EvoDevo: Graph Computer Genetics

Your Laptop Can Now Analyze Big Data

New software makes it possible to do in minutes on a small computer what used to be done by large clusters of computers.

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JOHN PAVLUS

Tuesday, July 17, 2012

Maximilian Bode

Computer scientists from Carnegie Mellon University have devised a framework for running large-scale computations for tasks such as social network or Web search analysis efficiently on a single personal computer.

The software could help developers working on many modern tasks: for example, designing a new recommendation engine using social network connections. In order to make effective recommendations—"your friends liked this movie, so here is another movie that you haven't seen yet, but you will probably like"—the software has to be able to analyze the connections between the members of a social network. This type of task is called graph computation, and it is increasingly common. But working with large-scale data sets (such as online social networks) usually requires the processing horsepower of many computers clustered together, such as those offered by Amazon's cloud-based EC2 service.

The new software, called GraphChi, exploits the capacious hard drives that are becoming ever more common in personal computers. A graph would normally be stored in temporary memory (RAM) for analysis. With GraphChi, the hard drive performs this task instead.

"PCs don't have enough RAM to hold an entire Web graph, but they do have hard drives, which can hold a lot of information," says Carlos Guestrin, codirector of Carnegie Mellon's Select Lab, where GraphChi was developed. But hard drives are slow compared to RAM for reading and writing data, which tends to slow down computation. So Guestrin's student Aapo Kyrola designed a faster, less random method of accessing the hard drive.

According to Guestrin, a Mac Mini running GraphChi can analyze Twitter's social graph from 2010—which contains 40 million users and 1.2 billion connections—in 59 minutes. "The previous published result on this problem took 400 minutes using a cluster of about 1,000 computers," Guestrin says.

As technology gets more networked, and data sets get larger, graph computation is becoming more and more relevant in many domains, says David A. Bader, a graph computation expert at Georgia Tech. "Trying to understand how the human brain works or trying to make sense of medical patient records involve graph computing," he says.

Graph analysis also drives the development of new web products, says Jeremy Kepner, a researcher at MIT. "Document search, ad placement, route planning, travel reservations, and cyber security all rely on graph analysis," he says. "Enabling web developers to construct these analyses on their desktop computers catalyzes these industries and accelerates product development."

Guestrin adds that GraphChi can handle "streaming graphs," which more accurately model large networks by showing how relationships change over time. Bader and others at Georgia Tech have created a graph computation framework, called Stinger, that's optimized for supercomputers working with massive streaming graphs.

"The scales of these problems will obviously keep growing," says Guestrin. But he says GraphChi is capable of effectively handling many large-scale graph-computing problems without resorting to cloud-based solutions or supercomputers.

"A researcher in computational biology could do large-scale computations on their PC; a developer working on a data-center algorithm can test it on their laptop before pushing it to the cloud," Guestrin says. "Big data is everywhere now, but some big data isn't as big as it once was, relatively speaking. Tools like GraphChi will let many companies and startups solve all their graph-computing needs on a single machine. It's cost effective, and it drives innovation, too."

Ecology of Disease

http://www.nytimes.com/2012/07/15/sunday-review/the-ecology-of-disease.html?ref=science

The Ecology of Disease

Olaf Hajek

By JIM ROBBINS

Published: July 14, 2012 114 Comments

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THERE’S a term biologists and economists use these days — ecosystem services — which refers to the many ways nature supports the human endeavor. Forests filter the water we drink, for example, and birds and bees pollinate crops, both of which have substantial economic as well as biological value.

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If we fail to understand and take care of the natural world, it can cause a breakdown of these systems and come back to haunt us in ways we know little about. A critical example is a developing model of infectious disease that shows that most epidemics — AIDS, Ebola, West Nile, SARS, Lyme disease and hundreds more that have occurred over the last several decades — don’t just happen. They are a result of things people do to nature.

Disease, it turns out, is largely an environmental issue. Sixty percent of emerging infectious diseases that affect humans are zoonotic — they originate in animals. And more than two-thirds of those originate in wildlife.

Teams of veterinarians and conservation biologists are in the midst of a global effort with medical doctors and epidemiologists to understand the “ecology of disease.” It is part of a project called Predict, which is financed by the United States Agency for International Development. Experts are trying to figure out, based on how people alter the landscape — with a new farm or road, for example — where the next diseases are likely to spill over into humans and how to spot them when they do emerge, before they can spread. They are gathering blood, saliva and other samples from high-risk wildlife species to create a library of viruses so that if one does infect humans, it can be more quickly identified. And they are studying ways of managing forests, wildlife and livestock to prevent diseases from leaving the woods and becoming the next pandemic.

It isn’t only a public health issue, but an economic one. The World Bank has estimated that a severe influenza pandemic, for example, could cost the world economy $3 trillion.

The problem is exacerbated by how livestock are kept in poor countries, which can magnify diseases borne by wild animals. A study released earlier this month by the International Livestock Research Institute found that more than two million people a year are killed by diseases that spread to humans from wild and domestic animals.

