Fresh Insight into Evolution

Studies of genetic recombination suggest that genetic shuffling varies by gender.

Genetic recombination: When cells divide to produce eggs and sperm, a process called meiosis, corresponding maternal and paternal chromosomes pair up and swap small pieces of DNA. (Paired chromosomes are depicted above.) This ensures a constant source of genetic diversity, which drives evolution. Credit: Technology Review

It's a tantalizing thought worthy of X-Men-inspired daydreams: are some of us, for better or for worse, evolving faster than others? Growing evidence suggests that rates of genetic recombination--one of the driving forces of human evolution--vary greatly between individuals. Two new studies shed further light on the inner workings of this gene-shuffling process, highlighting differences in the way men and women rearrange the DNA that they pass on to their children. The findings could help scientists understand disorders such as miscarriage and Down syndrome, which are linked to errors in recombination.

During recombination, corresponding maternal and paternal chromosomes align within cells and swap bits of DNA. These cells eventually develop into sperm and eggs, endowing future offspring with a different configuration of genes than their parents. "Recombination constitutes one of the most powerful means by which new combinations of genetic variants are generated in the genome," says Kari Stefansson, chief executive officer of deCODE Genetics, in Iceland, and senior author of one of the studies.

Previous research shows that recombination is often localized to specific spots on the genome, known as hot spots. Some people's genomes undergo this swap more than other people's, with apparently profound consequences. In 2005, Stefansson's group at deCODE found that women with higher recombination rates had more children, suggesting that evolution has selected for molecular mechanisms that create diversity.

Scientists study recombination by comparing genetic variation in parents and their children. New techniques to analyze huge numbers of genetic variations, commonly used to identify genes linked to disease, are now allowing a more detailed analysis of recombination than ever before. (See "Genes for Several Common Diseases Found.") In one such study, published Thursday in the online version of the journal Science, researchers from the University of Chicago generated a high-resolution map of recombination hot spots by analyzing the DNA of 725 people. The volunteers came from 82 families of Hutterites, a genetically similar group of European immigrants who settled in the Dakotas in the 19th century.

That map allowed researchers to analyze how specific hot spots varied between men and women, and parents and children. "Some individuals use some hot spots more than others," says Graham Coop, a researcher at the University of Chicago who led the work. Coop and his collaborators also found that men and women had different recombination rates and tended to use different hot spots for recombination. In addition, that pattern of hot-spot usage seemed to be inherited. "That suggests differences in recombination machinery between indviduals," says Coop. He ultimately hopes to identify the genes that control recombination.

Stefansson and his colleagues do just that in a second study, also published Thursday in Science. The researchers scanned the genomes of 20,000 people for specific genetic variations linked to recombination rate. They identified two variations within a gene known as RNF212 that together accounted for 22 percent and 6.5 percent of paternal and maternal variation, respectively. Little is known about the function of the gene.

Surprisingly, these variations had opposite effects in men and women: the mutation that increased recombination in women did the opposite in men, and vice versa. The findings suggest an evolutionary mechanism for keeping control of genetic diversity. "It's important to increase diversity, but if it goes unchecked, it's likely to lead to instability in the genome that could be dangerous," says Stefansson. "If you have the same sequence variant influencing recombination in one direction in men and the other direction in women, you have put together a mechanism to keep recombination rates within certain limits."

Both studies shed light on the basic underpinnings of human evolution, which could ultimately impact human health. For example, abnormal recombination can result in miscarriage. Older women, who have higher rates of miscarriage, tend to have children whose genomes show evidence of higher recombination rate. A better understanding of the mechanisms underlying this observation could eventually lead to new fertility treatments.

http://www.technologyreview.com/Biotech/20139/

Social Search

A new website will offer personalized search results based on the user's social network.

