Science Tuesday, er, Friday: Unexpected surprises...

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Fossil Find Challenges Theories on T. Rex
By HENRY FOUNTAIN, The New York Times, September 18, 2009

Paleontologists said Thursday that they had discovered what amounted to a miniature prototype of Tyrannosaurus rex, complete with the oversize head, powerful jaws, long legs — and, as every schoolchild knows, puny arms — that were hallmarks of the king of the dinosaurs.

But this scaled-down version, which was about nine feet long and weighed only 150 pounds, lived 125 million years ago, about 35 million years before giant Tyrannosaurs roamed the earth. So the discovery calls into question theories about the evolution of T. rex, which was about five times longer and almost 100 times heavier.



“The thought was these signature Tyrannosaur features evolved as a consequence of large body size,” Stephen L. Brusatte of the American Museum of National History, an author of a paper describing the dinosaur published online by the journal Science, said at a news conference. “They needed to modify their entire skeleton so they could function as a predator at such colossal size.”

The new dinosaur, named Raptorex kriegsteini, “really throws a wrench into this observed pattern,” Mr. Brusatte said.

The nearly complete fossil was found in northeastern China and bought by a collector, Henry J. Kriegstein, who alerted Paul C. Sereno, a paleontologist at the University of Chicago and lead author of the paper. The fossil, which was illicitly excavated, will be returned to a museum in China.

Dr. Sereno said the fossil was that of a young adult, about 5 or 6 years old and near the end of its growth period. Besides the oversized head, jaws and legs, it had long shinbones and long, compressed feet that helped it run fast after smaller dinosaurs and other prey. “We see this all, to our great surprise, in an animal that is basically the body weight of a human,” Dr. Sereno said.

Raptorex, like T. rex, would have killed animals with its teeth and jaws. The forelimbs would not have been the primary means for attacking prey. In fact, Dr. Sereno said, the forelimbs would have gotten smaller as the head got larger. “This is an agile, fast-running animal,” he said. “By adding a lot of weight at the top, something has to give way. What gave way was the forelimb.”

Thomas R. Holtz Jr., a paleontologist at the University of Maryland who was not involved in the work, said the discovery helped “clear up the origin of the characteristic features of the Tyrannosaurs.”

Dr. Holtz, who cautioned that the findings needed to be independently confirmed, noted that there had been a gap in the family tree between earlier, more primitive Tyrannosaurs that had relatively short legs and long arms and the later giants with opposite features. “This clarifies the sequence,” he said.





Remarkable Creatures: In a Shark’s Tooth, a New Family Tree
By SEAN B. CARROLL, The New York Times, September 15, 2009

“Like a locomotive with a mouth full of butcher knives.”

That is how a shark expert, Matt Hooper, described Carcharodon megalodon to the police chief in Peter Benchley’s novel “Jaws.” He was referring to the 50-foot-long, 50-ton body and enormous six- to seven-inch-long teeth that made the extinct megalodon shark perhaps the most awesome predator that has ever roamed the seas.

Hooper had just gotten his first glimpse of the massive great white shark that was terrorizing the residents of Amity Island. Hooper explained that the Latin name for the great white was Carcharodon carcharias and that “the closest ancestor we can find for it” was megalodon. So maybe, he speculated, this creature wasn’t merely a great white, but a surviving sea monster from an earlier era.

Hooper was toying with a simple and long-established idea: that the most feared predator in the ocean today, the great white shark, evolved from megalodon, the most fearsome predator of a few million years ago.

That is how the two species had been viewed, until recently, when new ways of looking at shark teeth, and new shark fossils from a Peruvian desert, convinced most experts that great whites are not descended from a megatoothed megashark. Rather, they evolved from a more moderate-size, smooth-toothed relative of mako sharks.



If true, then the mouth full of flesh-ripping razor blades that are the stuff of nightmares, and box-office blockbusters, are also a great example of one of the most interesting phenomena in the story of life, convergent evolution — the independent evolution of similar adaptations by different creatures.

