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: 13407 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: 299 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.   -------------- "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! ) -------------- Bye.

Alan Fox Posts: 1552 Joined: Aug. 2005 (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 Posts: 6436 Joined: Jan. 2006 (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 -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (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 -------------- Bye.

clamboy Posts: 299 Joined: May 2006 (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. -------------- Must... not... scratch... mosquito bite.

Louis Posts: 6436 Joined: Jan. 2006 (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 -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (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 -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (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 -------------- Bye.

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

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

Louis Posts: 6436 Joined: Jan. 2006 (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 -------------- Bye.

"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. -------------- Editor, Red and Black Publishers 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? -------------- Editor, Red and Black Publishers 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 -------------- Bye.

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Dec. 17 2006,22:24    Quote (Louis @ 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. Nothing so sinister.  I was scrolling through and I saw the pretty pictures and the long post and GoP popped into my head.   A quick second look revealed the truth and I had a little chuckle which I thought I'd share with you.  No need to threaten censorship as you see.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Dec. 18 2006,03:30    Skeptic, I know what you meant re GoP. I was being humourous. Mi apologias for not being clear enough Not censorship by any stretch of the imagination. Asking for some irrelevant posts to be moved to the bathroom wall isn't censorship, it's porting irrelevant garbage to the relevant place. Make your last post your finalno science poston this thread please. And I have no power or authority here, I can only ask Steve or Wes to do this. They can, and quite probably will, say no. I just have a fervent hope that on one thread we can focus on, ya know, the science rather than the trolling. Any chance? Any at all? Please. I have asked very nicely several times. By the very virtue of having this conversation we're doing exactly what I hoped we wouldn't. Louis -------------- Bye.

Alan Fox Posts: 1552 Joined: Aug. 2005 (Permalink) Posted: Dec. 18 2006,04:08    Quote (Louis @ Dec. 17 2006,12:16) 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 No, just observing that if the mousetrap argument had been applied to abiogenesis, it would have been less easy to refute. I was just remarking that there is quite a narrow window for abiogenesis to occur between a cool and wet enough earth and the first evidence of stromatolites. I can see that it did happen. I can believe that it was a natural process, but I doubt we will ever know how it happened. So room for "Goddidit" for those that need that hypothesis. I am far from up-to-speed on the latest theories and developments, anyway. Robert Shapiro sold me the idea that abiogenesis is a much tougher nut to crack than evolution; he is also doubtful that "RNA world" will turn out to be a succesful hypothesis.

deadman_932 Posts: 3094 Joined: May 2006 (Permalink) Posted: Dec. 18 2006,04:47    For those that have access to book/journal stacks in uni's or colleges: Osawa, Syozo, "Evolution of the Genetic Code"  (Oxford University Press, Oxford, 1995). mechanisms of molecular evolution of the genetic code. “Contribution of Cosmic Rays, Radiation, Lightning and Geothermal Heat to Prebiotic Synthesis on the Primitive Earth” In: The Role of Radiation in the Origin and Evolution of Life (Akaboshi, M., Fujii, N. & Navarro-Gonzalez, R. (Eds.)) (Kyoto University Press, Kyoto), pp. 9-24. Terada, R., Imai, E., Honda, H., Hatori, K. & Matsuno, K., 1999 “Fixation of Carbon Dioxide in Hydrothermal Environments: Synthesis of Formic and Acetic Acids” Viva Origino 27, 197-208. Matsuno,Koichiro:  “Submarine Hydrothermal Vents Preparing the Emergence of Life and Likelihood in the Laboratory Experiments?” Genetics - Biological Science 53-7, 6-7 Imai, E., Honda, H., Hatori, K. & Matsuno, K., 1999. “Autocatalytic Synthesis of Oligoglycine in a Simulated Submarine Hydrothermal System” Origins Life Evol. Bioshere 29, 249-259. Much of Matsuno's work is available for online reading here, too: http://bio.nagaokaut.ac.jp/~matsuno/preprint.html For some online reading: http://www.gla.ac.uk/Project/originoflife/index.htm http://www.origins.rpi.edu/research.html http://www.resa.net/nasa/origins_life.htm http://www.lcb.uu.se/~dave/publications.html http://www.chemistry.ucsc.edu/Projects/origin/home.html http://www.astrobiology.com/ http://adsabs.harvard.edu/cgi-bin....be00373 article on the stability of aminos in space (hit pdf link) such articles can be found in http://www.adsabs.harvard.edu/ , including lots of interesting stuff on chirality of prebiotic molecules, or http://adsabs.harvard.edu/cgi-bin....format=  (on "The Astrobiology of Nucleobases") good stuff , Maynard. http://mcb.harvard.edu/BioLinks.html (for dealing with bio terms) -------------- AtBC Award for Thoroughness in the Face of Creationism

deadman_932 Posts: 3094 Joined: May 2006 (Permalink) Posted: Dec. 18 2006,05:50    I found these in another text file I had on abiogenesis/origins of life stuff: Martin W, Russell MJ. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philos Trans R Soc Lond B Biol Sci. 2003;358:59–85 http://www.gla.ac.uk/project....ell.pdf Other origin of life PDF's available at this site I had mentioned in previous post: http://www.gla.ac.uk/projects/originoflife/html/2001/pdf_articles.htm Mulkidjanian, A., et al (2003) Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. Evol Biol. 2003; 3: 12. Published online at http://www.pubmedcentral.nih.gov/article....ols=bot   ***see also the reference list cited in this article Montmorillionite Clays and catalysis http://www.ncbi.nlm.nih.gov/entrez....2458736 and http://www.ncbi.nlm.nih.gov/entrez....5570708 Clays seem pretty interesting in terms of autocatalysis and early cell formation, etc. By the way, the Santa Fe Institute got a nice fat grant to study Life Origins last year, in conjunction with some other Uni's   Quote October 18, 2005 -- The Directorate for Biological Sciences at the National Science Foundation (NSF) announced that the Santa Fe Institute (SFI)--along with collaborating institutions George Mason University, University of Colorado, University of Illinois at Urbana-Champaign, Arizona State, and Carnegie Institution of Washington--has been awarded a five-year Frontiers in Integrative Biological Research (FIBR) grant for their joint project, "The Emergence of Life: from Geochemistry to the Genetic Code." and some links to relevant papers can be found at : http://www.googlesyndicatedsearch.com/u....afe.edu Note: If anyone hates PDF's as much as I do, and the slowness of Adobe Acrobat ( yeah, I know you can strip out a bunch of crap it loads , but it's still cumbersome) --get  the free Foxit pdf reader at http://www.foxitsoftware.com/pdf/rd_intro.php -------------- AtBC Award for Thoroughness in the Face of Creationism

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Dec. 18 2006,06:02    Alan, {thwack} Our Dawkins Who Art Mostly in Oxford, Richard be thy name...{thwack} Ok enough funny. I'd agree that in certain senses abiogenesis is a tougher nut to crack than evolutionary biology. But not in all senses.The senses in which I think this is the case are due to things like time taken for certain evolutionary processes etc. We can synthesise self replicating molecules quicker than nature can evolve them for example, these are things accomplishable in a human lifespan. So in some senses abiogenesis is an easier nut to crack. However, as I allude to above unlike evolutionary biology in abiogenesis research we simply don't have the fossils in the same sense. We have a different problem, instead of lacking fossil chemicals in their entirety, we are drowned by huge amounts of chemical noise from which a signal is almost impossible to distinguish. We also have a really unique situation in that we have a really good idea of what sorts of chemicals were available on early earth and in space, and we have a really good idea of what is available now. We have a comparitively poor idea about which paths were taken between the two points! We do however have many great ideas about which paths COULD have been taken. If you consider how complex a topic we're dealing with that's a pretty advanced state of knowledge. Granted it isn't a step by step process of what definitely, but are you sure you're not asking for something that you cannot get in order to avail yourself of the "poof goddidit" loophole? After all, we don't have a step by step process of the relationship between humans and out last common ancestor with chimps. Does this provide a "goddidit" loophole? Of course not! We don't actually need the step by step "photograph" of each link, the relatonship is demonstrated by different evidence. The DNA, fingerprints, footprints, fibre traces etc left by a burglar demonstrate his or her presence in the burgled domicile as well (in fact vastly better) than a CCTV picture. The emotional appeal of a CCTV picture is a different beast, but it is of lesser evidenciary significance. I'm curious as to why you seem to need to single out abiogenesis as more friendly to the Beheian mousetrap ideas. More friendly in your personal estimation perhaps, but very far from being actually more friendly. Cheers Louis -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Dec. 18 2006,06:06    Deadman, Thanks very much indeed for all of that. Not least the pdf reader alternative! Louis -------------- Bye.

Mike PSS Posts: 428 Joined: Sep. 2006 (Permalink) Posted: Dec. 18 2006,08:14    Quote (Louis @ Dec. 17 2006,18:08) 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?" Ahhhh... so many ways to respond to Mr. Cleese.  Shall it be classic MP?  Some of the stage work?  Films (I was thinking Kevin Klinesque at first since the psedo-psychological rantings could produce some chuckles).  Naw, I choose the simple route. [Normal Manuel voice] "Qué?" [/Normal Manuel voice] ***************************** My comment, although sparse in detail, is angled more on the 'energy pump' aspects of any first self-replication survivor.  With your references and others I see a few alternatives for the energy source, and eventual energy stream, for our first bugs. 1.  Sulfide/Sulfate energy source.  Originating source from the hydrothermal vents that have most likely existed on earth since the oceans first formed. (O.K. Sulphur for you East Atlantists, I'll also state that Al-U-Min-E-Um is more correct but becoming more archaic.  Color....   errrrr  Colour me surprised that you cling on to this usage as "MORE" correct) 2.  Water surface energy source, maybe a CO2 or hydrocarbon source. 3.  Specific catalysis products in some specific area.  This source could be a vent from a large deposit of hydrides (H2 product is possible) or other such chemistry where a catalysis starts the breakdown of an older geologic deposit after some specific geologic change (uplift exposure to air/rain, fold exposure to water, volcanism through formerly stable areas, metamorphic change, etc...). The first 'energy pump' piece of abiogenesis would have to be a simple system and the self-replicator may have located itself in an area where unstable (read higher-energy) sources of chemicals occur so that the first 'energy pump' consisted of simple autocatalytic (or catalytic, see below) one-step reaction. Another aspect of these conditions is the availability of catalysts.  Although autocatalytic processes are an easier condition, a catalytic process may be necessary in these early conditions.  As Deadman referenced...   Quote Montmorillionite Clays and catalysis http://www.ncbi.nlm.nih.gov/entrez....2458736 and http://www.ncbi.nlm.nih.gov/entrez....5570708 Clays seem pretty interesting in terms of autocatalysis and early cell formation, etc. Deadman, just had one correction on your comment.  Autocatalysis implies no external factors.  The presence of clays (Fe, Mg, Mn, etc...) would be external catalysis only. Anyway, the first replicator could use an available catalytic source (say a clay ball) located near a source of higher-energy molecules (list above) to source its energy for life. I'll become more verbose on this thread to bore the he11 out of everyone. Mike PSS I'm a BSc chemical engineer and spent the last 10 years working in industrial production.  My first seven was with phosphate fertilizer manufacture.  Interesting process; -first making 8000 tons per day (tpd) of sulfuric acid by burning liquid sulphur (SO2) then catalysing to SO3 then scrubbing to H2SO4 (98%). -then using all that sulfuric acid to attack 12,000 tpd of phosphate ore (the drag lines at the mines are massive) becoming phosphoric acid and gypsum. -combine the phosphoric acid with liquid ammonia and you get 7,500 tpd of a high quality Di-ammonium Phosphate (18-46-0) or Mono-ammonium Phosphate (10-50-0). Big equipment, big material balances and big energy swings in every process.  Lots of fun after the lab scale processes taught in school.

