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Permalink Reply by doone on April 26, 2012 at 7:54am

Credit Where It’s Due

By mistermix April 26th, 2012

The White House issued a veto threat against CISPA, the latest attempt to turn file sharers into terrorists. Earlier this year, the White House also effectively killed SOPA by announcing that it opposed that bill, and it looks like CISPA has met the same fate.

In addition to being the right thing to do, I don’t think the DC press appreciates how important opposition to these bills is to the “youth vote”, which in this case is probably anybody under 80 who uses the Internet. SOPA and CISPA are two cases where having Obama in the White House has made a difference.

Permalink Reply by doone on April 26, 2012 at 12:06pm

UNLOCKING THE MYSTERIES OF LIFE?

More problematic is the reality that the human genome is still a vast catalogue of the unknown and scarcely known. The Human Genome Project’s most startling finding was that human genes, as currently defined, make up less than 2 percent of all the DNA on the genome, and that the total number of genes is relatively small. Scientists had predicted there might be 80,000 to 140,000 human genes, but the current tally is fewer than 25,000 — as one scientific paper put it, somewhere between that of a chicken and a grape. The remaining 98 percent of our DNA, once dismissed as “junk DNA,” is now taken more seriously. Researchers have focused on introns, in the gaps between the coding segments of genes, which may play a crucial role in regulating gene expression, by switching them on and off in response to environmental stimuli. Gene regulation, whether by introns or by regulator genes, forms one aspect of the burgeoning field of epigenetics, which concerns itself with the process of differential gene expression. In a classic study published in 2004, biologists at McGill University in Montreal identified a regulatory sequence in rat pups that lowered stress hormone production when the mother groomed them; their production of the hormone stayed low throughout their lives. Moreover, the researchers could adjust the gene in healthy adults to increase their stress, and in agitated adults to lower it. Though not their intention, the study provided the genetic evidence to prove Freud right: what happens in childhood has a lasting, though theoretically reversible, biological effect on adult behaviour.

more from Mark Czarnecki at The Walrus here.

Posted by Morgan Meis at 11:53 AM | Permalink

Permalink Reply by doone on April 26, 2012 at 3:18pm

Rare protozoan from sludge in Norwegian lake does not fit on main branches of tree of life

http://www.sciencedaily.com/releases/2012/04/120426104853.htm

April 26, 2012

ScienceDaily (Apr. 26, 2012) — Humankind's remotest relative is a very rare micro-organism from south-Norway. The discovery may provide an insight into what life looked like on earth almost one thousand million years ago.

Biologists all over the world have been eagerly awaiting the results of the genetic analysis of one of the world's smallest known species, hereafter called the protozoan, from a little lake 30 kilometer south of Oslo in Norway.

When researchers from the University of Oslo, Norway compared its genes with all other known species in the world, they saw that the protozoan did not fit on any of the main branches of the tree of life. The protozoan is not a fungus, alga, parasite, plant or animal.

"We have found an unknown branch of the tree of life that lives in this lake. It is unique! So far we know of no other group of organisms that descend from closer to the roots of the tree of life than this species. It can be used as a telescope into the primordial micro-cosmos," says an enthusiastic associate professor, Kamran Shalchian-Tabrizi, head of the Microbial Evolution Research Group (MERG) at the University of Oslo.

His research group studies tiny organisms hoping to find answers to large, biological questions within ecology and evolutionary biology, and works across such different fields as biology, genetics, bioinformatics, molecular biology and statistics.

World's oldest creature

Life on Earth can be divided up into two main groups of species, prokaryotes and eukaryotes. The prokaryote species, such as bacteria, are the simplest form of living organisms on Earth. They have no membrane inside their cell and therefore no real cell nucleus. Eukaryote species, such as animals and humankind, plants, fungi and algae, on the other hand do.

The family tree of the protozoan from the lake near Ås starts at the root of the eukaryote species.

"The micro-organism is among the oldest, currently living eukaryote organisms we know of. It evolved around one billion years ago, plus or minus a few hundred million years. It gives us a better understanding of what early life on Earth looked like.," Kamran says to the research magazine Apollon.

How they move

The tree of life can be divided into organisms with one or two flagella. Flagella are important when it comes to a cell's ability to move. Just like all other mammals, human sperm cells have only one flagellum. Therefore, humankind belongs to the same single flagellum group as fungi and amoebae.

