. These days, the CrispR/Cas9 method of DNA editing developed in 2012 means that a researcher might encounter this same gene in another quite different plant, without being aware that it is indeed the patented brocoli molecule. So, from a legal viewpoint, we're in a totally new ballpark, where the concept of patenting naturally-occurring genes is fuzzy to the point of being nonsensical.

Wednesday, January 6, 2016

Can we "enhance" humans by means of customized genes ?

I've preferred to leave the verb "enhance" in inverted commas, because geneticists are frankly playing at behaving as a divinity, and nobody knows with certainty yet whether these scientists are God or the Devil. Or maybe a bit of both. Consequently, many observers consider that it's still too early to say whether or not we have the right to perform so-called human gene editing.

A conference on these questions took place in Washington on December 1–3, sponsored by Britain’s Royal Society, the Chinese Academy of Sciences and the US National Academies. Click here for a Scientific American website on this subject.

In my recent blog post about the French scientist Emmanuelle Charpentier [display], I mentioned a celebrated method known as the CRISPR–Cas9 system, for which she was a contributor. This technology has made DNA modification so simple that amateur biologists working in home laboratories are starting to fiddle with it, and to "hack genomes". Not surprisingly, the CRISPR-Cas9 method appears to have played a central role in the Washington conference.

Tuesday, December 22, 2015

Is genealogy all about genes?

That's not meant to be a trick question, but it is surely a tricky question. And I'm not at all certain that I can indeed reply correctly and intelligently. Both the ancient term "genealogy" (study of generations of ancestors) and the relatively modern biological word "gene" (one of the many molecular elements of an individual's DNA) are inspired by the same root: γενεά ‎(geneá, "generation, descent"). So, the obvious answer to my question is yes: the study of genealogy is surely concerned by some kind of an examination of an individual's DNA. Having made that point, I'm obliged to say that, for the moment, the concrete associations between conventional family-history preoccupations and modern genetic methods are not at all obvious.

It's well known that many everyday family-history enthusiasts are tempted to pay fees to US laboratories specializing in genetic enhancements to everyday genealogy, usually of a complex nature. I made this decision several years ago, without fully understanding the exact advantages that I might (or might not) acquire. I can now say that I derived few avantages of the kind I was expecting, and nothing proves to my mind that the alleged missions of such companies are as sound as they make themselves out to be. On the other hand, an unexpected family-history event enabled me to discover that this kind of enhancement of ordinary family-history research can give rise to a startling result. I'm talking of the extraordinary Courtenay affair concerning the chance discovery of my paternal great-grandfather.

On page 48 of The Ancestor's Tale by Richard Dawkins, there's a precise and brilliant explanation of "a telling difference between gene trees and people trees". Here, for example, is a "people tree" of my own childhood family in Australia:

That's me on the middle left, then my brother followed by our three sisters. Now, the questions introduced by Dawkins could be put as follows: In the case of a specific gene that's responsible for such-and-such an aspect of the character of a particular child, did that child inherit that gene from our father or from our mother, and was it the same gene that was inherited (from the same parent) by the other four siblings?

The answers to those two questions astonished me greatly when I first encountered them, and I'm sure that many people might be surprised, for they prove beyond any doubt whatsoever that siblings in a sole "people tree" do not necessarily acquire their specific character traits from the same "gene trees". To put it bluntly, brothers and sisters do not necessarily share identical character traits. Let us imagine, for example, my brother's genes that played a role in making him behave character-wise in a particular fashion. It is perfectly thinkable that none of Don's siblings had inherited comparable genes. Don's gene might have come, for example, from the father of Enid Kathleen Walker, whereas my corresponding version of this gene might have come, say, from the mother of King Mepham Skyvington.

This appears to me as a highly significant and fundamental law of inheritance, which should not be ignored.

Friday, December 26, 2014

Escaping from DNA detection

Over the last month or so, in the context of my work on a future book about Gamone, I’ve been investigating haphazardly and half-heartedly the genealogy of various local families, just to obtain (if possible) a slightly less fuzzy idea of who’s who. At one point, I happened to say to one of our female municipal representatives that it would be an interesting idea if some of the people here were to carry out DNA-testing, in order to gain a better understanding of the evolution of certain time-honored families. It was if I had suggested that they should grab a shotgun and fire at their feet.

In my enthusiasm for science and technology in general, and for genetics in particular, it’s true that I often tend to forget that many of my fellow citizens look upon DNA analysis as some kind of necessarily evil. For them, it belongs to the morbid category of crime detection, forensic tests, unsolved murders, Big Brother… At a less dramatic level, DNA analysis is likely to land you in trouble when it reveals that you’re not really the individual you thought you were, and that your alleged biological ancestors weren’t exactly the individuals they claimed to be. Eons of prehistoric experiences have taught us that there’s no point in waking up sleeping dogs. There are things that are better left unknown. And how might a genealogist such as myself disagree? Click here for a summary of a sleeping dog that was rudely awakened in our Skyvington household, recently, by DNA analysis.

Maybe, therefore, we should look into ways of protecting ourselves from the inevitably nasty consequences of DNA testing. Click here to see an imaginative video on this theme.

Why doesn’t a bright scientist simply invent a gadget (maybe a smartphone app) that would simply neutralize our personal DNA, turning it off (a little like unsubscribing from a Facebook account), so that nobody—not even Islamic jihadists or North Koreans—would be capable of attacking us?

Happy Winter Solstice greetings to all of my friends
in the Northern Hemisphere,
and complementary Summer Solstice greetings
to those in the Antipodes.