The idea of a close relationship between great whites and megalodon started in 1835, when Louis Agassiz, a Swiss paleontologist and fish expert, formally named the giant species. The huge fossil teeth of megalodon had been known for centuries and were once believed to be the fossilized tongues of dragons. Agassiz, noting that great white shark teeth and the fossil megalodon teeth were both serrated, lumped megalodon into the same genus, Carcharodon, (from the Greek karcharos, meaning sharp or jagged, and odous, meaning tooth).

Agassiz was not, however, making an evolutionary judgment. In 1835, a young Charles Darwin was just then visiting the Galapagos Islands. There would be no theory of evolutionary descent for nearly 25 years. In fact, the brilliant Agassiz, who later became a professor at Harvard and the leading figure of natural history in the United States, forever resisted Darwin’s revolutionary ideas. Rejecting biological evolution, Agassiz defined species as a “thought of God.” His classification scheme signified nothing about shark origins.

But over the next century, the idea that great whites evolved from megalodon took hold. Because shark skeletons are largely made of nonmineralized cartilage that isn’t preserved in the fossil record, the principal evidence has come from their teeth. Shark teeth are heavily mineralized, preserve well, and sharks may shed thousands of them over their lifetime. Megalodon teeth are highly sought by collectors, so we have lots of their teeth.

Great white teeth reach a maximum size of about two and half inches. Scary enough, but adult megalodon teeth dwarf them. The most obvious characteristics the species’ teeth have in common are their pointed shape and serrations. The points facilitate the puncturing of flesh and grasping of prey. The fine, regularly spaced serrations aid in cutting and ripping it into pieces.

Based primarily on these characteristics and some similarities in specific tooth shapes and roots, many experts supported the idea that great whites were, in effect, dwarf megalodons.

But a small minority had their doubts. It was noted that great white teeth also bore similarities to the teeth of an extinct mako shark, Isurus hastalis, some of which had weak serrations. An alternative proposal for great white origins was offered — that they evolved from an extinct group of mako sharks.

Many debates about interpretations of the appearances of structures in the fossil record boil down to the emphasis on different characters by different researchers, the great white origins debate included. It is often similar to a discussion at a family reunion of which child looks more like one parent or grandparent. It depends upon the feature and the viewer.

Such subjective arguments are hard to settle without more quantitative measures. Kevin Nyberg and Gregory Wray of Duke University and Charles Ciampaglio of Wright State University used new computer-assisted imaging and measurement methods to better assess the similarities and differences among great white, megalodon and extinct mako teeth. They determined that the extinct mako and great white teeth and roots were similar in shape and clearly distinct from megalodon.

Furthermore, high-resolution electron microscopy revealed that the shape and spacing of serrations of great white teeth were markedly different from those in megalodon teeth. The serrations that impressed Agassiz now appear to be just a superficial resemblance. The great white did not inherit its sharp cutting tools from megalodon.

Rather, it appears that great whites evolved from a less ferocious-looking ancestor and independently evolved sharp serrations. A remarkably well-preserved fossil of what a great white ancestor may have looked like was recently brought to light. The desert region of southwestern Peru is a graveyard of marine animals from the past 40 million years, including spectacularly preserved whales, dolphins, walruses, seals, turtles and sharks. It was there that Gordon Hubbell, a shark expert, collected the four-million-year-old fossil that had not only its jaws intact with 222 teeth, but also 45 vertebrae — both rarities for shark fossils and rare opportunities for shark experts.

The preservation of the teeth in their proper place, as opposed to being found scattered in sediments, allowed an unprecedented analysis of individual teeth and the pattern of tooth development in the shark. Similarities were found to both extinct mako sharks and living great whites, including weak serrations, suggesting that the Peruvian fossil might be a transitional form, a link between a smooth-toothed mako ancestor and the great white.

The serrations of great white teeth undoubtedly evolved to exploit expanding populations of marine mammals. That adaptation appears to have given the predators an advantage as they, like megalodon in its day, enjoy a broad oceanwide distribution. At least for now.