On the other hand it is believed that our distant relatives from the family branches of plants, algae and excavates (single-celled parasites) originally had two flagella.

The protozoan from Ås has four flagella. The family it belongs to is somewhere between excavates, the oldest group with two flagella, and some amoebae, which is the oldest group with only one flagellum.

"Were we to reconstruct the oldest, eukaryote cell in the world, we believe it would resemble our species. To calculate how much our species has changed since primordial times, we have to compare its genes with its nearest relatives, amoebae and excavates," says Shalchian-Tabrizi.

Caught with a tasty morsel

The protozoan is not easy to spot. It lives down in the sludge at the bottom of a lake.

It is 30 to 50 micrometres long and can only be seen with a microscope. When Professor Dag Klaveness of MERG wants to catch the protozoan he sticks a pipe down into the lakebed, removes a column of sludge and pours a bile green algae mixture over it.

The algae are such tempting morsels for the small protozoa that they swim up.

"We can then pick them out, one by one, with a pipette," says Klaveness.

There are not many of them. And the University of Oslo biologists have not found them anywhere else other than in this lake.

"We are surprised. Enormous quantities of environmental samples are taken all over the world. We have searched for the species in every existing DNA database, but have only found a partial match with a gene sequence in Tibet. So it is conceivable that only a few other species exist in this family branch of the tree of life, which has survived all the many hundreds of millions of years since the eukaryote species appeared on Earth for the first time."

Not very sociable

The protozoan lives off algae, but the researchers still do not know what eats the protozoan. Nor do they know anything about its life cycle. But one thing is certain:

"They are not sociable creatures. They flourish best alone. Once they have eaten the food, cannibalism is the order of the day," notes Klaveness.

The protozoan has a special cell indentation. It looks like a groove.

"The species has the same intracellular structure as excavates. And it uses the same protuberances as amoebae to catch its food. This means that the species combines two characteristics from each family branch of the main eukaryote groups. This further supports the hypothesis that the species from this lake belongs to a primordial group. Perhaps it descended from the antecedents of both the excavates and amoeba?" asks Shalchian-Tabrizi.

The protozoan was discovered as early as 1865, but it is only now that, thanks to very advanced genetic analyses, researchers understand how important the species is to the history of life on Earth.

Breeding enormous quantities of the protozoan

Dag Klaveness has, together with research fellow Jon Bråte, managed to breed large quantities of the species. No one has done this before. Klaveness has spent the last 40 years specialising in breeding organisms that are difficult to breed or that are difficult to isolate from other species.

Breeding is important if we want to analyse the creature's genes. More than just a few are needed for a genetic test. Researchers have needed to breed large quantities. The work is demanding and has taken many months.

The protozoan's favourite food is green algae, but since both the protozoan and the green algae are eukaryote species, i.e. species with real cell nuclei, it is easy to confuse the genes of the protozoan with those of its food in the gene sequencing. Therefore, Klaveness has chosen to feed the protozoan with blue green bacteria, which are genetically very different to the protozoan. Blue green bacteria are not exactly its favourite dish, but the protozoan can only choose between eating or dying.

Blue green bacteria are prokaryotes, i.e. species without membranes or real cell nuclei. This allows the researchers to differentiate between the genes of the protozoan and its food in the gene sequencing.

Klaveness has a number of vats of the protozoan in the laboratory. The algae mixture sinks to the bottom. The protozoan dives down when it wants to eat.

In optimum conditions they divide every second day. However, with blue green bacteria on the menu, which is just as boring as if you only got carrots for several months and nothing else, the protozoan grows much more slowly.

When the protozoa have reproduced enough, they are centrifuged out and gene sequenced. The genes are then compared with equivalent gene sequences from other species. "We have gene sequenced 300,000 parts of the genome (the total genetic material), but we still do not know how large the genome is. We are currently only looking for the most important parts," explains Kamran Shalchian-Tabrizi.

Traces from primordial times

The problem is that DNA sequences change a lot over time. Parts of the DNA may have been wiped away during the passing of the years. Since the protozoan is a very old species, an extra large amount of gene information is required.

