Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity—heat agitation and the cause-and-effect determinism of nature’s orderliness—cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical.
References
[1]
Rizzotti, M. Defining Life: The Central Problem in Theoretical Biology; University of Padova Press: Padova, Italy, 1996; p. 208.
[2]
Joyce, G.F. Origins of Life: The Central Concepts See Forward; Jones and Bartlett: Boston, MA, USA, 1994.
[3]
Trevors, J.T.; Psenner, R. From self-assembly of life to present-day bacteria: A possible role for nanocells. FEMS Microbiol. Rev.？2001, 25, 573–582, doi:10.1111/j.1574-6976.2001.tb00592.x.
[4]
Monnard, P.; Deamer, D. Membrane self-assembly processes: Steps toward the first cellular life. Anat. Rec.？2002, 268, 196–207, doi:10.1002/ar.10154.
[5]
Deamer, D.; Dworkin, J.P.; Sandford, S.A.; Bernstein, M.P.; Allamandola, L.J. The first cell membranes. Astrobiology？2002, 2, 371–381, doi:10.1089/153110702762470482.
Segre, D.; Ben-Eli, D.; Deamer, D.W.; Lancet, D. The lipid world. Orig. Life Evol. Biosph.？2001, 31, 119–145, doi:10.1023/A:1006746807104.
[8]
Fischer, A.; Oberholzer, T.; Luisi, P.L. Giant vesicles as models to study the interactions between membranes and proteins. Biochim. Biophys. Acta？2000, 1467, 177–188, doi:10.1016/S0005-2736(00)00217-0.
[9]
Luisi, P.L.; Walde, P.; Oberholzer, T. Lipid vesicles as possible intermediates in the origin of life. Curr. Opin. Colloid Interface Sci.？1999, 3, 33–39.
[10]
Deamer, D.W. The first living systems: A bioenergetic perspective. Microbiol. Mol. Biol. Rev.？1997, 61, 239–261.
[11]
Oberholzer, T.; Wick, R.; Luisi, P.L.; Biebricher, C.K. Enzymatic RNA replication in self-reproducing vesicles: An approach to a minimal cell. Biochem. Biophys. Res. Commun.？1995, 207, 250–257, doi:10.1006/bbrc.1995.1180.
[12]
Chakrabarti, A.C.; Deamer, D.W. Permeation of membranes by the neutral form of amino acids and peptides: Relevance to the origin of peptide translocation. J. Mol. Evol.？1994, 39, 1–5.
[13]
Chakrabarti, A.C.; Breaker, R.R.; Joyce, G.F.; Deamer, D.W. Production of RNA by a polymerase protein encapsulated within phospholipid vesicles. J. Mol. Evol.？1994, 39, 555–559, doi:10.1007/BF00160400.
[14]
Wick, R.; Luisi, P.L. Enzyme-containing liposomes can endogenously produce membrane-constituting lipids. Chem. Biol.？1996, 3, 277–285, doi:10.1016/S1074-5521(96)90107-6.
[15]
Luisi, P.L. Autopoiesis: A review and a reappraisal. Naturwissenschaften？2003, 90, 49–59.
[16]
Dyson, F.J. A model for the origin of life. J. Mol. Evol.？1982, 18, 344–350, doi:10.1007/BF01733901.
[17]
Dyson, F.J. Origins of Life, 2nd ed. ed.; Cambridge University Press: Cambridge, UK, 1998.
[18]
Guimaraes, R.C. Linguistics of biomolecules and the protein-first hypothesis for the origins of cells. J. Biol. Phys.？1994, 20, 193–199, doi:10.1007/BF00700436.
[19]
De Duve, C. A research proposal on the origin of life. Orig. Life Evol. Biosph.？2003, 33, 559–574, doi:10.1023/A:1025760311436.
[20]
Lahav, N. The synthesis of primitive ‘living’ forms: Definitions, goals, strategies and evolution synthesizers. Orig. Life Evol. Biosph.？1985, 16, 129–149, doi:10.1007/BF01809467.
[21]
Shapiro, R. A replicator was not involved in the origin of life. IUBMB Life？2000, 49, 173–176.
[22]
Pattee, H.H. Dynamic and linguistic modes of complex systems. Int. J. Gen. Syst.？1977, 3, 259–266, doi:10.1080/03081077708934771.
[23]
Rocha, L.M. Syntactic autonomy: Or why there is no autonomy without symbols and how self-organizing systems might evolve them. Ann. N. Y. Acad. Sci.？2000, 207–223.
