Ïîëåçíîå:
Êàê ñäåëàòü ðàçãîâîð ïîëåçíûì è ïðèÿòíûì
Êàê ñäåëàòü îáúåìíóþ çâåçäó ñâîèìè ðóêàìè
Êàê ñäåëàòü òî, ÷òî äåëàòü íå õî÷åòñÿ?
Êàê ñäåëàòü ïîãðåìóøêó
Êàê ñäåëàòü òàê ÷òîáû æåíùèíû ñàìè çíàêîìèëèñü ñ âàìè
Êàê ñäåëàòü èäåþ êîììåð÷åñêîé
Êàê ñäåëàòü õîðîøóþ ðàñòÿæêó íîã?
Êàê ñäåëàòü íàø ðàçóì çäîðîâûì?
Êàê ñäåëàòü, ÷òîáû ëþäè îáìàíûâàëè ìåíüøå
Âîïðîñ 4. Êàê ñäåëàòü òàê, ÷òîáû âàñ óâàæàëè è öåíèëè?
Êàê ñäåëàòü ëó÷øå ñåáå è äðóãèì ëþäÿì
Êàê ñäåëàòü ñâèäàíèå èíòåðåñíûì?
Êàòåãîðèè:
ÀðõèòåêòóðàÀñòðîíîìèÿÁèîëîãèÿÃåîãðàôèÿÃåîëîãèÿÈíôîðìàòèêàÈñêóññòâîÈñòîðèÿÊóëèíàðèÿÊóëüòóðàÌàðêåòèíãÌàòåìàòèêàÌåäèöèíàÌåíåäæìåíòÎõðàíà òðóäàÏðàâîÏðîèçâîäñòâîÏñèõîëîãèÿÐåëèãèÿÑîöèîëîãèÿÑïîðòÒåõíèêàÔèçèêàÔèëîñîôèÿÕèìèÿÝêîëîãèÿÝêîíîìèêàÝëåêòðîíèêà
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S ≈ 5 × 1022 × 1021 × 3 × 1017 ≈ 1,5 × 1061⇐ ÏðåäûäóùàÿÑòð 124 èç 124
Ïðåäïîëîæèì, ÷òî äëÿ íà÷àëà áèîëîãè÷åñêîé ýâîëþöèè òðåáóåòñÿ óíèêàëüíûé n -ìåð. Êîëè÷åñòâî âîçìîæíûõ ïîñëåäîâàòåëüíîñòåé, ñîñòîÿùèõ èç n íóêëåîòèäîâ, N = 4 n ≈ 100,6 n. Ìîæíî îæèäàòü, ÷òî óíèêàëüíûé n -ìåð âîçíèêíåò â Í-îáëàñòè E ðàç:
E = S / N = 1,5 × 1061/100,6n
è
n = log (E × 1,5 × 1061)/0,6
Ïîäñòàâèâ E = 1, ïîëó÷àåì n ≈ 102 (íóêëåîòèäà). Çàìåòèì, ÷òî, òàê êàê âåëè÷èíà n ïðÿìî ïðîïîðöèîíàëüíà ëîãàðèôìó S, îöåíêà áóäåò ìàëî çàâèñåòü îò íà÷àëüíûõ ïðåäïîëîæåíèé î âåëè÷èíå ïåðåìåííûõ; íàïðèìåð, èçìåíåíèå S íà ïîðÿäîê âåëè÷èíû ïðèâåäåò ê óâåëè÷åíèþ èëè óìåíüøåíèþ n ìåíåå ÷åì íà 2 íóêëåîòèäà. Ìîæíî ïðåäñòàâèòü ñåáå ðèáîçèì-ðåïëèêàçó, ñîñòîÿùóþ èç ïðèáëèçèòåëüíî ñòà íóêëåîòèäîâ; òàêèì îáðàçîì, â ïðèíöèïå ñïîíòàííîå ïîÿâëåíèå òàêîâîé â êîíå÷íîé âñåëåííîé, ñîñòîÿùåé èç åäèíñòâåííîé Í-îáëàñòè, íåëüçÿ èñêëþ÷àòü â íàøåé «èãðóøå÷íîé» ìîäåëè (è ñíîâà, ñêîðîñòü ñèíòåçà ÐÍÊ, ïðèíÿòàÿ çäåñü, íàìåðåííî ñèëüíî ïåðåîöåíåíà). Äëÿ ïîÿâëåíèÿ ïðèìèòèâíîé ñèñòåìû ñîïðÿæåííîé ðåïëèêàöèè-òðàíñëÿöèè, ÷òî â äàííîì êîíòåêñòå ðàññìàòðèâàåòñÿ êàê ðåâîëþöèîííàÿ ñòàäèÿ, òðåáîâàíèÿ ãîðàçäî æåñò÷å. Êàê ìèíèìóì, íåîáõîäèìî ñïîíòàííîå ïîÿâëåíèå ñëåäóþùåãî:
• Äâå ðÐÍÊ, ñ îáùèì ðàçìåðîì íå ìåíåå 1000 íóêëåîòèäîâ. • Ïðèìåðíî 10 ïðèìèòèâíûõ àäàïòåðîâ ïî 30 íóêëåîòèäîâ êàæäûé, â öåëîì îêîëî 300 íóêëåîòèäîâ. • Ïî ìåíüøåé ìåðå îäíà ÐÍÊ, êîäèðóþùàÿ ðåïëèêàçó, ðàçìåðîì ïðèìåðíî 500 íóêëåîòèäîâ (îöåíêà ñíèçó).  ïðèíÿòîé ìîäåëè, n = 1800, è â ðåçóëüòàòå E < 10–1018.
Äðóãèìè ñëîâàìè, äàæå â íàøåé èãðóøå÷íîé ìîäåëè, êîòîðàÿ ïðåäïîëàãàåò ñèëüíî ïðåóâåëè÷åííóþ ñêîðîñòü ñèíòåçà ÐÍÊ, âåðîÿòíîñòü ñëó÷àéíîãî çàðîæäåíèÿ ñèñòåìû òðàíñëÿöèÿ – ðåïëèêàöèÿ â åäèíñòâåííîé Í-îáëàñòè áóäåò P < 10–1018. Î÷åâèäíî, ýòà âåðñèÿ ðåâîëþöèîííîé ñòàäèè ìîæåò ðàññìàòðèâàòüñÿ òîëüêî â êîíòåêñòå âñåëåííîé ñ áåñêîíå÷íûì (èëè, ïî ìåíüøåé ìåðå, î÷åíü áîëüøèì) êîëè÷åñòâîì Í-îáëàñòåé. Ìîäåëü, ðàññìîòðåííàÿ çäåñü, íè â êîåì ñëó÷àå íå ïðåäïîëàãàëàñü ðåàëèñòè÷íîé. Îíà òîëüêî èëëþñòðèðóåò ðàçíèöó â òðåáîâàíèÿõ, íàêëàäûâàåìûõ íà âåðîÿòíîñòü âîçíèêíîâåíèÿ ðàçíûõ âåðñèé ðåâîëþöèîííûõ ñèñòåì, è ñëåäîâàòåëüíî, ñâÿçü ýòîé âåðñèè ñ ðàçíûìè êîñìîëîãè÷åñêèìè ìîäåëÿìè âñåëåííîé.
Òàáëèöà II-1. Íîâûå îïðåäåëåíèÿ è íîâûå èíòåðïðåòàöèè èçâåñòíûõ îïðåäåëåíèé â ìîäåëè ÌÌÌ.
