Early Evolution Course

An interdisciplinary seminar course at the Weizmann Institute of Science, Israel

Lecture hours:

Thursday 11:00-13:00 (Wolfson lecture hall)
First meeting – 16 November 2000

Lecturers

Prof. Doron Lancet

Prof. Ehud Shapiro
Dr. Guy Sella

Teaching Assistants

Barak Shenhav
Daniel Segre
Ron Kafri

For questions, comments,
picking topic, etc.

Barak Shenhav, barak.shenhav@weizmann.ac.il,
Tel. 3098

Credits

 2


Talks, Olds, Syllabus, Requirements, Grade, Registration, Plan, MATLAB, Links, Books

News

30-Jan-2001          Matlab sessions will take place on 16:00 and not 11:00 as previously announced (no change in days and place).

Talks

Prof. Doron Lancet - What is biology?

Prof. Ehud Shapiro - What is computing?

Dr. Guy Sella - What is life?

Daniel Segre - Origin of life without biopolymers

Students Talks (schedule)

Group 1 - Qusi-species, Error threshold & Hypercycles

Group 2A - RNA world, In vitro evolution & Ribozymes

Group 2B - RNA landscape

Group 3A - Von Neumann automaton

Group 3B - Self-replication in silicon & Cellular automata

Group 4 - Evolution & Self-organization

Group 5A, Group 5B - Self-organization, Reproduction, Metabolism first & Mutual catalysis (A & B)

Group 6 - Lipid world

Group 7A - Energetics

Group 7B - Information

Group 8 - Lambda calculus & Pi calculus

Group 9A - Tierra

Group 9B - Artificial life

Group 10 - Minimal Cell

Group 11 - Prebiotic Chemistry

Group 12 – Auto-catalitic and Mutual-catalitic Biopolymers

Olds

9-Nov-2000          Groups, references and schedule might change!

10-Nov-2000        Group 8 (Lambda calculus & Pi calculus) is currently complete.

16-Nov-2000        Group 3 (Von Neumann automaton, Self-replication in silicon & Cellular automata) and group 4 (Evolution &
Self-organization) are currently
complete.

17-Nov-2000        New subject for student talk is available (“Minimal Cell”). Note change in course schedule.

19-Nov-2000        Group 4 (Evolution & Self-organization) is open again.

19-Nov-2000        Group 2 (In vitro evolution, Ribozymes & RNA landscape) is currently complete.

20-Nov-2000        Note some changes in references of groups 4, 5 and 6

21-Nov-2000        Group 4 (Evolution & Self-organization) is complete, again.

21-Nov-2000        Group 5 (Self-organization, Reproduction, Metabolism first & Mutual catalysis) is complete.

20-Nov-2000        Group 2 is divided to two sub-groups. Other groups will be divided soon.

21-Nov-2000        New subject for student talk is available (“Prebiotic Chemistry”).

21-Nov-2000        Note some changes in schedule and references

10-Nov-2000        You should register as soon as possible.

24-Nov-2000        More Changes in schedule and references

14-Dec-2000         Questionnaire (to be submitted by 28-Dec-2000)

3-Jan-2001            Barak’s son 0th birthday

11-Jan-2001          Barak’s son is named Dor

18-Jan-2001          Matlab sessions were rescheduled

30-Jan-2001          Matlab sessions will take place on 16:00 and not 11:00 as previously announced (no change in days and place).

30-Jan-2001          Note the project description

30-Jan-2001          Note the course grading policy.

Syllabus:

The origin of life is one of the major remaining mysteries facing science. The course will review computer science, biological and chemical literature related to this question, including the work of computer science pioneer John von Neumann, physicists such as Freeman Dyson and biological chemists such as Stuart Kauffman, Harold Morowitz and Manfred Eigen. Topics related to prebiotic evolution and to the emergence of life will be discussed. This will include theoretical models of self-reproducing automata, self-reproducing molecular assemblies, simulations of microscopic physico-chemical properties of mutually catalytic networks, homeostatic ensembles, quasi-species and hypercycles. Also to be included will be Artificial Life approaches involving formal languages (e.g. lambda-calculus), chemical kinetics simulations akin to molecular dynamics, as well as the origin of the genetic code. The molecular version of the chicken-egg paradox will be reviewed in light of realistic prebiotic scenarios, on Earth and elsewhere. This course and seminar is intended for students of Mathematics, Biology, Chemistry and Physics.

