Nigel Goldenfeld's Group: Physical and Quantitative Biology






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Physical biology is the study of living systems from a physical sciences perspective. In Nigel Goldenfeld's group, this means using approaches from statistical physics to explore the collective properties of biological systems, in particular how they evolve and behave as complex spatially-extended dynamical systems. Because biological systems have, by definition, the capacity to evolve, they exhibit biocomplexity -- a higher level of complexity than occurs in purely physical systems.

Quantitative biology is the study of living systems using precise measurements and theoretical techniques, and is not necessarily physical biology, although it often is. Goldenfeld works closely with biological colleagues in an effort to bring precision and predictability to the interplay between conceptual modeling, theory and experiment.

Nigel Goldenfeld's group is housed in the Department of Physics, the Center for the Physics of Living Cells, and the Institute for Genomic Biology, where he leads the Theme on Biocomplexity.

Examples of the group's work are briefly summarized below:

Scaling laws in ecology: A fundamental problem in ecology is the estimation of biodiversity.  Empirically, it is found that the number of species S in a biome of area A scales with a power law of A.  Typically, this power law is found to be  in the range 0.2-0.25 although other values are sometimes found, depending on the nature of the habitat.  This species-area law is an example of a universal scaling law in biology, obeyed with good precision over more than 10 orders of magnitude in scale.  The universal nature of the species-area law suggests that there is a general mechanism for its occurrence.  We have recently discovered that species-area law relationships can follow ubiquitously from very general mathematical properties of species correlation functions, especially clustering.  Ongoing work involves computational models of ecosystems to test these properties, and to extend the predictions to addressing the hotly-debated issue of species abundance distributions.

Microbial ecology: Microbial ecology is still in its infancy and is only now beginning to emerge from the era of simply estimating diversity from environmental DNA.  Trends that we are exploring include the quantification of community-wide genomes (metagenomics) in diverse ecosystems and computer-intensive statistical methods for estimating microbial abundance distributions cheaply and quickly from environmental DNA stored in clone libraries.  Our field work is primarily carried out at the geothermal hot spring system at Mammoth, Yellowstone National Park, which exhibits a spectacular diversity gradient downstream of the actual vent.  The Mammoth Hot Spring system creates a spectacular carbonate landscape that represents a fascinating pattern formation problem in its own right. We are studying the dynamics of carbonate precipitation also, using minimal models incorporating fluid and precipitation dynamics. This work is conducted in collaboration with Professor Bruce Fouke in the Geology department.

Evolution of the genetic code: Over the last decade, it has become clear that the canonical genetic code is not a "frozen accident", but has been highly optimized with respect to a property of amino acids known as the "polar requirement", first measured by Carl Woese.  Recent work has documented convincingly this optimal property, but relatively little attention has been paid to the mechanisms by which this optimization might have occurred.  Our research has been exploring the possibility that at least some of this optimization arose during an era in which lateral gene transfer was rampant in the community of primitive organisms from which emerged the Last Universal Common Ancestor.  On the basis of genetic algorithm simulations of a caricature of translation, we have found that lateral gene transfer is a far more effective optimization process than conventional vertical descent.  Ongoing research is exploring more detailed measures of the genetic code, more realistic models of genome dynamics, and molecular dynamics calculations to explore the significance of the polar requirement.  This work is conducted in collaboration with Professors Carl Woese (Microbiology) and Zaida Luthey-Schulten (Chemistry).

Microbial speciation: Whether or not microbes exhibit well-defined species is a hotly-debated question, that will become experimentally accessible as more and more microbial genomes are sequenced.  We have been exploring dynamical mechanisms for global sequence divergence in microbes, leading to "speciation" through competition between recombination and mutation.  Through simple models and genetic algorithm simulations, we have identified a mechanism for sequence divergence even in the absence of selection, via the propagation of fronts along genomes.  We are currently exploring the phase diagram of microbial genomes and performing bioinformatics studies of available genomes of closely-related strains in order to identify markers of our new mechanism.

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