Tuesday, July 31, 2012
Thursday, July 26, 2012
DNA and Fossils Tell Differing Tales of Human Origins
By NICHOLAS WADE NY TIMES
After decades of digging, paleoanthropologists looking for fossilized human bones have established a reasonably clear picture: Modern humans arose in Africa some 200,000 years ago and all archaic species of humans then disappeared, surviving only outside Africa, as did the Neanderthals in Europe. Geneticists studying DNA now say that, to the contrary, a previously unknown archaic species of human, a cousin of the Neanderthals, may have lingered in Africa until perhaps 25,000 years ago, coexisting with the modern humans and on occasion interbreeding with them.
The geneticists reached this conclusion, reported on Thursday in the journal Cell, after decoding the entire genome of three isolated hunter-gatherer peoples in Africa, hoping to cast light on the origins of modern human evolution. But the finding is regarded skeptically by some paleoanthropologists because of the absence in the fossil record of anything that would support the geneticists’ statistical calculations.
Two of the hunter-gatherers in the study, the Hadza and Sandawe of Tanzania, speak click languages and carry ancient DNA lineages that trace to the earliest branchings of the human family tree. The third group is that of the forest-dwelling pygmies of Cameroon, who also have ancient lineages and unusual blood types.
The geneticists, led by Joseph Lachance and Sarah A. Tishkoff of the University of Pennsylvania, decoded the entire genomes of five men from each of these groups. The costs of whole-genome sequencing have fallen so much that the technique can now be applied to populations for the first time, said Dr. Tishkoff, who paid the company Complete Genomics around $10,000 for each of the 15 genomes. Among the DNA sequences special to pygmies, Dr. Tishkoff and colleagues found a variant of the usual gene that controls development of the pituitary gland, the source of the hormones that control reproduction and growth. This could be the cause of the pygmies’ short stature and early age of reproduction, the researchers say.
The genomes of the pygmies and the Hadza and Sandawe click-speakers contained many short stretches of DNA with highly unusual sequences. Through mutation, the genomes of species that once had a common ancestor grow increasingly unlike one another. Dr. Tishkoff’s team interprets these divergent DNA sequences as genetic remnants of an interbreeding with an archaic species of human. Genetic calculations suggest the interbreeding took place between 20,000 and 80,000 years ago.
From calculations of the amount of divergence in the DNA, the geneticists estimate that the archaic species split from the ancestors of modern humans about 1.2 million years ago, about the same time as did the ancestors of the Neanderthals, who dominated Europe during the end of the last ice age.
But the archaic species has a different DNA sequence from that of Neanderthals, whose genome has been reconstructed from DNA surviving in ancient bones, and so may be a sister species, the geneticists say.
Inquiries into human origins are on strong ground when genetic data and fossil evidence point in the same direction, but at present geneticists and paleoanthropologists have somewhat different stories to tell. All human fossil remains in Africa for the last 100,000 years, and probably the last 200,000 years, are of modern humans, providing no support for a coexistent archaic species. Another team of geneticists reported in 2010 the finding that Neanderthals had interbred 100,000 years ago with Europeans and Asians, but not Africans. This, too, conflicted with the fossil evidence in implying that modern humans left Africa 100,000 years ago, some 55,000 years before the earliest known fossil evidence of this exodus.
In a report still under review, a third group of geneticists says there are signs of Neanderthals having interbred with Asians and East Africans. But Neanderthals were a cold-adapted species that never reached East Africa.
These three claims of interbreeding have opened up a serious discordance between geneticists and paleoanthropologists. For digesting the geneticists’ claims, “sup with a long spoon,” advised Bernard Wood, a paleoanthropologist at George Washington University.
Richard Klein, a paleoanthropologist at Stanford University, said the new claim of archaic and modern human interbreeding “is a further example of the tendency for geneticists to ignore fossil and archaeological evidence, perhaps because they think it can always be molded to fit the genetics after the fact.”
Dr. Klein said the claims of interbreeding could be “a methodological artifact” in the statistical assumptions on which the geneticists’ calculations are based. The flaw may come to light when enough inconsistent claims are published. “Meanwhile, I think it’s important to regard such claims skeptically when they are so clearly at odds with the fossil and archaeological records,” he said.
Dr. Tishkoff said that she agreed on the need for caution in making statistical inferences, and that there are other events besides interbreeding, like a piece of DNA getting flipped around the wrong way, that can make a single DNA sequence look ancient. “But when you see it at a genomewide level, it’s harder to explain away,” she said.
