'Junk DNA' has a purpose, new map of human genome reveals

Vast sections of the human genome that were previously thought to have no useful function and were dismissed as "junk DNA" are in fact involved in key biochemical processes, an international team has found.
The five-year Encyclopedia of DNA Elements, or ENCODE, project has attempted to catalogue the bulk of genetic material that does not fall under the category of protein-coding genes, the building blocks necessary for life that comprise only two per cent of the human genome.
The results of their efforts, published Wednesday in a series of papers in the journals Nature, Genome Research and Genome Biology, are being widely seen as the most significant contribution to understanding the human genome since the last sequence was completed in 2003.

Genes only a tiny part of genome

Genes make up only about two per cent of the human genome and have been well catalogued as part of the Human Genome Project begun in the 1990s, but little has been known about the purpose of the other 98 per cent.

"During the early debates about the Human Genome Project, researchers had predicted that only a few per cent of the human genome sequence encoded proteins, the workhorses of the cell, and that the rest was junk. We now know that this conclusion was wrong," said Eric D. Green, director of the National Human Genome Research Institute in Bethesda, Md., a part of the National Institutes of Health, which funded the ENCODE project to the tune of $288 million since 2003.
"ENCODE has revealed that most of the human genome is involved in the complex molecular choreography required for converting genetic information into living cells and organisms."
The effort to identify the functions of the genetic material that lies between the roughly 20,000 protein-coding genes involved hundreds of scientists at dozens of institutions in the U.S., U.K., Japan, Singapore and Spain.

DNA 'switches' regulate genes

The researchers found that about 80 per cent of the human genome has at least one biochemical activity associated with it. Much of that activity consists of telling protein-coding genes when and where in the body they should turn on and off.
About 18 per cent of DNA is involved in regulating protein-coding genes.
"Every cell in the body has the same genes, but different kinds of cells, such as liver or heart, switch on different combinations of genes," said John A. Stamatoyannopoulos, professor of genome sciences and medicine at the University of Washington who worked on the ENCODE project, in a press release.

"When cells become unhealthy, these combinations change. Understanding how genes turn on and off is therefore vital to deciphering their role in both normal health and disease.
"The instructions for how genes are controlled are contained in small DNA 'switches' that are scattered around the 98 per cent of the genome that does not contain genes. Mapping and decoding these instructions is a central mission of the ENCODE project."
The researchers located more than four million of these DNA 'switches,' information that should help scientists better understand how to prevent, diagnose and treat disease.
To help them understand the relationship between disease-associated genetic changes and the gene-controlling switches scattered around the genome, the researchers collected DNA maps from 349 tissue samples covering all major organ systems in adults and all stages of human development and compared them against genetic studies of more than 400 common diseases and clinical traits.
"They found that most disease-associated genetic changes occurred within gene-regulating switches, often located far away from the genes they control," a University of Washington press release said. "Most changes affected circuits active during early human development, when body tissues are most vulnerable."

Database publicly available online

The ENCODE scientists made their data publicly available in a vast database that has been posted on the ENCODE project portal as well as on the websites of the University of California, Santa Cruz Genome Browser, the National Center for Biotechnology Information, and the European Bioinformatics Institute.

'The ENCODE catalogue is like Google Maps for the human genome.'— Elise Feingold, National Human Genome Research Institute

The journal Nature diverged from its usual practice and presented the findings of the six core papers published by the ENCODE consortium as a series of thematic threads accessible through an interactive online "ENCODE Explorer."
Another 24 associated papers that came out of the research appeared in the journals Genome Research and Genome Biology.
"The ENCODE catalogue is like Google Maps for the human genome," said Elise Feingold, a program director at the National Human Genome Research Institute who helped start the ENCODE Project, in a news release.
"Simply by selecting the magnification in Google Maps, you can see countries, states, cities, streets, even individual intersections, and by selecting different features, you can get directions, see street names and photos, and get information about traffic and even weather.
"The ENCODE maps allow researchers to inspect the chromosomes, genes, functional elements and individual nucleotides in the human genome in much the same way."

