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  Topic: Abiogenesis discussion thread, No trolls please, we're adults< Next Oldest | Next Newest >  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 15 2006,11:33   

HUGENESS WARNING.

Dear All,

Abiogenesis is a fascinating and hugely varied topic. There are valid contributions possible from almost all fields of science.

From the outset I imagine that, since this is intended to be a technical and drama free thread it won't make huge numbers, which is fine. What I want to gather together is the ideas, data and opinions of the relevant experts and people on this board. We have a huge variety of experienced scientists including physicists, mathematicians, biologists and a chemist or two. I have every expectation that a rational conversation can ensue.

To that end I politely request that this is a troll free thread. The board currently has 2.5 trolls as far as I can tell: AFDave, Ghost of Paley, and Skeptic on his bad days. I am asking that these people do not post on this thread. Troll away in the rest of the board by all means, but just for once realise that your "contributions" such as they are, are neither desired nor required.



The nasty bits over with, I'll kick things off:

For life as we know it now on earth to have arisen, in general terms, abiogenesis has several hurdles to overcome. In no specific order:

1) A self replicating molecule or self replicating series of molecules or a series of interacting molecules that template the synthesis of other molecules.

2) Some form of cellular encapsulation, which at least must incoporate a semi permeable membrane or barrier.

3) A series of effector molecules/physical scaffolding/chemoselective processes which allow for a relatively high level of "copying fidelity".

Since this is a conversation not a monologue I'll leave it there. There are more hurdles and more specific examples of them, but I'd rather people contributed.

So the first question I'd like to pose is, based on the evidence what order do people think that the key events in abiogenesis happened? What form did they take? Why?

Encapsulation before self replication? Inorganic templating of reactions before self replication? Systems of effector molecules before high fidelity replication?

Louis

P.S. Some references people might be interested in.Most require subscription. To the Bat Library!

Selected papers by Leslie Orgel:

Record 1 of 128
Author(s): Orgel, LE
Title: Geothermal synthesis and metabolism
Source: ASTROBIOLOGY, 6 (2): 297-298 APR 2006

Record 2 of 128
Author(s): Orgel, LE
Title: The, origin of the RNA world
Source: FASEB JOURNAL, 20 (4): A36-A36 Part 1 MAR 6 2006

Record 3 of 128
Author(s): Orgel, L
Title: Genesis: The scientific quest for life's origins
Source: NATURE, 439 (7079): 915-915 FEB 23 2006

Record 4 of 128
Author(s): Leman, LJ; Orgel, LE; Ghadiri, MR
Title: Amino acid dependent formation of phosphate anhydrides in water mediated by carbonyl sulfide
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128 (1): 20-21 JAN 11 2006

Record 5 of 128
Author(s): Leman, L; Orgel, L; Ghadiri, MR
Title: Amino acid condensation mediated by carbonyl sulfide.
Source: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 228: U693-U693 023-GEOC Part 1 AUG 22 2004

Record 6 of 128
Author(s): Leman, L; Orgel, L; Ghadiri, MR
Title: Carbonyl sulfide-mediated prebiotic formation of peptides
Source: SCIENCE, 306 (5694): 283-286 OCT 8 2004

Record 7 of 128
Author(s): Orgel, LE
Title: Prebiotic chemistry and the origin of the RNA world
Source: CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, 39 (2): 99-123 MAR-APR 2004

Record 8 of 128
Author(s): Orgel, LE
Title: Prebiotic adenine revisited: Eutectics and photochemistry
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 34 (4): 361-369 AUG 2004

Record 9 of 128
Author(s): Orgel, LE
Title: Some consequences of the RNA world hypothesis
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 33 (2): 211-218 APR 2003

Record 10 of 128
Author(s): Orgel, LE
Title: Is cyanoacetylene prebiotic?
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 32 (3): 279-281 JUN 2002

Record 11 of 128
Author(s): Hill, A; Orgel, LE
Title: Synthesis of adenine from HCN tetramer and ammonium formate
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 32 (2): 99-102 APR 2002

Record 12 of 128
Author(s): Orgel, LE
Title: Restaging the origins
Source: BIOFUTUR, (219): 32-36 FEB 2002

Record 13 of 128
Author(s): Wen, K; Orgel, LE
Title: The specificity of peptide chain extension by N-carboxyanhydrides
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 31 (3): 241-248 JUN 2001

Record 14 of 128
Author(s): Kozlov, IA; Orgel, LE; Nielsen, PE
Title: Remote enantioselection transmitted by an achiral peptide nucleic acid backbone
Source: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 39 (23): 4292-+ 2000

Record 15 of 128
Author(s): Orgel, L
Title: Origin of life - A simpler nucleic acid
Source: SCIENCE, 290 (5495): 1306-1307 NOV 17 2000

Record 16 of 128
Author(s): Orgel, LE
Title: Self-organizing biochemical cycles
Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 97 (23): 12503-12507 NOV 7 2000

Record 17 of 128
Author(s): Arrhenius, G; Bada, JL; Joyce, GF; Lazcano, A; Miller, S; Orgel, LE
Title: Origin and ancestor: Separate environments
Source: SCIENCE, 283 (5403): 792-792 FEB 5 1999

Record 18 of 128
Author(s): Orgel, LE
Title: The origin of life - a review of facts and speculations
Source: TRENDS IN BIOCHEMICAL SCIENCES, 23 (12): 491-495 DEC 1998

Record 19 of 128
Author(s): Orgel, LE
Title: Polymerization on the rocks: Theoretical introduction
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 28 (3): 227-234 JUN 1998

Record 20 of 128
Author(s): Hill, AR; Bohler, C; Orgel, LE
Title: Polymerization on the rocks: Negatively-charged alpha-amino acids
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 28 (3): 235-243 JUN 1998

Record 21 of 128
Author(s): Liu, R; Orgel, LE
Title: Polymerization on the rocks: beta-amino acids and arginine
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 28 (3): 245-257 JUN 1998

Record 22 of 128
Author(s): Liu, RH; Orgel, LE
Title: Polymerization of beta-amino acids in aqueous solution
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 28 (1): 47-60 FEB 1998

Record 23 of 128
Author(s): Orgel, LE
Title: The origin of life - How long did it take?
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 28 (1): 91-96 FEB 1998

Record 24 of 128
Author(s): Joyce, GF; Orgel, LE
Title: The origins of life - A status report
Source: AMERICAN BIOLOGY TEACHER, 60 (1): 10-12 JAN 1998

Record 25 of 128
Author(s): Liu, RH; Orgel, LE
Title: Oxidative acylation using thioacids
Source: NATURE, 389 (6646): 52-54 SEP 4 1997

Record 26 of 128
Author(s): Liu, RH; Orgel, LE
Title: Efficient oligomerization of negatively-charged beta-amino acids at -20 degrees C
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 119 (20): 4791-4792 MAY 21 1997

Record 27 of 128
Author(s): Orgel, LE
Title: Prion replication and secondary nucleation
Source: CHEMISTRY & BIOLOGY, 3 (6): 413-414 JUN 1996

Record 28 of 128
Author(s): Ferris, JP; Hill, AR; Liu, RH; Orgel, LE
Title: Synthesis of long prebiotic oligomers on mineral surfaces
Source: NATURE, 381 (6577): 59-61 MAY 2 1996

Record 29 of 128
Author(s): Bohler, C; Hill, AR; Orgel, LE
Title: Catalysis of the oligomerization of O-phospho-serine, aspartic acid, or glutamic acid by cationic micelles
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 26 (1): 1-5 FEB 1996

Record 30 of 128
Author(s): Kolb, V; Orgel, LE
Title: Phosphorylation of glyceric acid in aqueous solution using trimetaphosphate
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 26 (1): 7-13 FEB 1996

Record 31 of 128
Author(s): BOHLER, C; NIELSEN, PE; ORGEL, LE
Title: TEMPLATE SWITCHING BETWEEN PNA AND RNA OLIGONUCLEOTIDES
Source: NATURE, 376 (6541): 578-581 AUG 17 1995

Record 32 of 128
Author(s): ORGEL, LE
Title: UNNATURAL SELECTION IN CHEMICAL-SYSTEMS
Source: ACCOUNTS OF CHEMICAL RESEARCH, 28 (3): 109-118 MAR 1995

Record 33 of 128
Author(s): ORGEL, LE
Title: THE ORIGIN OF LIFE ON THE EARTH
Source: SCIENTIFIC AMERICAN, 271 (4): 77-83 OCT 1994

Record 34 of 128
Author(s): ORGEL, LE
Title: MOLECULAR REPLICATION
Source: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 207: 26-GEOC Part 1 MAR 13 1994

Record 35 of 128
Author(s): HILL, AR; ORGEL, LE; WU, TF
Title: THE LIMITS OF TEMPLATE-DIRECTED SYNTHESIS WITH NUCLEOSIDE-5'-PHOSPHORO(2-METHYL)IMIDAZOLIDES
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 23 (5-6): 285-290 DEC 1993

Record 36 of 128
Author(s): ORGEL, LE
Title: GENOME ORGANIZATION AND EVOLUTION
Source: GENE, 135 (1-2): 27-27 DEC 15 1993

Record 37 of 128
Author(s): ORGEL, LE
Title: WRATH AVERTED
Source: NATURE, 363 (6430): 577-577 JUN 17 1993

Record 38 of 128
Author(s): ORGEL, LE; CRICK, FHC
Title: ANTICIPATING AN RNA WORLD - SOME PAST SPECULATIONS ON THE ORIGIN OF LIFE - WHERE ARE THEY TODAY
Source: FASEB JOURNAL, 7 (1): 238-239 JAN 1993

Record 39 of 128
Author(s): WU, T; ORGEL, LE
Title: NONENZYMATIC TEMPLATE-DIRECTED SYNTHESIS ON HAIRPIN OLIGONUCLEOTIDES .3. INCORPORATION OF ADENOSINE AND URIDINE RESIDUES
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 114 (21): 7963-7969 OCT 7 1992

Record 40 of 128
Author(s): ORGEL, LE
Title: MOLECULAR REPLICATION
Source: NATURE, 358 (6383): 203-209 JUL 16 1992

