Tuesday, June 23, 2015

Who ya callin’ bird brain?

http://www.washingtonpost.com

Are crows the smartest animals of all?
Many scientists think that corvids — the family of birds that includes crows, ravens, rooks and jays — may be among the most intelligent animals on Earth, based on their ability to solve problems, make tools and apparently consider both possible future events and other individuals’ states of mind.
“There’s a lot of research that has been done with both ravens and crows because they are such intelligent species,” said Margaret Innes, an assistant curator at the Maryland Zoo in Baltimore.
Even in humans, defining and measuring intelligence is difficult, and it’s more complicated in other species, which have very different body shapes and have evolved for their niche in the environment. However, scientists who study cognition have defined a few measures of intelligence: recognizing oneself in a mirror, solving complex problems, making tools, using analogies and symbols, and reasoning about what others are thinking.
For a long time, biologists expected most of these mental feats to be unique to primates. The great apes — chimpanzees, orangutans and gorillas — succeed at nearly all of these tasks, from making and using tools to learning large vocabularies of symbols, as well as recognizing themselves in mirrors
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Crows: Smart as your average 7-year-old?
In this study by the University of Auckland and the University of Cambridge, crows drop objects into tubes filled with water, raising the water level and obtaining a food reward. Researches found that this species of crows can solve a science puzzle about as well as the average 7-year-old kid. (University of Auckland, University of Cambridge)
 
A select few other mammals also meet most of the accepted criteria for intelligence. Dogs and dolphins, for instance, are very good at tasks involving social intelligence, such as communication, conflict resolution and reasoning about what others are thinking. Dolphins are also capable of basic tool use — for instance, carrying sea sponges in their mouths to shield their noses from scrapes and bumps as they forage on the ocean floor.
However, the greatest intellectual rival to the brainy apes may be a noisy scavenger with a sharp beak, bright eyes and a brain about the size of a walnut: the crow and its corvid relatives.
Clever problem-solvers
Crows and ravens are clever problem-solvers, expert toolmakers and adept social movers, but scientists haven’t reached a consensus about how corvid minds handle abstract thinking or how closely their mental processes resemble those of humans.
Researchers from the University of Iowa and Lomonosov Moscow State University in Russia reported early this year that crows can use analogies to match pairs of objects. To reach that conclusion, the scientists trained crows to recognize whether two objects were identical or different, which the birds indicated by pressing one button when shown pictures of objects that matched and a different button when the objects didn’t match. Once all the birds were good at matching objects, researchers showed the crows images of pairs of objects. Some images depicted matched pairs, while others depicted two mismatched objects with different shapes or colors. In response, crows could press buttons to choose between a matched pair or a mismatched pair.
The researchers wanted to see if crows could figure out the relationship between pairs of objects and then choose a pair with the same relationship: matched or mismatched. For instance, a crow looking at a mismatched pair would then select the mismatched pair from their response choices. Nearly 78 percent of the time, the birds succeeded. According to the researchers, the birds recognized that the relationship between the two pairs of objects was the same. In other words, they were making analogies.
Other scientists contend that a type of reasoning less sophisticated than analogies could have produced the same results. For instance, the crows in the analogy test could have simply chosen images with similar characteristics, such as objects of the same color, instead of reasoning about the relationship between the objects, to get the correct answer.
Some behaviors, like those employed in the analogy test, could have more than one explanation, and until recently, scientists could only see what the birds did, then make inferences about the mental processes behind the behavior.