Requirements:

The participants will be divided in to interdisciplinary teams of 2-3 students. Each team should is expected to give a talk and submit a project.

Talk

·        Meet its instructor few weeks prior to the oral presentation.

·        Give an oral presentation.

·        Provide the presentation slides in a web publishable format (such as PowerPoint).

Project

·         The project should be related to the subject of the teams talk, although projects, which are not related to the presentation, can be considered. A typical project will present a phenomenon or illustrate an idea on the basis of a simulation. It is preferred that the ideas for projects will come from the team (course staff could be consulted).

·         A typical submission will include (other formats or types of projects can also be considered upon early approval):

o       A short (~2 paragraphs) presentation of the question that motivates the study.

o       A short description of the model underlying the simulation.

o       The output/s of the simulation presented in comprehendible form.

o       A short account explaining the essence of the results.

o       A short discussion (a few paragraphs) explaining how the study enlightened the motivating question.

o       The ‘source’ of the simulation (preferably MATLAB sources).

o       Instructions how to ’use’ the simulation.

·         To make sure the planned project meets the course's requirements, each group will meet Prof. Lancet, Prof. Shapiro, or Dr. Guy Sella, to discuss the proposed project at the stage of ideas and plans, before any significant work is done.

·         The projects will be submitted by e-mail.

Grade:

The course and seminar grade will be based on:

·        Project (25%)

·        Oral presentation (75%)

·        Participation

Registration:

If you are considering attending this course (even not for credits), please assist us by sending an E-mail to Barak Shenhav, with the following details:

·        Last name

·        First Name

·        E-mail

·        Faculty and department

·        M.Sc. / Ph.D / other:

·        Credit / Active participant / Free student

·        Student talk you would like to join

Thanks for your collaboration.

Plan:

Week

Given By

Topics

1

16 Nov 2000

Prof. Doron Lancet

What is biology?

2

23 Nov 2000

Prof. Ehud Shapiro

What is computing?

3

30 Nov 2000

Dr. Guy Sella

What is life?

Daniel Segre

Compositional inheritance: origin of life without biopolymers

4

7 Dec 2000

Student Group 2A (Prof. Doron Lancet)

RNA world, In vitro evolution & Ribozymes

Student Group 1
(Dr. Guy Sella)

Qusi-species, Error threshold & Hypercycles

5

14 Dec 2000

Student Group 3B
(Prof. Ehud Shapiro)

Self-replication in silicon & Cellular automata

Student Group 3A
(Prof. Ehud Shapiro)

Von Neumann automaton

6

21 Dec 2000

Student Group 10
(Prof. Ehud Shapiro)

Minimal cell

Student Group 4
(Prof. Doron Lancet)

Evolution & Self-organization

7

28 Dec 2000

Student Group 12 (Prof. Doron Lancet)

Auto-catalitic and Mutual-catalitic Biopolymers

Student Group 2B (Dr. Guy Sella)

RNA landscape

8

4 Jan 2001

Student Group 5A
(Dr. Guy Sella)

Self-organization, Reproduction, Metabolism first & Mutual catalysis (A)

9

11 Jan 2001

Student Group 5B
(Dr. Guy Sella)

Self-organization, Reproduction, Metabolism first & Mutual catalysis (B)

Dr. Guy Sella

Genetic Code

10

18 Jan 2001

Student Group 11
(Prof. Doron Lancet)

Prebiotic Chemistry

Student Group 6
(Prof. Doron Lancet)

Lipid world

11

25 Jan 2001

Student Group 7A
(Ron Kafri)

Energetics

Student Group 7B
(Ron Kafri)

Information

12

1 Feb 2001

Aviv Regev

 

Student Group 8
(Prof. Ehud Shapiro & Aviv Regev)

Lambda calculus & Pi calculus

13

8 Feb 2001

Student Group 9A
(Barak Shenhav)

Tierra

Student Group 9B
(Barak Shenhav)

Artificial Life

MATLAB:

Elective MATLAB tutorials will be given in the Ebner computer room (next to Ebner lecture hall).