Ëèòåðàòóðà
(1948) O Polozhenii V Biologicheskoi Nauke. Stenograficheskii Otchet Sessii Vsesoyuznoi Akademii Selskohozyastvennyh Nauk Imeni V. I. Lenina. (On the Situation in Biological Science. A Transcript of the Session of the V. I. Lenin All-Union Academy of Agricultural Sciences, July 31-August 7, 1948. Moscow, USSR: The State Agricultural Literature Publishers. ‘t Hooft, G. (1993) Dimensional Reduction in Quantum Gravity. gr-qc/9310026. Adami C. (2002) What Is Complexity? Bioessays 24: 1,085—1,094. Adl, S. M., A. G. Simpson, M. A. Farmer, R. A. Andersen, O. R. Anderson, J. R. Barta, S. S. Bowser, G. Brugerolle, R. A. Fensome, S. Fredericq, T. Y. James, S. Karpov, P. Kugrens, J. Krug, C. E. Lane, L. A. Lewis, J. Lodge, D. H. Lynn, D. G. Mann, R. M. McCourt, L. Mendoza, O. Moestrup, S. E. Mozley-Standridge, T. A. Nerad, C. A. Shearer, A. V. Smirnov, F. W. Spiegel, and M. F. Taylor. (2005) The New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists. J Eukaryot Microbiol 52: 399–451. Agol V. I. (1974) Towards the System of Viruses. Biosystems 6: 113–132. Agol V. I., and A. P. Gmyl. (2010) Viral Security Proteins: Counteracting Host Defences. Nat Rev Microbiol 8: 867–878. Ahlquist P. (2006) Parallels among Positive-Strand RNA Viruses, Reverse-Transcribing Viruses and Double-Stranded RNA Viruses. Nat Rev Microbiol 4: 371–382. Alic N., N. Ayoub, E. Landrieux, E. Favry, P. Baudouin-Cornu, M. Riva, and C. Carles. (2007) Selectivity and Proofreading Both Contribute Significantly to the Fidelity of RNA Polymerase III Transcription. Proc Natl Acad Sci USA 104: 10,400—10,405. Allen, E. E., and J. F. Banfield. (2005) Community Genomics in Microbial Ecology and Evolution. Nat Rev Microbiol 3: 489–498. Alperovitch-Lavy, A., I. Sharon, F. Rohwer, E. M. Aro, F. Glaser, R. Milo, N. Nelson, and O. Beja. (2011) Reconstructing a Puzzle: Existence of Cyanophages Containing Both Photosystem-I and Photosystem-II Gene Suites Inferred from Oceanic Metagenomic Datasets. Environ Microbiol 13: 24–32. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. (1997) Gapped Blast and Psi-Blast: A New Generation of Protein Database Search Programs. Nucleic Acids Res 25: 3,389—3,402. Altstein, A. D. (1987) Origin of the Genetic System. Mol Biol 21: 309–322. Amaral, P. P., M. E. Dinger, T. R. Mercer, and J. S. Mattick. (2008) The Eukaryotic Genome as an RNA Machine. Science 319: 1,787—1,789. Anantharaman, V., E. V. Koonin, and L. Aravind. (2002) Comparative Genomics and Evolution of Proteins Involved in RNA Metabolism. Nucleic Acids Res 30: 1,427—1,464. Anfinsen, C. B. (1973) Principles That Govern the Folding of Protein Chains. Science 181: 223–230. Aquadro, C. F. (1997) Insights into the Evolutionary Process from Patterns of DNA Sequence Variability. Curr Opin Genet Dev 7: 835–840. Aravind, L., V. Anantharaman, S. Balaji, M. M. Babu, and L. M. Iyer. (2005) The Many Faces of the Helix-Turn-Helix Domain: Transcription Regulation and Beyond. FEMS Microbiol Rev 29: 231–262. Aravind, L., L. M. Iyer and E. V. Koonin. (2006) Comparative Genomics and Structural Biology of the Molecular Innovations of Eukaryotes. Curr Opin Struct Biol 16: 409–419. Aravind, L., and E. V. Koonin. (1999) DNA-Binding Proteins and Evolution of Transcription Regulation in the Archaea. Nucleic Acids Res 27: 4,658—4,670. Aravind, L., and E. V. Koonin. (2001) The DNA-Repair Protein Alkb, Egl-9, and Leprecan Define New Families of 2-Oxoglutarate – and Iron-Dependent Dioxygenases. Genome Biol 2: RESEARCH0007. Aravind, L., R. Mazumder, S. Vasudevan, and E. V. Koonin. (2002) Trends in Protein Evolution Inferred from Sequence and Structure Analysis. Curr Opin Struct Biol 12: 392–399. Aravind, L., R. L. Tatusov, Y. I. Wolf, D. R. Walker, and E. V. Koonin. (1998) Evidence for Massive Gene Exchange Between Archaeal and Bacterial Hyperthermophiles. Trends Genet 14: 442–444. Aravind, L., D. R. Walker, and E. V. Koonin. (1999) Conserved Domains in DNA Repair Proteins and Evolution of Repair Systems. Nucleic Acids Res 27: 1,223—1,242. Assis, R., and A. S. Kondrashov. (2009) Rapid Repetitive Element-Mediated Expansion of piRNA Clusters in Mammalian Evolution. Proc Natl Acad Sci USA 106: 7,079—7,082. Assis, R., A. S. Kondrashov, E. V. Koonin, and F. A. Kondrashov. (2008) Nested Genes and Increasing Organizational Complexity of Metazoan Genomes. Trends Genet 24: 475–478. Atkins, J. F., R. F. Gesteland, and T. R. Cech, eds. (2010) RNA Worlds: From Life’s Origins to Diversity in Gene Regulation. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Auster, P. (1991) The Music of Chance. New York: Penguin. Autexier, C., and N. F. Lue. (2006) The Structure and Function of Telomerase Reverse Transcriptase. Annu Rev Biochem 75: 493–517. Baaske, P., F. M. Weinert, S. Duhr, K. H. Lemke, M. J. Russell, and D. Braun. (2007) Extreme Accumulation of Nucleotides in Simulated Hydrothermal Pore Systems. Proc Natl Acad Sci USA 104: 9,346—9,351. Babu, M., N. Beloglazova, R. Flick, C. Graham, T. Skarina, B. Nocek, A. Gagarinova, O. Pogoutse, G. Brown, A. Binkowski, S. Phanse, A. Joachimiak, E. V. Koonin, A. Savchenko, A. Emili, J. Greenblatt, A. M. Edwards, and A. F. Yakunin. (2011) A Dual Function of the CRISPR-Cas System in Bacterial Antivirus Immunity and DNA Repair. Mol Microbiol 79: 484–502. Ball, P. (2011) A Metaphor Too Far. Nature doi:10.1038/news.2011.115. Bailey, K. A., F. Marc, K. Sandman, and J. N. Reeve. (2002) Both DNA and His-tone Fold Sequences Contribute to Archaeal Nucleosome Stability. J Biol Chem 15: 9293–9301. Baltimore, D. (1971) Expression of Animal Virus Genomes. Bacteriol Rev 35: 235–241. Bangham, C. R., and T. B. Kirkwood. (1993) Defective Interfering Particles and Virus Evolution. Trends Microbiol 1: 260–264. Barabasi, A. L. (2002) Linked: The New Science of Networks. New York: Perseus Press. Barabasi, A. L., and Z. N. Oltvai. (2004) Network Biology: Understanding the Cell’s Functional Organization. Nat Rev Genet 5: 101–113. Barbrook, A. C., C. J. Howe, D. P. Kurniawan, and S. J. Tarr. (2010) Organization and Expression of Organellar Genomes. Philos Trans R Soc Lond B Biol Sci 365: 785–797. Baross, J. A., and S. A. Hoffman. (1985) Submarine Hydrothermal Vents and Associated Gradient Environments As Sites for the Origin and Evolution of Life. Origins of Life 15: 327–345. Barrangou, R., C. Fremaux, H. Deveau, M. Richards, P. Boyaval, S. Moineau, D. A. Romero, and P. Horvath. (2007) CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes. Science 315: 1,709—1,712. Barrick, J. E., D. S. Yu, S. H. Yoon, H. Jeong, T. K. Oh, D. Schneider, R. E. Lenski, and J. F. Kim. (2009) Genome Evolution and Adaptation in a Long-Term Experiment with Escherichia coli. Nature 461: 1243–1247. Barrow, J. D., and F. J. Tipler. (1988) The Anthropic Cosmological Principle. Oxford: Oxford University Press. Barrowman, J., D. Bhandari, K. Reinisch, and S. Ferro-Novick. (2010) Trapp Complexes in Membrane Traffic: Convergence Through a Common Rab. Nat Rev Mol Cell Biol 11: 759–763. Barton, N. H. (2000) Genetic Hitchhiking. Philos Trans R Soc Lond B Biol Sci 355: 1,553—1,562. Barton, N. H., and J. B. Coe. (2009) On the Application of Statistical Physics to Evolutionary Biology. J Theor Biol 259: 317–324. Basu, M. K., E. Poliakov, and I. B. Rogozin. (2009) Domain Mobility in Proteins: Functional and Evolutionary Implications. Brief Bioinform 10: 205–216. Beardmore, R. E., I. Gudelj, D. A. Lipson, and