DNA can provide your mugshot — Huh? Wha?

Leaving a hair at a crime scene could one day be as damning as leaving a photograph of your face. Researchers have developed a computer program that can create a crude three-dimensional model of a face from a DNA sample.

Using genes to predict eye and hair colour is relatively easy. But the complex structure of the face makes it more valuable as a forensic tool — and more difficult to connect to genetic variation, says anthropologist Mark Shriver of Pennsylvania State University…who led the work…

Shriver and his colleagues took high-resolution images of the faces of 592 people of mixed European and West African ancestry living in the United States, Brazil and Cape Verde. They used these images to create 3D models, laying a grid of more than 7,000 data points on the surface of the digital face and determining by how much particular points on a given face varied from the average: whether the nose was flatter, for instance, or the cheekbones wider. They had volunteers rate the faces on a scale of masculinity and femininity, as well as on perceived ethnicity.

Next, the authors compared the volunteers’ genomes to identify points at which the DNA differed by a single base, called a single nucleotide polymorphism (SNP). To narrow down the search, they focused on genes thought to be involved in facial development, such as those that shape the head in early embryonic development, and those that are mutated in disorders associated with features such as cleft palate. Then, taking into account the person’s sex and ancestry, they calculated the statistical likelihood that a given SNP was involved in determining a particular facial feature.

This pinpointed 24 SNPs across 20 genes that were significantly associated with facial shape. A computer program the team developed using the data can turn a DNA sequence from an unknown individual into a predictive 3D facial model…Shriver says that the group is now trying to integrate more people and genes, and look at additional traits, such as hair texture and sex-specific differences…

At the moment, such genetic analyses are limited, imprecise. If you think scientists will leave it alone you don’t understand curiosity. If you think someone like the FBI or any other Alphabetoid snoop will leave it alone you don’t understand paranoia.

The blog is on hiatus for a couple of days — UPDATED

Eideard icon

I get to celebrate my birthday, Thursday morning, under the hands of a plastic surgeon specializing in eye repair. Courtesy of age – and my Italian grandma’s genes. 🙂

I won’t be allowed to peer at a computer screen or television for a few days afterwards – and this is not the time for experiments with dictating blog posts to my iMac or iPad.

I should be back by the beginning of next week, Monday, 18 February.

UPDATE: 16/Feb — Peering out from inside this gray head, the surgery appears to have gone well. I can see better, a more complete field of vision than I have had in a number of years. Prognosis from the experts – doctor’s visit next week.

UPDATE: 18/Feb — Eyes appear to be working better than ever. Next Tuesday morning – the 26th – will tell the in-depth medical side of the procedures. And the removal of stitches [ouch].

Meanwhile, I’m resuming a limited schedule of posting – extending back out to all the blogs where I contribute over the next few days.

UPDATE: 26/Feb — Stitches removed this afternoon. I’m happy with progress. The doctor is happy with progress. Complete field of vision – and it will only continue to improve over next few months. The doc is going to use me as his poster child.

Scientists build anew on remains of junk DNA theory

The genetic “control panel” of the human body that regulates the activity of our 23,000 genes has been revealed for the first time in a scientific tour de force that could revolutionise the understanding and treatment of hundreds of diseases.

Scientists have once and for all swept away any notion of “junk DNA” by showing that that the vast majority of the human genome does after all have a vital function by regulating the genes that build and maintain the body.

Junk DNA was a term coined 40 years ago to describe the part of the genome that does not contain any genes, the individual instructions for making the body’s vital proteins. Now, this vast genetic landscape could hold hidden clues to eradicating human disease, scientists said.

Hundreds of researchers from 32 institutes around the world collaborated on the immense effort to decipher the hidden messages within the 98 per cent of the human genome without any genes and was thought, therefore, to have no function.

They have concluded in a series of 30 research papers published simultaneously today, in Nature, Science and other journals, that this so-called junk DNA is in fact an elaborate patchwork of regulatory sequences that act as a huge operating system for controlling the genome

“We see that 80 per cent of the genome is actively doing something. We found that a much bigger part of the genome – a surprising amount in fact – is involved in controlling when and where proteins are produced,” Dr. Ewen Birney said.

