Archive for category Systems Biology

Systems Biology Videos

Selected videos at the cutting edge of science. Genetic diversity reflects evolutionary pressures from environmental changes, principally climate and diet. These drivers explain why populations and individuals vary and why one-size-fits-all dietary guidelines and public health nutrition approaches derive from out-of-date reductionist science. Nutritional therapy is person-centred, recognising individuality and the complex network of environmental factors which influence health status.

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Systems Biology and Human Health

Despite clear scientific support for the fact that human biology shares many of the characteristics of complex adaptive systems  which requires a systems biology approach for full understanding, the orthodox linear medical model which sees the body as a machine with simple effects localised to a single cause persists strongly in conventional medical approaches to healthcare. See the paper on “Non-linear dynamics for clinicians: chaos theory, fractals, and complexity at the bedside” in the Lancet here: and another example of an article in Nature on systems biology of the cell here:

Complex adaptive systems are known to be highly flexible and are constantly poised on the edge of being a coherent organized system and collapsing into what appears like chaos. They thrive in their instability allowing them to adapt at the edge of chaos. They are non-linear and attempts to control them can be destructive. They cannot be broken down into separate, more simple parts and small stimuli can lead to disproportionately large changes in the entire system.

A good example of a such as system is the human autonomic nervous system as measured by heart rate variability. It is well understood that when a human heart beats healthily, it follows a chaotic pattern. When it beats too uniformly, it is a sign of chronic stress and ill health. See a full paper on heart rate variability, standards of measurement, physiological interpretation, and clinical use by the  Task Force of the European Society of Cardiology and the North American Society of Pacing and Electrophysiology here: and more discussion in Scientific American here:  Chaos and fractals in human physiology:

Another example is the human immune system and especially how it interacts with the complex adaptive system known as the gut microflora “ecosystem.” Scientists are now starting to use quantitative computing methods based on non-linear models of dynamic complexity theory to predict the changes resulting from stimuli on this internal ecosystem. See “The emerging medical ecology of the human gut microbiome in Trends in Ecology & Evolution, 2012 here:

Please watch the videos in the order they appear starting at number 1.

1) TEDMED 2012 – Albert-László Barabási

Albert-László Barabási is a Distinguished University Professor at Northeastern University, where he directs the Center for Complex Network Research, and holds appointments in the Departments of Physics, Computer Science and Biology, as well as in the Department of Medicine, Harvard Medical School and Brigham and Women Hospital, and is a member of the Center for Cancer Systems Biology at Dana Farber Cancer Institute. A Hungarian born native of Transylvania, Romania, he received his Masters in Theoretical Physics at the Eötvös University in Budapest, Hungary and was awarded a Ph.D. three years later at Boston University. After a year at the IBM T.J. Watson Research Center, he joined Notre Dame as an Assistant Professor, and in 2001 was promoted to the Professor and the Emil T. Hofman Chair. Barabási latest book is “Bursts: The Hidden Pattern Behind Everything We Do” (Dutton, 2010) available in five languages. He has also authored “Linked: The New Science of Networks” (Perseus, 2002), currently available in eleven languages, is co-author of “Fractal Concepts in Surface Growth” (Cambridge, 1995), and the co-editor of “The Structure and Dynamics of Networks” (Princeton, 2005). His work lead to the discovery of scale-free networks in 1999, and proposed the Barabasi-Albert model to explain their widespread emergence in natural, technological and social systems, from the cellular telephone to the WWW or online communities. His work on complex networks have been widely featured in the media, including the cover of Nature, Science News and many other journals, and written about in Science, Science News, New York Times, USA Today, Washington Post, American Scientist, Discover, Business Week, Die Zeit, El Pais, Le Monde, London’s Daily Telegraph, National Geographic, The Chronicle of Higher Education, New Scientist, and La Republica, among others. He has been interviewed by BBC Radio, National Public Radio, CBS and ABC News, CNN, NBC, and many other media outlets.