Now, researcher John Marzluff and his colleagues at the University of Washington are using positron emission tomography, or PET, scans to study which parts of a crow’s brain are active when it performs such tasks as recognizing friendly and unfriendly birds. And he says that another team of researchers, at the University of California at Davis, is preparing to use the same technique to study the brain activity of New Caledonian crows, a species that makes sophisticated tools. The team hopes to actually see the crows’ brains at work while they’re crafting tools.
Birds’ minds
Corvids seem to understand that other birds have minds like theirs, and their decisions often take into account what others might know, want or intend, according to several studies of crows, ravens and jays. Psychologists call this a theory of mind, and it’s a fairly sophisticated cognitive ability. Humans don’t develop it until late in childhood. Crows and their fellow corvids are social animals, much like primates, so theory of mind probably offers significant evolutionary advantages.
For one thing, it may help prevent food theft. Crows and ravens often hide food in caches and retrieve it later. “You can actually see them watching both the other birds that they are with and the humans, and if they sense that they have been seen, they will take that food and they’ll go and hide it somewhere else,” Innes said of the Maryland Zoo’s ravens. The birds appear to realize that watchers will know where they’ve hidden the food and might use that knowledge to steal it later.
Studies of several corvid species have documented this re-caching, as it is called. Skeptics of the birds’ advanced intelligence say simpler mental processes might prompt re-caching, such as making an association between being seen and later having a cache stolen.
Innes, however, is convinced that the re-caching is a sign that ravens have a theory of mind, based on her observation of re-caching behavior in ravens at the Maryland Zoo. “Definitely,” she said. “I think it definitely indicates that.”
Other test results are harder to dismiss as simple association. When researchers in Austria hid food behind a partition, ravens found it, apparently by noticing where the humans were looking and following their gazes to the hidden food. “You’re using the person’s gaze to infer information about something you can’t see,” Marzluff said.
Brain imaging studies could settle the question, Marzluff said, because advanced cognition in all animals uses different areas of the brain than simpler associative learning.
Feathered craftsmen
Corvids’ toolmaking is much more clearly the product of sophisticated cognition, according to biologists who study them.
Several animals use found objects to get food, such as otters and sea gulls that use rocks to crack shellfish, and apes that use sticks to fish termites out of nests. But deliberately crafting tools is a much more sophisticated skill. Only four species are known to actually make tools: humans, chimpanzees, orangutans — and New Caledonian crows. Although other corvid species have learned to make and use tools in labs, only the crows found on the Pacific island of New Caledonia have been found to actually make tools in the wild.
With their beaks, the crows sharpen forked twigs into hooks for scooping larvae and worms out of holes in wood. The crows often spend more than a minute finding the right stick and then sculpting it into the right shape. Even chimpanzees don’t craft their tools so meticulously, and some researchers say that the crows’ work is on par with very early human tools such as spears and sharpened digging sticks.
New Caledonian crows even take steps to avoid losing their carefully crafted tools. Biologists recently discovered that the birds sometimes stash their hooks in holes, or simply stand on them, when they aren’t in use. The crows are especially careful when the risk of losing their tools is greatest, such as when the birds forage in high branches.
The aptitude for toolmaking is probably an instinct for most corvids, as it is for humans. Corvids use found objects as tools — ravens and crows, for example, drop nuts onto flat rocks to crack the shells — and nearly all corvids seem to have a knack for solving physical problems. In one set of experiments, captive crows figured out how to bend wires into hooks to retrieve food from a tube. And captive rooks, close relatives of crows and ravens, have done the same thing.
It’s unsurprising that chimpanzees and orangutans share so many abilities with humans, because they are very closely related to us, but it’s striking that corvids share so many skills once believed to set humans apart. After all, birds and mammals have spent the last 300 million years evolving on different paths, which produced very different brain structures and bodies.
Parts of the brain that evolved earlier than 300 million years ago, such as the primitive structures in the brainstem that control basic bodily functions, look the same in most animals, including primates and corvids. But structures that developed more recently, like those involved in cognition, are organized very differently in birds than are they are in mammals.
Mammalian brains have evolved with what is called a laminar structure, in which brain cells are organized in six layers that make up the cerebral cortex, or forebrain. The cerebral cortex handles cognitive tasks, and it’s especially well developed in humans and our fellow apes, as well as other intelligent animals such as dolphins and dogs. In the bird brain, a structure called the nidopallium caudolaterale handles cognitive tasks, and it’s especially well developed in corvids.
“All three of those animals have very large forebrains relative to the rest of their brains, for their particular group,” Marzluff said. “Certainly the forebrain of a bird and a mammal differ, but they have the same sorts of functions — that is, you know, higher-level thought and processing of sensory information.”
In birds’ brains, cells form clusters called nuclei instead of layers. For years, biologists held that the layered cerebral cortex gave mammals some cognitive advantages, but research on corvids has cast doubt on that assumption.
Bird brains
That such distantly related animals with such different brains could evolve such similar abilities is surprising, but when two different species face similar evolutionary pressures, natural selection can lead to similar traits. Biologists call this convergent evolution, and it’s the same process by which birds and bats both evolved wings. At some point, biologists say, the ancestor of today’s corvids must have found itself in an ecological niche where intelligence boosted the odds of survival, so corvid brains evolved with cognitive abilities similar to those of primates.
Convergent evolution may have led to similar wiring despite the differences in physical structure between bird and mammalian brains. The network of connections between areas of the brain looks very similar in corvids and primates, and one recently published paper compared bird and primate brains to Apple and PC computers. “At one level of analysis, they do the same things in a similar way, but viewed from another perspective, their operating systems are indeed different,” wrote the author, Cambridge University psychologist Nicola Clayton.
In the coming years, the differences and similarities between corvids’ mental operating systems and those of mammals will be analyzed with brain imaging. At that point, said Marzluff, we may have “some of those answers” to the question of how smart crows really are.

Sunday, June 21, 2015

Southern California red crab invasion intensifies

crabs
Red crabs swarming 1 mile off San Clemente. 
Photo: ©Geoff Glenn

The invasion of pelagic red crabs along the Southern California coast has intensified during the past week, and judging by photos circulating on the Web, there seems to be no end in sight.
The brightly colored crustaceans, which typically exist in deep water and much farther south, have flooded coastal waters in San Diego and Orange County, and washed onto beaches and into harbors, creating an enormous mess while wreaking minor havoc in the surf zone.

crabsdonna
Donna Kalez stoops amid thousands of red crabs at Salt Creek. 

