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

Friday, February 5, 2010

Nativity rites

Jean Sarkozy, the president's son, married his adolescent sweetheart, Jessica Sebaoun-Darty. The following photo shows the father and the son, accompanied by their respective wives.

A son, Solal, was born to Jessica and Jean on 13 January 2010. A few days ago, I saw in the press that the baby was subjected to the Jewish tradition of circumcision, which I find archaic and physically revolting. The Christian rite of baptism is less bloody, but just as stupid today, at the start of the third millennium. In both cases, an innocent child is being enthroned as a member of an elite body of religious believers, and this membership is being established solemnly at a time when the tiny creature at the heart of the ceremony is not yet capable of any degree of intellectual discernment. What utter nonsense, perpetrated by mindless adults!

In a recent article entitled Little gods [display], I mentioned my reading a book by the great atheist author Christopher Hitchens. On the question of circumcision, I was moved by the parts of that book in which Hitchens condemns "child abuse" in the form of "sexual mutilation". He even gives us the gory details of the way in which circumcision has been performed, as recently as 2005 in New York, by certain Hasidic fundamentalist foreskin-removers. Nasty stuff!

I predict a day in the not-too-distant future when a joyful nativity rite of a new non-religious kind will become, as it were, standard practice. The DNA of the newly-born individual will be examined and stored permanently (as permanently as possible) in a great database of the kind that would bring joy to the heart of a Mormon genealogist. And this rite would symbolize (literally, you might say, since the DNA sample is in fact a huge set of symbols) the baby's passage into the great planetary congregation of humanity.

For the moment, those who come closest to this nativity rite are the researchers in genealogy who get their DNA tested (like me). But it remains a relatively superficial affair, since only the Y-chromosome of males and the mitochondrial DNA of females are in fact examined. And it's a private firm that holds on to the DNA samples. So, I can't really count upon the hope—if ever that were my intention (which it isn't)—of my being cloned at some future time.

No sooner had I finished writing this article than I came upon a CNN story [click the baby photo to display it] indicating that US babies appear to have their DNA tested systematically, with medical reasons in mind... much to the distress of certain parents.

Insofar as humans seem to like ceremonies based upon rites of passage of various kinds (birth, marriage, death, etc), I can well imagine creative Americans (the sort of people who have transformed Halloween into a planetary event) who would find ways of transforming the baby's DNA test into a kind of celebration, with music, food and drinks, solemn speeches and even short readings from the books of Dawkins, performed by students of genetics. This new nativity rite could be called DNAtion (rhymes with creation, confirmation and ordination).

Thursday, December 31, 2009

Ray of hope for our devils

For many years, the marsupial known as the Tasmanian devil has been the victim of a terrible form of facial cancer that is so contagious that it could well drive these precious creatures to extinction.

An article in The New York Times reveals the existence of a ray of hope [display]. It has always saddened my heart to hear that these fabulous beats have been suffering and dying, and it would be utterly marvelous if modern genetics could save them.

In another cancer domain, concerning human beings, scientists at the UK-based Wellcome Trust Sanger Institute have catalogued the genetic maps of skin and lung cancer, and identified specific DNA mutations that can lead to malignant tumors.

There's something beautifully harmonious in the idea that we humans and the Tasmanian devils are all awaiting the magic benefits of scientific research. There's no sense in our praying, of course, since devils—like atheists—don't seek salvation from God.

Thursday, October 22, 2009

Warming my toes with Darwin & Dawkins

When Badger suggests, in a comment to my First fire article [display], that I might be curling up my toes in front of the fireplace instead of pursuing Antipodes, he has hit the proverbial nail on its head. I have indeed got into the pleasant habit, over the last week, of sitting in front of the fire of an evening and soaking in slowly—as if I were appreciating a fine wine—the powerful words of the Richard Dawkins book that I evoked recently in the article entitled Latest Dawkins book [display]. I found it hard to imagine a priori that Dawkins still had room to produce yet another book on his usual themes of Darwinism and genes, but all I can say is that the master has succeeded brilliantly, surprising me in ways that I would never have imagined.

