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Thursday, May 31, 2007

New discoveries may lead to ALS cure

DISEASE REPLICATED, CONTRIBUTING CELL FOUND IN 2 STUDIES

By Jamie Talan
NEWSDAY

Scientists at Columbia University Medical Center have identified a new player in the motor neuron disease that claimed the life of baseball legend Lou Gehrig, and their scientific collaborators at Harvard Medical School have used stem-cell technology to re-create the disease process in a lab dish.

These developments, reported this week in two papers in the journal Nature Neuroscience, could help unravel the causes of the fatal disease and allow scientists to test the effects of drugs against damaged motor neurons grown from stem cells in the lab.

There are 30,000 Americans with ALS (amyotrophic lateral sclerosis), and it is always fatal. The average survival after diagnosis is five years, and there are no treatments that halt or prevent motor neurons in the brain from dying. Paralysis results because the brain no longer can talk to these neurons that control muscles.

Until recently, ALS researchers have focused on the motor neurons themselves.

But Columbia scientist Serge Przedborski, co-director of the Center for Motor Neuron Biology and Disease, and his colleagues showed that non-neuronal support cells called astrocytes that carry the mutant form of the ALS gene can on their own cause normal motor neurons to get sick and die. That means, said Przedborski, that astrocytes are intimately involved in the disease process. If so, this discovery could provide a new route to developing treatments to prevent or slow the disease.

The team identified a toxic molecule in the astrocytes that seems to trigger damage to motor neurons, and scientists are now working to name the rogue molecule. The Columbia researchers are collaborating with Harvard scientists to unravel the puzzle of ALS.

In the Harvard study, Kevin Eggan and Tom Maniatis used embryonic stem cells to make a population of diseased motor neurons grow.

"We thought that embryonic stem cells could provide a system in which to study ALS," said Eggan, of Harvard's Stem Cell Institute. Indeed, the stem cells were coaxed into making motor neurons from the mutant form of the SOD1 gene, the most common familial ALS gene.

The pathology in the Petri dish was similar to that seen in a mouse with the disease. These specialized stem cells can make billions of motor neurons that will succumb to the damage caused by the mutated gene, the scientists said. Motor neurons are labeled with a green fluorescent protein, which makes them easy to identify.

"This is a viable approach," said Eggan, referring to the use of the green protein. "It's difficult to pick out damaged motor neurons from animal models. We will be able to use this system to do drug screening."

Much of the excitement over stem cells has surrounded their role in possible therapies. This study shows that stem cells also can be used to understand diseases, the researchers said. Eggan likens the study of disease to the way investigators used to figure out why a plane crashed.
Engineers would rush to the crash scene and study the broken pieces. Often, there was so much damage that it was impossible to figure out the events that led to the crash. Today, black boxes on planes collect those missing early events and have helped enormously in putting the pieces together.

The embryonic stem cells that carry disease genes, Eggan said, are the equivalent of the plane's black box. "These cells allow us to replay the early events of the disease process."

Wednesday, May 30, 2007

Know Thyself—Man, Rat or Bot

By Sharon Begley
Newsweek

April 23, 2007 issue - Whether it is an eerily human bot in a virtual-reality game, an animal looking at you with soulful eyes or a patient in a vegetative state, the question nags and nags and won't go away: is there a thinking, self-aware, conscious mind in there?

Not one that merely exhibits intelligence, since silicon chips do calculations that leave the human brain in the dust and even discover mathematical proofs. And not one merely capable of empathy or grief or cooperation, which chimps, elephants and species in between all manage.

No, the capacity that distinguishes humans has come down to something Augustine identified 1,600 years ago when he asked what "can be the purport of the injunction, know thyself? I suppose it is that the mind should reflect upon itself."

It's called metacognition—the ability to think about your thoughts, to engage in self-reflection, to introspect. It was long thought to be not just something that we have more of or do better than machines or animals, but that we have and they lack.

To know what you know is not only the mark of a skilled game-show contestant who is quick (but not too quick) on the buzzer, but also of consciousness, the last stand for human exceptionalism.

Now, however, this claim is on the rocks as both animals and machines show signs that they can engage in self-reflection.

