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

Thursday, February 19, 2009

DNA test

To celebrate the birthday of Charles Darwin, I finally decided to order a DNA test. As everybody knows, the results will reveal the particular species of monkey from which I descend, and the jungle in which my ancestors lived, maybe even the kind of trees in which they built their homes. Besides that, this DNA test will no doubt confirm that I have an exceptionally high level of extremely healthy and active intelligence genes, and that I was genetically endowed to be a really superior guy from every point of view. Based upon hard facts, the test will no doubt also explain scientifically (for those who were not already aware of this particular aspect of my being) why I've always had a terrific sensual effect upon beautiful women, a little like Julio Iglesias (but without the singing) or George Clooney (without the Nescafé ads). And I'll be getting all this great information sent to my doorstep, direct from Arizona, for no more than 120 euros.

Well, the results of the test might not be quite like that. So maybe I should set aside my wishful thinking and describe the DNA test in a more modest down-to-earth way.

[Click the logo to visit the Family Tree DNA website.]

I lost no time in choosing a company to carry out my test because, in the genealogical domain, there aren't really very many companies around. The laboratories that you hear of in the news—when scientists talk, say, about cracking the genome of Neanderthals or the possibility of cloning furry mammoths—are not concerned with the DNA of ordinary mortals such as you and me. Most of the high-profile companies that advertise their high-priced services in DNA analysis are medically-oriented, which means that they're capable of obtaining personal data about your genetic makeup that might just prevent your descendants, one of these days, from purchasing life insurance, finding a partner and procreating, or even getting certain jobs. Apart from that, though, it's great to know yourself better from a health viewpoint. As far as genealogy is concerned, most people seem to agree that the Arizona-based company called Family Tree DNA is the ideal door to knock on, because they propose an infrastructure enabling you to meet up with other individuals with comparable DNA profiles.

One of the first sobering things you learn, when you step into the domain of genealogical DNA tests, is that specialists refer to the precious molecular fragments used in their analyses as junk DNA. Now, this doesn't mean that they think your ancestors are trash. Even if a living prince were to use DNA testing to confirm that he descended from a long-dead king, this would be done by means of junk DNA. The adjective "junk" simply draws attention to the curious fact (well, it's curious for newcomers) that the fragments of the DNA double helix yielding the most information as far as family links are concerned lie outside the all-important sequences of genetic coding that determine what kind of hereditary makeup we have. Between the genes, in our lengthy strand of DNA, there's a vast quantity of chemical "noise" (to borrow the term used by communications engineers), which doesn't play any role in determining our inherited nature. Well, this junk part of our DNA reveals certain patterns that remain constant from a father to his sons. These patterns get copied in the Y-chromosome, found only in males. Consequently, if the DNA of two males happens to contain identical patterns of this kind, that means that their paternal ancestral lines reach back to a unique male individual.

What does this mean at a practical level? Let me give you an example. In an article written in August 2007 entitled Dorset ancestral anecdotes [display], I mentioned an old pump organ that I discovered (and actually played) in the village of Blandford.

The label on the instrument mentioned a William Skivington, proprietor of a local music shop.

The UK census of 1861 mentions this fellow and his family, and refers to him as a piano tuner. I'm surely a relative of this individual, who lived from 1827 to 1912, but I've not yet been able to determine our exact links. Now, let's imagine an unlikely discovery. Let's suppose that, inside the organ in the Blandford folk museum, we happened to find a trace of blood that had been left there long ago when William Skivington hit his thumb with a hammer while repairing the instrument. Normally, if this fellow were indeed a distant cousin of mine, we should find that junk DNA recovered from the spot of blood in the organ has the same markers as in my own DNA test.

OK? Well, that fictitious scenario does not in fact describe the usual way in which genealogical researchers go about using the results of DNA tests. Although this approach would be theoretically sound, we don't generally go around searching in pump organs or cemeteries for specimens of the blood of our supposed ancestors. I would be more interested in coming upon a fellow who's living today, let's say a certain Fred Skivington settled over in Canada, who is convinced—through sound documentary evidence—that he is a descendant of the Dorset piano-tuner William Skivington. In such a situation, if Fred's DNA markers coincided with mine, then this would reveal that I, too, am related to the William of Blandford.

I'm obliged to admit, though, that it would be very tempting to have an opportunity of fossicking around in some of the ancient tombs over in the village of Skeffington in Leicestershire. You never know what kind of junk you might dig up there...

Friday, February 13, 2009

Announcements in genetics

Over the last 24 hours, the Creator seems to have joined in the Darwin Day celebrations by performing a neat little act of synchronicity, in the form of two interesting announcements in the genetics domain.

First, an official French report states that, according to recent research, genetically-modified corn can be consumed with no risks by humans.

Second, scientists in Germany reveal that they have fully reconstructed the genome of Neanderthals.

This good news suggests that if—as I hope—we end up cloning a new community of Neanderthal citizens, we should have no trouble in feeding them.

Thursday, February 12, 2009

Darwin Day

A few evenings ago, I saw an extraordinary 50-minute French-language TV documentary entitled Espèces d'espèces (Kinds of species), explaining how humans are cousins of countless creatures, organisms, plants, bacteria, etc. We have in common the undeniable fact (unknown, of course, to Charles Darwin) that we're all built out of strands of stuff called DNA.

An ingenious underlying element of the movie, which exploits superb graphics, was a novel representation of the "tree" of species in the form of a kind of big spherical cauliflower, which could have been mistaken for the fat brain of some mysterious giant creature. In fact, this "tree" might indeed be imagined, metaphorically, as the brain of a primordial virtual species that we can call DNA. The root of the tree has a lovely name: LUCA, the Last Universal Common Ancestor of the myriad DNA-based species that have existed on the planet Earth.

Although this has nothing to do with Darwin Day, that name reminds me, of course, of one of my favorite songs. So let me use that association as a pretext to celebrate Darwin Day by including in this post the famous song of Suzanne Vega... who is certainly one of the loveliest specimens of Homo sapiens I've ever admired.

Getting back to the "tree", we're obliged to admit that Homo sapiens is nothing more than a tiny blob on the outer surface of the cauliflower "cortex". We are neither more nor less important (whatever that might mean) than countless other blobs representing everything from whales, elephants and giant oak trees down to tiny insects and unicellular organisms such as bacteria.