Sessions

·          Session I - The MATLAB environment, variables, basic operators, scripts and control structures (HTML, PowerPoint)

·          Session II - 2-D and 3-D plots, functions and debugging (HTML, PowerPoint)

Schedule

·        Sunday, 28 January (11:00-13:00) – Session I (Hebrew)

·        Sunday, 4 February (16:00-18:00) - Session I (English)

·        Sunday, 11 February (16:00-18:00) - Session II (Hebrew)

·        Sunday, 18 February (16:00-18:00) – Session II (English)

Teach yourself MATLAB

Learning MATLAB” by MathWorks.

Getting MATLAB

Contact Boris Lourie from Weizmann institute computer center (tel 2443).

Useful links:

Origin of Life

Previous course – The course given in Weizmann on 1998-1999.

Artificial Life

Moshe Sipper – Starting point for artificial life and Self-replication in silicon.

Artificial Life Online 2.0 – Starting point for artificial life and Self-replication in silicon.

MATLAB

Mathworks – The official site of MATLAB.

Relevant books:

Freeman J. Dyson, Origins of Life, Oct. 1999 (2nd ed), Cambridge Univ. Press

 

John Maynard Smith, Eors Szathmary, The Origins of Life: From the Birth of Life to the Origin of Language, Nov. 2000, Oxford Univ. Press

Moshe Sipper, Evolution of Parallel Cellular Machines: The Cellular Programming Approach, (Lecture Notes in Computer Science 1194), Apr 1997, Springer Verlag

David W. Deamer, Gail R. Fleischaker, Origins of Life, Jan 1994, Jones & Bartlett Pub.

Christian De Duve, Vital Dust: Life As a Cosmic Imperative, Jan 1996, Basic Books

Iris Fry, The Emergence of Life on Earth: A Historical and Scientific Overview, Feb. 2000 Rutgers Univ Press

Stuart A. Kauffman, Investigations, Oct 2000, Oxford Univ Press

Stuart A. Kauffman, At Home in the Universe : The Search for Laws of Self-Organization and Complexity, May 1996, Oxford Univ Press

Stuart A. Kauffman, The Origins of Order: Self-Organization and Selection

in Evolution, May 1993, Oxford Univ Press

Christopher Wills, Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Apr. 2000, Perseus Press

Alexander Graham Cairns-Smith, Seven Clues to the Origin of Life: A Scientific Detective Story, Feb. 1991, Cambridge Univ. Press

Werner R. Loewenstein, The Touchstone of Life: Molecular Information, Cell Communication, and the Foundations of Life, Jan. 1999, Oxford Univ. Press

 

Aleksandr Ivanovich Oparin, Origin of Life, 1953 (2nd Ed.), Dover Publications Inc.

 

Noam Lahav, Biogenesis: Theories of Life's Origin, Dec. 1998 (Paperback) Jan 1999 (Hardcover), Oxford Univ. Press

 

Christian De Duve, A Guided Tour of the Living Cell

 

Christian De Duve, Blueprint for a Cell : The Nature and Origin of Life, Jan 1991, Carolina Biological Supply Co.

 

Armand H. Delsemme, Christian De Duve, Our Cosmic Origins : From the Big Bang to the Emergence of Life and Intelligence, Oct 2000,

Cambridge Univ. Press

 

William Poundstone, The Recursive Universe: Cosmic Complexity and the Limits of Scientific Knowledge

 

Manfred Eigen, Ruthild Winkler-Oswatitsch (Contributor), Paul

Woolley (Translator), Steps Towards Life: A Perspective on Evolution, Jun. 1996 (Reprint), Oxford Univ. Press

 

Manfred Eigen, The Hypercycle: A Principle of

Natural Self Organization

 

Harold J. Morowitz, Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis (Bio-Origins Series)

 

Harold J. Morowitz, Mayonnaise and the Origin of Life : Thoughts of Minds and Molecules, Feb 1991, Ox Bow Press

 

Christian De Duve, Blueprint for a Cell: The Nature and Origin of Life, Jan. 1991, Carolina Biological Supply Co.