Monday, February 18, 2013

Unexpected links

A few days ago, a friendly reader of my blog sent me a link to a list of online genealogical resources [here]. I replied that an all-important resource was glossed over in the list. Genealogical research is often dominated by black swan happenings, in the sense suggested by Nassim Nicholas Taieb: that's to say, totally unexpected events that upset the nice and tidy little applecart upon which the researcher had been basing his beliefs.

The biggest black swan that has alighted upon my genealogical research over recent months concerned my Pickering relatives (through the family of my paternal grandmother). On 3 March 2012, my bucolic blog post entitled Vicar's garden [display] evoked the rural existence of our forebear Henry Latton [1737-1798],  the vicar of Woodhorn in Northumberland. I ended that blog post by saying that the vicar would have surely disapproved of my science-based atheism.

Be that as it may, my dear great-great-great-great-grandfather did not deserve to be murdered by bandits while returning from an afternoon of betting on the horses at Newbiggin-by-the-Sea.

Six months after having evoked this Latton ancestor, I got an unexpected e-mail from an unknown Englishman named Latton who told me an amazing tale. He alleged that his own grandfather, known to him as John Edward Latton, was in fact the same individual designated in my document They Sought the Last of Lands [display] as John Edward Latton Pickering [1851-1926]. In other words, my correspondent was saying that we had a skeleton in one of our family-history closets: a respected Londoner (archivist at the Inner Temple law library) who had invented a new name for himself (borrowed from our Latton ancestors) and forged a marriage certificate enabling him to become a full-fledged bigamist and raise a second family in parallel to his first one. Needless to say, I've got over the surprise by now, and I'm looking forward to meeting up with my new English cousin when he drops in at Gamone with his wife this summer.

That wasn't the only recent black swan. In April 2012, I became really excited about a possible research avenue aimed at elucidating the mystery of the Norman origins of the Skeffington family. In blog posts entitled Patriarch [display] and Skeffington/Verdun links [display], I evoked the identity of a celebrated Norman family with close attachments to the Leicestershire village of Skeffington at the time of the Conquest. I concluded my first blog post, on 27 April 2012, as follows:
Another fascinating question emerges. Is it thinkable that our patriarch Bertram de Verdun might have descendants today in France and elsewhere? Well, to put it mildly, judging from what I've seen through a rapid visit to the Genea website, it would appear that the community of my so-called "genetic cousins" includes many present-day members of the old nobility of Normandy and France.

When I asked that "fascinating question", I had not yet started to look around in France with the aim of contacting living de Verdun descendants. From this point on in the present blog post, I'm obliged to be deliberately vague, because I wish to avoid mentioning names that would be picked up by search engines. Let me explain in roundabout terms that, in April 2011, French police had come upon a nasty crime scene in the city whose mayor was our present prime minister, Jean-Marc Ayrault. They unearthed the bodies of a mother and her four teenage kids. As for the father, he has totally disappeared. Most people consider that the father—whom I shall refer to as X—is indeed the culprit. On the other hand, X's sister is convinced that her brother never murdered his wife and children. In the ongoing crusade aimed at protecting the honor of her brother, this determined lady is assisted by her husband... who happens to bear exactly the same ancient Norman name as the Conqueror's companion associated with the Leicestershire village of Skeffington, evoked in the "fascinating question" that I have just quoted. For all I know, X's brother-in-law could well be a direct descendant of the 11th-century personage who interests me. Naturally, in the context of my Skeffington research, I would be interested in the possibility of examining a description of the Y chromosomes of this present-day Frenchman. For the moment, though, such a request for DNA data would be out of place, and unwise.

POST SCRIPTUM: In the wake of my initial enthusiasm about the possibility that Bertram de Verdun might have been the "elusive patriarch" whom I've been seeking for so long, I now believe that this was a false track. Click here to download the latest version of chapter 1 of my slowly-emerging Skeffington One-Name Study.

Friday, September 7, 2012

Junk's not junk

For ages, it has been said that humans use only a small percentage of their cerebral potential. Personally, I've always been wary of this kind of evaluation. The experimental evidence for such a conclusion is obscure, to say the least. What would it mean, at a practical level, if my cerebral performances were suddenly doubled, say? Would I understand twice as many things as I did previously? Would I have a vision of our human existence that was twice as deep as my old way of looking at things? Would I be capable of thinking twice as rapidly as I used to? Would I be able to master new fields of learning? Would I now have a clear perception of things that once appeared fuzzy in my mind? Would I be clearly conscious of the fact that I was twice as smart as I used to be? Frankly, I've always imagined all that extra yet-unused brainpower as akin to the legendary multiple lives of a cat. It sounds like a great idea... up until you try to imagine what it might mean in practice.

More recently, I've often been similarly wary, indeed stupefied, when I've heard geneticists talk of so-called junk DNA. The idea is that only some 2 per cent of our precious genetic heritage plays an essential role in the synthesis of proteins and operational cells and organs. The remaining 98 per cent would appear to be biological "dark matter" that simply comes along for the ride, in an almost parasitical fashion.

Once upon a time, when scientists told us that the human body was largely composed of water, I used to wonder whether it might be possible to "dry out" a human being, by removing magically all this surplus wetness. Would the waterless creature work just as well? Or would he simply shrivel up and die like a fish discarded on a sunny riverbank? In a similar way, I wondered naively about all that junk stuff that I was carrying around with me. If it were completely useless in my survival, then we might imagine a zapping device capable of eliminating everything that wasn't essential. Normally, after being zapped, I would be reduced to a dwarf, with only 2 percent of my original volume, but I would remain just as smart as before... or even much smarter, if I decided to combine the junk-DNA-zapping with a foolproof method for gaining control of all my unused brainpower. I would be transformed into a mighty midget! As Hamlet said:
I could be bounded in a nutshell, and count myself a king of infinite space, were it not that I have bad dreams.
We adepts of genealogical research have always been stalwart admirers of junk DNA. Funnily enough, although specialists affirmed that all this vast quantity of code achieved nothing of a useful nature, it was nevertheless the object of mutations. And the analysis of such mutations in Y-chromosomes has enabled us to trace paternal lineages. So, the junk hasn't been as totally junky as you might imagine. For example, if ever I were able to discover the identity of the first fellow in England who procreated dozens of generations of descendants named Skeffington (Skevington, Skivington, Skyvington, etc), then my junk DNA would be far more precious, for me, than all the crown jewels in the Tower of London.

