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Tuesday, October 22, 2013

The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead

The Significance of the 2013 Nobel Prize in Chemistry and the Challenges Ahead

By PLOS Computational Biology
Posted: October 18, 2013

Following the announcement of the 2013 Nobel Prize in Chemistry, PLOS Computational Biology Editor-in-Chief Ruth Nussinov discusses the implications of this award for both the computational biology and wider biological community.

Last week, the 2013 Nobel Prize in Chemistry was awarded to Martin Karplus, Michael Levitt and Arieh Warshel for "the development of multiscale models for complex chemical systems". As the Royal Swedish Academy of Sciences noted "Chemists used to create models of molecules using plastic balls and sticks. Today, the modelling is carried out in computers. In the 1970s, Martin Karplus, Michael Levitt and Arieh Warshel laid the foundation for the powerful programs that are used to understand and predict chemical processes. Computer models mirroring real life have become crucial for most advances made in chemistry today." Further, "Today the computer is just as important a tool for chemists as the test tube. Simulations are so realistic that they predict the outcome of traditional experiments."

This event is a milestone for the broad community that PLOS Computational Biology represents. Along with Philip E. Bourne, the Founding Editor-in-Chief, and our Editorial Board, which proudly lists Michael Levitt among its members, I extend the warmest congratulations to the winners. Beyond the specific personal scientific achievements that have already been widely discussed, we must consider the more general and broader context of this unique prize. Here, I would like to present this Nobel Prize within this framework, emphasizing its magnitude and far reaching implications not only for computational biology, but for the biological community at large.

In recent decades, molecular biology has progressed by leaps and bounds. Huge technological advances have taken place in sequencing, in mapping structure and dynamics via EM, X-ray and NMR, in manipulating imaging of nuclei and cells, in sequencing single biomolecules, and more. These have led to fundamental new insights; biology and medicine have soared to new heights with the DNA double helix providing the molecular basis for genetics and Darwinism. Many steps were required to identify and untangle DNA-RNA-protein sequence -structure- function and reverse transcription processes, RNA enzymes, key multi-partnered scaffolding molecules important under normal physiological conditions and in disease, their structures, mutations, and the principles and mechanisms of their dynamic regulation, and other landmark developments. These involved technological breakthroughs and greater understanding of the specific mechanisms involved. Most of the Nobel prizes in chemistry and medicine in recent years have been awarded at these junctures.

Vast amounts of information on sequences and structures are yet to be explained and pose a challenge for computational biology. Recently this has been compounded by interdisciplinary studies of the nervous system, posing questions such as how it is structured, how it develops, how it works, the mechanisms of signal processing, and more, all at multiple levels, ranging from the molecular and cellular levels to the systems and cognitive levels. Thus, even if we gain in-depth insight into static properties such as the genomic data and structural snapshots of proteins (DNA and RNA) at different levels of resolution, the truly monumental challenge of understanding their dynamics still looms ahead. And eventually, this is how cells, tissues and organisms develop and work.

The systems in question operate at all scales: force fields and free energy landscapes relevant for protein folding and function, large complexes, biomolecular recognition involving proteins, DNA, RNA, lipids, post-translational (and DNA) modifications, and interactions with small molecules. On a larger scale we see cellular locomotion, cell division and trafficking, and cell-cell recognition. Further, beyond these, lurks the working of the complex cell as a cohesive unit: the cellular network controls metabolism and regulation, intra- and inter-cellular signaling and the neural circuits of nerve cells, where the activity of one cell directly influences many others. All are dynamic, all change with the cellular environment and all present a daunting challenge. The relevant time scales range from femtosecond for simple chemical reactions to the eons of evolution; however, all operate with the same underlying physical principles of conformational variability and selection.

At each time scale and corresponding physical size we strive to identify the relevant moving parts and degrees of freedom and to formulate effective Рthough often approximate- rules for their mutual interactions and resulting motion. Solving, understanding, and computing the dynamic behavior at any given scale is of great interest in its own right and provides approximate dynamical input for the next scale, which is one rung above it. Only at the lowest, most basic scale of individual atoms and electrons are the dynamical rules (electrostatics and Schr̦dinger's equation) completely well defined. And the all-important work cited by the Nobel Prize Committee and which is carried out by our community is roughly at the first/second level, making it of fundamental importance.