 


Group 1: Lotka-Volterra, Qusi-species, Error threshold & Hypercycles

Members:

Mor Dolev (Molecular genetics)

Jan Ihmels (Molecular genetics)

Paper Summaries:

·        Hofbauer and Sigmund, "The theory of evolution and dynamical systems",p. 77-87

·        M. Eigen, P.Schuster, "The Hypercycle", Springer-Verlag, 1979

·        J. Maynard Smith, "Hypercycles and the origin of life", Nature 20:445-6, 1979

·        M. Eigen, “Steps towards life : A Perspective on Evolution”, Oxford Univ Press, 1996

·        M. Eigen, "Self-organization of matter and the evolution of biological macromolecules", Naturwissenschaften. 1971 Oct; 58(10): 465-523

·        M. Eigen, "Natural selection: a phase transition?", Biophys Chem. 2000 Jul 15;85(2-3):101-23

Presentation:

HTML, PowerPoint

Project:

Group 2A: RNA world, In-vitro evolution & Ribozymes

Members:

Yanir Rubinstein (CS)

Ilana Schanin (Science Teaching)

Yifat Kolikant (Science Teaching)

Paper Summaries:

·        W.Gilbert, "The RNA world", Nature, 319, p.618, 1986

·        G.F.Joyce, "The rise and fall of the RNA world", The New Biologist, Vol.3, pp.399-407, 1991.

·        G.F.Joyce, "RNA evolution and the origins of life", Nature, 338, p.217

·        L.E.Orgel, "Molecular replication", Nature, 358, p.203, 1992

Presentation:

HTML, PowerPoint

Project:

Group 2B: RNA landscape

Members:

Adi Salomon (Chemistry)

Issac Berith (Biochemistry)

Hani Neuvirth (CS)

Paper Summaries:

·         W. Fontana and P. Schuster, “Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping”, J. Theor. Biol., 194, 491-515 (1998)

·        W. Fontana and P. Schuster, “Continuity in Evolution: On the Nature of Transitions”, Science, 280, 1451-1455 (1998).

·        P. Schuster, W. Fontana, P. F. Stadler and I. Hofacker, “From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures”, Proc. Roy. Soc. (London) B, 255, 279-284 (1994)

·        M. Huynen, P. F. Stadler and W. Fontana, “Smoothness within Ruggedness: The role of neutrality in adaptation”, PNAS, 93, 397-401 (1996)

·        W. Fontana, T. Griesmacher, W. Schnabl, P. F. Stadler and P. Schuster, “Statistics of Landscapes Based on Free Energy, Replication and Degradation Rate Constants of RNA Secondary Structures”, Chemical Monthly, 122, 795-819 (1991)

·        Fontana W, Stadler PF, …, Schuster P. "RNA folding and combinatory landscapes", Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar; 47(3): 2083-2099

Presentation:

HTML, PowerPoint

Project:

Group 3A: Von Neumann automaton

Members:

Olga Grinchtein (CS)

Evgeniy Bart (CS)

Paper Summaries:

·        A.W.Burks, "Von Neumann's self-reproducing automata", Essay 1 from Essays on Cellular Automata, ed. By A.W.Burks, Univ. of Illinois Press

·        J. Beuchat, J. Haenni, “Von Neumann’s 29-State Cellular Automaton: A Hardware Implementation”, IEEE Transactions On Education, Vol. 43 (3), 2000.

J.Signorini, “How a SIMD machine can implement a complex cellular automaton? A case study: von Neumann’s 29-state cellular automaton”, IEEE Proc. Supercomput.,1989.

