Posts Tagged ‘Bioinformatics’

Brief curriculum vitae of Francisco Varela

Friday, May 15th, 2009

1965 Bachelor of Engineering Physics, Cornell University

1970 Ph.D., Biology, Princeton University

1969-1972 Assistant Professor, University of Chicago

1972-1979 Associate Professor of Biological Sciences, Purdue University

1979-1986 Professor of Biological Sciences, Purdue University

1986-2002 Professor of Ecology and Evolutionary Biology, University of Arizona

1989-2002 Regents Professor, University of Arizona

Who is Arthur Winfree

Friday, May 15th, 2009

Arthur Taylor Winfree (May 15, 1942 - November 5, 2002) was a noted theoretical biologist at the University of Arizona. He was born in St. Petersburg, Florida, United States.

Winfree was noted for his work on the mathematical modeling of biological phenomena: from cardiac arrhythmia and circadian rhythms to the self-organization of slime mold colonies and the Belousov-Zhabotinsky reaction. Winfree was a MacArthur Fellow from 1984 to 1989 and shared the 2000 Norbert Wiener Prize in Applied Mathematics with Alexandre Chorin.

He was the father of Erik Winfree, another MacArthur Fellow and currently a professor at the California Institute of Technology.

Work of Francisco Varela

Friday, May 15th, 2009

Varela was primarily trained as a biologist, and was fundamentally influenced by his teacher and fellow Chilean, Humberto Maturana, also a biologist with a strong philosophical orientation.

Varela wrote and edited a number of books and numerous journal articles in biology, neurology, cognitive science, mathematics, and philosophy. He was a founding member of the Integral Institute, a thinktank dedicated to the cross-fertilization of ideas and disciplines.

Varela was a proponent of the embodied philosophy which argues that human cognition and consciousness can only be understood in terms of the enactive structures in which they arise, namely the body (understood both as a biological system and as personally, phenomenogically experienced) and the physical world with which the body interacts. He introduced into neuroscience the concepts of neurophenomenology, based on the phenomenological writings of Edmund Husserl and of Maurice Merleau-Ponty, and on “first person science,” in which observers examine their conscious experience using scientifically verifiable methods.

Biography of Francisco Varela

Friday, May 15th, 2009

Francisco Varela was born in 1946 in Santiago in Chile. Like his mentor Humberto Maturana, Varela studied first medicine then biology at the University of Chile, then did a Ph.D. in biology at Harvard University. His thesis, defended in 1970 and supervised by Torsten Wiesel, was titled Insect Retinas: Information processing in the compound eye.

After the 1973 military coup led by Augusto Pinochet, Varela and his family spent 7 years in exile in the USA before returning to Chile to become a Professor of biology.

Varela became a Tibetan Buddhist in the 1970s, initially studying with the meditation master Chögyam Trungpa Rinpoche, founder of Vajradhatu and Shambhala Training, and later with Tulku Urgyen Rinpoche, a Nepalese meditation master of higher tantras.

In 1986, he settled in France, where he at first taught cognitive science and epistemology at the École Polytechnique, and neuroscience at the University of Paris. From 1988 until his death, he led a research group at the CNRS (Centre National de Recherche Scientifique).

He died in 2001 in Paris of Hepatitis C after having written an account of his 1998 liver transplant.[1]. Varela had four children, including the actress, environmental spokesperson, and model Leonor Varela.

Who is Francisco Varela

Friday, May 15th, 2009

Francisco Javier Varela García (September 7, 1946 – May 28, 2001), was a Chilean biologist, philosopher and neuroscientist who, together with his teacher Humberto Maturana, is best known for introducing the concept of autopoiesis to biology.

Who is Eörs Szathmáry

Friday, May 15th, 2009

Eörs Szathmáry (born 1959) is a Hungarian theoretical evolutionary biologist at Collegium Budapest (Institute for Advanced Study and at the Department of Plant Taxonomy and Ecology of Eötvös Loránd University, Budapest. He is the co-author with John Maynard Smith of The Major Transitions in Evolution.