Today, we can't evoke Darwin without thinking of one of his most brilliant offspring (metaphorically speaking): Richard Dawkins.

The TV documentary described an excursion that consisted of moving back from our Homo sapiens blob, down into the heart of the cauliflower, in pursuit of encounters with the ancestors of our various cousins. This is the same fabulous journey imagined by Dawkins in his book The Ancestor's Tale, mentioned in my article of August 13, 2008 entitled Exotic pilgrimage [display].

If you click on the portrait of Dawkins, you can see a delightful talk on atheism... which is so closely associated with Darwinism and the DNA species "tree" that I tend to think of them as part and parcel of a unique philosophy of enlightenment. And here's another nice Dawkins video:

To end this birthday post, here are links to an imaginary interview with Darwin [access] and a Scientific American article on the legacy of Darwin [access].

Wednesday, February 11, 2009

Marvelous creatures

There's a popular saying in French: "Tell me what you read, and I'll tell you who you are." In fact, it's an entire family of sayings, generated by replacing "read" by any other verb that enters your imagination. For example, a widespread variant: "Tell me what you eat, and I'll tell you who you are." The general idea is that such-and-such an aspect of your behavior is immensely revealing in a global sense.

I would be happy if the following subtle variation on this saying were to be applied, by friends, to me: "William, tell me what you admire in such-and-such a creature, and I'll tell you who you are." If friends were to address me in this manner, and they were to listen to what I had to say, their analyses of my trivial statements would have the sanctity of a prayer. They would be spot on. Take this splendid American goat, for example:

This female animal—whom I shall name Jeanie (with a single "n", please; see my PS), evoking genes—was created by means of genetic engineering. In other words, she's a kind of visitor from outer space. She looks like a goat, and she probably behaves like a goat. Humans who are so hungry that they're prepared to eat goat meat might even decide to kill this animal, cut up her carcass, cook the fragments and eat them... and they would surely conclude that the dear departed creature actually tasted like a goat. But Jeanie is no ordinary goat, for her DNA incorporates a human gene! And it wouldn't be wise to serve Jeanie up on a plate and eat her. Because your delicately-engineered asshole (not to mention more distinguished elements of your anatomy) might suddenly start to glow in a phosphorescent green, or send out Technicolor sparks, or anything whatsoever... because we simply do not know how genetically-engineered creatures such as Jeanie might fit into our archaic world. Consequently, it would be wise, at least for the moment, to prevent Jeanie from going out on the town of a Saturday evening, and screwing around with any old billy-goat at all.

Meanwhile, Jeanie provides us with huge quantities of a precious protein called antithrombin, capable of preventing fatal blood clots in certain sick humans. Jeanie might be obliged to remain forever cloistered in a convent, like a saint with genetic stigmata, but the benefits of her existence impinge upon countless humans.

So, there you are. I've told you what I admire about the marvelous goat Jeanie. But frankly, even though you might have certain ideas on the subject, I don't think it's all that important to talk, now, about who I might be. Because everybody knows...

POST SCRIPTUM: Why have I christened this fine goat Jeanie? In 1952, a Hollywood musical incorporated a catching soft song with the refrain: "I dream of Jeanie with her light brown hair."

The tender female in question was a pale-skinned romantic Old World lass, initially portrayed by an ethereal Andrea Leeds in Swanee. Well, by chance, at that time (when I was starting high school in Grafton), my paternal grandparents, Pop and Ma, happened to employ an Aboriginal girl named Jeanie in their house at 12 Robinson Avenue. Now, lovely Jeanie (whom I remember so well) was uniformly ebony from top to bottom, including her thick black hair. In a dimly-lit bedroom, you would catch no more than the glimmer in her eyes and a flash of her pearl-white teeth. The refined sense of humor of my grandfather (whose manners remained forever strictly Victorian) extended often to mentioning with a grin, but ever so politely, their dear "Jeanie with her light brown hair".

Saturday, December 6, 2008

Correlation between balls and brains

When I was a teenager in Australia, a good way of insulting a fellow was to call him a dickhead. I must admit, though, that I never really knew whether this was intended to mean that his head had the same shape as a penis, or an equivalent degree of intelligence, or a similar vocation in life, or some other more subtle resemblance.

Today, scientific research carried out in the UK has revealed that men of higher intelligence appear to have sperm of better quality. Results indicated that smart males who obtained higher notes in IQ tests tended to produce a greater quantity of sperm with greater mobility.

Now, if you're anything like me, I'll bet you were surprised to learn—in that last sentence—that mobility is an important factor in the clinical evaluation of sperm. We don't generally tend to imagine that these little critters need to travel to and from work every day, or that they like to go out driving in the countryside of a weekend. Well, the truth of the matter is that a lazy sperm who is not constantly up and about, in the style of an early bird catching worms, serves no useful purpose. The unique raison d'être of a self-respecting sperm is to track down an egg, crack it open and devour it in a single gulp, sunny side up. There's lots of tough competition from other sperms, who are totally lacking in brotherly love. In their search for an egg, they jostle and trample one another violently, like US shoppers stampeding into a Wal-Mart on sales day. Suffice it to say: May the best sperm win! We're talking of the most mobile young chap, in top physical form, with first-class sporting footware, at the wheel of the procreative equivalent of a red Ferrari. The brutal battle between competing sperms is a terribly vicious affair... like the Democratic primaries in the USA or the installation of a governing committee in the French Socialist party. Weak-hearted sperms, those that have let their regular gym work slip, those that drink, or those that have wasted their physical resources hanging around in bars with loose women, don't stand a chance. The quest for the egg, like the Graal, is even more terrifyingly Herculean than the Triwizard Tournament in Harry Potter and the Goblet of Fire.

The "dickhead" epithet might therefore be a disguised compliment, designating a superior male with balls in his brain (or maybe rather brains in his balls), whose gushing intellect and spurts of wisdom have the same volume and mobility as his sperm. In any case, this correlation between superior intelligence and award-winning sperm has an interesting corollary. Normally, according to Darwinian evolution, top-quality sperm should have a greater survival value, and it should be giving rise to more and more offspring with superior intelligence. In other words, our planet should be subjected to a relentless phenomenon of ever-increasing intelligence. Spiraling brilliance, wisdom, creativity... you name it. Frankly, I don't know. From my personal viewpoint, I'm convinced that, in our marvelous modern world, there are indeed more and more... dickheads.