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Dec. 18 2006,09:43    abiogenesis is a much tougher nut to crack in this sense: Behe's whole argument, with or without the mousetrap, is a God-of-the-gaps argument. In terms of the evolution of various complex structures from less complex precursors, he's already said that he'll accept nothing less than a mutation-by-mutation account of how it happened. Which is ridiculous, of course, and at odds with what he wrote in "Darwin's Black Box", the gist of which - as I recall, anyway; I consider it not worth my while to go back and check - is that no plausible paths are even conceivable. So, just like the transitional fossil charade, where any series of N transitional fossils between point A and point B implies N+1 gaps, any awake reader can see that Behe is just pre-moving the goalposts. So the gaps in which he's trying to hide God get to be elastic to the point of meaninglessness. Abiogenesis is different, though. There is no point A, so the gap in which God resides is much more spacious, and there's not the same sense that it's getting smaller with every new issue of Nature. -------------- Must... not... scratch... mosquito bite.

deadman_932 Posts: 3094 Joined: May 2006 (Permalink) Posted: Dec. 18 2006,12:06    Hah, yeah, you're right, Mike -- I had autocatalysis on the brain after looking through some of the Santa Fe material I have -- I should have simply said "catalysis." Per Russel on Behe's (and Dembski's) facile rewriting of claims -- Behe and Dembski have both not merely moved the goalposts, but they've essentially put wheels on them. Classic God-of-the-Gappism. And yeah, he does say what you stated, concerning multiple systems, pp. 39-50 and onward of "Black Box." See also http://www.don-lindsay-archive.org/creation/behe.html and section 4.2 of http://www.talkorigins.org/design/faqs/nfl/#defense by Richard Wein -------------- AtBC Award for Thoroughness in the Face of Creationism

"Rev Dr" Lenny Flank Posts: 2560 Joined: Feb. 2005 (Permalink) Posted: Dec. 18 2006,17:47    Quote (Louis @ Dec. 17 2006,18:44) esp on counter creationism and **Viking Piss. ** Tee hee --- those who came late to this party are probably scratching their heads wondering that the #### you're talking about.   -------------- Editor, Red and Black Publishers www.RedandBlackPublishers.com

Alan Fox Posts: 1552 Joined: Aug. 2005 (Permalink) Posted: Dec. 21 2006,04:59    Quote I'm curious as to why you seem to need to single out abiogenesis as more friendly to the Beheian mousetrap ideas. More friendly in your personal estimation perhaps, but very far from being actually more friendly. Hi Louis Been too busy to respond, lately. In case the thread is not yet moribund: Friendly is not what I feel towards Behe or his mousetrap. Russell puts it neatly. Say a Mars probe was able to recover and bring back soil samples. Resulting analysis may show: 1) No evidence of life (I know the "one white crow" argument, it was a big sample ) 2) Evidence of lifeforms, carbon-based, DNA, proteins, same chirality. 3) Evidence of lifeforms, like nothing on Earth. Would I be right in concluding from 1, Life is a rare, maybe unique event. We may never explain its origin. From 2, panspermia looks a strong possibility and abiogenesis could still be a unique event that occurred elsewhere than on Earth. From 3, we are not alone and the Universe is teeming with life. I also find the thermal vent hypothesis more compelling than a warm pond. You have the high temperatures, minerals and nutrients close to cold therefore stabilising water with convection currents quickly moving chemicals away from the "manufacturing" hot-spots, preventing them from quickly breaking down again.

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Dec. 21 2006,15:59    I have to go out of my way to thank Louis once again for this thread, and I guess GoP for the original idea.  Here's my reading list for the holidays: Aquagenesis - Ellis Biocosm - Gardner The Plausibility of Life - Kirschner and Gerhart The Spark of Life - Wills and Bada Independent Birth of Organisms - Senepathy I'll check in after the holidays and add my comment of substance, til then Happy Holidays, Merry Christmas, Happy Hanakkah, Happy Boxing Day, Happy New Year and for our resident atheists Happy Anti-Christmas. Talk to you all next year.

stephenWells Posts: 127 Joined: April 2006 (Permalink) Posted: Dec. 21 2006,16:05    Quote (Mike PSS @ Dec. 18 2006,08:14) (O.K. Sulphur for you East Atlantists, I'll also state that Al-U-Min-E-Um is more correct but becoming more archaic.  Color....   errrrr  Colour me surprised that you cling on to this usage as "MORE" correct) Oddly, that element was originally called alumium (cf. sodium, potassium), aluminum is a more easily pronounced Americanism, aluminium is then a back-formation from that to recover the -ium ending. So, the ^^%^% with it, everyone's wrong

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Dec. 22 2006,09:51    Alan, My bad for being confused. I think in each of your three examples, as you note, the sample size is too small to make "global" or "universal" claims about the feasibility or otherwise of abiogenesis. They would however all be fascinating data points in "local" abiogenesis research. I'm really cautious about making massive "universal" inferences from limited sets of data. For example the idea of universal and local homogeneity of physical processes/"laws" is based on a huge series of observations from pretty much every field of human enquiry. Observations of life/lack of life on Mars and its comparison to earthly life are a miniscule subset of the possible data. Finding life on Mars would be fascinating and may tell us a huge amount about local abiogenesis (or not). The comment of Russell's about there being no point A baffles me to to be honest. The only reason that this gap appears to be unchanged by every issue of Nature is that chemists rarely publish in Nature! Ok so that's not a serious point at all! What I am really confused about is this "no point A" stuff. Maybe it's my dumb chemist brain but I see one HELLOVA lot of point As. Perhaps you and Russell could expand on this for me because I'm confused. (Possibly due to current state of crippling hangover but I digress). Louis -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Dec. 22 2006,11:18    Mike PSS, Re: hydrothermal vent and Fe/S chem as an early source of energy for early organisms, yup absolutely, a great candidate. And Fe/S chemistry has some interesting facets that might be really key. The lability of some S based ligands in Fe complexes for example. I guess I'm thinking vastly simpler in terms of what the Ur-replicator might have been. I don't see them needing an "external" energy source probably because I'm thinking of them as simple chemical reactions in the sense described in my kinetics post previously. I.e. the enthalpy difference between reactants and product is the driving force for reaction, and the fact that the reaction is catalysed/autocatalysed lowers the activation energy and favours one reaction pathway over others. This is why I am asking for people's ideas of orders of events. Because I don't see that a self replicating molecular system is much of a hurdle at all. The combination of this with encapsulation and that system then "repoducing" is a different bag. My guess is that this is a really tricky step and absolutely requires the soort of energy pumps you describe. The templating of clays/minerals is I agree a really key to either a self replicating system (although it's not necessary, but could be very helpful) and/or encapsulating a chemical system. In fact were I to make a guess it would be that encapsulation happened early in abiogenesis because a relatively "high tech" replicating system would be positively hampered by encapsulation. So my first general guess is roughly thus: 1) A simple self replicating system develops which is either initially autocatalytic or templated/catalysed in some fashion. If templated/catalysed the template or catalyst must be capable of being encapsulated with the self replicating system (this is why I am a fan of polymeric carbohydrates as structures for templation, and guess what, these are "simple" polymers, "spring loaded" to polymerise at the anomeric position, the monomers are found in space/abiotic systems and their formation is diastereoselective). 2) This simple replicating system is then encapsulated in some fashion (micelles, mineral absorption etc). The barrier/walls of the capsule must be at least semi permeable and must permit the influx of reactants (this isn't as hard as it sounds. Think osmosis) 3) The encapsulated replicating system is subject to natural selection (more stable/fecund etc systems persist at the expense of crappier ones). This is the stage I think your energy pump idea is really valuable. Systems which can more efficiently use the resources around them, who's kinetics are simple/robust enough to take advantage of external energy sources will tend to work better. Whaddya think? Louis P.S. I speeek-ah Eeenglish verrry goood. I-ah learn eeet from-ah boook. P.P.S. Sulfur and aluminium are the IUPAC standards. Even us Brits behave ourselves when it comes to IUPAC! -------------- Bye.

Mike PSS Posts: 428 Joined: Sep. 2006 (Permalink) Posted: Dec. 22 2006,13:32    Louis, This is the point I need to do some more reading from the assigned list.  The details of the next point of discussion start to get fuzzy in my mind because I lose sight of everything going on at once.  Holiday reading I guess. Sticking to the thermal vent environment might be helpful for the moment. My initial thoughts about your 1) 2) 3) scenario are: 1)  Plausible for carbs.  Easy to polymerise and easy to find in the environment we're talking about.  I think the polymer chemistry in this step is what will set up step 2) as a first Ur-replicator. 2)  The polymerisation products in step 1) may form the encapsulation layer here.  A branched polymer or co-polymer is an option to consider for incorporation within the encapsulation layer with one branch backbone adapting to the miscelle barrier and the other branch backbone internal and/or external to the barrier (the first resemblance of an interbarrier receptor).  As new variants of polymer chains are included in the miscelle then new chemical reactive functions may appear depending on backbone structure and chain endings.  Now we would have a system incorporating the full variety of organic chemistry in the vent environment. 3)  The energy pump system is probably an Ionic Pump type found in cell functions today.  The Ion source is produced in the vent or the exposed Fe catalyst source.  One item I thought of is that the miscelle formation would change the water conditions inside the miscelle formed in 2) so that the Ionic Pump system has a greater energy release or different product mix (maybe moving the equilibrium or solubility of the products one way or the other).  The Ionic Pump system would also have to maintain the internal miscelle conditions so that this reaction could be sustained. Just musings for now.  I'll see how good this holds up in the literature. Mike PSS

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Dec. 22 2006,13:35    Quote The comment of Russell's about there being no point A baffles me to to be honest. The only reason that this gap appears to be unchanged by every issue of Nature is that chemists rarely publish in Nature! Ok so that's not a serious point at all! What I am really confused about is this "no point A" stuff. Nothing all that profound, really. I'm just noting that evolution is all about getting from one form to another by "descent with modification". So it's no big deal (unless your mind is stunted by religious indoctrination) to get from Australopithecus to Homo, or even from worms to chickens. In each case the "point A" is pretty well known and understood. But for abiogenesis, "point A" is nonliving, nonreproducing, precursors of unknown composition, in an unknown environment. And "point B", the bacteria-like creatures reflected in the earliest fossil stromatolites (I guess that's the earliest we have, but I'm not expert or even current on this stuff), (1) is not very well known or understood itself, and (2) represents a much huger leap than any other "point A - point B" pair plausibly addressed by any real science. It's sort of like giving a Martian detailed directions to get to the Empire State Building, starting with "Go north on 1st Avenue to 34th Street...." -------------- Must... not... scratch... mosquito bite.

