Robot biologist solves complex problem from scratch

First it was chess. Then it was Jeopardy.

Now computers are at it again, but this time they are trying to automate the scientific process itself.

An interdisciplinary team of scientists at Vanderbilt University, Cornell University and CFD Research Corporation, Inc., has taken a major step toward this goal by demonstrating that a computer can analyze raw experimental data from a biological system and derive the basic mathematical equations that describe the way the system operates. According to the researchers, it is one of the most complex scientific modeling problems that a computer has solved completely from scratch.

The paper that describes this accomplishment is published in the October issue of the journal Physical Biology and is currently available online.

The work was a collaboration between John P. Wikswo, the Gordon A. Cain University Professor at Vanderbilt, Michael Schmidt and Hod Lipson at the Creative Machines Lab at Cornell University and Jerry Jenkins and Ravishankar Vallabhajosyula at CFDRC in Huntsville, Ala.

The “brains” of the system, which Wikswo has christened the Automated Biology Explorer (ABE), is a unique piece of software called Eureqa developed at Cornell and released in 2009. Schmidt and Lipson originally created Eureqa to design robots without going through the normal trial and error stage that is both slow and expensive. After it succeeded, they realized it could also be applied to solving science problems.

One of Eureqa’s initial achievements was identifying the basic laws of motion by analyzing the motion of a double pendulum. What took Sir Isaac Newton years to discover, Eureqa did in a few hours when running on a personal computer.

In 2006, Wikswo heard Lipson lecture about his research. “I had a ‘eureka moment’ of my own when I realized the system Hod had developed could be used to solve biological problems and even control them,” Wikswo said. So he started talking to Lipson immediately after the lecture and they began a collaboration to adapt Eureqa to analyze biological problems.

“Biology is the area where the gap between theory and data is growing the most rapidly,” said Lipson. “So it is the area in greatest need of automation.”

Software passes test

The biological system that the researchers used to test ABE is glycolysis, the primary process that produces energy in a living cell. Specifically, they focused on the manner in which yeast cells control fluctuations in the chemical compounds produced by the process.

The researchers chose this specific system, called glycolytic oscillations, to perform a virtual test of the software because it is one of the most extensively studied biological control systems. Jenkins and Vallabhajosyula used one of the process’ detailed mathematical models to generate a data set corresponding to the measurements a scientist would make under various conditions. To increase the realism of the test, the researchers salted the data with a 10 percent random error. When they fed the data into Eureqa, it derived a series of equations that were nearly identical to the known equations.

“What’s really amazing is that it produced these equations a priori,” said Vallabhajosyula. “The only thing the software knew in advance was addition, subtraction, multiplication and division.” …

via Robot biologist solves complex problem from scratch.

Woman shoots, kills bow-and-arrow-armed intruder

An auxiliary Florida Highway Patrol trooper shot and killed her neighbor Monday night after he came into her home armed with a bow and arrow and asked for money.

Sean Harris, 24, of the 4200 block of Lynn Ora Drive was taken to Sacred Heart Hospital, where he died about 9:45 p.m. Monday.

Auxiliary Trooper Tabbatha Nussbaumer was in the shower in her upstairs bathroom when her 9-year-old son told her a man he didn’t recognize was in the house, the Pensacola Police Department said.

When Nussbaumer left her bathroom, Harris was at the bottom of the stairs holding the bow and arrow, police said.

Nussbaumer said Harris asked for money.

In an effort to get Harris out the house, Nussbaumer told him she had money in her truck. As Nussbaumer went out the front door, Harris followed and removed his clothes, police said.

Nussbaumer’s truck was parked on the street. Police said Nussbaumer removed a handgun from the truck, turned around, faced Harris, who was standing a few feet from her, and shot him as he walked toward her, police said.

When police arrived on Lynn Ora Drive, Harris was lying nude in the street. He was shot once in the lower abdomen. An autopsy is set for today.

The Police Department’s investigation into the shooting is continuing.

via Woman shoots, kills bow-and-arrow-armed intruder | Pensacola News Journal | pnj.com.

Something a little more than what is reported was going on, seems to me.

Gregory Liascos, Portland’s Alleged ‘Moss Man,’ Fails To Show Up For Trial

Authorities say an Oregon burglary suspect dubbed “Moss Man” failed to show up at his trial, and a warrant has been issued for his arrest.

Gregory Liascos of Portland earned the “Moss Man” moniker after police say he was arrested in full-body camouflage last October outside the Rice Northwest Museum of Rocks and Minerals.

Police say the 36-year-old Portland man had cut a hole in a museum wall and was trying to break in.

Officers found a bike and a backpack, but they didn’t find the suspect until a police dog bit what appeared to be the ground. It was Liascos in a “ghillie” suit, a head-to-toe camouflage outfit used by military snipers to blend in with vegetation.