Scientific explanation of psychopathy cuts jail time

Serial sex offender Raymond Henry Garland, considered one of Australia's most dangerous sexual predators, was officially diagnosed a psychopath last week. Psychiatrist Joan Lawrence told the Brisbane District Court that Garland had an "almost 100 per cent chance of violent reoffending." Garland has been dealt four indefinite sentences – but research out today suggests that biological evidence of psychopathy could alter the length of such sentences.

Brain scans and genetic tests are becoming a common feature of courtroom battles, as biological evidence is increasingly used to explain a person's criminal behaviour. For example, last year an Italian woman convicted of murdering her sister had her lifetime sentence reduced to 20 years on the basis of brain and genetic tests, which provided biological explanations for her aggressive behaviour.

But does the inclusion of such evidence affect the sentencing of psychopaths – people with a disorder currently thought to be untreatable? Any evidence could act as a double-edged sword, says James Tabery at the University of Utah. A so-called biomechanism to explain psychopathic behaviour could be used to argue that a person is less culpable for their actions, reducing their sentence. On the other hand, the defendant could be seen as more likely to reoffend and receive a longer sentence.

Testing the sword

To find out "which way the sword was going to cut", Tabery, together with psychologist Lisa Aspinwall and law professor Teneille Brown, also at Utah, sent out a survey to 181 US judges based in a number of different states.

Each judge was asked to sentence a convicted criminal diagnosed as a psychopath. The team's fictional character was based on Stephen Mobley, who robbed and then killed a Domino's pizza store manager in 1991. Mobley went on to brag about the crime, and even got the word "Domino" tattooed on his back. Psychologists claimed that his behaviour and lack of remorse was psychopathic and untreatable. At the time, Mobley's request to submit a genetic-based defence for his behaviour was denied, says Tabery. "The Georgia State Supreme Court said [genetic evidence] wouldn't have made any difference," he says. "He was sentenced to death."

In Tabery's fictional case, a man was found guilty of the similar crime of aggravated battery, although the victim was not killed but left with permanent brain damage. The criminal was diagnosed as a psychopath by a psychiatrist. Half of the judges were given additional evidence from a second psychiatrist, who said that the man's behaviour was the result of a genetic mutation that caused a structural abnormality in his brain. Half of each group of judges received the diagnosis as a form of defence, pleading the man's lack of control and culpability over his actions. The other judges saw the diagnosis as part of a prosecution which argued that the man was likely to reoffend.

Shorter sentences

Without a diagnosis, the judges surveyed said they would have given the man a sentence of about nine years. Once he had been diagnosed as an untreatable psychopath, however, the average sentence jumped to 14 years. When judges were presented with biological evidence of the genetic mutation, this sentence was lowered to around 13 years, regardless of whether the evidence was presented by the prosecution or defence.

"We saw both sides of the double-edged sword in play," says Tabery. "The addition of a biological mechanism slightly reduces the sentence compared to just the diagnosis of psychopathy, but it's still significantly higher than what judges said their average sentences are for aggravated battery."

Stephen Morse, professor of law and psychiatry at the University of Pennsylvania in Philadelphia, says that the issue of free will in responsibility for one's actions should be "beside the point" in a court room. "Having free will or not having it is not part of any legal doctrine, and needs never be proven or disproven."

But if biological evidence can swing sentences, should all psychopaths be given the option to include brain scans and genetic tests in their defence? Or should the use of such evidence be ruled out entirely? "Different states and different judges vary in how they process this information," says Tabery.

Morse thinks this variation is a real problem in the criminal justice system. "It's usually up to the judge to decide what factors to balance at sentence, how they should be weighed and what evidence to consider, and that results in very varied sentencing," he says. "I think there should be less discretion involved in sentencing, although judges hate the idea."

Journal reference: Science, DOI: 10.1126/science.1219569

Gaze-tracking illusion lets you draw with your eyes

IMAGINE drawing or writing on a screen with just your eyes. That's what a novel gaze-tracking software promises to do for people with locked-in syndrome.