"It is often the case with such ancient organisms that features they share in common with other known species have been wiped away from the DNA sequence because of long-term mutations. You can compare it with tarmacing. If you tarmac a road enough times, you will no longer see the cobblestones. Therefore, you have to collect large gene sequences to find common traces from prehistoric times."

Research fellow Sen Zhao was responsible for the extensive, statistical calculations. In order to calculate the family link they have used information from the research group's own Bioportal in cooperation with the high performance computing group at the University of Oslo.

Resolving evolutionary mysteries

Kamran Shalchian-Tabrizi explains that the tree of life can provide fundamental answers to great evolutionary mysteries.

"In order to understand what a species is today, we have to understand how they have changed genetically. The tree of life allows us to explain cellular change processes by connecting the genome and morphology (appearance) with its way of life."

Among other things, Shalchian-Tabrizi wants to use the protozoan to investigate when photosynthesis arose among eukaryote organisms. Photosynthesis takes place in chloroplast.

Chloroplasts were originally free-living, blue green bacteria. If the researchers find genetic residues of these bacteria in the protozoan from Ås, this may indicate that photosynthesis arose earlier than supposed.

"There are many likely scenarios, but we still do not know the answer," acknowledges Shalchian-Tabrizi.

The researchers also want to question when other characteristics arose, e.g. mitochondria, which are the energy motors of our cells.

Purifying drinking water in Japan

In recent years researchers have found some apparently matching examples of the protozoan from Ås in Japan and South East Asia. A researcher from Japan arrived in Oslo with a glass of the species solely so that Klaveness could breed them.

"We are now going to gene sequence these organisms, because it is not certain that the genes are the same, even if the morphology is similar," says Klaveness.

The Japanese hope that the protozoan can be used to purify drinking water by removing toxic, blue green bacteria.

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Story Source:

The above story is reprinted from materials provided by University of Oslo, via AlphaGalileo. The original article was written by Yngve Vogt.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

Permalink Reply by doone on April 26, 2012 at 3:19pm

sciencedaily.comhttp://www.sciencedaily.com/releases/2012/04/120425192742.htm

Number line is learned, not innate human intuition

Now, challenging a mainstream scholarly position that the number-line concept is innate, a study suggests it is learned.

The study, published in PLoS ONE April 25, is based on experiments with an indigenous group in Papua New Guinea. It was led by Rafael Nunez, director of the Embodied Cognition Lab and associate professor of cognitive science in the UC San Diego Division of Social Sciences.

"Influential scholars have advanced the thesis that many of the building blocks of mathematics are 'hard-wired' in the human mind through millions of years of evolution. And a number of different sources of evidence do suggest that humans naturally associate numbers with space," said Nunez, coauthor of "Where Mathematics Comes From" and co-director of the newly established Fields Cognitive Science Network at the Fields Institute for Research in Mathematical Sciences.

"Our study shows, for the first time, that the number-line concept is not a 'universal intuition' but a particular cultural tool that requires training and education to master," Nunez said. "Also, we document that precise number concepts can exist independently of linear or other metric-driven spatial representations."

Nunez and the research team, which includes UC San Diego cognitive science doctoral alumnus Kensy Cooperrider, now at Case Western Reserve University, and Jurg Wassmann, an anthropologist at the University of Heidelberg who has studied the indigenous group for 25 years, traveled to a remote area of the Finisterre Range of Papua New Guinea to conduct the study.

The upper Yupno valley, like much of Papua New Guinea, has no roads. The research team flew in on a four-seat plane and hiked in the rest of the way, armed with solar-powered equipment, since the valley has no electricity.

The indigenous Yupno in this area number some 5,000, spread over many small villages. They are subsistence farmers. Most have little formal schooling, if any at all. While there is no native writing system, there is a native counting system, with precise number concepts and specific words for numbers greater than 20. But there doesn't seem to be any evidence of measurement of any sort, Nunez said, "not with numbers, or feet or elbows."

Neither Hard-Wired nor "Out There"

Nunez and colleagues asked Yupno adults of the village of Gua to complete a task that has been used widely by researchers interested in basic mathematical intuitions and where they come from. In the original task, people are shown a line and are asked to place numbers onto the line according to their size, with "1" going on the left endpoint and "10" (or sometimes "100" or "1000") going on the right endpoint. Since many in the study group were illiterate, Nunez and colleagues followed previous studies and adapted the task using groups of one to 10 dots, tones and the spoken words instead of written numbers.