L. D. Hurst. (2011) Metabolic Trade-Offs and the Maintenance of the Fittest and the Flattest. Nature [Epub ahead of print]. Beeby, M., B. D. O’Connor, C. Ryttersgaard, D. R. Boutz, L. J. Perry, and T. O. Yeates. (2005) The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles. PLoS Biol 3: e309. Begley, T. J., and L. D. Samson. (2003) Molecular Biology: A Fix for RNA. Nature 421: 795–796. Behe, M. J. (2006). Darwin’s Black Box: The Biochemical Challenge to Evolution. New York: Free Press. Behm-Ansmant, I., I. Kashima, J. Rehwinkel, J. Sauliere, N. Wittkopp, and E. Izaurralde. (2007) mRNA Quality Control: An Ancient Machinery Recognizes and Degrades mRNAs with Nonsense Codons. FEBS Lett 581: 2,845—2,853. Beiko, R. G., and N. Hamilton. (2006) Phylogenetic Identification of Lateral Genetic Transfer Events. BMC Evol Biol 6: 15. Beiko, R. G., T. J. Harlow, and M. A. Ragan. (2005) Highways of Gene Sharing in Prokaryotes. Proc Natl Acad Sci USA 102: 14,332—14,337. Beringer, M., and M. V. Rodnina. (2007) The Ribosomal Peptidyl Transferase. Mol Cell 26: 311–321. Bezier, A., M. Annaheim, J. Herbiniere, C. Wetterwald, G. Gyapay, S. Bernard-Samain, P. Wincker, I. Roditi, M. Heller, M. Belghazi, R. Pfister-Wilhem, G. Periquet, C. Dupuy, E. Huguet, A. N. Volkoff, B. Lanzrein, and J. M. Drezen. (2009) Polydnaviruses of Braconid Wasps Derive from an Ancestral Nudivirus. Science 323: 926–930. Bhattacharya, D., J. M. Archibald, A. P. Weber, and A. Reyes-Prieto. (2007) How Do Endosymbionts Become Organelles? Understanding Early Events in Plastid Evolution. Bioessays 29: 1,239—1,246. Bidle, K. D., and P. G. Falkowski. (2004) Cell Death in Planktonic, Photosynthetic Microorganisms. Nat Rev Microbiol 2: 643–655. Biebricher, C. K., and M. Eigen. (2005) The Error Threshold. Virus Res 107: 117–127. Bigot, Y., S. Samain, C. Auge-Gouillou, and B. A. Federici. (2008) Molecular Evidence for the Evolution of Ichnoviruses from Ascoviruses by Symbiogenesis. BMC Evol Biol 8: 253. Bjedov, I., O. Tenaillon, B. Gerard, V. Souza, E. Denamur, M. Radman, F. Taddei, and I. Matic. (2003) Stress-Induced Mutagenesis in Bacteria. Science 300: 1,404—1,409. Blanchard, S. C., R. L. Gonzalez, H. D. Kim, S. Chu, and J. D. Puglisi. (2004) tRNA Selection and Kinetic Proofreading in Translation. Nat Struct Mol Biol 11: 1,008—1,014. Blasius, M., S. Sommer, and U. Hubscher. (2008) Deinococcus Radiodurans: What Belongs to the Survival Kit? Crit Rev Biochem Mol Biol 43: 221–238. Blencowe, B. J. (2006) Alternative Splicing: New Insights from Global Analyses. Cell 126: 37–47. Bokov, K., and S. V. Steinberg. (2009) A Hierarchical Model for Evolution of 23s Ribosomal RNA. Nature 457: 977–980. Bolotin, A., B. Quinquis, A. Sorokin, and S. D. Ehrlich. (2005) Clustered Regularly Interspaced Short Palindrome Repeats (Crisprs) Have Spacers of Extrachro mosomal Origin. Microbiology 151: 2,551—2,561. Bonner, J. T. (2004) Perspective: The Size-Complexity Rule. Evolution 58: 1,883—1,890. Bostrom, Nick. (2002) Anthropic Bias: Observation Selection Effects in Science and Philosphy. New York and London: Rutledge. Bourc’his, D., and O. Voinnet. (2010) A Small-RNA Perspective on Gametogenesis, Fertilization, and Early Zygotic Development. Science 330: 617–622. Bousso, R. (2006) Holographic Probabilities in Eternal Inflation. Phys Rev Lett 97: 19,1302. Bousso, R., and J. Polchinski. (2004) The String Theory Landscape. Sci Am 291: 78–87. Bowman, G. R., V. A. Voelz, and V. S. Pande. (2011) Taming the Complexity of Protein Folding. Curr Opin Struct Biol 21: 4—11. Branco, M. R., and A. Pombo. (2007) Chromosome Organization: New Facts, New Models. Trends Cell Biol 17: 127–134. Brinkmann, H., and H. Philippe. (2007) The Diversity of Eukaryotes and the Root of the Eukaryotic Tree. Adv Exp Med Biol 607: 20–37. Brisson, D. (2003) The Directed Mutation Controversy in an Evolutionary Context. Crit Rev Microbiol 29: 25–35. Brochier-Armanet, C., B. Boussau, S. Gribaldo, and P. Forterre. (2008) Mesophilic Crenarchaeota: Proposal for a Third Archaeal Phylum, the Thaumarchaeota. Nat Rev Microbiol 6: 245–252. Bromham, L., and D. Penny. (2003) The Modern Molecular Clock. Nat Rev Genet 4: 216–224. Brookfield, J. F. (2009) Evolution and Evolvability: Celebrating Darwin 200. Biol Lett 5: 44–46. Brouns, S. J., M. M. Jore, M. Lundgren, E. R. Westra, R. J. Slijkhuis, A. P. Snijders, M. J. Dickman, K. S. Makarova, E. V. Koonin, and J. van der Oost. (2008) Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes. Science 321: 960–964. Bruggeman, F. J., and H. V. Westerhoff. (2007) The Nature of Systems Biology. Trends Microbiol 15: 45–50. Burger, R., M. Willensdorfer, and M. A. Nowak. (2006) Why Are Phenotypic Mutation Rates Much Higher Than Genotypic Mutation Rates? Genetics 172: 197–206. Burki, F., K. Shalchian-Tabrizi, and J. Pawlowski. (2008) Phylogenomics Reveals a New «Megagroup» Including Most Photosynthetic Eukaryotes. Biol Lett 4: 366–369. Bushman, F. (2001) Lateral DNA Transfer: Mechanisms and Consequences. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Cairns, J., J. Overbaugh, and S. Miller. (1988) The Origin of Mutants. Nature 335: 142–145. Cairns, J., G. S. Stent, and J. D. Watson, eds. (1966) Phage and the Origins of Molecular Biology, Cold Spring Harbor, NY: CSHL Press. Carmel, L., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. (2007) Three Distinct Modes of Intron Dynamics in the Evolution of Eukaryotes. Genome Res 17: 1,034—1,044. Carroll, L. (1872). Through the Looking Glass and What Alice Found There. London: Macmillan. Carroll, S. (2010) From Eternity to Here: The Quest for the Ultimate Theory of Time. New York: Penguin. Carter, B. (1974) Large Number Coincidences and the Anthropic Principle in Cosmology in Confrontation of Cosmological Theories with Observational Data. M. S. Longair, editor. Dordrecht: D. Reidel, pp. 291–298. Casino, P., V. Rubio, and A. Marina. (2010) The Mechanism of Signal Transduction by Two-Component Systems. Curr Opin Struct Biol 20: 763–771. Cavalier-Smith, T. (1998) A Revised Six-Kingdom System of Life. Biol Rev Camb Philos Soc 73: 203–266. Cech, T. R. (2002) Ribozymes, the First 20 Years. Biochem Soc Trans 30: 1,162—1,166. Chan, C. X., A. E. Darling, R. G. Beiko, and M. A. Ragan. (2009) Are Protein Domains Modules of Lateral Genetic Transfer? PLoS One 4: e4524. Chargaff, E. (1978) Heraclitean Fire: Sketches from a Life Before Nature. New York: Rockefeller University Press. Charlebois, R. L., and W. F. Doolittle. (2004) Computing Prokaryotic Gene Ubiquity: Rescuing the Core from Extinction. Genome Res 14: 2,469—2,477. Chen, I., P. J. Christie, and D. Dubnau. (2005) The Ins and Outs of DNA Transfer in Bacteria. Science 310: 1,456—1,460. Cheng, L. K., and P. J. Unrau. (2010) Closing the Circle: Replicating RNA with RNA. Cold Spring Harb Perspect Biol 2: a002204. Chernikova, D., S. Motamedi, M. Csuros, E. V. Koonin, and I. B. Rogozin. (2011) A Late Origin of the Extant Eukaryotic Diversity: Divergence Time Estimates Using Rare Genomic Changes. Biol Direct, in press. Ciccarelli, F. D., T. Doerks, C. von Mering, C. J. Creevey, B. Snel, and P. Bork. (2006) Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science 311: 1,283—1,287. Clapier, C. R., and B. R. Cairns. (2009) The Biology of Chromatin Remodeling Complexes. Annu Rev Biochem 78: 273–304. Claverie, J. M. (2006) Viruses Take Center Stage in Cellular Evolution. Genome Biol 7: 110. Collins, L., and D. Penny. (2005) Complex Spliceosomal Organization Ancestral to Extant Eukaryotes. Mol Biol Evol 22: 1,053—1,066. Cortez, D., P. Forterre, and S. Gribaldo. (2009) A Hidden Reservoir of Integrative Elements Is the Major Source of Recently Acquired Foreign Genes and Orfans in Archaeal and Bacterial Genomes. Genome Biol 10: R65. Costanzo, G., S. Pino, F. Ciciriello, and E. Di Mauro. (2009) Generation of Long RNA Chains in Water. J Biol Chem 284: 33,206—33,216. Costanzo, G., R. Saladino, C. Crestini, F. Ciciriello, and E. Di Mauro. (2007) Nucleoside Phosphorylation by Phosphate Minerals. J Biol Chem 282: 16,729—16,735. Cox, C. J., P. G. Foster, R. P. Hirt, S. R. Harris, and T. M. Embley. (2008) The Archaebacterial Origin of Eukaryotes. Proc Natl Acad Sci USA 105: 20,356—20,361. Cox, M. M., and J. R. Battista. (2005) Deinococcus Radiodurans – the Consummate Survivor. Nat Rev Microbiol 3: 882–892. Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227: 561–563. Crick, F. H. (1958) On Protein Synthesis. Symp Soc Exp Biol 12: 138–163. Crick, F. H. (1968) The Origin of the Genetic Code. J Mol Biol 38: 367–379. Csuros, M., and I. Miklos. (2009) Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model. Mol Biol Evol 26: 2,087—2,095. Csuros, M., I. B. Rogozin, and E. V. Koonin. (2011) Resonstructed HumanLike Intron Density in the Last Common Ancestor of Eukaryotes. PLoS Comput Biol, in press. D’Herelle, F. (1922). The Bacteriophage; Its Role in Immunity. Baltimore: Williams and Wilkins. Dagan, T., and W. Martin. (2006) The Tree of One Percent. Genome Biol 7: 118. Daly, M. J. (2009) A New Perspective on Radiation Resistance Based on Deinococcus Radiodurans. Nat Rev Microbiol 7: 237–245. Danchin, A. (2003). The Delphic Boat: What Genomes Tell Us. Cambridge, MA: Harvard Univ Press. Darwin, C. (1859) On the Origin of Species. London: Murray. Darwin, C. (1872) Origin of Species. New York: The Modern Library. Daubin, V., and H. Ochman. (2004) Bacterial Genomes As New Gene Homes: The Genealogy of Orfans in E. Coli. Genome Res 14: 1,036—1,042. Davidov, Y., and E. Jurkevitch. (2009) Predation Between Prokaryotes and the Origin of Eukaryotes. Bioessays 31: 748–757. Daviter, T., K. B. Gromadski, and M. V. Rodnina. (2006) The Ribosome’s Response to Codon-Anticodon Mismatches. Biochimie 88: 1,001—1,011. Dawkins, R. (1996) The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design. London: W.W. Norton & Co. Dawkins, R. (2006) The Selfish Gene: 30th Anniversary Edition – with a New Introduction by the Author. Oxford: Oxford University Press. Dayhoff, M. O., W. C. Barker, and L. T. Hunt. (1983) Establishing Homologies in Protein Sequences. Methods Enzymol 91: 524–545. de Nooijer, S., B. R. Holland, and D. Penny. (2009) The Emergence of Predators in Early Life: There Was No Garden of Eden. PLoS ONE 4: e5507. de Souza, S. J., M. Long, R. J. Klein, S. Roy, S. Lin, and W. Gilbert. (1998) Toward a Resolution of the Introns Early/Late Debate: Only Phase Zero Introns Are Correlated with the Structure of Ancient Proteins. Proc Natl Acad Sci USA 95: 5,094—5,099. de Visser, J. A., and S. F. Elena. (2007) The Evolution of Sex: Empirical Insights into the Roles of Epistasis and Drift. Nat Rev Genet 8: 139–149. Deckert, G., P. V. Warren, T. Gaasterland, W. G. Young, A. L. Lenox, D. E. Graham, R. Overbeek, M. A. Snead, M. Keller, M. Aujay, R. Huber, R. A. Feldman, J. M. Short, G. J. Olsen, and R. V. Swanson. (1998) The Complete Genome of the Hyperthermophilic Bacterium Aquifex Aeolicus. Nature 392: 353–358. Delarue, M., O. Poch, N. Tordo, D. Moras, and P. Argos. (1990) An Attempt to Unify the Structure of Polymerases. Protein Eng 3: 461–467. Delaye, L., and A. Moya. (2010) Evolution of Reduced Prokaryotic Genomes and the Minimal Cell Concept: Variations on a Theme. Bioessays 32: 281–287. Deleuze, G., and F. Guattari. (1987) Thousand Plateaus: Capitalism and Schizophrenia. Minneapolis, MN: University of Minnesota Press. Denamur E. and I. Matic. (2006) Evolution of Mutation Rates in Bacteria. Mol Microbiol 60: 820–827. Dennett, D. C. (1996) Darwin‘s Dangerous Idea: Evolution and the Meanings of Life. New York: Simon & Schuster. Deppenmeier, U., A. Johann, T. Hartsch, R. Merkl, R. A. Schmitz, R. Martinez-Arias, A. Henne, A. Wiezer, S. Baumer, C. Jacobi, H. Bruggemann, T. Lienard, A. Christmann, M. Bomeke, S. Steckel, A. Bhattacharyya, A. Lykidis, R. Overbeek, H. P. Klenk, R. P. Gunsalus, H. J. Fritz, and G. Gottschalk. (2002) The Genome of Methanosarcina Mazei: Evidence for Lateral Gene Transfer Between Bacteria and Archaea. J Mol Microbiol Biotechnol 4: 453–461. Deveau, H., J. E. Garneau, and S. Moineau. (2010) CRISPR/Cas System and Its Role in Phage-Bacteria Interactions. Annu Rev Microbiol 64: 475–493. Diaz, R., C. Vargas-Lagunas, M. A. Villalobos, H. Peralta, Y. Mora, S. Encarnacion, L. Girard, and J. Mora. (2011) argC Orthologs from Rhizobiales Show Diverse Profiles of Transcriptional Efficiency and Functionality in Sinorhizobium Meliloti. J Bacteriol 193: 460–472. Ding, S. W. (2010) RNA-Based Antiviral Immunity. Nat Rev Immunol 10: 632–644. Dlakic, M. and A. Mushegian. (2011) Prp8, the Pivotal Protein of the Spliceosomal Catalytic Center, Evolved from a Retroelement-Encoded Reverse Transcriptase. RNA [Epub ahead of print]. Dobzhansky, T. (1951). Genetics and the Origin of Species. New York: Columbia University Press. Dobzhansky, T. (1973) Nothing in Biology Makes Sense Except in the Light of Evolution. The American Biology Teacher 35: 125–129. Dong, H., and C. G. Kurland. (1995) Ribosome Mutants with Altered Accuracy Translate with Reduced Processivity. J Mol Biol 248: 551–561. Doolittle, R. F. (1995) The Multiplicity of Domains in Proteins. Annu Rev Biochem 64: 287–314. Doolittle, W. F. (1999a) Lateral Genomics. Trends Cell Biol 9: M5—8. Doolittle, W. F. (1999b) Phylogenetic Classification and the Universal Tree. Science 284: 2,124—2,129. Doolittle, W. F. (2000) Uprooting the Tree of Life. Sci Am 282: 90–95. Doolittle, W. F., and E. Bapteste. (2007) Pattern Pluralism and the Tree of Life Hypothesis. Proc Natl Acad Sci USA 104: 2,043—2,049. Doolittle, W. F., and J. R. Brown. (1994) Tempo, Mode, the Progenote, and the Universal Root. Proc Natl Acad Sci USA 91: 6,721—6,728. Doolittle, W. F., and C. Sapienza. (1980) Selfish Genes, the Phenotype Paradigm and Genome Evolution. Nature 284: 601–603. Doolittle, W. F., and O. Zhaxybayeva. (2009) On the Origin of Prokaryotic Species. Genome Res 19: 744–756. Doudna, J. A., and T. R. Cech. (2002) The Chemical Repertoire of Natural Ribozymes. Nature 418: 222–228. Douzery, E. J., E. A. Snell, E. Bapteste, F. Delsuc, and H. Philippe. (2004) The Timing of Eukaryotic Evolution: Does a Relaxed Molecular Clock Reconcile Proteins and Fossils? Proc Natl Acad Sci USA 101: 15,386—15,391. Draghi, J. A., T. L. Parsons, G. P. Wagner, and J. B. Plotkin. (2010) Mutational Robustness Can Facilitate Adaptation. Nature 463: 353–355. Drake, J. W. (1991) A Constant Rate of Spontaneous Mutation in DNA-Based Microbes. Proc Natl Acad Sci USA 88: 7,160—7,164. Drake, J. W., and J. J. Holland. (1999) Mutation Rates Among RNA Viruses. Proc Natl Acad Sci USA 96: 13,910—13,913. Dronamraju, K. R., ed. (1968) Haldane and Modern Biology. Baltimore, Johns Hopkins University Press. Drummond, D. A., J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. (2005) Why Highly Expressed Proteins Evolve Slowly. Proc Natl Acad Sci