2) Emergence – Complexity from Simplicity, Order from Chaos (1 of 2)

3) Emergence – Complexity from Simplicity, Order from Chaos (2 of 2)

4) Modeling Complex Adaptive Systems – John Holland PhD

John H. Holland is professor of computer science and engineering and professor of psychology at the University of Michigan; he is also external professor and member of the executive committee of the board of trustees at the Santa Fe Institute. Professor Holland was made a MacArthur fellow in 1992 and is a fellow of the World Economic Forum. He serves on the Advisory Board on Complexity at the McDonnell Foundation. Professor Holland has been interested for more than 40 years in what are now called complex adaptive systems (CAS). He formulated genetic algorithms, classifier systems, and the Echo models as tools for studying the dynamics of such systems. His books Hidden Order (1995) and Emergence (1998) summarize many of his thoughts about complex adaptive systems. Research Interests include the study of cognitive processes and complex adaptive systems in general, using mathematical models and computer simulation.


5) 2011 Allen Institute of Brain Science Symposium – Dr Eric Schadt

Chairman, Department of Genetics and Genomic Sciences; Director, Institute of Genomics and Multiscale Biology; Jean C. and James W. Crystal Professor of Genomics, Mount Sinai School of Medicine, New York City.

Dr. Eric Schadt, a visionary in the use of computational biology in genomics, joined the Mount Sinai School of Medicine in August 2011. His focus is on generating and integrating large-scale, high-dimension molecular, cellular, and clinical data to build more predictive disease models that will improve the ability to diagnosis and treat diseases.

His efforts are motivated by the genomics and systems biology research he led as Executive Scientific Director of Genetics at Rosetta Inpharmatics, a subsidiary of Merck & Co., to elucidate common human diseases and drug response using novel computational approaches applied to genetic and molecular profiling data. His research helped revolutionize a field in statistical genetics (the genetics of gene expression), has energized the systems biology field, and has led to a number of discoveries relating to the causes of common human diseases. When Dr. Schadt left Merck in 2009, more than 50% of all the company’s new drug discovery programs in the metabolic space were derived from his work.

Since June 2009, Dr. Schadt has served as Chief Scientific Officer (CSO) of Pacific Biosciences, overseeing the firm’s scientific strategy including creating the vision for next-generation sequencing applications of the company’s technology. He currently retains that position, and Mount Sinai will use technology platforms from Pacific Biosciences to query biological data.

Dr. Schadt is a founding member of Sage Bionetworks, an open access genomics initiative designed to build and support databases and an accessible platform for creating innovative, dynamic disease models.

Dr. Schadt has co-authored numerous studies on gene expression and analysis published in peer-reviewed medical journals including Nature, Nature Genetics and The New England Journal of Medicine (NEJM).

Recently appointed Fellow to the Institute of Systems and Synthetic Biology, Imperial College London, Dr. Schadt received a Ph.D. in bio-mathematics from the University of California, Los Angeles (UCLA) (requiring Ph.D. candidacy in molecular biology and mathematics); an M.A. in pure mathematics from the University of California, Davis (UCD); and a B.S. in applied mathematics/computer science from California Polytechnic State University.

6) Mitochondrial Paradigm for Degenerative Diseases, Aging and Cancer Research on Aging – Dr Douglas Wallace

Dr. Douglas Wallace is the Director of the Center for Molecular & Mitochondrial Medicine and Genetics, University of California at Irvine. He is one of the nation’s leading genetics researchers, helping to discover how defects in inherited genes contribute to neurodegenerative diseases such as Parkinson’s and Alzheimer’s. Through his research, Wallace has shown that defects in mitochondrial genes are major contributors to degenerative diseases, cancer and aging. A recent study of his, published in the Proceedings of the National Academy of Sciences, shows a link between mtDNA mutations and prostate cancer. He’s using that link now to test non-toxic drugs to kill prostate cancer in mice.

7) Scaling Laws in Biology and Other Complex Systems – Geoffrey H West PhD

Science Board, Science Steering Committee Distinguished Professor and Past President, Santa Fe Institute. Geoffrey West is a theoretical physicist whose primary interests have been in fundamental questions in physics, especially those concerning the elementary particles, their interactions and cosmological implications. West served as SFI President from July 2005 through July 2009. Prior to joining the Santa Fe Institute as a Distinguished Professor in 2003, he was the leader, and founder, of the high energy physics group at Los Alamos National Laboratory, where he is one of only approximately ten Senior Fellows.