Record 41 of 128
Author(s): HILL, AR; ORGEL, LE
Title: PHOTOOXIDATION OF OLIGODEOXYNUCLEOTIDES BY UO2(2+)
Source: BIOCONJUGATE CHEMISTRY, 2 (6): 431-434 NOV-DEC 1991

Record 42 of 128
Author(s): HILL, AR; KUMAR, S; PATIL, VD; LEONARD, NJ; ORGEL, LE
Title: WHICH 3-RIBOFURANOSYL-SUBSTITUTED PURINE 5'-PHOSPHATES UNDERGO TEMPLATE-DIRECTED OLIGOMERIZATION
Source: JOURNAL OF MOLECULAR EVOLUTION, 32 (6): 447-453 JUN 1991

Record 43 of 128
Author(s): WU, TF; ORGEL, LE
Title: DISULFIDE-LINKED OLIGONUCLEOTIDE PHOSPHOROTHIOATES - NOVEL ANALOGS OF NUCLEIC-ACIDS
Source: JOURNAL OF MOLECULAR EVOLUTION, 32 (4): 274-277 APR 1991

Record 44 of 128
Author(s): TOHIDI, M; ORGEL, LE
Title: POLYMERIZATION OF THE CYCLIC PYROPHOSPHATES OF NUCLEOSIDES AND THEIR ANALOGS
Source: JOURNAL OF MOLECULAR EVOLUTION, 30 (2): 97-103 1990

Record 45 of 128
Author(s): ORGEL, LE
Title: NUCLEIC-ACIDS - ADDING TO THE GENETIC ALPHABET
Source: NATURE, 343 (6253): 18-20 JAN 4 1990

Record 46 of 128
Author(s): ORGEL, LE
Title: EVOLUTION OF THE GENETIC APPARATUS - A REVIEW
Source: COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY, 52: 9-16 1987

Record 47 of 128
Author(s): ORGEL, LE
Title: RNA CATALYSIS AND THE ORIGINS OF LIFE
Source: JOURNAL OF THEORETICAL BIOLOGY, 123 (2): 127-149 NOV 21 1986

Record 48 of 128
Author(s): ORGEL, LE
Title: DID TEMPLATE-DIRECTED NUCLEATION PRECEDE MOLECULAR REPLICATION
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 17 (1): 27-34 1986

Record 49 of 128
Author(s): ORGEL, LE
Title: ACCURACY IN MOLECULAR PROCESSES - ITS CONTROL AND RELEVANCE TO LIVING SYSTEMS - KIRKWOOD,TBL, ROSENBERGER,RF, GALAS,DJ
Source: NATURE, 324 (6094): 219-219 NOV 20 1986

Record 50 of 128
Author(s): ORGEL, LE
Title: REPLICATION MODELS
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 16 (3-4): 438-438 1986

Record 51 of 128
Author(s): ACEVEDO, OL; ORGEL, LE
Title: TEMPLATE-DIRECTED LIGATION OF OLIGONUCLEOTIDES ON HYDROXYAPATITE - A MODEL FOR COMPLEXATION IN A PRIMITIVE OCEAN
Source: ORIGINS OF LIFE AND EVOLUTION OF THE BIOSPHERE, 16 (3-4): 441-441 1986

Record 52 of 128
Author(s): HAERTLE, T; ORGEL, LE
Title: THE TEMPLATE PROPERTIES OF SOME OLIGODEOXYNUCLEOTIDES CONTAINING CYTIDINE AND GUANOSINE
Source: JOURNAL OF MOLECULAR EVOLUTION, 23 (2): 108-112 1986

Record 53 of 128
Author(s): ACEVEDO, OL; ORGEL, LE
Title: TEMPLATE-DIRECTED OLIGONUCLEOTIDE LIGATION ON HYDROXYLAPATITE
Source: NATURE, 321 (6072): 790-792 JUN 19 1986

Record 54 of 128
Author(s): HAERTLE, T; ORGEL, LE
Title: TEMPLATE-DIRECTED SYNTHESIS ON THE OLIGONUCLEOTIDE D(C7-G-C7)
Source: JOURNAL OF MOLECULAR BIOLOGY, 188 (1): 77-80 MAR 5 1986

Record 55 of 128Author(s): ZIELINSKI, WS; ORGEL, LE
Title: OLIGOMERIZATION OF 3'-AMINO-3'-DEOXYNUCLEOTIDES IN AQUEOUS-SOLUTION
Source: BIOCHEMISTRY, 24 (13): 3376-3376 1985

Record 56 of 128
Author(s): SCHWARTZ, AW; ORGEL, LE
Title: TEMPLATE-DIRECTED POLYNUCLEOTIDE SYNTHESIS ON MINERAL SURFACES
Source: JOURNAL OF MOLECULAR EVOLUTION, 21 (3): 299-300 1985

Record 57 of 128
Author(s): SCHWARTZ, AW; ORGEL, LE
Title: TEMPLATE-DIRECTED SYNTHESIS OF NOVEL, NUCLEIC ACID-LIKE STRUCTURES
Source: SCIENCE, 228 (4699): 585-587 1985

Record 58 of 128
Author(s): CHU, BCF; ORGEL, LE
Title: NONENZYMATIC SEQUENCE-SPECIFIC CLEAVAGE OF SINGLE-STRANDED-DNA
Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 82 (4): 963-967 1985

Record 59 of 128
Author(s): CHEN, CB; INOUE, T; ORGEL, LE
Title: TEMPLATE-DIRECTED SYNTHESIS ON OLIGODEOXYCYTIDYLATE AND POLYDEOXYCYTIDYLATE TEMPLATES
Source: JOURNAL OF MOLECULAR BIOLOGY, 181 (2): 271-279 1985

Record 60 of 128
Author(s): GRZESKOWIAK, K; WEBB, TR; ORGEL, LE
Title: TEMPLATE-DIRECTED SYNTHESIS WITH 2-AMINOADENOSINE
Source: JOURNAL OF MOLECULAR EVOLUTION, 21 (1): 81-83 1984

Record 61 of 128
Author(s): JOYCE, GF; VISSER, GM; VANBOECKEL, CAA; VANBOOM, JH; ORGEL, LE; VANWESTRENEN, J
Title: CHIRAL SELECTION IN POLY©-DIRECTED SYNTHESIS OF OLIGO(G)
Source: NATURE, 310 (5978): 602-604 1984

Record 62 of 128
Author(s): JOYCE, GF; INOUE, T; ORGEL, LE
Title: NON-ENZYMATIC TEMPLATE-DIRECTED SYNTHESIS ON RNA RANDOM COPOLYMERS - POLY(C,U) TEMPLATES
Source: JOURNAL OF MOLECULAR BIOLOGY, 176 (2): 279-306 1984

Record 63 of 128
Author(s): ORGEL, LE
Title: AN RNA-POLYMERASE MODEL
Source: CHEMICA SCRIPTA, 21 (1-5): 85-85 1983

Record 64 of 128
Author(s): ORGEL, LE
Title: THE ORIGIN OF LIFE AND THE EVOLUTION OF MACROMOLECULES
Source: FOLIA BIOLOGICA, 29 (1): 65-77 1983

Record 65 of 128
Author(s): INOUE, T; ORGEL, LE
Title: A NON-ENZYMATIC RNA-POLYMERASE MODEL
Source: SCIENCE, 219 (4586): 859-862 1983

Record 66 of 128
Author(s): ORGEL, L
Title: DARWINISM AT THE VERY BEGINNING OF LIFE
Source: NEW SCIENTIST, 94 (1301): 149-151 1982

Record 67 of 128
Author(s): FAKHRAI, H; VANROODE, JHG; ORGEL, LE
Title: SYNTHESIS OF OLIGOGUANYLATES ON OLIGOCYTIDYLATE TEMPLATES
Source: JOURNAL OF MOLECULAR EVOLUTION, 17 (5): 295-302 1981

Record 68 of 128
Author(s): BRIDSON, PK; ORGEL, LE
Title: CATALYSIS OF ACCURATE POLY©-DIRECTED SYNTHESIS OF 3'-5'-LINKED OLIGOGUANYLATES BY ZN2+
Source: JOURNAL OF MOLECULAR BIOLOGY, 144 (4): 567-577 1980

Record 69 of 128
Author(s): ORGEL, LE; CRICK, FHC; SAPIENZA, C
Title: SELFISH DNA
Source: NATURE, 288 (5792): 645-646 1980

Record 70 of 128
Author(s): ORGEL, LE
Title: VANADIUM AS PROTECTION AGAINST PREDATION
Source: TRENDS IN BIOCHEMICAL SCIENCES, 5 (8): R10-R10 1980

Record 71 of 128
Author(s): LOHRMANN, R; BRIDSON, PK; BRIDSON, PK; ORGEL, LE
Title: EFFICIENT METAL-ION CATALYZED TEMPLATE-DIRECTED OLIGONUCLEOTIDE SYNTHESIS
Source: SCIENCE, 208 (4451): 1464-1465 1980

Record 72 of 128
Author(s): ORGEL, LE; CRICK, FHC
Title: SELFISH DNA - THE ULTIMATE PARASITE
Source: NATURE, 284 (5757): 604-607 1980

Record 73 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: SELF-CONDENSATION OF ACTIVATED DINUCLEOTIDES ON POLYNUCLEOTIDE TEMPLATES WITH ALTERNATING SEQUENCES
Source: JOURNAL OF MOLECULAR EVOLUTION, 14 (4): 243-250 1979

Record 74 of 128
Author(s): WEBER, AL; ORGEL, LE
Title: FORMATION OF DIPEPTIDES FROM AMINO-ACIDS AND THE 2'(3')-GLYCYL ESTER OF AN ADENYLATE
Source: JOURNAL OF MOLECULAR EVOLUTION, 13 (3): 185-191 1979

Record 75 of 128
Author(s): WEBER, AL; ORGEL, LE
Title: FORMATION OF PEPTIDES FROM GLYCINE THIOESTERS
Source: JOURNAL OF MOLECULAR EVOLUTION, 13 (3): 193-202 1979

