Mathematical biology

Big question

What was the environment like in which life first arose? What was the temperature, the acidity and the mineral content of the primordial soup in which life first evolved? New information about the primordial environment could help us narrow down the possible mechanisms by which life first arose on earth.

Basic idea

The genetic code is the code that all organisms, from carrots to humans, use to interpret the 64 codons as commands for the production of the 20 amino acids (and the stop). There is evidence that the genetic code is a passively error correcting code in the information theoretic sense. So I asked, what can we learn from the structure of the code about the environment that shaped it? Basically, I suggested to interpret the genetic ode as the oldest available fossil (because it has not changed since our last common ancestor) and to analyze it as such. Its structure should be able to tell us about the evolutionary pressures that were at work when the code formed. With my student Sasha Gutfraind, I published work showing that the code structure indicates that it evolved in organisms that were probably not in a hot environment. (We inferred this when we found the code to be ill adapted to protect organisms from the pattern of mutations that is typical for organisms that are in hot environments - those organisms have an elevated frequency of G's and C's because these base pairs are thermodynamically more stable due to their triple bond). In very recent work with my collaborator J. Jestin we used this approach to study the concentrations of magnesium (Mg) and manganese (Mn) cations in the primordial environment.

Selected publications

  • J.-L. Jestin, A. Kempf, Optimization Models and the Structure of the Genetic Code, Journal of Molecular Evolution 69, pp.452-457 (2009).
  • A. Gutfraind, A. Kempf, Error-reducing Structure of the Genetic Code Indicates Code Origin in Non-thermophile Organisms, Orig. Life Evol. Biosph., 38, 75 (2008)
  • J.-L. Jestin, A. Kempf, Degeneracy in the genetic code: how and why?, Genes, Genomes and Genomics 1, 100-103 (2007)