USA 102: 14,338—14,343. Drummond, D. A., A. Raval, and C. O. Wilke. (2006) A Single Determinant Dominates the Rate of Yeast Protein Evolution. Mol Biol Evol 23: 327–337. Drummond, D. A., and C. O. Wilke. (2008) Mistranslation-Induced Protein Misfolding As a Dominant Constraint on Coding-Sequence Evolution. Cell 134: 341–352. Drummond, D. A., and C. O. Wilke. (2009) The Evolutionary Consequences of Erroneous Protein Synthesis. Nat Rev Genet 10: 715–724. Dupuy, C., E. Huguet, and J. M. Drezen. (2006) Unfolding the Evolutionary Story of Polydnaviruses. Virus Res 117: 81–89. Echols, H. (1981) SOS Functions, Cancer, and Inducible Evolution. Cell 25: 1–2. Eckerle, L. D., X. Lu, S. M. Sperry, L. Choi, and M. R. Denison. (2007) High Fidelity of Murine Hepatitis Virus Replication Is Decreased in nsp14 Exoribonuclease Mutants. J Virol 81: 12,135—12,144. Eddy, S. R. (2002) Computational Genomics of Noncoding RNA Genes. Cell 109: 137–140. Edwards, R. A., and F. Rohwer. (2005) Viral Metagenomics. Nat Rev Microbiol 3: 504–510. Eigen, M. (1971) Self-organization of Matter and the Evolution of Biological Macromolecules. Naturwissenschaften 58: 465–523. Eigen, M., B. F. Lindemann, M. Tietze, R. Winkler-Oswatitsch, A. Dress, and A. von Haeseler. (1989) How Old Is the Genetic Code? Statistical Geometry of tRNA Provides an Answer. Science 244: 673–679. Eisen, J. A., J. F. Heidelberg, O. White, and S. L. Salzberg. (2000) Evidence for Symmetric Chromosomal Inversions Around the Replication Origin in Bacteria. Genome Biol 1: RESEARCH0011. Eldredge, N., and S. J. Gould. (1997) On Punctuated Equilibria. Science 276: 338–341. Ellington, A. D., X. Chen, M. Robertson, and A. Syrett. (2009) Evolutionary Origins and Directed Evolution of RNA. Int J Biochem Cell Biol 41: 254–265. Ellis, R. J. (2003) Protein Folding: Importance of the Anfinsen Cage. Curr Biol 13: R881—883. Embley, T. M., and W. Martin. (2006) Eukaryotic Evolution, Changes and Challenges. Nature 440: 623–630. Esser, C., N. Ahmadinejad, C. Wiegand, C. Rotte, F. Sebastiani, G. Gelius-Dietrich, K. Henze, E. Kretschmann, E. Richly, D. Leister, D. Bryant, M. A. Steel, P. J. Lockhart, D. Penny, and W. Martin. (2004) A Genome Phylogeny for Mitochondria Among Alpha-Proteobacteria and a Predominantly Eubacterial Ancestry of Yeast Nuclear Genes. Mol Biol Evol 21: 1,643—1,660. Esser, C., W. Martin, and T. Dagan. (2007) The Origin of Mitochondria in Light of a Fluid Prokaryotic Chromosome Model. Biol Lett 3: 180–184. Falkowski, P. G., T. Fenchel, and E. F. Delong. (2008) The Microbial Engines That Drive Earth’s Biogeochemical Cycles. Science 320: 1,034—1,039. Falnes, P. O. (2005) RNA Repair – the Latest Addition to the Toolbox for Macro-molecular Maintenance. RNA Biol 2: 14–16. Fedor, M. J., and J. R. Williamson. (2005) The Catalytic Diversity of RNAs. Nat Rev Mol Cell Biol 6: 399–412. Felsenstein, J. (1996) Inferring Phylogenies from Protein Sequences by Parsimony, Distance, and Likelihood Methods. Methods Enzymol 266: 418–427. Felsenstein, J. (2004). Inferring Phylogenies. Sunderland, MA: Sinauer Associates. Feschotte, C. (2010) Virology: Bornavirus Enters the Genome. Nature 463: 39–40. Field, M. C., and J. B. Dacks. (2009) First and Last Ancestors: Reconstructing Evolution of the Endomembrane System with Escrts, Vesicle Coat Proteins, and Nuclear Pore Complexes. Curr Opin Cell Biol 21: 4—13. Fields, B. N., P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, S. E. Straus, and D. M. Knipe. (2001). Fields Virology. New York: Lippincott Williams & Wilkins. Fisher Box, J. (1978) R. A. Fisher: The Life of a Scientist. New York: Wiley. Fisher, R. A. (1930) The Genetical Theory of Natural Selection. New York: Oxford University Press. Fitch, W. M. (1970) Distinguishing Homologous from Analogous Proteins. Syst Zool 19: 99—113. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J. F. Tomb, B. A. Dougherty, J. M. Merrick et al. (1995) Whole-Genome Random Sequencing and Assembly of Haemophilus Influenzae Rd [See Comments]. Science 269: 496–512. Flores, R., S. Delgado, M. E. Gas, A. Carbonell, D. Molina, S. Gago, and M. De la Pena. (2004) Viroids: The Minimal Non-Coding RNAs with Autonomous Replication. FEBS Lett 567: 42–48. Fontanari, J. F., M. Santos, and E. Szathmary. (2006) Coexistence and Error Propagation in Pre-Biotic Vesicle Models: A Group Selection Approach. J Theor Biol 239: 247–256. Forterre, P. (1999) Displacement of Cellular Proteins by Functional Analogues from Plasmids or Viruses Could Explain Puzzling Phylogenies of Many DNA Informational Proteins. Mol Microbiol 33: 457–465. Forterre, P. (2002) A Hot Story from Comparative Genomics: Reverse Gyrase Is the Only Hyperthermophile-Specific Protein. Trends Genet 18: 236–237. Forterre, P. (2006) Three RNA Cells for Ribosomal Lineages and Three DNA Viruses to Replicate Their Genomes: A Hypothesis for the Origin of Cellular Domain. Proc Natl Acad Sci USA 103: 3,669—3,674. Forterre, P., and D. Prangishvili. (2009) The Great Billion-Year War Between Ribosome – and Capsid-Encoding Organisms (Cells and Viruses) As the Major Source of Evolutionary Novelties. Ann N Y Acad Sci 1,178: 65–77. Foster, P. L. (2000) Adaptive Mutation: Implications for Evolution. Bioessays 22: 1,067—1,074. Foster, P. L. (2007) Stress-Induced Mutagenesis in Bacteria. Crit Rev Biochem Mol Biol 42: 373–397. Fowles, J. (1969). The French Lieutenant’s Woman. Boston: Little & Brown. Fox, S. W. (1976) The Evolutionary Significance of Phase-Separated Microsystems. Orig Life 7: 49–68. Frank, A. C., H. Amiri, and S. G. Andersson. (2002) Genome Deterioration: Loss of Repeated Sequences and Accumulation of Junk DNA. Genetica 115: 1—12. Fraser, C. M., J. D. Gocayne, O. White, M. D. Adams, R. A. Clayton, R. D. Fleischmann, C. J. Bult, A. R. Kerlavage, G. Sutton, J. M. Kelley, et al. (1995) The Minimal Gene Complement of Mycoplasma Genitalium. Science 270: 397–403. Fredrick, K., and H. F. Noller. (2002) Accurate Translocation of mRNA by the Ribosome Requires a Peptidyl Group or Its Analog on the tRNA Moving into the 30s P-Site. Mol Cell 9: 1,125—1,131. Freeland, S. J., and L. D. Hurst. (1998) The Genetic Code Is One in a Million. J Mol Evol 47: 238–248. French, S. L., T. J. Santangelo, A. L. Beyer, and J. N. Reeve. (2007) Transcription and translation are coupled in Archaea. Mol Biol Evol 24: 893–895. Friedberg, E. C., G. C. Walker, W. Siede, R. D. Wood, R. A. Schulz, and T. Ellenberger. (2005) DNA Repair and Mutagenesis. Washington, D.C.: ASM Press. Fritz-Laylin, L. K., S. E. Prochnik, M. L. Ginger, J. B. Dacks, M. L. Carpenter, M. C. Field, A. Kuo, A. Paredez, J. Chapman, J. Pham, S. Shu, R. Neupane, M. Cipriano, J. Mancuso, H. Tu, A. Salamov, E. Lindquist, H. Shapiro, S. Lucas, I. V. Grigoriev, W. Z. Cande, C. Fulton, D. S. Rokhsar, and S. C. Dawson. (2010) The Genome of Naegleria Gruberi Illuminates Early Eukaryotic Versatility. Cell 140: 631–642. Frost, L. S., and G. Koraimann. (2010) Regulation of Bacterial Conjugation: Balancing Opportunity with Adversity. Future Microbiol 5: 1,057—1,071. Frost, L. S., R. Leplae, A. O. Summers, and A. Toussaint. (2005) Mobile Genetic Elements: The Agents of Open Source Evolution. Nat Rev Microbiol 3: 722–732. Fuerst, J. A. (2005) Intracellular Compartmentation in Planctomycetes. Annu Rev Microbiol 59: 299–328. Futuyma, D. (2005). Evolution. Sunderland, MA: Sinauer Associates. Gago, S., S. F. Elena, R. Flores, and R. Sanjuan. (2009) Extremely