Steviepinhead Posts: 532 Joined: Jan. 2006 (Permalink) Posted: Dec. 22 2006,15:27    You guys have been working on this for a whole week now, and you still have no definitive result...? And yet you Darwinists are arrogant enough to call yourselves "scientists"! The only thing this little exercise demonstrates is that life must be complexly specified if abiogenesis can't be solved through such massive application of brainpower over such an enormous length of time... </troll-mimickry>

deadman_932 Posts: 3094 Joined: May 2006 (Permalink) Posted: Dec. 22 2006,16:22    Speaking of troll mimicry:   Quote The energy pump system is probably an Ionic Pump type found in cell functions today.   YEAH I GOT YER PUMP RIGHT HERE Just for you, Louis. Ah, memories.   By the way, here's something to read : "Genesis: The Scientific Quest for Life's Origin"  by Robert Hazen, a colleague of theoretical biologist Harold Morowitz and physicist James Trefil at George Mason U. -- it has an iffy title ( at least to my taste) but it's pretty good , and it's fun, and most importantly, it's FREE. A doc. file is available here :   http://hazen.gl.ciw.edu/publica....ownload or you can look at it in HTML online here:  http://209.85.165.104/search?....nk&cd=8 -------------- AtBC Award for Thoroughness in the Face of Creationism

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Dec. 25 2006,23:38    My holiday reading is raising more questions than it answers, which is fantastic, but I have one in particular that I keep coming back to.  I'm not sure if it falls under evolutionary biology, genetics or molecular biology but given the diversity on this board I think we've got them all covered. My question relates to conserved genes and specifically those that are conserved in vastly different species.  Is it the commonly held assumption that these genes are just remnants that are not expressed or are they actually active genes?  I'm thinking in terms of a conserved gene similar in both single-celled organisms and higher mammals.  Would they just be latent in the mammal or are they actually expressed and participate in some basic process?  I know generalities aren't very useful but I'm just trying to get some idea if there are any trends in these cases or a consenses of thought on conserved genes.

Chris Hyland Posts: 705 Joined: Jan. 2006 (Permalink) Posted: Dec. 26 2006,03:14    There a quite a few genes that are conserved over all domains of life, such as those involved in DNA and protein production, transcription and translation, and central metabolism. There are also a lot of genes that are used across a lot of species for different purposes, as recent analysis of the sea urchin and amoeba genomes has shown. For those with plenty of time on their hands I highly recommend 'The principles of life' by Tibor Ganti. A good review is here.

ericmurphy Posts: 2460 Joined: Oct. 2005 (Permalink) Posted: Dec. 26 2006,15:07    Quote (skeptic @ Dec. 25 2006,21:38) My question relates to conserved genes and specifically those that are conserved in vastly different species.  Is it the commonly held assumption that these genes are just remnants that are not expressed or are they actually active genes?  I'm thinking in terms of a conserved gene similar in both single-celled organisms and higher mammals.  Would they just be latent in the mammal or are they actually expressed and participate in some basic process? I can't imagine that a gene that is not expressed or that otherwise serves no function would be conserved. A functionless gene would not be subjected to selection pressure, and therefore could mutate without restriction. -------------- 2006 MVD award for most dogged defense of scientific sanity "Atheism is a religion the same way NOT collecting stamps is a hobby." —Scott Adams

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Dec. 26 2006,15:52    Quote I can't imagine that a gene that is not expressed or that otherwise serves no function would be conserved. A functionless gene would not be subjected to selection pressure, and therefore could mutate without restriction Conversely, if a gene, or stretch of DNA sequence is conserved significantly (i.e. statistically significantly) better than "filler" like intronic sequences, or unexpressed pseudogenes, you can be pretty sure that it either has a significant function, or at least has until the most recent generations. This is one area where ToE makes useful predictions, but afdavism comes up, once again, empty-handed. -------------- Must... not... scratch... mosquito bite.

"Rev Dr" Lenny Flank Posts: 2560 Joined: Feb. 2005 (Permalink) Posted: Dec. 26 2006,18:14    Quote (skeptic @ Dec. 25 2006,23:38) My question relates to conserved genes and specifically those that are conserved in vastly different species.  Is it the commonly held assumption that these genes are just remnants that are not expressed or are they actually active genes? There are several genes that are conserved across virtually all life, and others that are conserved across virtually all multicellular life.  In nearly every case, these are basic central "housekeeping" genes that perform the most basic and vital cell functions.  Since they work well enough to get the job done, there's not much point in changing them.  At the cellular biochemical level, all life is pretty much the same -- a banana cell isn't very different from a human cell. They all have to do the same basic biochemical tasks, and since they're all descended from each other, the simplest solution is to keep doing the same thing, over and over and over.  (It's the NON-descendents, like virii and the most primitive prokaryotes, who show different biochemistries). As for multicellular organisms, all the really important stuff happened in the pre-Cambrian (how to make cells stick together into one body, how to form various internal layers, how to determine front from back and up from down).  Since then, multicellular life has consisted simply of minor variations on the same theme -- multicellular animals are just tubes with various numbers of things sticking out the sides.  At the basic biochemical level, a flatworm and a human simply are not that different from each other. -------------- Editor, Red and Black Publishers www.RedandBlackPublishers.com

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Dec. 26 2006,21:11    So essentially we're looking at a "Why reinventing the wheel" scenario?  Something that troubles me is that all the differences would then be improvements of original genes without much actual innovation.  I'm sure this must be the general case and exceptions exist.  Whatever the case I surely plan on looking into this more.

"Rev Dr" Lenny Flank Posts: 2560 Joined: Feb. 2005 (Permalink) Posted: Dec. 26 2006,22:07    Quote (skeptic @ Dec. 26 2006,21:11) So essentially we're looking at a "Why reinventing the wheel" scenario?  Something that troubles me is that all the differences would then be improvements of original genes without much actual innovation.  I'm sure this must be the general case and exceptions exist.  Whatever the case I surely plan on looking into this more. Actually most of the major innovations are the result of gene duplication, followed by variation in the duplicated gene. When it comes to basic genes like HOX genes, a small change (a single duplication, for instance) can have a large effect on the final phenotype. Or, in the case of the appearance of eukaryotes, the major innovations came from symbiosis, and weren't genetic at all. But at the basic biochemical level, there isn't much room for improvement.  Those genes are highly conserved because they work well just the way they are. -------------- Editor, Red and Black Publishers www.RedandBlackPublishers.com

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Dec. 26 2006,23:32    I don't really see this thread going very far, but you might enjoy my response to Jonathan Sarfati regarding Imai et al (1999) “Boiled Creationist with a Side of Hexaglycine: Sarfati on Imai et al. (1999)." -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Dec. 29 2006,21:21    Another question, what's are earliest evidence for DNA?  I know we're limited by the nature of the fossil record but what direct evidence do we have right now?

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Dec. 30 2006,01:29    ya see?  I just refuse to try to explain this any more.  OOL demands a solid grasp of geochemistry, and biochemistry.  Plus, you had better do some solid astrochemistry as well. OOL is far more difficult than the standard creationist crap.  It is much more difficult in the first place, and then you must be ready to deal with the creationist lies and blunders.  I have a 35 page bibliography (and growing) and I have had to limit my attention to areas that I think will be most productive.   It is just too much! This is how ID really started.  With Thaxton, C. B., Walter L. Bradley, R. L. Olsen 1984 The Mystery of Life’s Origin.  New York: Philosophical Library. It was not Johnson, Behe, or Dembski. Edited by Dr.GH on Dec. 30 2006,01:31 -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Alan Fox Posts: 1552 Joined: Aug. 2005 (Permalink) Posted: Dec. 30 2006,05:18    Dr Hurd You appear to agree with Robert Shapiro on the intractability of the OOL problem. Would you agree with him that "RNA world" is not a convincing hypothesis? Does the "thermal vent" idea appeal?

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Dec. 30 2006,07:18    All, I haven't deserted this thread, and despite Dr GH's pessimism for its prospects (ironic when considering the critique of Safarti's garbage) when I get a chance I have a "proper" post to make. Cheers Louis -------------- Bye.

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Dec. 30 2006,10:19    Nor have I, I've been busy with background reading and the holidays. Lol, if anyone cared.

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Dec. 30 2006,11:29    Nor have I. If the library's open today, I plan on checking out Shapiro's book. Holidays are too crazy, though. Has anyone read the Hazen book, "Gen-e-sis"? -------------- Must... not... scratch... mosquito bite.

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Dec. 30 2006,17:28    Good news! I got Shapiro's book, Hazen's, and - for good measure - "Investigations" by Stuart Kauffman (2000) with an adjacent Dewey decimal number and correspondingly related content. -------------- Must... not... scratch... mosquito bite.