Presentation:

HTML, PowerPoint

Project:

Group 3B: Self-replication in silicon & Cellular automata

Members:

Jason Friedman (CS)

Byung-Woo Hong (CS)

Paper Summaries:

·        M.Sipper, “Fifty years of research on self replication – an overview”, Artificial Life, 4, 237 (1998)

·        G.Tempesti, D.Mange, A.Stauffer, “Self-Replication and Self-Repairing Multicellular Automata”, Artificial Life, 4, 259 (1998)

·        C.G.Langton, “Self-reproduction in cellular automata”, Physica D, 10, 135-144 (1984)

·        C.G.Langton, “Studying artificial life with cellular automata”, Physica D, 22, 120-149 (1984)

Presentation:

HTML, PowerPoint, videos: Pump (19Mb), Glider (17Mb), Shoter (80Mb), Langton (81Mb)

Project:

Group 4: Evolution & Self-organization

Members:

Lior Noy (CS)

Max Chvalevsky (CS)

Khalil Kashkush (Plant sciences)

Paper Summaries:

·        A.I.Oparin, "Evolution of self-assembly of probionts", BioSystems, 12, 133-145,1980

·        A.I.Oparin, "The origin of the first organisms", chapter from The Origin of Life on the Earth, Oliver and Boyd, 1957, p.347

·        A.I.Oparin, "Origin of prebiological systems", chapter from Genesis and Evolutionary Development of Life, Academic Press, 1968, pp.101-125

·        T.H.Jukes, “Oparin and Lysenko”, J Mol Evol. 1997 Oct;45(4):p339-40.

·        Miller SL, Schopf JW, Lazcano A. “Oparin's ‘Origin of Life’: sixty years later”, J Mol Evol. 1997 Apr;44(4):351-3

·        Lazcano A.,”chemical evolution and the primitive soup: did Oparin get it all right? ”, J Theor Biol. 1997 Jan 21;184(2):219-23

Presentation:

HTML, PowerPoint

Project:

Group 5A: Self-organization, Reproduction, Metabolism first & Mutual catalysis

Members:

Gilad Doitsh (Molecular genetics)

Yaki Setty (Bioinfomatics)

Eran Keydar (CS)

Paper Summaries:

·        F.Dyson, "A model for the origin of life", J.Mol.Evol, 1982

·        F.Dyson, "Origins of life", Cambridge Univ.Press, 2000.

·        F. Stadler, W. Fontana, J. H. Miller, “Random Catalytic Reaction Networks”, Physica D, 63, 378-392 (1993)

·        W. Fontana , “Functional Self-Organization in Complex Systems”, 1990 Lectures in Complex Systems, SFI Studies in the Sciences of Complexity, Lecture Notes Vol. III, L.Nadel and D.Stein (eds.), pp. 407-426, Addison-Wesley, 1991

Presentation:

HTML, PowerPoint

Project:

Group 5B: Self-organization, Reproduction, Metabolism first & Mutual catalysis

Members:

Ya'ara Goldschmidt (Bioinfomatics)

Shai Mor (CS)

Paper Summaries:

·        Kauffman, "Autocatalytic sets of proteins", J.theor.Biol., 119, 1-24, 1986

·        Kauffman, "Origin of Order", Oxford University Press, 1998

·        R.J.Bagley and J.D.Farmer, "Spontaneous emergence of a metabolism", in Artificial Life II, SFI studies in the science of complexity, ed. by C.G.Langton et al., Addison-Wesley, 1991

·        M. Huynen, P. F. Stadler, W. Fontana, “Smoothness within Ruggedness: The role of neutrality in adaptation”, PNAS, 93, 397-401 (1996)

·        J.D. Farmer, S. Kauffman and N.H. Packard, “Autocatalytic Replication of Polymers”, Physica D, 22, 50-67 (1986)

Presentation:

HTML, PowerPoint

Project:

Group 6: Lipid world

Members:

Mark Vilensky (Environmental Sciences)

Iris Visoly-Fisher (Materials & Interfaces)

Neri Minsky (LS)

Paper Summaries:

·        C.Tanford, "The hydrophobic effect and the organization of living matter", Science, 200, p1012-1018, 1978

·        P.A.Bachmann et al., "Autocatalytic self-replicating micelles as a model for prebiotic structures", Nature 357, p57-59, 1992

·        Ourisson, G. and Y. Nakatani. “The terpenoid theory of the origin of cellular life: the evolution of terpenoids to choloesterol.” Chemistry & Biology, 1, p11-23, 1994.