Defects in this part of the genome could be responsible for a range of illnesses, from diabetes and Crohn’s disease to disorders of the immune system, such as lupus. Knowing about them could lead to a fundamental reappraisal of what goes wrong in scores of difficult conditons, said John Stamatoyannopoulous of Washington University in Seattle, another leader of the consortium.

Bravo! As happens so often, study and experimentation pries away prominence of a small body of knowledge only to open the door to new studies magnitudes larger and broader. Gonna need more molecular biologists, gang.

Science welcomes Megavirus, the world’s most ginormous virus

There are many weird viruses on this planet, but none weirder–in a fundamentally important way–than a group known as the giant viruses.

For years, they were hiding in plain sight. They were so big – about a hundred times bigger than typical viruses – that scientists mistook them for bacteria. But a close look revealed that they infected amoebae and built new copies of themselves, as all viruses do. And yet, as I point out in A Planet of Viruses, giant viruses certainly straddle the boundary between viruses and cellular life.

Flu viruses may only have ten genes, but giant viruses may have 1,000 or more. When giant viruses invade a host cell, they don’t burst open like other viruses, so that their genes and proteins can disperse to do their different jobs. Instead, they assemble into a “virus factory” that sucks in building blocks and spits out large pieces of future giant viruses. Giant viruses even get infected with their own viruses. People often ask me if I think viruses are alive. If giant viruses aren’t alive, they sure are close.

Ever since giant viruses were first unveiled seven years ago, scientists have argued about the origins of these not-so-wee beasties. Many of their genes are different from those found in cellular life forms, or even other viruses. It’s possible that giant viruses amassed their enormous genetic armamentarium over billions of years, picking up genes from long-extinct host or swapping them with other viruses we have yet to find. Other scientists have suggested that giant viruses started out giant – or even bigger than they are today. Some have even argued that they represent a new domain of life, although others aren’t so sure.

A new study suggests that giant viruses are indeed ancient. It is the work of a team of French researchers led by Jean-Michel Claverie, who went searching for new giant viruses in the waters near a marine biology station in Chile. They found a new kind so different from other giant viruses that they gave it a name of its own: Megavirus.

Carl Zimmer’s blog post is enjoyable – as ever.

RTFA for the methods Claverie’s research crew used to isolate Megavirus. And look forward to the next installment in this adventure.

Paving way for evolution on demand — inorganic biology

Life forms have been created that carry strands of genetic material designed and built from scratch in the lab, paving the way for on-demand “evolution” of organisms.

Scientists made sections of chromosomes, the long molecules that bear DNA, and transferred them into yeast cells, of the kind normally used in baking. The cells adopted the new genetic code as part of their normal cellular machinery and, to the scientists’ surprise, appeared as healthy as their natural counterparts.

The feat is a big step towards the manufacture of completely synthetic organisms that could be designed to churn out biofuels, vaccines and industrial chemicals, said Jef Boeke, who led the study at Johns Hopkins University in Maryland…”We have created a research tool that not only lets us learn more about yeast biology, but also holds out the possibility of someday designing genomes for specific purposes, like making new vaccines or medications”…

Boeke’s work centred on a yeast known as Saccharomyces cerevisiae, one of the most well-understood organisms in the field of genetics. It has 16 chromosomes that together carry around 6000 genes…

Once the first chromosome was finalised, Boeke’s team took a second chromosome and edited that in a similar way.

In the next stage of the experiment, Boeke’s team used feedstocks of chemicals to manufacture the new chromosomes from scratch. They then dropped these into growing colonies of yeast cells, which replaced parts of their natural chromosomes with the synthetic versions.

The yeast cells’ genetic makeover was modest, amounting to changes in only one percent of the organism’s entire genome, but Boeke was still intrigued to see the organisms thrive.

“They are remarkably healthy and to us that’s incredibly exciting because it means our design is sound and we can play all the games we are fantasising about,” Boeke told the Guardian. The study is reported in the journal, Nature…

The process has more practical implications, by allowing scientists to direct the evolution of yeast cells, until they are better than those in use by industry.