"Rev Dr" Lenny Flank Posts: 2560 Joined: Feb. 2005 (Permalink) Posted: Dec. 30 2006,18:21    Quote (Dr.GH @ Dec. 30 2006,01:29) This is how ID really started.  With Thaxton, C. B., Walter L. Bradley, R. L. Olsen 1984 The Mystery of Life’s Origin.  New York: Philosophical Library. It was not Johnson, Behe, or Dembski. Yes and no.  Thaxton was probably the first to use the term "intelligent design", but as far as the ID movement itself, it's Johnson who gets the "credit".   See:  "The Birth of Intelligent Design 'Theory' ", at: http://www.geocities.com/lflank/designhistory.htm -------------- Editor, Red and Black Publishers www.RedandBlackPublishers.com

deadman_932 Posts: 3094 Joined: May 2006 (Permalink) Posted: Dec. 30 2006,18:23    Russell: Excellent, I plan on getting a few of the suggested works here myself. Being an archaeologist, I didn't get enough background in the basic chem/organic chem/bio/blah,blah, blah classes I took, but I AM fanatically interested in the hard sciences, subscribe to Nature and Science, read constantly and don't mind being guided by more informed people towards a better understanding of the issues. Any other relevant suggested works would be helpful, since you guys already know the territory I'm just entering -------------- AtBC Award for Thoroughness in the Face of Creationism

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Dec. 30 2006,20:08    Iris Fry, 2000 "The Emergence of Life on Earth: A Historical and Scientific Overview" Rutgers University Press This is still the best single cover book available.  This is sad actually, because there is a huge amount of new work that needs to be presented to general readers. (Hazen has too many personal issues that he lets into his book).   Shapiro has made a career out of being negative.  Every ship needs an anchor, and Shapiro is the anchor for OOL. That is not for me. I am in the process of writing up some material, and I have descided to use it as a doctoral proposal. No need to tell me- I think that it is very weird too: GREs, orals, at my age.  I must be sick. Maybe I'll recover.  But if I am to personally follow this, I need a lab and graduate students have access to labs. Edited by Dr.GH on Dec. 30 2006,20:10 -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

deadman_932 Posts: 3094 Joined: May 2006 (Permalink) Posted: Dec. 30 2006,21:18    Gary: Thanks! I've got a lot of purchasing and reading to do after I recover from this weekend-- I should have demanded book certificates again for Xmas, grrr.   -------------- AtBC Award for Thoroughness in the Face of Creationism

Ichthyic Posts: 3325 Joined: May 2006 (Permalink) Posted: Jan. 04 2007,00:24    Quote No need to tell me- I think that it is very weird too: GREs, orals, at my age.  I must be sick. Maybe I'll recover.  But if I am to personally follow this, I need a lab and graduate students have access to labs. you're a braver man than I, Gunga Din. I find working with non-profit research groups associated with universities to give me decent access to labs when needed. the university appreciates NOT having to support your ass through getting another degree, as well. If you can't find a relevant NGO to work with, you might try making one yourself and going that way. I did that, and found it to actually be far easier than getting my degree was, that's for sure. just a thought, and best of luck either way. -------------- "And the sea will grant each man new hope..." -CC

Alan Fox Posts: 1552 Joined: Aug. 2005 (Permalink) Posted: Jan. 04 2007,04:40    Has anyone read Hubert Yockey's book, Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life 2005 Cambridge University Press ISBN 13 978-0-521-80293-2? His web-site seems to be down but I came across this comment by him in an email published by a critic Quote If you send me your postal address I shall send you the Computers & Chemistry paper. That will explain why the recent data on the genomes of human and other organisms provide a mathematical proof of "Darwinism" beyond a reasonable doubt.

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 04 2007,14:08    I have read it through once, and will probably make a second pass.  I am not ready to make much about it other than to note that Yockey knows much more about physics and math than about chemistry or biology.  However, he thinks that there is not real difference between math and biology therefore he is (in his imagination) an expert in biology and biochemistry. Edited by Dr.GH on Jan. 04 2007,14:09 -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Steviepinhead Posts: 532 Joined: Jan. 2006 (Permalink) Posted: Jan. 04 2007,16:16    I just finished Hazen's Genesis.  It's charming, anecdotal, does provide a very sketchy and spotty overview of the history and breadth of the subject, and spends--in general--way too much time trying to tie Hazen, his colleagues and pals, and his lab to every important ongoing inquiry in the field. He gives a decent sense of the major positions and disputes in the field, of what we can already feel pretty confident of (much more than what the typical creationists frothing about "abiological" issues would ever admit), and of the many areas that remain to be pursued and pinned down. Nothing really wrong with any of that--the bit about walking on the tideflats and estimating sand-grain size and coverage, and correlating it all with emergent patterns of sand-ripples is accessible amateur science at its best, and several of the descriptions of "how exactly (read: once over lightly) we went about performing that particular experiment" are entertaining and interesting, you-are-there, accounts. But.  There's just way too little nitty-gritty chemistry.  Too many photos of people and not enough good illos/diagrams of the concepts.  Science is people and personality-driven, to some large degree, and we all have some level of People-magazine fascination with that aspect of things, but this book had way too much of the rubbing-elbows-with-the-stars and not enough length, detail, and meat. I wasn't left with a whole lot more "take-home" info than I picked up out of a couple of deDuve's books a decade ago, plus just half-assedly following the topic in pop-science books and mags and news articles since then. (Hint: You'd do as well, really, to go to the most recent Tangled Web and read the first entry.) I'm like deadman, I think.  I'm probably not going to be able to follow/keep up with a detailed chemical analysis (and certainly won't have the fonts, etc., to contribute to one, even if I had some of the other background).  But, dammit, I want to SEE it anyway.  And give it a shot.  And pretend to myself I can kinda-sorta follow what's being said.  And ask questions.  And go to the links and the cites if I'm really motivated. One of the key things that some of the discussions on AtBC and Pharyngula and TO and other such places teaches is that--if you're not a complete pinhead or utterly unteachable/unlearnable (like DaveyDoodles)-- "you"--the broadly-educated, curious layperson--are not incapable of reaching and following the primary literature of science and scholarship, when necessary. Finding that this was true in a general sense (some earlier, unintegrated experiences from earlier well-done "how to" manuals had intimated the prospect)--which happened to me about ten-twelve years ago, back in the bricks-and-mortar library era--was a personal revelation for me!  One that I attempted to pass onto my then-junior high/high school aged kids while it might still do them some real good, and have attempted--in appropriate social situations--to pass onto other friends, relatives, acquaintances: while we obviously are all, in our specialized world, highly dependent on experts for any number of services and guidance, and while we should not make the mistake that, simply because we can kinda-sorta "follow" what these people are saying, we are instantly no-sweat-involved "one of them," you don't "just" have to take everybody's word for it: if it's important enough to you, you can access and, to some extent, weigh the evidence yourself. Or at least track an articulate, evidence-weighing discussion/debate among the real scientists well enough to come away with some sense of who's bs-ing you and themselves and who's not. (This process is, of course, for many reasons we seem unable to get across to the likes of davey, light-years away from going to some single marginalized source of "expert" info and privileging it over every other source in the world.) Anyway, bring on the nitty-gritty, you real scientists.  Please.  And thanks!

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Jan. 05 2007,18:28    Thanks, Pihhead. I just finished Shapiro's book, and had much the same reaction. Very little to sink one's teeth into. And, with the added disadvantage of being >20 years old, I can't really recommend it, except for historical interest. It does have some interesting history about Lysenkoism in the Soviet Union, which turns out to have a significant impact on the whole field. Oparin, who is basically the father of the discipline was a Lysenkoist. I was about to start Hazen, but in light of Stevie P's review, I think I'll skip straight to Kauffman's "Investigations". I do note, though, that the foreword to Hazen's book was written by David Deamer, one of my professors in graduate school whom I especially admired. -------------- Must... not... scratch... mosquito bite.

Steviepinhead Posts: 532 Joined: Jan. 2006 (Permalink) Posted: Jan. 05 2007,20:04    Deamer comes off well in Hazen's book. Again, I enjoyed the book, as far as it went.  It just wasn't the toothsome, incisive chomp at the latest data that I was hoping it would be.

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Jan. 05 2007,21:53    A quick leafing through the book tells me it will be more "toothsome" than the Shapiro book, though. Maybe to really get into the nitty gritty, we'll have to read recent issues of "Origins of Life and Evolution of the Biosphere", or perhaps some of the 128 references listed by Louis in his thread opener. I feel like I need a little big-picture orientation, though, before I can put into proper perspective questions like "is cyanoacetylene prebiotic?". -------------- Must... not... scratch... mosquito bite.

MichiganRuss Posts: 2 Joined: Jan. 2007 (Permalink) Posted: Jan. 10 2007,18:26    Glad I found this thread. OOL research is a fascinating topic area for me. I think there are numerous directions from which to approach it that could offer incite.  Incite might be our best we can hope for in the short term since we do lack the exact details of the primary chemistries on the early earth.  Fortunately, incite can offer great directionality to further inquiry if that incite stimulates curiosity to the point of goading a researcher into following a line of inquiry long enough for it to bear fruit. In considering OOL, since we are dealing with unknown processes and conditions, we are essentially working in the abstract.  We are basically attempting to ferret out the nature of the pre-cellular material processing.  When we talk of specifics - what reaction kinetics are necessary for a specific molecular species to predominate in a solution, for instance - we need expert knowledge of chemistry.  However, at this point, even the chemistry experts are looking for a guide in the form of a plausibility argument for how the transition to cellular life occurred.  In this process of creative guessing, anyone with the ability to combine the basic capabilities of chemical species - get longer, get shorter, fold, match shapes, make reactions easier, make reactions harder, prefer reacting with some other chemicals, be stable, be unstable, among others - in, perhaps uncharacteristic, tinker toy kinds of ways, potentially has the ability to offer incite into the origin of life.  So, to those of you who have prefaced your posts with self-deprecating comments about your understanding of chemistry or the current state of OOL research I say start looking at it in a more creative, more abstract way.  The current state of OOL research is more about looking for a way to proceed than it is about discovering the answer.  Realistically, the spark that illuminates the most promising path forward may well be ignited by observing soap bubbles or watching a kite line entangled in a tree. The sciences like chemistry and physics have demonstrated for us that the chemistry of living things is not distinct from the chemistry of non-living things.  This provides us with all the reason we need to pursue the earthly - as opposed to pre-existing life riding to earth on a comet - origin of life as a legitimate discipline with hope of success.  That progress toward the goal of understanding the OOL on this planet might be slow can be understood and accepted when we consider how ill-prepared we still are, even in the scientific community, to deal with the level of complexity associated with living things.  When I say complexity, I simply mean the capacity to simultaneously account for the behavior of a large number interacting entities. The difficulty of predicting behaviors becomes apparent when we look at three-atom water, for instance.  Water is composed of one oxygen bonded to two hydrogen atoms.  The characteristics of water are "emergent" properties of the combining of those three atoms in that exact way. The properties of molecular water are very different from those of molecular hydrogen, very different from those of molecular oxygen, and very different from any mixture of the two.  Then, too, the specific configurations of the atomic species in water itself make for still different emergent properties of water as a gas, as a liquid or as a solid. Just as water is an emergent property of oxygen combined with hydrogen in exact proportions under specific conditions, life, too, is a product of emergence - emergence at many levels.  At the atomic level, life depends on the emergent properties of sodium and calcium ions interacting with water.  At the molecular level life depends on characteristics of water, amino acids, nucleic acids, and glucose to name a few.  At the macromolecular level lipids,  DNA, RNA, and proteins for instance, all exhibit properties quite distinct from their component sub units. Emergence continues through the sub-cellular, organelle, cellular, organ, organ system, organism, society, and ecosystem levels. To me, this is a fascinating topic and I hope others find it as engaging as I do. ---------------------- For the purposes of discussion, here, what do we consider life?  Are self-replicating molecular species alive?  Is a cell wall required?  Can any series of reactions be considered living if they are not enclosed in a cell wall but still result in the production of a specific molecule?  Are we looking for literal inheritability in that a "parent" creates a duplicate "daughter" genetic molecule and passes it to its progeny?  Is a microsphere alive if it reproduces simply by swelling and breaking in half? Which comes first metabolism or inheritability?  Can they be the same thing? Thanks, MichiganRuss

