Mar 19, 2011

Biology's 'dark matter' hints at fourth domain of life

Step far enough back from the tree of life and it begins to look quite simple. At its heart are just three stout branches, representing the three domains of life: bacteria, archaea and eukaryotes. But that's too simple, according to a band of biologists who believe we may be on the verge of discovering the fourth domain of life.

The bold statement is the result of an analysis of water samples collected from the world's seas. Jonathan Eisen at the University of California, Davis, Genome Center has identified gene sequences hidden within these samples that are so unusual they seem to have come from organisms that are only distantly related to cellular life as we know it. So distantly related, in fact, that they may belong to an organism that sits in an entirely new domain.

Most species on the planet look like tiny single cells, and to work out where they fit on the tree of life biologists need to be able to grow them in the lab. Colonies like this give them enough DNA to run their genetic analyses. The problem is, the vast majority of these cells species – 99 per cent of them is a reasonable bet – refuse to be cultured in this way. "They really are the dark matter of the biological universe," says Eisen.

Life's dark matter

To probe life's dark matter, Eisen, Craig Venter of the J. Craig Venter Institute in Rockville, Maryland, and their colleagues have resorted to a relatively new technique called metagenomics. This can "sequence the crap out of any DNA samples", whether they are collected from the environment or come from lab cultures, says Eisen.

When Eisen and Venter used the technique on samples collected from the Global Ocean Sampling Expedition, they found that some sequences belonging to two superfamilies of genes – recA and rpoB – were unlike any seen before.

"The question is, what are they from?" says Eisen. Because the team has no idea what organism the genes belong to, the question remains unanswered. There are two possibilities, he says. "They could represent an unusual virus, which is interesting enough. More interestingly still, they could represent a totally new branch in the tree of life."

The exciting but controversial idea has met with mixed reactions. "It's a very good piece of careful work," says Eugene Koonin at the National Center for Biotechnology Information in Bethesda, Maryland.

Younger than they look?

But some think any talk of a fourth domain of cellular life is premature. Radhey Gupta at McMaster University in Hamilton, Ontario, Canada, calls the finding "very exciting", but cautions that there are other explanations.

For instance, the sequences could be from cellular organisms living in unique habitats that caused their genes to undergo rapid evolution. That would give the false impression that the "new" life forms diverged from all others a very long time ago.

"There is still debate [over] how to clearly distinguish the three proposed domains of life, and how they are interrelated," Gupta says. "The suggestion [of] a fourth domain will only add to the confusion."

Eric Bapteste at Pierre and Marie Curie University in Paris, France, is far more receptive. "The facts are that there is lots of genetic diversity, and unquestionably most of it is unknown to us," he says. "It's legitimate to consider that there's genuinely new stuff out there."

Further analysis of the samples could determine whether the two gene families studied have evolved unusually rapidly or are from a cellular organism with a universally bizarre genome, he says.

Read more at New Scientist

How not to change a climate sceptic's mind

HOW do you get your point across over an issue as contentious as climate change? As a hearing in the US Congress last week showed, the evidence alone is not enough.

At issue was the authority of the Environmental Protection Agency to regulate greenhouse gas emissions. Republicans in the House and Senate are backing bills that would strip the EPA of that right, which is based on findings that rising carbon dioxide levels pose a threat to health and the environment.

At the hearing, House Democrats hoped to counter these moves by calling a cast of climatologists to explain the weight of scientific evidence for climate change. A meeting of minds it was not. The effort seemed only to harden Republican scepticism.

For Dan Kahan of the Cultural Cognition Project at Yale University, the result was predictable. He has previously shown that simply explaining the science behind contentious issues drives the two sides further apart. But Kahan's work also suggests how warring parties can move towards consensus.

Kahan grades people on two scales of cultural belief: individualists versus communitarians, based on the different importance people attach to the public good when balanced against individual rights; and hierarchists versus egalitarians, based on their views on the stratification of society. Republicans are more likely to be hierarchical-individualist, while Democrats are more often egalitarian-communitarian.

People's views on contentious scientific issues tend to reflect their position on these scales. For example, egalitarian-communitarians tend to accept the evidence that climate change is a threat, while hierarchical-individualists reject it.