Record 76 of 128
Author(s): SLEEPER, HL; LOHRMANN, R; ORGEL, LE
Title: TEMPLATE-DIRECTED SYNTHESIS OF OLIGOADENYLATES CATALYZED BY PB2+ IONS
Source: JOURNAL OF MOLECULAR EVOLUTION, 13 (3): 203-214 1979

Record 77 of 128
Author(s): ORGEL, LE
Title: SELECTION INVITRO
Source: PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES, 205 (1161): 435-442 1979

Record 78 of 128
Author(s): SLEEPER, HL; LOHRMANN, R; ORGEL, LE
Title: FORMATION OF IMIDAZOLIDES OF DINUCLEOTIDES UNDER POTENTIALLY PREBIOTIC CONDITIONS
Source: JOURNAL OF MOLECULAR EVOLUTION, 11 (2): 87-93 1978

Record 79 of 128
Author(s): WEBER, AL; ORGEL, LE
Title: AMINO-ACID ACTIVATION WITH ADENOSINE 5'-PHOSPHORIMIDAZOLIDE
Source: JOURNAL OF MOLECULAR EVOLUTION, 11 (1): 9-16 1978

Record 80 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: PREFERENTIAL FORMATION OF (2'-5')-LINKED INTERNUCLEOTIDE BONDS IN NON-ENZYMATIC REACTIONS
Source: TETRAHEDRON, 34 (7): 853-855 1978

Record 81 of 128
Author(s): ORGEL, LE
Title: GENE-DUPLICATION AND ORIGIN OF PROTEINS WITH NOVEL FUNCTIONS
Source: JOURNAL OF THEORETICAL BIOLOGY, 67 (4): 773-773 1977

Record 82 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: REACTIONS OF ADENOSINE 5'-PHOSPHORIMIDAZOLIDE WITH ADENOSINE-ANALOGS ON A POLYURIDYLIC ACID TEMPLATE - UNIQUENESS OF 2'-3'-UNSUBSTITUTED BETA-RIBOSYL SYSTEM
Source: JOURNAL OF MOLECULAR BIOLOGY, 113 (1): 193-198 1977

Record 83 of 128
Author(s): EHLER, KW; GIRARD, E; ORGEL, LE
Title: REACTIONS OF POLYFUNCTIONAL AMINO-ACIDS WITH N,N'-CARBONYLDIIMIDAZOLE IN AQUEOUS-SOLUTION - OLIGOPEPTIDE FORMATION
Source: BIOCHIMICA ET BIOPHYSICA ACTA, 491 (1): 253-264 1977

Record 84 of 128
Author(s): BIEMANN, K; ORO, J; TOULMIN, P; ORGEL, LE; NIER, AO; ANDERSON, DM; SIMMONDS, PG; FLORY, D; DIAZ, AV; RUSHNECK, DR; BILLER, JA
Title: SEARCH FOR ORGANIC AND VOLATILE INORGANIC-COMPOUNDS IN 2 SURFACE SAMPLES FROM CHRYSE-PLANITIA REGION OF MARS
Source: SCIENCE, 194 (4260): 72-76 1976

Record 85 of 128
Author(s): GIBBS, DE; ORGEL, LE
Title: TRIPLE HELICES FORMED BY POLYURIDYLIC ACID WITH SOME AMINO DEOXYADENOSINE DERIVATIVES
Source: JOURNAL OF MOLECULAR EVOLUTION, 8 (1): 55-58 1976

Record 86 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: POLYMERIZATION OF NUCLEOTIDE ANALOGS - REACTION OF NUCLEOSIDE 5' PHOSPHORIMIDAZOLIDES WITH 2'-AMINO-2'-DEOXYURIDINE
Source: JOURNAL OF MOLECULAR EVOLUTION, 7 (4): 253-267 1976

Record 87 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: TEMPLATE-DIRECTED SYNTHESIS OF HIGH MOLECULAR-WEIGHT POLYNUCLEOTIDE ANALOGS
Source: NATURE, 261 (5558): 342-344 1976

Record 88 of 128
Author(s): GREEN, D; ORGEL, L
Title: RESEARCH ON ORIGIN OF LIFE
Source: TRENDS IN BIOCHEMICAL SCIENCES, 1 (3): N54-N55 1976

Record 89 of 128
Author(s): ORGEL, LE
Title: PREBIOTIC POLYNUCLEOTIDES AND POLYPEPTIDES
Source: ISRAEL JOURNAL OF CHEMISTRY, 14: 11-16 1975

Record 90 of 128
Author(s): LOHRMANN, R; RANGANATHAN, R; SAWAI, H; ORGEL, LE
Title: PREBIOTIC PEPTIDE-FORMATION IN SOLID-STATE .1. REACTIONS OF BENZOATE ION AND GLYCINE WITH ADENOSINE 5'-PHOSPHORIMIDAZOLIDE
Source: JOURNAL OF MOLECULAR EVOLUTION, 5 (1): 57-73 1975

Record 91 of 128
Author(s): SAWAI, H; ORGEL, LE
Title: OLIGONUCLEOTIDE SYNTHESIS CATALYZED BY ZN2+ ION
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 97 (12): 3532-3533 1975

Record 92 of 128
Author(s): ORGEL, LE; LOHRMANN, R
Title: PREBIOTIC CHEMISTRY AND NUCLEIC-ACID REPLICATION
Source: ACCOUNTS OF CHEMICAL RESEARCH, 7 (11): 368-377 1974

Record 93 of 128
Author(s): VERLANDE.MS; ORGEL, LE
Title: ANALYSIS OF HIGH MOLECULAR-WEIGHT MATERIAL FROM POLYMERIZATION OF ADENOSINE CYCLIC 2',3'-PHOSPHATE
Source: JOURNAL OF MOLECULAR EVOLUTION, 3 (2): 115-120 1974

Record 94 of 128
Author(s): BURTON, FG; LOHRMANN, R; ORGEL, LE
Title: POSSIBLE ROLE OF CRYSTALS IN ORIGINS OF LIFE .7. ADSORPTION AND POLYMERIZATION OF PHOSPHORAMIDATES BY MONTMORILLONITE CLAY
Source: JOURNAL OF MOLECULAR EVOLUTION, 3 (2): 141-150 1974

Record 95 of 128
Author(s): ORGEL, LE
Title: COMMENTS ON DIRECTED PANSPERMIA AND SEAWATER AND ORIGIN OF LIFE - REPLY
Source: ICARUS, 21 (4): 518-518 1974

Record 96 of 128
Author(s): HANDSCHU.GJ; LOHRMANN, R; ORGEL, LE
Title: EFFECT OF MG2+ AND CA2+ ON UREA-CATALYZED PHOSPHORYLATION REACTIONS
Source: JOURNAL OF MOLECULAR EVOLUTION, 2 (4): 251-262 1973

Record 97 of 128
Author(s): VERLANDE.MS; LOHRMANN, R; ORGEL, LE
Title: CATALYSTS FOR SELF-POLYMERIZATION OF ADENOSINE CYCLIC 2', 3'-PHOSPHATE
Source: JOURNAL OF MOLECULAR EVOLUTION, 2 (4): 303-316 1973

Record 98 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: PREBIOTIC ACTIVATION PROCESSES
Source: NATURE, 244 (5416): 418-420 1973

Record 99 of 128
Author(s): CRICK, FHC; ORGEL, LE
Title: DIRECTED PANSPERMIA
Source: ICARUS, 19 (3): 341-346 1973

Record 100 of 128
Author(s): OSTERBER.R; ORGEL, LE; LOHRMANN, R
Title: FURTHER STUDIES OF UREA-CATALYZED PHOSPHORYLATION REACTIONS
Source: JOURNAL OF MOLECULAR EVOLUTION, 2 (2-3): 231-234 1973

Record 101 of 128
Author(s): FULLER, WD; ORGEL, LE; SANCHEZ, RA
Title: STUDIES IN PREBIOTIC SYNTHESIS .7. SOLID-STATE SYNTHESIS OF PURINE NUCLEOSIDES
Source: JOURNAL OF MOLECULAR EVOLUTION, 1 (3): 249-& 1972

Record 102 of 128
Author(s): ORGEL, LE
Title: POSSIBLE STEP IN ORIGIN OF GENETIC CODE
Source: ISRAEL JOURNAL OF CHEMISTRY, 10 (2): 287-& 1972

Record 103 of 128
Author(s): FULLER, WD; SANCHEZ, RA; ORGEL, LE
Title: STUDIES IN PREBIOTIC SYNTHESIS .6. SYNTHESIS OF PURINE NUCLEOSIDES
Source: JOURNAL OF MOLECULAR BIOLOGY, 67 (1): 25-& 1972

Record 104 of 128
Author(s): BISHOP, MJ; ORGEL, LE; LOHRMANN, R
Title: PREBIOTIC PHOSPHORYLATION OF THYMIDINE AT 65 DEGREES C IN SIMULATED DESERT CONDITIONS
Source: NATURE, 237 (5351): 162-& 1972

Record 105 of 128
Author(s): ANDERSON, DM; BIEMANN, K; SHULMAN, GP; TOULMIN, P; UREY, HC; OWEN, T; ORGEL, LE; ORO, J
Title: MASS-SPECTROMETRIC ANALYSIS OF ORGANIC COMPOUNDS, WATER AND VOLATILE CONSTITUENTS IN ATMOSPHERE AND SURFACE OF MARS - VIKING MARS LANDER
Source: ICARUS, 16 (1): 111-& 1972

Record 106 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: UREA-INORGANIC PHOSPHATE MIXTURES AS PREBIOTIC PHOSPHORYLATING AGENTS
Source: SCIENCE, 171 (3970): 490-& 1971

Record 107 of 128
Author(s): DOWLER, MJ; FULLER, WD; SANCHEZ, RA; ORGEL, LE
Title: PREBIOTIC SYNTHESIS OF PROPIOLALDEHYDE AND NICOTINAMIDE
Source: SCIENCE, 169 (3952): 1320-& 1970