A co-author, Joshua M. Akey of the University of Washington in Seattle, said he was “reasonably confident that what we are seeing in Africa does represent archaic introgression.” The archaic sequences make up only 2.5 percent of the genomes of the living hunter-gatherers, and there is no evidence that they are being favored by natural selection. They may, therefore, have no effect on a person’s physical form, which could explain why the fossils show little sign of them, Dr. Akey said.
Although all known African fossils are of modern humans, a 13,000-year-old skull from the Iwo Eleru site in Nigeria has certain primitive features. “This might have indicated interbreeding with archaics,” said Chris Stringer, a paleoanthropologist at the Natural History Museum in London. “For half of Africa we really have no fossil record to speak of, so I think it’s quite likely there were surviving archaic forms living alongside modern humans.”
Paleoanthropologists like Dr. Klein consider it “irresponsible” of the geneticists to publish genetic findings about human origins without even trying to show how they may fit in with the existing fossil and archaeological evidence. Dr. Akey said he agreed that genetics can provide only part of the story. “But hopefully this is just a period when new discoveries are being made and there hasn’t been enough incubation time to synthesize all the disparities,” he said.
Monday, July 09, 2012
A Blip That Speaks of Our Place in the Universe
By LAWRENCE M. KRAUSS NY Times
ASPEN, Colo. — Last week, physicists around the world were glued to computers at very odd hours (I was at a 1 a.m. physics “party” here with a large projection screen and dozens of colleagues) to watch live as scientists at the Large Hadron Collider, outside Geneva, announced that they had apparently found one of the most important missing pieces of the jigsaw puzzle that is nature.
The “Higgs particle,” proposed almost 50 years ago to allow for consistency between theoretical predictions and experimental observations in elementary particle physics, appears to have been discovered — even as the detailed nature of the discovery allows room for even more exotic revelations that may be just around the corner.
It is natural for those not deeply involved in the half-century quest for the Higgs to ask why they should care about this seemingly esoteric discovery. There are three reasons.
First, it caps one of the most remarkable intellectual adventures in human history — one that anyone interested in the progress of knowledge should at least be aware of.
Second, it makes even more remarkable the precarious accident that allowed our existence to form from nothing — further proof that the universe of our senses is just the tip of a vast, largely hidden cosmic iceberg.
And finally, the effort to uncover this tiny particle represents the very best of what the process of science can offer to modern civilization.
If one is a theoretical physicist working on some idea late at night or at a blackboard with colleagues over coffee one afternoon, it is almost terrifying to imagine that something that you cook up in your mind might actually be real. It’s like staring at a large jar and being asked to guess the number of jelly beans inside; if you guess right, it seems too good to be true.
The prediction of the Higgs particle accompanied a remarkable revolution that completely changed our understanding of particle physics in the latter part of the 20th century.
Just 50 years ago, in spite of the great advances of physics in the previous half century, we understood only one of the four fundamental forces of nature — electromagnetism — as a fully consistent quantum theory. In just one subsequent decade, however, not only had three of the four known forces succumbed to our investigations, but a new elegant unity of nature had been uncovered.
It was found that all of the known forces could be described using a single mathematical framework — and that two of the forces, electromagnetism and the weak force (which governs the nuclear reactions that power the sun), were actually different manifestations of a single underlying theory.
How could two such different forces be related? After all, the photon, the particle that conveys electromagnetism, has no mass, while the particles that convey the weak force are very massive — almost 100 times as heavy as the particles that make up atomic nuclei, a fact that explains why the weak force is weak.
What the British physicist Peter Higgs and several others showed is that if there exists an otherwise invisible background field permeating all of space, then the particles that convey some force like electromagnetism can interact with this field and effectively encounter resistance to their motion and slow down, like a swimmer moving through molasses.
As a result, these particles can behave as if they are heavy, as if they have a mass. The physicist Steven Weinberg later applied this idea to a model of the weak and electromagnetic forces previously proposed by Sheldon L. Glashow, and everything fit together.
This idea can be extended to the rest of particles in nature, including the protons and neutrons and electrons that make up the atoms in our bodies. If some particle interacts more strongly with this background field, it ends up acting heavier. If it interacts more weakly, if acts lighter. If it doesn’t interact at all, like the photon, it remains massless.
If anything sounds too good to be true, this is it. The miracle of mass — indeed of our very existence, because if not for the Higgs, there would be no stars, no planets and no people — is possible because of some otherwise hidden background field whose only purpose seems to be to allow the world to look the way it does.