After confirming the Yupno participants' understanding of numbers with piles of oranges, the researchers gave the number-line task to 14 adults with no schooling and six adults with some degree of formal schooling. There was also a control group of participants in California.

The researchers found that unschooled Yupno adults placed numbers on the line (or mapped numbers onto space), but they did it in a categorical manner, using systematically only the endpoints: putting small numbers on the left endpoint and the mid-size and large numbers on the right, ignoring the extension of the line -- an essential component of the number-line concept. Schooled Yupno adults used the line's extension but not quite as evenly as adults in California.

"Mathematics all over the world -- from Europe to Asia to the Americas -- is largely taught dogmatically, as objective fact, black and white, right/wrong," Nunez said. "But our work shows that there are meaningful human ideas in math, ingenious solutions and designs that have been mediated by writing and notational devices, like the number line. Perhaps we should think about bringing the human saga to the subject -- instead of continuing to treat it romantically, as the 'universal language' it's not. Mathematics is neither hardwired, nor 'out there.'"

Out-of-Body Time

The researchers ran several experiments while in Gua, Papua New Guinea, including those that examine another fundamental concept: time.

When talking about past, present and future, people all over the world show a tendency to conceive of these notions spatially, Nunez said. The most common spatial pattern is the one found in the English-speaking world, in which people talk about the future as being in front of them and the past behind, encapsulated, for example, in expressions such as the "week ahead" and "way back when." (In earlier research, Nunez found that the Aymara of the Andes seem to do the reverse, placing the past in front and the future behind.)

In their time study with the Yupno, now in press at the journal Cognition, Nunez and colleagues find that the Yupno don't use their bodies as reference points for time -- but rather their valley's slope and terrain. Analysis of their gestures suggests they co-locate the present with themselves, as do all previously studied groups. (Picture for a moment how you probably point down at the ground when you talk about "now.") But, regardless of which way they are facing at the moment, the Yupno point uphill when talking about the future and downhill when talking about the past.

Interestingly and also very unusually, Nunez said, the Yupno seem to think of past and future not as being arranged on a line, such as the familiar "time line" we have in many Western cultures, but as having a three-dimensional bent shape that reflects the valley's terrain.

"These findings suggest that how we think about abstract concepts is even more flexible than previously thought and is profoundly affected by language, culture and environment," said Nunez.

"Our familiar notions on 'fundamental' concepts such as time and number are so deeply ingrained that they feel natural to us, as though they couldn't be any other way," added former graduate student Cooperrider. "When confronted with radically different ways of construing experience, we can no longer take for granted our own. Ultimately, no way is more or less 'natural' than the Yupno way."

The research was supported by a UC San Diego Academic Senate grant, an Institute for Advanced Studies in Berlin fellowship, a UCSD Friends of the International Center fellowship, and the Marsilius Kolleg Heidelberg.

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The above story is reprinted from materials provided by University of California, San Diego, via Newswise.

Note: Materials may be edited for content and length. For further information, please contact the source cited above.

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Journal Reference:

1. Núñez R, Cooperrider K, Wassmann J. Number Concepts without Number Lines in an Indigenous Group of Papua New Guinea. PLoS ONE, 7(4): e35662 DOI:10.1371/journal.pone.0035662

Note: If no author is given, the source is cited instead.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

Permalink Reply by archaeopteryx on May 11, 2012 at 3:48pm

RE: "the Aymara of the Andes seem to do the reverse, placing the past in front and the future behind" - though is may seem convoluted thinking to us, it actually makes sense if one can step outside our cultural paradigm - one can see the past, whereas, one cannot see the future.

archaeopteryx

Permalink Reply by doone on April 27, 2012 at 6:31am

WHY PYGMIES OF AFRICA ARE SO SHORT

From MSNBC:

Why the Pygmies of West Africa have such short stature, while neighboring groups don't, has been somewhat of a mystery. Now new research suggests unique changes in the Pygmy's genome have both led to adaptations for living in the forest as well as kept them short. Researchers analyzed the genomes, the "building code" that directs how an organism is put together, of Western African Pygmies in Cameroon, whose men average 4 feet, 11 inches tall, and compared them with their neighboring relatives, the Bantus, who average 5 feet, 6 inches, to see whether these differences were genetic or a factor of their environment.