Saturday, November 29, 2008

Lively neighborhood

This is the road a few kilometers up above Gamone. The cliff in the background has a name like a movie star: Tina Dalle. In fact, dalle is the French word for a stone slab. This particular cliff, which I can see quite clearly from the slopes behind my house, is used as a training site by the French rock-climbing federation. In the foreground, the road snakes through a couple of small tunnels just before it reaches the plateau of Presles.

In the middle of the vast tree-studded plateau beyond Presles, these moss-covered limestone rocks are the entrance to a splendid cavern called Prélétang, which was used as a shelter, for millennia, both by wild animals and Neanderthals. The latter, who spent most of their time down in the valley, would only venture up to Prélétang during the summer months. Unfortunately, I arrived here a little too late to meet up with such residents.

Back in those days—during a relatively warm period, some 50 millennia ago, at the end of the fourth and final Ice Age—all the members of Neanderthal families would go out together, in summer, on hunting excursions. So, the plateau up above Choranche must have been quite a lively place. By comparison, today, I saw only a single hunter at Gamone, searching for an elusive wild boar, and I heard no more than two or three shots... which were nevertheless sufficient to terrify my dog Sophia, whose archaic brain has learned over eons of time that loud bangs of all kinds spell trouble and danger.

Before the arrival of the Neanderthals, Prélétang was occupied above all by cave bears, for whom the cavern was an ideal place for hibernation. Bones of these animals were found inside Prélétang, and one is tempted to imagine a Neanderthal family, seated around a fire at the entrance to the cavern and chomping into bear steaks. Alas, the Neanderthals would have found it difficult to kill such huge beasts. So, the bear bones probably resulted from attacks by wolves or cave lions, or maybe simply old age.

What's that block of colors doing in the middle of my Stone Age reverie? Answer: They're the graphical representations used in my recently-acquired genetics bible, described in my article entitled Big book [display], to designate the four kinds of bases found in the nucleotides of a strand of DNA. In simple terms, you can call them the four "letters" of the "alphabet" of life on the planet Earth. All kinds of life, with no exceptions: plants, bacteria, insects, fish, frogs, birds, bears, Neanderthals, you, me, etc. Even Sarah Palin and Pope Benedict XVI are said to be composed of DNA. Indeed, as far as can be ascertained, the only allegedly living entities (?) that might not be built out of strands of adenine, thymine, guanine and cytosine are God, the Holy Ghost, angels, cherubim and maybe various fantastic creatures such as elves, centaurs, fairies, leprechauns, unicorns, mermaids, etc... although I hasten to admit that the basic problem concerning all these entities is that scientists have not yet been able to carry out enough serious laboratory testing.

Now, what was it that got me started talking about such questions? DNA. You see, certain researchers are starting to evoke the possibility of using their skills in genetic engineering, combined with a few archaic tufts of hair, say, to rebuild all kinds of marvelous creatures that we have long imagined as extinct.

What's that big fellow doing in the middle of the computer screen? Well, he's one of the first candidates for reconstruction that comes to mind, because scientists have just announced that they've finally deciphered more than three-quarters of the genome of the woolly mammoth, using specimens of hair from an animal that died in Siberia at about the same time, 20 millenia ago, that naked apes like me started to arrive in Choranche, where they may have wondered why all the Neanderthals had apparently disappeared. (Don't ask me. For all I know, they may have moved down to the French Riviera.)

Nobody, of course, is going to attempt to synthesize a latter-day mammoth from scratch, as it were. The only feasible technique for producing something that might look like a woolly mammoth consists of taking an elephant cell and modifying its DNA so that it starts to resemble the genome of the extinct animal.

Californian scientists have also recovered and successfully analyzed the DNA in the tooth of a cave bear that lived over 40 thousand years ago. So, there's another candidate for genetic resurrection. But will researchers be content with recreating a few wild beasts? Well, the Max Planck Institute for Evolutionary Anthropology and a Roche company in Connecticut have just spent two years sequencing the Neanderthal genome, which is 99.5 percent identical to our human genome. It would be perfectly feasible to take a chimpanzee cell and nudge its DNA into emerging as something that looked like Neanderthal stuff.

I'm sure that a latter-day Neanderthal would feel perfectly at home here on the slopes of Choranche. Besides, I've got a spare bedroom at Gamone, I can dish up all kinds of food (once my guests tell me what they like and don't like to eat), and I would be prepared to drive him/her up to Prélétang for summer hunting excursions. The only minor problem is that I can't be certain beforehand that my dog Sophia might not be racist. That would surprise me, though. Besides, I'm sure that Neanderthals would be nice neighbors.

Wednesday, November 19, 2008

Big book

For a long time, particularly since my discovery of the extraordinary books of Richard Dawkins, I've thought it would be a good idea for me to get acquainted with the technical details of genetics: that's to say, of molecular biology. My reading matter in this domain was starting to get a little antiquated. Above all, much of it was poorly written stuff, and this is no longer acceptable in a field where authors are expected to write almost as well as Dawkins. What I wanted was simple: a good textbook about genetics, DNA, etc... Well, in this morning's mail, Amazon supplied me with exactly what I was looking for.

This huge book looks fabulous. The bible! Just what I need. Didactic with superb graphics. The only problem is that I won't be able to read it in bed of a late evening. It weighs a ton, and the paper product doesn't even include the latest chapters, supplied on a DVD. Great stuff as a substitute for evening TV.

Thursday, October 30, 2008

The world is afraid

Here in France, many people are holding their breath, anguished by the thought that something might happen in the unpredictable USA, between now and next Tuesday evening, to prevent Barack Obama from becoming president. In browsing through the Internet press, I have the impression that the Western world at large shares this same fear that something might go wrong at the last minute: either electoral fraud or simply the unspoken refusal to elect a black man. The most terrifying scenario of all, as many commentators have pointed out, would be the election of McCain, followed closely by his death, resulting in the appointment of Mrs Moose to replace him.

Concerning Sarah Palin, there would appear to be no limits to her ignorance and stupidity, combined with a stubborn belief in herself. She's the proverbial dumb bitch, capable of making even George W Bush look like a bright guy. She accompanies her hot air with winks, no doubt believing that common folk will find her smart and cute. And a lot of other dumb Americans probably do find her smart and cute, because she reminds them of the nice fuzzy image they have of themselves. In a policy speech on what she thinks of as misdirected federal funds, Palin wrinkled her silly forehead while looking for examples of wrongful spending, and blurted out: "Things like fruit fly research in Paris, France. I kid you not." [Note the archaic teenage colloquialism, meant to make her sound savvy.]