·        D.Segre, D.Ben-Eli, D.W.Deamer, D.Lancet, “The Lipid World”, Origins Life Evol. Biosphere, in press

·        P.L.Luisi et al. "Enzymatic RNA synthesis in self-reproducing vesicles: an approach to the construction of a minimal synthetic cell"

·        D.Segre', D.Lancet, O.Kedem and Y.Pilpel, "Graded Autocatalysis Replication Domain (GARD): kinetic analysis of self-replication in mutually catalytic sets", Origins Life Evol.Biosphere, 28:501-514, 1998

Presentation:

Project:

Group 7A: Energetics

Members:

Kobi Benenson (CS)

Amit Lotan

Paper Summaries:

·        Rees DC, Howard JB, “Structural bioenergetics and energy transduction mechanisms”, J MOL BIOL 293: (2) 343-350 OCT 22 1999

·        Kurzynski M, “Importance of intramolecular protein dynamics to kinetics of biochemical processes”, CELL MOL BIOL LETT 4: (1) 117-130 1999

·        Mogi K, “On the absolute meaning of the energy scale similar-to-kT in the thermal interference involved in enzyme-coupled reactions”, P ROY SOC LOND A MAT 445: (1925) 529-541 JUN 8 1994

·        Yamato I, “Ordered binding model as a general tight coupling mechanism for bioenergy transduction – a hypothesis”, P JPN ACAD B-PHYS 69: (8) 218-223 OCT 1993

·        Otsuka J, Nozawa Y, “Self-reproducing system can behave as Maxwell's demon: Theoretical illustration under prebiotic conditions”, J THEOR BIOL 194: (2) 205-221 SEP 21 1998

Presentation:

HTML, PowerPoint

Project:

Group 7B: Information

Members:

Michel Vidal-Naquet (CS)

Ella Zak (Materials and Interfaces)

Paper Summaries:

·        Ebeling W, Feistel R, “Theory of self-organization and evolution – the role of entropy, value and information”, J NON-EQUIL THERMODY 17: (4) 303-332 1992

·        Wagensberg J, “Complexity versus uncertainty: The question of staying alive”, BIOL PHILOS 15: (4) 493-508 SEP 2000

Presentation:

HTML (part 1), HTML (part 2), PowerPoint (part 1), PowerPoint (part 2)

Project:

Group 8: Lambda calculus & Pi calculus

Members:

Amos Korman (CS)

Ofer Feinerman (Physics)

Yoav Rodeh (CS)                      

Paper Summaries:

·        W.Fontana and L.W.Buss, "What would be conserved if 'the tape were played twice'?", 1994

·        W.Fontana, "Algorithmic Chemistry", Artificial Life II, p.159, 1991

·        P.F.Stadler, et al., "Random catalytic reaction networks"

·        W. Fontana et al., "Beyond digital naturalism", Artificial Life, 1994

Presentation:

HTML, PowerPoint

Project:

Group 9A: Tierra

Members:

Alex Shpunt (CS)

Nizan Horesh

Elad Glienart

Paper Summaries:

·        C.ADAMI, “Learning and complexity in genetic auto-adaptive systems”, PHYSICA D 80: (1-2) 154-170, 1995

Links:

Tierra home page

Presentation:

HTML, PowerPoint, Movie (2Mb)

Project:

Group 9B: Artificial life

Members:

Ann Rapoport (CS)

Eyal Lev (CS)

Orna Fallik (Science Teaching)

Paper Summaries:

·        G.Nuno, H.Pereira, J.A.Lima, A.Rosa, “Gaia: an artificial life environment for ecological systems simulations”, Artificial life V, MIT press, p.124, 1996

·        K.Downing and P.Zvirinsky, "The simulated evolution of biochemical guilds: reconciling Gaia theory and natural selection”, Artificial Life 5 (4) 291

