IBM Researchers: chip design advance

Project Seeks to Replace Copper Wires With Lasers and Tiny Silicon Circuits; Intel and Universities Have Similar Efforts
By PAUL GLADER And DON CLARK


Researchers at International Business Machines Corp. are claiming an important advance that could change the way computer chips communicate, sharply boosting speed while lowering energy consumption. The goal is to use pulses of light rather than copper wires to exchange information between chips—and to build the needed components out of silicon rather than costly, esoteric materials.


IBM's advance involves a key component called an avalanche photodetector, which converts light into electricity. The researchers say they used silicon and the element germanium to create a photodetector that is among the fastest and least power-hungry of its kind. They are publishing their findings in the scientific journal Nature. IBM isn't alone in the pursuit. Researchers at universities and companies including Intel Corp. and start-up Luxtera Inc., have also been working on improving chip performance using silicon-based optical components.


"This is the next wave of computing," said Richard Doherty, an analyst at market-research firm Envisioneering Group and a patent holder in optical communications. "By 2020, it may be the dominant way Google, governments, banks and other large users are doing their computing." Optical communications involve encoding information on streams of light particles generated by lasers. The technology uses thin glass fibers rather than bulky cables, yet creates connections that allow more data to flow at higher speed.

Such benefits are the reason long-distance phone wires were replaced with fiber-optic cables, a technology developed in the 1970s. Companies like Luxtera already sell silicon-based optical devices for linking up computers. Researchers are racing to miniaturize optical components so they can be built into microprocessors.


Intel has built a series of optical components from silicon and related materials, including a prototype avalanche photodetector it announced in December 2008. IBM says its version can detect 40 gigabits of data a second—four times the speed of Intel's—and operates at 1.5 volts rather than 30 volts. "That can save a huge amount of power," said Yurii Vlasov, the lead scientist on the IBM research. He said IBM's photodetector can detect weak pulses and amplify them without adding unwanted noise, a previous problem with the technology.


Mario Paniccia, director of Intel's photonics technology lab, called IBM's advance another sign of progress in the field. "As a scientist, I think this is all great," he said. "It just drives more competition."


Mr. Vlasov said it could be five years until the technology makes its way into chips for high-end server systems. It could take another five years before it is used in consumer products such as cellphones, he said.

* TECHNOLOGY
* MARCH 4, 2010

IBM: IBM scientists Fengnian Xia, Yurii Vlasov and Solomon Assefa were part of the team behind the research.

As impressive as the chip is, I love this picture: a Chinese, a Russian, and  an Ethiopian; that the US at its best.

Sun, Stimulus and a Sneeze

The tendency to sneeze when suddenly exposed to sunlight or other bright light may be caused by an extra-sensitive visual cortex, the part of the brain that receives visual signals, according to a study in PLoS ONE. The so-called "photic sneeze reflex" or ACHOO (Autosomal Cholinergic Helio-Ophthalmic Outburst) syndrome affects an estimated one in four people. The study, which compared the reactions of 10 photic sneezers and 10 control subjects, appears to be the first to examine the condition. The researchers measured the electrical activity of the participants' brains while they were shown a shifting pattern of white and black squares. At around 60 milliseconds after each shift and again 140 milliseconds later, the visual cortices of sneeze-prone subjects showed significantly higher activity than those of the control subjects.

Caveat: A larger study is needed to verify the findings. More precise measurements are needed to identify which particular areas of the visual cortex drive the response.
 
Read the Study: When the Sun Prickles Your Nose: An EEG Study Identifying Neural Bases of Photic Sneezing

U.S. Scientists Given Access to Cloud Computing

February 5, 2010
U.S. Scientists Given Access to Cloud Computing
By JOHN MARKOFF


The National Science Foundation and the Microsoft Corporation have agreed to offer American scientific researchers free access to the company’s new cloud computing service.


A goal of the three-year project is to give scientists the computing power to cope with exploding amounts of research data. It uses Microsoft’s Windows Azure computing system, which the company recently introduced to compete with cloud computing services from companies like Amazon, Google, I.B.M. and Yahoo. These cloud computing systems allow organizations and individuals to run computing tasks and Internet services remotely in relatively low-cost data centers.


The new program was announced on Thursday at a news conference in Washington.


Neither Microsoft nor the foundation was willing to place a dollar amount on the agreement, but Dan Reed, the corporate vice president for technology strategy and policy at Microsoft, said that the company was prepared to invest millions of dollars in the service and that it could support thousands of scientific research programs.


Access to the service will come in grants from the foundation to new and continuing scientific research. Microsoft executives said they planned eventually to make the new service global.


The government has traditionally supported a group of scientific computing centers at universities and laboratories around the country. These centers have typically housed supercomputers capable of solving scientific and engineering problems quickly. In recent years, however, increasing emphasis has been placed on computing systems capable of storing and analyzing vast amounts of data.


“It’s all about data,” said Jeannette M. Wing, assistant director of computer and information science and engineering directorate at the science foundation. “We are generating streams and rivers of data.”


Genetic sequencing systems are capable of generating as much as a terabyte, 1,000 gigabytes, of information a minute, Dr. Wing said.


Microsoft made its commitment to scientific computing two years after a similar service was introduced by Google and I.B.M. Several scientists familiar with the Microsoft project said the software company was hoping to differentiate the new service by offering scientists a set of custom applications that simplified access to Azure and the use of older software applications like Microsoft Excel.