Existing eye-writing systems involve focusing on a letter then blinking to select it. Moving your eyes smoothly enough to trace out words is hard because your eyes constantly make jerky motions known as saccades, unless you are tracking a moving object.

Jean Lorenceau at the Pierre and Marie Curie University in Paris, France, has found a way to fool your eyes into making smooth movements by using an optical illusion called "reverse phi motion".

Phi motion is the effect that turns a series of still photos into a movie, but reverse phi motion is weirder. Take a film of a moving white dot then turn the dot in every other frame black. The film will appear to run backwards. Lorenceau's system manipulates the illusion to trick you into thinking you are moving a dot around the screen with your eyes, so the motion is smooth. A gaze-tracking camera follows the right eye's movements to control a cursor on the screen. This lets you trace out numbers, letters or drawings. "It's like surfing, you move your eyes to get on the wave and once you're on you just slide with it," Lorenceau says.

Is this Richard III, England's last Plantagenet king?

What exactly has been found?
The body of an adult male has been excavated from what is believed to be ruins of the choir area of the Grey Friars church in Leicester. It's now a car park in the city centre, but was used as a church in the late 15th century. Some records suggest that Richard III, the last Plantagenet king of England, was buried here.

So how do we know it's him? Has the body got a hunched back?
We don't know it's him – yet – but yes, the skeleton does show signs of spinal curvature. Contemporary accounts, reinforced later by Shakespeare, described Richard III as being "hunchbacked". The newly found body appears to have scoliosis, a form of spinal curvature that would have made the man's right shoulder appear higher than the left shoulder. The classic "hunchback" is caused by kyphosis but there is no evidence of this in the Leicester skeleton.

Any other evidence?
Yes. The man who became this skeleton took a beating. He has a small penetrating wound to the top of the head, and a much larger wound where a slice has been cut off the skull at the side and back – consistent with the swing of a blade. On 22 August 1485, Richard III was killed at the Battle of Bosworth Field by blows that some accounts describe as being so violent they drove his helmet into his head.

The Leicester skeleton also has a barbed iron arrowhead stuck in its upper back. But the middle ages were violent times, so again this is only supporting evidence.

Can DNA testing determine if the body is Richard III?
Perhaps. The Richard III Society says it has located someone – Londoner Michael Ibsen – who is apparently the 17th great grand-nephew of Richard III, in the female line. Ibsen's late mother Joy Ibsen is purportedly a direct descendent of the King's eldest sister, Anne. Richard's male relatives were executed.

Leicester University geneticists hope to extract mitochondrial DNA taken from the skeleton's teeth and compare it with DNA from Ibsen. Mitochondrial DNA is transmitted only through the female line, so if Ibsen really is a direct descendent, his mtDNA can be compared with that from the skeleton.

Mitochondrial DNA is present in thousands of copies per cell, so is easier to extract from degraded tissue than nuclear DNA, which is only present in one copy, in the nucleus. MtDNA was used, for example, to identify the remains of Jesse James, the 19th century American outlaw. But in that case, the living maternal relatives were a great grandson and great-great grandson. With Richard III, many more generations have passed, so the challenges are that much greater.

How can we be sure Joy Ibsen is a direct descendent?
This is one of the shakiest parts of the project, relying as it does on historical records stretching back hundreds of years. The family tree linking Ibsen with Richard III's sister was made by historian John Ashdown-Hill. Kevin Schürer at Leicester University is leading the team assessing the historical evidence to try and corroborate Ibsen's genealogy.

"It's prudent to have a second set of eyes go over the tree and to use other historical data to try and verify it," says geneticist Turi King at Leicester University, who is working on extracting the ancient DNA. Until we know how much mtDNA we can get out of the skeleton, we won't know whether we can say if it is related to Michael Ibsen or not.