[24]
Rocha, L.M. The physics and evolution of symbols and codes: Reflections on the work of howard pattee. Biosystems？2001, 60, 1–4, doi:10.1016/S0303-2647(01)00103-4.
[25]
Rocha, L.M. Evolution with material symbol systems. Biosystems？2001, 60, 95–121, doi:10.1016/S0303-2647(01)00110-1.
[26]
Rocha, L.M.; Hordijk, W. Material representations: From the genetic code to the evolution of cellular automata. Artif. Life？2005, 11, 189–214, doi:10.1162/1064546053278964.
[27]
Rocha, L.M.; Joslyn, C. Simulations of Embodied Evolving Semiosis: Emergent Semantics in Artificial Environments. In Proceedings of the 1998 Conference on Virtual Worlds and Simulation, San Diego, CA, USA, 11–14 January 1998; Landauer, C., Bellman, K.L., Eds.; The Society for Computer Simulation International: San Diego, CA, USA; pp. 233–238.
[28]
Pereto, J. Controversies on the origin of life. Int. Microbiol.？2005, 8, 23–31.
[29]
Ruiz-Mirazo, K.; Pereto, J.; Moreno, A. A universal definition of life: Autonomy and open-ended evolution. Orig. Life Evol. Biosph.？2004, 34, 323–346, doi:10.1023/B:ORIG.0000016440.53346.dc.
[30]
Ruiz-Mirazo, K.; Umerez, J.; Moreno, A. Enabling conditions for ‘open-ended evolution’. Biol. Philos.？2008, 23, 67–85.
[31]
Smith, J.M. The 1999 crafoord prize lectures. The idea of information in biology. Q. Rev. Biol.？1999, 74, 395–400.
[32]
Smith, J.M. The concept of information in biology. Philos. Sci.？2000, 67, 177–194. (entire issue is an excellent discussion).
[33]
Szathmary, E. From RNA to language. Curr. Biol.？1996, 6.
[34]
Szathmary, E. Biological information, kin selection, and evolutionary transitions. Theor. Popul. Biol.？2001, 59, 11–14, doi:10.1006/tpbi.2000.1503.
[35]
Francois, J. The Logic of Living System: A History of Heredity; Allen Lane: London, UK, 1974.
[36]
Alberts, B.; Bray, D.; Lewis, J.; Raff, M.; Roberts, K.; Watson, J.D. Molecular Biology of the Cell; Garland Science: New York, NY, USA, 2002.
Wolpert, L.; Smith, J.; Jessell, T.; Lawrence, P. Principles of Development; Oxford University Press: Oxford, UK, 2002.
[39]
Stegmann, U.E. Genetic information as instructional content. Phil. Sci.？2005, 72, 425–443, doi:10.1086/498472.
[40]
Barbieri, M. Biology with information and meaning. Hist. Philos. Life Sci.？2004, 25, 243–254, doi:10.1080/03919710312331273045.
[41]
Abel, D.L. Is Life Reducible to Complexity? In Fundamentals of Life; Palyi, G., Zucchi, C., Caglioti, L., Eds.; Elsevier: Paris, France, 2002; pp. 57–72.
[42]
Abel, D.L.; Trevors, J.T. Three subsets of sequence complexity and their relevance to biopolymeric information. Theor. Biol. Med. Model. 2005, 2. Available online: http://www.tbiomed.com/content/2/1/29 (accessed on 26 December 2011).
[43]
Chen, S.; Zhang, Y.E.; Long, M. New genes in drosophila quickly become essential. Science？2010, 330, 1682–1685.
[44]
Freiberg, C.; Wieland, B.; Spaltmann, F.; Ehlert, K.; Brotz, H.; Labischinski, H. Identification of novel essential Escherichia coli genes conserved among pathogenic bacteria. J. Mol. Microbiol. Biotechnol.？2001, 3, 483–489.
[45]
Razin, S.; Yogev, D.; Naot, Y. Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev.？1998, 62, 1094–1156.
[46]
Pattee, H.H. Clues from Molecular Symbol Systems. In Dahlem Workshop Reports: Life Sciences Research Report 19: Signed and Spoken Language: Biological Constraints on Linguistic Form; Bellugi, U., Studdert-Kennedy, M., Eds.; Verlag Chemie GmbH: Dahlem Konferenzen, Weinheim, Germany, 1980; pp. 261–274.
[47]
Gánti, T. The Principles of Life; Oxford University Press: Oxford, UK, 2003; p. 200.
