Showing posts with label DNA. Show all posts
Showing posts with label DNA. Show all posts

Friday, September 21, 2012

Identity keys in the genealogical domain

A new kind of personal identity key has come into existence over the last few years. I refer to it as your Y-key, pronounced to rhyme with "crikey". It's a unique identifier that is used in DNA testing in the genealogical domain. A Y-key points to an individual's set of Y-chromosome marker values stored in a global database.

For the moment, since few individuals have bothered to obtain their Y-chromosome marker values, the keys are quite short. For example, my own Y-key is a short string of five alphanumeric characters: RJ6XS. Click here to access the Ysearch.org database, created by the Family Tree DNA company. For the moment, it's the only Y-chromosome database of which I'm aware. Anybody who knows that my Y-key is RJ6XS can rapidly access my set of 67 marker values.

Once Y-keys became a commonplace phenomenon, messages of the following kind could be used in genealogical contexts:

My Y-key is RJ6XS.

Can anybody tell me if a Y-key exists for Winston Churchill?

Please send me your mother's Y-key.

The latter example raises an obvious question: What is the sense of a Y-key in the case of a female individual? Well, it's simply the Y-key of her father or her brothers.

In years to come, I would imagine that Y-keys will become as commonplace as social security numbers. But they will only ever concern a small minority of people: namely, those who are interested in genealogy.

Friday, September 7, 2012

Junk's not junk

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

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

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

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


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


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

Monday, June 11, 2012

Dogs in God's city

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

All this Biblical stuff is most smelly dogshit.

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

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

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

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

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

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

Saturday, July 30, 2011

Smart boss

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

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

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

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

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

Monday, March 21, 2011

Unbearable tragedy

Having got rid of that lousy pun in my title (a silly way of trying to attenuate my great distress), I hasten to point out that I've truly been projected into a terrible state of sadness by the sudden and unexpected death of the marvelous little bear Knut. His disappearance is totally unthinkable, but we must think just that.

Much will be said in the near and distant future about Knut and his friend Thomas Doerflein… both of whom have now left us. The love story of Knut and Thomas was utterly fabulous. I have rarely been the (remote) spectator of any relationship of a comparable depth and intensity between an allegedly wild beast and a human. But critics will seek to demolish (and rightly so, I feel) the very concept of zoos.

Try to access a serious video account of this amazing relationship, as distinct from the popular publicity stuff about Knut put out by the Berlin Zoo. I've seen such a video on French TV, but I don't know whether it's available on DVD. [Maybe informed readers might comment on this question.] Meanwhile, my message for Knut and Thomas:
We humble observers on the planet Terra cannot fail to sense today that your DNA is being intermingled for Eternity as stardust, and setting out on a fabulous journey through the Cosmos, far from Berlin and the Arctic, into realms where you will belong—at home together—forever.

Saturday, February 12, 2011

Darwin Day

In The Origin of Species, Charles Darwin wrote timidly:

Light will be thrown on the origin of man and his history.

As Richard Dawkins points out in A Devil's Chaplain, Darwin's monumental understatement is on a par with the famous words of James Watson and Francis Crick in 1953, on the potential of their discovery of the structure of DNA:

This structure has novel features which are of considerable biological interest. […] It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.

Great scientists rarely shout. They rarely need to.

Saturday, August 28, 2010

British tribes

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

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

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

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

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

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

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

Saturday, July 31, 2010

Much ado about nothing

In catastrophic dreams, at moments, the entire universe becomes unstuck, turned upside-down. Then, a moment later, everything is back in place, as it has always been. At present, our DNaydreams seem to be a bit like that.

For ages, at a homely level, I've been jumping up and down and shouting about the promises of DNA-testing in the genealogical domain. Well, the truth of the matter is that nothing much at all has happened lately in this domain. Not a single male named Skeffington or Skyvington (or something like that) has responded to my appeals for DNA collaboration. You can't get genealogical blood out of a stone of apathy. So, there we are. I don't even seem to be able to persuade Pickering and Walker relatives to participate in this kind of research. Consequently, the global results are zero. This lack of collaboration doesn't disturb me unduly, in the sense that it doesn't impinge upon my knowledge of the history of my ancestors. At most, it casts a veil upon the quality of my communications with genetic cousins and fellow-researchers.

At a more profound level, it's interesting to learn that a brilliant individual can herald in an amazing new age by having his genome analyzed and published… only to find that this potentially-awesome revelation fizzles out into nothingness. The world feared that Craig Venter, in publishing his personal genome, might be selling his soul to the Devil. Well, the least that might be said is that the Devil is taking his time in pinning down the possible weaknesses of Craig Venter. If indeed it was the Devil who invested in this kind of research, then his ROI (return on investment) would appear to be dismal for the moment. Not enough to call out the troops of the Vatican. Not enough to send Venter to Hell… or even to Heaven, for that matter.

Click the portrait of Venter to access a fascinating English-language interview by Der Spiegel. You'll learn exactly how and why nothing has really happened. In fact, this absence of spectacular fallout is convenient. There are exciting and indeed awesome times when the best thing that could possibly happen is… nothing.

Friday, February 19, 2010

"InDNA" Jones in Egypt

In former times, the hero of this tale would have been Tutankhamun himself, of course.

These days, one has the impression that a more powerful Egyptian chief than the New Kingdom pharaoh has arisen, and is stealing the archaeological limelight at times.

The name of the all-powerful boss of Egyptian antiquities is Zahi Hawass. He's the man who's presently blocking (for reasons I fail to grasp) an examination of the interior of the Great Pyramid of Giza that might confirm the extraordinary construction theory put forward by the French architect Jean-Pierre Houdin. On this subject, see my article of 27 November 2008 entitled How did they do it? [display]

Hawass has the look and style (and the hat, too) of the movie archaeologist Indiana Jones. As of a fortnight ago, I think that Hawass deserves a nickname: "InDNA". He revealed, in a press conference, that genetic tests indicate that Tutankhamun was the fruit of an incestuous affair between Akhenaten and his sister. The name of this lady is unknown, but we might suppose that young Tut simply called her Mummy [shameful pun].

Today, everybody knows that it's not a good idea for brothers and sisters to procreate, because human chromosomes can get horribly screwed up in situations of that kind. For example, it appears that Tutankhamun, who died at the age of 19, suffered from malaria, a cleft lip and an inherited bone disease that caused him to have a club foot. As if that weren't enough, he was represented in paintings as an androgynous creature. Of course, you don't notice any of these genetic flaws when you admire the dead pharaoh through his funeral mask and mummy swaddling. But you can't hide anything from DNA tests.

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.