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Ruwansha Galagedara
Origin of life
• All known organisms share the same essential features of genome
replication, gene expression, basic anabolic reactions, and
membrane-associated ATPase mediated energy production
• Monophyletic origin of all known forms of life
• Sets of genes encoding the components of above complex traits were
fixed a long time ago
• What was first? Replication or Metabolism?
Demetrius, L. (1997).
Modularity
• Modularity refers to the relative independence of a biological
component or network
Kussell, E., & Vucelja, M. (2014), Perunov, N., Marsland, R. A., & England, J. L. (2016).
Evolutionary rate
• Kussel & Vucelja
• E. coli Long-term Experimental Evolution Projects
• Examine mutators and the evolution of mutation rates.
• Mutators are bacterial strains with significantly higher mutation rates than
commonly encountered in wild populations.
• In laboratory experiments, mutators have been found to evolve spontaneously,
and can become a dominant majority in a bacterial population.
• Discuss an analogy between population dynamics and polymer
thermodynamics, which identifies a key phase transition that underlies a
number of results relevant to adaptation in fluctuating environments.
• This analogy to understand the emergence of mutators as a function of
fluctuation frequency, selective strength, and mutation rates.
Statistical physics of Evolution
• Stella & Hirsch’s study
• A precise mathematical analogy can be drawn between certain
evolutionary and thermodynamic systems, allowing application of the
powerful machinery of statistical physics to analysis of a family of
evolutionary models.
• Shows that the frequencies of adaptive and deleterious substitutions at
steady state are equal.
• A free fitness function provides an analytical expression for the balance
between natural selection and stochastic drift
• Another study - Analysis of complete Archaeal and Bacterial genomes
unraveled compositional and sequence signals related to molecular
mechanisms of stability and adaptation unaffected by selective sequencing
or by the comparison of orthologs. Overall, codon bias works stronger in
Archaea and is mostly utilized in thermophilic adaptation of nucleic acids.
Stella, G. and Hirsh, A. E. (2005), Goncearenco, A., Ma, B. G., & Berezovsky, I. N. (2014).
Example: The energy–speed–accuracy trade-off in
sensory adaptation
• In biochemical networks, there are many `futile cycles', in which two
pathways run simultaneously in opposite directions dissipating
chemical energy with no apparent function.
• Here, they have showed that these cycles, are crucial in powering
accurate adaptation
• The study reveals a general relation among energy dissipation rate,
adaptation speed and the maximum adaptation accuracy