[48]
Jablonka, E.; Lamb, M. Epigenetic Inheritance and Evolution; Oxford University Press: Oxford, UK, 1995.
[49]
Jablonka, E.; Szathmary, E. The evolution of information storage and heredity. Trends Ecol. Evol.？1995, 10, 206–211, doi:10.1016/S0169-5347(00)89060-6.
[50]
Palyi, G.; Zucchi, C.; Caglioti, L. Proceedings of the Workshop on Life: A Satellite Meeting before the Millennial World Meeting of University Professors. Modena, Italy, 3–8 September 2000.
[51]
Palyi, G.; Zucchi, C.; Caglioti, L. Fundamentals of Life; Elsevier: Paris, France, 2002.
[52]
Yockey, H.P. Origin of life on earth and shannon’s theory of communication. Comput. Chem.？2000, 24, 105–123.
[53]
Yockey, H.P. Information Theory, Evolution, and the Origin of Life. In Fundamentals of Life; Palyi, G., Zucchi, C., Caglioti, L., Eds.; Elsevier: Paris, France, 2002; pp. 335–348.
[54]
Yockey, H.P. On the Role of Information Theory in Mathematical Biology, Radiation on Biology and Medicine, Geneva Presentation Volume; Addison Wesley Publication Company: Boston, MA, USA, 1958.
[55]
Yockey, H.P. Information Theory with Applications to Biogenesis and Evolution. In Biogenesis Evolution Homeostasis; Locker, A., Ed.; Springer-Verlag: New York, NY, USA, 1973. Heidelberg and Berlin, Germany.
[56]
Yockey, H.P. An application of information theory to the central dogma and the sequence hypothesis. J. Theor. Biol.？1974, 46, 369–406, doi:10.1016/0022-5193(74)90005-8.
[57]
Yockey, H.P. A calculation of the probability of spontaneous biogenesis by information theory. J. Theor. Biol.？1977, 67, 377–398, doi:10.1016/0022-5193(77)90044-3.
[58]
Yockey, H.P. On the information content of cytochrome c. J. Theor. Biol.？1977, 67, 345–398, doi:10.1016/0022-5193(77)90043-1.
[59]
Yockey, H.P. Information Theory and Molecular Biology; Cambridge University Press: Cambridge, UK, 1992; p. 408.
[60]
Mayr, E. The Place of Biology in the Sciences and Its Conceptional Structure. In The Growth of Biological Thought: Diversity, Evolution, and Inheritance; Mayr, E., Ed.; Harvard University Press: Cambridge, MA, USA, 1982; pp. 21–82.
[61]
Mayr, E. Introduction, pp. 1-7; Is Biology an Autonomous Science? pp. 8-23. In Toward a New Philosophy of Biology, Part 1; Mayr, E., Ed.; Harvard University Press: Cambridge, MA, USA, 1988.
[62]
Monod, J. Chance and Necessity; Knopf: New York, NY, USA, 1972.
[63]
Bohr, N. Light and life. Nature？1933, 131, 421–423, doi:10.1038/131421a0.
[64]
Küppers, B.-O. Information and the Origin of Life; MIT Press: Cambridge, MA, USA, 1990; p. 215.
[65]
Bedau, M.A. An aristotelian account of minimal chemical life. Astrobiology？2010, 10, 1011–1020, doi:10.1089/ast.2010.0522.
[66]
Barbieri, M. The Organic Codes: An Introduction to Semantic Biology; Cambridge University Press: Cambridge, UK, 2003.
[67]
Barbieri, M. The definitions of information and meaning: Two possible boundaries between physics and biology (Translated from Italian). Rev. Biol. Biol. Forum？2004, 97, 91–110.
[68]
Barbieri, M. Life is ‘artifact-making’. J. Biosemiotics？2005, 1, 113–142.
[69]
Barbieri, M. Is the Cell a Semiotic System? In Introduction to Biosemiotics: The New Biological Synthesis; Barbieri, M., Ed.; Springer-Verlag New York, Inc.: Secaucus, NJ, USA, 2006.
[70]
Barbieri, M. Introduction to Biosemiotics: The New Biological Synthesis; Springer-Verlag: Dordrecht, The Netherlands, 2006.
[71]
Barbieri, M. Semantic biology and the mind-body problem: The theory of the conventional mind. Biological Theory？2006, 1, 352–356, doi:10.1162/biot.2006.1.4.352.