The Nipah virus in South Asia, and the closely related Hendra virus in Australia, both in the genus of henipah viruses, are the most urgent examples of how disrupting an ecosystem can cause disease. The viruses originated with flying foxes, Pteropus vampyrus, also known as fruit bats. They are messy eaters, no small matter in this scenario. They often hang upside down, looking like Dracula wrapped tightly in their membranous wings, and eat fruit by masticating the pulp and then spitting out the juices and seeds.

The bats have evolved with henipah over millions of years, and because of this co-evolution, they experience little more from it than the fruit bat equivalent of a cold. But once the virus breaks out of the bats and into species that haven’t evolved with it, a horror show can occur, as one did in 1999 in rural Malaysia. It is likely that a bat dropped a piece of chewed fruit into a piggery in a forest. The pigs became infected with the virus, and amplified it, and it jumped to humans. It was startling in its lethality. Out of 276 people infected in Malaysia, 106 died, and many others suffered permanent and crippling neurological disorders. There is no cure or vaccine. Since then there have been 12 smaller outbreaks in South Asia.

In Australia, where four people and dozens of horses have died of Hendra, the scenario was different: suburbanization lured infected bats that were once forest-dwellers into backyards and pastures. If a henipah virus evolves to be transmitted readily through casual contact, the concern is that it could leave the jungle and spread throughout Asia or the world. “Nipah is spilling over, and we are observing these small clusters of cases — and it’s a matter of time that the right strain will come along and efficiently spread among people,” says Jonathan Epstein, a veterinarian with EcoHealth Alliance, a New York-based organization that studies the ecological causes of disease.

That’s why experts say it’s critical to understand underlying causes. “Any emerging disease in the last 30 or 40 years has come about as a result of encroachment into wild lands and changes in demography,” says Peter Daszak, a disease ecologist and the president of EcoHealth.

Emerging infectious diseases are either new types of pathogens or old ones that have mutated to become novel, as the flu does every year. AIDS, for example, crossed into humans from chimpanzees in the 1920s when bush-meat hunters in Africa killed and butchered them.

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Jim Robbins is a frequent contributor to the Science section of The New York Times.

Using Genetic Codes to Detect and Trace Food Poisoning

Harnessing Gene Codes as Sleuths of Food Ills

By SABRINA TAVERNISE

Published: July 12, 2012

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WASHINGTON — A new public database aims to catalog the genetic codes of 100,000 types of bacteria found in food, vastly increasing the amount of data that scientists can use to trace the causes of food-borne illness.

The free database, being set up at the University of California, Davis, will enable scientists to pinpoint not only what food carries the bacteria responsible for a given outbreak — raw tuna in sushi, for example — but also what country it came from. And while responses to such outbreaks have typically taken weeks, the new database is expected to reduce that to days.

“It’s actually a big deal from a scientific standpoint,” said Steven M. Musser, the Food and Drug Administration official who announced plans for the database on Thursday.

Genetic sequencing is new. To date scientists have identified as many as 3,000 sequences, and only about 1,000 are related to food.

The Centers for Disease Control and Prevention has the largest such database, but the gene maps it contains are only partial, not enough to determine which food the illness came from or its geographic origin, said Dr. Musser, director of the office of regulatory science at the F.D.A.’s Center for Food Safety and Applied Nutrition.

Cataloging gene codes is time-consuming. Salmonella alone has about 2,700 different strains, almost three times as many as all the sequences for food-borne bacteria that have been cataloged to date. Dr. Musser said his laboratory had cataloged just 500 in about three years of work. It is contributing those sequences to the project, all related to salmonella.

But the database, which includes contributions from the disease centers and from the biotechnology company Agilent Technologies, aims to have mapped 100,000 sequences in five years, making it the single largest genome project in the world, said Bart C. Weimer, a professor of microbiology at U.C. Davis who is directing the project.

The cost of such work has dropped sharply in recent years, he said, but having enough people trained to sort through all the data was the main concern.

The first sequencing started in March, Dr. Weimer said, shortly after researchers at the F.D.A. and at the university realized they were working simultaneously on similar things and decided to join forces.

“You need a big volume of information to make an impact in the public health arena,” he said. “That improves accuracy and the capability of doing things fast.”

A version of this article appeared in print on July 13, 2012, on page A10 of the New York edition with the headline: Harnessing Gene Codes As Sleuths Of Food Ills.

Salmon Genetically changing

OBSERVATORY

Alaskan Salmon Evolve Along With the Climate

By NICHOLAS BAKALAR

Published: July 16, 2012

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Alaskan salmon are apparently evolving to adapt to climate change.

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Chris Gash

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Researchers have suspected that temperature-driven changes in migration and reproduction behaviors — which have happened in many species — may be evidence of natural selection at work. Now there is genetic evidence to confirm the hypothesis.

For their study, published online last week in Proceedings of the Royal Society B, the scientists studied Alaska pink salmon in a small stream near Juneau where there have been complete daily counts of all adult fish since 1971.

The salmon migrated in two distinct populations, one appearing toward the end of August, the other starting in September. In 1979, scientists introduced a neutral genetic marker into the later-migrating population so it could be identified and tracked without affecting its fitness.