“They were pinching me out there,” Ethan Mudge, an amateur surfer told the Orange County Register, in reference to a contest last Sunday at Salt Creek in Orange County. “They were hard to paddle through.”
The crabs’ influx, which began about a month ago, is linked either to a strengthening El Niño, a warm-water phenomenon originating in the equatorial eastern Pacific, or another warm-water event referred to by scientists as the “warm blob.”

crab2
Red crab hides in the kelp. Photo: ©Geoff Glenn

crab
A lone red crab swims near a kelp bed.
 Photo: ©Geoff Glenn

Not since the powerful El Niño of 1997-98 has there been a red crab invasion in Southern California that came close to resembling this one.
In Orange County, so many crabs are ending up beaches, where they promptly die, that a stench wafts across the air.
“I’m really hoping they come in and rake them up,” Mary Olsen, a Newport Beach resident, told the Register. “Once they die, they just really smell.”
But not far offshore, the critters are still alive and represent a feast for bluefin tuna.

crabsdana

Red crabs can measure about 5 inches. 
Photo: Dana Wharf Sportfishing

Anglers are venturing out to hook and spear tuna, while photographers are diving in to take advantage of a rare opportunity to photograph these mysterious crustaceans beneath the surface.
To be sure, the images that appear with this post, all used with permission, help shine the light on Pleuroncodes Planipes, a.k.a. red crab and tuna crab.

 crabs-jim-grant-photo
The red crab invasion began last month in San Diego. 
Photo: ©Jim Grant
It’s actually a type of squat lobster, and one of the most abundant species of micronekton (actively swimming organisms, larger than plankton), residing in the California Current.
They can measure about 5 inches and represent a food source for not only tuna, but marlin, sharks, yellowtail, and even some whales. Their typical range is from Chile in South America, to Baja California.
They’re not heavily fished commercially, but some of the larger specimens are marketed as langostino. Those that are dying on SoCal beaches, though, seem to be fit only for starving gulls.
–Note: Underwater photos are courtesy of Geoff Glenn Photography. Click on these links to follow him on Facebook and Instagram

Friday, June 19, 2015

Cambodia trains rats to detect landmines

AFP

An African rat pictured helping to sniff out landmines in Chimoio, Mozambique on June 24, 2005
Cambodia is training an elite squad of rats, imported from Africa, to sniff out landmines and other unexploded ordnance in the once war-wracked kingdom, authorities said on Friday.
A team of 15 rats, some weighing up to 1.2 kilograms, were imported from Tanzania in April with the help of a Belgian non-governmental organisation, which trains rats to sniff out mines, Heng Ratana, director general of Cambodian Mine Action Center (CMAC), told AFP.
"If the rats pass the test, we will use them... if they are not qualified, we will end the program," Ratana told AFP.
He said there have been claims of success in using rats to sniff landmines -- as well as detect tuberculosis -- in several African countries including Tanzania, Mozambique and Angola.
The rats are now being trained by experts in northwestern Siem Reap province, home to Cambodia's famed Angkor temples complex.
But one of the rodents has already died probably because of the change in climate, he said.
Experts plan to begin testing the rats over the next few weeks.
The rodents will be put through their paces on a number of tasks, including to establish if they can sense all types of mine, whether they can detect buried ordnance and how fast they work, he said.
"They will test the rats in actual landmine fields," he said.
"At this stage, it is too early to say if we can use the rats," Ratana said, adding that two Cambodian mine experts had been trained in Tanzania and they were now sharing their expertise with their colleagues.
Nearly three decades of civil war gripped Cambodia from the 1960s, leaving the poverty-stricken nation both one of the most heavily bombed and heavily mined countries in the world.
Last month, a new Cambodian underwater demining team pulled an American-made bomb from the Mekong River for the first time as the country battles the wartime legacy of unexploded mines that have killed thousands -- detonating when trodden on.
Teams of deminers face the unenviable task of trying to locate and safeguard huge quantities of unexploded ordnance that has killed nearly 20,000 people and wounded double that number since 1979.
According to Cambodian government statistics, 154 people were killed or injured by leftover mines in 2014, and 111 the year before.