Meanwhile, researchers concerned with the human genome have just announced that it is high time for us to realize that so-called junk DNA is anything but that. These researchers have been participating in a huge research project known as Encode: a consortium, based at the University of Santa Cruz in California, that is building a huge databse of the various bits and pieces of the genome.

DNA strings that don't code the synthesis of proteins take care of a multitude of necessary behind-the-scenes activities such as switching genes on or off, and regulating the context in which genes carry out their functions. Suggesting that DNA segments are "junk" simply because they don't have a star role in the coding of proteins is as silly as saying, for example, that the fabulous Avatar movie was created solely by a single director, or a pair of actors, and that all the background support was of no importance.

I liked the comments of an observer who referred to research in genetics by means of a sporting metaphor. "We're still in the warm-up, the first couple of miles of this marathon."

Friday, August 31, 2012

Opening chapter of Skeffington study

I've more-or-less terminated the opening chapter of my Skeffington One-Name Study, entitled Elusive patriarch [download], dealing with the half-century that followed the Norman Conquest in Leicestershire, in the vicinity of the village of Skeffington.

As the title of this opening chapter suggests, I haven't been able to track down and identify the patriarch of the Skeffington family in England. So, you might say that the hero of my document is totally absent. On the other hand, as I've often suggested, the widespread adoption of genealogical genetics (Y-chromosome profiles) could well add totally new dimensions to this quest. For the moment, I seem to have no potential relatives whatsoever in the Y-chromosome database, so the current score of my Skeffington matching is a huge zero. In fact, the match hasn't even got under way yet, since I'm still the sole player on the field. My chapter 1 might become interesting in the future, for certain small groups of readers, when the techniques of genealogical genetics have become commonplace.

Wednesday, August 15, 2012

What, no rock 'n' roll in the caves?

Svante Pääbo, 57, is a Swedish geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig.

In my blog post of 26 December 2010 entitled Prehistoric encounters [display], I mentioned the existence in Siberia, 30 millennia ago, of humanoid creatures—on an evolutionary par with Neanderthals—known as Denisovans. It was Pääbo's team that revealed the existence of these people, in March 2010, using mtDNA [mitochondrial DNA] that was lurking in a single Denisovan finger bone.

Two months later, Pääbo's team published a draft sequence of the Neanderthal genome. Noticing that a certain quantity of DNA is common to both Neanderthals and modern humans whose ancestors had moved beyond Africa, Pääbo's team announced that it was likely that a certain degree of sexual promiscuity had characterized relationships between Neanderthals and humans in the course of their many millennia together, side by side, on the planet Earth.

                          — photo Jochen Tack/Alamy

That idea doesn't surprise me at all. On the contrary. I can well imagine a randy Cro-Magnon gentleman running into a horny Neanderthal lady, on his way home from the hunt at the end of a wintry afternoon, and paraphrasing in his imagination the well-known Canada Dry words: "It looks like whisky, smells like whisky, and tastes like whisky."

I imagine myself in the Cro-Magnon's place, on the horns of a dilemma. Regardless of the respective species (or races, or whatever) of the Neanderthal wench and me, I would have surely decided, there and then, that a little bit of Guinness would be good for me... and for her, too, no doubt.

Now, I learn today from The Guardian [access] that certain sourpuss scientists are abandoning this delightful idea of intertribal rock 'n' roll. They suggest that the DNA stuff shared by Neanderthals and us humans was surely a remnant of code that existed already in our most recent common ancestor, half a million years ago, before we had differentiated into Neanderthals and humans. Their reasoning is perfectly plausible, but it strikes me as somewhat puritanical. I far prefer the friendly idea of a whole lotta prehistoric shakin' goin' on.

Monday, June 11, 2012

Dogs in God's city

Dogs, in the context of conventional religions, have often had a hard time. An antiquated version of Revelations, on the very last page of my ugly King James Bible, states:
I am Alpha and Omega, the beginning and the end, the first and the last.
Blessed are they that do his commandments, that they may have right to the tree of life, and may enter in through the gates into the city.
For without are dogs, and sorcerers, and whoremongers, and murderers, and idolaters, and whosoever loveth and maketh a lie.
So, in a heavenly context, dogs would be "without" (along with perverts, sorcerers, fornicators, murderers and idolaters)... just like the body of Jesus with respect to his tomb in Jerusalem. [One of my favorite jokes. A pious lady visiting the ornate tomb of the Holy Sepulcher asks her guide, a priest: "Is there anyone inside?" Priest: "Lady, if He's in, then I'm out."]

All this Biblical stuff is most smelly dogshit.

I remain astonished—as I said in my blog post entitled Is the Bible good English literature? [display]—that a great evolutionary zoologist such as Richard Dawkins might seriously appreciate the alleged literary qualities of this kind of antiquated twaddle.

Within Buddhism, of course, the situation for dogs is not much better. If I understand correctly, Buddhists place dogs at the extreme lower end of the spiritual scale (or whatever it might be called). I evoked this horrifying canine disparagement in my blog post entitled Tea for two expats [display].

In God's Own City, Jerusalem, the authorities are fed up with those nice droppings of angels, commonly referred to as dog shit. And they plan to use a genetics database to identify culprits.