In the 1980s, the genetically marked late migrators made up about a third of the population. But as streams started warming earlier in the year, the proportion began to decrease rapidly — to just 5 percent by 2011 — even though overall abundance did not change.

These were rapid changes, not gradual evolutionary shifts. The late-migrating fish practically disappeared within a few years.

“It’s sort of reassuring that organisms have the potential to adapt to the really major changes that are occurring,” said the lead author, Ryan P. Kovach, a doctoral student at the University of Alaska, Fairbanks. “But the fact that climate change is already forcing evolutionary changes should be raising red flags for resource managers and the general public alike.”

GMO Apples that never brown up-NYT

That Fresh Look, Genetically Buffed

By ANDREW POLLACK

Published: July 12, 2012 239 Comments

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A small company is trying to bring to market a genetically engineered apple that does not turn brown when sliced or bruised. But it has much of the rest of the apple industry seeing red.

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James Best Jr./The New York Times

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Okanagan Specialty Fruits

Conventional slices alongside nonbrowning Arctic Apples.

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The company, Okanagan Specialty Fruits, says the nonbrowning apple will prove popular with consumers and food service companies and help increase sales of apples, in part by making sliced apples more attractive to serve or sell.

While Americans have been eatinggenetically engineered foods since the 1990s, those have been mainly processed foods. The Arctic Apple, as it is being called, could become one of the first genetically engineered versions of a fruit that people directly bite into.

But the U.S. Apple Association, which represents the American apple industry, opposes introduction of the product, as do some other industry organizations. They say that, while they do not believe that the genetic engineering is dangerous, it could undermine the fruit’s image as a healthy and natural food, the one that keeps the doctor away and is as American as, well, apple pie.

“We don’t think it’s in the best interest of the apple industry of the United States to have that product in the marketplace at this time,” said Christian Schlect, president of the Northwest Horticultural Council, which represents the tree-fruit industry in and around Washington State, which produces about 60 percent of the nation’s apples.

The Agriculture Department is expected on Friday to opena 60-day public comment period on Okanagan’s application for regulatory approval of the genetically modified apple trees. A public comment period just ended in Canada, where the company is also seeking approval.

Neal Carter, the founder and president of the company, which is based in the Okanagan Valley of British Columbia, said the nonbrowning apples could improve industry sales, much as baby carrots did for carrot sales.

A whole apple is “for many people too big a commitment,” he said. “If you had a bowl of apples at a meeting, people wouldn’t take an apple out of the bowl. But if you had a plate of apple slices, everyone would take a slice.”

Consumption of fresh apples in the United States has fallen from about 20 pounds a year for each person in the late 1980s to about 16 pounds now, according to the Agriculture Department.

Apple slices are already becoming more popular as a healthful snack, sold in bags in supermarkets and included by McDonald’s in its Happy Meals for children. The slices are often coated with vitamin C and calcium to prevent browning and preserve crispness. But that can affect the taste, Mr. Carter said.

He also said that growers would have fewer apples rejected by supermarkets because of the minor bruising that is common from handling of the fruit.

Arctic Apples, which would first be available in the Golden Delicious and Granny Smith varieties, contain a synthetic gene that sharply reduces production of polyphenol oxidase, an enzyme responsible for the browning.

The gene does not come from another species. Rather, it contains DNA sequences from four of the apple’s own genes that govern production of polyphenol oxidase. Putting an extra copy of a gene into a plant can activate a self-defense mechanism known as RNA interference that shuts down both the extra copy and the endogenous gene.

Some critics say the lack of browning could conceal problems with an apple that consumers may want to know about.

“Is it a rotten apple that looks fresh?” said Lucy Sharratt, coordinator of the Canadian Biotechnology Action Network, a coalition of groups critical of genetically engineered crops. Ms. Sharratt also said the genetic engineering was “designed to turn the apple into an industrialized product” that could be sold in plastic bags instead of as whole fresh fruit.

Mr. Carter said the injury from bruising or slicing was not harmful to consumers. If the apple were truly rotten from a bacterial or fungal infection, it would still change colors.

“The stuff that is really bad and people won’t want to eat will still be bad,” he said.

Biology and Amelia Earhart mixed together in the S. Pacific

http://en.wikipedia.org/wiki/Nikumaroro

Artificial Reefs in Delaware from subway cars...great repurposing idea

Saturday, March 26, 2011

Subway Cars Dumped Into Sea To Make Artificial Reef

Posted by Kaushik at 7:01 AM

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Photographer Stephen Mallon took photos of New York City's discarded subway cars as they are tossed into the ocean, over a period of two and a half years, for his photo series Next Stop Atlantic. The initiative, headed by the Delaware Department of Natural Resources and Environmental Control, has deposited hundreds of the vacant vessels in an effort to jump start a new reef 16 miles off the state’s coast.

The concept has already shown great promise, transforming “a barren stretch of ocean floor into a bountiful oasis, carpeted in sea grasses, walled thick with blue mussels and sponges, and teeming with black sea bass and tautog.” The reef is currently composed of 714 cars and continues to grow, creating “a thriving community in what was once an underwater desert”.

Source: Inhabitat, MyModernMet