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  • Comets in the dark ages

    Fri, 2009-01-16 11:35 -- John Hawks

    Here's a story from earlier this month in New Scientist:

    MULTIPLE comet impacts around 1500 years ago triggered a "dry fog" that plunged half the world into famine.

    Historical records tell us that from the beginning of March 536 AD, a fog of dust blanketed the atmosphere for 18 months. During this time, "the sun gave no more light than the moon", global temperatures plummeted and crops failed, says Dallas Abbott of Columbia University's Lamont-Doherty Earth Observatory in New York

    It seems to me that the ability to find possible impacts has really increased, with finer-resolution cores and ways of finding the microscopic ejecta. Regardless of the scale of effects of any given instance, it will be nice when we can get some idea of the rate of such events through the past several tens of thousands of years.

  • A history of cattle breeding by the book?

    Wed, 2009-01-14 10:16 -- John Hawks

    Ancient DNA technology may make it possible to test some very interesting hypotheses about recent evolutionary change in human populations.

    Meanwhile, several people are reporting the potential of DNA from museum specimens for testing hypotheses about ancient or extinct populations. Today's news includes a story introducing the term "museomics" -- otherwise known as the metagenomics of museum specimens, including the DNA of taxidermed specimens and their pathogens and commensal bacterial populations:

    [Webb] Miller and his team used state-of-the-art DNA sequencing technology to analyze the hair of two preserved specimens: a female thylacine that died at the London Zoo in 1893, and a male brought to the National Zoo in 1902 that died three years later.

    Although the two thylacines were continents apart, their mitochondrial DNA — a portion of the genome passed on via the maternal line — was nearly identical, illustrating the species' ultra-low genetic diversity around the turn of the 20th century.

    Brandom Keim of Wired blogs that medieval parchment preserves enough DNA for analysis:

    Initial tests showed that the animal skin pages contained enough intact DNA to make analysis worthwhile. So [Tim] Stinson and his brother Mike Stinson, a biologist at Southside Virginia Community College, skin samples taken from five pages of a 15th century French prayer book. Preserved mitochondrial DNA revealed that the pages came from two closely related calves.

    Those results, said Stinson, are a proof of principle that it's possible to create a DNA database from manuscripts of known age and origin. Monastic paperwork tended to be dated, so DNA from those works could be cross-indexed with that of literary works from tomes of unknown provenance, producing a taxonomy of manuscript manufacture.

    Sourcing manuscripts is pretty exciting to historians, no doubt, who must otherwise rely on indicators such as handwriting style and dialect.

    But the results may be equally useful for understanding the processes of animal breeding in medieval Europe. Today's domesticated breeds are a remnant of a much larger diversity of local breeds that once existed. People bred animals both locally by selection and across large regions by introducing favored animals from long distances. Sometimes they favored diversity -- and considering the revival of interest in legacy breeds like Highland cattle.

    As an example, today's European swine include a blend of genes from ancient European domesticates, and hogs introduced from China during the 18th and 19th centuries (Giuffra et al. 2000). That introgression probably caused some substantial improvements in the hog population, but has helped to reduce genetic variation and move the population from its medieval structure to a more homogenized gene pool.

    Gregory Cochran and I gave a short description of the history of cattle domestication and ongoing gene flow in our 2006 paper about introgression (Hawks and Cochran 2006). With four original cattle species in different parts of Eurasia, and the possibility of continued gene flow among imported breeds as well as the original progenitor species of European cattle, the aurochs (still known in early medieval times), the population history of European breeds may harbor a lot of complexity during the last 1000 years. Finding the medieval distribution of today's genes -- even if the only result is a mitochondrial DNA distribution -- might help us understand the distribution in which favored traits originated and were selected.

    References:

    Giuffra E, Kijas JMH, Amarger V, Carlborg Ö, Jeon J-T, Andersson L. 2000. The origin of the domestic pig: Independent domestication and subsequent introgression. Genetics 154:1785-1791.

    Hawks J, Cochran G. 2006. Dynamics of adaptive introgression from archaic to modern humans. PaleoAnthropology 2006:101-115.

  • Cliometrics from Cicero

    Tue, 2008-12-02 08:34 -- John Hawks

    I happened to be reading about the scholastic revival of Cicero, in the book Ad Infinitum: A Biography of Latin by Nicholas Ostler. It's a really interesting book and I'll be reviewing it here later.