“We’re trying to figure out how to engage the majority of scientists,” said Dr. Reed, who directed several of the nation’s scientific computing centers before joining Microsoft.


Simplicity of use is one Microsoft goal. Programming modern cloud systems for full efficiency has been difficult. The company is trying to overcome this difficulty in creating a variety of software tools for scientists, said Ed Lazowska, a University of Washington computer scientist who works with the Microsoft researchers.


Dr. Lazowska said the explosion of data being collected by scientists had transformed the staffing needs of the typical scientific research program on campus from a half-time graduate student one day a week to a full-time employee dedicated to managing the data. He said such exponential growth in cost was increasingly hampering scientific research.

Chatter of Monkeys

January 12, 2010
Deciphering the Chatter of Monkeys
By NICHOLAS WADE

Walking through the Tai forest of Ivory Coast, Klaus Zuberbühler could hear the calls of the Diana monkeys, but the babble held no meaning for him.

That was in 1990. Today, after nearly 20 years of studying animal communication, he can translate the forest’s sounds. This call means a Diana monkey has seen a leopard. That one means it has sighted another predator, the crowned eagle. “In our experience time and again, it’s a humbling experience to realize there is so much more information being passed in ways which hadn’t been noticed before,” said Dr. Zuberbühler, a psychologist at the University of St. Andrews in Scotland.

Do apes and monkeys have a secret language that has not yet been decrypted? And if so, will it resolve the mystery of how the human faculty for language evolved? Biologists have approached the issue in two ways, by trying to teach human language to chimpanzees and other species, and by listening to animals in the wild.

The first approach has been propelled by people’s intense desire — perhaps reinforced by childhood exposure to the loquacious animals in cartoons — to communicate with other species. Scientists have invested enormous effort in teaching chimpanzees language, whether in the form of speech or signs. A New York Times reporter who understands sign language, Boyce Rensberger, was able in 1974 to conduct what may be the first newspaper interview with another species when he conversed with Lucy, a signing chimp. She invited him up her tree, a proposal he declined, said Mr. Rensberger, who is now at M.I.T.

But with a few exceptions, teaching animals human language has proved to be a dead end. They should speak, perhaps, but they do not. They can communicate very expressively — think how definitely dogs can make their desires known — but they do not link symbolic sounds together in sentences or have anything close to language.

Better insights have come from listening to the sounds made by animals in the wild. Vervet monkeys were found in 1980 to have specific alarm calls for their most serious predators. If the calls were recorded and played back to them, the monkeys would respond appropriately. They jumped into bushes on hearing the leopard call, scanned the ground at the snake call, and looked up when played the eagle call.

It is tempting to think of the vervet calls as words for “leopard,” “snake” or “eagle,” but that is not really so. The vervets do not combine the calls with other sounds to make new meanings. They do not modulate them, so far as is known, to convey that a leopard is 10, or 100, feet away. Their alarm calls seem less like words and more like a person saying “Ouch!” — a vocal representation of an inner mental state rather than an attempt to convey exact information.

But the calls do have specific meaning, which is a start. And the biologists who analyzed the vervet calls, Robert Seyfarth and Dorothy Cheney of the University of Pennsylvania, detected another significant element in primates’ communication when they moved on to study baboons. Baboons are very sensitive to who stands where in their society’s hierarchy. If played a recording of a superior baboon threatening an inferior, and the latter screaming in terror, baboons will pay no attention — this is business as usual in baboon affairs. But when researchers concoct a recording in which an inferior’s threat grunt precedes a superior’s scream, baboons will look in amazement toward the loudspeaker broadcasting this apparent revolution in their social order.

Baboons evidently recognize the order in which two sounds are heard, and attach different meanings to each sequence. They and other species thus seem much closer to people in their understanding of sound sequences than in their production of them. “The ability to think in sentences does not lead them to speak in sentences,” Drs. Seyfarth and Cheney wrote in their book “Baboon Metaphysics.”

Some species may be able to produce sounds in ways that are a step or two closer to human language. Dr. Zuberbühler reported last month that Campbell’s monkeys, which live in the forests of the Ivory Coast, can vary individual calls by adding suffixes, just as a speaker of English changes a verb’s present tense to past by adding an “-ed.”

The Campbell’s monkeys give a “krak” alarm call when they see a leopard. But adding an “-oo” changes it to a generic warning of predators. One context for the krak-oo sound is when they hear the leopard alarm calls of another species, the Diana monkey. The Campbell’s monkeys would evidently make good reporters since they distinguish between leopards they have observed directly (krak) and those they have heard others observe (krak-oo).

Even more remarkably, the Campbell’s monkeys can combine two calls to generate a third with a different meaning. The males have a “Boom boom” call, which means “I’m here, come to me.” When booms are followed by a series of krak-oos, the meaning is quite different, Dr. Zuberbühler says. The sequence means “Timber! Falling tree!”

Dr. Zuberbühler has observed a similar achievement among putty-nosed monkeys that combine their “pyow” call (warning of a leopard) with their “hack” call (warning of a crowned eagle) into a sequence that means “Let’s get out of here in a real hurry.”