Sixth mass extinction is here: US study

AFP
The world is embarking on its sixth mass extinction with animals disappearing about 100 times faster than they used to, scientists warned, and humans could be among the first victims
The world is embarking on its sixth mass extinction with animals disappearing about 100 times faster than they used to, scientists warned, and humans could be among the first victims (AFP Photo/Asit Kumar)
Miami (AFP) - The world is embarking on its sixth mass extinction with animals disappearing about 100 times faster than they used to, scientists warned Friday, and humans could be among the first victims.
Not since the age of the dinosaurs ended 66 million years ago has the planet been losing species at this rapid a rate, said a study led by experts at Stanford University, Princeton University and the University of California, Berkeley.
The study "shows without any significant doubt that we are now entering the sixth great mass extinction event," said co-author Paul Ehrlich, a Stanford University professor of biology.
And humans are likely to be among the species lost, said the study -- which its authors described as "conservative" -- published in the journal Science Advances.
"If it is allowed to continue, life would take many millions of years to recover and our species itself would likely disappear early on," said lead author Gerardo Ceballos of the Universidad Autonoma de Mexico.
The analysis is based on documented extinctions of vertebrates, or animals with internal skeletons such as frogs, reptiles and tigers, from fossil records and other historical data.
The modern rate of species loss was compared to the "natural rates of species disappearance before human activity dominated."
It can be difficult to estimate this rate, also known as the background rate, since humans don't know exactly what happened throughout the course of Earth's 4.5 billion year history.
For the study, researchers used a past extinction rate that was twice as high as widely used estimates.
If the past rate was two mammal extinctions per 10,000 species per 100 years, then the "average rate of vertebrate species loss over the last century is up to 114 times higher than it would be without human activity, even when relying on the most conservative estimates of species extinction," said the study.
"We emphasize that our calculations very likely underestimate the severity of the extinction crisis because our aim was to place a realistic lower bound on humanity's impact on biodiversity."
The causes of species loss range from climate change to pollution to deforestation and more.
According to the International Union for Conservation of Nature, about 41 percent of all amphibian species and 26 percent of all mammals are threatened with extinction.
"There are examples of species all over the world that are essentially the walking dead," Ehrlich said.
The study called for "rapid, greatly intensified efforts to conserve already threatened species, and to alleviate pressures on their populations -- notably habitat loss, over-exploitation for economic gain and climate change."

Tuesday, June 16, 2015

Florida Beachgoers Warned About Deadly Bacteria — That’s Also Found in Raw Shellfish


Florida Beachgoers Warned About Deadly Bacteria — That’s Also Found in Raw Shellfish
Eight people have been infected by vibrio vulnificus in Florida this year, and two people have died — one from eating raw seafood and another from “multiple exposures” to the bacteria. (Photo: Getty Images)
If you’ve eaten at a restaurant that serves raw seafood, you’ve probably noticed this warning on the menu, or something similar: “Eating raw or undercooked shellfish can put you at a higher risk of foodborne illness.”
Before you brush off the message, consider this: The state of Florida has issued a warning about vibrio vulnificus, an often deadly bacteria that can be transmitted by eating undercooked or raw shellfish such as oysters, clams, or crabs.
Eight people have been infected by the bacteria in Florida this year, and two have died — one from eating raw seafood and another from “multiple exposures” to the bacteria. (The bacteria killed at least seven people in Florida last year, but the state says that number is underreported.)
Vibrio vulnificus can also be contracted by wading in bacteria-infected water with an open wound, but ingesting raw seafood is by far the biggest culprit, infectious disease specialist Dr. Amesh A. Adalja, an assistant professor at the University of Pittsburgh Medical Center, tells Yahoo Health.
Most people who contract this bacteria will experience vomiting, diarrhea, and abdominal pain, but it can also infect the bloodstream, causing fever, chills, decreased blood pressure, and blistering skin lesions.
This bacteria also has a high mortality rate. According to the Centers for Disease Control and Prevention, vibrio vulnificus bloodstream infections are fatal 50 percent of the time.
Before you panic, know this: Most people who died from vibrio vulnificus had liver disease or had compromised immune systems. However, anyone can become infected.
Vibrio vulnificus is most common in warm waters in Gulf states, Adalja says, but he points out that 100 percent of Chesapeake Bay oysters have vibrio vulnificus in them. “It’s not uncommon; just not everybody who comes into contact with it gets infected,” he says.
According to Adalja, some people may be genetically predisposed to infection, adding, “The more raw shellfish you eat, the more likely you are to get vibrio vulnificus.”
Michael Doyle, director of the Center for Food Safety at the University of Georgia, tells Yahoo Health that you should be wary of eating raw oysters in general. “It’s considered to be a potential high risk, whether you’re immunocompromised or not,” he said.
However, he says, there is one way you can make sure your raw shellfish is safe: Look for foods that undergo high-pressure processing. This process inactivates harmful microbes that could be in your shellfish, including vibrio vulnificus, but doesn’t kill the oysters. “You still have a fresh flavor, but they’re pasteurized,” Doyle says, noting that more restaurants are buying these types of oysters.  
If you experience symptoms of vibrio vulnificus infection after eating oysters or raw shellfish, call your doctor immediately. “This can quickly spread systemically,” says Adalja. “Getting antibiotics quickly is crucial.”

Thursday, June 11, 2015

Some people can resist the ravages of HIV – here's how

 New Scientist
 
HIV (purple) mingling with a dendritic cell (purple)
 ((Image: AS&K VISUAL SCIENCE/SPL)

Just when all seems lost, our hero strikes back with such speed that the evil invader is vanquished. It could be the climax of a blockbuster movie, but it's more important than that. If this is how a handful of people are able to fight off HIV, we could have a route towards a blockbuster drug or vaccine.
Less than 1 per cent of people infected with HIV around the world are able to suppress its effects without taking drugs. These "elite controllers" are somehow able to keep the virus from replicating uncontrollably, thus preventing it from taking its terrible toll on their bodies.
Unsurprisingly, ever since these people were first identified, researchers have been hoping to discover their immune system's secret, in the hope of bottling it for the other 99 per cent of people with HIV.