In the latest study, scientists tested for introspection in rats. Jonathon Crystal and Allison Foote of the University of Georgia trained rats to push one lever when they heard a short burst of static, and a second lever when they heard a long burst. The reward for a right answer was six food pellets.

A wrong answer yielded nothing. But refusing to answer—like a student fleeing an exam room upon seeing the impossible questions—earned the rat a consolation prize of three morsels.

Clearly, the smart strategy was to respond if sure of the answer, but pass if not.
The rats got almost perfect scores when they had to identify two-second or eight-second bursts. But when they heard static of intermediate duration and had to choose "long" or "short," they were twice as likely to decline the test and take the three pellets; they knew what they didn't know.

To make sure the rats were truly introspecting, the scientists then eliminated the opt-out choice and required the rats to choose "long" or "short" for the medium bursts.

The animals got half right, no better than guessing, which suggests that when they opted out it was indeed because they had assessed the contents of their mind—do I know this?—and made the rational choice, the scientists report in Current Biology.

"Rats can reflect on their internal mental states," says Crystal. "They know when they don't know." Other scientists have gotten similar results with dolphins and rhesus monkeys, who also decline to take a test when they don't know the answer. They think about thinking.
CONTINUED

Thursday, May 24, 2007

Shoe, diary discoveries spur on search for Earhart

Clues emerge in '37 mystery
By Richard Pyle, Associated Press April 1, 2007
NEW YORK -- It's the coldest of cold cases, and yet 70 years after Amelia Earhart disappeared, clues are still turning up.

Long-dismissed notes of a shortwave distress call beginning, "This is Amelia Earhart . . ."
The previously unknown diary of an Associated Press reporter, surfacing after decades.

And a team that has already found aircraft parts and a woman's shoe on a remote South Pacific atoll, hoping to return in July to find more evidence, perhaps DNA.

For nearly 18 hours, Earhart's twin-engine Lockheed Electra drummed steadily eastward over the Pacific, and as sunrise etched a molten strip of light along the horizon, navigator Fred J. Noonan marked the time and calculated the remaining distance to Howland Island.

It was July 2, 1937, and the two were near the end of a 2,550-mile trek from Lae, New Guinea, the longest leg of a "World Flight" begun 44 days earlier in Oakland, Calif. At the journey's end there a few days hence, Earhart would become the first female pilot to circumnavigate the globe.

Noonan, a former Pan American Airways navigator, estimated when the plane would reach an imaginary "line of position" running northwest-southeast through Howland, where they were to rest and refuel for the onward flight to Hawaii.

" Two hundred miles out," Earhart radioed to the Coast Guard cutter Itasca waiting off Howland.

What nobody knew -- not Earhart and not the Itasca -- was that her plane's radio-reception antenna had been ripped away during takeoff from Lae's bumpy dirt runway. The Itasca could hear Earhart, but she was unable to hear anything.

Also listening aboard the Itasca was James W. Carey, a 23-year-old University of Hawaii student who had been hired by the Associated Press to cover Earhart's Howland stopover.

He had been keeping a diary, a fact unknown to Earhart scholars until September 2006, when a typewritten copy was bought on eBay by a member of the International Group for Historic Aircraft Recovery, or TIGHAR.

The nonprofit organization rejects the official verdict that the fliers were lost at sea, believing instead that they may have crash-landed on an uninhabited atoll called Gardner Island, in the Phoenix Islands 350 miles south of Howland, and lived for a time as castaways.

"Even though the diary doesn't answer the big question, it's an incredible discovery," said TIGHAR's executive director, Ric Gillespie, who has led eight expeditions to the island since 1989 and plans another one this July if his group can raise enough money.

The diary, he said, presents "a firsthand witness about what went on during those desperate hours and days."
Earhart left Lae on July 1. Early the next day, Carey wrote in his diary: "Up all last night following radio reports -- scanty . . . heard voice for first time 2:48 a.m. -- 'sky overcast.' All I heard. At 6:15 a.m. reported '200 miles out.' "Continued...

Tuesday, May 15, 2007

100 new deep-sea species found near Australia

First Published: 00:00 IST(3/1/2007)
Last Updated: 20:26 IST(28/6/2003)

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A joint Australian-New Zealand research voyage has discovered more than 100 new deep-sea species ranging from ferocious-looking fanged creatures to rubber-like bottom dwellers, officials said on Friday.