Apes have larger brains than monkeys and might be expected to produce more calls. But if there is an elaborate code of chimpanzee communication, their human cousins have not yet cracked it. Chimps make a food call that seems to have a lot of variation, perhaps depending on the perceived quality of the food. How many different meanings can the call assume? “You would need the animals themselves to decide how many meaningful calls they can discriminate,” Dr. Zuberbühler said. Such a project, he estimates, could take a lifetime of research.

Monkeys and apes possess many of the faculties that underlie language. They hear and interpret sequences of sounds much like people do. They have good control over their vocal tract and could produce much the same range of sounds as humans. But they cannot bring it all together.

This is particularly surprising because language is so useful to a social species. Once the infrastructure of language is in place, as is almost the case with monkeys and apes, the faculty might be expected to develop very quickly by evolutionary standards. Yet monkeys have been around for 30 million years without saying a single sentence. Chimps, too, have nothing resembling language, though they shared a common ancestor with humans just five million years ago. What is it that has kept all other primates locked in the prison of their own thoughts?

Drs. Seyfarth and Cheney believe that one reason may be that they lack a “theory of mind”; the recognition that others have thoughts. Since a baboon does not know or worry about what another baboon knows, it has no urge to share its knowledge. Dr. Zuberbühler stresses an intention to communicate as the missing factor. Children from the youngest ages have a great desire to share information with others, even though they gain no immediate benefit in doing so. Not so with other primates.

“In principle, a chimp could produce all the sounds a human produces, but they don’t do so because there has been no evolutionary pressure in this direction,” Dr. Zuberbühler said. “There is nothing to talk about for a chimp because he has no interest in talking about it.” At some point in human evolution, on the other hand, people developed the desire to share thoughts, Dr. Zuberbühler notes. Luckily for them, all the underlying systems of perceiving and producing sounds were already in place as part of the primate heritage, and natural selection had only to find a way of connecting these systems with thought.

Yet it is this step that seems the most mysterious of all. Marc D. Hauser, an expert on animal communication at Harvard, sees the uninhibited interaction between different neural systems as critical to the development of language. “For whatever reason, maybe accident, our brains are promiscuous in a way that animal brains are not, and once this emerges it’s explosive,” he said.

In animal brains, by contrast, each neural system seems to be locked in place and cannot interact freely with others. “Chimps have tons to say but can’t say it,” Dr. Hauser said. Chimpanzees can read each other’s goals and intentions, and do lots of political strategizing, for which language would be very useful. But the neural systems that compute these complex social interactions have not been married to language.

Dr. Hauser is trying to find out whether animals can appreciate some of the critical aspects of language, even if they cannot produce it. He and Ansgar Endress reported last year that cotton-top tamarins can distinguish a word added in front of another word from the same word added at the end. This may seem like the syntactical ability to recognize a suffix or prefix, but Dr. Hauser thinks it is just the ability to recognize when one thing comes before another and has little to do with real syntax.

“I’m becoming pessimistic,” he said of the efforts to explore whether animals have a form of language. “I conclude that the methods we have are just impoverished and won’t get us to where we want to be as far as demonstrating anything like semantics or syntax.”

Yet, as is evident from Dr. Zuberbühler’s research, there are many seemingly meaningless sounds in the forest that convey information in ways perhaps akin to language.

Doomsday? not in 2012

NASA said last week that the world was not ending — at least anytime soon. Last year, CERN, the European Center for Nuclear Research, said the same thing, which I guess is good news for those of us who are habitually jittery. How often do you have a pair of such blue-ribbon scientific establishments assuring us that everything is fine?

On the other hand, it is kind of depressing if you were looking forward to taking a vacation from mortgage payments to finance one last blowout.

Interactive Graphic The Long Count

The announcements by the National Aeronautics and Space Administration, in the form of several Web site postings and a video posted on YouTube, were in response to worries that the world will end on Dec. 21, 2012, when a 5,125-year cycle known as the Long Count in the Mayan calendar supposedly comes to a close.

The doomsday buzz reached a high point with the release of the new movie “2012,” directed by Roland Emmerich, who previously inflicted misery on the Earth from aliens and glaciers in “Independence Day” and “The Day After Tomorrow.”

Some people's imagination jis way too vivid.

A Discipline in Denial

Earlier this month, Sen. Tom Coburn of Oklahoma swooped in on the National Science Foundation budget, offering an amendment that would ban the organization from "wasting any federal research funding on political-science projects." The assumption that the money was better spent on "real science," seemed to cause the entire quarrelsome field of political scientists to rise as one in righteous opposition.

Senator Coburn strikes again.

Querulous academics often are their own worst enemies in these funding battles. They quickly wax hysterical, unaware that platitudes about supporting "free inquiry" do not cut much with the general public. Should NSF be spending $188,206 to support a study of "candidate ambiguity and voter choice," designed to ascertain how politicians benefit from being vague?

188 thousand out of a budget totaling 2.5 trillion dollars; wow, that will make an impact. Seems more pf an anti-intellectual charade than budgetary discipline. Coburn's at it again.

Still, the political scientists have a point. The program has been going since the early 1960s, and the dollar amounts have always been relatively small—the money for political science projects have amounted to $112 million over a 10-year period, compared to NSF's budget request for 2010 of more than $7 billion.

188 thousand out of 7 billion equals 0.00269%

There are other reasons to think that this battle may be ill-chosen. The very program under fire supported the work of Elinor Ostrom, who won a Nobel Prize in economics this year for her work advancing the role of free institutions, rather than governments, in managing natural resources—an analysis Mr. Coburn might find valuable.