High Mutation Rate of a Hammerhead Viroid. Science 323: 1,308. Galhardo, R. S., P. J. Hastings, and S. M. Rosenberg. (2007) Mutation As a Stress Response and the Regulation of Evolvability. Crit Rev Biochem Mol Biol 42: 399–435. Galperin, M. Y. (2005) A Census of Membrane-Bound and Intracellular Signal Transduction Proteins in Bacteria: Bacterial Iq, Extroverts and Introverts. BMC Microbiol 5: 35. Garriga, J., and A. Vilenkin. (2001) Many Worlds in One. Phys. Rev. D 64: 043,511. Garriss, G., M. K. Waldor, and V. Burrus. (2009) Mobile Antibiotic Resistance Encoding Elements Promote Their Own Diversity. PLoS Genet 5: e1000775. Gavrilets, S. (2004) Fitness Landscapes and the Origin of Species. Princeton, NJ: Princeton University Press. Ge, F., L. S. Wang, and J. Kim. (2005) The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer. PLoS Biol 3: e316. Gell-Mann, M. (1995) The Quark and the Jaguar: Adventures in the Simple and the Complex New York: St. Martin’s Griffin. Gibson, C. M., and M. S. Hunter. (2010) Extraordinarily Widespread and Fantastically Complex: Comparative Biology of Endosymbiotic Bacterial and Fungal Mutualists of Insects. Ecol Lett 13: 223–234. Gilbert, W. (1978) Why Genes in Pieces? Nature 271: 501. Gillespie, J. H. (2000) The Neutral Theory in an Infinite Population. Gene 261: 11–18. Giovannoni, S. J., H. J. Tripp, S. Givan, M. Podar, K. L. Vergin, D. Baptista, L. Bibbs, J. Eads, T. H. Richardson, M. Noordewier, M. S. Rappe, J. M. Short, J. C. Carrington, and E. J. Mathur. (2005) Genome Streamlining in a Cosmopolitan Oceanic Bacterium. Science 309: 1,242—1,245. Glansdorff, N., Y. Xu, and B. Labedan. (2008) The Last Universal Common Ancestor: Emergence, Constitution and Genetic Legacy of an Elusive Forerunner. Biol Direct 3: 29. Gliboff, S. (2005) Protoplasm… Is Soft Wax in Our Hands: Paul Kammerer and the Art of Biological Transformation. Endeavour 29: 162–167. Gogarten, J. P., W. F. Doolittle, and J. G. Lawrence. (2002) Prokaryotic Evolution in Light of Gene Transfer. Mol Biol Evol 19: 2,226—2,238. Gogarten, J. P., H. Kibak, P. Dittrich, L. Taiz, E. J. Bowman, B. J. Bowman, M. F. Manolson, R. J. Poole, T. Date, T. Oshima, et al. (1989) Evolution of the Vacuolar H+-Atpase: Implications for the Origin of Eukaryotes. Proc Natl Acad Sci USA 86: 6,661—6,665. Gogarten, J. P., and J. P. Townsend. (2005) Horizontal Gene Transfer, Genome Innovation and Evolution. Nat Rev Microbiol 3: 679–687. Gorbalenya, A. E., V. M. Blinov, A. P. Donchenko, and E. V. Koonin. (1985) An NTP-Binding Motif Is the Most Conserved Sequence in a Highly Diverged Monophyletic Group of Proteins Involved in Positive Strand RNA Viral Replication. Molek Genetika, Microbiol Virusol 11: 30–36. Gorbalenya, A. E., L. Enjuanes, J. Ziebuhr, and E. J. Snijder. (2006) Nidovirales: Evolving the Largest RNA Virus Genome. Virus Res 117: 17–37. Gorbalenya, A. E., and E. V. Koonin. (1989) Viral Proteins Containing the Purine NTP-Binding Sequence Pattern. Nucleic Acids Res 17: 8,413—8,440. Gorbalenya, A. E., F. M. Pringle, J. L. Zeddam, B. T. Luke, C. E. Cameron, J. Kalmakoff, T. N. Hanzlik, K. H. Gordon, and V. K. Ward. (2002) The Palm Subdomain-Based Active Site Is Internally Permuted in Viral RNA-Dependent Rna Polymerases of an Ancient Lineage. J Mol Biol 324: 47–62. Gould, S. J. (1997) The Exaptive Excellence of Spandrels as a Term and Prototype. Proc Natl Acad Sci USA 94: 10,750—10,755. Gould, S. J. (1997). Full House: The Spread of Excellence from Plato to Darwin. San Francisco: Three Rivers Press. Gould, S. J. (2002). The Structure of Evolutionary Theory. Cambridge, MA: Harvard University Press. Gould, S. J., and R. C. Lewontin. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proc R Soc Lond B Biol Sci 205: 581–598. Graur, D., and W. Martin. (2004) Reading the Entrails of Chickens: Molecular Timescales of Evolution and the Illusion of Precision. Trends Genet 20: 80–86. Gray, M. W., J. Lukes, J. M. Archibald, P. J. Keeling, and W. F. Doolittle. (2010) Cell Biology. Irremediable Complexity? Science 330: 920–921. Grilli, J., B. Bassetti, S. Maslov, and M. C. Lagomarsino. (2011) Joint Scaling Laws in Functional and Evolutionary Categories in Prokaryotic Genomes. arXiv:1101.5814v1 [q-bio.GN]. Grishin, N. V., Y. I. Wolf, and E. V. Koonin. (2000) From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins. Genome Res 10: 991—1,000. Groll, M., M. Bochtler, H. Brandstetter, T. Clausen, and R. Huber. (2005) Molecular Machines for Protein Degradation. Chembiochem 6: 222–256. Guth, A. (1998) The Inflationary Universe. Boston: Basic Books. Guth, A. H. (1998) The Inflationary Universe: The Quest for a New Theory of Cosmic Origins. New York: Perseus Book Group. Guth, A. H. (2001) Eternal Inflation. Ann N Y Acad Sci 950: 66–82. Guth, A. H., and D. I. Kaiser. (2005) Inflationary Cosmology: Exploring the Universe from the Smallest to the Largest Scales. Science 307: 884–890. Haeckel, E. (1997). The Wonders of Life: A Popular Study of Biological Philosophy. London: General Books, LLC. Haldane, J. B. S. (1928) The Origin of Life. Rationalist Annual 148: 3—10. Hale, C. R., P. Zhao, S. Olson, M. O. Duff, B. R. Graveley, L. Wells, R. M. Terns, and M. P. Terns. (2009) RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex. Cell 139: 945–956. Halfmann, R., and S. Lindquist. (2010) Epigenetics in the Extreme: Prions and the Inheritance of Environmentally Acquired Traits. Science 330: 629–632. Hampl, V., L. Hug, J. W. Leigh, J. B. Dacks, B. F. Lang, A. G. Simpson, and A. J. Roger. (2009) Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic «Supergroups.» Proc Natl Acad Sci USA 106: 3,859—3,864. Harrison, P. M., and M. Gerstein. (2002) Studying Genomes Through the Aeons: Protein Families, Pseudogenes, and Proteome Evolution. J Mol Biol 318: 1,155—1,174. Hartl, D. L., and A. G. Clark. (2006) Principles of Population Genetics. Sunderland, MA: Sinauer Associates. Hartung, S., and K. P. Hopfner. (2009) Lessons from Structural and Biochemical Studies on the Archaeal Exosome. Biochem Soc Trans 37: 83–87. Hawking, S. W. (1988) A Brief History of Time: From the Big Bang to Black Holes. London: Bantam. Hawking, S. W., and L. Mlodinow. (2010) The Grand Design. London: Bantam. Hazkani-Covo, E., R. M. Zeller, and W. Martin. (2010) Molecular Poltergeists: Mitochondrial DNA Copies (Numts) in Sequenced Nuclear Genomes. PLoS Genet 6: e1000834. Hilario, E., and J. P. Gogarten. (1993) Horizontal Transfer of Atpase Genes – the Tree of Life Becomes a Net of Life. Biosystems 31: 111–119. Hochstrasser, M. (2009) Origin and Function of Ubiquitin-Like Proteins. Nature 458: 422–429. Hollick, J. B. (2010) Paramutation and Development. Annu Rev Cell Dev Biol 26: 557–579. Holmes, E. C. (2009) The Evolution and Emergence of RNA Viruses. Oxford: Oxford University Press. Horie, M., T. Honda, Y. Suzuki, Y. Kobayashi, T. Daito, T. Oshida, K. Ikuta, P. Jern, T. Gojobori, J. M. Coffin, and K. Tomonaga. (2010) Endogenous Non-Retroviral RNA Virus Elements in Mammalian Genomes. Nature 463: 84–87. Huber, C., W. Eisenreich, S. Hecht, and G. Wachtershauser. (2003) A Possible Primordial Peptide Cycle. Science 301: 938–940. Hudder, A., L. Nathanson, and M. P. Deutscher. (2003) Organization of Mammalian Cytoplasm. Mol Cell Biol 23: 9,318—93,26. Hulen, C., and J. Legault-Demare. (1975) In Vitro Synthesis of Large Peptide Molecules Using Glucosylated Single-Stranded Bacteriophage