Yet people's views do change if the right person is offering the evidence. Kahan investigated attitudes for and against giving the human papillomavirus (HPV) vaccine to schoolgirls to prevent cervical cancer - another divisive issue. After he presented people with both sides of the argument, he found that 70 per cent of egalitarian-communitarians thought it was safe, compared with 56 per cent of hierarchical-individualists.

When the "pro" argument was presented as coming from an expert painted as being in the egalitarian-communitarian camp, and the "anti" view came from a hierarchical-individualist, the split widened to 71 versus 47 per cent. But strikingly, swapping the experts around caused a big shift: 61 per cent of hierarchical-individualists then rated the vaccine as safe, compared to 58 per cent of egalitarian-communitarians. In short, evidence from someone you identify with sways your view.

In practice, it is hard to find experts who will give "unexpected" testimony. But when the evidence was presented by experts with a variety of backgrounds, views were not so starkly polarised, with 65 per cent of egalitarian-communitarians and 54 per cent of hierarchical-individualists agreeing that the vaccine is safe.

Read more at New Scientist

Mar 18, 2011

Italy Celebrates 150 Years of Unification

Italy never saw so many national flags waving in the air as on March 17, 2011.

Posted across windows and balconies all over the country, thousands of green, white and red flags celebrated the 150th anniversary of the country’s unification.

As a nation-state, Italy is younger than the United States. The home of the ancient Roman empire became a nation as a whole just 150 years ago, on March 17, 1861.

On that day, Victor Emmanuel II became the first king of a unified Italy. It was the culmination of the Risorgimento, the movement for independence that for years struggled to free the country from foreign rule and unite several micro-states.

Indeed, before 1861, Italy was, in the words of the Austrian statesman Metternich, a "mere geographical expression."

The country was just a patchwork of city-states and regions ruled by the pope and a variety of monarchs.

Established as a monarchy with a parliamentary government (the Italian Republic was founded in 1946), the new state had its first capital in Turin. Four years later, in 1865, the capital was moved to Florence and then, in 1871, to Rome.

A number of events have marked the anniversary, including parades, fireworks, jets streaming green, white and red smoke trails across the sky, and historical re-enactments recalling the campaign of Risorgimental hero Giuseppe Garibaldi to bring Italy's deeply different states together.

“Without unity our nation would have been swept away by history,” said Italian President Giorgio Napolitano.

Despite heavy rain in many cities, hundreds of thousands celebrated singing the national anthem, “Brothers of Italy,” as green-white-red light projections covered the facade of the main monuments.

“From North to South, all proud of the three-color flag,” wrote the daily La Repubblica.

The newspaper reported the results of a national poll, which found about 90 percent of Italians are happy about the country’s unification.

Read more at Discovery News

God's Wife Edited Out of the Bible -- Almost

God had a wife, Asherah, whom the Book of Kings suggests was worshiped alongside Yahweh in his temple in Israel, according to an Oxford scholar.

In 1967, Raphael Patai was the first historian to mention that the ancient Israelites worshiped both Yahweh and Asherah. The theory has gained new prominence due to the research of Francesca Stavrakopoulou, who began her work at Oxford and is now a senior lecturer in the department of Theology and Religion at the University of Exeter.

Information presented in Stavrakopoulou's books, lectures and journal papers has become the basis of a three-part documentary series, now airing in Europe, where she discusses the Yahweh-Asherah connection.

"You might know him as Yahweh, Allah or God. But on this fact, Jews, Muslims and Christians, the people of the great Abrahamic religions, are agreed: There is only one of Him," writes Stavrakopoulou in a statement released to the British media. "He is a solitary figure, a single, universal creator, not one God among many ... or so we like to believe."

"After years of research specializing in the history and religion of Israel, however, I have come to a colorful and what could seem, to some, uncomfortable conclusion that God had a wife," she added.

Stavrakopoulou bases her theory on ancient texts, amulets and figurines unearthed primarily in the ancient Canaanite coastal city called Ugarit, now modern-day Syria. All of these artifacts reveal that Asherah was a powerful fertility goddess.