I say “for now” because great whites are declining along with most shark species, some of which have experienced alarming drops in their numbers in just the past two decades. Biologists are not sure what caused the once dominant megalodon to become extinct two million years ago, but there will be no debate about who is to blame if today’s top predator is gone tomorrow.

Sean B. Carroll is a molecular biologist and geneticist and the author of several books, most recently “Remarkable Creatures: Epic Adventures in the Search for the Origin of Species.” He will be writing a column of the same title for Science Times, more or less monthly, on the remarkable creatures that scientists study and the remarkable creatures that many scientists are (or were). He is an investigator of the Howard Hughes Medical Institute at the University of Wisconsin.





New Clues to Sex Anomalies in How Y Chromosomes Are Copied
By NICHOLAS WADE, The New York Times, September 15, 2009

The first words ever spoken, so fable holds, were a palindrome and an introduction: “Madam, I’m Adam.”

A few years ago palindromes — phrases that read the same backward as forward — turned out to be an essential protective feature of Adam’s Y, the male-determining chromosome that all living men have inherited from a single individual who lived some 60,000 years ago. Each man carries a Y from his father and an X chromosome from his mother. Women have two X chromosomes, one from each parent.

The new twist in the story is the discovery that the palindrome system has a simple weakness, one that explains a wide range of sex anomalies from feminization to sex reversal similar to Turner’s syndrome, the condition of women who carry only one X chromosome.

The palindromes were discovered in 2003 when the Y chromosome’s sequence of bases, represented by the familiar letters G, C, T and A, was first worked out by David C. Page of the Whitehead Institute in Cambridge, Mass., and colleagues at the DNA sequencing center at Washington University School of Medicine in St. Louis.

They came as a total surprise but one that immediately explained a serious evolutionary puzzle, that of how the genes on the Y chromosome are protected from crippling mutations.



Unlike the other chromosomes, which can repair one another because they come in pairs, one from each parent, the Y has no evident backup system. Nature has prevented it from recombining with its partner, the X, except at its very tips, lest its male-determining gene should sneak into the X and cause genetic chaos.

Discovery of the palindromes explained how the Y chromosome has managed over evolutionary time to discard bad genes: it recombines with itself. Its essential genes are embedded in a series of eight giant palindromes, some up to three million DNA units in length. Each palindrome readily folds like a hairpin, bringing its two arms together. The cell’s DNA control machinery detects any difference between the two arms and can convert a mutation back to the correct sequence, saving the Y’s genes from mutational decay.

After Dr. Page discovered the palindromes, he wondered whether the system had weaknesses that might explain the male sex chromosome anomalies that are a major object of his studies. In the current issue of Cell, with Julian Lange and others, he describes what they call the “Achilles’ heel” of the Y chromosome and the wide variety of sexual disorders that it leads to.

The danger of the palindrome protection system occurs when a cell has duplicated all its chromosomes prior to cell division, and each pair is held together at a site called the centromere. Soon, the centromere will split, with each half and its chromosome tugged to opposite sides of the dividing cell.

Before the split, however, a serious error can occur. Palindromes on one Y chromosome can occasionally reach over and form a fatal attraction with the counterpart palindrome on its neighbor. The two Y’s fuse at the point of joining, and everything from the juncture to the end of the chromosome is lost

The double-Y’s so generated come in a range of lengths, depending on which of the palindromes makes the unintended liaison. Like other chromosomes, the Y has a left arm and a right arm with the centromere in between. The male-determining gene lies close to the end of the left arm. If the palindromes at the very end of the right arm make the join, a very long double-Y results in which the two centromeres are widely separated. But if the joining palindromes are just to the right of the centromere, a short double-Y is formed in which the two centromeres lie close together.

Dr. Page detected among his patients both short and long double-Y’s and those of all lengths in between. He and his colleagues then noticed a surprising difference in the patients’ sexual appearance that depended on the length between the centromeres of their double-Y’s.