The latest insights come from experiments on specialised dendritic cells that "teach" the immune system to destroy infected or faulty cells. We already knew that elite controllers have CD8 T-cells – components of the immune system – that react more strongly to HIV than T cells of other people, but we didn't know why, says Xu Yu at the Ragon Institute, a collaboration between Massachusetts General Hospital, MIT and Harvard set up to study these unusual individuals .

Riot, then backlash

Yu's team infected colonies of dendritic cells with HIV and compared those from elite controllers with those of HIV-negative people, people with HIV receiving antiretroviral drugs, and those that weren't.
Normally, immune cells neutralise invading viruses by destroying viral RNA and DNA as it starts to build up. This is what happened in all the dendritic cells the team tested – except those from elite controllers. In these colonies the virus appeared to run riot, producing copious amounts of genetic material. "It seemed as though the virus was escaping from detection, and that's our most paradoxical finding," says Yu.
But then came the equally unexpected backlash. When they eventually swung into action, dendritic cells from elite controllers produced large quantities of antiviral compounds called type 1 interferons. Other people's dendritic cells responded much more sluggishly.
And the elite controllers' cells were still pumping out interferons two days later, long after the other cells' response had petered out. "Both the speed and the ability to sustain the defence were what marked out the elite controller cells," says Yu.
The interferon spewing from the elite controllers' cells also triggered the rapid proliferation of CD8 T cells, priming them to attack any other cells containing HIV.

No stealthy approach

"It tells us what the difference is in elite controller cells, and it sounds pretty key, but it doesn't tell us why it happens," says Sarah Rowland-Jones at the University of Oxford. She suspects that the extra viral DNA that built up in the elite controllers' cells may have made the infection more obvious to the immune system. In contrast, other people's immune cells destroyed most but not all of the HIV, potentially allowing the infection to continue unnoticed.
Yu says her team hopes to capitalise on the discovery by seeking ways to make dendritic cells from ordinary patients mimic the HIV response seen in elite controllers. They are now screening novel molecules and adjuvants – substances given alongside vaccines – to identify any that do the trick. These could then be tested to see if they provide the extra kick needed to prime the immune system against HIV.

[BBC Science Documentary] THE HISTORY OF COMPUTER HACKING - Technology d...



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How a history of eating human brains protected this tribe from brain disease


