darwin, self-organization and molecules
TRANSCRIPT
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Darwin, self-organization and molecules
Peter Schuster
Institut für Theoretische Chemie, Universität Wien, Austriaand
The Santa Fe Institute, Santa Fe, New Mexico, USA
Darwin and the Origin of Life
San Sebastian - Donostia, 22.05.2009
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Web-Page for further information:
http://www.tbi.univie.ac.at/~pks
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Color patterns on animal skins and wings
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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Alan M. Turing, 1912-1954
Change in local concentration =
= diffusion + chemical reaction
A.M. Turing. 1952. The chemical basis of morphogenesis. Phil.Trans.Roy.Soc.London B 237:37-72.
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Belousov-Zhabotinskii reaction 1959Liesegang rings 1895
Turing pattern: Boissonade, De Kepper 1990
Pattern formation through chemical self-organization:
Liesegang rings through precipitation from oversaturatedsolutions,
space-time patterns of the Belousov-Zhabotinskii reaction,
and stationary Turing pattern.
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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mother presumptivefather
daughter
Skin patterns in an inbred strain of cats
Parents and daughter
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Bates‘ mimicry Müller‘s mimicry
Different forms of mimicry observed in nature
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Bates‘ mimicry
milk snake
false coral snake
Different forms of mimicry observed in nature
Emsley‘s or Mertens‘ mimicry
coral snake
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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Three necessary conditions for Darwinian evolution:
1. Multiplication
2. Variation
3. Selection
Empirically recognized principle of natural selection
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1.01
12 =−
=f
ffs
Two variants with a mean progeny of ten or eleven descendants
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01.0,02.0,1.0;1)0(,9999)0( 21 === sNN
Selection of advantageous mutants in populations of N = 10 000 individuals
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time
Charles Darwin, The Origin of Species, 6th edition. Everyman‘s Library, Vol.811, Dent London, pp.121-122.
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Modern phylogenetic tree: Lynn Margulis, Karlene V. Schwartz. Five Kingdoms. An Illustrated Guide to the Phyla of Life on Earth. W.H. Freeman, San Francisco, 1982.
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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Genotype, GenomeGCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAGATCTGGAGGTCCTGTGTTCGATCCACAGAATTCGCACCA
Phenotype
Unf
oldi
ng o
f th
e ge
noty
pe
geneticsepigeneticsenvironment
biochemistrymolecular biologystructural biology
molecular evolutionmolecular genetics
systems biologybioinfomatics
Gerhard Braunitzerhemoglobin sequence
systems biology
‘the new biology is the chemistry of living
matter’
Linus Pauling andEmile Zuckerkandlmolecular evolution
ManfredEigen
James D. Watson undFrancis H.C. Crick
DNA structure
DNA
RNA
Thomas CechRNA catalysis
Max Perutz
John Kendrew
protein
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James D. Watson, 1928-, and Francis H.C. Crick, 1916-2004
Nobel prize 1962
1953 – 2003 fifty years double helix
The three-dimensional structure of a short double helical stack of B-DNA
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DNA structure and DNA replication
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Point mutation
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Point mutation
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Point mutation
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Reconstruction of phylogenies through comparison of molecular sequence data
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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RNA sample
Stock solution: Q RNA-replicase, ATP, CTP, GTP and UTP, buffer
Time0 1 2 3 4 5 6 69 70
Application of the serial transfer technique to RNA-evolution in the test tube
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An example of ‘artificial selection’ with RNA molecules or ‘breeding’ of biomolecules
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tobramycin
RNA aptamer, n = 27
Formation of secondary structure of the tobramycin binding RNA aptamer with KD = 9 nM
L. Jiang, A. K. Suri, R. Fiala, D. J. Patel, Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chemistry & Biology 4:35-50 (1997)
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The three-dimensional structure of the tobramycin aptamer complex
L. Jiang, A. K. Suri, R. Fiala, D. J. Patel, Chemistry & Biology 4:35-50 (1997)
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1. Pattern formation in physics and chemistry
2. Pattern formation in biology
3. Darwins natural selection and the origin of life
4. Molecular biology and evolution
5. Evolution in the test tube
6. Complexity in biology
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The bacterial cell as an example for a simple form of autonomous life
Escherichia coli genome:
4 million nucleotides
4460 genes
The structure of the bacterium Escherichia coli
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August Weismann, 1834-1914
Separation of germ line and soma
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Cascades, A B C ... , and networks of genetic control
Turing pattern resulting from reaction-diffusion equation ?
Intercelluar communication creating positional information
Development of the fruit fly drosophila melanogaster: Genetics, experiment, and imago
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E. coli: Genome length 4×106 nucleotidesNumber of cell types 1Number of genes 4 460
Four books, 300 pages each
Man: Genome length 3×109 nucleotides
Number of cell types 200
Number of genes 30 000
A library of 3000 volumes, 300 pages each
Complexity in biology
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Wolfgang Wieser. 1998. ‚Die Erfindung der Individualität‘ oder ‚Die zwei Gesichter der Evolution‘. Spektrum Akademischer Verlag,Heidelberg 1998
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(REL
ATIV
E BR
AIN
MAS
S x
1000
)2/3
BRITISH TIT
Alan C. Wilson.1985. The molecular basis of evolution.Scientific American 253(4):148-157.
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Evolution does not design with the eyes of an engineer, evolution works like a tinkerer.
François Jacob. The Possible and the Actual. Pantheon Books, New York, 1982, and
Evolutionary tinkering. Science 196 (1977), 1161-1166.
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The difficulty to define the notion of „gene”.
Helen Pearson,Nature 441: 399-401, 2006
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ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816, 2007
ENCODE stands forENCyclopedia Of DNA Elements.
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Web-Page for further information:
http://www.tbi.univie.ac.at/~pks
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