Biological Treatment and Downstream Processing of Perchlorate
Information and Information Processing in Biological Systems
Transcript of Information and Information Processing in Biological Systems
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Information and Information Processingin Biological Systems
Peter Schuster, Eörs Szathmáry, and Avshalom Elitzur
Institut für Theoretische Chemie, Universität Wien, Austria,
Collegium Budapest – Institute for Advanced Study , Ungarn, and
Bar-Ilan University, Israel
Europäisches Forum Alpbach
Alpbach, 18.– 25.08.2005
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Web-Pages for further information:
http://www.tbi.univie.ac.at/~pkshttp://www.colbud.hu/fellows/szathmary.shtml
http://faculty.biu.ac.il/~elitzua/
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Program
Friday, Aug.19:9:00-9:30 Peter Schuster, Evolution and Information9:30-10:15 Avshalom Elitzur, Information, Complexity and the Physics of Life10:15-10:30 Coffee Break10:30-11:30 Avshalom Elitzur, Information, Complexity and the Physics of Life11:30-12:00 Discussion
Saturday, Aug.20:9:00-10:00 Eörs Szathmáry, Genetics and Genes. Mendel 1865 and Today10:00-10:30 Coffee Break10:30-11:30 Peter Schuster, Multiplication, Mutation and Selection11:30-12:00 Discussion
Monday, Aug.22:9:00-10:00 Eörs Szathmáry, Error Propagation in Cellular Information Processing10:00-10:30 Coffee Break10:30-12:00 Avshalom Elitzur, Peter Schuster, and Eörs Szathmáry,
Physics, Biology, Evolution and Information –Panel Discussion
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Program
Tuesday, Aug.23:9:00-10:00 Peter Schuster, Evolution Experiments in the Laboratory10:00-10:30 Coffee Break10:30-12:00 Contribution by Participants and Discussion
Wednesday, Aug.24:9:00-10:00 Eörs Szathmáry, Development – From Cells to Organisms10:00-10:30 Coffee Break10:30-12:00 Contribution by Participants and Discussion19:00- Informal Discussion at Hotel Alpbach
Thursday, Aug.25:9:00-9:30 Peter Schuster, Primitive Forms of Learning9:30-9:45 Hans Flohr, Semantic Information9:45-10:30 Eörs Szathmáry, Language10:30-11:00 Coffee Break11:00-12:00 Avshalom Elitzur, Peter Schuster, and Eörs Szathmáry,
Summary of the Seminar and Panel Discussion
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Evolution and Information
Peter Schuster, Institut für Theoretische Chemie, Universität Wien
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Genotype, Genome
Phenotype
Unf
oldi
ng o
f th
e ge
noty
pe
Highly specific environmental conditions
Developmental program
Collection of genes
Evolution
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Genotype, GenomeGCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAGATCTGGAGGTCCTGTGTTCGATCCACAGAATTCGCACCA
Phenotype
Unf
oldi
ng o
f th
e ge
noty
pe
Highly specific environmental conditions
Biochemistrymolecular biologystructural biology
molecular evolutionmolecular genetics
systems biology bioinfomatics
Max PerutzHemoglobin sequenceGerhard Braunitzer
Molecular evolutionLinus Pauling andEmile Zuckerkandl
The exciting RNA story
evolution of RNA molecules,ribozymes and splicing,
the idea of an RNA world,selection of RNA molecules,
RNA editing,the ribosome is a ribozyme,
small RNAs and RNA switches.
Omics‘the new biology is
the chemistry ofliving matter’
James D. Watson undFrancis H.C. Crick
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Earlier abstract of the ‚Origin of Species‘
Alfred Russell Wallace, 1823-1913Charles Robert Darwin, 1809-1882
The two competitors in the formulation of evolution by natural selection
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Key ingredients in Darwin‘s theory of evolution are:
(i) Variations occurring spontaneously and not themselves produced by the environment,
(ii) Competition for resources, so that only the best adapted survive to reproduce, and, therefore
(iii) Selection by the environment, of which variants will survive and increase in number.