Man and yeast have this ancient relationship. We’ve been brewing beer and making bread since before the written word,” said Boeke. “Nowadays, a major share of fermentation is done using yeast, and that’s everything from making vaccines to chemicals and biofuel production.

“All of those industries are actively looking for yeast that makes their favourite product better, whether it’s more efficiently, with a higher yield, or in special conditions.

“Industrial geneticists are always looking for new tools for their toolbox and this will become an important part of that.”

It’s the usual race between public and private universities on one side – and industry on the other. The dialectic of progress crosses forth-and-back between the two. But, with society’s current focus on everything from biofuels to vaccines, the likelihood of successes grows as fast as does the yeast.

As humans evolved – we had sex with all of our relatives!

Our species may have bred with a now extinct lineage of humanity before leaving Africa, scientists say.

Although we modern humans are now the only surviving lineage of humanity, others once roamed the Earth, making their way out of Africa before our species did, including the familiar Neanderthals in West Asia and Europe and the newfound Denisovans in East Asia. Genetic analysis of fossils of these extinct lineages has revealed they once interbred with modern humans, unions that may have endowed our lineage with mutations that protected them as we began expanding across the world about 65,000 years ago.

Now researchers analyzing the human genome find evidence that our species hybridized with a hitherto unknown human lineage even before leaving Africa, with approximately 2 percent of contemporary African DNA perhaps coming from this lineage. In comparison, recent estimates suggest that Neanderthal DNA makes up 1 percent to 4 percent of modern Eurasian genomes and Denisovan DNA makes up 4 percent to 6 percent of modern Melanesian genomes.

“We need to modify the standard model of human origins in which a single population transitioned to the anatomically modern state in isolation — a garden of Eden somewhere in Africa — and replaced all other archaic forms both within Africa and outside Africa without interbreeding,” researcher Michael Hammer, a population geneticist at the University of Arizona in Tucson, told LiveScience. “We now need to consider models in which gene flow occurred over time…”

We think there were probably thousands of interbreeding events,” Hammer said. “It happened relatively extensively and regularly.”

I don’t think the “extensive and regular” part is a surprise either. It may upset some boring, straight-laced and narrow-minded pundits; but, evolution doesn’t pay any attention to ideology.

How genes jump from crop to crop – a new model

Bees do it, humans do it – move genes among crop plants, that is. But until now, researchers and growers had a hard time getting a grip on the factors that determine how much of this gene flow happens in an agricultural landscape.

A new data-driven statistical model that incorporates the surrounding landscape in unprecedented detail describes the transfer of an inserted bacterial gene via pollen and seed dispersal in cotton plants more accurately than previously available methods…

The transfer of genes from genetically modified crop plants is a hotly debated issue. Many consumers are concerned about the possibility of genetic material from transgenic plants mixing with non-transgenic plants on nearby fields. Producers, on the other side, have a strong interest in knowing whether the varieties they are growing are free from unwanted genetic traits.

Up until now, realistic models were lacking that could help growers and legislators assess and predict gene flow between genetically modified and non-genetically modified crops with satisfactory detail.

This study is the first to analyze gene flow of a genetically modified trait at such a comprehensive level. The new approach is likely to improve assessment of the transfer of genes between plants other than cotton as well.

“The most important finding was that gene flow in an agricultural landscape is complex and influenced by many factors that previous field studies have not measured,” said Heuberger. “Our goal was to put a tool in the hands of growers, managers and legislators that allows them to realistically assess the factors that affect gene flow rates and then be able to extrapolate from that and decide how they can manage gene flow.”

Continue reading

U.S. to decide – if we’re allowed to decide – to eat redesigned fish


Two fish the same age. Same-size portions on the dinner plate? No differences.

U.S. health officials are set to rule on whether a faster-growing, genetically engineered fish is safe to eat in a decision that could deliver the first altered animal food to consumers’ dinner plates.

The fish, made by Aqua Bounty Technologies Inc, is manipulated to grow twice as fast as traditional Atlantic salmon, something the company says could boost the nation’s fish sector and reduce pressure on the environment.