The sickness spread at funerals.
The Fore people, a once-isolated tribe in eastern Papua New Guinea, had a long-standing tradition of mortuary feasts — eating the dead from their own community at funerals. Men consumed the flesh of their deceased relatives, while women and children ate the brain. It was an expression of respect for the lost loved ones, but the practice wreaked havoc on the communities they left behind. That’s because a deadly molecule that lives in brains was spreading to the women who ate them, causing a horrible degenerative illness called “kuru” that at one point killed 2 percent of the population each year.
The practice was outlawed in the 1950s, and the kuru epidemic began to recede. But in its wake it left a curious and irreversible mark on the Fore, one that has implications far beyond Papua New Guinea: After years of eating brains, some Fore have developed a genetic resistance to the molecule that causes several fatal brain diseases, including kuru, mad cow disease and some cases of dementia.
The single, protective gene is identified in a study published Wednesday in the journal Nature. Researchers say the finding is a huge step toward understanding these diseases and other degenerative brain problems, including Alzheimer’s and Parkinson’s.
The gene works by protecting people against prions, a strange and sometimes deadly kind of protein. Though prions are naturally manufactured in all mammals, they can be deformed in a way that makes them turn on the body that made them, acting like a virus and attacking tissue. The deformed prion is even capable of infecting the prions that surround it, reshaping them to mimic its structure and its malicious ways.
The prions’ impact on their hosts is devastating and invariably fatal. Among the Fore, the prions riddled their victims’ brains with microscopic holes, giving the organ an odd, spongy texture. In cattle, prions cause mad cow disease — they are responsible for the epidemic in Britain of the late ’80s and ’90s that required hundreds of thousands of cattle to be destroyed. They have been linked to a bizarre form of fatal insomnia that kills people by depriving them of sleep. And they’re the source of the degenerative neurological disorder Creutzfeldt-Jakob disease (CJD), characterized by rapid dementia, personality changes, muscle problems, memory loss and eventually an inability to move or speak.
The vast majority of prion-diseases are “sporadic,” seemingly appearing without cause. But a lead author of the Nature study, John Collinge, said in an interview with Nature that a portion of cases are inherited from one’s parents, and an even smaller percentage are acquired from consuming infected tissue. Variant CJD, often called the “human mad cow disease,” is caused by eating beef from infected cows.
Prions are especially insidious because there’s no way of stopping them, science writer D.T. Max, author of a book on prions and fatal familial insomnia, told NPR in 2006. In the hierarchy of pathogens, they’re even more elusive and difficult to quash than a virus. They can’t be treated with antibiotics or radiation. Formalin, usually a powerful disinfectant, only makes them more virulent. The only way to clean a prion-contaminated object is with massive amounts of extremely harsh bleach, he said. But that technique isn’t helpful in treating a person who has already been infected.
The study by Collinge and his colleagues offers a critical insight into ways that humans might be protected from the still-little-understood prions. They found it by examining the genetic code of those families at the center of the Fore’s kuru epidemic, people who they knew had been exposed to the disease at multiple feasts, who seemed to have escaped unscathed.
When the researchers looked at the part of the genome that encodes prion-manufacturing proteins, they found something completely unprecedented. Where humans and every other vertebrate animal in the world have an amino acid called glycine, the resistant Fore had a different amino acid, valine.
“Several individuals right at the epicenter of the epidemic, they have this difference that we have not seen anywhere else in the world,” Collinge told Nature.
That minute alteration in their genome prevented the prion-producing proteins from manufacturing the disease-causing form of the molecule, protecting those individuals from kuru. To test whether it might protect them from other kinds of prion disease, Collinge — the director of a prion research unit at University College London — and his team engineered the genes of several mice to mimic that variation.
When the scientists re-created the genetic types observed in humans — giving the mice both the normal protein and the variant in roughly equal amounts — the mice were completely resistant to kuru and to CJD. But when they looked at a second group of mice that had been genetically modified to produce only the variant protein, giving them even stronger protection, the mice were resistant to every prion strain they tested — 18 in all.
“This is a striking example of Darwinian evolution in humans, the epidemic of prion disease selecting a single genetic change that provided complete protection against an invariably fatal dementia,” Collinge told Reuters.
The Fore aren’t the only people to demonstrate prion resistance. More than a decade ago, Michael Alpers — a specialist on kuru who has studied the Fore since the 1960s and was a co-author of the Nature study — conducted similar research on prion protein genes in humans worldwide. In a study published in Science, he found that people as far-flung as Europe and Japan exhibited the genetic protection, indicating that cannibalism was once widespread and that prehistoric humans probably dealt with waves of kuru-like epidemics during our evolution.
But the gene found in the Fore is special because it seems to render mutant prion-producing proteins (the kind that would be passed down from one’s parents, causing inherited prion diseases) incapable of producing any kind of prion whatsoever. It also stops the wild-type protein — the phenotype that most people have — from making malformed prions.
Scientists say that the benefits of this discovery don’t stop at prion diseases, which are relatively rare — only about 300 cases are reported each year in the United States. According to Collinge, the process involved in prion diseases — prions changing the shape of the molecules around them and linking together to form long chains called “polymers” that damage the brain — is probably responsible for the deadly effects of all kinds of degenerative brain illnesses: Alzheimer’s, Parkinson’s and dementia chief among them.
According to the World Health Organization, there are 47.5 million people worldwide living with dementia. An additional 7.7 million are diagnosed each year.
If Collinge and his colleagues can understand the molecular mechanisms by which prions do their work — and how the prion-resistant gene stops them — they might better understand the misshapen proteins that are afflicting millions with those other degenerative brain illnesses.
Eric Minikel, a prion researcher at the Broad Institute in Cambridge, Mass., who was not involved in the study, was impressed by the finding.
“It is a surprise,” he told Nature. “This was a story I didn’t expect to have another chapter.”

South Korea reported a 10th death from the MERS virus on Thursday, although officials say they believe the disease has peaked.

SEOUL, South Korea (AP) —
The victim was a 65-year-old man who had been treated for lung cancer and was hospitalized in the same facility as another MERS patient, the Health Ministry said.
The outbreak of Middle East respiratory syndrome has caused panic in South Korea. It has infected more than 120 people since the first case, a 68-year-old man who had traveled to the Middle East, was diagnosed on May 20.
About 3,800 people remained isolated Thursday after possible contact with infected people, according to the ministry. More than 2,600 schools and kindergartens across South Korea were closed.
On Wednesday, experts from the World Health Organization and South Korea urged the schools' reopening as the outbreak in the country has so far been contained to hospitals and there is no evidence of sustained transmission in the community.
South Korean officials believe the outbreak may have peaked, although they say the next few days will be crucial to determining whether their efforts to isolate patients and control the disease have worked. Three people diagnosed with MERS were released from hospitals Thursday, bringing the total discharged to seven.
President Park Geun-hye postponed her planned U.S. visit scheduled next week to focus on coping with the outbreak.
Most of the deaths so far have been of people who had been suffering from pre-existing medical conditions, such as respiratory problems or cancer.
Experts think MERS can spread in respiratory droplets, such as by coughing. But transmissions have mainly occurred through close contact, such as living with or caring for an infected person.
MERS has mostly been centered in Saudi Arabia and has a death rate of about 40 percent among reported cases. It belongs to the family of coronaviruses that includes the common cold and SARS, and can cause fever, breathing problems, pneumonia and kidney failure.