Record 108 of 128
Author(s): SULSTON, J; LOHRMANN, R; ORGEL, LE; SCHNEIDE.H; WEIMANN, BJ; MILES, HT
Title: NON-ENZYMIC OLIGONUCLEOTIDE SYNTHESIS ON A POLYCYTIDYLATE TEMPLATE
Source: JOURNAL OF MOLECULAR BIOLOGY, 40 (2): 227-& 1969

Record 109 of 128
Author(s): SCHNEIDE.H; LOHRMANN, R; SULSTON, J; WEIMANN, BJ; ORGEL, LE; MILES, HT
Title: NON-ENZYMIC SYNTHESIS OF DEOXYADENYLATE OLIGONUCLEOTIDES ON A POLYURIDYLATE TEMPLATE
Source: JOURNAL OF MOLECULAR BIOLOGY, 37 (1): 151-& 1968

Record 110 of 128
Author(s): SCHNEIDE.H; LOHRMANN, R; ORGEL, LE; SULSTON, J; WEIMANN, BJ
Title: PARTIAL RESOLUTION OF DL-ADENOSINE BY TEMPLATE SYNTHESIS
Source: SCIENCE, 162 (3855): 809-& 1968

Record 111 of 128
Author(s): HALMANN, M; SANCHEZ, R; ORGEL, LE
Title: CYANOGEN AND CYANAMIDE INDUCED CONDENSATION OF D-RIBOSE AND ORTHOPHOSPHATE
Source: ISRAEL JOURNAL OF CHEMISTRY, 6: P4-& 1968

Record 112 of 128
Author(s): WEIMANN, BJ; LOHRMANN, R; ORGEL, LE; SCHNEIDE.H; SULSTON, JE
Title: TEMPLATE-DIRECTED SYNTHESIS WITH ADENOSINE-5'-PHOSPHORIMIDAZOLIDE
Source: SCIENCE, 161 (3839): 387-& 1968

Record 113 of 128
Author(s): LOHRMANN, R; ORGEL, LE
Title: PREBIOTIC SYNTHESIS - PHOSPHORYLATION IN AQUEOUS SOLUTION
Source: SCIENCE, 161 (3836): 64-& 1968

Record 114 of 128
Author(s): FERRIS, JP; SANCHEZ, RA; ORGEL, LE
Title: STUDIES IN PREBIOTIC SYNTHESIS .3. SYNTHESIS OF PYRIMIDINES FROM CYANOACETYLENE AND CYANATE
Source: JOURNAL OF MOLECULAR BIOLOGY, 33 (3): 693-& 1968

Record 115 of 128
Author(s): SANCHEZ, RA; FERRIS, JP; ORGEL, LE
Title: STUDIES IN PREBIOTIC SYNTHESIS .4. CONVERSION OF 4-AMINOIMIDAZOLE-5-CARBONITRILE DERIVATIVES TO PURINES
Source: JOURNAL OF MOLECULAR BIOLOGY, 38 (1): 121-& 1968

Record 116 of 128
Author(s): ORGEL, LE
Title: EVOLUTION OF GENETIC APPARATUS
Source: JOURNAL OF MOLECULAR BIOLOGY, 38 (3): 381-& 1968

Record 117 of 128
Author(s): REID, C; ORGEL, LE; PONNAMPE.C
Title: NUCLEOSIDE SYNTHESIS UNDER POTENTIALLY PREBIOTIC CONDITIONS
Source: NATURE, 216 (5118): 936-& 1967

Record 118 of 128
Author(s): REID, C; ORGEL, LE
Title: SYNTHESIS OF SUGARS IN POTENTIALLY PREBIOTIC CONDITIONS
Source: NATURE, 216 (5114): 455-& 1967

Record 119 of 128
Author(s): BECK, A; LOHRMANN, R; ORGEL, LE
Title: PHOSPHORYLATION WITH INORGANIC PHOSPHATES AT MODERATE TEMPERATURES
Source: SCIENCE, 157 (3791): 952-& 1967

Record 120 of 128
Author(s): SANCHEZ, RA; FERRIS, JP; ORGEL, LE
Title: STUDIES IN PREBIOTIC SYNTHESIS .2. SYNTHESIS OF PURINE PRECURSORS AND AMINO ACIDS FROM AQUEOUS HYDROGEN CYANIDE
Source: JOURNAL OF MOLECULAR BIOLOGY, 30 (2): 223-& 1967

Record 121 of 128
Author(s): SANCHEZ, RA; FERRIS, JP; ORGEL, LE
Title: CYANOACETYLENE IN PREBIOTIC SYNTHESIS
Source: SCIENCE, 154 (3750): 784-& 1966

Record 122 of 128
Author(s): FERRIS, JP; ORGEL, LE
Title: STUDIES IN PREBIOTIC SYNTHESIS .I. AMINOMALONONITRILE AND 4-AMINO-5-CYANOIMIDAZOLE
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 88 (16): 3829-& 1966

Record 123 of 128
Author(s): SANCHEZ, R; FERRIS, J; ORGEL, LE
Title: CONDITIONS FOR PURINE SYNTHESIS - DID PREBIOTIC SYNTHESIS OCCUR AT LOW TEMPERATURES
Source: SCIENCE, 153 (3731): 72-& 1966

Record 124 of 128
Author(s): FERRIS, JP; ORGEL, LE
Title: AN UNUSUAL PHOTOCHEMICAL REARRANGEMENT IN SYNTHESIS OF ADENINE FROM HYDROGEN CYANIDE
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 88 (5): 1074-& 1966

Record 125 of 128
Author(s): BECK, A; ORGEL, LE
Title: PHOTOCHEMICAL SYNTHESIS OF CONDENSED PHOSPHATES
Source: NATURE, 208 (5014): 1000-& 1965

Record 126 of 128
Author(s): FERRIS, JP; ORGEL, LE
Title: AMINOMALONONITRILE AND 4-AMINO-5-CYANOIMIDAZOLE IN HYDROGEN CYANIDE POLYMERIZATION AND ADENINE SYNTHESIS
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 87 (21): 4976-& 1965

Record 127 of 128
Author(s): BECK, A; ORGEL, LE
Title: FORMATION OF CONDENSED PHOSPHATE IN AQUEOUS SOLUTION
Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 54 (3): 664-& 1965

Record 128 of 128
Author(s): FERRIS, JP; ORGEL, LE
Title: REACTIONS OF BROMOMALONONITRILE WITH BASES
Source: JOURNAL OF ORGANIC CHEMISTRY, 30 (7): 2365-& 1965

Selected papers by Julius Rebek

Record 1 of 24
Author(s): Rebek, J
Title: Some got away, but others didn't...
Source: JOURNAL OF ORGANIC CHEMISTRY, 69 (8): 2651-2660 APR 16 2004

Record 2 of 24
Author(s): Hof, F; Craig, SL; Nuckolls, C; Rebek, J
Title: Molecular encapsulation
Source: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 41 (9): 1488-1508 2002

Record 3 of 24
Author(s): Chen, J; Korner, S; Craig, SL; Lin, S; Rudkevich, DM; Rebek, J
Title: Chemical amplification with encapsulated reagents
Source: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99 (5): 2593-2596 MAR 5 2002

Record 4 of 24
Author(s): Tokunaga, Y; Rudkevich, DM; Santamaria, J; Hilmersson, G; Rebek, J
Title: Solvent controls synthesis and properties of supramolecular structures
Source: CHEMISTRY-A EUROPEAN JOURNAL, 4 (8): 1449-1457 AUG 1998

Record 5 of 24
Author(s): Wintner, EA; Rebek, J
Title: Autocatalysis and the generation of self-replicating systems
Source: ACTA CHEMICA SCANDINAVICA, 50 (6): 469-485 JUN 1996

Record 6 of 24
Author(s): WINTNER, EA; TSAO, B; REBEK, J
Title: EVIDENCE AGAINST AN ALTERNATIVE MECHANISM FOR A SELF-REPLICATING SYSTEM
Source: JOURNAL OF ORGANIC CHEMISTRY, 60 (24): 7997-8001 DEC 1 1995

Record 7 of 24
Author(s): CONN, MM; REBEK, J
Title: THE DESIGN OF SELF-REPLICATING MOLECULES
Source: CURRENT OPINION IN STRUCTURAL BIOLOGY, 4 (4): 629-635 AUG 1994

Record 8 of 24
Author(s): WINTNER, EA; CONN, MM; REBEK, J
Title: SELF-REPLICATING MOLECULES - A 2ND GENERATION
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 116 (20): 8877-8884 OCT 5 1994

Record 9 of 24
Author(s): CONN, MM; WINTNER, EA; REBEK, J
Title: NEW EVIDENCE FOR TEMPLATE EFFECTS IN A SELF-REPLICATING SYSTEM
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 116 (19): 8823-8824 SEP 21 1994

Record 10 of 24
Author(s): CONN, MM; WINTNER, EA; REBEK, J
Title: TEMPLATE EFFECTS IN NEW SELF-REPLICATING MOLECULES
Source: ANGEWANDTE CHEMIE-INTERNATIONAL EDITION IN ENGLISH, 33 (15-16): 1577-1579 SEP 2 1994

Record 11 of 24
Author(s): KUBIK, S; MEISSNER, RS; REBEK, J
Title: SYNTHESIS OF ALPHA,ALPHA-DIALKYLATED AMINO-ACIDS WITH ADENINE OR THYMINE RESIDUES - A NEW MILD AND FACILE HYDROLYSIS OF HYDANTOINS
Source: TETRAHEDRON LETTERS, 35 (36): 6635-6638 SEP 5 1994

Record 12 of 24
Author(s): REBEK, J
Title: SYNTHETIC SELF-REPLICATING MOLECULES
Source: SCIENTIFIC AMERICAN, 271 (1): 48-& JUL 1994

Record 13 of 24
Author(s): HUC, I; CONN, MM; WINTNER, EA; REBEK, J
Title: INTRODUCING GENERAL BASE CATALYSIS IN A SELF-REPLICATING SYSTEM
Source: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 206: 390-ORGN Part 2 AUG 22 1993

