'Robot biologist' solves complex problem from scratch

ScienceDaily (Oct. 14, 2011) — 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."

Beyond Adam

The ability to generate mathematical equations from scratch is what sets ABE apart from Adam, the robot scientist developed by Ross King and his colleagues at the University of Wales at Aberystwyth. Adam runs yeast genetics experiments and made international headlines two years ago by making a novel scientific discovery without direct human input. King fed Adam with a model of yeast metabolism and a database of genes and proteins involved in metabolism in other species. He also linked the computer to a remote-controlled genetics laboratory. This allowed the computer to generate hypotheses, then design and conduct actual experiments to test them.

"It's a classic paper," Wikswo said.

In order to give ABE the ability to run experiments like Adam, Wikswo's group is currently developing "laboratory-on-a-chip" technology that can be controlled by Eureqa. This will allow ABE to design and perform a wide variety of basic biology experiments. Their initial effort is focused on developing a microfluidics device that can test cell metabolism.

"Generally, the way that scientists design experiments is to vary one factor at a time while keeping the other factors constant, but, in many cases, the most effective way to test a biological system may be to tweak a large number of different factors at the same time and see what happens. ABE will let us do that," Wikswo said.

The project was funded by grants from the National Science Foundation, National Institute on Drug Abuse, the Defense Threat Reduction Agency and the National Academies Keck Futures Initiative.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Vanderbilt University.

Journal Reference:

Michael D Schmidt, Ravishankar R Vallabhajosyula, Jerry W Jenkins, Jonathan E Hood, Abhishek S Soni, John P Wikswo, Hod Lipson. Automated refinement and inference of analytical models for metabolic networks. Physical Biology, 2011; 8 (5): 055011 DOI: 10.1088/1478-3975/8/5/055011

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

'Robot biologist' solves complex problem from scratch

ScienceDaily (Oct. 14, 2011) — 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."

Beyond Adam

The ability to generate mathematical equations from scratch is what sets ABE apart from Adam, the robot scientist developed by Ross King and his colleagues at the University of Wales at Aberystwyth. Adam runs yeast genetics experiments and made international headlines two years ago by making a novel scientific discovery without direct human input. King fed Adam with a model of yeast metabolism and a database of genes and proteins involved in metabolism in other species. He also linked the computer to a remote-controlled genetics laboratory. This allowed the computer to generate hypotheses, then design and conduct actual experiments to test them.

"It's a classic paper," Wikswo said.

In order to give ABE the ability to run experiments like Adam, Wikswo's group is currently developing "laboratory-on-a-chip" technology that can be controlled by Eureqa. This will allow ABE to design and perform a wide variety of basic biology experiments. Their initial effort is focused on developing a microfluidics device that can test cell metabolism.

"Generally, the way that scientists design experiments is to vary one factor at a time while keeping the other factors constant, but, in many cases, the most effective way to test a biological system may be to tweak a large number of different factors at the same time and see what happens. ABE will let us do that," Wikswo said.

The project was funded by grants from the National Science Foundation, National Institute on Drug Abuse, the Defense Threat Reduction Agency and the National Academies Keck Futures Initiative.

Recommend this story on Facebook, Twitter,
and Google +1:

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Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Vanderbilt University.

Journal Reference:

Michael D Schmidt, Ravishankar R Vallabhajosyula, Jerry W Jenkins, Jonathan E Hood, Abhishek S Soni, John P Wikswo, Hod Lipson. Automated refinement and inference of analytical models for metabolic networks. Physical Biology, 2011; 8 (5): 055011 DOI: 10.1088/1478-3975/8/5/055011

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Edible carbon dioxide sponge: All-natural nanostructures could address pressing environmental problem

ScienceDaily (Sep. 25, 2011) — A year ago Northwestern University chemists published their recipe for a new class of nanostructures made of sugar, salt and alcohol. Now, the same team has discovered the edible compounds can efficiently detect, capture and store carbon dioxide. And the compounds themselves are carbon-neutral.

The porous crystals -- known as metal-organic frameworks (MOFs) -- are made from all-natural ingredients and are simple to prepare, giving them a huge advantage over other MOFs. Conventional MOFs, which also are effective at adsorbing carbon dioxide, are usually prepared from materials derived from crude oil and often incorporate toxic heavy metals.

Other features of the Northwestern MOFs are they turn red when completely full of carbon dioxide, and the carbon capture process is reversible.

The findings, made by scientists working in the laboratory of Sir Fraser Stoddart, Board of Trustees Professor of Chemistry in the Weinberg College of Arts and Sciences, are published in the Journal of the American Chemical Society (JACS).

"We are able to take molecules that are themselves sourced from atmospheric carbon, through photosynthesis, and use them to capture even more carbon dioxide," said Ross S. Forgan, a co-author of the study and a postdoctoral fellow in Stoddart's laboratory. "By preparing our MOFs from naturally derived ingredients, we are not only making materials that are entirely nontoxic, but we are also cutting down on the carbon dioxide emissions associated with their manufacture."

The main component, gamma-cyclodextrin, is a naturally occurring biorenewable sugar molecule that is derived from cornstarch.

The sugar molecules are held in place by metals taken from salts such as potassium benzoate or rubidium hydroxide, and it is the precise arrangement of the sugars in the crystals that is vital to their successful capture of carbon dioxide.