Wednesday, June 10, 2015

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Scientists just found soft tissue inside a dinosaur fossil. Here's why that's so exciting.

http://www.vox.com/

Dinosaur fossils, it was long thought, are simple objects. The fossilization process leaves the overall shape of a dinosaur's bones intact, but all the microscopic structures inside them — the blood cells, connective fibers, and other sorts of soft tissue — inevitably decay over time.
But that view is changing — and it's possible that many ancient fossils may preserve more detail than meets the eye. The sort of biological tissue now being found in some fossils could tell us about dinosaur anatomy, behavior, and evolution in ways that weren't possible just a few years ago.
dino collagen
(Sergio Bertazzo)
The photo above, from a new study published today in Nature Communications and led by Sergio Bertazzo of Imperial College London, shows an extremely zoomed-in view of a 75-million-year-old theropod claw, taken from the London Natural History Museum's collection. When researchers scraped tiny pieces off the fossil and looked at them under an electron microscope, they found tiny structures that look a lot like collagen fibers present in our own ligaments, tendons, and bones.
In other dinosaur fossils, the researchers found features that resemble red blood cells. Tests showed that they have a similar chemical composition to the blood of an emu (a bird thought to be a relatively close relative to dinosaurs).
 (Bertazzo et. al. 2015)
The idea that dinosaur fossils might harbor soft tissue first surfaced about a decade ago, when paleontologist Mary Schweitzer found evidence of blood cells preserved inside T. rex fossils.
But what's so exciting about this new study is that the fossils used, unlike Schweitzer's, aren't particularly well-preserved. Susannah Maidment, one of the paleontologists who worked on the paper, called them "crap" specimens. If they have preserved soft tissue inside them, it could be a sign that thousands of other fossils in museum collections do too.

How paleontologists found blood inside dinosaur fossils

t rex
For hundreds of years, most paleontologists never considered that their fossils might preserve these sorts of microscopic soft-tissue features. It was assumed that the proteins and other molecules they're made of would deteriorate in just a few million years.
What's more, looking inside them to confirm this would require that people damage the fossil, either by breaking it open or by dissolving the hard, mineralized outside, as Schweitzer did with her T. rex. "No right-thinking paleontologist would do what Mary did with her specimens," paleontologist Thomas Holtz told Smithsonian for a 2006 story on Schweitzer's discovery. "We don’t go to all this effort to dig this stuff out of the ground to then destroy it in acid."
t rex
Soft tissue extracted from a T. rex fossil by Schweitzer appeared to contain blood cells. (Schweitzer et al., 2005/Science)
Schweitzer did so after a veterinarian at a conference happened to see microscope slides of T. rex bone slices and observed that there were red blood cells inside it. But her claim remained controversial among paleontologists — even after her 2006 paper, which presented more thorough testing.
More recent chemical analysis has provided further evidence that the
T. rex bones do indeed contain blood cells, and Schweitzer has since found soft tissue preserved inside an 80-million-year-old hadrosaur. It's still unclear exactly how this soft tissue is able to survive, but some hypothesize that iron molecules might bind to proteins in the tissue, making it more stable.
This newest paper, conducted with weathered, run-of-the-mill fossils rather than pristine ones, suggests that this process might be the rule, not the exception. If so, these findings could be the first of many to come.

Dinosaur blood and proteins could tell us about their behavior and evolution

t rex
You can only learn so much about an organism from its bones. As much as we've discovered from the hundreds of thousands of dinosaur fossils excavated around the world, we're still debating whether dinosaurs were warm- or cold-blooded and how many of them had feathers.
Peering inside these dinosaurs' bones — to look at their blood cells, connective tissue, and other microscopic features — could dramatically improve our understanding of their biology as a whole. The structure of their blood cells, for instance, could hint at their behavior and physiology in ways that their bones simply can't.
The tissue might help scientists better understand evolutionary relationships between species
The new information might also help scientists better understand evolutionary relationships between species. In the study, researchers found that the proteins inside the collagen-like fibers are well-preserved, with the specific sequence of amino acids that they're built from largely intact. Amino acid sequences in proteins gradually evolve over time and vary from species to species, somewhat like DNA — so analyzing them in dinosaurs could lead to better knowledge about the evolutionary relationships between them and other species, like birds.
But there's one thing we can't do with this soft tissue: extract dinosaur DNA and make Jurassic Park a reality. Compared with collagen fibers and red blood cells, DNA is much, much smaller and more fragile.
Perhaps DNA could also be more readily preserved than thought. But scientists currently estimate that it has a half-life of just 521 years, and dinosaurs largely died off 65 million years ago.