But consumer advocates and food safety experts are worried that splicing and dicing fish genes may have the opposite effect, leading to more industrial farming and potential escapes into the wild. Side effects from eating such fish are also unknown, with little data to show it is safe, they say…

There are no data which say, however, that eating these fish is unsafe at all. The rest is pundit-babble.

The small Massachusetts-based biotechnology company is seeking Food and Drug Administration approval to sell its salmon, called AquAdvantage, to fish farmers nationwide.

If given the green light, the salmon could be followed by the company’s engineered trout and tilapia…

“This is an Atlantic salmon in every measurable way,” said Aqua Bounty Chief Executive Ronald Stotish. “When you look at the fish, it’s impossible to see the difference.”

And that’s the kicker. As it is with GM beef or pork – or any other genetically-engineered animal protein that’s moved far enough along towards production to sit on a platter before the FDA.

My enviro brothers and sisters have one serious question to answer before this old political insurgent is convinced to back their fears. Prove to me you can come up with any test which can differentiate between the engineered protein and the stuff swimming past my kinfolk’s farm up on PEI. Let’s cook it and eat it, smell it and taste it, feed it to test animals for several years [again?] and show me where it’s different.

Then, I won’t think you’re wasting my time – and that of a public who could use a break on the cost of good food.

Do bad drivers have bad genes?


Dr. Cramer

Bad drivers may in part have their genes to blame. A recent study found that people with a particular gene variant performed more than 20 percent worse on a driving test than people without it—and a follow-up test a few days later yielded similar results. About 30 percent of Americans have the variant.

These people make more errors from the get-go, and they forget more of what they learned after time away,” says Steven Cramer, University of California, Irvine, neurology associate professor and senior author of the study…

“We wanted to study motor behavior, something more complex than finger-tapping,” says Stephanie McHughen, graduate student and lead author of the study. “Driving seemed like a good choice because it has a learning curve and it’s something most people know how to do.”

The driving test was taken by 29 people—22 without the gene variant and seven with it. They were asked to drive 15 laps on a simulator that required them to learn the nuances of a track programmed to have difficult curves and turns. Researchers recorded how well they stayed on the course over time. Four days later, the test was repeated.

Results showed that people with the variant did worse on both tests than the other participants, and they remembered less the second time. “Behavior derives from dozens and dozens of neurophysiologic events, so it’s somewhat surprising this exercise bore fruit,” Cramer says…

A test to determine whether someone has the gene variant is not commercially available.

“I’d be curious to know the genetics of people who get into car crashes,” Cramer says. “I wonder if the accident rate is higher for drivers with the variant.”

Ooh! I know a few people who absolutely would be caught out in a test like this. It explains a lot.

Gene-related heart disease on the rise in India


Daylife/AP Photo

Hindu priest Pandjitee is not overweight, does not smoke or drink and follows a strict vegetarian diet. Yet three years ago he was suddenly struck by a heart attack.

Pandjitee is among a growing number of Indians who are at risk of heart disease because of a genetic mutation that affects one in 25 people in India. The mutation almost guarantees the development of the disease and Indians suffer heart attacks at an earlier age, often without prior symptoms or warning.

Now researchers say India, a country with more than one billion people, will likely account for 60 per cent of heart disease patients worldwide, by 2010.

A study among Asian Indian men showed that half of all heart attacks in this population occur under the age of 50 years and 25 percent under the age of 40, according to the Indian organization, Medwin Heart Foundation…

The major causes of heart disease are tobacco use, physical inactivity, and an unhealthy diet often linked to the developed world.

So in a country that traditionally frowns upon smoking and embraces the idea of a vegetarian diet, it was unexpected to find such a high percentage of the disease.

Fair amount of detail in the article. Enough to get you thinking about extra caution if you are Indian.

Presses me to reflect upon the number of illnesses our species experiences now that we live longer. In prehistory, or even before the advent of modern medicine and medical technology increasing lifespan – many illnesses weren’t significant in how they affected the whole population.