[72]
Barbieri, M. Has Biosemiotics Come of Age? In Introduction to Biosemiotics: The New Biological Synthesis; Barbieri, M., Ed.; Springer: Dorcrecht, The Netherlands, 2007; pp. 101–114.
[73]
Barbieri, M. Is the Cell a Semiotics System? In Introduction to Biosemiotics: The New Biological Synthesis; Barbieri, M., Ed.; Springer: Dordrecht, The Netherlands, 2007; pp. 179–208.
[74]
Barbieri, M. Biosemiotic Research Trends; Nova Science Publishers, Inc.: New York, NY, USA, 2007.
[75]
Barbieri, M. The Codes of Life: The Rules of Macroevolution (Biosemiotics); Springer: Dordrecht, The Netherlands, 2007.
[76]
Barbieri, M. Biosemiotics: A new understanding of life. Naturwissenschaften？2008, 95, 577–599, doi:10.1007/s00114-008-0368-x.
[77]
Barbieri, M. Cosmos and history: Life is semiosis; the biosemiotic view of nature. J. Nat. Soc. Philos.？2008, 4, 29–51.
[78]
Johnson, D.E. Chapter 10: What Might be a Protocell’s Minimal “Genome”? In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biol. Res. Div.: New York, NY, USA, 2011; pp. 287–303.
[79]
Abel, D.L. What is Protobiocybernetics? In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biolog. Res. Div.: New York, NY, USA, 2011; pp. 1–18. Chapter 1.
[80]
Abel, D.L. The Three Fundamental Categories of Reality. In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biolog. Res. Div.: New York, NY, USA, 2011; pp. 19–54. Chapter 2.
[81]
Abel, D.L. The Cybernetic Cut and Configurable Switch (Cs) Bridge. In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biol. Res. Div.: New York, NY, USA, 2011; pp. 55–74. Chapter 3.
[82]
Abel, D.L. What Utility does Order, Pattern or Complexity Prescribe? In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biol. Res. Div.: New York, NY, USA, 2011; pp. 75–116. Chapter 4.
[83]
Abel, D.L. Linear Digital Material Symbol Systems (Mss). In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biol. Res. Div.: New York, NY, USA, 2011; pp. 135–160. Chapter 6.
[84]
Abel, D.L. The Formalism > Physicality (F > P) Principle. In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: New York, NY, USA, 2011; pp. 325–356. Chapter 12.
[85]
Abel, D.L. The biosemiosis of prescriptive information. Semiotica？2009, 2009, 1–19, doi:10.1515/semi.2009.026.
[86]
Abel, D.L. Prescriptive Information (PI). Available online: http://www.scitopics.com/Prescriptive_Information_PI.html (accessed on 26 December 2011).
[87]
Abel, D.L. The First Gene: The Birth of Programming, Messaging and Formal Control; LongView Press-Academic: Biolog. Res. Div.: New York, NY, USA, 2011; p. 389.
[88]
Abel, D.L. Moving ‘Far from Equilibrium’ in a Prebitoic Environment: The Role of Maxwell’s Demon in Life Origin. In Genesis—In the Beginning: Precursors of Life, Chemical Models and Early Biological Evolution; Seckbach, J., Gordon, R., Eds.; Springer: Dordrecht, The Netherlands, 2011.
Abel, D.L. To What Degree can We Reduce “Life” Without “Loss of Life”? In Workshop on Life: A Satellite Meeting before the Millenial World Meeting of University Professor; Palyi, G., Caglioti, L., Zucchi, C., Eds.; University of Modena: Modena, Italy, 2000.
[91]
Abel, D.L. Life Origin: The Role of Complexity at the Edge of Chaos. In Washington Science 2006; Chandler, J., Kay, P., Eds.; Headquarters of the National Science Foundation: Arlington, VA, USA, 2006.
[92]
Abel, D.L. Complexity, self-organization, and emergence at the edge of chaos in life-origin models. J. Wash. Acad. Sci.？2007, 93, 1–20.
[93]
Abel, D.L. The Capabilities of Chaos and Complexity. In Society for Chaos Theory: Society for Complexity in Psychology and the Life Sciences; International Conference at Virginia Commonwealth University: Richmond, VA, USA, 2008.
[94]
Henry, C.; Overbeek, R.; Stevens, R.L. Building the blueprint of life. Biotechnol. J.？2010, 5, 695–704, doi:10.1002/biot.201000076.