Research exploiting the insect in question, Drosophila, has contributed greatly to modern genetics, and so-called vinegar flies are still playing a role in this domain. The US embryologist Thomas Hunt Morgan used these tiny red-eyed creatures to investigate mutations, and he was the first geneticist to be awarded the Nobel Prize in Physiology or Medicine, in 1933, for his discoveries on the role of chromosomes in heredity.

Palin is such an idiot that she can't even realize that research in genetics might one day put an end to trisomy 21, from which one of her own kids suffers. Appalled by Palin's words, the White House correspondent for Newsweek, Richard Wolffe, said: "This is the most mindless, ignorant, uninformed comment we have seen from Governor Palin so far, and there has been a lot of competition for that prize." Personally, I would prefer to give Palin the jackpot prize for her beliefs in so-called creationism: you know, all that shit about Adam and Eve walking around with dinosaurs some six thousand years ago. In any case, no matter what outstanding stupidity awards we give her, that woman is clearly an American catastrophe.

Tuesday, September 16, 2008

Is there such a thing as French blood?

The question in my title is deliberately rhetorical and provocative, merely to draw attention. It's like a newspaper heading such as: Must man who bit dog wear muzzle? A more rigorous down-to-earth title for the present post would have been: Are there correlations between DNA and the geographical origins of Europeans? It would appear that the answer to that intriguing question is yes. In any case, what I want to do in this post is to summarize what I've understood—if anything at all—about this question, and about the answers provided by research assisted by the GlaxoSmithKline pharmaceutical company. Maybe readers who are better versed in genetics than me might correct possible blunders in what I have to say... or they might consider that this subject is so fuzzy that it's better not to say anything at all.

Let's start at the beginning. We all know that the basic stuff of life, DNA, can be imagined as a lengthy "word" written by means of only four "letters". In the following fragment of DNA, I've represented the four "letters" by arbitrary colors:

Now, let me drop the inverted commas around "letter": a metaphor for nucleotide. From one human being to another, throughout the planet, 99% of DNA sequences are identical. But every now and again, for such-and-such a fragment of DNA, one of the letters might be different, as illustrated here:

As you can see, in the normal fragment of DNA, the third letter is green, whereas in the case of the individual we've just encountered, the third letter is red. If this kind of variation occurs for at least one in every hundred new individuals they examine, geneticists refer to the changed letter as an SNP, pronounced "snip". In the case of humans, potential snips are commonplace. They probably number around 3 million. But, as I said, for any particular snip, only a small proportion of humans will possess the changed letter. Concerning the vast majority of snips, geneticists have no idea whatsoever of the consequences upon an individual, if any, of the changed letter. On the other hand, certain snips have been identified as sources of possible health problems, meaning that they can be used as medical indicators... which is why snips are of interest to pharmaceutical companies such as GlaxoSmithKline.

Let's get back to the question of European geography. The research project was headed by Manfred Kayser, a geneticist at Erasmus University at Rotterdam in the Netherlands. Researchers were able to use a vast collection of European DNA samples that had been obtained by GlaxoSmithKline in the context of their constant hunt for genes responsible for side effects brought about by certain pharmaceutical products. Within the DNA sample for each European studied by Kayser's teams (including researchers at the University of California, Los Angeles), half a million snips were examined. When I say "examined", that merely means that the researchers noted whether each snip letter, for that individual, was normal or anomalous. The result of this analysis was a huge collection of yes/no snip data for each person being studied. Using conventional number-crunching methods, all this data was reduced in such a way that the individual's snip profile could be represented as a point on a two-dimensional graph. And the researchers added an elementary item of information to each point: namely, the place where that individual happened to be born.

Well, the results were astounding. All the points corresponding to individuals born in France formed a cluster, which was located alongside another cluster of the points corresponding to individuals born in Italy, and so on... In other words, the geneticists' graph of snip profiles was equivalent to a geographical map of Europe! Consequently, it's a fact that, if a new human candidate were to be examined, and his snip profile happened to fall inside the French cluster, there's a good chance that he's a Frenchman.

In fact, there's very little genetic diversity within Europe, because people have remained largely within their territorial borders. Not surprisingly, the researchers found that the greatest diversity existed in Mediterranean Europe, whereas Scandinavian, British and Irish data was more uniform. Noah Rosenberg, a geneticist at the University of Michigan in Ann Arbor, concluded: "A pattern in which genes mirror geography is essentially what you would expect from a history in which people moved slowly and mated mainly with their close neighbors."

It's important to understand that this research has little to do with chromosomes, genes and inheritance. It's simply a matter of the statistical analysis of snip data, correlated with geography. It would be crazy to imagine that the researchers are suggesting, for example, that there's a "French gene" that might be injected into an Englishman (Heaven forbid!) to transform him into a Parisian. That would be just as crazy as the idea of a "lipstick gene" for pigs.

Thursday, August 28, 2008

Professional bias

The expression "professional bias" designates a mental conditioning brought about by the particularities of one's job. A contrived example is that of a race-car driver, say, who overtakes dangerously when he's out driving in the family automobile with his wife and kids.

Long ago, I started to suspect the existence of professional bias due to computer programming. I recall seeing a case of this, for the first time, in the conversational behavior of a colleague in Paris. He would periodically abandon the current topic about which he had been speaking in order to explore such-and-such an aspect in detail. Then, at the end of his detailed exploration, he would return to what he had been saying earlier on. On such occasions, he would inform his listeners that he was implementing the familiar programming concept referred to as a stack. He would do this by pointing out explicitly the moment at which he was about to "push down" (hide momentarily) the initial topic, and then, later on, the moment at which the hidden topic was about to "pop up" (reappear) once again. Insofar as a stack can be composed of multiple levels, which might be exploited in an irregular order, it can quickly become tedious for a listener confronted with a conversationalist with this kind of professional bias.