    Meanwhile, I saw this story come across the tubes:

    The good news is that Philip Kay knows how the Romans got themselves into financial bother. The bad news is no one knows how they got themselves out of it.

    ...

    The monetary historian is giving a lecture today in which he will reveal how Cicero, the Roman orator, gave a speech in 66BC in which he alluded to the credit crunch. Cicero was arguing that Pompey the Great should be given military command against Mithridates VI, king of Pontus on the Black sea coast of what is now Turkey. He reminded his audience of events in 88BC, when the same Mithridates invaded the Roman province of Asia, on the western coast of Turkey. Cicero claimed the invasion caused the loss of so much Roman money that credit was destroyed in Rome itself.

    The orator told his audience: "Defend the republic from this danger and believe me when I tell you - what you see for yourselves - that this system of monies, which operates at Rome in the Forum, is bound up in, and is linked with, those Asian monies; the loss of one inevitably undermines the other and causes its collapse."

    So, don't despair. The glorious days of empire may still be before us!

  • Hail, great Copernithal!

    Thu, 2008-11-20 18:08 -- John Hawks

    OK, so they've identified the body of Copernicus.

    So, in the next stage, Swedish genetics expert Marie Allen analyzed DNA from a vertebrae, a tooth and femur bone and matched and compared it to that taken from two hairs retrieved from a book that the 16th-century Polish astronomer owned, which is kept at a library of Sweden's Uppsala University where Allen works.

    "We collected four hairs and two of them are from the same individual as the bones," Allen said.

    Which sort of makes you wonder about the other two hairs...

    Anyway, naturally if we're going to start cloning extinct creatures, naturally we'll want to recreate the League of Extraordinary Scientists. Now, I don't know if Copernicus is going to be up to your standards; maybe you go for Newton, Einstein and Galileo first. But maybe if you want additional reinforcement that we aren't the center of the universe, you might build your Neandertal clone using a Copernican template. Although "Copernithal" sounds kind of like a pharmaceutical product of some kind.

  • Quote: Simpson on geneticists and paleontologists

    Wed, 2008-10-22 11:42 -- John Hawks

    From the introduction of G. G. Simpson, 1943, Tempo and Mode in Evolution, p. xv:

    The attempted synthesis of paleontology and genetics, an essential part of the present study, may be particularly surprising and possibly hazardous. Not long ago paleontologists felt that a geneticist was a person who shut himself in a room, pulled down the shades, watched small flies disporting themselves in milk bottles, and thought that he was studying nature. A pursuit so removed from the realities of life, they said, had no significance for the true biologist. On the other hand, the geneticists said that paleontology had no further contributions to make to biology, that its only point had been the completed demonstration of the truth of evolution, and that it was a subject too purely descriptive to merit the name "science." The paleontologist, they believed, is like a man who undertakes to study the principles of the internal combustion engine by standing on a street corner and watching the motor cars whiz by.

    Now paleontologists and geneticists are learning tolerance for each other, if not understanding. As a paleontologist, I confess to inadequate knowledge of genetics, and I have not met a geneticist who has demonstrated much grasp of my subject; but at least we have come to realize that we do have problems in common and to hope that difficulties encountered in each separate type of research may be resolved or alleviated by the discoveries of the other.

  • Billiard-ball genetics

    Thu, 2008-10-16 15:57 -- John Hawks

    I picked up a copy of Julian Huxley's Evolution: The Modern Synthesis this week at a book sale. It's funny -- the book was a review copy and bears the following bookplate:

    To The Literary Editor:

    Direct quotation in reviews is limited to 500 words or less unless special permission is given.

    Well, I hope that the statute of limitations on the bookplate has passed, because I'm going to quote a lot more than 500 words out of this over the next few weeks.

    I'll start with a passage from the first chapter. It brings to mind Mayr's famous comment about "bean bag genetics," but I find Huxley's approach at once more sympathetic and insightful about the nature of inheritance opposed to the way scientists describe inheritance:

    In the early days of Mendelian research, phrases such as "in fowls, the character rose-comb is inherited as a Mendelian dominant" were current. So long as such phrases are recognized as mere convenient shorthand, they are harmless; but when they are taken to imply the actual genetic transmission of the characters, they are wholly incorrect.