Apple's iPhone 5 hits right buttons, but lacks surprises

The iPhone 5 is on display after its introduction during Apple Inc.'s iPhone media event in San Francisco Wednesday. It was designed to be thinner than the current 4S model, with a taller screen, but several other new features on the iPhone are already on other smartphones. (Beck Diefenbach/Reuters)
It may have been the worst kept secret in technology history. So much so that when the iPhone 5 finally made its debut on Wednesday in San Francisco, many observers were disappointed because there were no surprises.
The much-ballyhooed device — on sale in Canada through Bell, Rogers, Telus and their sub-brands on Sept. 21 — is packed with everything that was expected: a four-inch screen that's half an inch bigger than its predecessors and slightly sharper, an A6 processor that's twice as fast as the iPhone 4S, and long-term evolution (LTE) cellular connectivity that will make for much zippier downloads.
It's also got a slightly better camera that can now take panoramic photos, and it's thinner and lighter too — about 20 per cent less weighty than the 4S.
On the software side, the iPhone 5 will have better email organization, FaceTime video calling over cellular connections, easy photo stream sharing, a new Maps app and a nifty folder called Passbook, where all sorts of electronic tickets, boarding passes and coupons can be stored.

All told, virtually every specification and feature had been leaked, pieced together by tech detectives or shared by Apple prior to the event. So why the disappointment?

Victim of its own success

Apple has, in many ways, become a victim of its own success. Over the past five years since the launch of the original iPhone, it has grown into the biggest company in the world by market capitalization. Its product launches are thus the most heavily scrutinized — and hyped — events in the technology world.
With each successive event, onlookers grow increasingly curious as to whether the company will again hit a home run, or whether there will be signs that its golden touch might finally be running out, like it eventually has to. Against that backdrop, it's difficult to surprise people.
In some ways, the iPhone 5 is playing catch-up. Some of its capabilities are already found in other phones that have been on the market for months. Several Android devices, for example, do panoramic photos and run on LTE networks.
Other devices are using near-field communication, a wireless technology that lets ph
ones share photos or make mobile payments simply by touching them to a sensor. Apple obviously decided to forego NFC with this version, but that’s evidence that the infrastructure for mobile payments is not yet sufficiently developed, according to Forrester Research analysts Frank Gillett.

"[Apple] are very well positioned to break records come February when they announce what happened during the Christmas season. My vote is it will do very well."—Kaan Yigit, president of Solutions Research Group

When mobile payments start to gain traction, as they could over the next year, Apple will then add the capability, he added. It's a wait-and-see approach.
So, will consumers rush to snap up the iPhone 5, despite the lack of surprises? Many analysts believe so. One report earlier this week suggested the new gadget could singlehandedly boost the U.S. economy.

3.6 million iPhones in Canada

According to Toronto-based tracking firm Solutions Research Group, there are approximately 3.6 million iPhones in circulation in Canada, accounting for about a third of all smartphones. Over the next 12 months, the company expects about 1.5 million new iPhone users to come into the fold, the vast majority of whom will be buying the latest device.
Based on surveys gauging buying intent, this coming Christmas period is going to be the biggest season for smartphones in some time.
"[Apple] are very well positioned to break records come February when they announce what happened during the Christmas season," says Solutions Research Group president Kaan Yigit. "My vote is it will do very well."
So what exactly is it about the iPhone 5 that will have people lining up? After spending some time with the new device at a hands-on session after the press conference, it's clear that its weight — or, more specifically, lack thereof — will be a big selling point. The new phone is touted as being 20 per cent lighter than the 4S, but when holding the two at the same time, it's easy to think it's even lighter than that.
The main material is now anodized aluminum, with a lot less glass involved, which takes away a lot of the heft. The A6 processor is also smaller than its predecessor, so that's also saving weight.
Other than that, the iPhone 5 represents a series of incremental improvements. There's nothing earth-shattering, which is disappointing to those who want to be surprised, but it’s evidently going to be enough for the millions of consumers looking for a new phone.

