Seminar: Evolutionary Dynamics of Molecules – Übersicht

As minimal conditions for the emergence of an evolutionary dynamics, the three processes replication, mutation, and selection are needed. How can such an evolutionary dynamics emerge spontaneously with molecules under non-equilibrium conditions? This central question will be explored in the context of recent experimental and theoretical studies.

Papers as ZIP-File: Seminar 1-4, Seminar 5-8, Seminar 9-15  (last updated: Nov 18th)

Note: The Seminar on Jan 11, 2011 has been cancelled !

Schedule

19.10. -  Introduction and selection of topics (Dieter Braun & Ulrich Gerland)

List of Topics and Papers  (last updated: Nov 18th)

26.10. (Gerland)

1 - Why start with an RNA World? [Georg Urtel] Talk PDF Link to Movie

The RNA World, Gilbert, Nature 319, 618 (1986)

Additional Papers:

- The intervening sequence RNA of Tetrahymena is an enzyme, Zaug and Cech, Science 231, 470 (1986)

2.11. (Braun)

2 - Schemes of Simple Replication [Matthias Hiermaier]

A self-replicating hexadeoxynucleotide, von Kiedrowski, Angewandte Chemie International Ed, 25:932–935 (1986)

9.11. (Braun)

3 - Chemical Basis: Polymerization of Nucleotides [Christian Schwall]

Montmorillonite catalysis of 30–50 mer oligonucleotides: Laboratory demonstration of potential steps in the origin of the RNA world, Ferris, Origins of Life and Evolution of Biospheres, 32: 311-332 (2002)

Generation of Long RNA Chains in Water, Costanzo, Pino, Ciciriello and Di Mauro, Journal of biological chemistry, 284: 33206–33216 (2009)

Additional Papers:

- Montmorillonite Catalysis of RNA Oligomer Formation in Aqueous Solution. A Model for the Prebiotic Formation of RNA, Ferris and Ertem, J. Am. Chem. Soc. 115: 12270-12275 (1993)

- Molecular Complexity Favors the Evolution of Ribopolymers, Ciciriello, Costanzo, Pino, Crestini, Saladino and Di Mauro, Biochemistry 47:2732–2742 (2008)

16.11. (Braun)

4 - Catalyzed Replication [Nicolas Kuske]

RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension, Johnston, Bartel et.al., Science 292, 1319 (2001)

23.11. (Gerland)

5 - Future of the RNA World [Michael Hartmann]

Crawling out of the RNA world, Cell, 136, 599 (2009)

30.11. (Braun)

6 - Boundary conditons & Disequilibrium [Arne Hartz]

Model Consideration for the Origin of Life, Hans Kuhn, Naturwissenschaften 63, 68-80 (1976)

Additional Papers:

- The emergence of life from iron monosulphide bubbles at a submarine hydrothermal redox and pH front, Russell and Hall

- Elongation of Oligopeptides in a Simulated Submarine Hydrothermal System, Science, Matsuno et.al. (1999)

- Extreme accumulation of nucleotides in simulated hydrothermal pore systems, PNAS, Braun et.al. (2007)

- Thermal Trap for DNA Replication, PRL, Mast and Braun (2009)

7.12. (Gerland)

7 - Error Threshold [Erik Gawehn]

Bull et al. Quasispecies made simple. PLoS Comput Biol (2005) vol. 1 (6) pp. e61

Additional paper:

Error catastrophe and antiviral strategy, Manfred Eigen, PNAS 99:13374–13376 (2002)

+

13 - Mutation rates & Evolution of Viruses [Michael Rebhan]

Extremely High Mutation Rate of a Hammerhead Viroid, Gago, Elena, Flores and Sanjuán, Science, 323:1308 (2009)

14.12. (Gerland)

15 - RNA evolution [Nicolas Lenner]

W Fontana, P Schuster (1998) Continuity in evolution: On the nature of transitions. Science 280, 1451

Additional paper:

- L W Ancel, W Fontana (2000) Plasticity, evolvability, and modularity in RNA. J Exp Zool 288, 242

21.12. (Braun)

9 - Selection and exponentiality of growth [Francesco Alaimo]

Szathmary: Survival of Replicators with Parabolic Growth Tendency and Exponential Decay (2001)

Additional paper:

Szathmary and Kiedrowski: Selection versus Coexistence of Parabolic Replicators Spreading on Surfaces (2000)

11.1. (Gerland) - cancelled

10 - The origin of the genetic code [Franz Englbrecht]

How old is the genetic code? Statistical geometry of tRNA provides an answer, Eigen, Lindemann, Tietze, Winkler, Science 244, 673 (1989)

18.1. (Gerland)

11 - Emergence of cellularity [Friederike Möller] Talk PDF

The emergence of cells during the origin of life, Chen, Science, 314:1558 (2006)

Additional paper:

- The emergence of Competition between model protocells, Chen, Roberts, Szostak, Science 305:1474 (2004)

25.1. (Gerland)

12 - Proofreading [Johannes Nagele]

J J Hopfield (1974) Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. PNAS 71, 4135.

Additional papers:

- J J Hopfield, T Yamane, V Yue, S M Coutts (1976) Direct experimental evidence for kinetic proofreading in amino acylation of tRNAIle. PNAS 73, 1164.

-  T Yamane, J J Hopfield (1977) Experimental evidence for kinetic proofreading in the aminoacylation of tRNA by synthetase. PNAS 74, 2246.

1.2. (Braun)

8 - Hypercycles [Dominik Thalmeier] (after christmas, 1.2.)

Hypercycles and the origin of life, JM Smith, Nature 280:445-446 (1979).

Additional paper:

The hypercycle, M Eigen, P Schuster, Naturwissenschaften 65, 7-41 (1978)

pwd biophysics