Russell Posts: 1082 Joined: April 2005 (Permalink) Posted: Jan. 10 2007,21:41    The Kauffman book, "Investigations", is, indeed, all about abstractions, not the specifics of any chemical hypothesis. (I'm still reading, though. Not ready for a full report). A lot is made, especially by creationists, of how well the Miller-Urey experiment does or does not represent anything like Earth's atmosphere 4 bya. But there's not much point in trying to get "more realistic" conditions, since the Earth's surface is not and never was homogeneous. Did life first emerge near an undersea volcanic vent? The surface of a pond? What temperature? No way to know. It may have had its start in a very atypical environment. It's in the nature of life to break out of micro-environments and expand into - I like this term of Kauffman's - "the adjacent possible". That makes me think that, however much fun it is to entertain various chemical hypotheses, no consensus is likely to emerge in the foreseeable future. Maybe, on the other hand, we can intelligently assess more abstract treatments of the subject. Like, are there any compelling reasons to suppose a nucleic-acid first scenario? Or how could a "metabolism-only" scenario have the necessary self-replicating mechanisms to qualify as "life"? (For the purposes of this discussion, I guess the definition of "life" in my mind is something like a self-replicating entity that is genetically related to me, my cat, pond scum, E. coli...) Anyway, whatever the actual sequence of events (replicating, "naked" nucleic acids subsequently, somehow, acquiring cells; cells somehow replicating before acquiring nucleic acids?) DNA had to have its own origin somewhere, somewhen, somehow - likely as a modified RNA. And RNA had to have its origin. The genetic code had to have its origin... Any one of these origins would probably merit a more substantial discussion than The Big One, the ultimate origin of Life Itself. Unfortunately, even there I predict there's not going to be much of a consensus in my lifetime. -------------- Must... not... scratch... mosquito bite.

skeptic Posts: 1163 Joined: May 2006 (Permalink) Posted: Jan. 10 2007,22:06    With all my reading in the past couple weeks I've been kicking around an idea and since MichiganRuss has posed the question I'll let it rip.  Just to caution it is fairly radical.  What if life is DNA, RNA and proteins? I don't mean composed of but actually that is the only configuration that is life.  We're looking at scenarios of a primitive self-replicating molecule but we have no evidence that such a molecule can exist or ever has.  Just to be clear I'm not talking about crystals or polymers but a molecule that truely facilitates its own replication.  In fact, every form of life on the planet meets this criteria and we even have cases that partially meet this criteria and we do not consider them "alive" (viruses and prions).  This could be proof of common descent or just more simply that all life requires this configuration to be alive.  Even in our search beyond the planet we're looking for life similar to what we have here.  Would we even recognize life that wasn't compsed of DNA, RNA and proteins? Just a thought and certainly not a popular one but what really got it going for me is the fact that there are no other forms (or never have been as far as we know) of life on the planet.  Wouldn't it be reasonable to assume that in the past 3-4 billion years something new would have developed from the DNA, RNA, protein framework and we'd see a branch that was similar but different.  Wouldn't evolution and selection nearly guarantee this outcome unless such a configuration just flat out didn't function? Anyway, thought I'd show you guys what this background reading had done to my already crazy brain.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 11 2007,03:40    All, I'm collecting references for Big Post, please bear with me during this busy time! Skeptic, There are examples of self replicating non nucleotide, non protein chemical systems and molecules. Check out those Rebek refs I provided right at the start. Also, don't get as hung up on the semantics of "alive" or "life" like you're appearing to. The semantics aren't what's important. Quote Just a thought and certainly not a popular one but what really got it going for me is the fact that there are no other forms (or never have been as far as we know) of life on the planet.  Wouldn't it be reasonable to assume that in the past 3-4 billion years something new would have developed from the DNA, RNA, protein framework and we'd see a branch that was similar but different.  Wouldn't evolution and selection nearly guarantee this outcome unless such a configuration just flat out didn't function? Not necessarily no. First and foremost the reason abiogenesis is tough to find certain types of "fossil" evidence for, and one reason a plurality of different replicating systems don't exist in other organisms is this: we living organisms have a word for things like that: food. Second you have it bass ackwards. the nucleotide/protein/carbohydrate (everyone forgets the glycome for some reason. Very silly) system we have now is the most successful one that DID evolve, not the only possible one that could have evolved. One of the things we are trying to find out is what other systems could have developed, mainly because they could give us clues to the precise pathways taken to the current point. Never forget Mother Nature, whilst coy and cunning, is also cheap. If it ain't broke there's no need to fix it. At some point there was a replicating system that worked well, perhaps it was in isolation, perhaps it was first amongst equals, perhaps it was an out an out winner, perhaps it was a lucky underdog, this much we don't know. What we DO know is that it occured way in the past (i.e. it was an early event, possibly one prior to the evolution of more complex organisms), we know this because from the bottom of the ocean to the top of the highest mountain every organism encountered uses the same system of transferring inheritable information to the next generation. There are variations, but the underlying "basic" chemistry is the same. (Obviously this is the shorthand, potted version) We know that the most parsimonious explanation for this is common descent, i.e. that modern organisms have evolved from this Ur-replicator, or various Ur-replicators relatively closely aligned. The problem we have (as has been stated many times on this thread) is that we don;t know what specific path was taken nor which "hurdles" were passed in what order. What we DO know is what the likely hurdles are/were, what some mechanisms and paths that could have been taken are, and roughly what is needed to make those paths. To use a magic analogy it's like the guess the card trick done badly. We know that a card is involved (woohoo!, we even have some idea of whether it's a black card or red card. We're not sure of the suit, but interestingly we know that it's a picture card. See what I mean? Louis Louis -------------- Bye.

Ichthyic Posts: 3325 Joined: May 2006 (Permalink) Posted: Jan. 11 2007,15:33    Uh, Loius, Since Sal constantly conflates abiogenisis and the ToE, I invited him to participate in your thread. *ducks behind bar* ...but it's really unlikely he'll bother; he hates this place as he always gets shredded and has to go into retreat to put his mental blocks back in place. Just thought I'd give you a head's up, and apologize ahead of time for any collateral damage that might occur should he actually decide to spend time here. -------------- "And the sea will grant each man new hope..." -CC

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 11 2007,16:04    Icthyic, Oh now that's just mean. Are you not satisfied with the tards we already have? When I was an undergrad a friend of mine and I instigated the "Mormon Wars". We'd go to the high street bright and early on a Saturday afternoon, and sign ourselves up for visits by mormons and JWs using the other guy's identity and address. We'd specify an early visit. It got slightly out of hand. You have instigated their 21st century equivalent: "Tard Wars". You do realise that I am now going to have to go undercover and get Duane Gish to come to your house or arrange for you to be an authorised visitor for Hovind don't you? As if I'm not busy enough already. Louis -------------- Bye.

Ichthyic Posts: 3325 Joined: May 2006 (Permalink) Posted: Jan. 11 2007,16:20    I see I shouldn't have said anything. curse my honesty! oh well, at least it will make life interesting. I still think Sal won't bother, but if he does, you're welcome to take your best shot. -------------- "And the sea will grant each man new hope..." -CC

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 11 2007,17:12    {bring bring, bring bring} "Hello is that Duane? Hi it's your devoted disciple here.I don't suppose you could do me a favour could you....." "....You could? Oh that's super! Naked you say? Even better. The address you need is......" "Yup 5 am Saturday morning will be fine." Mwah ha haaa. {twirls moustache} Louis -------------- Bye.