Insofar as this book simply aims to supply readers with the actual evidence in favor of Darwinian evolution, Dawkins has written it in an almost colloquial style. Here's a humorous specimen: One Australian river turtle, indeed, gets the majority of its oxygen by breathing (as an Australian would not hesitate to say) through its arse.

There's a hell of a lot of good basic stuff about fossils and the way in which they're dated by radioactive "clocks". I don't know whether or not God exists, but the Devil surely does... otherwise I can think of no other reason to explain why Ardi waited up until the Dawkins book had just rolled off the press before making her coming-out. In a way, it's no sweat, because (a) it's easy to fit Ardi into the context presented by Dawkins; (b) it's nice for us lowly disciples to have an opportunity of feeling, if only for a short while, that we possess more information than the master; and (c) we'll be looking forward to a forthcoming book in which Dawkins will give us his reactions to Ardi.

To my mind, the best-written section of this book deals with embryology, and a quasi-magical phenomenon known as epigenesis, which concerns the processes enabling a single cell to "evolve" (nothing whatsoever to do with Darwinian evolution) into a living organism. We know that the single cell soon splits exponentially into countless essentially identical cells. But how do all these cells get their act together in such a way as to coalesce into a creature such as a dog or a human, or a rose bush? If we liken the end product (the creature or the plant) to a symphony performed buy an orchestra, and the cells to a vast set of musicians belonging to the orchestra, where's the conductor who makes sure that every performer is playing the required notes in a perfect manner? For that matter, where's the score? To approach such questions, Dawkins resorts to the fabulous metaphor of flocks of starlings in an aerial ballet:



The amazing conclusion is that each cell in the evolving organism, like each starling in the flock, is in fact doing its own thing. There is neither an explicit score, nor a unique conductor. This idea is hard to grasp. Computer programmers are accustomed to working in the domain of object-oriented programming, where you program a single relatively-simple object equipped with its own methods, whereupon you can instantiate that object as many times as you like, with differing parameters. This computer-based version of cloning provides a good paradigm of the starling phenomenon, or the process that enables ants to build vast and complex subterranean cities. And this is what biological epigenesis is all about.

Everybody knows that DNA can be likened to a string. But living tissues are highly-convoluted three-dimensional structures. So, in embryology, how do simple strings get folded into all the wonderful shapes of living creatures and plants? To tackle this question, Dawkins calls upon the metaphor of paper-folding, known as origami, of which there are many fascinating demonstrations on YouTube [click here for an origami rose].

The only negative element in this great new Dawkins book is his insertion of a four-page transcription of a TV interview between Dawkins and a female named Peggy Wright, president of Concerned Women for America. In the context of so much scientific poetry and wisdom, her presence is like a hair in the soup. Read the book, to see if you agree/disagree with me.

Saturday, July 4, 2009

Snippets and stutters

My title is a fanciful allusion to the two basic entities used in the fascinating domain of family-history research based upon DNA, which has interested me now for several months. There are so many novel concepts and bits of necessary know-how in this field that I've started to set them down in the form of a text, which might one day be of use to other newcomers.

The first thing you discover about this exciting new genealogical tool is that there are two quite different approaches:

-- A female can have her DNA tested to learn about her matriarchal line: that's to say, her mother, her mother's mother, the mother of her mother's mother, and so on. This testing uses mitochondrial DNA, designated in short as mtDNA.

-- A male can have his mtDNA tested in exactly the same way, and the results will be identical to those of his sisters. A male can also have his Y-chromosome tested, to learn about his father, his father's father, the father of his father's father, and so on.

Since a female researcher doesn't have Y-chromosomes, she can't be tested in this second way. But that's not a problem as long as she can call upon either her father, a brother or some other male relative on her paternal side to obtain such Y-chromosome information.

For the moment, personally, I've been tested only at this second level. The results are directly linked to the ancient origins of the Skyvington surname, which is currently being documented.