New Ring Discovered Around Saturn

A new ring of tiny dust particles has been discovered 8 million miles from Saturn's surface. The halo is approximately 50 times farther from Saturn than the other rings, and scientists believe it's the product of debris from small impacts on Saturn's moon Phoebe. Experts suggest the dust from the impacts then migrated toward the planet and was picked up by another of Saturn's moons, Iapetus. "The particles smack Iapetus like bugs on a windshield," explained a University of Virginia professor, adding that the discovery explains Iapetus' two-tone nature. The newly found disc is distinct not only in its size and distance, but also its angle: It is tilted 27 degrees to the plane encompassing Saturn's other rings, which is likely due to Phoebe's inclined path around the planet.

Read it at BBC

Fossils Shed New Light on Human Past

A partial skeleton of Ardipithecus ramidus graces the cover of the latest issue of the journal Science.






After 15 years of rumors, researchers made public fossils from a 4.4 million-year-old human forebear they say reveals that our ancestors were more modern than scholars had assumed, widening the evolutionary gulf separating humankind from apes and chimpanzees.

The highlight of the extensive fossil trove was a female skeleton a million years older than the iconic bones of Lucy, the primitive female figure that has long symbolized humankind's beginnings.


More interactive graphics and photos

Ardipithecus ramidus

October 2, 2009
Fossil Skeleton From Africa Predates Lucy
By JOHN NOBLE WILFORD

Lucy, meet Ardi.

Ardi, short for Ardipithecus ramidus, is the newest fossil skeleton out of Africa to take its place in the gallery of human origins. At an age of 4.4 million years, it lived well before and was much more primitive than the famous 3.2-million-year-old Lucy, of the species Australopithecus afarensis.

Since finding fragments of the older hominid in 1992, an international team of scientists has been searching for more specimens and on Thursday presented a fairly complete skeleton and their first full analysis. By replacing Lucy as the earliest known skeleton from the human branch of the primate family tree, the scientists said, Ardi opened a window to “the early evolutionary steps that our ancestors took after we diverged from our common ancestor with chimpanzees.”

The older hominid was already so different from chimps that it suggested “no modern ape is a realistic proxy for characterizing early hominid evolution,” they wrote.

The Ardipithecus specimen, an adult female, probably stood four feet tall and weighed about 120 pounds, almost a foot taller and twice the weight of Lucy. Its brain was no larger than a modern chimp’s. It retained an agility for tree-climbing but already walked upright on two legs, a transforming innovation in hominids, though not as efficiently as Lucy’s kin.

Ardi’s feet had yet to develop the arch-like structure that came later with Lucy and on to humans. The hands were more like those of extinct apes. And its very long arms and short legs resembled the proportions of extinct apes, or even monkeys.

Tim D. White of the University of California, Berkeley, a leader of the team, said in an interview this week that the genus Ardipithecus appeared to resolve many uncertainties about “the initial stage of evolutionary adaptation” after the hominid lineage split from that of the chimpanzees. No fossil trace of the last common ancestor, which lived some time before six million years ago, according to genetic studies, has yet come to light.

The other two significant stages occurred with the rise of Australopithecus, which lived from about four million to one million years ago, and then the emergence of Homo, our own genus, before two million years ago. The ancestral relationship of Ardipithecus to Australopithecus has not been determined, but Lucy’s australopithecine kin are generally recognized as the ancestral group from which Homo evolved.

Scientists not involved in the new research hailed its importance, placing the Ardi skeleton on a pedestal alongside notable figures of hominid evolution like Lucy and the 1.6-million-year-old Turkana Boy from Kenya, an almost complete specimen of Homo erectus with anatomy remarkably similar to modern Homo sapiens.

David Pilbeam, a professor of human evolution at Harvard University who had no role in the discovery, said in an e-mail message that the Ardi skeleton represented “a genus plausibly ancestral to Australopithecus” and began “to fill in the temporal and structural ‘space’ between the apelike common ancestor and Australopithecus.”

Andrew Hill, a paleoanthropologist at Yale University who was also not involved in the research, noted that Dr. White had kept “this skeleton in his closet for the last 15 years or so, but I think it has been worth the wait.” In some ways the specimen’s features are surprising, Dr. Hill added, “but it makes a very satisfactory animal for understanding the changes that have taken place along the human lineage.”

The first comprehensive reports describing the skeleton and related findings, the result of 17 years of study, are being published Friday in the journal Science. Eleven papers by 47 authors from 10 countries describe the analysis of more than 110 Ardipithecus specimens from a minimum of 36 different individuals, including Ardi.

The paleoanthropologists wrote in one of the articles that Ardipithecus was “so rife with anatomical surprises that no one could have imagined it without direct fossil evidence.”

A bounty of animal and plant material — “every seed, every piece of fossil wood, every scrap of bone,” Dr. White said — was gathered to set the scene of the cooler, more humid woodland habitat in which these hominids had lived.

This was one of the first surprises, said Giday WoldeGabriel, a geologist at Los Alamos National Laboratory, because it upset the hypothesis that upright walking had evolved as an adaptation to life on grassy savanna.

The discovery site, on what is now an arid floodplain along the middle stretch of the Awash River in Ethiopia, is 140 miles northeast of Addis Ababa and 45 miles south of Hadar, where Lucy was found in 1974 by Donald Johanson, with whom Dr. White collaborated in analyzing those fossils.