Record 14 of 24
Author(s): ROTELLO, V; FENG, Q; HONG, JI; REBEK, J
Title: MUTATION AND COMPETITION IN A SYNTHETIC SELF-REPLICATING SYSTEM
Source: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 204: 414-ORGN Part 2 AUG 23 1992

Record 15 of 24
Author(s): PARK, TK; FENG, Q; REBEK, J
Title: SYNTHETIC REPLICATORS AND EXTRABIOTIC CHEMISTRY
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 114 (12): 4529-4532 JUN 3 1992

Record 16 of 24
Author(s): FENG, Q; PARK, TK; REBEK, J
Title: CROSSOVER REACTIONS BETWEEN SYNTHETIC REPLICATORS YIELD ACTIVE AND INACTIVE RECOMBINANTS
Source: SCIENCE, 256 (5060): 1179-1180 MAY 22 1992

Record 17 of 24
Author(s): FAMULOK, M; NOWICK, JS; REBEK, J
Title: SELF-REPLICATING SYSTEMS
Source: ACTA CHEMICA SCANDINAVICA, 46 (4): 315-324 APR 1992

Record 18 of 24
Author(s): HONG, JI; FENG, Q; ROTELLO, V; REBEK, J
Title: COMPETITION, COOPERATION, AND MUTATION - IMPROVING A SYNTHETIC REPLICATOR BY LIGHT IRRADIATION
Source: SCIENCE, 255 (5046): 848-850 FEB 14 1992

Record 19 of 24
Author(s): REBEK, J
Title: MOLECULAR RECOGNITION AND THE DEVELOPMENT OF SELF-REPLICATING SYSTEMS
Source: EXPERIENTIA, 47 (11-12): 1096-1104 DEC 1 1991

Record 20 of 24
Author(s): ROTELLO, V; HONG, JI; REBEK, J
Title: SIGMOIDAL GROWTH IN A SELF-REPLICATING SYSTEM
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 113 (24): 9422-9423 NOV 20 1991

Record 21 of 24
Author(s): NOWICK, JS; FENG, Q; TJIVIKUA, T; BALLESTER, P; REBEK, J
Title: KINETIC-STUDIES AND MODELING OF A SELF-REPLICATING SYSTEM
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 113 (23): 8831-8839 NOV 6 1991

Record 22 of 24
Author(s): REBEK, J
Title: CLEFTS AS RECEPTOR AND ENZYME ANALOGS
Source: CIBA FOUNDATION SYMPOSIA, 158: 98-114 1991

Record 23 of 24
Author(s): TJIVIKUA, T; BALLESTER, P; REBEK, J
Title: A SELF-REPLICATING SYSTEM
Source: ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 199: 46-ORGN Part 2 APR 22 1990

Record 24 of 24
Author(s): TJIVIKUA, T; BALLESTER, P; REBEK, J
Title: A SELF-REPLICATING SYSTEM
Source: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 112 (3): 1249-1250 JAN 31 1990



Selected pubmed urls

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._DocSum

http://www.ncbi.nlm.nih.gov/entrez...._docsum

For some reason my computer was being funny about me linking things from WoS, so you'll have to look up the first 152 or so by hand, apologies. At least they have titles. There may also be some unintended duplicates.

--------------
Bye.

  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 15 2006,15:37   

what about on my good days?

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Dec. 15 2006,17:06   

Quote (skeptic @ Dec. 15 2006,15:37)
what about on my good days?

We'll need a slip from your doctor giving us a schedule of when your good days and your bad days are. Until then, our hands are tied.

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 15 2006,18:19   

Skeptic,

I know I'm possibly being naively optimistic but is there any remote hope of a serious conversation about a fascinating area of science, preferably troll free?

Sometimes you appear to be someone genuinely interested in a discussion and open to evidence, reason etc. Other times you appear to be the obliviot that Icthyic describes you as. If you can remain on topic and rational (unlike for example the recent religion thread) then by all means post away. There's probably some hope that you can do this. I've got no illusions that the troll or the creationist lies to kids merchant are capable of anything resembling reason, so if they post on thsi thread I'll ask for their posts to be ported to the bathroom wall. Whether that'll happen or not I don't know, but one can ask.

Any chance that after >20 views anyone has something to say about the science? The long list of refs I posted should be as good a basic overview of/introduction to the subject as I can muster at short notice.  There's some truly fascinating articles in there. I haven't read all the pub med ones at the end yet, but the Rebek and Orgel stuff I have read. They are part of the basis of a (hopefully successful) research proposal I am writing.

Louis

--------------
Bye.

  
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 15 2006,23:11   

Personally, I prefer the harder science threads but as you rightly observed they get much less play from the board as a whole and there's much less argument because you really have to know what you're talking about to create any lasting discussion.  I, for one, will greatly enjoy reading the references provided and see if I have anything meaningful to add or offer.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 16 2006,09:48   

Quote
Any chance that after >20 views anyone has something to say about the science?
Well, you did give a long reading list, and there's a lot to catch up on. But I guess I might add to your list of hurdles that have to be overcome: how was the link between particular nucleotides and particular amino acids forged? Perhaps that's more of a fine point compared with your 3 hurdles, but from my perch it looms pretty large.

--------------
Must... not... scratch... mosquito bite.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 16 2006,09:52   

By the way, Louis. I'm curious about your new avatar. Should I recognize this guy?  And should I be able to read his lips?

[edit] Having studied it more closely, I think he's saying "STFU". No?

--------------
Must... not... scratch... mosquito bite.

  
stevestory



Posts: 8880
Joined: Oct. 2005

(Permalink) Posted: Dec. 16 2006,10:02   

It looks like Penn Jillette saying STFU.

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 16 2006,11:31   

Russel,

1) My apologies, my comment wasn't as piqued as it sounds to me now. The curse of time and type. I merely meant that I thought there was a degree of keenness to discuss abiogenesis, and that (IMNSHO) it's better done troll free given the current circumstances. Sorry if I came across snarky, that wasn't my intent. Nor do I expect everyone to read all those references! I haven't read them all yet myself as I said. I am familiar with Orgel's and Rebek's work, but some of the others I linked are new to me. I think a fun thing to do would be to see if we could build (between all the people of disperate disciplines and expertise) an sort of consensus view. A drunken, soon to be hungover, ATBC abiogenetic scenario if you will.

I only bunged those references up for those people who had expressed some genuine interest in the current state of abiogenesis research. If people really want to get a splendid idea of what's going on, they really need look no further than Orgel's work, he really is one of the (if not THE) big fish in OOL research and has been for decades. I can only apologise for not knowing of any more accessible works on the subject. It's not a topic (unlike evolutionary biology for example) I have approached from a popular science position, mainly because it's so chemistry related I had all the journals available to me. EB I had to learn something about from scratch as it were, and so it's much easier to reference easy access online resources. Like I said elsewhere, if I get a chance over Giftmas (the coincidentally situated atheist holiday which celebrates presents) I'll write something up and post it, rather than violate a series of copyright laws by stealing the pdfs and plonking them on my website for all to grab.

2) [Victorian Brit]

Yes it is indeed Mr Penn Jillette. I believe the gentleman in question is expressing a dislike for funk music, by asking that we shut the funk up.  Unless of course I am very much mistaken. It's an excerpt I found on a different website taken from the television programme Mr Jillette and Mr Teller present about farming matters (or so I assume, the title of the show indicates a fascination with fertiliser). I believe Messrs Jillette and Teller to be manifestly unimpressed by a certain type of gentleperson obsessed with matters unproven and pseudoscientific. Although I must confess that despite watching the programme several times I have yet to make the connection between funk music, fertiliser and said irrational persons. I am sure 'twill come to me in time.

[/Victorian Brit]

Should my avatar be causing offense, it can of course be removed. All anyone has to do is ask. Even I can be eminently reasonable.....On occasion.......Well, sometimes.......Rarely. Ok I am a rude, unreasonable and intolerant bastard. Vastly too much time spent on the rugby pitch!

Louis

--------------
Bye.

  
clamboy



Posts: 155
Joined: May 2006

(Permalink) Posted: Dec. 16 2006,12:08   

Louis,

I hope that you will not mind me dropping the discussion down to the Homer Simpson level temporarily, but I have an opening question concerning this:

'3) A series of effector molecules/physical scaffolding/chemoselective processes which allow for a relatively high level of "copying fidelity".'

I understand that this is a hurdle, but how high is it? Since we are talking about repeating chemical processes occuring in (I assume) a basically stable environment, what is it that stands in the way of "copying fidelity"?

Please understand that my level of reading is Dawkins/Zimmer/Gould/Mayr/talkorigins, so while I am not completely ignorant I am certainly no expert. If you just want to point me to an lay person's "Guide to Problems with Copying Fidelity and How They Can Help Lower Your Monthly Payments," cool. Or if you want to sigh and give me your take, that would kick ass too. And I thank you.

  
"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Dec. 16 2006,18:30   

Quote (Louis @ Dec. 15 2006,18:19)
I know I'm possibly being naively optimistic but is there any remote hope of a serious conversation about a fascinating area of science, preferably troll free?

Alas, probably not.

There are two topics that are simply impossible to discuss without emotional hackles being raised --- religion, and politics.

Abiogenesis research, unfortunately, is intimately tied to both of those.

--------------
Editor, Red and Black Publishers
www.RedandBlackPublishers.com

  
bystander



Posts: 301
Joined: Oct. 2005

(Permalink) Posted: Dec. 16 2006,21:29   

I'm strictly an amateur here but I am curious that there is emphasis on how our DNA life came to be. Is there any research creating life of any kind? Also is there any freely available documents from the above?

Michael

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Dec. 16 2006,22:22   

Quote (stevestory @ Dec. 16 2006,10:02)
It looks like Penn Jillette saying STFU.

That must be why Teller never speaks.  :p

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Mike PSS



Posts: 428
Joined: Sep. 2006

(Permalink) Posted: Dec. 16 2006,23:55   

First, to stick my neck out, I haven't read the references (yet).

Has there been any agreement from the researchers involved about the environmental conditions at the time of abiogenesis?

If this is answered in the linked references then I'll find out eventually.

If not, shouldn't finding this out be condition 0) for your tract.