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 11 2007,17:21    I put this together almost 2 years ago, and it need to be updated.  But, I think that you can still get a quick start on the relevant literature in primary journals. Darwin's first edition of The Origin of Species made no particular mention of the origin of life. He does make some general observations in the conclusion of the sixth edition published in 1872. He writes,   Quote "I believe that animals are descended from at most only four or five progenitors, and plants from an equal or lesser number. Analogy would lead me one step further, namely, to the belief that all animals and plants are descended from some one prototype. But analogy may be a deceitful guide.  Nevertheless all living things have much in common, in their chemical composition, their cellular structure, their laws of growth, and their liability to injurious influences." And,   Quote "No doubt it is possible, as Mr. G.H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants." And a bit later, "Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual. When I view all beings not as special creations, but as the lineal descendants of some few beings which lived long before the first bed of the Cambrian system was deposited, they seem to me to become ennobled." The final sentence in the first edition, "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." was slightly modified in the Sixth to clearly indicate that the "Creator" was responsible for the origin of life. Some scholarly studies claim that Darwin regretted making this concession to his publishers. The general interest books on the origin of life (OOL) typically start with a lengthy discussion of the historical theories of life. Beginning with the Greeks and working our way toward the present, there are three most significant events: the invention of the microscope, the synthesis of urea, and the experiment by Pasteur in 1862. All the early thought on the origin of life can be reduced to a theory of spontaneous generation of life, or the creation of life by supernatural external agency. The invention, and improvements to the microscope between 1590 and 1674 CE profoundly changed mankind's conception of life and its complexity. This seemed to many as support for the spontaneous generation of life notion, as these microscopic life forms were thought as the simple "seed" for latter complex life. Anton van Leeuwenhoek's discovery of sperm also added to this "support" for the spontaneous generation theory. There was also the thought that the organic "stuff" of life was completely different from "inorganic" or mineral matter. Known as "vitalism," this concept was shown to be false by Wühler in 1832 when he made urea, a "live" compound, from inorganic stock chemicals. The most popular argument that creationists like to cite against results from modern origin of life research is that Pasteur demonstrated that the "spontaneous generation" theory was invalid. However, we should be quite clear that the Pasteur experiments showed that complex life forms do not form spontaneously. They did not address the origin of life as we currently understand the concept. The growing interest in the search for extra-terrestrial life as fueled more productive research on OOL in the last 15 years than has ever been done in history. The Emergence of Life on Earth: A Historical and Scientific Overview by Iris Fry, (2000 Rutgers University Press), is the best general reader book available on the topic. Even though it is only 5 years old, a second edition is warrented to bring her presentation up to date. There are quite a list of specifics that go into origin of life research, and very few research groups go far with more than a few. Just to list the key areas as I see them: 1) Composition of the Hadean/early Archean atmosphere. The key reference(s) here is: Genda, Hidenori & Abe, Yutaka 2003 “Survival of a proto-atmosphere through the stage of giant impacts: the mechanical aspects" Icarus 164, 149-162 (2003). Holland, Heinrich D. 1984 The Chemical Evolution of the Atmoshphere and Oceans, Princeton Series in Geochemistry Princeton University Press Holland, Heinrich D. 1999 “When did the Earth’s atmosphere become oxic? A Reply." The Geochemical News #100: 20-22 (see Ohmoto 1997 ) Kasting, J. F., J. L. Siefert, 2002 “Life and the Evolution of Earth's Atmosphere" Science 296:1066 Pepin, R. O. 1997 Evolution of Earth's Noble Gases: Consequences of Assuming Hydrodynamic Loss Driven by Giant Impact Icarus 126, 148-156 (1997). There are a few others, but anyone reading those above will get the basics. The result is that there was a reducing atmosphere, and ocean system with highly reducing oases. A recent paper Rosing, Minik T. and Robert Frei 2003 U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis" Earth and Planetary Science Letters, online 6 December 03 presents data that suggest there were very early oxygenic life forms in marine basins that most likely (to me anyway) were wiped out. So, with a reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun, we can ask the next question which is, 2) What was the source for "organic" molecules? The classic paper was of course Stanley Miller's 1953 paper Miller, Stanley L., 1953 “A Production of Amino Acids Under Possible Primitive Earth Conditions�? Science vol. 117:528-529 With a bit more information included in: Miller, Stanley, Harold C. Urey 1959 “Organic Compound Synthesis on the Primitive Earth�? Science vol 139 Num 3370: 254-251 Miller showed that a very simple set up that mimicked some key asspects of the early Earth could rapidly produce amino acids, among other things. This result has been one of the most often repeated (and confirmed) experiments I have ever encountered. In spite of this, creationists regularly claim that it is invalid. Jonathan Wells, a fellow of the creationist "Discovery Institute" claims to have refuted the Miller/Urey experiment (and all of what he called Darwinist "icons." But, the atmosphere is not the only synthesis location. For example Amend, J. P. , E. L. Shock 1998 “Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems�? Science Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662. Blank, J.G. Gregory H. Miller, Michael J. Ahrens, Randall E. Winans 2001 “Experimental shock chemistry of aqueous amino acid solutions and the cometary delivery of prebiotic compounds�? Origins of Life and Evolution of the Biosphere 31(1-2):15-51, Feb-Apr Chyba, Christopher F., Paul J. Thomas, Leigh Brookshaw, Carl Sagan 1990 "Cometary Delivery of Organic Molecules to the Early Earth" Science Vol. 249:366-373 Engel, Michael H., Bartholomew Nagy, 1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838. Matthews CN. 1992 Hydrogen cyanide polymerization: a preferred cosmochemical pathway. J. Br. Interplanet Soc. 45(1):43-8 Schoonen, Martin A. A., Yong Xu 2001 “Nitrogen Reduction Under Hydrothrmal Vent Conditions: Implications for the Prebiotic Synthesis of C-H-O-N Compounds�? Astrobiology 1:133-142 So amino acids are easy and plentiful on a pre-life (abiotic) Earth. But, we need more than just amino acids- sugars, nucleic acids, and lipids are also needed. I'll take those next. Let's see.. I guess this is 2a) amino acids 2.b) sugars Why do we need sugars? Well, the biggest reason is that without five carbon sugar our building life form can't make a "memory" like RNA or DNA. I'll get to the details later. First, where are the sugars? Weber AL. 1997 Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia. Origins of Life and Evolution of the Biosphere 28: 259-270. {I know the title says "amino acid" but sugar is in there. Hint: formose is a kind of sugar. } Cooper, George, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel 2001 Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth Nature 414, 879 - 883 (20 Dec 2001) Letters to Nature Cody, George D., Nabil Z. Boctor, Timothy R. Filley, Robert M. Hazen, James H. Scott, Anurag Sharma, Hatten S. Yoder Jr. 2000 “Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate"  Science v.289 : 1337-1340 Sephton, Mark A. 2001 Meteoritics: Life's sweet beginnings? Nature 414, 857 - 858 (20 Dec ) News and Views Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A. 2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia) Stanley Miller, and collegues suggested an earlier substitute for sugar in : Lazcano, Antonio, Stanley L. Miller 1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time�? Cell vol 85:793-798 Nelson, K. E., M. Levy, S. L. Miller 2000 “Peptide nucleic acids rather than RNA may have been the first genetic molecule" PNAS-USA v.97, 3868-3871 There are many more articles, but the bottom line reads "We got sugar." OK, I'll do nucleic acid bases next. There aren't many that are used on Earth, just five. There are a large number of creationist's books and web sites that claim there is some huge stability problem with nucleic acid base synthesis. This is a nice demonstration of how creationists copy eachother, since there are only a handfull of creationists with the education to even understand what this means. None that I know of have actually done research in the directly relevant area. Their claims generally can be traced back to a legit scientist, Robert Shapiro. Two of his representitive publications are: Shapiro, Robert 1986 "Origins: A Skeptics Guide to the Creation of Life on Earth" New York: Summit Books Shapiro, Robert 1999 Prebiotic Cytosine Synthesis: A Critical Analysis and Implications for the Origin of Life. Proceedings of the National Academy of Science 96 (8): 4396 *Side reactions make cytosine synthesis unlikely, but see Nelson et al (2001) The 1986 book is very out of date, and very popular with creationists. The 1999 Shapiro paper has also been answered. Levy and Miller raise a question of their own in: Levy, M and Miller, S.L., 1998 The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38, But, like superior scientists, they answer the questions they raise. The following are a selections of research articles that address the pre-biotic origin of nucleic acid bases: Fuller, W. D., Sanchez, R. A. & Orgel, L. E. Studies in prebiotic synthesis. VI. Synthesis of purine nucleosides. J. Mol. Biol. 67, 25-33 (1972). Robertson, MP, Miller SL. 1995 An efficient prebiotic synthesis of cytosine and uracil. Nature 375, 772 - 774 () Nelson K.E., Robertson M.P., Levy M, Miller S.L. 2001 Concentration by evaporation and the prebiotic synthesis of cytosine. Orig Life Evol Biosph Jun;31(3):221-229 For our fans following along at home, there are aspects of nucleoside synthesis in the earlier referenced papers as well. So, we got plenty of nucleic acid bases. 2c) lipids. Lipids are the stuff of membranes, they are what keeps inside in, and outside out.  Today they are made by simple cells and moved up the food chain. So where did they come from 3.7 billion years (or so) ago? One major source seems to be from meteors. Deamer, D. W. 1985. Boundary structures are formed by organic components of the Murchison carbonaceous chondrite. Nature 317:792-794. Deamer, D. W., and Pashley, R. M. 1989. Amphiphilic components of carbonaceous meteorites. Orig. Life Evol. Biosphere 19:21-33. Krishnamurthy, R., Pitsch, S. & Arrhenius, G. 1999 Mineral induced formation of pentose-2,4-bisphosphates. Origins Life Evol. Biosph. 29, 139-152 (). Dworkin, Jason P., David W. Deamer, Scott A. Sandford, and Louis J. Allamandola 2001 “Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices�? PNAS 98: 815-819 Pizzarello, Sandra, Yongsong Huang, Luann Becker, Robert J. Poreda, Ronald A. Nieman, George Cooper, Michael Williams 2001 “The Organic Content of the Tagish Lake Meteorite�? Science, Vol. 293, Issue 5538, 2236-2239, September 21, 2001 Segre' D., Ben-Eli D. Deamer D. and Lancet D. 2001 “The Lipid World�? Origins Life Evol. Biosphere 31, 119-145. So now that we got 'em, what do they do once they are on Earth? They make things. Martin M. Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak 2003 Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division Science October 24; 302: 618-622. (in Reports) D.W. Deamer 1997 "The First Living Systems - A Bioenergetic Perspective", ; Microbiology and Molecular Biology Reviews, 61(2): 239; June Chakrabarti, A.C., R.R. Breaker, G.F. Joyce, & D.W. Deamer 1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 ( December) Khvorova A, Kwak YG, Tamkun M, Majerfeld I, Yarus M. 1999. RNAs that bind and change the permeability of phospholipid membranes. Proceedings of the National Academy of the Sciences USA 96:10649-10654. Yarus M. 1999. Boundaries for an RNA world. Current Opinion in Chemical Biology 3:260-267. Walter P, Keenan R, Scmitz U. 2000. SRP-Where the RNA and membrane worlds meet. Science 287:1212-1213. So far, we have amino acids, riobose and/or other 5 carbon sugar substitutes (pentoses), we have lipid membranes which encapsulate mineral particles and "organic" molecules.  This is without any needed "interventions" and is purely the result of ordinary chemistry. But, there are more things that need to happen before there is life on Earth. Point 3) formation of complex systems 3a) Chirility Pastuer discovered that most amino acids came in two forms which can be identified by how they refract light. We label theses L- (for levo or left) adn D- (for dextro, or right). The interesting thing is that life on Earth uses the L form of amino acids, and hardly ever uses the D- form. A solution of just one form is called "chiral" and a mix of forms about 50/50 is called racimic. The kinds (L or D) are called enantomers. The nucleic acid bases I mentioned earlier are also found in L- and D- forms, only in this case life on Earth only uses the D- form. Creationists like to present this as a profound mystery that is supposed to "prove" that they are correct. I want to mention a neat instance where both left and right amino acids are used in a living thing. It is very rare, but it does happen. Next time a creationist claims to be an "expert" and that amino acid chirility "proves" something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclucive L- amino acids. Before we go forward another couple of basic chemical facts need to be added to the discussion. First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racimization" becuse eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attatched to one another, or better yet, if they are also attatched to a mineral or metal atom, racimization can be very slow. Very, very slow. This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form. The advantage comes from a surprising direction: outer space. Cronin, J. R. & Pizzarello, S., 1999. Amino acid enantomer excesses in meteorites: Origin and significance. Advances in Space Research 23(2): 293-299. Service, RF,   1999. Does life's handedness come from within? Science 286: 1282-1283. Antonio Chrysostomou, T. M. Gledhill,1 François Ménard, J. H. Hough, Motohide Tamura and Jeremy Bailey 2000 "Polarimetry of young stellar objects -III. Circular polarimetry of OMC-1" Monthly Notices of the Royal Astronomical Society Volume 312 Issue 1 Page 103 - February Michael H. Engel and Bartholomew Nagy, 1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838. Jeremy Bailey, Antonio Chrysostomou, J. H. Hough, T. M. Gledhill, Alan McCall, Stuart Clark, François Ménard, and Motohide Tamura 1998 Circular Polarization in Star- Formation Regions: Implications for Biomolecular Homochirality Science 1998 July 31; 281: 672-674. (in Reports) Chyba, Christopher F. 1997 Origins of life: A left-handed Solar System? Nature 389, 234- 235 (18 Sep 1997) Engel, M. H., S. A. Macko 1997 Isotopic evidence for extraterrestrial non- racemic amino acids in the Murchison meteorite. Nature 389, 265 - 268 (18 Sep) Letters to Nature That should do for that. The next question is can the advantage of L- amino acids be conserved in the formation of more complex molecules called "peptides?" Yep. Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 Enantiomeric cross-inhibition in the synthesis of oligonucleotides on a nonchiral template. J. Am. Chem. Soc. 119, 1494-1495 Saghatelion A, Yokobayashi Y, Soltani K, Ghadiri MR, 2001"A chiroselective peptide replicator", Nature 409: 797-51, Feb Singleton, D A,& Vo, L K, 2002 “Enantioselective Synthsis without Discrete Optically Active Additives�? J. Am. Chem. Soc. 124, 10010-10011 Yao Shao, Ghosh I, Zutshi R, Chmielewski J. 1998 Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature. Dec 3;396(6710):447-50. And there seems to be other L- selction advantages as well. For example: Hazen, R.M., T.R. Filley, and G.A. Goodfriend. 2001. Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality. Proceedings of the National Academy of Sciences 98 (May 8):5487. So chirility doesn't seem to be a big problem. This is far different from the way creationists present this. They cite a few out of date reports and then falsely claim that chiral life is impossible by natural means. But what about the nucleic acid bases? A new paper has just laid out the next step: Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A. 2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia) Pizzarello, Sandra, Arthur L. Weber 2004 Prebiotic Amino Acids as Asymmetric Catalysts Science Vol 303, Issue 5661: 1151, 20 February 2004 It turns out that the selective advatage of L- amino acids will force the selection of D- nucleic acids, and the whole reaction can proceed under common, natural conditions. Well, we have all the pieces. Our planet was formed from massive collisions of planetoids that had undergone independent evolution and weathering which retained much of their atmospheres to add to the growing planet Earth. We have amino acids, sugars, nucleic acid bases, lipids and minerals under an anoxic to reducing atmosphere and ocean with a thin hot crust and a UV rich cold Sun. Plus, remember that the Moon is closer and orbiting faster producing massive tidal flows compared to modern times. Will these combine to make any thing? Yep, they sure will: Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2). Synthesis of long prebiotic oligomers on mineral surfaces [see comments] Nature, 381, 59-61. Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR. 1996 “A self-replicating peptide." Nature Aug 8;382(6591):525-8 A.C. Chakrabarti, R.R. Breaker, G.F. Joyce, & D.W. Deamer 1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 (1994 December) Smith, J.V. Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars Proceedings of the National Academy of Sciences of the United States of America 95(7): 3370-3375; March 31, 1998 Smith, J.V., Arnold, F.P., Parsons, I., Lee, M.R. Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal-hemical modeling, formation of first cells, and geological clues Proceedings of the National Academy of Sciences of the United States of America 96(7): 3479-3485; March 30, 1999 Blochl, Elisabeth, Martin Keller, Gunter Wächtershäuser , Karl Otto Stetter 1992 “Reactions depending on iron sulfide and linking geochemistry with biochemistry" PNAS-USA v.89: 8117-8120 Dyall, Sabrina D., Patricia J. Johnson 2000 “Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis." Current Opinion in Microbiology 3:404-411 Huber, Claudia, Gunter Wächtershäuser 1998 “Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life�? Science v.281: 670-672 Imai, E., Honda, H., Hatori, K., Brack, A. and Matsuno, K. 1999 “Elongation of oligopeptides in a simulated submarine hydrothermal system“ Science 283(5403):831–833. Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR, 1997 Emergence of symbiosis in peptide self- replication through a hypercyclic network. Nature, 390: 591-4 Someone asked why I posted so many references. There are several reasons. First, that is how science is done, we build on the work of others. Second, when we use referenced data to make a point clear we state the source of our information up front. Anyone can read these papers. If they want, they can argue that I have misread the article, or that the article itself has been refuted by more up-to-date information. Third, a common creationist claim is that there is no valid research on the origin of life, or that the research done is inconclucive. The references I have cited are evidence that these claims are false. Fourth, except for some historical references, my sources are mostly less than 10 years old. This is in direct contrast to the selective use by creationist writers such as Jon Sarfati, or Jon Wells, who use a few out of date and refuted articles to puff up their nonsense. So, there you have it. -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