[95]
Dorman, C.J. Regulation of transcription by DNA supercoiling in Mycoplasma genitalium: Global control in the smallest known self-replicating genome. Mol. Microbiol.？2011, 81, 302–304, doi:10.1111/j.1365-2958.2011.07718.x.
[96]
Butt, A.M.; Tahir, S.; Nasrullah, I.; Idrees, M.; Lu, J.; Tong, Y. Mycoplasma genitalium: A comparative genomics study of metabolic pathways for the identification of drug and vaccine targets. Infect. Genet. Evol.？2011, 12, 53–62.
[97]
Pennisi, E. Genomics. Synthetic genome brings new life to bacterium. Science？2010, 328, 958–959, doi:10.1126/science.328.5981.958.
[98]
McCutcheon, J.P. The bacterial essence of tiny symbiont genomes. Curr. Opin. Microbiol.？2010, 13, 73–78, doi:10.1016/j.mib.2009.12.002.
[99]
Kwok, R. Genomics: DNA’s master craftsmen. Nature？2010, 468, 22–25, doi:10.1038/468022a.
Zhang, W.; Baseman, J.B. Transcriptional regulation of Mg_149, an osmoinducible lipoprotein gene from Mycoplasma genitalium. Mol. Microbiol.？2011, 81, 327–339, doi:10.1111/j.1365-2958.2011.07717.x.
[103]
Zhang, W.; Baseman, J.B. Transcriptional response of Mycoplasma genitalium to osmotic stress. Microbiology？2011, 157, 548–556, doi:10.1099/mic.0.043984-0.
[104]
Abel, D.L.; Trevors, J.T. More than Metaphor: Genomes are Objective Sign Systems. In Biosemiotic Research Trends; Barbieri, M., Ed.; Nova Science Publishers: New York, NY, USA, 2007; pp. 1–15.
[105]
Abel, D.L. What is life? (under Definitions). Available online: http://www.lifeorigin.info (accessed on 26 December 2011).
[106]
Abel, D.L. Constraints vs. controls. Open Cybern. Syst. J. 2010, 4, pp. 14–27. Available online: http://www.benthamscience.com/open/tocsj/articles/V004/14TOCSJ.pdf (accessed on 26 December 2011).
[107]
Abel, D.L.; Trevors, J.T. Self-organization vs. self-ordering events in life-origin models. Phys. Life Rev.？2006, 3, 211–228, doi:10.1016/j.plrev.2006.07.003.
[108]
Johnson, D.E. Programming of Life; Big Mac Publishers: Sylacauga, AL, USA, 2010; p. 127.
[109]
Rocha, L.M. Evidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and Embodiment in Cognitive and Biological Systems; State University of New York: Binghamton, NY, USA, 1997.
[110]
Whitehead, A.N. Symbolism: Its Meaning and Effect; Macmillan: New York, NY, USA, 1927.
[111]
Cassirer, E. The Philosophy of Symbolic Forms, Vol 3: The Phenomena of Knowledge; Yale University Press: New Haven, CT, USA, 1957.
[112]
Harnad, S. The symbol grounding problem. Phys. D？1990, 42, 335–346, doi:10.1016/0167-2789(90)90087-6.
Pattee, H.H.; Kull, K. A biosemiotic conversation: Between physics and semiotics. Sign Sys. Stud.？2009, 37, 311–331.
[115]
Cairns-Smith, A.G. Seven Clues to the Origin of Life; Cambridge University Press: Cambridge, UK, 1990; p. 130. Canto ed.
[116]
Segre, D.; Ben-Eli, D.; Lancet, D. Compositional genomes: Prebiotic information transfer in mutually catalytic noncovalent assemblies. Proc. Natl. Acad. Sci. USA？2000, 97, 4112–4117.
[117]
Segre, D.; Lancet, D. Composing life. EMBO Rep.？2000, 1, 217–222, doi:10.1093/embo-reports/kvd063.
[118]
Segre, D.; Lancet, D.; Kedem, O.; Pilpel, Y. Graded autocatalysis replication domain (gard): Kinetic analysis of self-replication in mutually catalytic sets. Orig. Life Evol. Biosph.？1998, 28, 501–514, doi:10.1023/A:1006583712886.
[119]
Durston, K.K.; Chiu, D.K.Y. Functional Sequence Complexity in Biopolymers. In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: Biol. Res. Div.: New York, NY, USA, 2011; pp. 117–133. Chapter 5.