Australian Environment Minister David Kemp announced the discoveries, which included many species either unrecognised or new to science.

The voyage was conducted on the New Zealand research ship RV Tangaroa, which for the past month explored underwater mountain ranges and peaks off Lord Howe and Norfolk Islands east of Australia.

The exploration found more than 500 fish species and 1,300 invertebrate species, Kemp said.
"Of these, more than 100 species are unrecognised and many represent species new to science," he said.

Discoveries included creatures given names like blobfish, prickly dogfish, viperfish, fangtooths, slickheads, giant sea spiders, goblin shrimp and jewel squid.

The haul also included the fossilised tooth of an extinct "megalodon" -- a shark twice the size of the Great White, according to shark expert Peter Last.

"The tooth had been lying on the seafloor for millions of years before being picked up in a deep-sea bottom sled," Last said.

Tuesday, May 8, 2007

Research links T-Rex to chicken

T-Rex fossil yields clues to evolutionary puzzle:
study
AFP

CHICAGO, April 12, 2007 (AFP) - US researchers have identified microscopic traces of soft tissue taken from a 68 million-year-old T-rex fossil in a startling discovery that is yielding clues to evolutionary links between dinosaurs and birds, a study released Thursday said.

The tiny protein fragments were extracted from the leg bone of a Tyrannosaurus rex that was discovered in the western state of Montana in 2003, but it wasn't until recently that scientists were able to definitively identify them as traces of prehistoric dinosaur collagen.

The collagen should have degraded millions of years before according to conventional wisdom, but paleontologists at North Carolina State University were fairly confident that what they had was the "barely detectable" remains of dinosaur soft tissue based on their chemical and molecular analyses.

However, they could not definitively say that, so they turned to biochemist John Asara at Beth Israel Deaconess Medical School in Boston to make that determination.

It took Asara a year and a half, but he was finally able to sequence the amino acids in the collagen proteins - a proxy for DNA analysis - and conclude that the T-rex femur did indeed contain traces of collagen, a fibrous protein found in bone.

When the researchers compared those amino acid sequences to those of similar proteins in several contemporary animals, they found that the T-rex sequence had similarities to those of chickens, and to a lesser extent frogs and newts. That finding bolsters a recent and controversial proposal that birds and dinosaurs are evolutionarily related, and change that hypothesis to a theory, the researchers said.

"Most people believe that birds evolved from dinosaurs, but that's all based on the architecture of the bones," said John Asara, who is director of mass spectrometry at Beth Israel Deaconess Medical School.

"This allows you to get the chance to say Wait, they really are related because their sequences are related.' We didn't get enough sequences to definitively say that, but what sequences we got support that idea."

More broadly, the discovery challenges long-held assumptions about the process of fossilization, which in turn opens up new avenues of investigation in the field, the researchers said.

Until now it was assumed that organic matter such as proteins could not survive past a million years, but this discovery shows that ancient proteins can provide genetic clues to organisms that are millions and millions of years old even if they are only marginally viable as they were in this case.

"For centuries, it was believed that the process of fossilization destroyed any original material, consequently no one looked carefully at really old bones," said Mary Schweitzer, an assistant professor of paleontology at North Carolina State University in Raleigh, and one of several researchers who worked on the project. But if molecular data from fossils can be retrieved and analyzed, it may be able to verify current ideas about relationships between fossil and living organisms and between groups of distinct organisms that have no modern descendants.

"This interplay between the fossil record and the molecular record is going to become more and more useful in understanding both ends of the evolution of life on this planet," she told journalists on a teleconference.

"It's really exciting." On a more practical level, the findings will probably change the way paleontologists view and treat future fossils, said Lewis Cantley, professor of systems biology at Harvard School of Medicine.

"I think what this says is that when people make new discoveries now, if they want to get maximum information out, they have to immediately handle material in a way that first of all will avoid contamination and second, ensure that whatever is there gets well preserved because it can be interrogated."

Inevitably, a lot will depend on the condition of the fossil. This fossil was preserved in sandstone 60 feet below the ground and the porosity of the sandstone may have been a factor in the survival of these soft tissues, the researchers said.