Credit: Technology Review

People are flocking to online social networks. Facebook, for example, claims an average of 250,000 new registrations per day. But companies are still hunting for ways to make these networks more useful--and profitable. In the past year, Facebook has introduced new services aimed at taking advantage of users' online contacts (see "Building onto Facebook's Platform"), and Yahoo announced plans for an e-mail service that shares data with social-networking sites. (See "Yahoo's Plan for a Smarter In-Box.") Now a company called Delver, which presented at Demo earlier this week, is working on a search engine that uses social-network data to return personalized results from the larger Web.

Liad Agmon, CEO of Delver, says that the site connects information about a user's social network with Web search results, "so you are searching the Web through the prism of your social graph." He explains that a person begins a search at Delver by typing in her name. Delver then crawls social-networking websites for widely available data about the user--such as a public LinkedIn profile--and builds a network of associated institutions and individuals based on that information. When the user enters a search query, results related to, produced by, or tagged by members of her social network are given priority. Lower down are results from people implicitly connected to the user, such as those relating to friends of friends, or people who attended the same college as the user. Finally, there may be some general results from the Web at the bottom. The consequence, says Agmon, is that each user gets a different set of results from a given query, and a set quite different from those delivered by Google.

"We have no intention of competing with the Googles of the world, because Google is doing a very good job of indexing the Web and bringing you the Wikipedia page of every search query you're looking for," says Agmon. He says that Delver will free general search queries such as "New York" or "screensaver" from the heavy search-engine optimization that tends to make those kinds of queries return generic, ad-heavy results on Google. "[As a user], you're always thinking, how can I trick Google into bringing me the real results rather than the commercial results?" Agmon says. "With this engine, we don't need to trick it at all. You can go back to these very naive and simple queries because the results come from your network. Your network is not trying to optimize results; they just publish or bookmark pages which they find interesting." As a consequence, the results lean toward user-generated content and items tagged through sites such as del.icio.us.

A person can improve the results he gets from Delver by registering and allowing it access to connections made on sites where information is usually kept private, Agmon says. Registered users can also add connections found through Delver, such as a friend of a friend who consistently leads to interesting sites. Although the registration feature will be available, Agmon says that it's important that people be able to use the site without registering, so it will be available to more casual Web users. One consequence of this design as it currently stands is that it's possible to search the Web as someone other than yourself. Agmon acknowledges the possibility and its potential for use and abuse, but he notes that once a person builds a profile, he must log in to search, and that identity can no longer be used as a proxy.

Help from friends: Before querying Delver (above), a user enters her name to allow the site to search for information about her social network and connections. Once the network is built, the user can search and receive results ranked by ties to her social network. The query "New York," for example, is more likely to return a friend's home video uploaded to YouTube than to return the home page of a five-star hotel.

Clay Shirky, a professor in the Interactive Telecommunications Program at New York University, points out that Google itself is already a form of social search, due to its dependence on links. "I think the question is, what value do you get out of being more explicitly social?" he says. Since personalized results are one of Delver's main selling points, Shirky says, it's important to be aware of when a user wants personalized results, and when that might not be desirable. "The further we are away from our own areas of expertise and concern, I think the less we care that our results be different," he says. "If I want to know what happened in the Crimean War, and you want to know what happened in the Crimean War, we're pretty happy that the Wikipedia link is the number-one link, because we'll get a good overview. If you're a Crimean War scholar, on the other hand, you're probably not happy about that."

Shirky says that he is suspicious of the claim that social search sites can return better results for general search queries. "People's tastes are more different than the same in environments with large amounts of freedom," he says. He worries that social search results to a general query like "music" might return either a cacophony of songs that would be all over the map in terms of style, or a list of the top 40 songs no one needs to search to find. A better situation might arise for someone looking for "bluegrass music," Shirky says, provided the user is someone, such as a bluegrass musician, who is likely to have a network well versed in the subject.