How Facebook can help hide your identity

When you think of privacy protection, chances are Facebook does not immediately spring to mind. But anonymity researchers are suggesting that social networks may hold the key to better anonymous online interactions.
Existing anonymity tools, such as Tor, work by routing a user's internet traffic through a random chain of other computers called a circuit. Any one individual computer in this circuit can only ever see information about the machine one place ahead of it or one place behind it. This mechanism keeps the originator of the request anonymous: online activities very quickly become divorced from their source. Information that was put into the circuit from one machine comes out into the internet from an entirely different machine, with no way to trace a path back to the originator. That's the theory, anyway.
In reality, however, tracing the originator is fairly simple. To reverse-engineer the identity of a person through the anonymisation network, all an interested organisation needs to do is place a large number of its own machines into the anonymisation chain. The data then can then be pieced together to reveal the source. This is known as a Sybil attack.
That's a problem because while Tor is often used for illegal file sharing, online anonymity has been crucial - for example, in allowing secure communication during the Arab Spring.
To thwart eavesdroppers, researchers from the University of Texas, the University of California, Berkeley, and the University of Illinois at Urbana-Champaign took advantage of a unique property of Facebook: its ability to connect you to friends. Their system, called Pisces, uses graphs of social network connections to make sure that only trusted nodes are used to make the random circuit, providing a safe route to the internet that excludes snooper nodes.
Pisces's reliance on social connections does confer some disadvantages. First, it won't work for users without a reasonably wide social network. It also requires users' social contacts to participate, although the researchers are trying to use friends-of-friends in the trust network to improve both of these issues.
"The incorporation of social trust will likely be an important consideration in the design of the next generation of deployed anonymity systems," the researchers say.

Journal reference: arXiv: 1208.6326v1

Paying for healthcare benefits only the rich with the new OBAMACARE

TALK about a flip-flop. Having initially promised to reverse it, Republican nominee Mitt Romney now says that if he wins the presidency, he will retain some elements of "ObamaCare".

Romney may find some clues on what to keep in The Lancet, which last week published research showing that having all Americans take out health insurance is the only way to get a healthcare system that truly benefits everyone (doi.org/jbv).

In countries such as China, Vietnam, the Philippines, India and Ghana, up to half of all costs are paid "out of pocket", that is, directly at the time of treatment. Data from 120 countries, cited in another paper (doi.org/jbw), showed that for each 10 per cent increase in government health expenditure per head, 5 per cent fewer women die in childbirth. But for each extra 10 per cent paid out of pocket, there were 11 more deaths per 1000 women.

The key to effective universal healthcare is to have pooled finances, through either direct taxation related to income or mandatory insurance, says Bill Savedoff of the Center for Global Development in Washington DC, lead author of one of the papers. "If everyone pays out of pocket, the rich get the care they want but the poor don't," he says. "When you combine people's payments into a pool, you start to be able to manage care for whole populations."

Sexually frustrated queens become commoners

Species: Acromyrmex echinatior
Habitat: Casually swapping lifestyles in wild areas from Mexico to Panama

There are few things more galling than finding oneself in reduced circumstances. If you grow up wealthy and privileged, it's awful to suddenly be on the breadline, your only source of amusement being a constant stream of cheap jokes about racial stereotypes. Someone even made a TV show about it.

If you're in that situation, console yourself with the knowledge that it could be worse – your fellows might have written you off as a waste of space and decided to kill you. That's what usually happens to ant queens that don't manage to leave their home colony.

Callous as this behaviour might seem, it makes evolutionary sense. Ant queens are only good for one thing – making more ants – so if they're not doing it the colony has no use for them. But the failed queens of one species have found a way to live out their lives: as humble workers.

Ant farms

Acromyrmex echinatior ants live in one of the most complex societies on Earth. They are leaf-cutter ants: they collect huge volumes of leaves from the area around their nest, and cultivate a special fungus on them. The ants eat the fungus and nothing else. Leaf-cutter colonies often have several different worker castes: the larger ones collect the leaves and the smaller ones tend the fungal gardens.