Translation: "If you didn't clean it up, then it's you who left the shit."

This means that all dogs in Jerusalem will be required to supply their DNA specifications (a fine idea in the perspective of future yet-undefined biological research). Then a squad of turd inspectors (employment conditions and salaries not yet specified) will spend their working days gathering biological data on the Holy City's latest dog shit. And dog-owners will be fined whenever their animals are found to have defecated on the municipal territory.

I laugh out loud at the image of Israeli turd inspectors sticking their noses inadvertently and unknowingly into UFOs [unidentified fallen objects] such as non-canine excrement (including human shit). Within the category of possible turds, we have no theological right to exclude the possibility of authentic angels' poo (bearing small white wings), or even (God be blessed!) a tiny turd or two from the good old Holy Ghost himself. All these possibilities are based, of course, upon the predictions of high-quality Byzantine science.

Wednesday, November 30, 2011


In a blog post of 9 August 2010 entitled Sophia's future companion at Gamone [display], I explained that the elegant name Fitzroy, which I would give to my young Border Collie a year ago, was in fact the surname of one of my ancient ancestors: a bastard son of King John.

The term Fitz means "son of", and roy is Old French for "king". The bastard Fitz who was my ancestor—often specified as Richard Fitzjohn Chilham—is mentioned briefly in this delightful book:

Well, I often get around to imagining my dog as a descendant, not of a king, but of a wolf. So, I often call him either FitzLoup (in French) or simply FitzWolf. These reveries started recently in my imagination when I thought about an amazing story told by Richard Dawkins in The Ancestor's Tale [pages 29-31] and then repeated in The Greatest Show on Earth [pages 73-76].

It's the story of an experiment carried out by the Soviet scientist Dmitri Belyaev [1917-1985] using a beautiful domestic animal, the Russian Silver Fox, bred for the fur trade.

[First parenthetical remark. What a horrible idea: killing such a glorious animal just to be able to transform its skin and fur into a coat.]

[Second parenthetical remark. The geneticist Belyaev was a man whom we might admire a priori, since he was sacked because he disagreed with the quackery of the Stalinist agronomist Trofim Lysenko.]

Belyaev's experiment was aimed at studying the concept of tameness in successive generations of his foxes. The basic experimental procedure consisted of offering food to fox cubs and trying to fondle them. According to their reactions, the young animals were classed in three categories:

(1) The wildest cubs would either flee or act aggressively, maybe by biting the experimenter's hand.

(2) Certain cubs would accept the food and the experimenter's caresses, but grudgingly, as it were, with no apparent enthusiasm.

(3) The tamest category of cubs would, not only accept the food, but exhibit a positive reaction to the experimenter's caresses, by wagging their tails and crouching down in front of him.

Only fox cubs in this third category would be used for breeding the next generation. And so on…

Not surprisingly, this breeding strategy produced cubs that were tamer and tamer. But the experiments resulted in consequences—we might say side effects—of a totally unexpected kind. The new generations of tame foxes started to look somewhat different to their relatively wilder genetic cousins. In a nutshell, the tame foxes started to look like Border Collies! Truly, it was magic… but simply genetic magic! While the silver foxes were being bred uniquely for tameness, their genes "threw in for free"—as it were—a whole host of genetically-connected features that were apparently linked rigorously with tameness.

Nature speaks to us with her eons of accumulated wisdom: If you want a tame fox, then what we have to offer you is a dog-like fox! Nature might have added: Take it or leave it! Me, I say enthusiastically that I'll take it, because my marvelous tame wolf is Fitzroy… whose fur warms me for a delightful instant when he jumps up onto my knees in front of the fireplace.

Often, I'm overwhelmed when I observe at close range the intense human-like gaze of Fitzroy, which has infinitely more profundity and meaning than the dumb expression of less-introspective animals.

Fitzroy is surely just a few magic chemicals away from being capable of discussing Dawkins with me… but that minor metamorphosis is likely to necessitate a few million years, to say the least, with all the risks of the long road. Frankly, Fitzroy and I tend to agree (not to mention the tacit approval of Sophia) that, for the moment, it's best we stay put.

Saturday, October 22, 2011

What science is saying

These days, the general public is being offered countless presentations of scientific conclusions concerning the origins of human beings. The tone of some of these presentations is so clear, and their contents are so striking, that most people should grasp what is being said, and be impressed by the scope and depth of such explanations. I would imagine that most young people react seriously to such presentations, whereas many adults probably find ways of shielding themselves from the impact of revolutionary facts capable of disturbing them.

Near the start of The Magic of Reality, Richard Dawkins presents readers with a spectacular thought experiment: that's to say, a virtual project carried out, not in a laboratory, but in your imagination. You're asked to stack up portraits of your father, your father's father, your father's father's father, and so on: that's to say, all your paternal male ancestors. The huge stack of images—extending backwards in time—might be laid out on bookshelves, enabling you to browse through them in an orderly fashion to examine the portrait of any specific male ancestor.

If you browsed back to the portrait of your 4,000-greats-grandfather, you would discover a bearded dark-skinned fellow not unlike men you might see today, say, in a Moroccan village. If you browsed back much further, to the portrait of your 50,000-greats-grandfather, you would come upon an individual who looks like the proverbial caveman. Dawkins then asks you to browse all the way back to your 185-million-greats-grandfather. What might he look like? With the help of brilliant illustrations from Dave McKean, Dawkins supplies an answer, which might shock certain readers:

This portrait of a grandpappy is far removed from the typical paintings of distinguished oldtimers in the portrait galleries of aristocratic families. The ancestor who most impressed me was our long-snouted 45-million-greats-grandfather, shown here having a snack:

To appreciate these ancestral illustrations and explanations, you really must get a copy of this splendid Dawkins book, which is packed with all kinds of fascinating tales (including myths) and science stuff.