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 17 2006,09:42   

Clamboy,

No need for sighs on my part, that's an excellent question. Also my own understanding has yet to acheive Homer Simpson's lofty heights, so no worries there. I hope I don't come across as being so arrogant that an honest enquiry is somehow beneath me. I'm not, it ain't. I just have no time for trolls. You ain't a troll, ergo no problem. The only reason I know anything about evolutionary biology or counter creationism (for example) is because a handful of very knowledgable folk like PZ, Wes, Lenny, Larry etc explained things to me and others on T.O. with nigh on inhuman patience and clarity. We're not born knowing everything.....well women are but that's a different story.

As for how high the hurdle is, the honest answer is I don't know to any quantifiable degree. I think, based on how you phrased your question a little diversion into why this hurdle even exists is appropriate.

You say something that interests me, and strikes to the heart of your question:

Quote
Since we are talking about repeating chemical processes occuring in (I assume) a basically stable environment, what is it that stands in the way of "copying fidelity"?


WARNING MASSIVE BUT RELEVANT DETOUR INTO CHEMICAL KINETICS FOLLOWS

There's several fascinating things here.  The cartoon of a chemical reaction is something like:

Reactant A + Reactant B -------> Product C (perhaps + by product D)

The general assumption is that if you mix A and B in the same way in the same ratios, POP out comes C. Sadly nothing could be further from the truth. Well I say sadly, but it's what keeps me employed! I am not saying this is your assumption, obviously you appreciate that reality is more of a slag than this, just that this is a common assumption.*

A slightly less simplified understanding of a chemical reaction is shown in this diagram:



This again is a cartoon of a chemical reaction profile. Higher energy reactants on the left go to lower energy products on the right.  Incidentally, in this type of reaction,  the difference in energy between reactant and products ("less stable" reactants going to "more stable" products) is (at least partly) the driving force for the reaction. It's also one of the key reasons that the "entropy challenges" of the creationists are so vapid. The whole system's entropy rises as the difference between the energy or the reactants and products is emitted as EM radiation (or whatever). The enthalpy change is what compensates and drives the entropy change in this case. But I digress, and obviously things are a little more complicated than that.

Key features of that diagram to note: There appear to be two different "routes" from reactants to product, the large humped blue one (with a large Activation Energy [Ea]) and the double humped red one with two smaller activation energies. This is probably way beyond the intended use of that diagram, but this is a genuine possibility in a chemical reaction. The "repeating chemical processes" you refer to really aren't serial iterations if the same thing like a factory assembly line. I'll get to why in a second.

Here are a couple of Wikipedia links to relevant discussions of this stuff that you can read to go into slightly more depth than I'll go into here:

Reaction Kinetics

The Curtin-Hammett Principle (Sadly not the Kirk Hammett Principle, which involves better music)

Stub on microscopic reversibility

Activation Energy

Transition state

Hammond's Postulate (or Hammond Leffler Postulate)

Intermediate

Potential Energy Surface

Personally I prefer this online source however:

http://goldbook.iupac.org/

A brief summary of features: At the peak of each activation energy hump (imagine this as the resistance or inertia that one needs to overcome to get a reaction going, i.e. to get all the reactants into a reactive conformation) is what's called the "transition state" (or t/s for short). A transition state is a very short lived entity on the route from reactants to products, it's high in energy (at top o EA peak) and whether it's product-like or reactant-like affects both the kinetics and thermodynamics of the reaction. In the trough between two EA peaks (between two t/s's) we have a longer lived entity, a reaction intermediate (or simply intermediate). These can even be alternative products (for reasons I'll get to in a moment).

The take home message of this part is that a chemical reaction can be thought of (very simpistically, and not without some reservations) as a route from reactant to product. There are hills to climb (Activation energy), short lived views from the peaks (transition states) and relatively calm and stable troughs (intermediates) to the lower energy product.

The extended analogy is of a whole mountain range, rather than a transverse slice through it. This is a "potential energy surface" and to anyone who has done any physics or read any pop physics about gravity (rolling balls across rubber sheets and Mexican hats etc) this should be familiar.

I've tried to find some suitable pics on the web and not come up with anything perfect, so forgive me if these don't do it justice:





Ignore the x and z axes on the second diagram. Although they deal with a similar situation to the one under discussion, they're not 100% relevant and will only confuse the situation (read: make me type out a whole bunch of new shit! ).

The purpose of these pics is to give a mental picture of a 3D version of the 2D reaction cartoon above.

Imagine now that in the second diagram we have on the North West of the "diamond" side our reactants, and on the South West side our products, the y axis remains as energy, the pics of ball and stick molecules and the x and z axes can be ignored. You can see that progress from the NW side to the SE side could take a variety of routes, some with peaks that are more NW and some with peaks that are more SE. Peaks that are more "reactant like" and more "product like" respectively.

The mountain range analogy I am going to use is far from perfect, but I hope it will illustrate certain points. Imagine a team of 100 mountain climbers all in a race to get from base camp on the NW side of a range of mountains to the base camp on the SE side of the range of mountains. Our 100 climbers are at different levels of ability, fitness and bravery etc. A Boltzmann distribution of talent if you like, the majority are at the mean values of these various talents for the group, but there are outliers. As the starting whistle blows our climbers set off, some racing for nearby peaks, some racing across the relatively flat plains to distant peaks, some weaving through the valleys. As fortune would have it disaster strikes, a huge and raging storm hits the entire mountain range forcing our  climbers to  head for the nearest shelter. Those who have gone for the NWern peaks can either head back to the NW base camp, or if they have got over the peak or are near to the top take refuge in the most sheltered available valleys. These aren't perhaps as sheltered as the most SEern base camp, but are possibly more sheltered than the NWern base camp. Those who have either raced through valleys or over flats to more SEern peaks can seek refuge in the appropriate nearest valley, or if they have moved quickly or chosen a really quick route to the SE end, then they can settle in for brandy and relaxtion in the safety of the SE base camp. It's possible that some exceptionally quick and fit individuals might have found a route across a NWern peak that has a simple downward slope all the way to the SE base camp, and these superb specimins can join their chums.

This is a far more accurate image of how a reaction is than either of the previous cartoons, and I hope (combined with the more detailed wikipedia articles) goes some way to demonstrate why a chemical reaction isn't  simply an easily repeatable assembly line type process.

What relevance does this have for copying fidelity?

Well, first of all not all reactants are at the same energy level, in any population of molecules there is a Boltzmann distribution of energy states, only a proportion of which have sufficient energy to overcome the activation energy barrier, acheive a reactive conformation (a transition state for a specific reaction) and react to form a specific product. So if we are only considering ONE specific route through our mountain, only some of our climbers are capable of making it over the specific hurdles (EA) to get to the desired products.

Couple that to phenomena like microscopic reversibility (where the forward path through the mountains and the reverse path through the mountains are similarly difficult) and the Curtin-Hammett postulate (where two different routes through the mountains which end in two different endpoints are of similar difficulty) etc and you have a whole swathe of reasons why a chemical reaction is not a simple A + B---> C situation. And that's even before one considers that starting conditions, reaction conditions, issues of mixing and scale etc are going to be at least slightly different each time the reaction proceeds.

A good example of this is, again, the Soai reaction. The Soai reaction is an autocatalytic process with some fascinating kinetics. It's of particular interest to abiogenesis research, not because it is a presumed precursor, but because it illustrates how well understood, complex kinetic effects can lead to astounding consequences. We can also look at this reaction to illustrate a mixing effect.

The details of the Soai reaction aren't important for the purposes of this discussion, what is important is that the product (P) of the reaction can combine with the reagents to form (temporarily) a catalyst © which aids the formation of that product (P). I.e. it catalyses its own formation. Better than all of this is that the Soai reaction at first glance should produce a racemic mixture of products (an equal mixture of left handed and right handed products, i.e. an equal mixture of enantiomers). First an idea of scale. If we were running a reaction on the scale of one mole of reactants that means that in our reaction vessel there are about 6 x 10exp23 indidual molecules of each reactant (assuming equimolar amounts for the sake of simplicity). That's one fuck of a lot of molecules!

Just as in a coin toss game, if you tossed a coin 6 x 10exp23 times you'd expect to get roughly equal amounts of heads and tails, but exactly 50:50 is only one of a number of very probable mixtures of nearly 50:50 head:tails you could get. In reality, with such huge numbers, exactly, spot on, not one coin toss either way 50:50 perfect mixtures of heads and tails are very very rare. Same with chemical reactions. There is very rarely such a thing as a perfect 50:50 racemic mixture. One of the fascinating things about the Soai reaction is that we DON'T get racemic mixtures at all, we get scalemic mixtures (mixtures of enantiomers that are not 50:50). If we re-run the reaction on the same substrates several times we get enantiopure products. Not only is the Soai reaction autocatalytic but it is enantioselectively autocatalytic. That means that if we see a slight bias of one enantiomer, then subjecting that product mixture to the reaction conditions again will produce more of that enantiomer and not the other one. All this comes from a totally randomn effect: which product enantiomer gains a slight majority in the product mixture first, as the reaction proceeds.

So what this means is if we are flipping coins and the first coin we flip is a head then the system in which we are flipping coins amplfies that first chance coin toss, and we will get heads thereafter. If tails, then tails thereafter. Each coin toss in the Soai reaction is dependant on the first coin toss.

Now the sharp eyed amongst you will have spotted a problem. Why then don't we get complete enantioselection immediately? Why do we have to take the product mixture and resubmit it to the conditions to get complete enantioselection.  Back to our mountains! Instead of 100 climbers we now have 6 x 10exp23. As we send them through the mountains a huge number of them will reach the other side of the range by the same route at roughly the same time. In the reaction, we have each molecule of sufficient energy following the same reaction path to the products. Some will end up elsewhere in the mountain range, but a whole host of our reactants are turned into products. A whole lot of coins are being tossed at the same time.