    Even as shorthand, they may mislead. To say that rose-comb is inherited as a dominant, even if we know that we mean the genetic factor for rose-comb, is likely to lead to what I may call the one-to-one or billiard-ball view of genetics. There are assumed to be a large number of characters in the organism, each one represented in a more or less invariable way by a particular factor or gene, or a combination of a few factors. This crude particulate view is a mere restatement of the preformation theory of development: granted the rose-comb factor, the rose-comb character, nice and clear-cut, will always appear. The rose-comb factor, it is true, is not regarded as a sub-microscopic replica of the actual rose-comb, but is taken to represent it by some form of unanalysed but inevitable correspondence.

    The fallacy in this view is again revealed by the use of the difference method. In asserting that rose-comb is a dominant character, we are merely stating in a too abbreviated form the results of experiments to determine what constitutes the difference between fowls with rose-combs and fowls with single combs. In reality what is inherited as a Mendelian dominant is the gene in the rose-combed stock which differentiates it from the single-combed stock: we have no right to assert anything more as a result of our experiments than the existence of such a differential factor (Huxley 1943:19).

    I try to emphasize this point whenever I introduce genetics: we know about inheritance because of our observations on organisms, not because we have traced the molecular effects of every gene. As when we interpret sounds into language, we depend on contrasts to see the effects of alleles. I am always amazed when we learn something new about these molecular mechanisms underlying observable phenotypes, because they manifest in so many different ways.

    P. S. Yes, after all that, you deserve a picture of a rose-comb. But although Flickr has many, all are copyrighted, none Creative Commons. So, I won't republish, but here's a link to my favorite.

  • Something fishy about this Pompeii story

    Mon, 2008-09-29 18:22 -- John Hawks

    This is one doofy story:

    Remains of rotten fish entrails have helped establish the precise dating of Pompeii's destruction, according to Italian researchers who have analyzed the town's last batch of garum, a pungent, fish-based seasoning.

    OK, so far so good. But wait a minute! We have a perfectly good historical date from Pliny the Younger! August 24, 79 AD. There's not any chance that some kind of radiometric date is going to improve on that. So what's the deal?

    Doubts about the date of the eruption emerged a couple of years ago when archaeologists discovered a coin which seemed to refer to the 15th imperiatorial acclamation of Titus, believed to have occurred on Sept. 7, 79 A.D.

    OK, so the coin supposedly was later than the eruption, even though it was in the site. But wouldn't the simple explanation be that they struck the coins in advance of the event? Well, I guess there's also this:

    "Unfortunately, that coin can't be taken as a dating evidence, since it is hardly readable. I myself agree with Ciarallo's dating of the eruption, even though I think that a bit of mystery remains. However, it is not so important whether the eruption occurred in August or in October," Teresa Giove, a coin expert at Naples' Archaeological Museum, told Discovery News.

    So where does the fish sauce fit in?

    "Pompeii's last batch of garum [fish sauce] was made with bougues, a fish that was cheap and easy to find on the market in those summer months. Still today, people living in this region make a modern version of garum, called "colatura di alici" or anchovy juice, in July when this fish abounds on the markets," Ciarallo said.

    The eruption froze the sauce right at the moment when the fish was left to macerate. No batches of finished garum were found, since the liquid evaporated in the heat from the eruption.

    "Since bogues abounded in July and early August and ancient Roman recipes recommend leaving the fish to macerate for no longer than a month, we can say that the eruption occurred in late August-early September, a date which is totally compatible with Pliny's account," Ciarallo said.

    OK, so they don't keep the sauce macerating for more than a month. And September 7 is...less than a month after early August. Uhh...what was the story here? Why were we doubting Pliny again? I mean, I admire the knowledge that goes into this, and it's pretty cool to analyze ancient fish sauce, but this story just wasted my time!

  • Book review: The Murder of Nikolai Vavilov, by Peter Pringle

    Thu, 2008-09-18 23:02 -- John Hawks

    Until this summer, I had only a vague idea of who Nikolai Vavilov was. I knew he had been Dobzhansky's mentor, and that like all Russian biologists, he had suffered at the hands of Lysenko. Otherwise, I had heard of Vavilov only in connection to an obscure quote from the introduction of Maynard Smith's Evolution and the Theory of Games:

    Suppose for example, that only two kinds of wings could ever develop -- rectangular and triangular. Natural selection would probably favor the former in vultures and the latter in falcons. But if one asked 'Why are birds' wings the shapes they are?', the answer would have to be couched primarily in terms of developmental constraints. If, on the other hand, almost any shape of wing can develop, then the actual shape, down to its finest details, may be explicable in selective terms.

