Scientists Develop New Computational Method To Investigate Origin Of Life

Scientists at Penn State have developed a new computational method that they say will help them to understand how life began on Earth. The team’s method has the potential to trace the evolutionary histories of proteins all the way back to either cells or viruses, thus settling the debate once and for all over which of these life forms came first. …

The team is focusing on an ancient group of proteins, called retroelements, which comprise approximately 50 percent of the human genome by weight and are a crucial component in a number of diseases, including AIDS. “Retroelements are an ancient and highly diverse class of proteins; therefore, they provide a rigorous benchmark for us to test our approach. We are happy with the results we derived, even though our method is in an early stage,” said Patterson. The team plans to make the algorithms that they used in their method available to others as open-source software that is freely available on the Web.

Scientists map out the evolutionary histories of organisms by comparing their genetic and/or protein sequences. Those organisms that are closely related and share a recent common ancestor have greater degrees of similarity among their sequences. In their paper, the researchers describe how they used 11 groups of the retroelement proteins — ranging from bacteria to human HIV — to trace the evolutionary histories of retroelements. Their method uses a computer algorithm to generate evolutionary profiles — also called phylogenetic profiles — that are compared all-against-all. For example, given four sequences, the new method compares profile A to profiles B, C, and D; it compares profile B to profiles C and D; and so on, for a total of six comparisons. The method then selects the regions of the profiles that match and creates a tree-like diagram, called a phylogenetic tree, based on the retroelements’ similarities to one another. The tree provides evolutionary distance estimates and, hence, phylogenetic relationships among retroelements. - ScienceDaily

Great! Some claim that humans are too complicated to have occurred by chance, and so, an all powerful man with a white beard must have created us. Perhaps techniques like this will solve the debate once and for all. They might even show that our DNA was intelligently altered by aliens several times during Earth’s evolution as some claim.

I wonder if the same technique could be used to show a person’s family tree in the entire picture of human evolution? Perhaps in a few years we will be able to access something like this on line. But first, we need a way (at home) to get one person’s 20,000-25,000 genes uploaded for a complete analysis.

Elephant Scores 87 Percent on Math Exam at Zoo

The elephant’s memory is legendary, but in a large, grey surprise to science the mighty Asian elephant turns out to have a distinct flair for maths as well

Under carefully controlled experimental conditions — essentially comprising a large cage and two buckets of assorted fruit — one elephant at Ueno Zoo in Tokyo managed to get its sums right 87 per cent of the time. A slightly less gifted pachyderm across the country in Kyoto scored a still respectable 69 per cent.

The curiously accurate adding skills of Elephas maximus have been discovered by Naoko Irie, a behavioural ecologist at the University of Tokyo putting the finishing touches to her doctoral thesis …“I couldn’t believe it at first,” said Irie, “They could instantly compare numbers like six and five.”

The elephants she subjected to the fruit-based arithmetic tests were as good at telling the difference between five and six as they were at spotting that five is greater than one, she said.

Speculation among scientists over why the elephant should have developed its limited but nonetheless impressive mathematical ability centres on the way in which the lumbering creatures move in herds. A basic counting ability, say experts, might act as a guarantee that no calf is left behind. - timesonline

The incredible journey taken by our genes

Sixty thousand years ago, a small group of African men and women took to the Red Sea in tiny boats and crossed the Mandab Strait to Asia. Their journey - of less than 20 miles - marked the moment Homo sapiens left its home continent. … Now scientists are completing a massive study of DNA samples from a quarter of a million volunteers in different continents in order to create the most precise map yet of mankind’s great diaspora. Last week, in Tallinn, Estonia, they outlined their most recent results. ‘As the ultimate ancestor begat son, who begat son and so on, they picked up mutations in their DNA that we can now pinpoint by gene analysis,’ said project leader Dr Spencer Wells. ‘When we look at these markers’ distributions we can see how our ancestors moved about.’ …

‘We can also see that just before humans left Africa, about 70,000 years ago, mankind was brought to the brink of extinction when Mount Toba, in Sumatra, erupted,’ said Wells. ‘It was the most powerful volcanic eruption for two million years and dropped thick ash and killed vegetation across the globe. Our research now shows Homo sapiens numbers dropped alarmingly at this time and we only just hung on as a species.’

Nevertheless, humanity bounced back, evolving new creative and intellectual gifts under the extreme selective pressures it then had to endure. …
One study by project scientists Pierre Zalloua and Chris Tyler-Smith has discovered a genetic marker typical of Europeans in modern Lebanese men. The inference is clear they say: this distinctive Y-chromosome was left behind by 11th-century Crusaders when they invaded Lebanon and then settled in the country. A similar sort of genetic legacy has been detected in regions where Gengis Khan ruled and which has been linked to the many male descendants he produced.