Our copying fidelity issue is like this. There are many routes through our reaction mountain range, not all are molecular climbers will follow the same path, nor do all our molecular climbers have the same energy. Some reactions will have low peaks and hugely easy to follow valleys to follow that means most of our climbers will swarm down those routes. Other reactions will have labyrinthian potential energy surfaces where significant numbers of our molecular climbers can get lost. In the case of the Soai reaction, in which the reagents are relatively simple molecules, the number of hidden valleys and alternative routes are far less that in the case of a long complex polymer. Well, to be truthful,  for the sake of simplicity in this case they are, there are subtleties that complicate things later on.

The take home message from all this is that even if all the chemical conditions are stable and similar each time you run the reaction, you can get different results due to the underlying kinetics and thermodynamics of the process. Of course these differences may be minor in some cases and major in others.

The next factor is the obvious one: things rarely ARE the same every time. Our broiling pot of abiogenetic froth might be a 30 Celsius one morning and 20 the next. A 10C difference in temperature equates to a roughly twofold difference in reaction rate (as a rule of thumb). Not only that but that 10 degree difference shifts our mean energy value in our Boltzmann distribution of energy values meaning that more or less (depending on if it gets hotter or colder) of our climbers have the energy to climb specific EA peaks. More than that, the higher energy we go (i.e. hotter) previously unaccessable peaks become possible opening up new avenues across our potential energy mountain range. And EVEN more than that changes in temperature may actually alter the mountain range itself, causing previously insignificant valleys and hidey holes to take on greater significance as more climber pour into them.

Changes in pH, temperature, pressure, mixing, chemical composition etc etc etc really do have a huge part to play in determining the course of a reaction.

MASSIVE BUT RELEVANT DETOUR INTO CHEMICAL KINETICS ENDS

Why is copying fidelity important?

Imagine our original type of cartoon system:

A + B -----> C

Now if we are looking at an autocatalytic system, it could run like this:

1) A + Reagents ------>  [A+catalyst complex]  -------> 2 A + byproducts

In this scenario A plus some reagents which are consumed in the reaction forms a catalytic complex which degrades to give the original A, plus another A plus the discarded, chewed up remains of the reagents. (Sounds like an ex-girlfriend of mine, but it's ok because I'M NOT  BITTER!!!! Ok only kidding, purely for humour folks. All my exes died mysteriously in freak boating accidents. Still kidding. It was food poisoning. Want some pie sweetheart?).

Imagine a different system:

2) A + Reagents ------>  [A+catalyst complex]  ------->  A + A' + byproducts

A' is very similar to A but not exactly the same. Now think about the following systems:

3) A' + Reagents ------>  [A+catalyst complex]  -------> 3 A' + byproducts

or

4) A' + Reagents ------>  B

In system 3) A' is a better catalyst of it's own formation than A, in system 4) it reacts to form B, something that is a dead end, i.e. not an autocatalytic system.

For the sake of this example we are assuming that the type and amounts of reagents consumed in the reaction, and the type and amounts of byproducts formed in reaction are the same or A and A'. If there is a limited quantity of reagents then this really is an evolutionary scenario. It's easy to see that if systems 2) and 3) are the case then in our broth of products A will a minor component of the broth and A' will be the major. So if the copying fidelity (i.e. autocatalytic ability of A to catalyse it's own formation and not the formation of other things) of A is like that in system 2) then A has problems!

The same applies if systems 2) and 4) are the case. System 1) is a nice one for A. But what if we have two similar systems:

1) A + Reagents ------FAST----> [A+catalyst complex]  -------> 2 A + byproducts

5) B + Reagents ------SLOW----> [B+catalyst complex]  -------> 2 B + byproducts

Both these reactions have similar profiles, similar fidelities, but A is quick and B is slow. Again we have competition for identical reagents. A will form a greater part of the product broth this time.

So the more fecund, fast and high fidelity systems will tend to form the majority of the products. If we are in a myre of hugely varied and complex webs of myriad reacting systems then those pathways through the myre which more efficiently catalyse themselves (or are more effectively catalysed by something else, or have more suitable kinetics/thermodynamics as described above) will tend to be those that use up all the available reagents.

So apologies for enormity, but I hope I have answered your questions to some degree. If I haven't, or if I've misunderstood them, please let me know. Now this gubbins is over with, the next answers will be much shorter I hope.

Cheers

Louis

*(Randomn aside whilst I think of it: whilst pop sci books abound for physics and biology and are really excellent, pop sci chem books are few and far between, and rarely do the subject justice. This interests me for several reasons, not the least of which is that what people consider chemistry affects all our lives vastly more intimately, immediately and significantly than does the most exciting reaches of popular physics or biology. Another reason is possible cash! )

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Alan Fox



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(Permalink) Posted: Dec. 17 2006,09:42   

For the less technical among us (me for instance) can I recommend "Planetary Dreams" (Wiley, 1999) by Robert Shapiro.

Simplistically, life was impossible on Earth prior to the condensation of water vapour and the first evidence of algal mats appears later, around 3.5 billion years ago. Common descent allows that all earthly life could have radiated out from those first simple life-forms. If you consider panspermia as a possibility it only regresses the problem and gives no answer. Personal incredulity then cuts in. Behe's mousetrap argument applied to abiogenesis seems a real obstacle. Unless some one can repeat the event in the lab, or life is found elsewhere in the universe, I don't expect any convincing hypotheses soon, if ever.

  
Louis



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(Permalink) Posted: Dec. 17 2006,09:50   

Lenny,

I think you are right, but that you have put it backwards. Abiogenesis has sweet fuck all to do with politics and religion.

Some people's religious dogma and political use of said dogma is so impoverished, narrow minded and destined to contradict observed and observable reality that they have manufactured a political controversy surrounding some aspects of science. It ain't science's fault. Just like it isn't a beaten wife's fault that her husband is a cruel bastard who gets his kicks beating women. That some people have wrongly conflated their religion and politics to a field of science does not mean that "she was asking for it".

Louis

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Louis



Posts: 6436
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(Permalink) Posted: Dec. 17 2006,10:28   

Bystander,

I've heard/read of some attempts to make no DNA based life/synthetic viruses. Indeed any attempt to make a non nucleic acid based replicating system could be seen to be the first forays into non-DNA based life. I think the reason that people work on synthetic DNA based life is because we can mimic what we already know. In that sense we are at the start of the process of actually making synthetic life. There is no reason it needs to be this way, we could start from the bottom up and make our own life. This is, however, vastly more difficult than trying to reverse engineer exisiting life back to it's simplest units. The idea is that the two approaches will meet in the middle.

Again, I really have to apologise for the non free nature of most (if not all) of the cited articles. I've come top down to abiogenesis as opposed to the normal way I approach topics. In other words the only things I know about it come from journals and the primary scientific literature. I was already working as a synthetic organic chemist before I got interested in abiogenesis, so I could sit at work and scour the lit as I would in my own field.  I'll try to find some more accessible things.

Louis

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clamboy



Posts: 155
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(Permalink) Posted: Dec. 17 2006,13:46   

Louis -

Thank you!!! I actually understood the vast majority of your post, and it certainly clarified the problem/hurdle of "copying fidelity" admirably.

And you didn't even have to pull some bogus probability estimates out of your ass!

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 17 2006,16:06   

Hey Louis -
Congratulations on starting what looks like it's going to be a very interesting thread.
Great reading list, and great intro in your 9:42 post today. (Lovely graphics, too! )
What exactly is your background, and your day job, if I may ask?

By the way, I had the honor of meeting Orgel several years ago at an RNA conference. Too bad I didn't know enough to ask him any really profound questions.

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Louis



Posts: 6436
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(Permalink) Posted: Dec. 17 2006,17:08   

Mike PSS,

Quote
Has there been any agreement from the researchers involved about the environmental conditions at the time of abiogenesis?

{snip}......{/snip}

If not, shouldn't finding this out be condition 0) for your tract.


I honestly don't know if there has been "agreement", depending on what one means by agreement. Are there a variety of plausible evidence based scenarios, one of which has yet to be 100% settled on by all relevant experts everywhere? Yes. So as for agreement the answer is yes and no!

Should this be condition 0) for my "tract"?

[Outraged John Cleese voice]

Well the first thought is "tract"? I'm fucking Jack Chick now am I? Tract? Kiss my heavily polished not particularly black arse! Tract. Fuck off.

[/Outraged John Cleese voice]

Ok so I'm kidding about, don't take the above to heart or in any way seriously.

What I think the question is is this:

"Is a complete description of the environmental conditions for the early earth, when we think abiogenesis occured, available?"

As far as I am aware, the answer is no a complete and perfect description isn't available for the early environmental conditions of earth. There are several descriptions which may be correct, but work is ongoing.

As for whether this is a necessary condition for understanding abiogenesis, the answer is no. We can work out likely scenarios, probable routes etc based on what we do know now. As for one hard and fast definitive answer to end all answers, sorry but I'm sure I don't need to tell you that science doesn't work like that. We have degrees of uncertainty ranging from the "pretty uncertain" to the "so certain it's extremely unlikely to be vastly different from this". Certain aspects of abiogenesis are at the latter end, certain aspects at the former.

We need to know the exact conditions of early earth to get an exact pathway. Something we may never be able to get, although I remain cheerfully optimistic. We don't need to know the exact conditions to be able to come up with a huge number or plausible pathways, which is the situation we are now in. In an analogous manner to that of clades and trees of relationships in evolutionary biology we cannot say to any degree of certainty that very archaic individual A was the direct ancestor of modern individual B. What we CAN say is that A and B share such traits that it is likely that A is representative of an organism ancestral to organism B. If A is slightly less archaic and we have DNA data then maybe we can come up with something more concrete. Otherwise we are left to making trees of parsimonious relationships and teasing out the actual paths by finding mutually independant lines of corrobotating evidence.

The same is true with abiogenesis. I can go into the lab and makeyou a self replicating molecular system. I can also go and make you an encapsulated system seperated from the rest of the universe by a semi permeable membrane. I can template these reactions on inorganic materials, and I can make effector/replicator systems and a whole swathe of autocatalytic systems. What I cannot do is claim with any basis in fact that any of these are DEFINITELY replicas of the precise route taken during abiogenesis, or even representative of the route taken. We don't have the "fossil" chemical evidence to say one way or another. What we DO have is some fascinating clues from geology and astrochemistry. I have some notes of this I might be able to dig out from the other house when and if I am next there.

