Inevitability of the emergence and persistence of genetic parasites caused by thermodynamic instability of parasite-free states

Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are thermodynamically unstable.

[1]  E. Koonin,et al.  Evolutionary Genomics of Defense Systems in Archaea and Bacteria. , 2017, Annual review of microbiology.

[2]  E. Koonin,et al.  Disentangling the effects of selection and loss bias on gene dynamics , 2017, Proceedings of the National Academy of Sciences.

[3]  E. Koonin,et al.  Reconstruction of the evolution of microbial defense systems , 2017, BMC Evolutionary Biology.

[4]  Kira S. Makarova,et al.  Diversity and evolution of class 2 CRISPR–Cas systems , 2017, Nature Reviews Microbiology.

[5]  E. Koonin.  Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence , 2017, Biology Direct.

[6]  J. Mellor,et al.  Is H3K4me3 instructive for transcription activation? , 2017, BioEssays : news and reviews in molecular, cellular and developmental biology.

[7]  G. Hartmann.  Nucleic Acid Immunity , 2016, Advances in Immunology.

[8]  E. Koonin,et al.  Coupling immunity and programmed cell suicide in prokaryotes: Life‐or‐death choices , 2016, BioEssays : news and reviews in molecular, cellular and developmental biology.

[9]  E. Koonin,et al.  Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question. , 2016, Studies in history and philosophy of biological and biomedical sciences.

[10]  E. Koonin.  Viruses and mobile elements as drivers of evolutionary transitions , 2016, Philosophical Transactions of the Royal Society B: Biological Sciences.

[11]  E. Koonin,et al.  Inevitability of Genetic Parasites , 2016, Genome biology and evolution.

[12]  Mike Boots,et al.  Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense , 2015, Current Biology.

[13]  E. Koonin,et al.  Classification of prokaryotic genetic replicators: between selfishness and altruism , 2015, Annals of the New York Academy of Sciences.

[14]  Matthew B. Sullivan,et al.  Rising to the challenge: accelerated pace of discovery transforms marine virology , 2015, Nature Reviews Microbiology.

[15]  E. Koonin,et al.  Evolution of adaptive immunity from transposable elements combined with innate immune systems , 2014, Nature Reviews Genetics.

[16]  Eugene V. Koonin,et al.  Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements , 2014, Microbiology and Molecular Reviews.

[17]  N. Friedman,et al.  Do all creatures possess an acquired immune system of some sort? , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[18]  E. Koonin,et al.  Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision , 2013, G3: Genes, Genomes, Genetics.

[19]  M. Sullivan,et al.  The global virome: not as big as we thought? , 2013, Current opinion in virology.

[20]  Sylvain Moineau,et al.  Revenge of the phages: defeating bacterial defences , 2013, Nature Reviews Microbiology.

[21]  E. Koonin,et al.  A virocentric perspective on the evolution of life , 2013, Current Opinion in Virology.

[22]  Kira S. Makarova,et al.  Comparative genomics of defense systems in archaea and bacteria , 2013, Nucleic acids research.

[23]  D. Mager,et al.  Transposable elements: an abundant and natural source of regulatory sequences for host genes. , 2012, Annual review of genetics.

[24]  Eugene V. Koonin,et al.  Evolution of microbes and viruses: a paradigm shift in evolutionary biology? , 2012, Front. Cell. Inf. Microbio..

[25]  Paulien Hogeweg,et al.  Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life. , 2012, Physics of life reviews.

[26]  E. Koonin,et al.  Systems biology of bacteriophage proteins and new dimensions of the virus world discovered through metagenomics , 2011, Genome Biology.

[27]  E. Koonin.  The Logic of Chance: The Nature and Origin of Biological Evolution , 2011 .

[28]  Paulien Hogeweg,et al.  On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems , 2011, PLoS Comput. Biol..

[29]  Adi Stern,et al.  The phage‐host arms race: Shaping the evolution of microbes , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.

[30]  Adi Stern,et al.  Self-targeting by CRISPR: gene regulation or autoimmunity? , 2010, Trends in genetics : TIG.

[31]  Sylvain Moineau,et al.  Bacteriophage resistance mechanisms , 2010, Nature Reviews Microbiology.

[32]  P. Forterre,et al.  The Great Billion‐year War between Ribosome‐ and Capsid‐encoding Organisms (Cells and Viruses) as the Major Source of Evolutionary Novelties , 2009, Annals of the New York Academy of Sciences.

[33]  V. Pande,et al.  On the application of statistical physics to evolutionary biology. , 2009, Journal of theoretical biology.

[34]  Paulien Hogeweg,et al.  Evolution of complexity in RNA-like replicator systems , 2008, Biology Direct.

[35]  John Stache,et al.  Demons , Engines and the Second Law , 2008 .

[36]  C. Suttle.  Marine viruses — major players in the global ecosystem , 2007, Nature Reviews Microbiology.

[37]  I. K. Jordan,et al.  Exaptation of protein coding sequences from transposable elements. , 2007, Genome dynamics.

[38]  C. Suttle.  Viruses in the sea , 2005, Nature.

[39]  Manfred Eigen,et al.  The error threshold. , 2005, Virus research.

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

[41]  Forest Rohwer,et al.  Global Phage Diversity , 2003, Cell.

[42]  G. Glazko,et al.  Origin of a substantial fraction of human regulatory sequences from transposable elements. , 2003, Trends in genetics : TIG.

[43]  Charles H. Bennett,et al.  Notes on Landauer's Principle, Reversible Computation, and Maxwell's Demon , 2002, physics/0210005.

[44]  C. Ofria,et al.  Evolution of digital organisms at high mutation rates leads to survival of the flattest , 2001, Nature.

[45]  T. O. Diener,et al.  The viroid: biological oddity or evolutionary fossil? , 2001, Advances in virus research.

[46]  E. Szathmáry.  The evolution of replicators. , 2000, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[47]  A. Read,et al.  The Economics of Immunity , 2000, Science.

[48]  C. Woese.  The universal ancestor. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[49]  E. Szathmáry,et al.  Group selection of early replicators and the origin of life. , 1987, Journal of theoretical biology.

[50]  J M Smith,et al.  Evolution and the theory of games , 1976 .

[51]  F. Kramer,et al.  Complete nucleotide sequence of a replicating RNA molecule. , 1973, Science.

[52]  S. Spiegelman,et al.  An approach to the experimental analysis of precellular evolution , 1971, Quarterly Reviews of Biophysics.

[53]  S. Spiegelman,et al.  Autocatalytic Synthesis of a Viral RNA in vitro , 1965, Science.

[54]  R. Landauer,et al.  Irreversibility and heat generation in the computing process , 1961, IBM J. Res. Dev..