Even so, it took the biochemists on the team a year and a half to sequence the amino acids in the proteins using highly sensitive mass spectrometry techniques that first broke the proteins down into fragments of 10 to 20 amino acids and then configured them into a sequence.

The study is published in the journal Science and was a collaborative effort between Schweitzer, Cantley and Asara, and Jack Horner, Regents Professor of Paleontology at Montana State University, who provided the fossil.

Thursday, May 3, 2007

Book Confirms Einstein's Belief in God

By
Kevin Jackson
Christian Post Reporter

A book chronicling the life history of Albert Einsten will be released this week and will reveal the deep religiosity of one of history’s greatest minds.

Einstein: His Life and Universe, written by Walter Isaacson, records not only the science behind the genius, but also the humanistic aspects of him, including a deep belief in God. An excerpt from his book was recently published in a Time magazine article titled “Einstein & Faith,” which specifically looked at the famed scientist’s theory on a higher being.

“But the awe part comes in his 50s when he settled into a deism based on what he called the ‘spirit manifest in the laws of the universe,’” wrote Isaacson in the book, “and a sincere belief in a ‘God who reveals Himself in the harmony of all that exists.’”

Through his discoveries in physics and other sciences, Einstein felt that there was undoubtedly a force behind all existence that created all the laws that the world abides by. He even criticized atheists who he argued are missing on the very present link between science and faith.

"There are people who say there is no God," the physicist told a friend, according to the biography. "But what makes me really angry is that they quote me for support of such views."
In a later letter he wrote, "The fanatical atheists are like slaves who are still feeling the weight of their chains which they have thrown off after hard struggle. They are creatures who – in their grudge against traditional religion as the 'opium of the masses' – cannot hear the music of the spheres."

Einstein was by no means a Christian. He had grown up as a German Jew, later leaving that faith. He did not believe in the Judeo-Christian concept of free will, but rather, that people were predetermined to act a certain way.

Despite, he still felt that people should act as if there was free will.

"I am compelled to act as if free will existed, because if I wish to live in a civilized society I must act responsibly," explained Einstein in Isaacson’s book. “I know that philosophically a murderer is not responsible for his crime, but I prefer not to take tea with him.”

In the biography, the author also shows how Einstein did feel compelled by the story of Jesus, seeing him as an integral part of history.

When asked whether he accepts the historical existence of Jesus, Einstein replied, “Unquestionably! No one can read the Gospels without feeling the actual presence of Jesus.
“His personality pulsates in every word,” he added. “No myth is filled with such life."
Current scientists today are also bridging the gap that many see between science and religion.

In an Apr. 6 commentary featured in CNN, Francis S. Collins, M.D., Ph.D., director of the Human Genome Project, shared about his Christian faith. He is also coming out with his own book, The Language of God: A Scientist Presents Evidence for Belief, to show how the two are related.

“I had always assumed that faith was based on purely emotional and irrational arguments,”
explained Collins in the commentary, “and was astounded to discover, initially in the writings of the Oxford scholar C.S. Lewis and subsequently from many other sources, that one could build a very strong case for the plausibility of the existence of God on purely rational grounds.”

In contrast to Einstein, however, the Human Genome director noted that reason alone is not enough to understand God or to prove his existence.

“Faith is reason plus revelation, and the revelation part requires one to think with the spirit as well as with the mind,” Collins wrote. “You have to hear the music, not just read the notes on the page. Ultimately, a leap of faith is required.”

When asked how he could both be a scientist as well as a Christian, Collins noted that the two are more than compatible with each other.

“Actually, I find no conflict here, and neither apparently do the 40 percent of working scientists who claim to be believers,” he explained. “I have found there is a wonderful harmony in the complementary truths of science and faith. The God of the Bible is also the God of the genome.”

Tuesday, May 1, 2007

New planets around Gliese 581

Category: planets

Posted on: April 25, 2007 12:26 PM,
by Chris Rowan

Unsurprisingly, there's lots of fuss about the new planet discovered around the red dwarf Gliese 581 (read the European Southern Observatory press release here). Planets, I should say, because they've actually confirmed two more in a system where they'd detected one already. The Gliese 581 system is now known to consist of:

One 15 Earth-mass planet, orbiting the host star in 5.4 days.

One 5 Earth-mass planet orbiting in 13 days.

One 8 Earth-mass planet, orbiting in 84 days.