[120]
Durston, K.K.; Chiu, D.K.; Abel, D.L.; Trevors, J.T. Measuring the functional sequence complexity of proteins. Theor. Biol. Med. Model. 2007, 4, p. 47. Available online: http://www.tbiomed.com/content/4/1/47 (accessed on 26 December 2011).
[121]
Durston, K.K.; Chiu, D.K.Y. A functional entropy model for biological sequences. Dyn. Contin. Discret. Impuls. Syst. Ser. B. 2005. Available online: http://www.newscholars.com/papers/Durston&Chiu%20paper.pdf (accessed on 26 December 2011).
[122]
Turing, A.M. On computable numbers, with an application to the entscheidungs problem. Proc. Roy. Soc. Lond. Math. Soc.？1936, 42, 230–265. correction in , 544-546., doi:10.1112/plms/s2-42.1.230.
[123]
Von Neumann, J. Functional Operators; Princeton University Press: Princeton, NJ, USA, 1950.
[124]
Von Neumann, J. The General and Logical Theory of Automata. In The World of Mathematics Vol 4; Newman, J.R., Ed.; Simon and Schuster: New York, NY, USA, 1956.
[125]
Von Neumann, J.; Aspray, W.; Burks, A.W. Papers of John Von Neumann on Computing and Computer Theory; MIT Press: Cambridge, MA, USA, 1987; p. xviii.
[126]
Von Neumann, J.; Churchland, P.M.; Churchland, P.S. The Computer and the Brain, 2nd ed. ed.; Yale University Press: New Haven, CT, USA, 2000; p. xxviii.
[127]
Wiener, N. Cybernetics; Wiley: New York, NY, USA, 1948.
[128]
Wiener, N. Cybernetics, Its Control and Communication in the Animal and the Machine, 2nd ed. ed.; MIT Press: Cambridge, MA, USA, 1961.
[129]
D’Onofrio, D.J.; An, G. A comparative approach for the investigation of biological information processing: An examination of the structure and function of computer hard drives and DNA. Theor. Biol. Med. Model.？2010, 7.
[130]
Conrad, M. Microscopic-macroscopic interface in biological information processing. Biosystems？1983, 16, 345–363, doi:10.1016/0303-2647(83)90017-5.
[131]
Wang, D. Discrepancy between mRNA and protein abundance: Insight from information retrieval process in computers. Comput. Biol. Chem.？2008, 32, 462–468, doi:10.1016/j.compbiolchem.2008.07.014.
[132]
Ramakrishnan, N.; Bhalla, U.S. Memory switches in chemical reaction space. PLoS Comput. Biol.？2008, 4.
[133]
Benenson, Y.; Adar, R.; Paz-Elizur, T.; Livneh, Z.; Shapiro, E. DNA molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA？2003, 100, 2191–2196.
[134]
Benenson, Y.; Paz-Elizur, T.; Adar, R.; Keinan, E.; Livneh, Z.; Shapiro, E. Programmable and autonomous computing machine made of biomolecules. Nature？2001, 414, 430–434, doi:10.1038/35106533.
[135]
Shannon, C. Part I and II: A mathematical theory of communication. Bell Syst. Tech. J.？1948, XXVII, 379–423.
[136]
Shannon, C. Part III: A mathematical theory of communication. Bell Syst. Tech. J.？1948, XXVII, 623–656.
[137]
Adami, C. Introduction to Artificial Life; Springer/Telos: New York, NY, USA, 1998; p. 374.
[138]
Bruza, P.D.; Song, D.W.; Wong, K.F. Aboutness from a common sense perspective. J. Am. Soc. Inf. Sci.？2000, 51, 1090–1105, doi:10.1002/1097-4571(2000)9999:9999<::AID-ASI1026>3.0.CO;2-Y.
[139]
Hjorland, B. Towards a theory of aboutness, subject, topicallity, theme, domain, field, content . . . and relevance. J. Am. Soc. Inf. Syst. Technol.？2001, 52, 774–778, doi:10.1002/asi.1131.
[140]
Johnson, D.E. Probability’s Nature and Nature’s Probability (a Call to Scientific Integrity); Booksurge Publishing: Charleston, SC, USA, 2010.
[141]
Oyama, S. The Ontogeny of Information: Developmenal Systems and Evolution (Science and Cultural Theory); Duke University Press: Durham, NC, USA, 2000.
[142]
Sarkar, S. Information in genetics and developmental biology: Comments on Maynard Smith. Philos. Sci.？2000, 67, 208–213.