Dr. Glashow, who along with Dr. Weinberg won a Nobel Prize in Physics, later once referred to this “Higgs field” as the “toilet” of modern physics because that’s where all the ugly details that allow the marvelous beauty of the physical world are hidden.
But relying on invisible miracles is the stuff of religion, not science. To ascertain whether this remarkable accident was real, physicists relied on another facet of the quantum world.
Associated with every background field is a particle, and if you pick a point in space and hit it hard enough, you may whack out real particles. The trick is hitting it hard enough over a small enough volume.
And that’s the rub. After 50 years of trying, including a failed attempt in this country to build an accelerator to test these ideas, no sign of the Higgs had appeared. In fact, I was betting against it, since a career in theoretical physics has taught me that nature usually has a far richer imagination than we do.
Until last week.
Every second at the Large Hadron Collider, enough data is generated to fill more than 1,000 one-terabyte hard drives — more than the information in all the world’s libraries. The logistics of filtering and analyzing the data to find the Higgs particle peeking out under a mountain of noise, not to mention running the most complex machine humans have ever built, is itself a triumph of technology and computational wizardry of unprecedented magnitude.
The physicist Victor F. Weisskopf — the colorful first director of CERN, the European Center for Nuclear Research, which operates the collider — once described large particle accelerators as the gothic cathedrals of our time. Like those beautiful remnants of antiquity, accelerators require the cutting edge of technology, they take decades or more to build, and they require the concerted efforts of thousands of craftsmen and women. At CERN, each of the mammoth detectors used to study collisions requires the work of thousands of physicists, from scores of countries, speaking several dozen languages.
Most significantly perhaps, cathedrals and colliders are both works of incomparable grandeur that celebrate the beauty of being alive.
The apparent discovery of the Higgs may not result in a better toaster or a faster car. But it provides a remarkable celebration of the human mind’s capacity to uncover nature’s secrets, and of the technology we have built to control them. Hidden in what seems like empty space — indeed, like nothing, which is getting more interesting all the time — are the very elements that allow for our existence.
By demonstrating that, last week’s discovery will change our view of ourselves and our place in the universe. Surely that is the hallmark of great music, great literature, great art ...and great science.
Lawrence M. Krauss, the director of the Origins Project at Arizona State University, is the author, most recently, of “A Universe From Nothing.”
Wednesday, July 04, 2012
A New Particle Could Be Physics’ Holy Grail
By DENNIS OVERBYE NY Times
ASPEN, Colo. — Physicists working at CERN’s Large Hadron Collider said Wednesday that they had discovered a new subatomic particle that looks for all the world like the Higgs boson, a potential key to an understanding of why elementary particles have mass and indeed to the existence of diversity and life in the universe.
“I think we have it,” Rolf-Dieter Heuer, the director general of CERN, said in an interview from his office outside Geneva, calling the discovery “a historic milestone.” His words signaled what is probably the beginning of the end for one of the longest, most expensive searches in the history of science. If scientists are lucky, the discovery could lead to a new understanding of how the universe began.
Dr. Heuer and others said that it was too soon to know for sure whether the new particle, which weighs in at 125 billion electron volts, one of the heaviest subatomic particles yet, fits the simplest description given by the Standard Model, the theory that has ruled physics for the last half-century, or whether it is an impostor, a single particle or even the first of many particles yet to be discovered. The latter possibilities are particularly exciting to physicists since they could point the way to new deeper ideas, beyond the Standard Model, about the nature of reality. For now, some physicists are calling it a “Higgslike” particle.
“It’s great to discover a new particle, but you have find out what its properties are,” said John Ellis, a theorist at CERN, the European Organization for Nuclear Research.
Joe Incandela, of the University of California, Santa Barbara, a spokesman for one of two groups reporting data on Wednesday, called the discovery “very, very significant.”
“It’s something that may, in the end, be one of the biggest observations of any new phenomena in our field in the last 30 or 40 years, going way back to the discovery of quarks, for example,” he said.
Here at the Aspen Center for Physics, a retreat for scientists that will celebrate its 50th birthday on Saturday, the sounds of cheers and popping corks reverberated early Wednesday against the Sawatch Range through the Roaring Fork Valley of the Rockies, as bleary-eyed physicists watched their colleagues read off the results in a webcast from CERN. It was a scene duplicated in Melbourne, Australia, where physicists had gathered for a major conference, as well as in Los Angeles, Chicago, Princeton, New York, London and beyond — everywhere that members of a curious species have dedicated their lives and fortunes to the search for their origins in a dark universe.