As for Africa, it has the most genetically diverse population of all the continents, as would be expected of humanity’s birthplace. And of those living today, the Khoisan people of southern Africa are probably the closest, genetically, to the founding mothers and fathers of humanity, say project scientists. - guardian

Study says eyes evolved for X-Ray vision

Humans and other large mammals — primates and large carnivores like tigers, for example — exist in cluttered environments like forests or jungles, and their eyes have evolved to point in the same direction. While animals with forward-facing eyes lose the ability to see what’s behind them, they gain X-ray vision, according to Mark Changizi, assistant professor of cognitive science at Rensselaer, who says eyes facing the same direction have been selected for maximizing our ability to see in leafy environments like forests.

All animals have a binocular region — parts of the world that both eyes can see simultaneously — which allows for X-ray vision and grows as eyes become more forward facing.

Demonstrating our X-ray ability is fairly simple: hold a pen vertically and look at something far beyond it. If you first close one eye, and then the other, you’ll see that in each case the pen blocks your view. If you open both eyes, however, you can see through the pen to the world behind it.

To demonstrate how our eyes allow us to see through clutter, hold up all of your fingers in random directions, and note how much of the world you can see beyond them when only one eye is open compared to both. You miss out on a lot with only one eye open, but can see nearly everything behind the clutter with both.

“Our binocular region is a kind of ’spotlight’ shining through the clutter, allowing us to visually sweep out a cluttered region to recognize the objects beyond it,” says Changizi, who is principal investigator on the project. “As long as the separation between our eyes is wider than - the width of the objects causing clutter — as is the case with our fingers, or would be the case with the leaves in the forest — then we can tend to see through it.” - pysorg

An Indonesian woman with metal wires “growing” out of her?

Her name is NOORSYAIDAH. A 40 years old kindergarten teacher from Sangatta, East Kutai. Her first symptoms started manifestating in 1991. The metal wires grew out of her chest and her belly. There was no explanation then (or even now). During the first week wires kept falling off from her body and were gone. A month later, the wires grew back again and from that time onward the wires did not fall. They kept growing!

One of her sisters said that she tried to help by trimming the wires. Alas, whenever she trimmed the wires, the wire retreated as if it were hiding and then popped up in another part of Noorsyaidah’s body. -myterytopia

Her attempt for recovery, from modern medics, alternative treatment to paranormals have been done, but still these wires that grew from within her stomach and chest does not dissapear.
Noorsyaidah had also tried going for treatment out of her hometown to the reknown hospital in her town. However, fate is not on this 40 year old woman from Kalimantan, Indonesia, as after these wires were pulled out of her body, they grew again in the next few days. “It’s up to God now” she said softly resigning to her fate. … Wires shape is just like any other wire that easily oxydized, length varying from 10-20 cm and they come in many colors from black, yellow and brown.- myinteretingfiles

This article is poorly written. What type of metal is this wire? Saying “just like any other wire” is not useful.

“There have been 4 Medical Specialists taking this matter seriously and have treated her in several ways.”

A real article would give at least the lead doctor’s name as well. Bad reporting. My guess is that she has some serious mental problems and is sticking these wires in herself.  Can anyone translate what is actually being said in the video? Are the doctors actually confused about her condition, or does she just have a personality disorder?

New technique finds a faster way to change one cell type into another

Harvard researchers have transformed one type of pancreas cell in living mice into another - the insulin- producing cells that are destroyed in type 1 diabetes - potentially giving stem cell scientists a powerful new way to one day grow replacement tissues for patients.

The technique, which the researchers said improved diabetic symptoms in the mice, is faster than another pioneering method, in which scientists turn mature adult cells into embryonic-like stem cells that have the capacity to become any cell in the body.

The new technique, reported online yesterday in the journal Nature, is years away from having benefits for diabetic patients, according to Douglas Melton, a co-author and co-director of the Harvard Stem Cell Institute. But other researchers said it was an exciting demonstration that could spur scientists to think more broadly about converting mature cells of all types into another type in the same organ - taking, for example, a bit of heart tissue and transforming it into cardiac muscle.  …

Two years ago, Japanese scientists altered stem cell science with their report that it was possible to reprogram a cell, turning it into an embryonic-like stem cell called an iPS cell, which was capable of turning into any cell in the human body. Melton’s team has shown it’s possible to skip that stem cell-like state altogether.

Melton and colleagues painstakingly identified which genes were likely to trigger the cell switch by sorting through more than 1,000 genes and winnowing them down to ones that played a role in the development of insulin-producing cells. They found that by injecting viruses carrying three genes into mice, they could turn the pancreatic cells into beta cells that produce insulin. - boston

Nice bit of bio hacking.

Kiron, A two-headed person born in Bangladesh

Police have been called in to control the crowds after a two-headed baby was born in Bangladesh. More than 150,000 people - almost double the size of the crowds at Wembley Stadium - have surrounded a hospital after news spread that a baby boy had been born with two heads. Police were called in to control the masses as the baby was moved from one hospital to another for security reasons. Officials feared that unless the baby was moved from the clinic in Bangladesh, where he was born, to a more secure hospital, the crowd would force their way in to gaze at the amazing sight.

