Chance and necessity do not explain the origin of life

Where and how did the complex genetic instruction set programmed into DNA come into existence? The genetic set may have arisen elsewhere and was transported to the Earth. If not, it arose on the Earth, and became the genetic code in a previous lifeless, physical—chemical world. Even if RNA or DNA were inserted into a lifeless world, they would not contain any genetic instructions unless each nucleotide selection in the sequence was programmed for function. Even then, a predetermined communication system would have had to be in place for any message to be understood at the destination. Transcription and translation would not necessarily have been needed in an RNA world. Ribozymes could have accomplished some of the simpler functions of current protein enzymes. Templating of single RNA strands followed by retemplating back to a sense strand could have occurred. But this process does not explain the derivation of “sense” in any strand. “Sense” means algorithmic function achieved through sequences of certain decision‐node switch‐settings. These particular primary structures determine secondary and tertiary structures. Each sequence determines minimum‐free‐energy folding propensities, binding site specificity, and function. Minimal metabolism would be needed for cells to be capable of growth and division. All known metabolism is cybernetic—that is, it is programmatically and algorithmically organized and controlled.

[1]  S. Mann,et al.  Ciba Foundation Symposium , 1997 .

[2]  Paul Schimmel,et al.  Mutational separation of two pathways for editing by a class I tRNA synthetase. , 2002, Molecular cell.

[3]  P. Schimmel,et al.  Formation of two classes of tRNA synthetases in relation to editing functions and genetic code. , 2001, Cold Spring Harbor symposia on quantitative biology.

[4]  P. Agris,et al.  Accurate Translation of the Genetic Code Depends on tRNA Modified Nucleosides* , 2002, The Journal of Biological Chemistry.

[5]  David C. Bradley The Genome Chose Its Alphabet With Care , 2002, Science.

[6]  Gerald F. Joyce,et al.  Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA , 1990, Nature.

[7]  Massimo Di Giulio On the origin of the genetic code. , 1992 .

[8]  M. Saraste,et al.  Evolution of energetic metabolism: the respiration-early hypothesis. , 1995, Trends in biochemical sciences.

[9]  H. Seligmann,et al.  Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code , 2002, Naturwissenschaften.

[10]  Guillaume Lecointre,et al.  Evolution of Amino Acid Metabolism Inferred through Cladistic Analysis* , 2003, Journal of Biological Chemistry.

[11]  M. Giulio The non-universality of the genetic code: the universal ancestor was a progenote. , 2001 .

[12]  Maciej Szymanski,et al.  Aminoacyl-tRNA synthetases database Y2K , 2000, Nucleic Acids Res..

[13]  Hubert P. Yockey,et al.  Origin of Life on Earth and Shannon's Theory of Communication , 2000, Comput. Chem..

[14]  S. Arrhenius Worlds in the Making , 1935, Nature.

[15]  M. Eigen Molecular self-organization and the early stages of evolution , 1971, Quarterly Reviews of Biophysics.

[16]  P. Schimmel,et al.  Oligonucleotide-directed peptide synthesis in a ribosome- and ribozyme-free system. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[17]  K. Dose,et al.  Hypotheses on the appearance of life on Earth (review). , 1986, Advances in space research : the official journal of the Committee on Space Research.

[18]  H. de Reuse,et al.  A noncognate aminoacyl-tRNA synthetase that may resolve a missing link in protein evolution , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[19]  P. Schimmel,et al.  Structure-specific tRNA Determinants for Editing a Mischarged Amino Acid* , 2003, Journal of Biological Chemistry.

[20]  M Di Giulio Genetic code origin and the strength of natural selection. , 2000, Journal of theoretical biology.

[21]  A. Banin,et al.  Soil and water and its relationship to the origin of life , 2005, Origins of life.

[22]  A. Cairns-smith,et al.  The origin of life and the nature of the primitive gene. , 1966, Journal of theoretical biology.

[23]  On the possible role of crystals in the origins of life , 1974, Journal of Molecular Evolution.

[24]  Hubert P. Yockey,et al.  Information theory, evolution and the origin of life , 2005, Inf. Sci..