    Biologists differ about which of these pictures is nearer the truth. My own position is intermediate. Clearly, not all variations are equally likely for a given species. This fact was well understood by Darwin, and was familiar to me when I was an undergraduate under the term 'Vavilov's law of homologous variation' (Maynard Smith 1982:7).

    Well, so much the more for mystery. A historical footnote to be remembered in an argument with Stephen Jay Gould. So I filed it in the back of my mind, since this kind of developmental constraint hypothesis has become more and more important in human evolution during the past few years. It turns out that the traits that differentiate some hominid species are in many cases the same traits that have the most variation within species.

    Anyway, it was enough to get my interest when Peter Pringle's new book, The Murder of Nikolai Vavilov, showed up in the local bookstore.

    When I flipped the book open, I found this description of Vavilov's desperate attempt to bring Dobzhansky back to the Soviet Union, from California where he had been working with Thomas Hunt Morgan:

    Nikolai Ivanovich [Vavilov] began to show irritation at Dobzhansky's hesitation.

    "Feodosy Georgievich, help us lift the country," one letter began. "This is a mission for all humanity. And start acting as a serious Soviet patriot. Truly the horizon here is wider and the future far more reliable than the comfort yet insecurity [of America]."

    ...

    When Dobzhansky wondered how he would cope with Marxist ideology, with the new pushed-ups [Lysenko's men] and their insistence that dialectics be applied to science, Vavilov dismissed his concerns. "Dialectic methodology is nothing but a plus, it allows one to stay in touch with life's demands... Of course, you must horse-shoe yourself into dialectics. It's an easy business and will bring you nothing but usefulness. I am going to send you my dialectic masterpiece in a few days, 'Linnaean Species as a System.' Perhaps dialecticians will criticize me for it, but at least for me the dialectic approach was useful (Pringle 2008:164-165).

    In the end, Dobzhansky refuses to return, and "No wonder!" you might well think. But the four-page passage really hooked me. How could this famous scientist have found himself in this position, accommodating such nonsense? The passage has a darker side: Vavilov succeeds in bringing another young geneticist back to Russia. Georgy Karpechenko returned to Vavilov's Institute only to be arrested and shot in the same purge that rounded up Vavilov himself.

    Tragic vignettes like this ring throughout the book. Yelena Barulina, Vavilov's lover and companion, desperate to find where he is imprisoned, flees Leningrad ahead of the German advance -- and unknowingly takes up residence a mere fifteen minutes from the prison where Vavilov lay dying of starvation. Vavilov forced to defend Mendelism in a hopeless show trial staged to Lysenko's triumph. Vavilov's brother, Sergei, a prominent physicist in his own right, promoted to the presidency of the USSR Academy of Sciences while plaintively trying to rehabilitate Nikolai's reputation and find out the truth about his death. Perhaps most of all, the starving workers at Vavilov's Leningrad Institute during the German siege, saving the precious worldwide collection of seeds and potatoes, planting some varieties in the public squares.

    Those details help to make the book a great story. But at the heart is a description of a truly visionary scientist. Vavilov was an innovator in genetics and plant breeding, but his advances came not only from careful experimentation but also from anthropology -- what we would today call an ethnohistorical approach.

    Early in his career, Vavilov became convinced that domesticated crops could be improved by introducing genes from the wild progenitor species and very early domesticated strains. This strategy was one of systematic introgression, with an aim to bring in genetic variants that would allow earlier ripening in colder climates, resistance to disease and drought, and higher germination rates. This strategy has since been followed to great effect, even today -- I wrote about here in connection to wheat. Vavilov believed that the most ancient areas of domestication would still harbor strains of crop plants that had greater genetic variation, with greater adaptation to their local microclimates. In particular, he thought that hilly or mountainous areas around the zones of initial domestication would be places to find very ancient cold-tolerant, dry-tolerant, and disease resistant strains. By breeding these genes into the major food crops of the Russian plain, Vavilov hoped to radically improve Soviet agriculture, stave off droughts and end the need to import food from Western powers.

    In all these things, Vavilov was entirely right. The modern conception of domestication and gene flow leads to almost exactly the same predictions. Moreover, Vavilov used historical and ethnographic observations to identify the early origins and dispersals of domesticates. He showed that the wheat in Ethiopia was not very diverse, casting doubt on its position as a primary center of domestication, while finding immense diversity in Central Asia and Afghanistan.