Liascos later said the whole thing was a mix-up, and that the outfit was a Halloween costume from his kids.

via Gregory Liascos, Portland’s Alleged ‘Moss Man,’ Fails To Show Up For Trial.

Moon dust declared in customs, Honolulu, Hawaii July 24, 1969

MIT: Life could exist if fundamental forces were different, New Universes constantly created

Modern cosmology theory holds that our universe may be just one in a vast collection of universes known as the multiverse. MIT physicist Alan Guth has suggested that new universes (known as “pocket universes”) are constantly being created, but they cannot be seen from our universe.

In this view, “nature gets a lot of tries — the universe is an experiment that’s repeated over and over again, each time with slightly different physical laws, or even vastly different physical laws,” says Jaffe.

Some of these universes would collapse instants after forming; in others, the forces between particles would be so weak they could not give rise to atoms or molecules. However, if conditions were suitable, matter would coalesce into galaxies and planets, and if the right elements were present in those worlds, intelligent life could evolve.

Some physicists have theorized that only universes in which the laws of physics are “just so” could support life, and that if things were even a little bit different from our world, intelligent life would be impossible. In that case, our physical laws might be explained “anthropically,” meaning that they are as they are because if they were otherwise, no one would be around to notice them.

MIT physics professor Robert Jaffe and his collaborators felt that this proposed anthropic explanation should be subjected to more careful scrutiny, and decided to explore whether universes with different physical laws could support life.

The MIT physicists have showed that universes quite different from ours still have elements similar to carbon, hydrogen, and oxygen, and could therefore evolve life forms quite similar to us, even when the masses of elementary particles called quarks are dramatically altered. …

The team found a few other congenial universes, including a family where the up and strange quarks have roughly the same mass (in our universe, strange quarks are much heavier and can only be produced in high-energy collisions), while the down quark would be much lighter. In such a universe, atomic nuclei would be made of neutrons and a hyperon called the “sigma minus,” which would replace protons. They published their findings in the journal Physical Review D last year.

Jaffe and his collaborators focused on quarks because they know enough about quark interactions to predict what will happen when their masses change. However, “any attempt to address the problem in a broader context is going to be very difficult,” says Jaffe, because physicists are limited in their ability to predict the consequences of changing most other physical laws and constants.

A group of researchers at Lawrence Berkeley National Laboratory has done related studies examining whether congenial universes could arise even while lacking one of the four fundamental forces of our universe — the weak nuclear force, which enables the reactions that turn neutrons into protons, and vice versa. The researchers showed that tweaking the other three fundamental forces could compensate for the missing weak nuclear force and still allow stable elements to be formed. …

via MIT: “New Universes are Being Constantly Created” (Today’s Most Popular).

American Friends of Tel Aviv University: “Ghostwriting” the Torah?

In both Jewish and Christian traditions, Moses is considered the author of the Torah, the first five books of the Bible. Scholars have furnished evidence that multiple writers had a hand in composing the text of the Torah. Other books of the Hebrew Bible and of the New Testament are also thought to be composites. However, delineating these multiple sources has been a laborious task.

Now researchers have developed an algorithm that could help to unravel the different sources that contributed to individual books of the Bible. Prof. Nachum Dershowitz of Tel Aviv University’s Blavatnik School of Computer Science, who worked in collaboration with his son, Bible scholar Idan Dershowitz of Hebrew University, and Prof. Moshe Koppel and Ph.D. student Navot Akiva of Bar-Ilan University, says that their computer algorithm recognizes linguistic cues, such as word preference, to divide texts into probable author groupings…

According to Prof. Dershowitz, the software searches for and compares details that human scholars might have difficulty detecting, such as the frequency of the use of “function” words and synonyms. Such details have little bearing on the meaning of the text itself, but each author or source often has his own style. This could be as innocuous as an author’s preference for using the word “said” versus “spoke.”

To test the validity of their method, the researchers randomly mixed passages from the two Hebrew books of Jeremiah and Ezekiel, and asked the computer to separate them. By searching for and categorizing chapters by synonym preference, and then looking at usage of common words, the computer program was able to separate the passages with 99 percent accuracy. The software was also able to distinguish between “priestly” materials — those dealing with issues such as religious ritual — and “non-priestly” material in the Torah, a categorization that is widely used by Bible scholars.

While the algorithm is not yet advanced enough to give the researchers a precise number of probable authors involved in the writing of the individual books of the Bible, Prof. Dershowitz says that it can help to identify transition points within the text where a source changes, potentially shedding new light on age-old debates. …

via American Friends of Tel Aviv University: “Ghostwriting” the Torah?.