I soon realized that I myself was afflicted with this professional bias, which happens to infuriate my ex-wife and our two children. I have an even worse affliction due to the same causes. Faced with an ordinary real-world challenge such as building a kitchen cupboard, say, I tend to consider that the task has been satisfactorily completed as soon as I've convinced myself that I know how to perform the task in question, rather than when the intended outcome of the project has indeed become a reality. I conceal this strange outlook, unwittingly, behind a verb that also infuriates my ex-wife and children. I speak of "mastering a situation", which is a synonym for knowing how to do something. Inversely, whenever I'm reprimanded because I haven't actually done something I should have done, I get upset by the suggestion that I might not "master the situation" in an ideal fashion. In my mind, the fact that the job has not in fact been performed yet is of lesser importance than my conviction that I know how to do it. These reactions are of course pure symptoms of professional bias due to excessive immersion in computer programming activities, where the only thing that counts is the existence of adequate algorithms for performing tasks, no matter whether or not the algorithms in question have actually been applied to solve specific problems, or carry out particular computational jobs. I would be a hopeless boss of a small company (or a big one, for that matter). When the employees complained that they hadn't received their pay checks, I would say: "What's all the fuss about? Everything's in perfect order, and our computer can print out the payroll rapidly at the flick of a switch! "

Sometimes I felt a little ill at ease to realize that my mind might be warped by my work. I was reminded of a brief image in a film where you have a rear view of a sexton who kneels down piously on his right knee every time he passes in front of the altar. When the camera swings around to provide us with a front view of the dear man, we discover that he has worn a knee-level hole in the right leg of his trousers. I wondered whether excessive computer thinking might not have worn a hole in my mind.

Things have advanced rapidly since the time when I had such qualms. From one end to the other of a book such as How the Mind Works by Steven Pinker, which is already over ten years old, the author—a professor psychology from the Massachusetts Institute of Technology—exploits the so-called computational theory of the mind, according to which everything aspect of human thinking can and must be explained in terms of computing-programming paradigms and machine metaphors. When I wrote Machina Sapiens back in 1976, I thought at times that I might be a bit reckless in imagining that computers might get around, one day, to "thinking" in a more-or-less human-like fashion. Today, on the contrary, I realize that I didn't go nearly far enough in suggesting that, since Man is a kind of machine, it is quite feasible to imagine machines that will end up behaving much like human beings. We realize, though, that the task will be extremely difficult, and probably take a long time, not because there's anything of a non-mechanical nature in a human being, but because Evolution has had an immensely long time to put together the spectacular machine called Homo sapiens.

This man, named Douglas A Melton, is a US researcher in genetics, co-director of the Harvard Stem Cell Institute, whose goal consists of creating cells that are missing or defective in certain patients, particularly those suffering from diabetes. Yesterday, the journal Nature revealed that Melton's group has made a great step towards modifying the function of adult cells. This operation is designated, by means of a pure computing metaphor, as reprogramming the function of the cells. The Washington Post described the breakthrough as follows:

Through a series of painstaking experiments involving mice, the Harvard biologists pinpointed three crucial molecular switches that, when flipped, completely convert a common cell in the pancreas into the more precious insulin-producing ones that diabetics need to survive.

Here, the notion of molecular "switches" being "flipped" sounds like electronic engineering. In fact, it is computer talk, reflecting the fact that the DNA in a cell can be considered as a purely digital storage device, like the memory of a computer.

Up until last year, researchers in medical genetics were obliged to work with authentic embryonic cells, and this disturbed religious folk who felt that scientists were acting unethically. Then there was the welcome discovery that adult cells of any kind could be transformed into an embryonic state, enabling them to be coaxed into developing into any kind of desired cell for experimental work. The outcome of the Harvard work is that it will be possible to avoid the necessity of returning to the embryonic level, since adult cells will be reprogrammed in such a way that they actually become cells of a related kind.

For the moment, Melton and his fellow researchers have been working only with the cells of mice. So, a lot of work still remains to be done before the successful creation of a revolutionary branch of medicine that might be referred to as genetic surgery. In that future domain, based upon the notion of reprogramming human cell functions, it's likely that the technicians will talk among themselves, to a large extent, in the jargon of computer programmers.

Monday, April 21, 2008

Gene business

In the fascinating domain of modern genetics, one of the most exciting activities costs next to nothing. I'm referring to the possibility of purchasing and reading a few books on this subject by Richard Dawkins. But other interesting branches of the gene business can be far more costly.

Apart from the fact that they are both celebrated scientists in the field of genetics, what do these two men have in common? Well, they are among the rare human beings whose personal genomes have been totally mapped.

Several US companies are now offering services in this domain, but the fees are rather high. [Click any of the following company logos to visit their websites.] If I understand correctly, it suffices to send them a sealed tube of your saliva.

The Knome company in Massachusetts offers you the same treatment as for the above-mentioned scientists: that's to say, your entire genome will be sequenced, analyzed and interpreted. But the job will set you back a third of a million dollars.

The services offered by Navigenics, 23andMe and deCODE are far simpler.

They are cheaper, too, starting around the thousand bucks level. Navigenics and 23andMe are located in California, whereas deCODE is based in Iceland.

In all cases, the results are supposed to provide you with interesting data about potential health problems caused by the inheritance of dubious genes. In certain cases, you might be able to compare your genetic profile with that of friends and relatives, and maybe acquire genealogical information.

At the low end of the scale, for a few hundred dollars, you can send a saliva sample to the so-called DNA Ancestry Project, but I'm not sure that you can necessarily expect rewarding results.

The ideal approach to the question of the likelihood of inherited health problems still consists of compiling family health data, such as the causes of death indicated on death records. And it's hard to see how DNA analysis could provide us with more meaningful facts than those obtained through conventional genealogical research.

Personally, I'll no doubt take a closer look at the DNA Ancestry Project, in the hope of obtaining enlightenment, if possible, on a genealogical question that has always intrigued me. My maternal background was marked by a striking marriage between a respectable and industrious man, probably Scottish, named Charles Walker [1807-1860] and a younger Irish girl, Ann Hickey [1822-1898], whose father and at least one brother were notorious criminals. [Click here to visit a website about these ancestors.] I've often wondered whether it might be possible, today, to determine how their respective genes were allocated to various descendants, including myself. Sometimes, I end up thinking that I might have received a disproportionately large dose of bad Hickey genes, making me rather different to more respectable relatives with nice Walker genes. Or vice versa. But this reasoning could well be bad science. Rather than a question of bad genes.

AFTERTHOUGHT It would be fitting that my relatives might have their word to say on this fundamental question... but I'm not at all sure that they read Antipodes, and I'm even less certain that these dear folk (who didn't even wish to help me obtain retirement benefits from the supposedly-rich Australian government) might like to get involved in DNA analysis. At times, I feel that I should put a practical cross on my Australian past. Since my French naturalization, I see sadly that this is actually happening.