The patients in whom the distance between the Y’s two centromeres is short are males. But the greater the distance between the centromeres, the more likely the patients are to be anatomically feminized. A few of the patients were so feminized that they had the symptoms of Turner’s syndrome, a condition in which women are born with a single X chromosome.

The explanation for this spectrum of results, in Dr. Page’s view, lies in how the double-Y’s are treated in dividing cells and in the consequences for determining the sex of the fetus.

When the centromeres are close together, they are seen as one and dragged to one side of the dividing cell. As long as the Y’s male-determining gene is active in the cells of the fetal sex tissue, or gonad, the gonads will turn into testes whose hormones will masculinize the rest of the body.

But when the centromeres lie far apart, chromosomal chaos results. During cell division, both centromeres are recognized by the cell division machinery, and in the tug of war the double-Y chromosome may sometimes survive and sometimes be broken and lost to the cell.

Such individuals can carry a mixture of cells, some of which carry a double-Y and some of which carry no Y chromosome. In the fetal gonads, that mixture of cells produces people of intermediate sex. In many of these cases the patients had been raised as female but had testicular tissue on one side of the body and ovarian tissue on the other.

In the extreme version of this process, the distribution of cells may be such that none of the fetal gonad cells possess a Y chromosome, even though other cells in the body may do so. Dr. Page and his colleagues found five of the feminized patients had symptoms typical of Turner’s syndrome. The patients had been brought to Dr. Page’s attention because their blood cells contained Y chromosomes. Evidently by the luck of the draw, the blood cell lineage had retained Y chromosomes but the all important fetal gonad cells had been denied them.

In 75 percent of women with Turner’s syndrome, the single X comes from the mother. “Since they are females, everyone imagines it’s Dad’s X that is missing,” Dr. Page said. “But it could easily be Dad’s Y.”

That the degree of feminization parallels the distance between the two centromeres of the double Y chromosome is “a fantastic experiment of nature,” Dr. Page said. Despite having studied the Y chromosome for nearly 30 years, he has learned that it is always full of surprises.

“I continue to see the Y as an infinitely rich national park where we go to see unusual things, and we are never disappointed,” he said.

Dr. Cynthia Morton, editor of the American Journal of Human Genetics, said the new explanation of Turner’s syndrome was plausible. “It’s another beautiful David Page contribution to the science of genetics,” Dr. Morton said.







Observatory: Fibers in a Cave Point to Ancient Craft Work
By HENRY FOUNTAIN, The New York Times, September 15, 2009

Archeologists looking for signs of what the ancient climate was like in the Caucasus Mountains have come across something else: signs of ancient craft work.

They found fibers of wild flax, up to 34,000 years old, in the Dzudzuana Cave in the former Soviet republic of Georgia. Some of the fibers were twisted and some were dyed, which indicates they were used for sewing clothes, weaving baskets or making ropes. That makes the fibers the oldest known to have been used by humans.



Ofer Bar-Yosef, an archaeologist with the Peabody Museum at Harvard and a lead author of a brief paper that describes the finding in Science, said the fibers were found during microscopic examination of samples of clay soil from layers of the cave dating from about 6,000 to 36,000 years ago.

Eliso Kvavadze, a paleobiologist with the National Museum of Georgia and another of the lead authors, was looking for pollen grains, which can provide information about climate variability.

In addition to pollen, Dr. Bar-Yosef said, Dr. Kvavadze found insect remains, microfossils of fungi and algae, and fur from a type of wild goat called a tur. “She found many things, but especially those flax fibers,” he said.

The clay soil in the cave remains wet most of the year, he said, which helped preserve the fibers. The most fibers were found in the older layers of the site, dating from 24,000 years ago and earlier. Some had multiple knots, others showed a fairly complex twisting pattern, and some showed evidence of having been cut. Among the dyed fibers were some in black, gray and turquoise and one in pink.

“The fibers clearly indicate these humans were making some kind of coats or ropes,” Dr. Bar-Yosef said. They are more evidence, he said, of what is known as the Upper Paleolithic Revolution, the period of major technological and social change that took place tens of thousands of years ago.