This Nobel Prize is the first given to work in computational biology, indicating that the field has matured and is on a par with experimental biology. It may also be the very first prize given in any area of the exact sciences for calculations. What is different in the present case? I believe that the answer is simple: the present calculations are of much greater interest to a much broader community. In endeavoring to imitate the basic processes of life in silico, great strides are being made toward understanding the secret of life. Computational biology, and simulations, for which Martin Karplus, Michael Levitt and Arieh Warshel shared the Nobel Prize, can carry the torch leading the sciences to decipher the elemental processes and help alleviate human suffering.

What are the challenges ahead? Are simulations with time scales of microseconds, milliseconds or beyond, under the current force field framework, capable of producing results in agreement with experiment, also for large and complex proteins like membrane receptors? Do the challenges also lie in the type of questions which are asked, for which such long time scale simulations can be useful in providing answers? Or is it the biology behind the questions that is also the key? Ultimately, as in experimental biology which also exploits methods and machines, it is likely to be all of the above. Computations are our treasured tool; they are not our aim. Merely running long molecular dynamics trajectories is unlikely to advance science.

PLOS Computational Biology joins the International Society of Computational Biology (ISCB) and our computational biology community in congratulating the awardees and celebrating this momentous event.

URL: http://blogs.plos.org/biologue/2013/10/18/the-significance-of-the-2013-nobel-prize-in-chemistry-and-the-challenges-ahead/

Contact Person: ISCB Admin (assistant@iscb.org)

Tuesday, October 15, 2013

FASEB Rallies Research Community to Urge Congress to End the Government Shutdown

Bethesda, MD—The Federation of American Societies for Experimental Biology (FASEB) issued an e-action alert this week to the 110,000 members of its 27 constituent societies urging the public to call their elected representatives with a simple message—Congress must work together to end the government shutdown, restore funding for the National Institutes of Health, the National Science Foundation, and other science agencies to pre-sequestration levels, and agree on a fiscal year (FY) 2014 budget thatsustains the prior investment in research. "Until Congress agrees on an FY 2014 budget and supports the biomedical research enterprise, we continue to lose ground in every area of scientific research," stated FASEB President Margaret K. Offermann, MD, PhD. More than 300 phone calls were made in the first 24 hours after the alert was distributed. Researchers are being urged to recruit friends, family members, and neighbors in the effort to restore funding for research.

In conjunction with the e-action alert, FASEB is running targeted ads in selected media markets asking citizens to take action to protect the nation's investment in science and engineering. FASEB has also developed a talk radio guide providing instructions on how to effectively engage in local talk radio shows. The guide includes talking points about biomedical research funding and sequestration. "We must continue to urge Congress to support the federal science agencies," stated the FASEB President.

FASEB is composed of 27 societies with more than 110,000 members, making it the largest coalition of biomedical research associations in the United States. Our mission is to advance health and welfare by promoting progress and education in biological and biomedical sciences through service to our member societies and collaborative advocacy.

URL: http://www.faseb.org

Contact Person: Lawrence Green (lgreen@faseb.org)

Thursday, October 10, 2013

Nobel Prize in Chemistry Awarded to Trio for Complex Computing Model

The Nobel Prize in Chemistry 2013 was awarded jointly to Martin Karplus, Michael Levitt and Arieh Warshel "for the development of multiscale computer models for complex chemical systems".


URL: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/press.html

Contact Person: Diane Kovats (dkovats@iscb.org)

Tuesday, October 1, 2013

FASEB Announces Second Annual Stand Up For Science Video Competition

FASEB Announces Second Annual Stand Up For Science Video Competition

Bethesda, MD - The Federation of American Societies for Experimental Biology (FASEB) is offering a $5,000 prize for a short video to inform Americans about how federal agencies, such as the National Institutes of Health and the National Science Foundation, fund research throughout the country.

"Many Americans are unaware of the critical role the U.S. federal government plays in supporting biological research and discovery," stated FASEB President Margaret "Kenny" Offermann MD, PhD. "It is important that we do not lose sight of the research discoveries that have changed our lives, how they were achieved, and what could be next. We must continue our investment in science."

The competition opens today, October 1, and video submissions will be accepted through November 30, 2013. The winning entrant will be announced in February 2014. FASEB encourages individuals and groups from around the country to participate.

More information about the contest and the entry form can be found on the Stand Up For Sciencecompetition website. Last year's winning entry, "What's Next," underscored the importance of federal funding to science and technology, and highlighted the adverse consequences of spending cuts on innovative research.

FASEB is composed of 27 societies with more than 110,000 members, making it the largest coalition of biomedical research associations in the United States. Our mission is to advance health and welfare by promoting progress and education in biological and biomedical sciences through service to our member societies and collaborative advocacy.


URL: http://www.faseb.org

Contact Person: Lawrence Green (lgreen@faseb.org)