information and information processing in biological systems

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

Web-Pages for further information:

http://www.tbi.univie.ac.at/~pkshttp://www.colbud.hu/fellows/szathmary.shtml

http://faculty.biu.ac.il/~elitzua/

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

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

Evolution and Information

Peter Schuster, Institut für Theoretische Chemie, Universität Wien

Genotype, Genome

Phenotype

Unf

oldi

ng o

f th

e ge

noty

pe

Highly specific environmental conditions

Developmental program

Collection of genes

Evolution

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

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

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.

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

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

time

Charles Darwin, The Origin of Species, 6th edition. Everyman‘s Library, Vol.811, Dent London, pp.121-122.

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

John Burdon Sanderson Haldane, 1892-1964

Sir Ronald Aylmer Fisher, 1890-1962 Sewall Wright, 1889-1988

The three scholars of theoretical population biology

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

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.

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

Canonical Watson-Crick base pairs:

cytosine – guanineuracil – adenine

W.Saenger, Principles of Nucleic Acid Structure, Springer, Berlin 1984

Complementary replication is the simplest copying mechanismof RNA.Complementarity is determined by Watson-Crick base pairs:

G C and A=U

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.

‚Replication fork‘ in DNA replication

The mechanism of DNA replication is ‚semi-conservative‘

Genetic recombination as the second mechanism of variation is the molecular basis

of Mendelian genetics.

Max Perutz, 1914-2002, at the opening of the Max Perutz-Library, ViennaBioCenter, in 1994Nobel Prize 1962

Information processing in the cell

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.

The citric acid or Krebs cycle (enlarged from previous slide).

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

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

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?