His main interest is theoretical evolutionary biology and focuses on the common principles of the major steps in evolution, such as the origin of life, the emergence of cells, the origin of animal societies, and the appearance of human language. Together with his mentor, John Maynard Smith, he has published two important books which serve as the main references in the field (The Major Transitions in Evolution, Freeman, 1995, and The Origins of Life, Oxford University Press, 1999). Both books have been translated into other languages (so far, German, French, Japanese, and Hungarian). He serves on the editorial board of several journals (Journal of Theoretical Biology, Journal of Evolutionary Biology, Origins of Life and Evolution of the Biosphere, Evolutionary Ecology and Evolution of Communication). Professor Szathmáry was awarded the New Europe Prize in 1996 by a group of institutes for advanced study. He used the prize to establish the NEST (New Europe School for Theoretical Biology) foundation, whose task is to help young Hungarian theoretical biologists. The Juhász-Nagy junior fellowship that he endowed in 1996 at Collegium Budapest also serves this purpose. In 1996 he was the Executive Vice-President of ICSEB V (Fifth International Congress of Systematic and Evolutionary Biology) that took place in Budapest, partially sponsored by CB. He served as President of the International Organisation for Systematic and Evolutionary Biology (IOSEB, 1996-2002). The Hungarian Academy of Sciences acknowledged his outstanding scientific contribution with the Academy Prize in 1999. He was invited to prestigious institutions, including the Wissenschaftskolleg zu Berlin and the College de France. He is a member of Academia Europaea and the Hungarian Academy of Sciences.

Professor Szathmáry’s main achievements include: (i) a mathematical description of some phases of early evolution; (ii) a scenario for the origin of the genetic code; (iii) an analysis of epistasis in terms of metabolic control theory; (iv) a demonstration of the selection consequences of parabolic growth; (v) a derivation of the optimal size of the genetic alphabet; (vi) a general framework to discuss the major transitions in evolution. Apart from books, he has published numerous papers in important journals, including Nature, Science, Proceedings of the National Academy of Sciences of the USA, and Journal of Theoretical Biology.

Awards and Honors of George Sugihara

Friday, May 15th, 2009

Sugihara is also the recipient of various international awards. Recently he was a Visiting Research Fellow at Merton College, Oxford and is currently appointed to the National Academies Board on Mathematical Sciences and it’s Applications

Research of Paulien Hogeweg

Friday, May 15th, 2009

Starting with asynchronous extensions of L-systems she pioneered agent-based modeling studying development of social structure in animal societies, using the opportunity based “ToDo” principle where agents “do what there is to do”, and a “DoDom” principle for dominance ranking also known as the winner-loser effect [2]. This type of research later became popular in artificial life.

When the first biological sequence data became available (from the EMBL) she developed a tree based algorithm for multiple sequence alignment [3], which is now common practice in sequence alignment and phylogeny. At about the same time she pioneered folding algorithms for predicting RNA secondary structures [4]. RNA folding was also introduce to allow for a non-linear genotype to phenotype mapping to study evolution on complex fitness landscapes [5].

The first phase-phase trajectory of a chaotic attractor in an ecological food-chain model of three differential equations appeared long before chaos became popular [6]. She pioneered the use of cellular automata for studying spatial ecological and evolutionary processes and demonstrated that spatial pattern formation can revert evolutionary selection pressures [7].

Extending the Cellular Potts model (CPM) to study morphogenesis and development she modeled the complete life cycle of Dictyostelium discoideum using simple rules for chemotaxis and differential adhesion [8]. This CPM approach is now used for modeling in various areas of developmental biology, and the migration of immune cells in lymphoid tissues. Finally the CPM is used for EvoDevo research.

Current work is on gene regulation networks, prebiotic evolution and properties of fitness landscapes of RNA replicators.

Biography of Paulien Hogeweg

Friday, May 15th, 2009

Paulien Hogeweg founded the Theoretical Biology & Bioinformatics group at Utrecht University in 1977 and has been its group leader until 2009. She graduated from the University of Amsterdam in 1969 and received her PhD at Utrecht University in 1976 on the thesis “Topics in Biological Pattern Analysis” on biological pattern formation and pattern recognition. The first part of her scientific career she collaborated intensively with Ben Hesper.

Who is Paulien Hogeweg

Friday, May 15th, 2009

Paulien Hogeweg (1943) is a Dutch theoretical biologist and complex systems researcher studying biological systems as dynamic information processing systems at many interconnected levels. Together with Ben Hesper she coined the term Bioinformatics in 1978 [1] as the study of informatic processes in biotic systems. The first use of this now so popular term was identified by the Oxford English dictionary. In her research she stands out as a pioneer, being the first to develop new concepts and computational approaches in various areas of biology.


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