qetzal Posts: 311 Joined: Feb. 2006 (Permalink) Posted: Jan. 11 2007,22:42    Great post, Dr. Hurd! One minor quibble, which I only point out so you can correct when you do an update. The section on chirality mentions nucleic acid bases in several places. The bases themselves are not chiral, of course. It's the attached sugars that are chiral. (The term for a base plus a sugar is a nucleoside. If a phosphate is also attached, it's a nucleotide.)

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 12 2007,01:18    Quote (qetzal @ Jan. 11 2007,22:42) Great post, Dr. Hurd! One minor quibble, which I only point out so you can correct when you do an update. The section on chirality mentions nucleic acid bases in several places. The bases themselves are not chiral, of course. It's the attached sugars that are chiral. (The term for a base plus a sugar is a nucleoside. If a phosphate is also attached, it's a nucleotide.) D'oh (or however Homer Simpson's standard line is written) You are correct- my bad. -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 12 2007,03:19    Dr GH, Thanks very much indeed for that excellent series of references and explanations. Great contribution. Louis P.S. I've just taken out a personal subscription to "Origin of Life and the Evolution of Biospheres", a really excellent Springer Journal. So expect my next set of refs to be "midly" biased! -------------- Bye.

MichiganRuss Posts: 2 Joined: Jan. 2007 (Permalink) Posted: Jan. 13 2007,23:12    Dr. GH, great post, lots of great stuff. <blockquote> The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclucive L- amino acids. </blockquote> What cried out to me for comment was the mixed L and D enantiomers in the Gramicidin A structure. The Gramicidin structure with chirality is shown at http://en.wikipedia.org/wiki/Gramicidin Does anybody here know much about Gramicidin A synthesis?  Is the synthesis done from actual L and D amino acids or does the pathway synthesize the resultant mixed L and D structure from non-amino acid pre-cursors?  Is much known about the genetics of the pathway?  Clearly, I've got some digging to do! ------------------------- One conception of the origin of life that truly fascinates me is the idea of self-replicating microspheres.  I guess we could envision a  microscopic bubble which forms automatically through simple mechanical actions like waves coming ashore or bubbles created in an underwater hot vent.  From several sources I've read pieces discussing the self-replicating nature of the spheres being due to the specific structure of the enclosing membrane.  I've often wondered if the structure of the membrane could be a means of heritability.  If the process of reproduction of the spheres was simply absorbing materials from the environment until the mechanical strain on the membrane was such that it split, then the initial structure of the mechanically formed sphere could determine rate of absorption and so, rate of reproduction. Membranes vary greatly as to the nature of their permeability, that is, what may pass through the membrane - size of species permitted through, chemical nature of species passed, orientation of the passed species, shape of passed molecules, flexibility, hydrogen bonding characteristics, among others.  The specific structure of the membrane, effects the contents of the sphere, rates of absorption, etc and thus the rate at which the volume of the contents surpass the divide threshhold.  I'm curious about the membrane itself, with its selecting capabilities, being the "genetic code" for the sphere. If the membrane could selectively take up ambient materials to perform a reproductive cycle with reasonable fidelity, would the flaws in the membrane constitute a form of variability on which natural selection could get a foothold? Its appeal to me is its simplicity: a crude bubble taking as long to reproduce as its environment and its membrane characteristics necessitate - months or years or even decades are conceivable; simple energy system - using chemical gradients to power the reproduction process; inherent variability in the reproduction process provides for built-in trial and error species testing; the environment alone being the natural selector - no predators, per se;  an environment which was a natural source of variability in membrane structure since new chemical species were constantly being introduced through terrestrial processes as well as through comet, asteroid and meteorite impacts. One aspect if this idea that keeps my interest is that in the presence of the correct chemical species - maybe some form of surfactant - all that would be necessary for the conditions to be favorable for the process to begin would be for the temperature to be low enough for the membranes to be stable in aqueous solution.  This idea correlates well with the observed age of the earliest cellular life on this planet - about 3.8 billion years ago.  Using an age of the earth of 4.5 billion years, this would have allowed a few hundred million years of surface cooling before the microsphere evolution began, then a few hundred million more years before anything evolved to be tough enough to survive in fossil form long enough for us to observe it. Another intriguing side of this is that if the microsphere evolution could take place, it would provide a safe haven for an environmentally isolated series of reactions to give rise to a more advanced form of physiology, perhaps even still using the membrane as the means of inheritance. I want to find out what you are thinking about this and about your favorite OOL ideas.  It might be fun to take one idea - this one or some other - and knock it around a while.  We could look at the membrane mechanics, the chemical specifics, molecules of heritability, physics, emergence, metabolism, physiology, kinetics, whatever perspective we want to follow.  Just a thought, but one that could be interesting. MichiganRuss

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 14 2007,01:13    I am nearly done writing up a lit review I plan to use as a gradstudent proposal at Scripps.  Miller and Orgel are still there, and there is even something that could interest Bada.  That would be a committee.  Failing that, I'll see if I can interest Deamer. Scripps is only an hours drive from my home, so that would be much better practically speaking.  At 56 YoA, I will not be dashing off to live in student housing.  Staying in the UC system might help me avoid some of the noxious BS of grad work as that is where I did my anthropology PhD.  I want to avoid the graduate teaching requirement for example.  I taught in universites and colleges of about 25 years.  I would like to skip the language exam, BTDT.  I believe that there is still a publication alternative to a dissertation which would save time.  When I earned my degree in 1976 I was able to get out in 7 quarters.  Saves money and saves time. If nothing else, I'll have a nice article with some apparently over looked biochem.  Most all the chemistry I have done has been using instrumental neutron activation analysis to study archaeological "stuff," clay, and pigments, the odd leaf or rock.  Well, lots of rocks.  But it was nearly 30 years since I seriously thought about organic or biochem. I had a lot of relearning. Gramicidin was my "jumping off point" 3 years ago as well.  My basic hypothesis is that the OOL was racemic, and that chirality was a later development.  After just more than a years work on this proposal, I have finally decided to stop worrying (I could be wasting my time) and just send the #### thing off.  I have run it past two colleagues who are better chemists than I am, so I have some assurance that I have not merely lost my mind.  (Other than the question of whether it is entirely sane to return to school when I am quite happy semiretired). I wish that we had the equivalent of the "prepublication" websites that the physicists use to such good effect.  I am really looking forward to feedback, and yes, I would like to establish priority. Edited by Dr.GH on Jan. 14 2007,01:16 -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 14 2007,02:09    Quote I guess we could envision a  microscopic bubble which forms automatically through simple mechanical actions like waves coming ashore or bubbles created in an underwater hot vent.  From several sources I've read pieces discussing the self-replicating nature of the spheres being due to the specific structure of the enclosing membrane. Think of waves crashing up aginst rocky coast.  Trillions of bubbles every few seconds.  With higher tides on a fairly fast cycle, you generate astronomical numbers of "trials" every day.  Every high tide leaves billions of trillions of oily bubbles exposed on the shore to dry out and also be soaked in UV light.  The products are recovered for further reactions on the next tide.   I have never been impressed with the so-called "cosmic upper bound"  What is the number Dembski likes to spout?  10^150?? This is supposed to represent the number of states that universe could possibly have given the number of particles in the universe and their possible states.  Piffle, piffle.  Lets say 10^15 bubbles per kilometer of shoreline (very modest), recycled/repeated 10^4 times every day for maybe 50 million years. The notion of how long is a shoreline is difficult, but let's pull a number out of the air; 10^6 kilometers (very modest).  We are well on the way without adding rivers, waterfalls, storms, wind caps, oceanic waves, under water thermal vents, geysers etc...  I think that every single bubble is a "trial."  Now repeat for a hundred billion galaxies with a hundred billion stars, for say ten billion years, just to bring us up to bat, and we have nearly 50/50 odds.  (unless it is very late at night and I can't add).  I doubt that every star has planets of that every planet could support life.  There are also good reasons we need to wait until there are metal rich star systems.  So even shedding a few orders of magnitude here and there, the odds are far from grim and we can top Borel's number of 10^50 cited by Dembski. Earlier I was asked if I were a pessimist about abiogenesis, and obviously I am not.  I am doubtful that we will be able to demonstrate that a "particular" pathway to life was inevitable, unique in the universe, or the particular one followed here on earth.  I know it happened, we are here aren't we? Edited by Dr.GH on Jan. 14 2007,02:19 -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Ichthyic Posts: 3325 Joined: May 2006 (Permalink) Posted: Jan. 15 2007,17:31    Quote I would like to skip the language exam, BTDT.   no worries; they made that optional a long time back - at least as far back as '88 in the UC system, as that's when i started and was told that right off.  They might ask for something else instead, though I doubt it. -------------- "And the sea will grant each man new hope..." -CC