Monday, June 4, 2007


In genealogy, there's a relatively unusual approach that consists of only taking into account your female ancestors. So, you disregard your father entirely and look only at your mother. Likewise, you disregard your maternal grandfather, and look only at your mother's mother. And so on. The set of ancestors that you obtain in this way describes your so-called uterine ancestry. In many ways, it's a sound approach to genealogy. In concerning yourself constantly and exclusively with the unique womb in which each female ancestor developed, you remain on relatively firm ground. After all, an error at a maternal level is less likely, for obvious reasons, than ambiguities or downright lies concerning the identity of somebody's father. Besides, the concept of matrilineality (as it is called in genealogical terminology) corresponds to our intuitive impression of having once emerged from the body of our mother. To put it in silly terms, most humans surely feel more like a well-hatched egg than a grown-up sperm, even though we've learned that we're a little bit of both.

The only problem about family-history research of a strictly uterine orientation is that, in societies where a married woman takes the surname of her husband, the researcher is likely to run out of data rather rapidly, at least much earlier than in investigations in which both male and female ancestors are being researched. In the case of my personal research, the disparity between a purely patrilineal and a purely matrilineal approach is flagrant. Concerning possible ancestors called Skyvington—or a variant of this patronymic such as Skivington, Skevington, Skiffington, Skeffington, etc—I've already filled a small book with research results. [Click here to visit this website.] But, when I concentrate solely on my uterine line, I find my maternal grandmother Mary Jane Kennedy [1888-1966], my Irish-born maternal great-grandmother Mary Eliza Cranston [1858-1926], my maternal great-great-grandmother Eliza Dancey [1821-1904], and then I run into an ancestor named Mary Adams about whom I know nothing whatsoever. And there's little chance of my ever learning the name of this Mary's mother. So, I've run up against a genealogical brick wall after four or five matrilineal generations.

Now, the uterine approach to genealogy has some strange but positive consequences when we look at things from a genetic viewpoint... which is, after all, a perfectly normal way in which to deal with family history. Every human baby inherits from its mother a stock of weird stuff, stored in every one of our cells, called mitochondria (in fact, a form of DNA), which can be thought of as tiny energy suppliers. Were it not for our mother's gift of mitochondria, our cells would be like factories without fuel, or cities without electricity. We would instantly collapse and die. Human males, like females, need mitochondria to survive. But a father, unlike a mother, does not transmit any of his stuff to his children. And, because mitochondrial DNA is only transmitted down uterine lines, this means that it can be used as a "marker" (that's not quite the right term) in the genealogical domain. By analyzing the mitochondria of two individuals, it's possible to ascertain whether they have a common uterine ancestor.

In the context of the famous tomb at Talpiot, this was the kind of analysis that enabled geneticists to declare that the individuals designated as Jesus and Mariamne (allegedly Mary of Magdala) were not related in a matrilineal sense. And this conclusion made it feasible to imagine this couple as man and wife.

In fact, the existence of mitochondria makes it possible to hypothesize the existence of common female ancestors—vastly more ancient than Biblical women—for all human beings living today. Genetic genealogists use a rather unromantic name to refer to the most recent female in this role: Mitochondrial Eve. She wasn't exactly a plump white-skinned European beauty. Mitochondrial Eve lived in Africa some 150 thousand years ago. Whatever she looked like, she's the lady to whom we can say thanks for passing on to us the primordial cell energy enabling humans to crawl out of their beds every morning, to make hay while the sun shines... before getting back into their beds of an evening, maybe to make more mitochondria.

Sunday, May 13, 2007

Sepulcher cult

Respect of the dead is one of the most ancient human principles that exists. In the splendid trilogy of films by Jacques Malaterre on the origins of humanity, there are reconstructions of the primeval impact of death at a personal level, that of the family and companions of the deceased. The notion of a sepulcher probably occurred in the beginning as a simple pile of rocks concealing the putrefying corpse. Much later, the concept of individual life after death was concocted, and the sepulcher cult reached an apogee in ancient Egypt. Along with the processes of embalming and mummification, and the erection of elaborate stone sepulchers, the Egyptians codified alleged happenings in their Underworld.

In this New Empire papyrus, the dog-headed god Anubis (whose head has often been described erroneously as that of a jackal) guides the deceased person to his judgment, which uses a balance.

Christians have taken over this Ancient Egyptian concept of a guide in their Saint Christopher, who is actually depicted in this image with a dog's head. Not so long ago, devout Catholic drivers used to attach a St Christopher medal above the dashboard of their vehicle, without realizing that the main role of the prototype personage consisted of guiding individuals into the afterlife! [What a pity that there don't seem to be any statistics revealing the proportion of accident deaths in which the driver was "protected" by a St Christopher medal.]

Getting back to the theme of elaborate sepulchers, I must admit, as a genealogy enthusiast, that I'm always happy to discover ancestral tombs, which are often a primary source of data. Sometimes, on the contrary, tombstones display less reliable information than what you can find in church and government records.

The raison d'être of my musings on sepulchers is to ask a rhetorical question: Should we, today, continue to employ traditional funerary rites that have come down to us from past epochs? Or should they be modernized? And the reason why this subject has arisen in my mind is the news item about a lot of folk having paid money to have a few grams of the ashes of some 200 loved ones sent into space aboard a telephone-sized rocket. The exact price: $495 dollars a gram. [Click here to see this story.] The capsule orbited Earth for two weeks, as planned, before floating back down to the surface of our planet by means of a parachute. But the hilarious aftermath of this afterlife business is that the parachute apparently touched down at a remote and rugged site in New Mexico, which means that the "ashstronauts" have not yet been found. Did the space vehicle and its dead occupants get damaged during their re-entry into the atmosphere? How long will they be able to survive in the harsh desert conditions if rescuers don't reach them soon? Will, in fact, they ever be found? These are terrible questions, which cannot yet be answered.

Personally, I'm convinced that it's high time to ditch all archaic concern for the material remains of the dead. We should realize that corpses are corpses, and ashes are ashes. No more, no less. I believe that much of the ugliness of death can be attenuated by facing up to the fact that a corpse contains no traces of the consciousness and personality of the individual we once knew. So, it's silly to think that the deceased person might, somehow or other, get a kick out of his/her posthumous ride through space.