[25]  M. Paecht-Horowitz,et al.  The polymerization of amino acid adenylates on sodium-montmorillonite with preadsorbed polypeptides , 2005, Origins of life and evolution of the biosphere.

[26]  Gerald F. Joyce,et al.  1 Prospects for Understanding the Origin of the RNA World , 1993 .

[27]  James R. Brown,et al.  Structure-Based Phylogeny of Class IIa tRNA Synthetases in Relation to an Unusual Biochemistry , 2001, Journal of Molecular Evolution.

[28]  P. E. Hare,et al.  Adsorption of amino acid entantiomers by Na-montmorillonite , 1981, Origins of life.

[29]  Jeremy J. Yang,et al.  The origin of intermediary metabolism. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[30]  J. Ferris,et al.  Mineral catalysis of the formation of dimers of 5′-AMP in aqueous solution: The possible role of montmorillonite clays in the prebiotic synthesis of RNA , 2005, Origins of life and evolution of the biosphere.

[31]  S. Freeland,et al.  Testing a biosynthetic theory of the genetic code: fact or artifact? , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[32]  M. Eigen New concepts for dealing with the evolution of nucleic acids. , 1987, Cold Spring Harbor symposia on quantitative biology.

[33]  M. Di Giulio,et al.  The Robust Statistical Bases of the Coevolution Theory of Genetic Code Origin , 2000, Journal of Molecular Evolution.

[34]  R. Guimarães The Organic Codes: an introduction to semantic biology , 2003 .

[35]  L. Hurst,et al.  The Genetic Code Is One in a Million , 1998, Journal of Molecular Evolution.

[36]  Maciej Szymanski,et al.  Aminoacyl-tRNA synthetases database , 2001, Nucleic Acids Res..

[37]  P. Schimmel,et al.  Getting tRNA synthetases into the nucleus. , 1999, Trends in biochemical sciences.

[38]  Mario Medugno,et al.  Physicochemical Optimization in the Genetic Code Origin as the Number of Codified Amino Acids Increases , 1999, Journal of Molecular Evolution.

[39]  I. Parsons,et al.  Biochemical evolution II: origin of life in tubular microstructures on weathered feldspar surfaces. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[40]  R. Shapiro,et al.  Prebiotic cytosine synthesis: a critical analysis and implications for the origin of life. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[41]  J P Wikswo,et al.  A low temperature transfer of ALH84001 from Mars to Earth. , 2000, Science.

[42]  S. Benner,et al.  Natural selection, protein engineering, and the last riboorganism: rational model building in biochemistry. , 1987, Cold Spring Harbor symposia on quantitative biology.

[43]  Paul Schimmel,et al.  Elucidation of tRNA‐dependent editing by a class II tRNA synthetase and significance for cell viability , 2003, The EMBO journal.

[44]  P. Schimmel,et al.  Active site of an aminoacyl-tRNA synthetase dissected by energy-transfer-dependent fluorescence. , 2001, Bioorganic & medicinal chemistry letters.

[45]  J. Ferris,et al.  Sequence- and Regio-Selectivity in the Montmorillonite-Catalyzed Synthesis of RNA , 2000, Origins of life and evolution of the biosphere.

[46]  Hyman Hartman,et al.  Speculations on the origin and evolution of metabolism , 1975, Journal of Molecular Evolution.

[47]  Catalytic RNA: structure and mechanism. , 1993, Biochemical Society transactions.

[48]  E. Friebele,et al.  Adsorption of protein and non-protein amino acids on a clay mineral: A possible role of selection in chemical evolution , 1980, Journal of Molecular Evolution.

[49]  F. Crick Origin of the Genetic Code , 1967, Nature.

[50]  Robert Shapiro Prebiotic ribose synthesis: A critical analysis , 2006, Origins of life and evolution of the biosphere.

[51]  T H Jukes,et al.  Evolutionary changes in the genetic code , 1990, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[52]  P Schuster,et al.  Hypercycles and compartments. Compartments assists--but do not replace--hypercyclic organization of early genetic information. , 1980, Journal of theoretical biology.

[53]  P. Schuster,et al.  Shaping space: the possible and the attainable in RNA genotype-phenotype mapping. , 1998, Journal of theoretical biology.