Asherah's connection to Yahweh, according to Stavrakopoulou, is spelled out in both the Bible and an 8th century B.C. inscription on pottery found in the Sinai desert at a site called Kuntillet Ajrud.

"The inscription is a petition for a blessing," she shares. "Crucially, the inscription asks for a blessing from 'Yahweh and his Asherah.' Here was evidence that presented Yahweh and Asherah as a divine pair. And now a handful of similar inscriptions have since been found, all of which help to strengthen the case that the God of the Bible once had a wife."

Also significant, Stavrakopoulou believes, "is the Bible's admission that the goddess Asherah was worshiped in Yahweh's Temple in Jerusalem. In the Book of Kings, we're told that a statue of Asherah was housed in the temple and that female temple personnel wove ritual textiles for her."

J. Edward Wright, president of both The Arizona Center for Judaic Studies and The Albright Institute for Archaeological Research, told Discovery News that he agrees several Hebrew inscriptions mention "Yahweh and his Asherah."

"Asherah was not entirely edited out of the Bible by its male editors," he added. "Traces of her remain, and based on those traces, archaeological evidence and references to her in texts from nations bordering Israel and Judah, we can reconstruct her role in the religions of the Southern Levant."

Read more at Discovery News

A real study of magicians’ fake movements

“Magicians trick us with their sleights of hand, reaching for objects that aren’t there and pretending to drop others that they’ve really kept hold of. This ability is all the more remarkable because research has shown how poor the rest of us are at faking reaching gestures and other movements. Now Cristiana Cavina-Pratesi and her colleagues have used motion-tracking technology to investigate how the magicians do it.

First off, ten magicians and ten controls reached for and picked up a wooden block, or mimed reaching and picking up an imaginary block situated next to the real one. Just as the participants began reaching, their sight was completely obscured by shutter glasses – this was to simulate the way that magicians often look away from where they’re reaching. The participants’ grasps were performed either with forefinger and thumb or little-finger and thumb, and markers were worn on these digits so they could be monitored with a motion-tracking system.

Just as has been found in earlier research, the controls’ pantomime grasping movements were quite distinct from the real thing – the ‘maximum grip aperture’ (the maximum gap between thumb and finger) was smaller, as was a metric called the ‘grip overshoot’, calculated from the position of the thumb and fingers during the actual grasp. In contrast, the magicians’ maximum grip aperture and grip overshoot were the same whether they actually grasped a real wooden block, or mimed grasping an imaginary one next to it.

Having confirmed that magicians’ fake movements really are like the real thing, a second experiment, involving batteries rather than wooden blocks, made things harder. This time, the miming condition was performed without a real, to-be-grasped object anywhere in sight. The seven magicians and seven controls performed their real grasps as before, but when the miming grasps were performed, the batteries were hidden away. Curiously, under these conditions, the magicians were no better at faking than the controls.

The researchers said this suggests that ‘the talent of magicians lies in their ability to use visual input from real objects to calibrate a grasping action toward a separate spatial location (that of the imagined object).’

How do they develop this ability? Cavina-Pratesi’s team think it reflects a flexibility in the magicians’ occipito-parietal system (located towards the back of the brain). ‘This flexibility,’ they said, ‘might exploit mechanisms similar to those underlying people’s ability to adapt to spatially displacing prisms through repeated target-directed movements.’ They’re referring here to the human ability to adapt to prism glasses that distort the visual world. At first the glasses are disorientating, but most people are able to adapt quickly. The researchers said future brain imaging studies will help reveal exactly what’s going on in the magicians’ brains as they perform their trickery.”

Read more at BPS Research Digest

Mar 17, 2011

Animal Leaders Improve With Age

Older animals make the best leaders, suggest studies on primates, whales and now elephants.

Advanced age can improve an individual's ability to detect threats, the research found, benefiting others if that individual is a leader.

"The findings highlight the importance of older individuals in natural populations -- not only in elephants, but most likely also in other large-brained, long-lived social species, such as whales and primates, where knowledge can be accumulated over time," said Karen McComb, lead author of the study, appearing in the latest Proceedings of the Royal Society B.