If that happened, it was feared, mother and baby would be crushed. In the past babies born with physical abnormalities have been viewed in countries such as Bangladesh and India as living gods. Last night the boy, named Kiron, was under police protection as doctors tried to determine whether he had any future. Kiron was born in a caesarean operation on Monday, weighing 5.5kg, in Keshobpur, 100 miles from the capital, Dhaka.

‘He has one stomach and he is eating normally with his two mouths,’ said gynaecologist Mohamad Abdul Bari.  ‘He has one genital organ and a full set of limbs.’ … Dr Bari said the baby developed from one embryo ‘but there was a developmental anomaly.’ … ‘We fear the crowds are going to grow even bigger as word spreads.

‘People are desperate to have a look at this baby. ‘We had to call the police to control the situation at the clinic and now the police are on 24-hour guard at the hospital.’ - dailymail

Kiron, similar to Abby and Britney Hensel, is two distinct people, Dicephalus conjoined twins … but Krion is even more fused. Amazing.  I hope they make it.  Here is some detail on how and when this happens.

Conjoined twinning, however, only arises when the twinning event occurs at about the primitive streak stage of development, at about 13-14 days after fertilisation in the human, and is exclusively associated with the monoamniotic monochorionic type of placentation. It is believed that the highest incidence of conjoined twinning is encountered in the human. While monozygotic twinning may be induced experimentally following exposure to a variety of agents, the mechanism of induction of spontaneous twinning in the human remains unknown. All agents that are capable of acting as a twinning stimulus are teratogenic, and probably act by interfering with the spindle apparatus. - nih

Would it really be an advantage to have two heads? Could one sleep while the other was awake, for example?

The number of birth defects in India is higher than you think…

The fourth annual meeting of World Alliance of Organisations for the Prevention of Birth Defects (WAOPB) was held here today for the first time outside Europe and America. … The world-level genetic scientists who participated in this meet were unanimous that every year, half a million babies with birth defects are born in India. The burden of genetic diseases is high in all countries but it is especially so in India and other developing countries, they observed. - expressindia

The number is lower in the US.

About 3% of U.S. babies — around 120,000 newborns per year — are born with any of 45 types of birth defects, says the CDC. - medscape

Then again, there are over 1.14 billion people in India and only 303 million in the US. The percentage of birth defects is higher in India, perhaps because it is more polluted or has poorer nutrition.  India’s poor has been encouraged to eat rats in one Indian state, Bihar.

Number of birth defects per year / Number of births per year (2008).

44,640 babies are born in India everyday * 365 = 16,365,600 babies in India/yr

(120,000 / 4,318,000) * 100 = 2.78% USA

(500,000 / 16,365,600) * 100 = 3.06 % India

Is this difference “statistically significant”?

Here is a visual comparison of the populations of US and India:

Here is a comparison showing the actual sizes of the land masses.

The population density is much greater in India.

Cats with Wings

While most cats are renowned for having nine lives, these moggies are clearly living on a wing and a prayer. The cute little devils began sprouting bumps on their backs, which later turned into wing-like growths, during a recent spell of hot weather in China’s Sichuan province. … genetic experts claim there is nothing angelic or magical about the condition, which doesn’t hinder the cat’s quality of life. They say the wings can form through poor grooming, a genetic defect or a hereditary skin condition.

Creepy or Cool? Robo-Rat, the first robot controlled by a biological brain

Grazing cattle display animal magnetism

Researchers have explained why cattle will tend to face the same direction when grazing - a behaviour long known to herdsmen and hunters but previously attributed to either prevailing winds or the sun’s position.

In fact, Reuters reports, they align their bodies along a north-south axis, suggesting the Earth’s magnetic field is the “polarizing factor”.

To prove it, Sabine Begall and colleagues at the University of Duisburg-Essen perused 8,510 Google Earth images encompassing 308 pastures and plains worldwide, plus “deer bed” impressions in snow created by around 3,000 deer in over 225 locations in the Czech Republic.

The team found that “whether grazing or resting, these animals face either magnetic north or south”. Since the direction of the wind and sun “varied widely where the images were taken”, it’s reasonable to suggest they’re reacting to the planet’s magnetic influence.

Begall and colleagues reported in the Proceedings of the National Academy of Sciences: “Our results call for an in-depth study of this phenomenon and challenge neuroscientists, biochemists and physicists to study the proximate mechanisms and biological significance of magnetic alignment.”

As Reuters notes, “birds, turtles and salmon are known to use the Earth’s magnetic field to guide their migrations, while rodents and one bat species have been found to possess an internal magnetic compass”. This is the first time, however, that large mammals have shown this kind of animal magnetism.

The team’s report does, though, suggest that humans and whales are “suspected of having an innate magnetic compass”, demonstrated by previous research showing that people who “sleep in an east-west position have far shorter rapid eye movement or REM sleep cycles… compared with north-south sleepers who got more REM sleep” - register