    Here, in this high plateau, sparsely populated by subsistence farmers, Vavilov had confirmed his initial suspicion about their ancestors; that some of them had fled the plains where wheat and barley, lentils and rye had originally been cultivated by the earliest farmers and had chosen to live in these natural mountain fortresses where they were better protected from wild beasts and attacks from unfriendly neighbors. The Pamirs was not a "center of origin" for these plants, but it was a "natural laboratory" where over millennia "peculiar forms" of food crops had been developed (Pringle 2008:58).

    To these, he would ultimately add maize diversity in Mexico, potatoes in Peru, and hemp across North Africa. And all the way, he collected seeds, always sending them back in great lots to Leningrad. By the time he had finished, he had amassed the greatest collection of domesticated seed diversity in the world, and had filled in the map of early centers of agriculture, documenting by crop diversity what archaeologists had yet to demonstrate by digging.

    Pringle describes the many sources of resistance to Vavilov's ideas. Years before Lysenko rose to power, many of the USSR's plant breeders had very different priorities from Vavilov. They wanted to find ways to transform new, economically useful crops not already found in the USSR, such as rubber, cinchona, or even bananas. His fieldwork in Soviet Central Asia and Afghanistan was difficult, relatively unglamorous, and drew suspicion that he was a Soviet spy. But his later extended trips to America, Mexico, Africa, and southern Europe, were more comfortable and brought much more international attention to his work. Some were jealous of this acclaim -- particularly after his "Law of Homologous Series" earned him the Order of Lenin and fawning comparisons to the most famous Russian scientist, Mendeleev.

    The Law itself derived from an important observation: related crop species, like wheat and rye, often had strains that had identical phenotypic variations -- awned and awnless, leaf shape, and stem size. These variations appeared to fall into a set series of categories -- a series that Vavilov compared to the periodic table of elements. Mendelian principles appeared to hold factors constant across species under different transformations. Today, we would indeed refer these similar variations to the topic of developmental constraints and shared genetic background.

    The book describes the rise of Lysenko and its contribution to Vavilov's fall. The two were intertwined for years, as Lysenko rose from uneducated field assistant to the supreme position in Soviet agriculture.

    Yet what surprised me the most was the way that Vavilov remained balanced on the knife's edge for so long, his ultimate fate looming on either side. His letters to Dobzhansky, read today, seem somehow out of character for a great scientist. But Vavilov was never a great scientist in his own mind; he always saw himself the humble servant of the state, forced to defend his science in the face of plain ignorance. He needed friends, and was protected from above for years until Stalin's will removed all defenders.

    It is Pringle's great accomplishment to have described the inevitable fall with such precision and suspense. I was amazed that Vavilov lasted as long as he did, with the vast apparatus of the police state collecting evidence against him for ten years or more. Equal to the amazement is the sadness that such a great scientist, with so many important insights, was drawn down by constant troubles, the arrests of assistants and colleagues, and finally the opprobrium Stalin himself. And yet through it all, he managed to run his Institute, keep his seed collection growing, and build a network of agricultural field stations across the Soviet Union.

    In the end, he was rehabilitated by Khrushchev, and later the records of Vavilov's interrogation and files were released. Pringle draws on these sources in chilling chapters describing how the great man was broken down, his closest colleagues shot, while others eagerly reported against him. There were moments when I turned away from the book in sadness, but truthfully, I couldn't put it down.

    References:

    Maynard Smith J. 1982. Evolution and the theory of games. Cambridge University Press, Cambridge UK.

    Pringle P. 2008. The murder of Nikolai Vavilov: The story of Stalin's persecution of one of the great scientists of the twentieth century. Simon and Schuster, New York.

  • Original landscape of American East

    Thu, 2008-09-04 22:30 -- John Hawks

    This New Scientist story is from January, but it's interesting -- streams and rivers across the eastern US were much more extensively terraformed by damming than ever thought:

    Their analysis revealed that by 1840, there were more than 65,000 dams between South Carolina and Maine.

    This revises the idea that the modern farming and damming practices are entirely responsible for certain observations:

    "After every rainstorm, our creeks and streams run like chocolate milk," says Walter. The belief has been that the mud is dragged off eroded farmland and rushed down streams that were straightened and inflated by industrialisation.

    But, Walter and Merritts say the sediment does not come from modern farms, but from those that capped the hills 300 years ago. Today, that mud still lines the ponds and streams, and every new storm simply dislodges it and moves it further downstream.

    (via Jerry Pournelle)

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.