A few evenings ago, on the Arte TV channel, I watched an interesting documentary on population genetics. Viewers were introduced to the fabulous possibilities of examining DNA specimens to determine the genealogy of various ethnic communities. Personally, I prefer to acquire my knowledge of population genetics and large-scale genealogy through reading books, articles and Internet stuff rather than depending on TV. I would imagine however that this documentary must have been an eye-opener for viewers who were unaware of state-of-the-art findings and thinking in this complex domain.

The subject was tackled in a controversial style (rightly, I believe) by insisting on the fact that the old-fashioned concept of human races is totally rejected by modern research. All human beings who exist today on the planet Earth are the biological descendants of a small group of Africans who were probably similar to the community known today as South African Bushmen. In a sense, therefore, we are all Africans! This poetic declaration charmed 80-year-old Desmond Tutu.

Certain facts are likely to amaze white-skinned Europeans and citizens of the New World, and maybe make us more humble. For example, there is no doubt whatsoever that our prehistoric ancestors were black-skinned, and that our present whiteness is a freakish new-fangled affair brought on by the physiological fact that fairer ex-Africans survived better in cold climates. So, alongside "black is beautiful", we might proclaim that "negro is normal", whereas "white is weird".

These days, research in population genetics is advancing so rapidly that certain major breakthroughs have occurred in the short time since the French TV documentary was completed. For example, there have been amazing revelations concerning the early date at which the ancestors of Australia's Aborigines left Africa. In the 1920s, a lock of hair was taken from an anonymous young Aboriginal male near Kalgoorlie. Well, this DNA specimen was sufficient to enable, recently, an analysis of the subject's genome. And it became obvious that the ancestors of Australia's Aborigines had in fact left Africa at least some 50 millennia ago: that's to say, well before the exodus that gave rise to communities of Homo sapiens in Asia and Europe.

A tribal elder described this DNA-based breakthrough as "just a white-fella story", and said he would continue to believe in the tribe's mythical creation legends.

Saturday, July 30, 2011

Smart boss

At the start of a recent Dilbert strip, I was surprised, indeed intrigued, to find the Pointy-Haired Boss referring to the sophisticated phenomenon of telomeres, which are the repetitive DNA sequences found at both ends of our chromosomes. After all, it was only in 2009 that the Australian-born biologist Elizabeth Blackburn was awarded (along with two colleagues) the Nobel Prize in Physiology or Medicine for the discovery of the way in which telomeres "protect" a chromosome whenever it replicates.

The boss's allusion to "short telomeres" evokes an hypothesis that has become widespread (although not yet fully confirmed) at the level of afflictions such as cancer and aging. The general idea is that a fragment at the extremity of a telomere is "sacrificed" during cell replication, and this insignificant destruction means that relatively important fragments further down the line will not be damaged, as they would be if the protective telomere "cap" were not present. In a healthy individual, this partial destruction of one end of the telomere is harmless, since it can rebuild itself later on. On the other hand, if an individual's telomeres have been reduced to an abnormally short length, then that person is a likely candidate—according to the above-mentioned hypothesis—for cancer and senescence.

I was surprised by the boss's knowledge of modern genetics. I didn't know that a narrow-minded man of his kind would have heard of telemeres. Maybe, if I had the habit of reading popular-science magazines, or stuff about health, I would have realized that telomeres have indeed become a household word. Incidentally, in the remaining frames of the Dilbert strip, the boss informs the job candidate that short telomeres are a sign that the individual in question values work above physical well-being.

[Click the image to access an article that the boss may have read.]

Another thing that intrigues me in this affair is the question of how an ordinary individual might learn that his telomeres are abnormally short. I've had my Y-chromosomes analyzed in a genealogical context [see description], but that trivial operation taught me nothing whatsoever concerning the length of my telomeres. Maybe individuals who have had their DNA examined in a wider medical context end up acquiring information about the length of their telomeres. In any case, I intend to carry on reading Dilbert comics in the hope of broadening my awareness of the marvels of modern medicine.

Friday, June 10, 2011

Gut bug villain identified

Germany has finally decided that bean sprouts are the source of the lethal strain of Escherichia coli.

But are German scientist well-informed and correct? After all the tergiversations, an observer of the devastating effects of Germany's outrageous Cucumbergate might have doubts.

In any case, it would be normal that Germany should pay cash for this erroneous rashness.

The notorious new strain of E. coli bacteria that came to light in Germany has caused acute diarrhea followed by a life-threatening affliction known as HUS (hemolytic-uremic syndrome), characterized by hemolytic anemia (breakdown of red blood cells) and acute uremia (kidney failure).

The designation of the deadly new strain, O104:H4, has nothing to do with the actual genome of this bacterium, which was sequenced in China at the BGI-Shenzhen laboratory. The O and H terms, designating the bacterium's serotype, refer to simple chemical substances called antigens that cover, respectively, the cell walls and tails of the bacteria, provoking defensive reactions (production of antibodies) from the immune system of the host in which the bacteria reside.

In fact, we humans have been living for ages with these terrifying E coli creatures, who've often become intimate friends. As the science-writer Robert Krulwich says so beautifully [click the bacteria images], they're our partners in the gigantic time-space adventure of existence, rather than our declared enemies, and we should respect them.

I nevertheless draw attention to a highly-pertinent document that I downloaded from the website of the University of California [find it by Google], suggesting that mungo bean seeds can be pathogenic, and that their inherent nastiness can move into sprouts in organic gardens. What more do we need to know or say?