Gen Suwa, a paleoanthropologist now at the University of Tokyo, made the first discovery in 1992: a single upper molar. Yohannes Haile-Selassie, an Ethiopian curator of anthropology at the Cleveland Museum of Natural History, uncovered the first skeletal bones. A preliminary report on the new species was published in 1994.

But the fossils, which are housed at the anthropology museum in Addis Ababa, were so plentiful, fragmentary and potentially significant that Dr. White held back from further public discussion of the research, even while discoveries of older fossils were being made.

One discovery was of an earlier species of Ardipithecus from elsewhere in Ethiopia. Other finds, perhaps from more than six million years ago and given other species names, were excavated in Chad and Kenya. Their bones indicate that they also walked upright, scientists say, but the fossils are too few to draw any definitive conclusions.

Ardi’s skull, Dr. Pilbeam said, appears to be more similar to the older Chad hominid than to younger australopithecines. This indicates that the fossils from Chad and Ethiopia possibly represent species of the Ardipithecus genus, or closely related genera.

From the new research, scientists inferred that Ardi was female, based on its small and lightly built skull and its canine teeth, which are small compared with other individuals at the site.

Dr. Suwa, a specialist in fossil teeth, said the more than 145 teeth collected at the site were of the size and shape and had wear patterns showing that the individuals were omnivorous eaters of plants and nuts, as well as small mammals, but were not as big consumers of fruits as are living chimps and gorillas. Ardi probably fed in trees and on the ground.

Dr. Suwa also noted that males had stubby canine teeth, more like those of modern humans, in contrast to the projecting tusklike upper canines of chimps and gorillas, suggesting that Ardipithecus teeth no longer functioned as weapons or displays in male-male or male-female conflicts. In fact, the male and female upper canines are similar.

This was seen as further evidence that the species had already evolved a distinctive trait of early prehumans. C. Owen Lovejoy, an anatomist at Kent State University and lead author of two of the journal reports, speculated that these hominids had a social system that involved less competition among males and that this suggested the beginning of pair bonding between males and females.

Dr. Pilbeam disputed this conjecture, saying, “This is a restatement of Owen Lovejoy’s ideas going back almost three decades, which I found unpersuasive then and still do.”

In his articles and an interview, Dr. Lovejoy described the five years he spent analyzing the Ardipithecus pelvis, which appeared to be in transition between a structure originally suited for life in trees and one modified for early upright walking. By contrast, the pelvis of the Lucy species had already evolved nearly all of the adaptations for bipedality.

Although the lower pelvis is still primitive, Dr. Lovejoy found, changes in the upper pelvis enabled the species to walk on two legs with a straightened hip, “but probably with less speed and efficiency than humans.” A few scientists think this walking evidence to be only circumstantial. The lower part of the pelvis, “still almost entirely apelike,” indicates retention of powerful hamstring muscles for climbing.

Dr. White, Berhane Asfaw of the Rift Valley Research Service in Ethiopia and other team members concluded that “despite the genetic similarities of living humans and chimpanzees, the ancestor we last shared probably differed substantially from any extant African ape.”

As Dr. Hill of Yale said, “It is always new specimens, particularly those from little known time periods or geographic areas, that provoke the greatest changes in our ideas.”

Looking ahead, Dr. White lamented that there were so few sites in Africa known to have fossil deposits six million to seven million years old. “We are getting so close to that common ancestor of hominids and chimps, and we’d love to find an earlier skeleton,” he said.

Why brain imp gets out

“That single thought is enough,” wrote Edgar Allan Poe in “The Imp of the Perverse,” an essay on unwanted impulses. “The impulse increases to a wish, the wish to a desire, the desire to an uncontrollable longing.”



In a few cases, the answer [to the question: am I sick?] may be yes. But a vast majority of people rarely, if ever, act on such urges, and their susceptibility to rude fantasies in fact reflects the workings of a normally sensitive, social brain, argues a paper published last week in the journal Science.

Whew.

Maybe not

A blood protein that only a short time ago was thought by some to be more important than cholesterol in heart disease now appears to be little more than a bystander.

The substance, C-reactive protein, or CRP, a marker of inflammation in the body, is unquestionably associated with heart disease: the more CRP in a person’s blood, the greater the likelihood of heart disease.

But in a paper to be published Wednesday in The Journal of the American Medical Association, researchers analyzing genetic data from more than 100,000 people conclude that their study “argues against” the notion that the protein causes heart disease.

Overreacting to news is nonsensical.

Science, Spirituality, and Some Mismatched Socks

One of quantum physics' crazier notions is that two particles seem to communicate with each other instantly, even when they're billions of miles apart. Albert Einstein, arguing that nothing travels faster than light, dismissed this as impossible "spooky action at a distance."

The great man may have been wrong.

Amazingly, 54 years afters his death, it can be said that he might have been wrong.

Quantum physics is the study of the very small -- atoms, photons and other particles. Unlike the cause-and-effect of our everyday physical world, subatomic particles defy common sense and behave in wacky ways.

That includes the fact that a photon, which is a particle of light, exists in a haze of multiple behaviors. They spin in many ways, such as "up" or "down," at the same time. Even trickier, it's only when you take a peek -- by measuring it -- that the photon fixes into a particular state of spin. Stranger still is entanglement. When two photons get "entangled" they behave like a joint entity. Even when they're miles apart, if the spin of one particle is changed, the spin of the other instantly changes, too. This direct influence of one object on another distant one is called non-locality.