T4d DNA Template. Nucleic Acids Res 2: 2,037—2,048. Humbard, M. A., H. V. Miranda, J. M. Lim, D. J. Krause, J. R. Pritz, G. Zhou, S. Chen, L. Wells, and J. A. Maupin-Furlow. (2010) Ubiquitin-Like Small Archaeal Modifier Proteins (Samps) in Haloferax Volcanii. Nature 463: 54–60. Hurst, L. D. (2002) The Ka/Ks Ratio: Diagnosing the Form of Sequence Evolution. Trends Genet 18: 486. Hurst, L. D., and N. G. Smith. (1999) Do Essential Genes Evolve Slowly? Curr Biol 9: 747–750. Hussain, T., V. Kamarthapu, S. P. Kruparani, M. V. Deshmukh, and R. Sankaranarayanan. (2010) Mechanistic Insights into Cognate Substrate Discrimination During Proofreading in Translation. Proc Natl Acad Sci USA 107: 22,117—22,121. Huxley, J. (2010) Evolution: The Modern Synthesis: The Definitive Edition. Cambridge: MIT Press. Huxley, T. H. (1860) Darwin on the Origin of Species. Westminster Review: 541–570. Irimia, M., D. Penny, and S. W. Roy. (2007) Coevolution of Genomic Intron Number and Splice Sites. Trends Genet 23: 321–325. Irimia, M., S. W. Roy, D. E. Neafsey, J. F. Abril, J. Garcia-Fernandez, and E. V. Koonin. (2009) Complex Selection on 5’ Splice Sites in Intron-Rich Organisms. Genome Res 19: 2,021—2,027. Iwabe, N., K. Kuma, M. Hasegawa, S. Osawa, and T. Miyata. (1989) Evolutionary Relationship of Archaebacteria, Eubacteria, and Eukaryotes Inferred from Phylogenetic Trees of Duplicated Genes. Proc Natl Acad Sci USA 86: 9,355—9,359. Iyer, L. M., A. M. Burroughs, and L. Aravind. (2006) The Prokaryotic Antecedents of the Ubiquitin-Signaling System and the Early Evolution of Ubiquitin-Like Beta-Grasp Domains. Genome Biol 7: R60. Iyer, L. M., E. V. Koonin, and L. Aravind. (2003) Evolutionary Connection Between the Catalytic Subunits of DNA-Dependent RNA Polymerases and Eukaryotic RNA-Dependent RNA Polymerases and the Origin of RNA Polymerases. BMC Struct Biol 3: 1. Iyer, L. M., E. V. Koonin, and L. Aravind. (2004a) Evolution of Bacterial RNA Polymerase: Implications for Large-Scale Bacterial Phylogeny, Domain Accretion, and Horizontal Gene Transfer. Gene 335: 73–88. Iyer, L. M., E. V. Koonin, D. D. Leipe, and L. Aravind. (2005) Origin and Evolution of the Archaeo-Eukaryotic Primase Superfamily and Related Palm-Domain Proteins: Structural Insights and New Members. Nucleic Acids Res 33: 3,875—3,896. Iyer, L. M., K. S. Makarova, E. V. Koonin, and L. Aravind. (2004b) Comparative Genomics of the Ftsk-Hera Superfamily of Pumping Atpases: Implications for the Origins of Chromosome Segregation, Cell Division and Viral Capsid Packaging. Nucleic Acids Res 32: 5,260—5,279. Jacob, F. (1977) Evolution and Tinkering. Science 196: 1,161—1,166. Jacob, F. (1993). The Logic of Life. Princeton: Princeton University Press. Jacob, F., and J. Monod. (1961) Genetic Regulatory Mechanisms in the Synthesis of Proteins. J Mol Biol 3: 318–356. Jain, R., M. C. Rivera, and J. A. Lake. (1999) Horizontal Gene Transfer Among Genomes: The Complexity Hypothesis. Proc Natl Acad Sci USA 96: 3,801—3,806. Jeffares, D. C., T. Mourier, and D. Penny. (2006) The Biology of Intron Gain and Loss. Trends Genet 22: 16–22. Jensen, L. J., P. Julien, M. Kuhn, C. von Mering, J. Muller, T. Doerks, and P. Bork. (2008) Eggnog: Automated Construction and Annotation of Orthologous Groups of Genes. Nucleic Acids Res 36: D250—254. Johansson, M., M. Lovmar, and M. Ehrenberg. (2008) Rate and Accuracy of Bacterial Protein Synthesis Revisited. Curr Opin Microbiol 11: 141–147. Johnson, L. J., and P. J. Tricker. (2010) Epigenomic Plasticity Within Populations: Its Evolutionary Significance and Potential. Heredity 105: 113–121. Johnson, N. (2009) Simply Complexity: A Clear Guide to Complexity Theory. New York: Oneworld Publications. Johnston, W. K., P. J. Unrau, M. S. Lawrence, M. E. Glasner, and D. P. Bartel. (2001) RNA-Catalyzed Rna Polymerization: Accurate and General RNA-Templated Primer Extension. Science 292: 1,319—1,325. Jordan, I. K., K. S. Makarova, J. L. Spouge, Y. I. Wolf, and E. V. Koonin. (2001) Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes. Genome Res 11: 555–565. Jordan, I. K., L. Marino-Ramirez, Y. I. Wolf, and E. V. Koonin. (2004) Conservation and Coevolution in the Scale-Free Human Gene Coexpression Network. Mol Biol Evol 21: 2,058—2,070. Jordan, I. K., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. (2002) Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria. Genome Res 12: 962–968. Juhas, M., J. R. van der Meer, M. Gaillard, R. M. Harding, D. W. Hood, and D. W. Crook. (2009) Genomic Islands: Tools of Bacterial Horizontal Gene Transfer and Evolution. FEMS Microbiol Rev 33: 376–393. Kaneko, K. (2007) Evolution of Robustness to Noise and Mutation in Gene Expression Dynamics. PLoS One 2: e434. Karev, G. P., Y. I. Wolf, A. Y. Rzhetsky, F. S. Berezovskaya, and E. V. Koonin. (2002) Birth and Death of Protein Domains: A Simple Model of Evolution Explains Power Law Behavior. BMC Evol Biol 2: 18. Karginov, F. V., and G. J. Hannon. (2010) The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea. Mol Cell 37: 7—19. Kasting, J. F., and S. Ono. (2006) Palaeoclimates: The First Two Billion Years. Philos Trans R Soc Lond B Biol Sci 361: 917–929. Kauffman, S. (1996) At Home in the Universe: The Search for the Laws of Self-Organization and Complexity. Oxford: Oxford University Press. Keating, K. S., N. Toor, P. S. Perlman, and A. M. Pyle. (2010) A Structural Analysis of the Group II Intron Active Site and Implications for the Spliceosome. RNA 16: 1–9. Keeling, P. J. (2007) Genomics. Deep Questions in the Tre of Life. Science 317: 1,875—1,876. Keeling, P. J., G. Burger, D. G. Durnford, B. F. Lang, R. W. Lee, R. E. Pearlman, A. J. Roger, and M. W. Gray. (2005) The Tree of Eukaryotes. Trends Ecol Evol 20: 670–676. Keeling, P. J., and J. D. Palmer. (2008) Horizontal Gene Transfer in Eukaryotic Evolution. Nat Rev Genet 9: 605–618. Keiler, K. C. (2008) Biology of Trans-Translation. Annu Rev Microbiol 62: 133–151. Kelley, D. S., J. A. Karson, G. L. Fruh-Green, D. R. Yoerger, T. M. Shank, D. A. Butterfield, J. M. Hayes, M. O. Schrenk, E. J. Olson, G. Proskurowski, M. Jakuba, A. Bradley, B. Larson, K. Ludwig, D. Glickson, K. Buckman, A. S. Bradley, W. J. Brazelton, K. Roe, M. J. Elend, A. Delacour, S. M. Bernasconi, M. D. Lilley, J. A. Baross, R. E. Summons, and S. P. Sylva. (2005) A Serpentinite-Hosted Ecosystem: The Lost City Hydrothermal Field. Science 307: 1,428—1,434. Kelly, S., B. Wickstead, and K. Gull. (2010) Archaeal Phylogenomics Provides Evidence in Support of a Methanogenic Origin of the Archaea and a Thaumarchaeal Origin for the Eukaryotes. Proc Biol Sci 278: 1009–1018. Khesin, R. B. (1984) Inconstancy of the Genome. Moscow: Nauka. Kim, V. N., J. Han, and M. C. Siomi. (2009) Biogenesis of Small RNAs in Animals. Nat Rev Mol Cell Biol 10: 126–139. Kimura, M. (1983) The Neutral Theory of Molecular Evolution. Cambridge: Cambridge University Press. Kimura, M. (1991) Recent Development of the Neutral Theory Viewed from the Wrightian Tradition of Theoretical Population Genetics. Proc Natl Acad Sci USA 88: 5,969—5,973. Kipling, R. (2009) Just So Stories: For Little Children. Oxford: Oxford University Press. Kirschner, M., and J. Gerhart. (1998) Evolvability. Proc Natl Acad Sci USA 95: 8,420—8,427. Knight, R. D., and L. F. Landweber. (2000) The Early Evolution of the Genetic Code. Cell 101: 569–572. Knoll, A. H., E. J. Javaux, D. Hewitt, and P. Cohen. (2006) Eukaryotic Organisms