·        E.M.A.Ronald, M. Sipper, M.S. Capcarrere, “Design, observation, surprise! a test of emergence”, Artificial Life 5 (3) 225

Links:

Artificial Life Online 2.0

Presentation:

HTML, PowerPoint

Project

Group 10: Minimal Cell

Members:

Ronen Zaidel Bar (Molecular Cell Biology)

Alexander Levitan (Plant Science)

Eti Meiri (Plant Science)

Paper Summaries:

·        C.A.Hutchison, S.N.Peterson, S.R.Gill, R.T.Cline, O.White, C.M.Fraser, H.O.Smith, J.C.Venter, “Global Transposon Mutagenesis and a Minimal Mycoplasma Genome”

·        V.C.Wasinger, J.D.Pollack , I.Humphery-Smith, “The proteome of Mycoplasma genitalium: Chapssoluble component”, Eur J Biochem 267:1571-1582, 2000

·        E.V.Koonin, “HOW MANY GENES CAN MAKE A CELL: The Minimal-Gene-Set Concept”, Annu. Rev. Genom. Hum. Genet. 1: 99-116, 2000

Presentation:

HTML, PowerPoint

Project:

Group 11: Prebiotic Chemistry

Members:

Mao Tang (Materials & interfaces)

Ravid Yiron-dar (Science Teaching)

Michael Montag (Structural Biology)

Paper Summaries:

·        S.L.Miller, H.C.Urey, "Organic Compound Synthesis on the Primitive Earth”, Science, 130, 245-251,1959

·        J.Oro, "Mechanism of Synthesis of Adenine from Hydrogen Cyanide under Possible Primitive Earth Conditions”, Nature, 191, 1193-1194, 1961

·        S.L.Miller, "A production of amino acids under possible primitive earth conditions", Science, 117, p.528-529, 1953

·        H.C.Urey, "On the early chemical history of the earth and the origin of life", PNAS, 38, pp.351-363, 1952

·        M.Levy and S.L.Miller, "The stability of the RNA bases: Implications for the origin of life", PNAS, 95, 7933-7938,1998

·        Schlesinger G, Miller SL, “Prebiotic synthesis in atmospheres containing CH4, CO, and CO2, Hydrogen cyanide, formaldehyde and ammonia”, J Mol Evol. 1983;19(5):383-90.

·        Sanchez RA, Ferris JP, Orgel LE, “Studies in prebiotic synthesis: Synthesis of purine precursors and amino acids from aqueous hydrogen cyanide”, J Mol Biol. 1967 Dec 14;30(2):223-53

·        Rabinowitz J, Chang S, Ponnamperuma C, “Phosphorylation by way of inorganic phosphate as a potential prebiotic process”, Nature. 1968 May 4;218(140):442-3

·        Reid C, Orgel LE, Ponnamperuma C. “Nucleoside synthesis under potentially prebiotic conditions”, Nature. 1967 Dec 2;216(118):936

·        Allen WV, Ponnamperuma C, “A possible prebiotic synthesis of monocarboxylic acids”, Curr Mod Biol. 1967 Mar;1(1):24-8

Presentation:

HTML (part 1), HTML (part 2), PowerPoint (part 1), PowerPoint (part 2)

Project:

Group 12: Auto-catalitic and Mutual-catalitic Biopolymers

Members:

Hagit Kornreich (Organic Chemistry)

Eylon Yavin (Organic Chemistry)

Ovadia Abed (Organic Chemistry)

Paper Summaries:

·        D.H.Lee et al., "A self replicating peptide", Nature 382, p.525, 1996

·        D.H.Lee et al., "Emergence of symbiosis in peptide self-replication through a hypercyclic network", Nature, 390, p.591, 1997

·        Sievers D, von Kiedrowski G., “Self-replication of complementary nucleotide-based oligomers”, Nature, 369, p.221-4, 1994

·        S.Kauffman, "Even peptides do it", Nature 382, p.496, 1996

Presentation:

HTML (part 1 & 2), HTML (part 3), PowerPoint (part 1 & 2), PowerPoint (part 3), Animation (part 1 & 2) , Animation (part 3)

Project:


Last updated on 11 February 2001