Nima Arkani-Hamed, a physicist at the Institute for Advanced Study in Princeton, said: “I was really impressed. It’s a triumphant day for fundamental physics. Now some fun begins!”
At CERN itself, 1,000 people stood in line all night to get into the auditorium, according to Guido Tonelli, a CERN physicist who said the atmosphere was like a rock concert. Peter Higgs, the University of Edinburgh theorist for whom the boson is named, entered the meeting to a standing ovation.
Confirmation of the Higgs boson or something very much like it would constitute a rendezvous with destiny for a generation of physicists who have believed in the boson for half a century without ever seeing it. And it affirms a grand view of a universe ruled by simple and elegant and symmetrical laws, but in which everything interesting in it, like ourselves, is a result of flaws or breaks in that symmetry.
According to the Standard Model, which has ruled physics for 40 years, the Higgs boson is the only visible and particular manifestation of an invisible force field, a cosmic molasses that permeates space and imbues elementary particles that would otherwise be massless with mass. Particles wading through it would gain heft.
Without this Higgs field, as it is known, or something like it, physicists say all the elementary forms of matter would zoom around at the speed of light, flowing through our hands like moonlight. There would be neither atoms nor life.
Physicists said that they would probably be studying the new Higgs particle for years. Any deviations from the simplest version of the boson — and there are hints of some already — could open a gateway to new phenomena and deeper theories that answer questions left hanging by the Standard Model: What, for example, is the dark matter that provides the gravitational scaffolding of galaxies? And why is the universe made of matter instead of antimatter?
“If the boson really is not acting standard, then that will imply that there is more to the story — more particles, maybe more forces around the corner,” Neal Weiner, a theorist at New York University, wrote in an e-mail. “What that would be is anyone’s guess at the moment.”
One intriguing candidate for the next theory they have been on the watch for is called supersymmetry, “SUSY” for short, which would come with a whole new laundry list of particles to be discovered, one of which might be the source of dark matter. In supersymmetry there are at least two Higgs bosons.
Dr. Incandela said, “The whole world thinks there is one Higgs, but there could be many of them.”
Michael Turner, a cosmologist at the University of Chicago and the chairman of the physics center board, said, “This is a big moment for particle physics and a crossroads — will this be the high water mark or will it be the first of many discoveries that point us toward solving the really big questions that we have posed?”
Wednesday’s announcement is also an impressive opening act for the Large Hadron Collider, the world’s biggest physics machine, which collides protons and only began operating two years ago. It is still running at only half-power.
Physicists had been holding their breath and perhaps icing the Champagne ever since last December. Two teams of about 3,000 physicists each — one named Atlas, led by Fabiola Gianotti, and the other CMS, led by Dr. Incandela — operate giant detectors in the collider, sorting the debris from the primordial fireballs left after proton collisions. Last winter they both reported hints of the same particle. They were not able, however, to rule out the possibility that it was a statistical fluke.
Since then the collider has more than doubled the number of collisions it has recorded.
The new results capped three weeks of feverish speculation and Internet buzz as the physicists, who had been sworn to secrecy, did a breakneck analysis of some 800 trillion proton-proton collisions over the last two years. They were racing to get ready for a major conference in Melbourne that started on Wednesday, where they had promised an update on the Higgs search.
In the end, the CERN council, which consists of representatives from each of CERN’s 20 member states, decided that the potentially historic announcement should come from the lab’s own turf first.
Up until last weekend, physicists from inside were reporting that they themselves did not know what the outcome would be, though many were having fun with the speculation.
“HiggsRumors” became one of the most popular hashtags on Twitter. The particle also acquired its own iPhone app, a game called “Agent Higgs.” Expectations soared when it was learned that the five surviving originators of the Higgs boson theory had been invited to the CERN news conference.
On the eve of the announcement, in what was an embarrassing moment for the lab where the Web was invented, a video of Dr. Incandela making his statement was posted to the Internet and then quickly withdrawn. Dr. Incandela said he had made a series of video presentations with alternate conclusions so that the video producers would not know the right answer ahead of time, but the one that was right just happened to get posted.
But the December signal was no fluke.
Like Omar Sharif materializing out of a distant blur of heated air into a man on a camel in “Lawrence of Arabia,” what was once a hint of a signal had grown over the last year, until it practically jumped off the chart. “I believe it now; I didn’t before,” said a physicist who was one of the first to see the new results but was not authorized to discuss them.