...The data revealed height had a genetic component related to Bantu ancestry: The more Bantu ancestry an individual from the Pygmy tribe had, the taller that individual tended to be. One part of the genome, on chromosome 3, was especially important in this trait, the researchers said. "We kept seeing a lot of them [these single-letter differences] highlight that region in chromosome 3," Tishkoff said. "It just seemed like a hot spot for selection and for very high differentiation and, as it turns out, very strong association with height as well."

Height genes 
The researchers zoomed in on the genes in this area of the genome. One of the genes they found had already been associated with height changes in other populations, but the rest hadn't. They found new changes in hormone pathways and immunity that seemed to correlate to the pygmy's short stature. These could have been selected for because of their influence on height or because changes in these genes play other roles in the body that were advantageous to the Pygmies, Tishkoff said. For example: An immunity component might be selected for because it helps the pygmies fight off infections, which are prevalent in their habitat. And the link to hormone pathways also makes sense, Tishkoff said, because changes to them could help the Pygmies reproduce at earlier ages. Shorter height could just be a byproduct of these changes.

More here.

Posted by Azra Raza at 06:00 AM | Permalink 

Permalink Reply by doone on April 27, 2012 at 9:39am

Sometimes Dumb Science Turns Out to be Pretty Smart

—By Kevin Drum

| Thu Apr. 26, 2012 10:12 PM PDT

Members of Congress love to grandstand about allegedly idiotic studies being funded by federal grants. But guess what? It turns out that a lot of this dumb sounding research ends up being pretty useful:

Federally-funded research of dog urine ultimately gave scientists and understanding of the effect of hormones on the human kidney, which in turn has been helpful for diabetes patients. A study called “Acoustic Trauma in the Guinea Pig” resulted in treatment of early hearing loss in infants. And that randy screwworm study? It helped researchers control the population of a deadly parasite that targets cattle — costing the government $250,000 but ultimately saving the cattle industry more than $20 billion, according to Cooper’s office.

More here.

Permalink Reply by doone on April 27, 2012 at 1:12pm

Permalink Reply by Michel on May 1, 2012 at 10:22am

This is a FANTASTIC animation!
I'll upload it as a Video, everyone should see this.

Permalink Reply by doone on April 28, 2012 at 8:07pm

Why Don't We Do It In The Yard?

Because private sex is part of human nature:

In his landmark book, The Evolution of Human Sexuality, anthropologist Donald Symons suggests that since men can never get enough of it, sex is a precious commodity and therefore best enjoyed covertly to avoid inciting covetousness. "This is for the same reason that during a famine anyone with food is likely to consume it in private," says Steven Pinker of Harvard University. "A sexual act, even among consenting adults, has a high probability of upsetting someone," he adds. Parents or community members may disapprove and for children it can lead to the creation of rival siblings.

Permalink Reply by doone on April 28, 2012 at 9:03pm

Estimated annual avian mortality from communication towers by Bird Conservation Region. High mortality estimates in Peninsular Florida and Southeastern Coastal Plain reflect the more numerous and taller communication towers in these regions. (Credit: Longcore et al. PLoS One; doi/10.1371/journal.pone.0034025.g006)

http://www.sciencedaily.com/releases/2012/04/120425193056.htm

Permalink Reply by doone on April 30, 2012 at 11:04am

How Homing Pigeons Get Home

A survey of the science:

Decades of studies with frosted lenses, magnetic coils or scent deprivation show they use pretty much every clue available. The most difficult one for us to comprehend may be the earth’s magnetic field.

Birds see it, but what it looks like to them, nobody knows. Work by Roswitha and Wolfgang Wiltschko in Germany, among others, suggests that this sense relies on quantum mechanics—that is, birds detect something happening in the eye at a subatomic level. Light striking the retina seems to stimulate chemical reactions that produce pairs of molecules with electrons that are "entangled," meaning they share certain quantum properties. One of those properties, called "spin," is affected by a magnetic field. That effect could tell the bird which way is north.

The above image is from an installation called "Suspended Together," by Saudi Arabian artist Manal Al Dowayan. Kawlture explains:

[E]ach dove carries on its body a permission document that allows a Saudi woman to travel. Notwithstanding their circumstances, all Saudi women are required to have this document, issued by their appointed male guardian.

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