searching-big-data-faster

Searching Big Data Faster

150826132013_1_540x360For more than a decade, gene sequencers have been improving more rapidly than the computers required to make sense of their outputs. Searching for DNA sequences in existing genomic databases can already take hours, and the problem is likely to get worse. Recently, Bonnie Berger’s group at MIT’s Computer Science and Artificial Intelligence Laboratory (CSAIL) has been investigating techniques to make biological and chemical data easier to analyze by, in some sense, compressing it. In the latest issue of the journal Cell Systems, Berger and colleagues present a theoretical analysis that demonstrates why their previous compression schemes have been so successful. They identify properties of data sets that make them amenable to compression and present an algorithm for determining whether a given data set has those properties. They also show that several existing databases of chemical compounds and biological molecules do indeed exhibit them.

“This paper provides a framework for how we can apply compressive algorithms to large-scale biological data,” says Berger, a professor of applied mathematics at MIT. “We also have proofs for how much efficiency we can get.” The key to the researchers’ compression scheme is that evolution is stingy with good designs. There tends to be a lot of redundancy in the genomes of closely related — or even distantly related — organisms.

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Study Investigates Whether Blind People Characterize Others by Race

Most people who meet a new acquaintance, or merely pass someone on the street, need only a glance to categorize that person as a particular race. But, sociologist Asia Friedman wondered, what can we learn about that automatic visual processing from people who are unable to see? “The visual process of assigning race is instantaneous, and it’s an example of automatic thinking — it happens below the level of awareness,” Friedman said. “With blind people, the process is much slower as they piece together information about a person over time. Their thinking is deliberative rather than automatic, and even after they’ve categorized someone by race, they’re often not certain that they’re correct.”

Friedman’s study breaks new ground, with little previous research done on the subject. An earlier study found that blind people think of race in visual terms, even though they rely on senses other than sight. But Friedman’s subjects generally did not think of race visually. Additionally, unlike the earlier study, which included only people who were born blind, Friedman’s study considered individuals who were born without sight as well as people who became blind later in life. Friedman found some differences between those groups.

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Editing Humanity

Susanne.Posel-Headline.News.Official- designer.baby.bloom.syndrome.fda.23andme_occupycorporatismThe genome is written in an alphabet of just four letters. Being able to read, study and compare DNA sequences for humans, and thousands of other species, has become routine. A new technology promises to make it possible to edit genetic information quickly and cheaply. This could correct terrible genetic defects that blight lives. It also heralds the distant prospect of parents building their children to order. The technology is known as CRISPR-Cas9, or just CRISPR. It involves a piece of RNA, a chemical messenger, designed to target a section of DNA; and an enzyme, called a nuclease, that can snip unwanted genes out and paste new ones in. Other ways of editing DNA exist, but CRISPR holds the promise of doing so with unprecedented simplicity, speed and precision.

It will be years, perhaps even decades, before CRISPR is being used to make designer babies. But the issues that raises are already the subject of fierce discussion. In April scientists in China revealed they had tried using CRISPR to edit the genomes of human embryos. Although these embryos could not develop to term, viable embryos could one day be engineered for therapeutic reasons or non-medical enhancement.

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Earliest Baboon Found in South Africa

image_3154_2-Papio-angusticepsA two-million-year-old partial skull of the extinct baboon Papio angusticeps has been unearthed at Malapa, in the Cradle of Humankind World Heritage Site, by a team of scientists headed by Dr Christopher Gilbert of Hunter College of the City University of New York. The specimen, according to the team, represents both the earliest baboon ever found and the only non-hominin primate yet recovered from Malapa.

Despite their evolutionary success, modern baboon origins in the fossil record have not well-understood or agreed upon. “According to molecular clock studies, baboons are estimated to have diverged from their closest relatives by 1.8 to 2.2 million years ago; however, until now, most fossil specimens known within this time range have been either too fragmentary to be definitive or too primitive to be confirmed as members of the living species Papio hamadryas,” said Dr Gilbert, who is the first author on the study published in the journal PLoS ONE.

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The Biological Origins of Sexual Orientation and Gender Identity

thebiologicaMale? Female? The distinction is not always clear. Exploring the scientific evidence for the biological origins of sexual orientation and gender identity must continue to both enhance patient care and fight discrimination. People often are unaware of the biological complexity of sex and gender, says Eric Vilain, MD (RES ’98, FEL ’99), PhD, director of the Center for Gender-Based Biology at UCLA, where he studies the genetics of sexual development and sex differences. “People tend to define sex in a binary way—either wholly male or wholly female—based on physical appearance or by which sex chromosomes an individual carries. But while sex and gender may seem dichotomous, there are in reality many intermediates.”

Dr. Vilain says that understanding this complexity is critical, as misperceptions affect the health and civil liberties of those who fall outside perceived societal norms. “Society has categorical views on what should define sex and gender, but the biological reality is just not there to support that,” he says.

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Cellphone Data Can Track Infectious Diseases

97771_webTracking mobile phone data is often associated with privacy issues, but these vast datasets could be the key to understanding how infectious diseases are spread seasonally, according to a study published in the Proceedings of the National Academy of Sciences.

Princeton University and Harvard University researchers used anonymous mobile phone records for more than 15 million people to track the spread of rubella in Kenya and were able to quantitatively show for the first time that mobile phone data can predict seasonal disease patterns. “One of the unique opportunities of mobile phone data is the ability to understand how travel patterns change over time,” said lead author C. Jessica Metcalf, assistant professor of ecology and evolutionary biology and public affairs at Princeton’s Woodrow Wilson School of Public and International Affairs. “And rubella is a well-known seasonal disease that has been hypothesized to be driven by human population dynamics, making it a good system for us to test.”

Overall, the results were in line with the researchers’ predictions; rubella is more likely to spread when children interact with one another at the start of school and after holiday breaks. Across most of the country, this risk then decreases throughout the rest of the school-term months. (The only anomaly was in Western Kenya where the risk during school breaks was relatively higher than when school was in session; the data were insufficient to clearly indicate why.)

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Wired For Habit

MIT-HabitFormation-1We are creatures of habit, nearly mindlessly executing routine after routine. Some habits we feel good about; others, less so. Habits are, after all, thought to be driven by reward-seeking mechanisms that are built into the brain. It turns out, however, that the brain’s habit-forming circuits may also be wired for efficiency. New research from MIT shows that habit formation, at least in primates, is driven by neurons that represent the cost of a habit, as well as the reward. “The brain seems to be wired to seek some near optimality of cost and benefit,” says Ann Graybiel, an Institute Professor at MIT and also a member of the McGovern Institute for Brain Research.

This study is the first to show that cost considerations are wired into the learning of habits.

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Do the Genes of Warriors Win the Evolution Battle?

“War—what is it good for? Absolutely nothing. Say it again.” So runs the 1970 pop song that Edwin Starr made famous and that’s now the obligatory soundtrack for every documentary about the Vietnam antiwar movement. For the historians, anthropologists and economists who study warfare, it’s more complicated than that. The sheer ubiquity of war across time and place suggest that it must be good for something. Evolutionary biologists take a longer view. They pose the basic Darwinian question: Does success in warfare enhance reproductive success, increasing the number of copies of genes that a man passes to future generations? Spectacular examples of this certainly exist. Ibn Saud, who unified Saudi Arabia in 1932 after a series of conquests, has thousands of descendants; tens of millions of humans appear to carry the genes of Genghis Khan.

But is there more systematic evidence that high rates of participation in warfare enhance reproductive success? In the long arc of human evolution, the most successful men at being fruitful and multiplying are unlikely to have been successful warriors.

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