ADDENDUM: This is a photo by Stew Milne for The New York Times. Click it to access an interesting US article on links between bean sprouts and the German bacterial outbreak. I learn that such events, in the USA, are referred to as sproutbreaks.

This fashionable foodstuff may indeed be most nutritious, and give the human consumer the pleasant sensation of being transformed into a herbivorous mammal (which we are not) akin to cows, horses and donkeys. What a pity that genetics in general, and bacteria in particular, don't have much respect for the latest nutritional fashions.

The Wikipedia article on the 2011 E. coli O104:H4 outbreak [display] is now well updated and informative... hopefully definitive.

Click the banner for an interesting and novel explanation of how the deadly bacteria might have set up home in our society.

Saturday, November 27, 2010

Nocturnal disturbance at Gamone

Once Fitzroy beds down for the night in his luxurious kennel, on a thick wad of sweet-smelling straw, he seems to sleep soundly. A couple of nights ago, exceptionally, he started to bark furiously around two o'clock in the morning. I opened the kitchen door so that Sophia could investigate. She has the advantage of seeing in the dark (I don't know how), whereas Fitzroy hasn't yet mastered that art. As for me, I looked around with a powerful flashlight, but I was unable to figure out what had woken up and disturbed Fitzroy.

The next morning, the two dogs were both in an aroused state, and barked frequently, as if a foreign presence were disturbing them.

I thought it might be the visiting pheasant, which I hadn't sighted for a couple of days. Or maybe it was a fox that had captured the pheasant. On the other hand, the direction of Sophia's muzzle suggested that the foreign presence might be located on the far side of Gamone Creek. Sure enough, I soon sighted a large roe deer. I even had time to race upstairs, fetch my Nikon, install a long-focus lens and take a couple of photos of the animal before it disappeared into the thicket.

For dogs, the scent of such an animal would seem to be both intense and alarming.

No sooner had I written the word "alarming" in the last sentence than I realized that it was quite stupid. But I won't remove it. My awareness of my mistaken use of this word illustrates the regular progress I'm making in becoming more and more naturally adapted to the evolutionary thinking of Richard Dawkins. The dogs are aroused by the scent of the deer for the simple reason that some of their archaic genes are screaming out (if genes can be thought of as capable of screaming) that the dogs should race out, attack this animal, kill it and eat its flesh. Wolves that reacted like that when they picked up the scent of deers ended up getting a good feed and surviving. On the other hand, wolves that didn't happen to get upset by the scent of deers were likely to starve, and die out instead of procreating. In other words, when little Fitzroy gets all adrenalized in the middle of the dark night, it's because his wolf genes are trying to persuade him that he should go out and capture a wild beast, to satisfy his hunger. But, insofar as Fitzroy's belly is already full of pasta and croquettes, his little dog's mind is puzzled about the logic of the signals being received from his muzzle and his archaic wolf genes. Ah, life is not necessarily easy when your closest ancestors were wild hungry wolves. It's easier for us humans because it's quite a long time since we dropped the habit of racing after deers in the middle of the night… if ever we behaved in such a way.

Once upon a time, I used to wonder how I might react if a glorious female creature were to sneak quietly into my bed while I was sound asleep, dreaming of Grecian nymphs. Would the powerful waves emitted by her presence react upon my archaic primate genes in such a way as to interrupt abruptly my snoring, and wake me up? Maybe they would. Maybe they wouldn't. To be perfectly honest, I've never had an opportunity of testing the experimental scenario I've just outlined. In any case, I'm sure as hell that I wouldn't start to bark or howl or race around crazily in the dark night. So, which of us males is better off, Fitzroy or me? It's hard to say...

BREAKING NEWS: Once again, at 2 o'clock in the middle of the night, Fitzroy spent half-an-hour barking. This morning, during our ritual walk up the road, the two dogs went out of their way to investigate scents in Gamone Creek up at the level of Bob's place, but without digging up anything. I've just been chatting with a hunter who strolled by with his dog, in the role of the advance scout (without a gun). He confirmed that there's a wild boar hiding in the creek up there, and that they plan to root him out later on in the day. So, we're promised a Wild West afternoon at Gamone, with gunshots, shouting and men and beasts scrambling down the slopes. I've often thought that what we need here at Choranche, particularly in the hunting season, is an elected sheriff. Meanwhile, with a wild boar in the neighborhood, the temporary winners are the roe deers and pheasants, which are considered by the hunters as relatively uninteresting small fry. Confronted by a terrified cornered boar, a hound can get its belly ripped open by the tusks of the beast. (Sophia and Fitzroy would scamper to safety before any such encounter.) The hunters no doubt appreciate this dimension of risk, and the aroma of blood. To my mind, it evokes bull-fighting accidents such as when a picador's horse is gored.

Saturday, August 28, 2010

British tribes

I've just been reading these two books, which tackle a fascinating subject: the genetic origins of the peoples of the British Isles.

Written by English authors—Stephen Oppenheimer and Bryan Sykes—both books were published in 2006. Curiously, each of the two authors gives the impression that he ignores the work of the other… even though they are both associated with the University of Oxford. They use both maternal (mitochondrial DNA) and paternal (Y-chromosome) data to reach their conclusions, which are rather similar. Basically, the people of Great Britain (England, Scotland and Wales) and Ireland are the descendants of settlers from the Iberian Peninsula (today's Spain and Portugal) who migrated up to the British Isles at the end of the Ice Age, some 15 millennia ago. In other words, our most ancient ancestors were the indigenous Cro-Magnons, rather than relatively recent colonists from the east. Among other things, this means that our indigenous European ancestors evolved spontaneously from being hunters and food-gatherers into the state of graziers and farmers. They were not simply replaced by eastern invaders who brought this know-how with them. As for legendary cultural phenomena such as the Celticism of the Gaelic-speaking lands, and the alleged Anglo-Saxon roots of the English, these must be thought of, genetically, as relatively-recent minor modifications, imported into the British Isles from the European continent, and limited largely to language.