Thursday, June 4, 2015

The paleontologist who worked on 'Jurassic World' is trying to create a real dinosaur within 5 to 10 years

Business Insider
Jack Horner Jurassic World
(Meet the media Guru/Flickr) Jack Horner, the paleontologist who worked on Jurassic World (and the rest of the Jurassic Park films), has plans to make a dinosaur.
Yes, this is for real. No, there isn't dinosaur DNA trapped in amber, waiting to be replicated and cloned.
But that's not the only way to make a dino, said Jack Horner, the paleontologist who worked on "Jurassic World" (and the rest of the "Jurassic Park" films), and he wants to make it happen.
How did we get to this point, where Horner — one of the main inspirations for Michael Crichton's "Jurassic Park" character Alan Grant — thinks we can make a live dinosaur within five to 10 years?
"It all started with 'Jurassic Park,'" Horner told Business Insider in an interview.
In 1993, the same year the first movie came out, he and then-graduate student Mary Schweitzer, who has continued to make some amazing discoveries in the field of paleontology, tried to extract DNA from dinosaur bones.
They failed. DNA basically starts coming apart as soon as a cell dies, says Horner, and no one has ever found intact dinosaur DNA — he doesn't think it's possible. "If you did the thing they did in 'Jurassic Park,'" says Horner (referring to the story's solution of filling in dino DNA gaps with frog DNA), "you'd basically have a frog."
About 20 years of genetics research later, however, Horner has another plan — and it relies on the fact that we have a more effective way to get "dinosaur" DNA.

Velociraptor Jurassic World
(Universal via YouTube) Picture this guy (or gal?), but smaller and feathered. \

Going back in time

We have creatures on the planet that are the direct descendants of dinosaurs: birds. And if you ask a paleontologist, birds are dinosaurs, specifically avian dinosaurs.
They might not look like dinosaurs, but birds have feathers, just like dinosaurs, including the ferocious velociraptor. Over time, their descendants' snouts turned into beaks, they stopped growing tails, and wings further evolved into modern bird wings.
But birds didn't necessarily lose the genes that code for tails or arms or snouts — instead, those same traits most likely exist in their genetic code, inactive, while the newer genes for wings, tail feathers, and beaks are expressed.
Horner thinks that we can suppress these new genes and express the atavistic, throwback dinosaurian genes instead. And his plan is to do this first with a well-researched bird that we're all familiar with, a chicken, giving us... a "chickenosaurus," as he described in a TED talk, or a "dino-chicken."
Picture it: a small, feathered creature, with a tail that helps it balance, small arms with claws, and a toothy snout, instead of a beak.
Remember, real velociraptors were just the size of a large turkey.
Horner has talked about pet dinosaurs for a while. Publishers of his book, "How to Build a Dinosaur: Extinction Doesn't Have to Be Forever" came out in 2009, originally planned to release it around the same time as "Jurassic Park 4."
Basically, Horner says, he's trying to discover the genetic pathways that turned birds into the modern creatures we know, so we can turn back the clock on a chicken's evolutionary history.
And as wild as this may sound, Horner's not the only one doing this type of work. A pair of Harvard and Yale scientists recently announced they'd found a way to turn chicken beaks back into dinosaur snouts. Skeptics think building a dino snout won't be so easy, and will involve as-yet undiscovered genetics. But the researchers counter that their work shows just how fast the science in this field is developing.
Horner says we can look at the beak study as a "proof of concept" that this reverse engineering process is feasible.
That Harvard-Yale team is working on the beak. In 2014, another group reported in PLOS Biology they'd figured out how dinosaur arms fused into wings. Horner is working on the tail. And he thinks that with the right funding, we can reverse-engineer and grow a dinosaur in five to ten years.

dna
(Shutterstock)

Creating something new

If researchers reverse-engineer a bird, they'd have some sort of dinosaur, though it would still be a new species — the process by which modern birds evolved happened over tens of millions of years, and the few changes we're talking about here probably wouldn't represent an exact creature that existed 65 million years ago.
And dinosaurs that weren't of the avian variety still wouldn't be represented. We have no modern descendant of a stegosaurus or a brontosaurus (newly restored to real dino status).
But the rapidly changing world of genetics could open up the possibility for creating animals just like, say, a triceratops.
Horner says that if we were interested, we could genetically engineer creatures like these, or like anything else we can figure out a genetic code for, even if it never existed in nature. Once we figure out the genes that create a trait, those genes could potentially be incorporated into an animal. We've already done this. Researchers used the genes from jellyfish to make rabbits that glow in the dark, and other researchers made mice with transparent skin. Once we know the code for a trait, we could use that to make a creature.
Horner uses a unicorn as an example — we'd just need to add genes for a horn. "We could probably get to a unicorn before we get to a dino-chicken," he says.

Chickens
(REUTERS/Stringer ) Your friendly neighborhood dinosaur relatives.

So why do it?

Though some of this might sound like it's totally out there, there are practical applications. If Horner's team figures out how to make a tail grow, that might unlock the ability to better understand the growth of vertebrae and neural tissue, with fascinating medical implications.
He also thinks "if we can make a dino-chicken, it's pretty cool." It might help get kids interested in genetics at a young age — what kid doesn't love dinosaurs?
Plus, Horner points out that we've been genetically modifying the genes of animals for thousands of years. We've just called it "breeding."
"People made chihuahuas out of wolves, for God's sake," he says.