in Proterozoic Oceans. Philos Trans R Soc Lond B Biol Sci 361: 1,023—1,038. Kobayashi, I. (1998) Selfishness and Death: Raison D’etre of Restriction, Recombination, and Mitochondria. Trends Genet 14: 368–374. Kobayashi, I. (2001) Behavior of Restriction-Modification Systems As Selfish Mobile Elements and Their Impact on Genome Evolution. Nucleic Acids Res 29: 3,742—3,756. Kogenaru, M., M. G. de Vos, and S. J. Tans. (2009) Revealing Evolutionary Pathways by Fitness Landscape Reconstruction. Crit Rev Biochem Mol Biol 44: 169–174. Kondrashov, F. A., I. B. Rogozin, Y. I. Wolf, and E. V. Koonin. (2002) Selection in the Evolution of Gene Duplications. Genome Biol 3: RESEARCH0008. Koonin, E. V. (1991) Genome Replication/Expression Strategies of Positive-Strand RNA Viruses: A Simple Version of a Combinatorial Classification and Predic tion of New Strategies. Virus Genes 5: 273–281. Koonin, E. V. (2003) Comparative Genomics, Minimal Gene-Sets and the Last Universal Common Ancestor. Nature Rev Microbiol 1: 127–136. Koonin, E. V. (2004) A Non-Adaptationist Perspective on Evolution of Genomic Complexity or the Continued Dethroning of Man. Cell Cycle 3: 280–285. Koonin, E. V. (2005) Orthologs, Paralogs and Evolutionary Genomics. Annu Rev Genet 39: 309–338. Koonin, E. V. (2006) The Origin of Introns and Their Role in Eukaryogenesis: A Compromise Solution to the Introns-Early Versus Introns-Late Debate? Biol Direct 1: 22. Koonin, E. V. (2007a) The Biological Big Bang Model for the Major Transitions in Evolution. Biol Direct 2: 21. Koonin, E. V. (2007b) The Cosmological Model of Eternal Inflation and the Transition from Chance to Biological Evolution in the History of Life. Biol Direct 2: 15. Koonin, E. V. (2007c) An RNA-Making Reactor for the Origin of Life. Proc Natl Acad Sci USA 104: 9,105—9,106. Koonin, E. V. (2009a) Evolution of Genome Architecture. Int J Biochem Cell Biol 41: 298–306. Koonin, E. V. (2009b) Intron-Dominated Genomes of Early Ancestors of Eukaryotes. J Hered 100: 618–623. Koonin, E. V. (2009c) On the Origin of Cells and Viruses: Primordial Virus World Scenario. Ann N Y Acad Sci 1,178: 47–64. Koonin, E. V. (2010a) The Origin and Early Evolution of Eukaryotes in the Light of Phylogenomics. Genome Biol 11: 209. Koonin, E. V. (2010b) Preview. The Incredible Expanding Ancestor of Eukaryotes. Cell 140: 606–608. Koonin, E. V. (2010c) Taming of the Shrewd: Novel Eukaryotic Genes from RNA Viruses. BMC Biol 8: 2. Koonin, E. V. (2010d) The Two Empires and the Three Domains of Life in the Postgenomic Age. Nature Education 3: 27. Koonin, E. V., and L. Aravind. (2002) Origin and Evolution of Eukaryotic Apoptosis: The Bacterial Connection. Cell Death Differ 9: 394–404. Koonin, E. V., L. Aravind, and A. S. Kondrashov. (2000a) The Impact of Comparative Genomics on Our Understanding of Evolution. Cell 101: 573–576. Koonin, E. V., and V. V. Dolja. (1993) Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences. Crit Rev Biochem Mol Biol 28: 375–430. Koonin, E. V., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, D. M. Krylov, K. S. Makarova, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, I. B. Rogozin, S. Smirnov, A. V. Sorokin, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. (2004) A Comprehensive Evolutionary Classification of Proteins Encoded in Complete Eukaryotic Genomes. Genome Biol 5: R7. Koonin, E. V., A. E. Gorbalenya, and K. M. Chumakov. (1989) Tentative Identification of RNA-Dependent RNA Polymerases of dsRNA Viruses and Their Relationship to Positive Strand RNA Viral Polymerases. FEBS Lett 252: 42–46. Koonin, E. V., and K. S. Makarova. (2009) CRISPR-Cas: An Adaptive Immunity System in Prokaryotes. F1000 Biol Rep 1: 95. Koonin, E. V., K. S. Makarova, and L. Aravind. (2001a) Horizontal Gene Transfer in Prokaryotes: Quantification and Classification. Annu Rev Microbiol 55: 709–742. Koonin, E. V., and W. Martin. (2005) On the Origin of Genomes and Cells within Inorganic Compartments. Trends Genet 21: 647–654. Koonin, E. V., and A. R. Mushegian. (1996) Complete Genome Sequences of Cellular Life Forms: Glimpses of Theoretical Evolutionary Genomics. Curr Opin Genet Dev 6: 757–762. Koonin, E. V., A. R. Mushegian, and K. E. Rudd. (1996) Sequencing and Analysis of Bacterial Genomes. Curr Biol 6: 404–416. Koonin, E. V., and A. S. Novozhilov. (2009) Origin and Evolution of the Genetic Code: The Universal Enigma. IUBMB Life 61: 99—111. Koonin, E. V., T. G. Senkevich, and V. V. Dolja. (2006) The Ancient Virus World and Evolution of Cells. Biol Direct 1: 29. Koonin, E. V., and Y. I. Wolf. (2006) Evolutionary Systems Biology: Links Between Gene Evolution and Function. Curr Opin Biotechnol 17: 481–487. Koonin, E. V., and Y. I. Wolf. (2008a). Evolutionary Systems Biology. Evolutionary Genomics and Proteomics. Ed. by M. Pagel and A. Pomiankowski. Sunder-land, MA: Sinauer Associates, Inc.: 11–25. Koonin, E. V., and Y. I. Wolf. (2008b) Genomics of Bacteria and Archaea: The Emerging Dynamic View of the Prokaryotic World. Nucleic Acids Res 36: 6,688—6,719. Koonin, E. V., and Y. I. Wolf. (2009a) The Fundamental Units, Processes and Patterns of Evolution, and the Tree of Life Conundrum. Biol Direct 4: 33. Koonin, E. V., and Y. I. Wolf. (2009b) Is Evolution Darwinian or/and Lamarckian? Biol Direct 4: 42. Koonin, E. V., and Y. I. Wolf. (2010a) The Common Ancestry of Life. Biol Direct 5: 64. Koonin, E. V., and Y. I. Wolf. (2010b) Constraints and Plasticity in Genome and Molecular-Phenome Evolution. Nat Rev Genet 11: 487–498. Koonin, E. V., Y. I. Wolf, and L. Aravind. (2000b) Protein Fold Recognition Using Sequence Profiles and Its Application in Structural Genomics. Adv Protein Chem 54: 245–275. Koonin, E. V., Y. I. Wolf, and L. Aravind. (2001b) Prediction of the Archaeal Exosome and Its Connections with the Proteasome and the Translation and Transcription Machineries by a Comparative-Genomic Approach. Genome Res 11: 240–252. Koonin, E. V., Y. I. Wolf, and G. P. Karev. (2002) The Structure of the Protein Universe and Genome Evolution. Nature 420: 218–223. Koonin, E. V., Y. I. Wolf, K. Nagasaki, and V. V. Dolja. (2008) The Big Bang of Picorna-Like Virus Evolution Antedates the Radiation of Eukaryotic Supergroups. Nat Rev Microbiol 6: 925–939. Koonin, E. V., and N. Yutin. (2010) Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses. Intervirology 53: 284–292. Kristensen, D. M., A. R. Mushegian, V. V. Dolja, and E. V. Koonin. (2010) New Dimensions of the Virus World Discovered Through Metagenomics. Trends Microbiol 18: 11–19. Krylov, D. M., Y. I. Wolf, I. B. Rogozin, and E. V. Koonin. (2003) Gene Loss, Protein Sequence Divergence, Gene Dispensability, Expression Level, and Interactivity Are Correlated in Eukaryotic Evolution. Genome Res 13: 2,229—2,235. Kuhn, T. S. (1962) The Structure of Scientific Revolutions. Chicago: University of Chicago Press. Kun, A., M. Santos, and E. Szathmary. (2005) Real Ribozymes Suggest a Relaxed Error Threshold. Nat Genet 37: 1,008—1,011. Kunin, V., L. Goldovsky, N. Darzentas, and C. A. Ouzounis. (2005) The Net of Life: Reconstructing the Microbial Phylogenetic Network. Genome Res 15: 954–959. Kunin, V., and C. A. Ouzounis. (2003) The Balance of Driving Forces During Genome Evolution in Prokaryotes. Genome Res 13: 1,589—1,594. Kurland, C. G. (2005) What Tangled Web: Barriers to Rampant Horizontal Gene Transfer. Bioessays 27: 7 Date: 2016-05-15; view: 488; Íàðóøåíèå àâòîðñêèõ ïðàâ |