I regret that both authors have resorted to nicknames for the various mtDNA and Y-chromosome haplogroups at the base of their vast research. For example, my personal DNA testing has placed me in a precise paternal haplogroup designated as R1b1b2a1b5. For Oppenheimer, on the other hand, I'm a member of the Ruisko tribe, which Sykes prefers to label the Oisin tribe. For serious adepts of DNA testing, the official haplogroup terminology is both necessary and sufficient, and the silly nicknames introduced by Oppenheimer and Sykes serve no useful purpose.

The existence of interesting in-depth studies such as those of Oppenheimer and Sykes evokes a common criticism that is often raised by people who are wary of the validity of all kinds of genealogical research, be it strictly personal (as when I explain with pride that my Skyvington patriarch in England came over with William the Conqueror, or that I've established another ancestral line running back up to this same Norman invader) or applied to the peoples of vast regions such as the British Isles. To get the gist of this criticism, look at the following pedigree chart (so-called because all the T-shaped signs can be imagined as goose tracks), in which my paternal ancestors are designated by blue dots, and my maternal ancestors by pink dots:

Now, it's all very well to determine the paternal tribe of the most ancient blue dot in our pedigree, and the maternal tribe of the earliest pink dot. But what about the respective tribes of the "infinite" (well, almost) horde of ancestors who aren't even apparent in my pedigree, let alone designated by any kind of dot? Surely, it's a grotesque over-simplification to allege that I belong to the Ruisko/Oisin tribe merely because of the blue dots in my pedigree. For example, let's imagine that one of my female ancestors happened to be a daughter of Boadicea, or that another had married Attila the Hun. Wouldn't perfectly-plausible family-history events such as these put a few gigantic flies in the ointment associated with the tidy little system of blue and pink dots? To put things in a more recent context, if I were suddenly to discover that one of my ancestors was a hitherto-unidentified offspring of Jack the Ripper, then my personal genetic package would owe no less to Jack and his clan than to any other distinguished tribe of Prehistory or Antiquity, and my inherited characteristics would certainly be more closely linked to those of the Ripper than to those of the Conqueror. Now, every serious researcher in genealogy should be perfectly aware of this common-sense situation. We describe the rare ancestral lines that we've been able to unearth, whereas we have nothing whatsoever to say (at least for the moment) about the vast network of untraced lines up into the mysterious past.

Getting back to the kind of research conducted by Oppenheimer and Sykes, isn't it a huge weakness to draw conclusions based merely upon the Y-chromosome and mtDNA profiles of present-day residents of the British Isles? If they had tested, say, a (fictive) London chap named George Skyvington and found that he (like me) was a descendant of the Ruisko/Oisin tribe, wouldn't they be drawing hasty and unsound conclusions by ignoring, as it were, that George might have had lots of other ancestors from quite remote tribes: Eskimos, American Red Indians, Chinese, Pacific Islanders, Tasmanian Aborigines, etc? Doesn't the absence of such perfectly-real ancestors cast a dark cloud of incompleteness or imperfection upon the global outcome of the research carried out by Oppenheimer and Sykes?

No, not at all. Don't forget that these researchers have been performing DNA tests upon large groups of people living in the British Isles. Consequently, if indeed our George Skyvington had ancestors belonging to "tribes" such as Eskimos, American Red Indians, etc, then it's possible that the existence of these ancestors will show up in the Y-chromosome and mtDNA data obtained from some of George's "genetic cousins"… about whom he probably knows nothing (and never will). Statistically, if the tested population is large enough (a criterion that can be determined mathematically), everything should come out in the wash, as it were. George's Eskimo and Red Indian ancestors won't be totally forgotten. They'll merely be associated with other tested individuals. And George won't even be tempted to complain about "his" ancestors being associated with total strangers, because he simply won't know that this has happened. Maybe George might even look at research results and say to himself: "My God, to think that, here in my native England, I'm living alongside descendants of Eskimos, American Red Indians, Chinese, Pacific Islanders, Tasmanian Aborigines, etc!"

Thursday, March 11, 2010

Scandinavian nuts and bolts

A recent article by Florence Williams in Slate [display] reveals apparent differences between Danish and Swedish males concerning the respective volumes of their genital resources.

Should the world at large be fascinated by this Swedish victory in the Prick and Balls Olympic event? The answer is no doubt yes. If things can shrivel up to such an extent between two neighboring nations, then we should try to understand what has happened... because the same sort of thing might just be happening in our own backyard, maybe even between neighbors with differing lifestyles. There's no smoke without a fire. So, there must be some set of underlying reasons why Swedes would appear to be getting it up better than Danes. It can't be the ambient climate, because it's much of a muchness. And it would be hard to imagine that cultural and lifestyle factors might account for this difference. There's no way in the world that you'll convince me that reading the delightful tales of Hans Christian Andersen, and eating Danish pastry, might have stealthily diminished the size of my John Thomas... and that the only way of getting things back to normal would consist of a strenuous acquaintance with the plays of August Swinberg and the films of Ingmar Bergman, combined with a massive daily intake of crisp bread and fermented fish, consumed in an Ikea environment.

Seriously: What exactly is it that might have influenced the respective qualities of the procreative devices of Danes and Swedes? That's an interesting question, but we don't yet know the answer. As they say in the classics, there will surely be a next episode...