These peculiar properties have already been proven in a lab and tapped to improve data encryption. They could also one day be used to build much faster computers. Some philosophers see quantum phenomena as a sign of far greater unknown forces at work and it bolsters their view that a spiritual dimension exists.

Einstein refused to believe that a photon could be in all states at once and set out to find an explanation for their seemingly odd behavior. God doesn't play dice with the universe, he said at the time. Danish physicist Neils Bohr, a big proponent of quantum uncertainty, shot back: "Quit telling God what to do."

Chemist Cites Advance in Stem-Cell Field

Scientists have reprogrammed mature skin cells into an embryonic-like state by using proteins instead of genes, a key advance aimed at overcoming safety concerns in one of the hottest areas of biological research.

Now, instead of reprogramming the cell with four introduced genes, researchers have achieved the same result by inserting four proteins associated with those genes. This technique is deemed to be safer because it doesn't require genetic manipulation.

Obama Walks Religious Tightrope

In the early days of his administration, President Barack Obama has developed an unusual pattern as he talks about religion: He regularly puts nonbelievers on the same footing as religious Americans.


It is a rare gesture for a U.S. political leader. But what makes Mr. Obama's outreach especially remarkable is that it is accompanied by public displays of faith that sometimes go beyond even those of his religiously oriented predecessor in the White House.

The outreach toward both ends of the religious spectrum makes for a complicated balancing act, one that runs the risk of alienating one group, the other, or possibly both.

They just can't figure him out. They keep using the same metrics, the same methods, as usual, and the results they get confuse them.

White House events, even those without a religious theme, often begin with a prayer. And the president said he would expand President George W. Bush's outreach to faith-based organizations.

At the same time, he has taken a series of policy steps that are troubling to religious conservatives, and pledged that decisions in his administration would be governed by science. He reversed Bush policies on funding for international family-planning groups and stem-cell research, and he has moved to rescind regulations that allow health-care workers to opt out of duties that offend their beliefs.

But even when taking these stands, which would be expected of a Democratic president, he often makes a point to say that he understands the other side.

Some don't understand that there is another side.

Bishop E.W. Jackson Sr. of Exodus Faith Ministries in Chesapeake, Va., a nondenominational church, finds Mr. Obama's acceptance of nonbelievers offensive. "I believe every American should worship however they wish," he said, "however to deny that the country is fundamentally Christian in its culture and its heritage is just not true."

Boo to you.

But Mr. Obama's frequent mentions of nonbelievers stand out, said Michael Lindsay, a Rice University sociologist who studies religion and culture. In some ways, says Mr. Lindsay, it represents the continuation of a pattern in American public discourse. "The last 50 years has been a gradual evolving notion of what constitutes religious diversity," he said. First, he said, Jews were included. Later, after immigration increased from Asia in the 1960s, politicians began mentioning Buddhism and Hinduism. But rarely have atheists been included, he said.

Vote on Challenge to Evolution

Where is Clarence Darrow when we need him?
Rev. Carl W. Rohlfs of the University United Methodist Church in Austin, left, talks with Texas Freedom Network President Kathy Miller, right, Thursday in Austin. The State Board of Education is voting on science-curriculum standards on the teaching of evolution.


We're still debating evolution? Maybe we should make sure the earth really rotates around the sun, unless we're in danger of falling off the edge of the earth while navigating. Geez.

The Texas Board of Education will vote this week on a new science curriculum designed to challenge the guiding principle of evolution, a step that could influence what is taught in biology classes across the nation.

"This is the most specific assault I've seen against evolution and modern science," said Steven Newton, a project director at the National Center for Science Education, which promotes teaching of evolution.

As Ralph Kiner once said about Casey Stengel, "if he were alive, he'd be turning over in his grave." This time it'd be Clarence Darrow.

Texas school board chairman Don McLeroy also sees the curriculum as a landmark -- but a positive one.

Dr. McLeroy believes that God created the earth less than 10,000 years ago. If the new curriculum passes, he says he will insist that high-school biology textbooks point out specific aspects of the fossil record that, in his view, undermine the theory that all life on Earth is descended from primitive scraps of genetic material that first emerged in the primordial muck about 3.9 billion years ago.

Huh? Never mind the separation of church and state, but this is ridiculous.

He also wants the texts to make the case that individual cells are far too complex to have evolved by chance mutation and natural selection, an argument popular with those who believe an intelligent designer created the universe.

Of course he couldn't possibly see that complexity arose across vast ages. Nah. God did it.

The textbooks will "have to say that there's a problem with evolution -- because there is," said Dr. McLeroy, a dentist. "We need to be honest with the kids."

That's rich: let's be honest.

Polls show many Americans are skeptical of or confused by evolution; in a recent survey by Gallup, 39% said they believe the theory, 25% said they didn't, and 36% had no opinion.

What can one possibly say about that? Well, 4 of 10 believe in evolution, 1 in 4 don't, and a third are skeptical, dumb or indifferent.








Someone sent this cartoon to the Wall Street Journal discussion of this article and topic.

The Fall and Rise of the Right Whale

SUNNIER DAYS A North Atlantic right whale and calf off Florida. The whale remains endangered, but its population has more than tripled in a century.