[143]
Sarkar, S. Biological Information: A Skeptical Look at Some Central Dogmas of Molecular Biology. In The Philosophy and History of Molecular Biology: New Perspectives; Sarkar, S., Ed.; Kluwer Academic Publishers: Dordrecht, The Netherlands, 1996; pp. 187–231.
[144]
Boniolo, G. Biology without information. Hist. Philos. Life Sci.？2003, 25, 255–273, doi:10.1080/03919710312331273055.
[145]
Salthe, S.N. Meaning in nature: Placing biosemitotics within pansemiotics. J. Biosemiotics？2005, 1, 287–301.
[146]
Salthe, S.N. What is the Scope of Biosemiotics? Information in Living Systems. In Introduction to Biosemiotics: The New Biological Synthesis; Barbieri, M., Ed.; Springer-Verlag New York, Inc.: Dordrecht, The Netherlands and Secaucus, NJ, USA, 2006.
[147]
Kurakin, A. Self-organization versus watchmaker: Molecular motors and protein translocation. Biosystems？2006, 84, 15–23, doi:10.1016/j.biosystems.2005.09.007.
[148]
Mahner, M.; Bunge, M.A. Foundations of Biophilosophy; Springer Verlag: Berlin, Germany, 1997.
[149]
Kitcher, P. Battling the Undead; How (and How Not) to Resist Genetic Determinism. In Thinking About Evolution: Historical Philosophical and Political Perspectives; Singh, R.S., Krimbas, C.B., Paul, D.B., Beattie, J., Eds.; Cambridge University Press: Cambridge, UK, 2001; pp. 396–414.
Hazen, R.M.; Griffin, P.L.; Carothers, J.M.; Szostak, J.W. Functional information and the emergence of biocomplexity. Proc. Natl. Acad. Sci. USA？2007, 104, 8574–8581, doi:10.1073/pnas.0701744104.
[152]
Sharov, A. Role of utility and inference in the evolution of functional information. Biosemiotics？2009, 2, 101–115, doi:10.1007/s12304-008-9032-2.
[153]
Davis, M. Computability and Unsolvability; McGraw-Hill: New York, NY, USA, 1958.
[154]
Abel, D.L. The capabilities of chaos and complexity. Int. J. Mol. Sci. 2009, 10, pp. 247–291. Available online: http://www.mdpi.com/1422-0067/10/1/247 (accessed on 26 December 2011).
[155]
Trevors, J.T.; Abel, D.L. Chance and necessity do not explain the origin of life. Cell Biol. Int.？2004, 28, 729–739, doi:10.1016/j.cellbi.2004.06.006.
[156]
Abel, D.L. ‘The cybernetic cut’: Progressing from description to prescription in systems theory. Open Cybern. Syst. J. 2008, 2, pp. 234–244. Available online: www.bentham.org/open/tocsj/articles/V002/252TOCSJ.pdf (accessed on 26 December 2011).
[157]
Beiter, T.; Reich, E.; Williams, R.; Simon, P. Antisense transcription: A critical look in both directions. Cell. Mol. Life Sci. (CMLS)？2009, 66, 94–112, doi:10.1007/s00018-008-8381-y.
[158]
Chen, J.; Sun, M.; Kent, W.J.; Huang, X.; Xie, H.; Wang, W.; Zhou, G.; Shi, R.Z.; Rowley, J.D. Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res.？2004, 32, 4812–4820.
Lluch-Senar, M.; Vallmitjana, M.; Querol, E.; Pinol, J. A new promoterless reporter vector reveals antisense transcription in Mycoplasma genitalium. Microbiology？2007, 153, 2743–2752, doi:10.1099/mic.0.2006/007559-0.
[161]
Slonczewski, J.L. Concerns about recently identified widespread antisense transcription in Escherichia coli. mBio？2010, 1.
[162]
Wade, J.T.; Dornenburg, J.E.; DeVita, A.M.; Palumbo, M.J. Reply to “concerns about recently identified widespread antisense transcription in Escherichia coli”. mBio？2010, 1.
[163]
Yelin, R.; Dahary, D.; Sorek, R.; Levanon, E.Y.; Goldstein, O.; Shoshan, A.; Diber, A.; Biton, S.; Tamir, Y.; Khosravi, R.; et al. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol.？2003, 21, 379–386, doi:10.1038/nbt808.
[164]
Dinger, M.E.; Pang, K.C.; Mercer, T.R.; Mattick, J.S. Differentiating protein-coding and noncoding RNA: Challenges and ambiguities. PLoS Comput. Biol.？2008, 4.