Cheers

Louis

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Louis



Posts: 6436
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(Permalink) Posted: Dec. 17 2006,17:16   

Alan,

Colour me extremely confused and/or shocked.

Are you saying that the witterings of the IDCists are valid when applied to abiogenesis due to your/their personal incredulity?

If you're not, please forgive me for even beginning to insinuate that you were! I shall say 10 "Hail Dawkins" and beat myself with a copy of "The Origin of Species" for a month.

If you are.......wuh wuh wuh wuh....gibber. Please explain.

Cheers

Louis

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Louis



Posts: 6436
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(Permalink) Posted: Dec. 17 2006,17:30   

Clamboy,

You understood my post? Shit, I'm glad one of us did! ;-)

Also glad to be of service.

As for probability estimates, I love them to bits. What I don't love is where creationists start from which is "it's weeeeeeeeealllllly unlikely thefore goddit". My probability estimate of abiogenesis by purely natural means based on the sum total of evidence we have now is: 1. We sure as shit don't have any evidence for any of the other oft touted hypotheses. ;-)

Louis

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Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Dec. 17 2006,17:35   

This guy seems to have thought in an organized way about an aspect of abiogenesis that's been lurking in the back of my mind in an inchoate way for some time.
Quote
Origins of Life and Evolution of Biospheres (2006) 36: 109–150

SURFACTANT ASSEMBLIES AND THEIR VARIOUS POSSIBLE ROLES
FOR THE ORIGIN(S) OF LIFE
PETER WALDE
Abstract.
A large number of surfactants (surface active molecules) are chemically simple compounds
that can be obtained by simple chemical reactions, in some cases even under presumably prebiotic
conditions. Surfactant assemblies are self-organized polymolecular aggregates of surfactants, in the
simplest case micelles, vesicles, hexagonal and cubic phases. It may be that these different types of
surfactant assemblies have played various, so-far underestimated important roles in the processes that
led to the formation of the first living systems.
Although nucleic acids are key players in the formation of cells as we knowthem today (RNAworld
hypothesis), it is still unclear howRNAcould have been formed under prebiotic conditions. Surfactants
with their self-organizing properties may have assisted, controlled and compartimentalized some of the
chemical reactions that eventually led to the formation of molecules like RNA. Therefore, surfactants
were possibly very important in prebiotic times in the sense that they may have been involved in
different physical and chemical processes that finally led to a transformation of non-living matter to
the first cellular form(s) of life. This hypothesis is based on four main experimental observations: (i)
Surfactant aggregation can lead to cell-like compartimentation (vesicles). (ii) Surfactant assemblies
can provide local reaction conditions that are very different from the bulk medium, which may lead to a
dramatic change in the rate of chemical reactions and to a change in reaction product distributions. (iii)
The surface properties of surfactant assemblies that may be liquid- or solid-like, charged or neutral,
and the elasticity and packing density of surfactant assemblies depend on the chemical structure of
the surfactants, on the presence of other molecules, and on the overall environmental conditions (e. g.
temperature). This wide range of surface characteristics of surfactant assemblies may allow a control
of surface-bound chemical reactions not only by the charge or hydrophobicity of the surface but also
by its “softness”. (iv) Chiral polymolecular assemblies (helices) may form from chiral surfactants.
There are many examples that illustrate the different roles and potential roles of surfactant assemblies
in different research areas outside of the field of the origin(s) of life, most importantly in
investigations of contemporary living systems, in nanotechnology applications, and in the development
of drug delivery systems. Concepts and ideas behind many of these applications may have
relevance also in connection to the different unsolved problems in understanding the origin(s) of
life.


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skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 17 2006,17:53   

Louis, sorry to say it but when I initially scrolled through your kinetics lecture I thought GoP had posted here, lol.

Anyway, only had time for a quick scan but looks good.  Keep it up!

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 17 2006,18:00   

Russell,

Thanks very much.

I missed a question of yours earlier:

Quote
But I guess I might add to your list of hurdles that have to be overcome: how was the link between particular nucleotides and particular amino acids forged? Perhaps that's more of a fine point compared with your 3 hurdles, but from my perch it looms pretty large.


This is one of the really interesting "modern, high tech" questions. I must confess I know vastly less about it than other areas of abiogenesis research, but I do know it's broadly part of the "RNA world" hypotheses, so looking in those refs of Orgel's that refer to that might help.

I think it's important to bear in mind just how high tech the DNA/protein/ribosome system is. I have a series of guesses about it, all of varying degrees of totally dumb. As far as I remember such a system must have had some sort of scaffolding to get going, and we don't know what that scaffolding is. I could be wrong about that.I need to read up. My guess based on what I remember is that we're looking in the wrong place by focussing on the genome and the proteome. I think the glycome, which is vastly more varied and contains hugely more "information" than either is the smoking gun. I also think that if we go back to the dead ends of primary metabolites in archea (i.e. secondary metabolites, natural products) we may also find some smoking guns there. I stress these are only midly informed guesses, and this whole section is a long way of saying "I don't know yet!".

The paper you cite about surfactants is a good example of a possible scaffold. Certainly simple bipolar molecules exist in space etc, and we know that at certain concentrations some molecules can aggregate to form micelles. They really are a good candidante in many ways. Also some of them are carbohydrate like (which is part of my reason to probe the glycome ;-) ).

My background is chemistry. My first taste of research was physical organometallic chemistry (My undergrad self despised organic chemists as being horribly limited and narrow, a bit stupid and dull. Oh how wrong I was! ). My second taste was synthetic organic chemistry both in industry and academia. I then realised how totally daft my undergrad opinion was as the universe literally opened out before me. Organic chemistry is far from limited. Basically I think I grew up! I then left industry to go back and do a PhD in natural product synthesis and I've never looked back. Since then I ahve yet again done a bit of academic work and most recently a bit of industry work. I haven't settled yet (hey I'm only a bairn at 32! ) Unfortunately getting into academic jobs as an organic chemist is frighteningly difficult compared to many if not most fields of study. I really don't know why this should be the case, or if it is the consequence of the market. Organic chem isn't somehow special or more advanced than say biology or particle physics, it just seems to be oversubscribed by people who want to be academics perhaps. What I do know is that I don't want to take the management track that some many of my friends have so that I can stay close to the research. It isn't the most lucrative or glorious career choice (despite the assurances of the entire pharma industry) but it is the most fun. Day job is in process chem at a big pharma atm, but not for much longer, I'm moving on. What's your background and day job?

I've yet to meet Orgel properly, although I have seen him talk and chatted anonymously as part of a crowd. He's someone I'd love to work for/with but I get the impression that would be a really hard position to acheive.

Louis

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Louis



Posts: 6436
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(Permalink) Posted: Dec. 17 2006,18:07   

Skeptic,

You thought I was GoP? Ow that hurts. Any serious contributions or are you simply befouling the thread because you've been asked not to? A bit childish no? Smarmy faux compliments irritate me anyway.

I'm guessing a simple email request can have your contributions to the thread ported, so please either say something worthwhile or keep it to yourself. Just allow the rational folks here their tiny bit of space and troll the rest of the board please. Is it really so much to ask?

Louis

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"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Dec. 17 2006,18:27   

Quote (Louis @ Dec. 17 2006,09:42)
The only reason I know anything about evolutionary biology or counter creationism (for example) is because a handful of very knowledgable folk like PZ, Wes, Lenny, Larry etc explained things to me and others on T.O. with nigh on inhuman patience and clarity.

I must interject here . . .   While I have always had a deep interest in science and the natural world, going back to the "Golden Book Encyclopedias" I got when I was eight or nine, I am not a scientist, nor do I play one on the Internet, and as far as knowledge of science goes, I am not fit to wipe the shoes of PZ, Wes or Larry.  :)

What I *am* pretty good at, though, is political organizing, and ID/creationism is, at root, a wholly-owned subsidiary of the Religious Right political movement.  Nothing more, nothing less, nothing else.  One does not need to know a lick of science to beat the IDers, because, at core, this fight simply ain't *about* science.  It's about political power, who gets to have it, and what they get to do with it once they've got it.

ID and the Religious Right died as an effective political movement because, in the final tally, no one supports it or its political goals.  Not even the Republicrat Party, with its one-party control of the White House, the entire Congress and most of the judiciary, could bring itself to actually  *pass* any of the fundie political agenda.

So, now that the politico-fundies are dead as mackerels, those of us with an interest in science can indulge in it for its own sake.  Finally.

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www.RedandBlackPublishers.com

  
"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Dec. 17 2006,18:31   

Quote (Louis @ Dec. 17 2006,09:50)
Lenny,

I think you are right, but that you have put it backwards. Abiogenesis has sweet fuck all to do with politics and religion.

Some people's religious dogma and political use of said dogma is so impoverished, narrow minded and destined to contradict observed and observable reality that they have manufactured a political controversy surrounding some aspects of science. It ain't science's fault. Just like it isn't a beaten wife's fault that her husband is a cruel bastard who gets his kicks beating women. That some people have wrongly conflated their religion and politics to a field of science does not mean that "she was asking for it".

Louis

Well, that is all true.  Nevertheless, even without the fundies, research into areas like abiogenesis and cosmology is, inextricably, wrapped up with lots of religious (and therefore political) complications.  It is simply unavoidable.

C'est la vie, n'est pa?

--------------
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www.RedandBlackPublishers.com

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 17 2006,18:44   

Bien sur. C'est vraiment le monde de nos temps. Malheureusement.

Lenny, I don't often say thanks for the education I recieved on T.O. and you were an instrumental part, esp on counter creationism and Viking Piss. Whilst I am totally bemused by the current Evangelical Atheist vs Chamberlain Group bunfight at the PT corral (mainly because we all agree on so very very much), I always want to recognise those that made the issues clearer rather than more obscure. Your political analogies and commentaries have been instrumental to my growing understanding, and for that I am eternally grateful.

Should I ever be on the same continent as you and the others again, beers will be forthcoming. It is the least I can do. I think an international Howlerfest is in order, along with my renewal of T.O. activity.

Louis

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