I can imagine a far more logical spatial trip towards posterity, which could even be organized while the individual is still alive. This would consist simply of using modern technology to obtain a digital copy of his/her genome and then beaming this into outer space by means of a high-energy transmitter, which might be called a Life Ray (as opposed to the death rays of a Star Trek kind). To keep it company on its never-ending journey through space, the genome could be associated with a digitized account of the genealogy and earthly achievements of the deceased. And why not even encapsulate in the Life Ray's message a digitized illustration of Anubis or Saint Christopher? The more the merrier on this excursion throughout Eternity!

Wednesday, April 18, 2007

Thin line between facts and Fascism

We're four days away from the first round of the French presidential elections. Since I'm not French, I won't be voting, but I have my personal aspirations and apprehensions. I would like to see a great victory for the Centrist François Bayrou, rather than the lightweight Socialist Ségolène Royal, because he appears to envisage French politics in a new light, without the eternal split between the Left and the Right. My vital hope, above all, is for the massive defeat of the Extreme Right of Jean-Marie Le Pen.

For the moment, the super favorite would appear to be Nicolas Sarkozy. I can understand this preference in the sense that many people would like to see France governed by a ferocious little bull terrier, which is exactly the image of Sarkozy. The possibility of a resurgence of Islamic terrorism in nearby Algeria promotes the case of a strongman such as Sarkozy, who doesn't beat around the bush when it comes to pointing a finger at societal outlaws, designated spontaneously as scum in need of Karcher-style cleansing.

In a recent interview with a philosopher, Sarkozy dropped an intellectual bombshell that was picked up immediately by everybody. First, in speaking of pedophiles, Sarkozy said: "One is born a pedophile. Besides, it's a problem in that we don't know how to handle this pathology." Then the pit bull turned to an adjacent subject: adolescent suicides. Here are the words of Sarkozy (my translation): "Some 1200 to 1300 young people commit suicide every year in France. They did so, not because their parents weren't taking care of them, but because they were genetically fragile, victims of a precursory pain." Programmed genetically to die. This is strong language, which brings to mind the terrible theme of eugenics.

Today, few people remember the unexpected but profound collaboration between the French Nobel prize-winner Alexis Carrell [1873-1944] and his young disciple, the American aviator Charles Lindbergh [1902-1974]. Carrell was a believer in eugenics: the science and potential technology of breeding humans like stud cattle. Hitler, among others, was fond of this theme.

Nicolas Sarkozy is a smart guy, and he knows where to stop, before going too far. He's perfectly aware (I hope) of the thin line that separates facts from Fascism.

Friday, March 9, 2007

Genealogy and genes

The Internet has changed genealogical research in both good and bad ways. First, the bad news. For me, it's summed up in the names of two money-making outfits named and Genes Reunited, which pester researchers constantly with publicity, trying to trap them into becoming paid-up members. These organizations lure newcomers into believing absurdly that family-history data will fall miraculously from the heavens, like rain, as soon as they join up.

On the positive side, I'm constantly thrilled by contacts from folk who've come upon one or other of my slowly-evolving websites concerning ancestors of my father and of my mother.

I'm eagerly awaiting delivery by Amazon of a new book: Stephen Oppenheimer, Saxons, Vikings and Celts: The Genetic Roots of Britain and Ireland. According to a review that appeared a few days ago, this medical geneticist from the University of Oxford claims that most present-day English, Irish, Scottish and Welsh people are highly similar from a genetic viewpoint. This leads to the interesting conclusion that Britain and Ireland have probably been inhabited for thousands of years by the same genetic stock, which would have been only marginally diluted later on by the arrivals of invaders described in history books: Celts, Romans, Angles , Saxons, Vikings and Normans. For the time being, Oppenheimer's views remain hypothetical, and other specialists in the genetic approach to genealogy have reached different conclusions.

Meanwhile, as Wednesday's votes are being counted in Northern Ireland, and Gerry Adams is waiting for a gesture of friendly conciliation from Ian Paisley, Ulster's tiny mind will no doubt find it impossible to conceive of the shocking notion that Catholics and Protestants might both be similarly-constituted human beings with identical genetic roots. Last night, French TV showed a brainwashed Belfast kid who was aghast, lost for words, when the reporter asked him if he could have friends on the other side of the wall. [Literally, the city is studded with walls to separate the communities.] We shouldn't even say it's religion that separates these two camps. It's just plain garden-variety ignorance and stupidity... of the kind that "inspired" many of our Australian bushranger "heroes".

Monday, March 5, 2007


When my Swedish cineast friend Eric M Nilsson visited me in December 2006, he shot a few images of me talking about Gamone, first in English, then in French. Click here to watch this video sequence. For me, it's amusing to see and hear myself speaking French. I'm not surprised that people notice instantly that I speak with an accent. The only individuals who never considered that I spoke French with an accent were my children, when they were kids. Apparently they would disagree with schoolmates who dared to suggest that I had an accent. For my children, their father spoke "normally".

At home, Christine and I always spoke French together, and with the children. So, they did not really grow up in a bilingual environment. But the intonations of my voice apparently rubbed off onto François, who became proficient at garbling in a way that sounded as if he might be speaking English. Meanwhile, he started studying English at school. One day, his teacher asked my wife: "Please explain something that has been puzzling me for ages. I often hear your son François speaking something that sounds like good English. Then, a moment later, I have the opposite impression, namely, that he doesn't understand English at all. Please tell me: Does François really speak English?" I love that story, because I knew my son well enough to appreciate exactly what was troubling his teacher. He has always been an instinctive actor, particularly apt at playing the roles of people he observed: in other words, a talented imitator. So, it was perfectly normal that he should start out by imitating the voice and accent of his father.

I've just finished reading a great book about imitation: The Meme Machine by Susan Blackmore. The term 'meme' (rhymes with 'cream') was invented in 1976 by Richard Dawkins in The Selfish Gene. It designates cultural entities that humans acquire by simply imitating other individuals who have already acquired such entities. For example, the art of using a mobile phone can be thought of as one of the countless memes in modern society. It so happens that I've never got around to acquiring that meme... mainly because nobody ever dials my mobile phone number, and I've not been sufficiently motivated to learn how to use this communications device... which I don't particularly like, preferring e-mail. When I ask my daughter to tell me the best way of learning how to use a mobile phone, she always explains that urban adolescents have seen how to use these gadgets simply by imitating the behavior of experienced friends who already knew how to use them. So, the art of using a mobile phone can indeed be thought of as a pure meme. And this meme has spread throughout society like an epidemic, through imitation.