[54]  G. Wächtershäuser,et al.  Groundworks for an evolutionary biochemistry: the iron-sulphur world. , 1992, Progress in biophysics and molecular biology.

[55]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[56]  J R Lepock,et al.  Astrophysical and biological constraints on radiopanspermia. , 1996, The Journal of the Royal Astronomical Society of Canada. Royal Astronomical Society of Canada.

[57]  M. Line The enigma of the origin of life and its timing. , 2002, Microbiology.

[58]  Gary J. Olsen,et al.  Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process , 2000, Microbiology and Molecular Biology Reviews.

[59]  L. Hurst,et al.  Early fixation of an optimal genetic code. , 2000, Molecular biology and evolution.

[60]  K. D. McKeegan,et al.  Evidence for life on Earth before 3,800 million years ago , 1996, Nature.

[61]  John Maynard Smith,et al.  Hypercycles and the origin of life , 1979, Nature.

[62]  L F Landweber,et al.  Selection, history and chemistry: the three faces of the genetic code. , 1999, Trends in biochemical sciences.

[63]  David S. Stevenson Co-evolution of the genetic code and ribozyme replication. , 2002, Journal of theoretical biology.

[64]  C V Forst,et al.  Replication and mutation on neutral networks , 2001, Bulletin of mathematical biology.

[65]  C. Ponnamperuma ORGANIC COMPOUNDS IN THE MURCHISON METEORITE , 1972, Annals of the New York Academy of Sciences.

[66]  A. Figureau,et al.  The logic of the genetic code: Synonyms and optimality against effects of mutations , 2004, Origins of life.

[67]  K. Kvenvolden,et al.  Evidence for Extraterrestrial Amino-acids and Hydrocarbons in the Murchison Meteorite , 1970, Nature.

[68]  V. I. Shcherbak,et al.  Arithmetic inside the universal genetic code. , 2003, Bio Systems.

[69]  M. Eigen Selforganization of matter and the evolution of biological macromolecules , 1971, Naturwissenschaften.

[70]  M. Giulio The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis , 2003, Origins of life and evolution of the biosphere.

[71]  B. Ganem RNA world , 1987, Nature.

[72]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.

[73]  Molecular self-organization and the early stages of evolution. , 1971, Experientia.

[74]  Michael J E Sternberg,et al.  Evolution of enzymes in metabolism: a network perspective. , 2002, Journal of molecular biology.

[75]  D. Deamer,et al.  Amphiphilic components of the murchison carbonaceous chondrite: Surface properties and membrane formation , 2005, Origins of life and evolution of the biosphere.

[76]  M Yarus,et al.  RNA-ligand chemistry: a testable source for the genetic code. , 2000, RNA.

[77]  V. Döring,et al.  Genetic Code Ambiguity , 2002, The Journal of Biological Chemistry.

[78]  P. Schimmel,et al.  A view into the origin of life: aminoacyl-tRNA synthetases , 2000, Cellular and Molecular Life Sciences CMLS.

[79]  J. Ferris,et al.  Formation of RNA Oligomers on Montmorillonite: Site of Catalysis , 2004, Origins of life and evolution of the biosphere.

[80]  Gerald F. Joyce,et al.  2 Prospects for Understanding the Origin of the RNA World , 1999 .

[81]  R. Shapiro Comments on `Concentration by Evaporation and the Prebiotic Synthesis of Cytosine' , 2002, Origins of life and evolution of the biosphere.

[82]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[83]  D. Inzé,et al.  A functional genomics approach toward the understanding of secondary metabolism in plant cells , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[84]  D. Clark,et al.  Combinatorial biocatalysis: taking the lead from nature. , 1999, Current opinion in biotechnology.

[85]  R. J. Williams,et al.  Introduction to silicon chemistry and biochemistry. , 1986, Ciba Foundation symposium.

[86]  G. Wächtershäuser,et al.  Evolution of the first metabolic cycles. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[87]  Aivo Lepland,et al.  Reassessing the evidence for the earliest traces of life , 2002, Nature.

[88]  J. Trevors Bacterial evolution and metabolism , 1997, Antonie van Leeuwenhoek.