McComb, a behavioral ecologist specializing in psychology at the University of Sussex, and colleagues conducted their experiments on 1500 African elephants living within 58 distinct family groups at Amboseli National Park in Kenya.

Using loudspeakers mounted on a fieldwork vehicle, the researchers played recorded male and female lion roars in the elephants' vicinity. During some experiments, the researchers would play the sounds of three lions roaring at once. Other than humans, lions are the main natural predators of elephants, with powerful male lions being more active hunters. Male lions are, on average, 50 percent larger than female lions.

While all of the elephants reacted more strongly to the sound of three lions, groups led by older matriarchs showed the greatest sensitivity to the more serious threat posed by male lions. These older female leaders, 60 years plus in age, not only listened intently, but they also rallied their group members into defensive maneuvers known as bunching and mobbing where the elephants act like a giant battering ram by charging the lion and harassing it.

"Our work emphasizes the importance of the knowledge that older individuals may possess, which can ultimately lead to benefits for individuals in groups that have older leaders," co-author Graeme Shannon of the University of Sussex told Discovery News.

The research highlights the value of older individuals in elephants-- and past work has suggested the same is true in humans. As Shannon points out, prior research on humans has found that "reasoning about social conflicts improves with age despite declines in many forms of cognitive processing."

Human societies in modern times often tend to revere youth culture. Throughout history and even now, however, "older individuals often emerge as leaders in tasks requiring specialized knowledge," the researchers point out.

The pattern appears to hold true for many other species, such as sperm whales, killer whales, broad-winged hawks, ravens and more.

Read more at Discovery News

Who Was St. Patrick?

How to celebrate St. Patrick's Day in the United States: Cover yourself in green (bonus points for shamrocks), put a smiling leprechaun cut-out on your front door, head to your local "Irish Pub" after work, get rowdy and wasted.

How to celebrate St. Patrick's Day in England: Eh, maybe pop down to the local pub for a nice pint.

How to celebrate St. Patrick's Day in Ireland: Go to church.

Those who recognize St. Patrick's Day celebrate it very differently depending on where they're from, and believe it or not, it's the United States that has turned the Emerald Isle's namesake tradition into a huge party scene, when its original intent was to be observed as a religious holiday.

For thousands of years, Irish Catholics have traditionally celebrated St. Patrick's Day by attending church in the morning and celebrating in the afternoon with a huge feast, honoring Ireland's patron saint. Even though March 17 falls in the middle of Lent when Catholics were forbidden to eat meat, this was waived in Ireland for feasting -- mostly on cabbage and Irish bacon, according to

Today, corned beef and cabbage is the traditional St. Patrick's Day meal, and in 2005, Americans consumed 2.4 billion pounds of cabbage, according to the U.S. Census Bureau.

But who was Saint Patrick? The truth is, much of his life is a mystery. One of the most famous legends of St. Patrick describes how he banished all snakes from the Emerald Isle into the ocean and they drowned. Philip M. Freeman, an expert in Celtic and classical studies at Washington University in St. Louis claims in his book, "St. Patrick of Ireland," that this legend is false.

What is known about St. Patrick is that he was born in England to wealthy parents near the end of the 4th century. At age 15, he was kidnapped by Irish pirates from his parents' estate in the Roman province of Britain, and sold into slavery in Ireland, where he spent six years in captivity, according to Freeman. After his escape, Patrick wrote in a letter of an "angel" speaking to him in a dream, telling him to become a missionary in Ireland, according to

After combing through two of Patrick's letters, Freeman confirms that Patrick attended training to become a priest in Ireland and was eventually made a bishop. He converted many of the Irish people from paganism to Christianity. St. Patrick is believed to have died on March 17, around 460 A.D., and many villagers across Ireland mourned his death on this day. From that, grew a celebration.

Like many other holidays, such as Halloween, St. Patrick's Day was recognized as a national holiday in the United States after thousands of Irish people immigrated to the country during the potato famine of the 1880s, bringing their traditions with them. Also like many other holidays, what began as small community affairs, St. Patrick's Day celebrations have exploded into full-on extravaganzas in the United States.