Friday, February 19, 2010

Basques are not as bizarre as all that

When I first arrived in France, I was amused to find people advising me, apparently in a serious manner, that the best way by far to learn French was in bed. And that's how I soon became a serious language student. For a long time, in this spirit, I've had a theory that the ideal way in which to acquire a certain understanding, not only of a foreign language, but of peoples and even regions, is through a female friend who's associated with the language, land or region in question. In any case, that's the way the cookie has always crumbled for me personally. Inversely, I've often thought that one of the explanations (cause or rather an effect?) of my aloofness concerning both my native land and the USA, for example, is the sad fact that I've never, at any moment, been involved in a passionate relationship with an Australian or an American. [This is not a distressed call for help!]


The ancient Basque Country covers a tiny corner of Spain and an even tinier corner of south-west France, in the vicinity of the Bay of Biscay. I've never had an opportunity of visiting this region. On the other hand, I had a Basque girlfriend in Paris for several years and, through her, I've always felt a kind of solidarity (no doubt superficial) with the Basque region and culture. Besides, as soon as she started to talk about her last visit to her relatives in the vicinity of Biarritz, she would abandon her usual lighthearted conversational style and adopt an almost solemn tone, as if to inform me that there should be no joking about her beloved region. It would have been unthinkable for me to make a remark of any kind concerning notorious events that were mentioned regularly by the media: the activities in Spain and France of partisans of the creation of an autonomous Basque nation.

Many Australians have heard of Basque beaches where surfing competitions take place. The sport that is most readily associated with this people is Basque pelota, derived from the quaint old game of "royal tennis".

Over recent decades, many curious legends have been circulating on the subject of the Basque people, who are often considered as a unique biological family, who might even be direct descendants of Cro-Magnon man. These legends probably came into existence initially because of the mysterious Basque language, which is indeed unique. It does not belong to the vast group of so-called Indo-European languages, and it appears to be unrelated to any other language in the world. Then, when blood tests appeared on the scene, it was found that 20 percent of Basques are Rh negative, as compared to only 15 percent among the English, and 3 percent among the Chinese. Even the great pioneer of population genetics Luigi Luca Cavalli-Sforza still looks upon this fact as evidence in favor of the Cro-Magnon hypothesis.

DNA testing then stepped into this arena, and it has clarified our ideas, and even changed them in many ways. Two days ago, a major article on the Basque question was published online [display]. It reveals that "a genome-wide survey does not show the genetic distinctiveness of Basques", who cannot be considered a genetic outsider. The authors of the article conclude that "interpretations on their origin may have to be revised". Now, I'm not sure that my former girlfriend would be happy to learn that there's nothing special about the Basques.

Much current research into the origins of Europeans concerns the famous R1b1b2 haplogroup, which is widespread throughout Europe. [I myself belong to the R1b1b2a1b5 subgroup, designated since the end of 2008 as the R-L21 family, with our own website.] Now, it has been known for quite a while that most Basques belong to this R1b1b2 haplogroup. The big question facing population geneticists has been this: What were the relative contributions to modern European populations of Paleolithic hunter-gatherers and Neolithic farmers from the Middle East? In other words, were our ancestors basically Old Stone Age hunter-gatherers who finally transformed their way of life when they heard about the possibility of becoming farmers? Or were our ancestors New Stone Age farmers who migrated to Europe, maybe only 10,000 years ago, from their Middle Eastern lands of origin? The answer seems to be that there was an equivalent dosage of both these origins. But in all cases, Y-chromosome research indicates that the origin of the Basques was no different to that of other Europeans.

So, how do specialists explain the Rh negative phenomenon? Well, it now appears that blood groups are not a trustworthy standard in population genetics, since they can be influenced, over the centuries, by the spread of diseases. And how do linguists explain the strange Basque language? For the moment, they can't...

Sunday, February 14, 2010

Inuk the Eskimo

It's truly fantastic to hear that scientists have used a specimen of permafrost-preserved hair to sequence the genome of a male, known henceforth as Inuk, who lived in Greenland some 4,000 years ago.

This feat was performed under the direction of two Danish geneticists, Morten Rasmussen and Eske Willerslev, and their results were confirmed by laboratories throughout the planet... including a DNA laboratory at Murdoch University in Perth and an Australian police laboratory in Canberra.

The basic article concerning this achievement, entitled Ancient human genome sequence of an extinct Palaeo-Eskimo, appeared in the journal Nature. [Click the banner to access the article.]

Inuk's paternal haplogroup is designated as Q1a, which characterizes peoples who migrated from Siberia into the New World some 5,500 years ago. He belonged to a cultural group called the Saqqaq. Funnily, this means that Inuk does not belong to the same family as modern Inuit populations. To obtain their spectacular results, the researchers had to identify over a third of a million SNPs (single-nucleotide polymorphisms, called "snips"). The most amazing aspect of these findings is that Inuk's genome provides the researchers with a lot of interesting facts about this man's physical features:

— His blood type was A+.

— He probably had brown eyes.

— His skin and hair were probably rather dark. Besides, he would have normally become bald at an early age.

— He probably had front teeth of a form designated as "shovel-graded".

— His earwax was probably of a dry kind, like that of Asians and Native Americans (as distinct from the wet earwax of other ethnic groups).

It's amusing to learn that, since none of the institutions involved in this project employ Saqqaq descendants, the chances of errors due to DNA contamination from laboratory assistants were practically zero.

In my recent article entitled Nativity rites [display], I made a plea in favor of the systematic DNA-testing of babies. My old friend Odile phoned me the next day to tell me that she thought I had "blown a fuse"... which suggests that many people still regard DNA-testing as a weird operation. No, I persist and sign this idea— which is not at all crazy—of nativity rites of a new kind, based upon a DNA record for the newborn child. When we observe the fascinating facts that can be gleaned from a DNA specimen that dates from four millennia ago, it becomes obvious that we should encourage the generalized registration of such fabulous individual "blueprints".