Let me explain rapidly the sense of my blog title:

-- In a strand of DNA, in a so-called junk region of the molecule (lying outside the coded sections that determine our nature), it can happen that a single letter is suddenly and mysteriously misspelled. For example, a meaningless "word" that has been spelled CAT since time immemorial suddenly reappears, in the DNA of an offspring, with a spelling error: say CGT. An error of this kind is called a single-nucleotide polymorphism [SNP, pronounced snip]. Now, this kind of mutation is extremely rare, but once such a mispelling occurs, the error is reproduced forever after. Some 16 to 18 millennia ago, there was a famous Y-chromosome snip referred to as M343, and one of the fellows with this trivial spelling error in his junk DNA happened to become the great-granddaddy of all of us western Europeans. So, if you find this M343 snip in your DNA, you can be fairly sure that some of your paternal ancestors once spent some time in western Europe.

-- In a strand of DNA, something akin to stuttering takes place when a tiny fragment is repeated several times, for no apparent reason. In a certain individual, a specific instance of such stuttering might involve, say, 14 repetitions, whereas another person might have a count of 13 or maybe 15. This stuttering is called short tandem repeats [STR, pronounced by naming separately each of the three letters: ess-tee-ahr]. Whenever the number of repeats is augmented (suddenly and mysteriously, as for snips, but far more often), the new value is reproduced in descendants of the mutated individual.

Let's leave things there for the moment, because I don't necessarily intend that Antipodes should be transformed into a series of biology lessons. But I'll return rapidly to these subjects, because I've been learning a lot of interesting things, over the last few days, about my paternal snippets and stutters.

Wednesday, May 20, 2009

Our concestor Ida

Like countless Earth-dwellers, I was moved by the fabulously beautiful image of our concestor Ida.

Even Google got into the act immediately, which proves (if need be) that the discovery and presentation of the fossil is a cosmic happening:

The term "concestor" was introduced into the terminology of tribal history (or genealogy, if you prefer) by Richard Dawkins in his monumental The Ancestor's Tale. It stands for "the (latest) common ancestor". For example, when a Skyvington in Choranche encounters, say, an individual named Skivington over in Canada, it's quite possible that their concestor was a 17th-century farmer named George over in Dorset, England. Researchers concerned with individuals X and Y are interested, above all, in identifying the latest concestor: that's to say, the common ancestor whose offspring split into two forever-separate lines, one of which ended up producing X, and the other, Y.

Juvenile Ida ("lovely Laura in her light green dress") looks a little like a modern lemur:

Let's say that 47-million-year-old Ida was almost a lemur... like our human ancestors, for that matter. But certain telltale features reveal that Ida had jumped onto the human, rather than the lemur, band wagon. She was surely one of us: an ancient member of our human tribe. Welcome aboard, Ida!

Thursday, April 16, 2009

My DNA data

I guess I could say that this is the first official certificate I've ever received from an American institution. And I didn't even have to do any hard work to obtain it. Now, this is terribly personal information, like the image of my skull in one of my early blog articles [display], which greatly disturbed my longtime friend Odile. But there's no personal copyright attached to my DNA certificate, and I wouldn't mind at all if this data were to get stolen by all kinds of hackers and scientists with secret plans to clone me.

The Texan folk who tested me have also supplied a nice little map showing how my ancestors moved away from the territory of our African patriarch known as Adam, and finally ended up here in France... where members of the family were called Cro-Magnon long before they got around to adopting a nicer surname, Skyvington. Without wishing to appear snobbish, I'm happy they made that name change, because Cro-Magnons were as common, back at that time, as today's Smiths and Duponts.

My folk are indicated by the arrow marked R1b, which means that they followed a long trail through central Asia before getting here. In fact, it's a mere 25 millennia since they moved away from the territory marked R, located in the vicinity of modern Kazakhstan, and set off westwards towards Europe.

For the moment, I haven't found any genetic cousins (individuals with exactly the same marker values) with a surname like mine, but I'm trying to persuade various Skivington and Skeffington men throughout the world to get tested. This genetic genealogy adventure will be followed up in my specialized Skeffington Genealogy blog [display] whose banner appears in the right-hand column of the present blog. At an anecdotal level, I've mentioned there that I was proud to learn that Richard Dawkins happens to be one of my genetic cousins.

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

Mothers

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.