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dx / dt = x - x
x
i i i
j j
; Σ = 1 ; i,j
f
f
i
j
Φ
Φ
fi Φ = (
= Σ
x - i )
j jx =1,2,...,n
[I ] = x 0 ; i i i =1,2,...,n ; Ii
I1
I2
I1
I2
I1
I2
I i
I n
I i
I nI n
+
+
+
+
+
+
(A) +
(A) +
(A) +
(A) +
(A) +
(A) +
fn
fi
f1
f2
I mI m I m++(A) +(A) +fm
fm fj= max { ; j=1,2,...,n}
xm(t) 1 for t
[A] = a = constant
Reproduction of individuals as basis of selection
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s = ( f2-f1) / f1; f2 > f1 ; x1(0) = 1 - 1/N ; x2(0) = 1/N
200 400 600 800 1000
0.2
00
0.4
0.6
0.8
1
Time [Generations]
Frac
tion
of a
dvan
tage
ous v
aria
nt
s = 0.1
s = 0.01
s = 0.02
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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4 4
2+ + 3+
2 2+
Dominant/recessive pair of allelesIntermediate pair of alleles
2 2+
F2 = F1 F1
F1
P
F1 = P P
P F1 ×Gregor Mendels laws of inheritance:Versuche über Pflanzen-Hybriden.Verhandlungen des naturforschenden Vereins in Brünn, 4: 3-47 (1865)Presented at the Meetings of 08.02. and 08.03.1965
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John Burdon Sanderson Haldane, 1892-1964
Sir Ronald Aylmer Fisher, 1890-1962 Sewall Wright, 1889-1988
The three scholars of theoretical population biology
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Theodosius Dobzhansky, 1900 – 1975
„Nothing in biology makes sense except in the light of evolution.“
Evolution is the comprehensive basis of macroscopic and molecular biology
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Ernst Mayr, 1904 – 2005
Author of the book:
‚The Origin of Biological Thought‘
The best known proponent of the ‚Neo-Darwinian‘ or synthetic theory of evolution which reconciled Darwinian evolutionary biology and Mendelian genetics.
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The three-dimensional structure of a short double helical stack of B-DNA
James D. Watson, 1928- , and Francis Crick, 1916-2004,Nobel Prize 1962
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Canonical Watson-Crick base pairs:
cytosine – guanineuracil – adenine
W.Saenger, Principles of Nucleic Acid Structure, Springer, Berlin 1984
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Complementary replication is the simplest copying mechanismof RNA.Complementarity is determined by Watson-Crick base pairs:
G C and A=U
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G
G
G
C
C
C
G
C
C
G
C
C
C
G
C
C
C
G
C
G
G
G
G
C
Plus Strand
Plus Strand
Minus Strand
Plus Strand
3'
3'
3'
3'
5'
3'
5'
5'
5'
Point Mutation
Insertion
Deletion
GAA AA UCCCG
GAAUCC A CGA
GAA AAUCCCGUCCCG
GAAUCCA
Mutations in nucleic acids represent one mechanism of variation of genotypes.
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‚Replication fork‘ in DNA replication
The mechanism of DNA replication is ‚semi-conservative‘
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Genetic recombination as the second mechanism of variation is the molecular basis
of Mendelian genetics.
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Max Perutz, 1914-2002, at the opening of the Max Perutz-Library, ViennaBioCenter, in 1994Nobel Prize 1962
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Information processing in the cell
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A B C D E F G H I J K L
1 Biochemical Pathways
2
3
4
5
6
7
8
9
10
The reaction network of cellular metabolism published by Boehringer-Ingelheim.
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The citric acid or Krebs cycle (enlarged from previous slide).
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Claude Elwood Shannon, 1916 – 2001
Formulated a theory of communication and transmittal of messages through channels including error propagation.
The constent of information is thenegative logarithm (to the basis 2) of the probability to receive a message chosen from a given set:
I = - 1.4427 log pk [bit]
Computer adapted alphabet: {0,1}; message: 001010111010100101101.....1
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Information content of a DNA sequence:
I = - 1.4427 log pk [bit],
where the bit refers to the binary alphabet: 0,1
GCGGATTTAGCTCAGTTGGGAGAGCGCCAGACTGAAGATCTGGAGGTCCTGTGTTCGATCCACAGAATTCGCACCA
N = 76 allows for
476 = 5708990770823839524233143877797980545530986496 =
= 5.709 1045 different sequences
I = - 1.4427 log (1/476) = 152 [bit] implying 2 bits per digit, since
the alphabet is
A,U,G,C
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Questions to be analyzed and dicussed in the seminar
How is biological information related to the physics of living matter and to the science of complexity?
How is biological information processed in present day organisms?
How did biological information originate in evolution?
Can the Darwinian mechanism explain the increase in biological complexity during evolution?
How did learning and language originate in societies?
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