Like honeybees, some termites and the famous naked mole rats, leaf-cutters are eusocial. In each colony only one female, the queen, reproduces. All the workers are sterile and work to preserve the colony. At first glance it seems like the workers have a raw deal, but because they are all closely related they are actually preserving their own genes.

Once a colony is established, it starts producing new queens. Their destiny is to leave the colony, find a male and mate with him, then found a new colony.

In most eusocial species, being a queen is a make-or-break existence. You either leave to start a new colony, or you die. The queen's body contains valuable nutrients: if they're not being used, she will put her genes to best use by giving the nutrients back to the colony.

Working girls

But not in colonies of A. echinatior, or the closely related A. octospinosus. Watching colonies in the wild, Volker Nehring of the University of Freiburg in Germany noticed several unmated queens living seemingly untroubled alongside the main queen.

Wondering what the virgin queens were getting up to, Nehring captured some newly-hatched queens and removed their wings, preventing them from leaving on their mating flights. The grounded queens began behaving like workers, taking care of larvae and attacking ants from other colonies. A. echinatior colonies don't have soldiers, and queens are bigger than workers so they are better than them at seeing off intruders.

The queens of other eusocial ants have lost the ability to behave like workers, so they can't adapt under such straitened circumstances. However, A. echinatior queens have retained their worker skills because they take an active role in setting up their own colonies.

While the virgin queens may only stay on sufferance, Nehring thinks they are quite safe from the other workers. Because leaf-cutter ants only eat fungus, they may have lost the ability to digest other foods. As a result, the workers probably couldn't eat the virgin queens even if they tried.

Journal reference: Current Biology, doi.org/jcc

Latest Smartphones

Latest mobiles

At a time when almost all telecom companies are vying for a better hold in the smartphone market, new smartphone handsets have been launched in the market keeping in mind the performance and luxury in mind. Here, we bring you some of the smartphones that have been launched lately.

Samsung ATIV S

*4.8" HD Super AMOLED display
*1GB of RAM
*16GB or 32GB of storage plus (7GB skydrive)
*Windows 8 OS
*8 MP camera with 1080p video at 30 fps; 1.9 MP front
*2,300mAh battery
*NFC and LTE connectivity
*Bluetooth
*USB
*Wi-Fi
*weighs 135g

Nokia Lumia 920

*Windows 8 OS
*4.5" 720p PureMotionHD+ display (curved glass)
*1.5GHz dual-core Krait processor
*Adreno 225 GPU with 1GB RAM
*PureMotion HD+ (screen color and brightness will adjusts automatically, depending on the ambient light)
*8 megapixel Carl Zeiss with image stabilisation
*1080p video recording (LED Flash)
*NFC and LTE connectivity
*32GB internal memory (+7GB SkyDrive cloud storage)
*USB
*Wi-Fi
*2,000 mAh battery
*weight 185 grams
*micro-SIM cards
*lacks memory expansion slot
*Wireless charging

Nokia Lumia 820

*4.3" AMOLED display of WVGA resolution
*Windows 8 OS
*1.5GHz Krait processor and 1GB of RAM
*1650mAh battery
*USB
*Wi-Fi
*Fatboy pillow charging (Wireless)
*8GB of built-in storage expanable (and 7GB of SkyDrive cloud storage)
*Carl Zeiss lens and an 8MP sensor
*LTE connectivity
*NFC-based features
*weighs 160gms

Motorola RAZR HD

*4.7" edge-to-edge Super AMOLED display (720p resolution)
*8 MP camera with 1080p video recording and LED flash
*Android 4.0 Ice Cream Sandwich (upgradable to Jelly Bean)
*1GB RAM and Adreno 225 GPU
*Pre-installed Chrome
*USB
*Wi-Fi
*2,530mAh battery (16 hrs talk time)
*weighs 146 gms

Motorola DROID RAZR MAXX HD

*3,300mAh battery (21 hrs talktime, 27 hours music streaming, 10 hours video streaming)
*weighs 157 gms
*NFC connectivity
*USB
*dual-band Wi-Fi
*Bluetooth 4.0
*HDMI port
*16GB of built-in memory