[165]
He, Y.; Vogelstein, B.; Velculescu, V.E.; Papadopoulos, N.; Kinzler, K.W. The antisense transcriptomes of human cells. Science？2008, 322, 1855–1857.
[166]
Shintani, S.; O’hUigin, C.; Toyosawa, S.; Michalová, V.; Klein, J. Origin of gene overlap: The case of tcp1 and acat2. Genetics？1999, 152, 743–754.
[167]
Sanna, C.; Li, W.-H.; Zhang, L. Overlapping genes in the human and mouse genomes. BMC Genomics？2008, 9.
[168]
Sabath, N.; Landan, G.; Graur, D. A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS ONE？2008, 3.
[169]
Herzel, H.; Weiss, O.; Trifonov, E.N. Sequence periodicity in complete genomes of archaea suggests positive supercoiling. J. Biomol. Struct. Dyn.？1998, 16, 341–345, doi:10.1080/07391102.1998.10508251.
[170]
Ohyama, T. DNA Conformation and Transcription; Landes Bioscience: Georgetown, TX, and New York, NY, USA, 2005.
[171]
Nurse, P. Life, logic and information. Nature？2008, 454, 424–426, doi:10.1038/454424a.
[172]
De Silva, A.P.; Uchiyama, S. Molecular logic and computing. Nat. Nano？2007, 2, 399–410, doi:10.1038/nnano.2007.188.
[173]
Korzeniewski, B. Cybernetic formulation of the definition of life. J. Theor. Biol.？2001, 209, 275–286, doi:10.1006/jtbi.2001.2262.
[174]
Korzeniewski, B. Confrontation of the cybernetic definition of a living individual with the real world. Acta Biotheor.？2005, 53, 1–28, doi:10.1007/s10441-005-7000-7.
[175]
Abel, D.L. The universal plausibility metric (Upm) & principle (Upp). Theor. Biol. Med. Model. 2009, 6. Available online: http://www.tbiomed.com/content/6/1/27 (accessed on 26 December 2011).
[176]
Abel, D.L. The Universal Plausibility Metric and Principle. In The First Gene: The Birth of Programming, Messaging and Formal Control; Abel, D.L., Ed.; LongView Press-Academic: New York, NY, USA, 2011; pp. 305–324. Chapter 11.
[177]
Dembski, W. The Design Inference: Eliminating Chance Through Small Probabilities; Cambridge University Press: Cambridge, UK, 1998.
[178]
Abel, D.L. The GS (Genetic Selection) Principle. Front. Biosci. 2009, 14, pp. 2959–2969. Available online: http://www.bioscience.org/2009/v14/af/3426/fulltext.htm (accessed on 26 December 2011).
[179]
Abel, D.L. The Genetic Selection (Gs) Principle. Available online: http://www.scitopics.com/The_Genetic_Selection_GS_Principle.html (accessed on 26 December 2011).
[180]
Kaplan, M. Decision Theory as Philosophy; Cambridge University Press: Cambridge, UK, 1996; p. 227.
[181]
Eigen, M.; Gardiner, W.C., Jr.; Schuster, P. Hypercycles and compartments. Compartments assists—But do not replace—Hypercyclic organization of early genetic information. J. Theor. Biol.？1980, 85, 407–411, doi:10.1016/0022-5193(80)90315-X.
[182]
Eigen, M.; Schuster, P. Comments on “growth of a hypercycle” by King (1981). Biosystems？1981, 13.
[183]
Eigen, M.; Schuster, P.; Sigmund, K.; Wolff, R. Elementary step dynamics of catalytic hypercycles. Biosystems？1980, 13, 1–22, doi:10.1016/0303-2647(80)90002-7.
[184]
Smith, J.M. Hypercycles and the origin of life. Nature？1979, 280, 445–446, doi:10.1038/280445a0.
[185]
Ycas, M. Codons and hypercycles. Orig. Life Evol. Biosph.？1999, 29, 95–108, doi:10.1023/A:1006549309688.
[186]
Melendez-Hevia, E.; Montero-Gomez, N.; Montero, F. From prebiotic chemistry to cellular metabolism—The chemical evolution of metabolism before darwinian natural selection. J. Theor. Biol.？2008, 252, 505–519, doi:10.1016/j.jtbi.2007.11.012.
[187]
Munteanu, A.; Sole, R.V. Phenotypic diversity and chaos in a minimal cell model. J. Theor. Biol.？2006, 240, 434–442, doi:10.1016/j.jtbi.2005.10.013.