Agmon says that Delver plans to make money by serving up personalized advertising along with its search results. The company also hopes to get income by licensing its search technology to socially oriented sites and by bringing up more meaningful search results within those sites. Delver is slated to launch next month, after its crawlers have had more time to collect data. Agmon says that he expects to open the site for an invitation-only preview by May.

http://www.technologyreview.com/Infotech/20138/

Analytics in Football

Will using complex statistical analysis give the New England Patriots an edge at game time?

Credit: Technology Review

Football coaches have never been known to be particularly intellectual, tending to favor their "gut feelings" over objective data. But that is slowly changing. Professional-football general managers and coaches are increasingly using analytics--the intensive use of data and statistics to make decisions--both in evaluating a player's performance and in calling plays during the game. Some experts credit part of the success of the New England Patriots, who are competing for their fourth Super Bowl in six seasons on Sunday, to this trend in analytics.

"It is generally accepted that the Patriots are one of the most analytically advanced franchises in the NFL," says Aaron Schatz, the creator of FootballOutsiders.com, a site that uses statistics to analyze the game.

Such heavy use of analytics has already transformed the management of professional baseball, and now it is making inroads into football. KC Joyner, author of Scientific Football 2007, a book that uses a performance-based metric system to analyze nearly every measureable statistic in the NFL, says that analytics began to emerge in football in the past five years as teams have gone from just analyzing game footage to putting a quantitative value on a player's performance.

One of the more widely used metrics is the quarterback rating. It is a complex rating that's computed based on complete passes, pass attempts, passing yards, touchdown passes, and interceptions. "This is a pretty critical metric since quarterbacks are one of the most important players," says Tom Davenport, a professor of IT and management at Babson College and author of Competing on Analytics: The New Science of Winning.

Teams continue to analyze video to track, tabulate, and calculate how many times the opposing team, for example, blitzes when its defense is in a nickel formation, but they are also starting to use video to track the number of times that a cornerback misreads a slant route or runs into another defender when covering a pick play. "It's not just about doing advanced scouting on teams' formations, but targeting players so teams say, 'We can run this play at this lineman,' or 'This cornerback can't cover this particular route,'" says Joyner.

Beyond targeting players, football is beginning to use analytics to select the best players for the lowest price. "The Patriots are particularly good at optimizing their payroll," says Davenport. "This is what a corporation would call human resource analytics, and in any sport, that is probably the single most important thing to do."

On the field, the Patriots do not shy away from using analytical data to make play-calling decisions--whether it is deciding to punt on fourth down, or deciding if they should go for one point or two after a touchdown, says Davenport. After the team's head coach, Bill Belichick, read a paper by well-known economist David Romer about how teams are generally too conservative on fourth down, he began using historical data to develop a table to determine when the team should punt and when it should go for the first down. In the past couple of years, Belichick has been one of the most aggressive coaches when it comes to going for it on fourth down, says Schatz.

Analytics in sports have been most commonly used in professional baseball. One early advocate was Bill James, a statistician who is now a senior advisor to the Boston Red Sox. "Bill James has been prolific in coming up with new metrics for team and player performance, gathering those statistics and publishing them," says Davenport.

But baseball lends itself to an analytical mind-set. "The sport is individually oriented and, thus, it is easier to measure the individual's contribution," says Davenport. "Plus, there is just a lot of data available, and when data emerges, people start taking advantage of it."

In football, the use of analytics is harder because there are only a few statistics that are popularly tracked, like yardage and downs. But football, like baseball, is now working to bridge the gap between what the "scouting eye" sees and what the numbers are saying, says Joyner. "Football is still in the early stages," he notes.

The analytics trend "is not going to take off in football until someone wins with metrics like the Red Sox did in baseball," says Joyner. "The Patriots are going to help, but what it will really take is a team to go from a losing record to winning the championship." Until that happens and everyone catches up, analytics are going to give teams that are already using the methods, like the Patriots, a competitive edge, he says.

http://www.technologyreview.com/Infotech/20132/?a=f