His long-term fascination in general scaling phenomena evolved into a highly productive collaboration on the origin of universal scaling laws that pervade biology from the molecular genomic scale up through mitochondria and cells to whole organisms and ecosystems. This led to the development of realistic quantitative models for the structural and functional design of organisms based on underlying universal principles. This work, begun at the Institute, has received much attention in both the scientific and popular press, and provides a framework for quantitative understanding of problems ranging from fundamental issues in biology (such as cell size, growth, metabolic rate, DNA nucleotide substitution rates, and the structure and dynamics of ecosystems) to questions at the forefront of medical research (such as aging, sleep, and cancer). Among his current interests is the extension of these ideas to understand quantitatively the structure and dynamics of social organizations, such as cities and corporations, including the relationships between economies of scale, growth, innovation and wealth creation and their implications for long-term survivability and sustainability.

He is a Fellow of the American Physical Society and was one of their Centenary Speakers in 2003. He has been a lecturer in many popular and distinguished scientist series worldwide, as well as at the World Economic Forum. Among recent honors he was a co-receiver of the Mercer Award from the Ecological Society of America, the Weldon Memorial Prize (2005), Oxford University and the Glenn Award for research on Aging. In 2006 he was named one of Time magazine’s”100 Most Influential People in the World” and his work selected as one of the breakthrough ideas of 2007 by the Harvard Business Review. He is the author of several books, a visiting Professor of Mathematics at Imperial College, London, and an Associate Fellow of the Said Business School at Oxford University.

West received his BA from Cambridge University in 1961 and his doctorate from Stanford University in 1966, where he returned in 1970 to become a member of the faculty. West is married to Jacqueline West, a psychologist in private practice; they have two children: Joshua, a geologist at Oxford University and an Olympic silver-medalist, and Devorah, a political scientist at the Brookings Institute.

8) Systems Approaches to Understanding Circadian Transcriptional Networks – Steven A. Kay PhD

Dr. Steve Kay is currently the Dean of the Division of Biological Sciences and holds the Richard C. Atkinson Chair in the Biological Sciences at the University of California, San Diego, and Distinguished Professor of Cell and Developmental Biology.  Previously, he was Chairman, Department of Biochemistry, Professor of Cell Biology and Director of the Institute for Childhood and Neglected Diseases at The Scripps Research Institute (TSRI) in La Jolla where he was a faculty member from 1996 to 2007.  His academic research concerns the molecular genetic basis of circadian rhythms in plants, animals and humans. He was also recently the Director of Discovery Research at the Genomics Institute of the Novartis Research Foundation (GNF), where he built a large Department of applying human genome science to biomedical research and drug discovery. Dr. Kay was also the founder, former Chief Technology Officer and Senior Vice President of Phenomix Corporation, a drug discovery and development company based in San Diego.

9) System Approaches to Biology and Medicine and the emergence of proactive P4 medicine – Dr Lee Hood 

Leroy Hood, MD, PhD, President and co-founder of the Institute for Systems Biology in Seattle, is a pioneer in systems approaches to biology and medicine. Dr. Hood’s research has focused on the study of molecular immunology, biotechnology and genomics. His professional career began at Caltech, where he and his colleagues developed the DNA sequencer and synthesizer and the protein synthesizer and sequencer–four instruments that paved the way for the successful mapping of the human genome and lead to his receiving this year’s prestigious Russ Prize, awarded by the Academy of Engineering. A pillar in the biotechnology field, Dr. Hood has played a role in founding more than fourteen biotechnology companies, including Amgen, Applied Biosystems, Darwin, The Accelerator and Integrated Diagnostics. He is a member of the National Academy of Sciences, the National Academy of Engineering, and the Institute of Medicine, one of only 10 people in the world to be elected to all three academies. In addition to having published more than 700 peer reviewed articles, he has coauthored textbooks in biochemistry, immunology, molecular biology and genetics, as well as a popular book on the human genome project, The Code of Codes. He is the recipient of numerous awards, including the Lasker Award, the Kyoto Prize and the Heinz Award in Technology. Dr. Hood has also received 17 honorary degrees from prestigious universities in the US and other countries.

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