North Atlantic right whales, which can grow up to 55 feet long and weigh up to 70 tons, were the “right” whales for 18th- and 19th-century whalers because they are rich in oil and baleen, move slowly, keep close to shore and float when they die.

They were long ago hunted to extinction in European waters, and by 1900 perhaps only 100 or so remained in their North American range, from feeding grounds off Maritime Canada and New England to winter calving grounds off the Southeastern coast.

Multimedia

Graphic Steering Clear

Audio Slide Show
A Slow Comeback for the Right Whale

From Bipolar Darkness, the Empathy to Be a Doctor

MANIC PHASE Dr. Alice W. Flaherty wrote everywhere, even on her arm.






Dr. Flaherty, now 45, is director of the movement disorders fellowship at Massachusetts General Hospital and an assistant professor of neurology at Harvard Medical School. But those technical descriptors do not begin to capture the way she uses the racing mind of her manic phases to drive her ideas into forceful, highly personal treatments.

The idea of using one's mania, instead of trying to suppress it, is fascinating.

“What made me empathic was my depressions,” she said recently. “People’s emotions were pounding me in the face. The mania is like wasps under the skin, like my head’s going to explode with ideas. But the depressions help the doctor aspect of me.”

Mania.

Letters run up the back of her wrist. They are one consequence of hypergraphia, the overwhelming urge to write; she writes during manias and edits during depressions. (She keeps the illness under control with medication.) Dr. Jerrold F. Rosenbaum, chief of psychiatry at Mass General, says he used to get notes from Dr. Flaherty on napkins.

What is the opposite of hypergraphia?

The wrist notes could be on any of a dozen topics. They may be more thoughts on empathic pain, or about research she is conducting on the side about light boxes and creativity in Harvard undergraduates.

Maybe they are about the informal consultation she made several years ago to an Off Broadway adaptation of “A Doll’s House,” directed by Lee Breuer, a former colleague of hers at the Radcliffe Institute at Harvard, where they were both fellows in 2005.

When weeping during a scene, the actress who played Nora was alarmed upon noticing that the mascara ran from her left eye more quickly than from her right. Dr. Flaherty reassured her that the neurology was normal: the right brain, which controls the opposite side of the body, also controls negative emotions. Therefore, one side seems, and is, sadder than the other. This will go in Dr. Flaherty’s next book, which will be about the neurobiology of illness behaviors ranging from hysteria to stoicism, and, of course, empathy.

I've noticed, now that I reflect on it, that when I weep, say while watching an emotional film scene, my right eye waters more than the left.

“For me,” Dr. Flaherty replied, “it wasn’t memory, but getting my brain to feel right. The psychiatrists said, ‘You should get used to this as your new normal,’ but I never did. It was always alienating when people said, ‘Oh, that’s just bipolar illness talking.’ No, hello — that’s me.”

That last point is so very important.

Behold the Appearance of the Invisibility Cloak

Magicians make things on stage vanish with mirrors and sleight of hand. Physicists are learning to make objects disappear by crafting artificial blind spots from strange new fabrics that deflect revealing electromagnetic waves.

Once perfected, these man-made vanishing points could make buildings disappear to cellphones to eliminate static, or make military missile launchers invisible to radar and infrared sensors.

Recommended Reading

In January, David R. Smith and his colleagues at Duke University reported research on an experimental invisibility device in Broadband Ground-Plane Cloak.

In Nature and Science, Xiang Zhang and his colleagues at the University of California, Berkeley, engineered 3-D metamaterials that can reverse the natural direction of visible and near-infrared light.

This month in Physics Review Letters, physicists at Hong University of Technology and Science devised a way to make things at a distance disappear from view.

A paper published this month in SIAM Review, "Cloaking Devices, Electromagnetic Wormholes, and Transformation Optics," presents an overview of the theoretical developments in cloaking from a mathematical perspective.

A more general primer on metamaterials appears in The Berkeley Science Review in (Meta)material World.

The U.S. Defense Advanced Research Projects Agency is exploring potential military applications. The U.S. Office of Naval Research is also investigating the topic.

The most amazing part of this article:
researchers are exploring whether metamaterials can be made that manipulate sound, seismic and water waves. Physicists led by the French National Center for Scientific Research are applying the principles to breakwater structures that could hide offshore platforms and small islands from tsunami waves. Their experimental dike can steer waves in water around things in the same way that light and microwaves can be redirected.

Limits on Stem Cell Research lifted

Obama Lifts Bush’s Strict Limits on Stem Cell Research

Multimedia

Graphic Easing Restrictions on Embryonic Stem Cells


March 10, 2009
News Analysis
Rethink Stem Cells? Science Already Has
By NICHOLAS WADE

With soaring oratory, President Obama on Monday removed a substantial practical nuisance that has long made life difficult for stem cell researchers. He freed biomedical researchers using federal money (a vast majority) to work on more than the small number of human embryonic stem cell lines that were established before Aug. 9, 2001.

In practical terms, federally financed researchers will now find it easier to do a particular category of stem cell experiments that, though still important, has been somewhat eclipsed by new advances.

Until now, to study unapproved stem cell lines, researchers had to set up separate, privately financed labs and follow laborious accounting procedures to make sure not a cent of federal grant money was used on that research. No longer. The lifting of such requirements “is just a major boon for the research here and elsewhere,” said Dr. Arnold Kriegstein, a stem cell researcher at the University of California, San Francisco.