[89]  Wenhua Huang,et al.  Synthesis of 35-40 mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. , 2003, Chemical communications.

[90]  G. Pályi,et al.  Fundamentals of Life , 2002 .

[91]  D. Whittet IS EXTRATERRESTRIAL ORGANIC MATTER RELEVANT TO THE ORIGIN OF LIFE ON EARTH? , 1997, Origins of life and evolution of the biosphere.

[92]  R S Root-Bernstein On the origin of the genetic code. , 1982, Journal of theoretical biology.

[93]  André Brack,et al.  Liquid water and the origin of life , 1993, Origins of life and evolution of the biosphere.

[94]  S. Benner,et al.  The last ribo-organism , 1987, Nature.

[95]  Jacques Monod,et al.  Chance and Necessity , 1970 .

[96]  Serge Massar,et al.  Optimality of the genetic code with respect to protein stability and amino-acid frequencies , 2001, Genome Biology.

[97]  H Baltscheffsky Major "anastrophes" in the origin and early evolution of biological energy conversion. , 1997, Journal of theoretical biology.

[98]  J. Ferris,et al.  Oligomerization of Ribonucleotides on Montmorillonite: Reaction of the 5′‐Phosphorimidazolide of Adenosine. , 1993 .

[99]  P. L. Hall Seven Clues to the Origin of Life , 1985 .

[100]  The coevolution theory of the origin of the genetic code , 2004 .

[101]  J. Greenberg,et al.  Can spores survive in interstellar space? , 1985, Nature.

[102]  P. Schuster Polynucleotide evolution, hypercycles and the origin of the genetic code. , 1984, Advances in space research : the official journal of the Committee on Space Research.

[103]  J. Wong,et al.  Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life. , 2003, Gene.

[104]  D. Deamer,et al.  Permeability of lipid bilayers to water and ionic solutes. , 1986, Chemistry and physics of lipids.

[105]  Early steps of metabolism evolution inferred by cladistic analysis of amino acid catabolic pathways. , 2002, Comptes rendus biologies.

[106]  J. T. Trevors,et al.  Hydrophobic medium (HM) water interface, cell division and the self-assembly of life , 2002, Theory in Biosciences.

[107]  P. Schimmel,et al.  Operational RNA Code for Amino Acids in Relation to Genetic Code in Evolution* , 2001, The Journal of Biological Chemistry.

[108]  John H. Holland,et al.  A Derived Markov Process for Modeling Reaction Networks , 2003, Evolutionary Computation.

[109]  T. Cech,et al.  The Ribosome Is a Ribozyme , 2000, Science.

[110]  M. Di Giulio,et al.  The Level and Landscape of Optimization in the Origin of the Genetic Code , 2001, Journal of Molecular Evolution.

[111]  S. Altman The road to RNase P , 2000, Nature Structural Biology.

[112]  P. Schimmel,et al.  Two Classes of tRNA Synthetases Suggested by Sterically Compatible Dockings on tRNA Acceptor Stem , 2001, Cell.

[113]  P. Schuster,et al.  How to search for RNA structures. Theoretical concepts in evolutionary biotechnology. , 1995, Journal of biotechnology.

[114]  J. Ferris,et al.  Oligomerization of uridine phosphorimidazolides on montmorillonite: A model for the prebiotic synthesis of rna on minerals , 1996, Origins of life and evolution of the biosphere.

[115]  J. Trevors Genetic material in the early evolution of bacteria. , 2003, Microbiological research.

[116]  J. Trevors Bacterial evolution and silicon , 1997, Antonie van Leeuwenhoek.

[117]  M. Eigen,et al.  Elementary step dynamics of catalytic hypercycles. , 1980, Bio Systems.

[118]  S. Freeland,et al.  The Case for an Error Minimizing Standard Genetic Code , 2003, Origins of life and evolution of the biosphere.

[119]  Dusting off panspermia , 1996, Nature.

[120]  W. Martin,et al.  On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[121]  J. Ferris,et al.  Clay Catalysis of Oligonucleotide Formation: Kinetics of the Reaction of the 5'-Phosphorimidazolides of Nucleotides with the Non-Basic Heterocycles Uracil and Hypoxanthine , 1999, Origins of life and evolution of the biosphere.