The first U.S. St. Patrick's Day parade took place in New York City on March 17, 1762, when Irish soldiers serving in the English military marched through the city. Now, over 100 cities across the country hold public festivities, according to the U.S. Census Bureau. Today, about 34.7 million Americans identify themselves as having Irish ancestry.

Read more at Discovery News

Record companies make claim against Limewire for $75 Trillion Does $75 trillion even exist? The thirteen record companies that are suing file-sharing company Lime Wire for copyright infringement certainly thought so. When they won a summary judgment ruling last May they demanded damages that could reach this mind-boggling amount, which is more than five times the national debt.

Manhattan federal district court judge Kimba Wood, however, saw things differently. She labeled the record companies’ damages request “absurd” and contrary to copyright laws in a 14-page opinion.

The record companies, which had demanded damages ranging from $400 billion to $75 trillion, had argued that Section 504(c)(1) of the Copyright Act provided for damages for each instance of infringement where two or more parties were liable. For a popular site like Lime Wire, which had thousands of users and millions of downloads, Wood held that the damage award would be staggering under this interpretation. “If plaintiffs were able to pursue a statutory damage theory predicated on the number of direct infringers per work, defendants’ damages could reach into the trillions,” she wrote. “As defendants note, plaintiffs are suggesting an award that is ‘more money than the entire music recording industry has made since Edison’s invention of the phonograph in 1877.”

Full story over at

Mar 15, 2011

Quake moved Japan by 8 feet

Japan’s recent massive earthquake, one of the largest ever recorded appears to have moved the island by about eight feet, around 2.4 Meters according to the US Geological Survey.

Friday’s 8.9 magnitude quake unleashed a terrifying tsunami that engulfed towns and cities on Japan’s northeastern coast, destroying everything in its path in what Prime Minister Naoto Kan said was an “unprecedented national disaster.”

The quake and its tectonic shift resulted from “thrust faulting” along the boundary of the Pacific and North America plates, according to the USGS.

Full Story at Psyorg

Are you prone to mind control?

“Are you easily influenced by what others do and say? If so, you’re just the type of person that hypnotists, magicians and mind-readers seek out as you’re more likely to fall for their mind tricks.

In this video, psychologist Richard Wiseman gives you the chance to find out how suggestible you are. Give it a go – even the most hardened skeptics might be surprised by the results.

If you tried the test, how far did your hands move? According to Wiseman, if they stayed level or shifted just a few inches apart then you aren’t that suggestible. But if they moved more than a few inches, you’re the perfect candidate for a magic trick.

The test can also reveal something about your character. “Non-suggestible types tend to be more down-to-earth, logical and enjoy puzzles and games. In contrast, suggestible types tend to have a good imagination, be sensitive, intuitive and find it easier to become absorbed in books and films,” says Wiseman.

To accompany his new book Paranormality, Wiseman has released a free set of psychological demonstrations where you can learn to perform mind tricks on others.”

Read more at New Scientist

Mar 14, 2011

Sperm Whales May Have Names

Subtle variations in sperm-whale calls suggest that individuals announce themselves with discrete personal identifier. To put it another way, they might have names.

The findings are preliminary, based on observations of just three whales, so talk of names is still speculation. But “it’s very suggestive,” said biologist Luke Rendell of Scotland’s University of St. Andrews. “They seem to make that coda in a way that’s individually distinctive.”

Rendell and his collaborators, including biologists Hal Whitehead, Shane Gero and Tyler Schulz, have for years studied the click sequences, or codas, used by sperm whales to communicate across miles of deep ocean. In a study published last June in Marine Mammal Sciences, they described a sound-analysis technique that linked recorded codas to individual members of a whale family living in the Caribbean.

In that study, they focused on a coda made only by Caribbean sperm whales. It appears to signify group membership. In the latest study, published Feb. 10 in Animal Behavior, they analyzed a coda made by sperm whales around the world. Called 5R, it’s composed of five consecutive clicks, and superficially appears to be identical in each whale. Analyzed closely, however, variations in click timing emerge. Each of the researchers’ whales had its own personal 5R riff.

The differences were significant. The sonic variations that were used to distinguish between individuals in the earlier study depended on a listener’s physical relationship to the caller: “If you record the animal from the side, you get a different structure than dead ahead or behind,” said Rendell. But these 5R variations held true regardless of listener position.