(new discoveries in bold; more details here)
It's the smallest of the two new discoveries which is hogging the limelight, because its orbit is within the zone where temperatures allow the presence of liquid water. It doesn't mean that there is any there, of course.

In fact, a mass doesn't give us much to go on in terms of what it's actually like.

What I find more interesting is the more general trend we're seeing in exoplanet discoveries.

It's only been a decade or so since we knew for sure that other planetary systems besides our own actually existed, although our instruments were only sensitive enough to detect "hot Jupiters" whose orbits grazed the surfaces of their host stars.

But as we've gradually developed more sensitive detection techniques, we're discovering less massive planets, with larger orbits, and even multiple bodies within the same system (although the lower relative mass of the star also made things easier in this case).

Clearly, what we've seen up to this point is a very selective view of what's out there, biased by the limitations of our telescopes; and suggests that as soon as we get the ability to detect smaller bodies in planetary systems more like our own, there's a real prospect that we will indeed start finding them.

Diabetes mystery... Geneti clues

Researchers uncover new risk factors
Boston Globe

Decades after scientists first realized that the risk of getting diabetes was partially inherited, discoveries of real genetic defects are suddenly coming rapid-fire.

Thursday, four separate scientific teams, including one led by Harvard researchers, reported three new genetic risk factors and confirmed five others identified over the last few years. An additional risk factor identified by one group has not yet been confirmed by others.

The discoveries open up new avenues to explain what breaks down in the body to cause type 2 diabetes. More than 20 million Americans suffer from diabetes and another 54 million are at risk. In the future, scientists said, the genetic findings may also help predict who will get the illness and lead to treatments tailored to each individual's genetic makeup.

"This is a milestone," said Dr. Larry C. Deeb, president for medicine and science of the American Diabetes Association, who was not involved in the research. "We're moving out of the darkness into understanding a lot more about diabetes."

The researchers identified some genetic areas that are not connected to any known mechanism behind diabetes, which harms the body's ability to control blood sugar and can lead to heart disease, blindness, and early death.

"No one had the first clue that these genetic changes were involved in the disease," said David Altshuler, associate professor of genetics and medicine at Harvard Medical School and a leader of one of the three collaborating teams.

Some of the genetic changes are in what scientists previously called "junk DNA," he said, areas of the genetic code that they previously thought were meaningless. "Our whole view of which parts of the human genome contribute to disease is being augmented."

Genetics accounts for about half the risk of getting type 2 diabetes, according to Altshuler. Environment and such behaviors as obesity and lack of exercise account for the remaining risk.
The eight confirmed genetic defects together account for about 5 percent of the risk of getting the illness, he said. "The picture that is emerging is of multiple genes, each with a modest effect" on diabetes, he added.

However, scientists from the National Institutes of Health found that in one group of subjects, people with the most defects had a four times higher risk of having diabetes than people with the fewest defects.

Scientists said much work remains before genetic testing for diabetes becomes useful for patients. Researchers also expect it may be up to a decade before new treatments result from the work.

"The pharmaceutical industry is absolutely salivating at all of these studies" because they suggest targets for new drugs, said Dr. Francis Collins, director of the National Human Genome Research Institute and a leader of another of the teams. "But there is a long lead time."

The results were published Thursday in the online editions of the journals Science and Nature Genetics. They are based on a new research technique called genomewide association studies, in which scientists compare genetic samples from thousands of individuals who have a specific illness with those who don't.

The work is also unusual because three of the four scientific groups collaborated to confirm their results, drawing on the largest database of DNA ever used to study diabetes and making the findings extremely solid.

"Only five years ago this work would have been unthinkable," said Collins.

Each of the four groups used genetic material from a different population, totaling tens of thousands of subjects.

The three groups that coordinated to confirm each other's results were led by scientists from Britain; the National Institutes of Health and Finland; and the Broad Institute at Harvard and MIT, Sweden, and the pharmaceutical company Novartis.

The three variations they found are near genes that appear to be related to regulation of insulin, which controls blood sugar, and to growth of the cells in the pancreas that produce insulin. In diabetes, the body becomes resistant to insulin or fails to make enough insulin, causing a problematic build-up of sugar in the blood stream. The actual effect of the genetic defects has yet to be determined.
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