[122]  Return of the 'last ribo-organism' , 1988, Nature.

[123]  A. Turing On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[124]  L. Orgel,et al.  Synthesis of long prebiotic oligomers on mineral surfaces , 1996, Nature.

[125]  S. Osawa,et al.  Recent evidence for evolution of the genetic code , 1992, Microbiological reviews.

[126]  R. Shapiro The improbability of prebiotic nucleic acid synthesis , 2004, Origins of life.

[127]  A. Cairns-smith Takeover mechanisms and early biochemical evolution. , 1977, Bio Systems.

[128]  H. Melosh Blasting rocks off planets , 1993, Nature.

[129]  J. Ferris,et al.  Sequence- and regioselectivity in the montmorillonite-catalyzed synthesis of RNA. , 2003, Journal of the American Chemical Society.

[130]  M. Baltscheffsky,et al.  H+‐proton‐pumping inorganic pyrophosphatase: a tightly membrane‐bound family , 1999, FEBS letters.

[131]  Robert Eugene Blankenship,et al.  The origin and evolution of oxygenic photosynthesis. , 1998, Trends in biochemical sciences.

[132]  M. Giulio Genetic Code Origin: Are the Pathways of Type Glu-tRNAGln \rightarrow Gln-tRNAGln Molecular Fossils or Not? , 2002, Journal of Molecular Evolution.

[133]  M. Yarus,et al.  Genetic code origins , 1989, Nature.

[134]  J. Ferris,et al.  Synthesis of RNA oligomers on heterogeneous templates , 1996, Nature.

[135]  J. Wong A co-evolution theory of the genetic code. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[136]  W. Good The role of water in the origin of life and its function in the primitive gene. , 1973, Journal of theoretical biology.

[137]  P. Schimmel,et al.  Aminoacyl-tRNA synthetases: potential markers of genetic code development. , 2001, Trends in biochemical sciences.

[138]  R Shapiro A Replicator Was Not Involved in the Origin of Life , 2000, IUBMB life.

[139]  Chun-Hsien Huang,et al.  Montmorillonite: A multifunctional mineral catalyst for the prebiological formation of phosphate esters , 2005, Origins of life and evolution of the biosphere.

[140]  F. Hoyle,et al.  The case for life as a cosmic phenomenon , 1986, Nature.

[141]  David Bradley Informatics. The genome chose its alphabet with care. , 2002, Science.

[142]  P. Ball Water, Water Everywhere , 2002 .

[143]  J. Barciszewski,et al.  The new aspects of aminoacyl-tRNA synthetases. , 2000, Acta biochimica Polonica.

[144]  P. Schimmel,et al.  Genetic code origins: tRNAs older than their synthetases? , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[145]  P. Schultz,et al.  Expanding the genetic code. , 2002, Chemical communications.

[146]  H. P. Yockey,et al.  Information Theory And Molecular Biology , 1992 .

[147]  B. K. Davis Evolution of the genetic code. , 1999, Progress in biophysics and molecular biology.

[148]  Laura F. Landweber,et al.  Genview and Gencode: a pair of programs to test theories of genetic code evolution , 2001, Bioinform..

[149]  M. Giulio The non-monophyletic origin of the tRNA molecule. , 1999 .

[150]  J. Schopf,et al.  Microfossils of the Early Archean Apex Chert: New Evidence of the Antiquity of Life , 1993, Science.

[151]  Robert Shapiro,et al.  Origins: A Skeptic's Guide to the Creation of Life on Earth , 1986 .

[152]  P. Schimmel,et al.  Ribozyme programming extends the protein code , 2002, Nature Biotechnology.

[153]  P. Davies The Origin of Life I: When and Where Did it Begin? , 2001, Science progress.

[154]  M. Di Giulio,et al.  The Historical Factor: The Biosynthetic Relationships Between Amino Acids and Their Physicochemical Properties in the Origin of the Genetic Code , 1998, Journal of Molecular Evolution.

[155]  S. Mann,et al.  Structural aspects of biogenic silica. , 1986, Ciba Foundation symposium.