Susan Blackmore is a fine writer, whose eclectic interests range from the psychology of consciousness through to meditation, paranormal phenomena and near-death experiences. The subject of her book, referred to as memetics, is a new discipline whose scope is awesome: the acquisition of all human behaviors and skills, from language through to the greatest achievements of the intellect. Since opening Blackmore's book a few days ago, I've had the constant impression that this is surely one of the most important books I've ever encountered, because it deals with every imaginable aspect of the whole human being. As I said, the underlying theme of memetics is that we've acquired everything that makes us human, all too human, simply by imitating others. (The general concept of imitation includes, of course, the possibility of reading books on a subject, and asking questions.) This ingenious explanation sounds almost too simple to be true.

Monday, December 25, 2006

The meaning of life

My title is misleading. A reader might imagine that I'm using the expression in the same style, say, as a distraught individual who cries out to a friend (or a priest or a psychiatrist): “Life has no meaning for me; I’ve decided to commit suicide.” There, it’s a question of “to be or not to be”: that's to say, meaning (or rather lack of meaning) à la Hamlet, à la Albert Camus:

There is but one truly serious philosophical problem and that is suicide. Judging whether life is or is not worth living amounts to answering the fundamental question of philosophy. All the rest—whether or not the world has three dimensions, whether the mind has nine or twelve categories—comes afterwards. These are games; one must first answer.

I first read those opening words of The Myth of Sisyphus when I was eighteen, out in Australia, and I was so impressed by the French Algerian-born author that I purchased several of his translated works, and even carried these books with me in my suitcases when I came to France in 1962... which was truly a case of bringing coals to Newcastle. Since then, I've totally revised my appreciation of the existentialist Nobel laureate. Like the US physicist Brian Greene [see The Fabric of the Cosmos], I’m no longer on the same wavelength—if ever this were the case—as Albert Camus. I don't, for a moment, consider that the pursuits of scientific research are mere "games" that should be put aside while an individual is deciding artistically (or otherwise) whether or not to blow his brains out. That suggestion, to my mind, is stupid, indeed grotesque. Besides, I'm not—and have never been—in the least bit suicidal. Human life on Earth—like all life in the Cosmos—is such a precious and fragile essence that one should not spill a drop of it.

The meaning of life is a clearcut affair for those who believe in Jesus... or any other divine entity, for that matter. Nonetheless, if a skull is ominously present, holding up the open Bible in this splendid depiction of Bruno in prayer (a curious visual reflection of the monk's own bald skull), this suggests that believers are constantly pursued by the gentle all-pervading presence of death, of human mortality. And this is normal. In extreme cases such as that of the Chartreux monks, whose earthly existence is characterized by a good dose of mortification, it might even be said that the global meaning of a monk’s life is to be found in the expected aftermath of his death.

But I said at the beginning that my title is misleading, since I was not referring to meaning of either the Hamlet/Camus or the Bruno kind. So, we might ask: What’s the meaning of “meaning” in my title? It’s a word whose archaic etymology is linked to the notion of mind. To look for the meaning of X is equivalent to asking: What do we have in mind when we refer to X? More precisely: What do we have in mind when we evoke the notion of living creatures such as plants, animals and Homo Sapiens?

That question found answers of a revolutionary kind in 1859, when Charles Darwin brought out a book with a long-winded title: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. Living creatures of a successful kind share a dominant feature. [That last sentence contains a hint of a pleonasm. If a creature is living vigorously—thriving, one might say—it is necessarily “of a successful kind”. Creatures that are not successful in life simply die out. Somebody once said that commuters only complain about trains that run late, whereas nobody ever talks about all the trains that run normally on time. On the great railway of life, it’s the opposite. We only meet up with creatures that have managed to get aboard the right train. All the rest disappear during the trip, and never reach their destination.]

As I was about to say, before getting led astray into talking about trains, thriving creatures share a dominant feature: that of being highly successful in the art of procreation. Years ago, when I was working in French TV, I found myself visiting the research laboratory of a French specialist in a bizarre discipline, linked to embryology, known as teratology: the study of monsters. He showed me his vast collection of malformed fetuses and babies, displayed in big jars of formaldehyde lined up on shelves along the walls of his laboratory. A teratologist uses a vocabulary of weird terms to designate the various kinds of monsters. If I remember correctly, “acephalous” indicates that the creature has no brain, and “cyclopean” means that there’s a single eye in the center of the forehead. I was impressed by a curious remark made by the teratologist: “Nature generally ensures that the most extreme kinds of malformations give rise to a creature that cannot survive. Consequently, we don’t normally encounter many striking teratological specimens in the everyday world around us.” Hearing these words, my mind flashed back to a lovely old Anglican hymn that we used to sing in the cathedral at Grafton:

All things bright and beautiful,
all creatures great and small,
all things wise and wonderful,
the Lord God made them all.

[See a quaint presentation of the words and music at]

I wondered whether the hymn would sound so nice if we changed a line:

all things weird and terrible...

Procreation is essentially a matter of copying genes, which is a process that may or may not be carried out in a two-parent sexual situation. The replicator device at the basis of all life—plants, animals and Homo Sapiens—is the DNA molecule, whose structure was explained by James Watson and Francis Crick in 1953.

Shortly before then, a mathematician named John von Neumann, working in the USA, produced operational computer-type models of the replication process, summed up in a famous book that was published posthumously: Theory of Self-Reproducing Automata. For those of us who were meeting up with the phenomenon of computers at that time [I first came in contact with IBM in 1957: the year of von Neumann’s death], the great Hungarian-born mathematician was something of a hero, because it was he who actually invented the fundamental concept of a stored computer program. And he also played a pioneering role in the theory of games... which may or may not have concerned the activities that Camus was designating in the quotation at the start of this post. We all felt that, in programming electronic machines to perform all kinds of tasks, we were exploiting an extraordinary art devised by von Neumann.

Today, if you were to ask me about the meaning of life, I would not hesitate in replying that one thing I have in mind (more than suicide or God or any other boring stuff), when I reflect upon the magic of all living things bright and beautiful (and otherwise), is John von Neumann’s work on self-reproducing automata.