The new particle has a mass of about 125.3 billion electron volts, in the units of mass and energy — Einstein showed they are the same — that are favored by physicists, about as much as a whole barium atom, according to the CMS group, and 126 billion according to Atlas.
Both groups said that the likelihood that their signal was a result of a chance fluctuation was less than one chance in 3.5 million, so-called “five sigma,” which is the gold standard in physics for a discovery.
On that basis, Dr. Heuer said that he had decided only Tuesday afternoon to call the Higgs result a “discovery.”
He said, “I know the science, and as director general I can stick out my neck.”
Dr. Incandela’s and Dr. Gianotti’s presentations were repeatedly interrupted by applause as they showed slide after slide of data bumps rising like mountains from the sea.
Dr. Gianotti said at one point: “Why are you applauding? I’m not done yet. This is just beginning. There is more to come.”
She noted that the mass of the putative Higgs made it easy to study its many behaviors and channels. “So,” she said, “thanks, nature.”
Gerald Guralnik, one of the founders of the Higgs theory, said he was glad to be at a physics meeting “where there is applause like a football game.”
Asked to comment after the announcements, Dr. Higgs seemed overwhelmed, saying, “For me, its really an incredible thing that’s happened in my lifetime.”
In quantum theory, which is the language of particle physicists, elementary particles are divided into two rough categories: fermions, which are bits of matter like electrons, and bosons, which are bits of energy and can transmit forces, like the photon that transmits light.
Dr. Higgs was one of six physicists, working in three independent groups, who in 1964 invented the notion of the cosmic molasses, or Higgs field. The others were Tom Kibble of Imperial College, London; Carl Hagen of the University of Rochester; Dr. Guralnik of Brown University; and Francois Englert and Robert Brout, both of Université Libre de Bruxelles.
One implication of their theory was that this cosmic molasses, normally invisible and, of course, odorless, would produce its own quantum particle if hit hard enough, by the right amount of energy. The particle would be fragile and fall apart within a millionth of a second in a dozen different ways depending upon its own mass.
Unfortunately, the theory did not say how much this particle should weigh, which is what made it so hard to find. The pesky particle eluded researchers at a succession of particle accelerators, including the Large Electron Positron Collider at CERN, which closed down in 2000, and the Tevatron at the Fermi National Accelerator Laboratory, or Fermilab, in Batavia, Ill., which shut down last year.
Along the way the Higgs boson achieved a notoriety rare for abstract physics. To the eternal dismay of his colleagues, Leon Lederman, the former director of Fermilab, called it the “God particle,” in his book of the same name, later quipping that he had wanted to call it “the goddamn particle.”
Finding the missing boson was one of the main goals of the Large Hadron Collider.
Both Dr. Heuer and Dr. Gianotti said they had not expected the search to succeed so quickly, a tribute, they said, to the people who had built the collider and the detectors and learned to run them efficiently. “It’s truly amazing,” said Lisa Randall, a prominent Harvard theorist.
Dr. Heuer recently extended the current run of the collider an extra three months, to the end of this year, during which the experimenters say they expect to triple their data on the new particle, narrowing its possible identities.
The collider will then shut down for two years for major repairs. When it starts up again, theories of both inner space and outer space could be up for grabs.
Although they have never been seen, Higgslike fields play an important role in theories of the universe and in string theory. Under certain conditions, according to the strange accounting of Einsteinian physics, they can become suffused with energy that exerts an antigravitational force. Such fields have been proposed as the source of an enormous burst of expansion, known as inflation, early in the universe and, possibly, as the secret of the dark energy that now seems to be speeding up the expansion of the universe.
Knowing more about the new particle will help put those theories on firmer ground, Dr. Turner of Chicago said.
So far, the physicists admit, they know little. The CERN results are mostly based on measurements of two or three of the dozen different ways, or “channels,” by which a Higgs boson could be produced and then decay.
There are hints, but only hints so far, that some of the channels are overproducing the Higgs while others might be underproducing, clues maybe that there is more than the Standard Model at work.
“This could be the first in a ring of discoveries,” Dr. Tonelli said.
CERN will be examining the rest of the channels over the coming months and years, and the idea that the Standard Model could be cracking is a prospect that physicists find thrilling. Only time, and a few more trillion proton collisions, will tell.
In an e-mail, Maria Spiropulu, a professor at the California Institute of Technology who works with the CMS team at CERN, wrote about the Higgs: “I personally do not want it to be standard model anything — I don’t want it to be simple or symmetric or as predicted. I want us all to have been dealt a complex hand that will send me (and all of us) in a (good) loop for a long time.”