Dr. George Q. Daley, who studies blood diseases at Children’s Hospital in Boston, said that he had derived 15 human embryonic stem cell lines using private money, and that for the first time he could now apply for grants from the National Institutes of Health to study these cells. In the last eight years, his lab has moved from 90 percent N.I.H. support to half N.I.H., half private financing. But private money is now drying up, he said, and new N.I.H. support will be particularly welcome.

However, the president’s support of embryonic stem cell research comes at a time when many advances have been made with other sorts of stem cells. The Japanese biologist Shinya Yamanaka found in 2007 that adult cells could be reprogrammed to an embryonic state with surprising ease. This technology “may eventually eclipse the embryonic stem cell lines for therapeutic as well as diagnostics applications,” Dr. Kriegstein said. For researchers, reprogramming an adult cell can be much more convenient, and there have never been any restrictions on working with adult stem cells.

For therapy, far off as that is, treating patients with their own cells would avoid the problem of immune rejection.

Members of Congress and advocates for fighting diseases have long spoken of human embryonic stem cell research as if it were a sure avenue to quick cures for intractable afflictions. Scientists have not publicly objected to such high-flown hopes, which have helped fuel new sources of grant money like the $3 billion initiative in California for stem cell research.

In private, however, many researchers have projected much more modest goals for embryonic stem cells. Their chief interest is to derive embryonic stem cell lines from patients with specific diseases, and by tracking the cells in the test tube to develop basic knowledge about how the disease develops.

Despite an F.D.A.-approved safety test of embryonic stem cells in spinal cord injury that the Geron Corporation began in January, many scientists believe that putting stem-cell-derived tissues into patients lies a long way off. Embryonic stem cells have their drawbacks. They cause tumors, and the adult cells derived from them may be rejected by the patient’s immune system. Furthermore, whatever disease process caused the patients’ tissue cells to die is likely to kill introduced cells as well. All these problems may be solvable, but so far none have been solved.

Restrictions on embryonic stem cell research originated with Congress, which, each year since in 1996, has forbidden the use of federal financing for any experiment in which a human embryo is destroyed. This includes the derivation of human stem cell lines from surplus fertility clinic embryos, first achieved by Dr. James Thomson of the University of Wisconsin in 1998.

President Clinton contemplated but never implemented a policy that would have allowed N.I.H.-financed researchers to study human embryonic stem cells derived by others. Research was able to begin only in August 2001, when President Bush, seeking a different way around the Congressional restriction, said researchers could use any lines established before that date.

Critics said the distinction between the Clinton and Bush policies lacked moral significance, given that each was intended to get around the Congressional ban, based on a religious and moral argument. The proposed Clinton policy amounted to: “Stealing is wrong, but it’s O.K. to use stolen property if someone else stole it.” The Bush policy was: “Stealing is wrong, but it’s O.K. to use stolen property if it was stolen before Aug. 9, 2001.”

Mr. Obama has put the proposed Clinton policy into effect, but Congressional restrictions remain. Researchers are still forbidden to use federal financing to derive new human embryonic stem cell lines. They will, however, be allowed to do research on new stem cell lines grown in a privately financed lab.

Stem cell research is the best known of several avenues of investigation into what is known as regenerative medicine. To regenerate the aging body with its own subtle repair systems, of which stem cells are one component, would be far more effective than the brute methods of drugs and surgery used today.

But scientists are still merely at the threshold of understanding how the body’s 200 different types of cell interact with one another. It seems likely to be years before biologists know all the settings that must be adjusted in a human cell’s chromosomes to make it become a well-behaved cone cell in the retina or a dopamine-making neuron of the type destroyed in Parkinson’s.

Despite the new interest in reprogrammed stem cells, human embryonic stem cells are still worth studying, both to track the earliest moments in disease and to help assess the behavior of the reprogrammed cells.

Beaker-Ready Projects? Colleges Have Quite a Few

From proposed animal research laboratories at the University of Arizona, the University of Nebraska and the University of Pennsylvania to empty floors in laboratory buildings at the University of California, Irvine, Ohio State University and Southern Illinois University, colleges across the country have hundreds of shovel- and beaker-ready projects in the sciences that could collectively cost tens of billions and begin within weeks.

Science is a critically important discipline.

When President Obama signed the $787 billion stimulus measure last Tuesday, one of the law’s most surprising provisions was a 36 percent increase in the budget for the National Institutes of Health. The law gives the health institutes $10.4 billion in addition to its annual budget of $29 billion, and the new money must be allocated by September 2010 on grants and other projects that can extend no more than two years.

36% increase, recognizing the importance of science. Monies must be allocated within 19 months and must be spent within two years. Sounds good to me,

The spending increase comes after six years of nearly flat research budgets at the N.I.H., the National Science Foundation, the Department of Energy and other agencies, and growing desperation at research universities, which depend on the agencies to underwrite much of their scientific faculty and laboratory infrastructure.

Since Bush's Iraq adventure began, such important funding as science and energy were neglected.

The agency must spend $1 billion to support construction projects at universities and $300 million to help buy equipment and scientific instruments. An additional $500 million will be spent on federal buildings, mostly at the N.I.H. campus in Bethesda, Md. University administrators said they were eager to get the money and promised that any grants they received would immediately stimulate local economies.

Immediately stimulate local economies; sounds good, no? Sounds good, yes.