“In terms of information transfer, the timing of the clicks is much less susceptible” to interference, said Rendell. “There is no doubt in my mind that the animals can tell the difference between the timing of individuals.” Moreover, 5R tends to be made at the beginning of each coda string as if, like old-time telegraph operators clicking out a call sign, they were identifying themselves. Said Rendell, “It may function to let the animals know which individual is vocalizing.”

Rendell stressed that much more research is needed to be sure of 5R’s function. “We could have just observed a freak occurrence,” he said. Future research will involve more recordings. “This is just the first glimpse of what might be going on.”

That individual whales would have means of identifying themselves does, however, make sense. Dolphins have already been shown to have individual, identifying whistles. Like them, sperm whales are highly social animals who maintain complex relationships over long distances, coordinating hunts and cooperating to raise one another’s calves.

Read more at Wired Science

Mar 13, 2011

In Times of Crisis, People Turn to Internet

The earthquake off the coast of Japan and the resulting tsunami has proven, yet again, how the Internet offers an information lifeline to the world in a time of crisis.

The Internet was designed so that U.S. military communications could withstand a nuclear war, but is proving equally resilient in the face of natural disasters and even seismic shifts in global politics.

As the waves smashed into the Japanese coastline following the 8.9-magnitude earthquake 130 kilometers (80 miles) east in the Pacific ocean on Friday, a tsunami of images was also soon hitting the web.

In scenes worthy of any Hollywood disaster movie, a massive wave was shown rolling in from the sea, and one of the most watched and shared videos was of water slowly engulfing the city of Sendai's airport.

Small aircraft, cars and trucks were shown scattered amongst the shattered debris of buildings like an unruly child's toy box.

And what looked like prefabricated factory units were shown floating under a bridge as drivers spun their cars and trucks around to try to outrun the waves.

Nearly five million people tuned in to video sharing site YouTube on Saturday to watch one raw, unedited video of the wave chewing away at Japan's coastline. Several other videos had notched up between three and four million hits.

Hundreds of people commented on the videos across the web and shared information, from social network giant Facebook to micro-blogging site Twitter -- as well as local, Japanese language websites.

And the Internet also functioned as a virtual crisis center as sites such as Google's people finder service helped locate loved ones and offered help and support to survivors.

As the floodwaters subsided, worried friends and relatives leapt onto their computers to find information about people who had not been heard from since the mighty wave crashed ashore.

Google's person finder service had notched up more than 81,000 records of people leaving messages seeking information on friends and family by 0300 GMT Sunday.

The site was updating, in English and Japanese, by the hundreds every few minutes.

A random search of the common Japanese surname "Sato" brought up hundreds of results, many of them for people living in Sendai -- the city that faced the brunt of the thunderous body of rolling water.

Gunduzhan posted a message seeking Aki Sato, a dentist from Sendai who studied at Ohu University in Koriyama. A photo of the pretty young woman was also posted on the site.

"Looking for Aki Sato," the post read. "Last heard from after earthquake but before tsunami."

Another post seeking Fatima Sato had some good news: "Mom is ok. She is on her way home."
The international and Japanese Red Cross also set up a similar site.

And micro-blogging site Twitter was updating every second with messages of good will, of condolences and offering aid.

Read more at Discovery News

Mobile phones could run for months between charges

A team of electrical engineers at Illinois University in the US believe their method will enable mobiles and laptops to run for up to 100 times longer between charges.

It focuses on changing the way a device's digital memory works, as this consumes much of the charge.

At the moment mobile phone memories contain thin metal wires. Every time information is accessed, electricity is passed through them to retrieve the data.

The electrical engineers thought that if the size of the components used to store and retrieve the information could be reduced, so could the amount of electricity.

They have discovered a way of using carbon nanotubes - tiny tubes 10,000 times thinner than a human hair - instead.

Feng Xiong, a graduate student on the team who was lead author on a paper, to be published in the journal Science, explained: "The energy consumption is essentially scaled with the volume of the memory bit.

"By using nanoscale contacts, we are able to achieve much smaller power consumption."

Read more at The Telegraph