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 15 2007,19:41    It has been a long long time.  I am trying to convince myself that it is a dumb idea. -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Ichthyic Posts: 3325 Joined: May 2006 (Permalink) Posted: Jan. 15 2007,20:55    *redface* I'm 42 and have been considering going back into a lab as well.  Not the first time. It's simply GOTTA be easier the second time around, right? right? *sigh* I do wonder if my memory would serve me well enough to pass an orals exam the second time around. are you sure you don't want to just go for a post-doc somewhere?  that might be a lot easier; talk to the guys at Scripps and see if there is room in somebody's lab, then go after some funding.  If anything looks positive, you might have an easier time going that route. BTW, that would effectively bypass all the irritating crap and get you focused strictly on the research.  the downside being that support is far more dependent on your own abilities. -------------- "And the sea will grant each man new hope..." -CC

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 16 2007,01:43    I'm changing jobs at the moment too. I'm very seriously considering bunking out of the pharmaceutical industry (great pay, get treated like a human being, research is directly vital* but occasionally dull) permanently and doing a postdoc with a view to permanent academic research (terrible pay, get treated like shit, research is occasionally directly vital, but very frequently exciting). Dr GH and Icthyic, if you guys do go back you have my eternal admiration and my support. Research is hard. Perhaps that's  why the IDCists don't do any. Louis *By "directly vital" I'll give you an example of what I mean. I've been working at late stage drug development in the pharma industry for the last 2 years. The company I'm working for has an anti-HIV drug in the final stages of filing. One of the projects I was briefly working on (so little credit to me, big credit to those guys working on it for ages) was this HIV drug. Our mandate: make the bulk synthetic route to this drug so cheap, so environmentally friendly, so efficient, that we can give it away for free to the third world. No one who isn't a synthetic chemist will realise just how tough that is, but everyone should realise just how directly vital such a piece of research could be. If it works millions of lives will be saved. That's one reason I love working in the pharma industry, despite all its many flaws, you know that what you are doing should have a real net positive effect on humans or animals. -------------- Bye.

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 16 2007,08:28    Louis, that is a great pep talk.  Wesley's wide ranging career is also inspiring.  The post-doc idea is good, the proposal then is either funded, or I get to go fishing.   I only had one friend with 2 PhDs.  His first was in math and he said he needed the second in ICS to "remove the stain" of the first. -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 16 2007,09:01    Dr GH, Erm I wasn't aware it WAS a pep talk, but YMMV! Either that or there's some sarcasm going on. Although since I'm so knackered today you could whack me around the head with a sarcastic clue by four and I'd still not get it, I'm probably hallucinating. (Writing a review on organocatalysis, up late dealing with stuff, mind is in meltdown) 2 PhDs would be a brilliant achievement though. Postdoccing would be easier in some senses. At least most academics think you border on being a human as a postdoc. But then as a PhD less is expected of you in terms of responsibility etc. The fishing element looks good. "Which agency funds this postdoc? NIH? NAS?" "Nah YTI" "YTI?" "Yellowfin Tuna Incorporated!" Louis -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: Jan. 22 2007,08:43    Dr GH, Any news on funding sources? Louis -------------- Bye.

Dr.GH Posts: 2324 Joined: May 2002 (Permalink) Posted: Jan. 22 2007,13:18    Quote (Louis @ Jan. 22 2007,08:43) Dr GH, Any news on funding sources? Louis Check back in June. -------------- "Science is the horse that pulls the cart of philosophy." L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

Dizzy Posts: 3 Joined: Mar. 2006 (Permalink) Posted: Feb. 13 2007,09:39    I hope you'll pardon a reply and stupid questions from a definite non-scientist, but: Quote 1) A self replicating molecule or self replicating series of molecules or a series of interacting molecules that template the synthesis of other molecules. It seems to me that this is a basic requirement for us to term anything as "bio" (living or life-like) at all...is that right? In that case, I would venture to guess that this would have to occur first, *except* that: Quote 3) A series of effector molecules/physical scaffolding/chemoselective processes which allow for a relatively high level of "copying fidelity". I don't quite understand this requirement.  If there is zero "copying fidelity," how can we understand a set of molecules to be "self-replicating" in the first place?  By identifying this as a requirement, doesn't it logically follow that 1) cannot occur without this? I feel like I'm missing some important subtlety or detail here...wonder if you can help me out. Quote 2) Some form of cellular encapsulation, which at least must incoporate a semi permeable membrane or barrier. Daniel Dennett (not a scientist, I know, but certainly more well-read than I am) takes an interesting perspective on one aspect of life: the separation, or "dividing line" between the organism and its environment. One property of living organisms seems to be that they expend energy to keep everything "inside" them ordered, essentially fighting against the increasing entropy of its environment and the universe at large. For us, I guess the "line" would be our skin, or our epithelial layer, which (as I understand it) covers every part of our body that is exposed to the environment and literally acts as a wall, allowing us to expunge "disorder" (waste) while keeping out disorderly material from our environment. But it seems like the line isn't quite as clear for some organisms; I think ants are an interesting example.  If one of the requirements for calling something "living" is the ability to replicate on its own, then a single worker ant isn't technically "alive," is it?  I.e., only one member of the colony, the queen, is actually capable of producing offspring. If we look at the colony at large, though, it's the colony that replicates, right?  If the queen dies, another ant becomes the queen so that the colony can continue to replenish itself.  Therefore, it seems to me that the ant *colony* is in fact the "living" entity, while individual ants are "parts" necessary to make it work. If that's true, then the "dividing line" isn't quite so clear anymore...the organism doesn't "end" at the exoskeleton of each individual ant, but includes a good portion of the environment, as well - e.g., the chemical trails that direct each ant to its task. All of this is a long-winded way of saying that, if a similar situation can apply at a molecular level (not sure if it can), then 2) may well have developed after 1) and 3).  Again, not being a biologist or chemist, I have no idea if this is actually possible, but at least conceptually, I can imagine it.

Steviepinhead Posts: 532 Joined: Jan. 2006 (Permalink) Posted: Feb. 13 2007,19:26    At least some of what you're cogitating about above was also mulled by Dawkins in The Extended Phenotype, or at least so it seems to my increasingly dim memory.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: April 24 2007,10:56    Hi All, Since what I am really interested in at the moment is abiogenesis I thought I'd revive this thread and use it to dump some of my developing thoughts etc on. I recently took out a personal subscription to "Origins of Life and Evolution of Biospheres", the journal of ISSOL, which is interesting at least, even if it isn't one of the most impacting journals out there. I've also just bought a book by Pier Luigi Luisi and it contains lots of info I didn't know (on a first pass rapid read) and hits on lots of topics I haven't visited since undergrad days. So with a view to expanding on fledgling ideas I have about abiogenesis involving topics such as organocatalysis and natural products, I hope nobody minds if I indulge myself here a little and bounce some ideas off our other resident chemists and hopefully off of everyone else as well. Since I cannot envisage a way to do this without chemical structures and diagrams, I'll be drawing them up and adding the images to the posts so I'd appreciate someone with the requisite internets knowledge telling me how I can get these images (i.e. ones not on the net already) into my posts. Are there hosting sites etc? Are they free? Also, since I'm going to be indulging myself if there are ny questions that come up I'll happily try to answer them, although I can't promise to be quick about it all the time. Cheers Louis -------------- Bye.

Louis Posts: 6436 Joined: Jan. 2006 (Permalink) Posted: April 24 2007,11:05    Dizzy, Sorry for taking so lon to get back to you. Quote I don't quite understand this requirement.  If there is zero "copying fidelity," how can we understand a set of molecules to be "self-replicating" in the first place?  By identifying this as a requirement, doesn't it logically follow that 1) cannot occur without this? I feel like I'm missing some important subtlety or detail here...wonder if you can help me out. You're quite right about "zero copying fidelity", but I'm talking about higher degrees of fidelity that are not necessarily 100%. You made me think of an interesting point which is there should be a copying fidelity threshold below which self replication is pointless and drowned out by noise. I'm working on an idea (on my own time, so it's really poorly thought out atm) at the moment about the side products of a less than 100% copying fidelity self replicating system being a positive benefit (after all one of the generators of genetic diversity in evolution is less than 100% copying fidelity, the same could be true of simpler chemical systems). This all relates to an idea about natural products I have but is very much in the really tentative stages. Your second point hits on a very key topic: just what IS "life". I think defining "life" is like defining "species": bloody difficult. Perhaps I'll get to it down thread! Thanks for you comments and I reckon your ideas have a lot of merit, the order of these events is a tricky thing to decide. Louis -------------- Bye.

Alan Fox Posts: 1552 Joined: Aug. 2005 (Permalink) Posted: April 24 2007,11:41    I recently read Shapiro's "Planetary Dreams". He seems to be advocating more space exploration as a way of developing OOL research, and confirming or eliminating "panspermia" possibilities as per the Drake equation.