"It turns out that a fairly unexpected event occurs when you put that many sugars next to each other in an alkaline environment -- they start reacting with carbon dioxide in a process akin to carbon fixation, which is how sugars are made in the first place," said Jeremiah J. Gassensmith, lead author of the paper and also a postdoctoral fellow in Stoddart's laboratory. "The reaction leads to the carbon dioxide being tightly bound inside the crystals, but we can still recover it at a later date very simply."

The fact that the carbon dioxide reacts with the MOF, an unusual occurrence, led to a simple method of detecting when the crystals have reached full capacity. The researchers place an indicator molecule, which detects changes in pH by changing its color, inside each crystal. When the yellow crystals of the MOFs are full of carbon dioxide they turn red.

The simplicity of the new MOFs, allied with their low cost and green credentials, have marked them as candidates for further commercialization. Ronald A. Smaldone, also a postdoctoral fellow in Stoddart's group and a co-author of the paper, added, "I think this is a remarkable demonstration of how simple chemistry can be successfully applied to relevant problems like carbon capture and sensor technology."

The National Science Foundation, the U.S. Department of Energy, the Engineering and Physical Sciences Research Council in the U.K., the King Abdulaziz City of Science and Technology (KACST) in Saudi Arabia and the Korea Advanced Institute of Science and Technology (KAIST) in Korea supported the research.

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The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Northwestern University. The original article was written by Megan Fellman.

Journal Reference:

Jeremiah J. Gassensmith, Hiroyasu Furukawa, Ronald A. Smaldone, Ross S. Forgan, Youssry Y. Botros, Omar M. Yaghi, J. Fraser Stoddart. Strong and Reversible Binding of Carbon Dioxide in a Green Metal–Organic Framework. Journal of the American Chemical Society, 2011; 110913144109022 DOI: 10.1021/ja206525x

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here

Edible carbon dioxide sponge: All-natural nanostructures could address pressing environmental problem

ScienceDaily (Sep. 25, 2011) — A year ago Northwestern University chemists published their recipe for a new class of nanostructures made of sugar, salt and alcohol. Now, the same team has discovered the edible compounds can efficiently detect, capture and store carbon dioxide. And the compounds themselves are carbon-neutral.

The porous crystals -- known as metal-organic frameworks (MOFs) -- are made from all-natural ingredients and are simple to prepare, giving them a huge advantage over other MOFs. Conventional MOFs, which also are effective at adsorbing carbon dioxide, are usually prepared from materials derived from crude oil and often incorporate toxic heavy metals.

Other features of the Northwestern MOFs are they turn red when completely full of carbon dioxide, and the carbon capture process is reversible.

The findings, made by scientists working in the laboratory of Sir Fraser Stoddart, Board of Trustees Professor of Chemistry in the Weinberg College of Arts and Sciences, are published in the Journal of the American Chemical Society (JACS).

"We are able to take molecules that are themselves sourced from atmospheric carbon, through photosynthesis, and use them to capture even more carbon dioxide," said Ross S. Forgan, a co-author of the study and a postdoctoral fellow in Stoddart's laboratory. "By preparing our MOFs from naturally derived ingredients, we are not only making materials that are entirely nontoxic, but we are also cutting down on the carbon dioxide emissions associated with their manufacture."

The main component, gamma-cyclodextrin, is a naturally occurring biorenewable sugar molecule that is derived from cornstarch.

The sugar molecules are held in place by metals taken from salts such as potassium benzoate or rubidium hydroxide, and it is the precise arrangement of the sugars in the crystals that is vital to their successful capture of carbon dioxide.

"It turns out that a fairly unexpected event occurs when you put that many sugars next to each other in an alkaline environment -- they start reacting with carbon dioxide in a process akin to carbon fixation, which is how sugars are made in the first place," said Jeremiah J. Gassensmith, lead author of the paper and also a postdoctoral fellow in Stoddart's laboratory. "The reaction leads to the carbon dioxide being tightly bound inside the crystals, but we can still recover it at a later date very simply."

The fact that the carbon dioxide reacts with the MOF, an unusual occurrence, led to a simple method of detecting when the crystals have reached full capacity. The researchers place an indicator molecule, which detects changes in pH by changing its color, inside each crystal. When the yellow crystals of the MOFs are full of carbon dioxide they turn red.

The simplicity of the new MOFs, allied with their low cost and green credentials, have marked them as candidates for further commercialization. Ronald A. Smaldone, also a postdoctoral fellow in Stoddart's group and a co-author of the paper, added, "I think this is a remarkable demonstration of how simple chemistry can be successfully applied to relevant problems like carbon capture and sensor technology."

The National Science Foundation, the U.S. Department of Energy, the Engineering and Physical Sciences Research Council in the U.K., the King Abdulaziz City of Science and Technology (KACST) in Saudi Arabia and the Korea Advanced Institute of Science and Technology (KAIST) in Korea supported the research.

Recommend this story on Facebook, Twitter,
and Google +1:

Other bookmarking and sharing tools:

Story Source:

The above story is reprinted (with editorial adaptations by ScienceDaily staff) from materials provided by Northwestern University. The original article was written by Megan Fellman.

Journal Reference:

Jeremiah J. Gassensmith, Hiroyasu Furukawa, Ronald A. Smaldone, Ross S. Forgan, Youssry Y. Botros, Omar M. Yaghi, J. Fraser Stoddart. Strong and Reversible Binding of Carbon Dioxide in a Green Metal–Organic Framework. Journal of the American Chemical Society, 2011; 110913144109022 DOI: 10.1021/ja206525x

Note: If no author is given, the source is cited instead.

Disclaimer: Views expressed in this article do not necessarily reflect those of ScienceDaily or its staff.

View the original article here