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Randomness in biology

  • THOMAS HEAMS (a1)
Abstract

Biology has contradictory relationships with randomness. First, it is a complex issue for an empirical science to ensure that apparently random events are truly random, this being further complicated by the loose definitions of unpredictability used in the discipline. Second, biology is made up of many different fields, which have different traditions and procedures for considering random events. Randomness is in many ways an inherent feature of evolutionary biology and genetics. Indeed, chance/Darwinian selection principles, as well as the combinatorial genetic lottery leading to gametes and fertilisation, rely, at least partially, on probabilistic laws that refer to random events. On the other hand, molecular biology has long been based on deterministic premises that have led to a focus on the precision of molecular interactions to explain phenotypes, and, consequently, to the relegation of randomness to the marginal status of ‘noise’. However, recent experimental results, as well as new theoretical frameworks, have challenged this view and may provide unifying explanations by acknowledging the intrinsic stochastic dimension of intracellular pathways as a biological parameter, rather than just as background noise. This should lead to a significant reappraisal of the status of randomness in the life sciences, and have important consequences on research strategies for theoretical and applied biology.

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This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

J. Ansel et al. (2008) Cell-to-cell stochastic variation in gene expression is a complex genetic trait. PLoS Genetics 4 e1000049.

A. M. Arias and P. Hayward (2006) Filtering transcriptional noise during development: concepts and mechanisms. Nature Reviews Genetics 7 3444.

M. Arndt , T. Juffmann and V. Vedral (2009) Quantum physics meets biology. HFSP Journal 3 386400.

H. Atlan and M. Koppel (1990) The cellular computer DNA: program or data. Bulletin of Mathematical Biology 52 335348.

A. V. Badyaev (2005) Stress-induced variation in evolution: from behavioural plasticity to genetic assimilation. Proceedings of the Royal Society B: Biological Sciences 272 877886.

P. Ball (2011) Physics of life: The dawn of quantum biology. Nature 474 272274.

D. C. Bennett (1983) Differentiation in mouse melanoma cells: initial reversibility and an on-off stochastic model. Cell 34 445453.

I. Bjedov et al. (2003) Stress-induced mutagenesis in bacteria. Science 300 14041409.

D. Brisson (2003) The directed mutation controversy in an evolutionary context. Critical Reviews in Microbiology 29 2535.

J. P. Capp (2012) Stochastic gene expression stabilization as a new therapeutic strategy for cancer. Bioessays 34 (3) 170–3.

H. H. Chang , M. Hemberg , M. Barahona , D. E. Ingber and S. Huang (2008) Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453 544547.

J. P. Changeux and A. Danchin (1976) Selective stabilisation of developing synapses as a mechanism for the specification of neuronal networks. Nature 264 705712.

J. P. Changeux , P. Courrege and A. Danchin (1973) A theory of the epigenesis of neuronal networks by selective stabilization of synapses. Proceedings of the National Academy of Sciences of the United States of America 70 29742978.

J. Chelly , J. P. Concordet , J. C. Kaplan and A. Kahn (1989) Illegitimate transcription: transcription of any gene in any cell type. Proceedings of the National Academy of Sciences of the United States of America 86 26172621.

M. B. Clark et al. (2011) The reality of pervasive transcription. PLoS Biology 9 e1000625.

R. S. Cox 3rd, M. J. Dunlop and M. B. Elowitz (2010) A synthetic three-color scaffold for monitoring genetic regulation and noise. Journal of Biological Engineering 4 10.

T. Cremer , M. Cremer , S. Dietzel , S. Müller , I. Solovei and S. Fakan (2006) Chromosome territories a functional nuclear landscape. Current Opinion in Cell Biology 18 307316.

C. Darwin and A. R. Wallace (1858) On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection. Journal of the Proceedings of the Linnean Society of London Zoology 3 4650.

E. H. Davidson et al. (2002) A genomic regulatory network for development. Science 295 16691678.

L. Delaye and A. Moya (2010) Evolution of reduced prokaryotic genomes and the minimal cell concept: variations on a theme. Bioessays 32 281287.

R. J. Ellis (2001) Macromolecular crowding: obvious but underappreciated. Trends in Biochemical Sciences 26 597604.

M. B. Elowitz , A. J. Levine , E. D. Siggia and P. S. Swain (2002) Stochastic gene expression in a single cell. Science 297 11831186.

G. S. Engel et al. (2007) Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems. Nature 446 782786.

M. L. Ferguson et al. (2012) Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states. Proceedings of the National Academy of Sciences of the United States of America 109 155160.

S. Fiering , E. Whitelaw and D. I. Martin (2000) To be or not to be active: the stochastic nature of enhancer action. Bioessays 22 381387.

M. I. Franco , L. Turin , A. Mershin and E. M. Skoulakis (2011) Molecular vibration-sensing component in Drosophila melanogaster olfaction. Proceedings of the National Academy of Sciences of the United States of America 108 37973802.

A. J. E. Gordon , J. A. Halliday , M. D. Blankschien , P. A. Burns , F. Yatagai and C. Herman (2009) Transcriptional Infidelity Promotes Heritable Phenotypic Change in a Bistable Gene Network. PLoS Biology 7: e1000044.

S. J. Gould and R. C. Lewontin (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proceedings of the Royal Society B: Biological Sciences 205 581598.

P. Guptasarma (1995) Does replication-induced transcription regulate synthesis of the myriad low copy number proteins of escherichia coli? Bioessays 17 987997.

T. P. Hettinger (2011) Olfaction is a chemical sense, not a spectral sense. Proceedings of the National Academy of Sciences of the United States of America 108 E349.

S. Hooshangi and R. Weiss (2006) The effect of negative feedback on noise propagation in transcriptional gene networks. Chaos 16 026108.

F. Jacob and J. Monod (1961) Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3 318356.

N. Jerne (1955) The natural selection theory of antibody formation. Proceedings of the National Academy of Sciences of the United States of America 41 849857.

M. Kaern , T. C. Elston , W. J. Blake and J. J. Collins (2005) Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 6 451464.

B. B. Kaufmann , Q. Yang , J. T. Mettetal and A. van Oudenaarden (2007) Heritable stochastic switching revealed by single-cell genealogy. PLoS Biology 5 e239.

A. Klug (1974) Rosalind Fanklin and the double helix. Nature 248 787788.

E. V. Koonin (2003) Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Reviews Microbiology 1 127136.

J. J. Kupiec (1997) A Darwinian theory for the origin of cellular differentiation. Molecular Genetics and Genomics 255 201208.

B. Laforge , D. Guez , M. Martinez and J. J. Kupiec (2005) Modeling embryogenesis and cancer: an approach based on an equilibrium between the autostabilization of stochastic gene expression and the interdependence of cells for proliferation. Progress in Biophysics and Molecular Biology 89 93120.

B. Lehner (2008) Selection to minimise noise in living systems and its implications for the evolution of gene expression. Molecular Systems Biology 4 170.

T. Lenormand , D. Roze and F. Rousset (2009) Stochasticity in evolution. Trends in Ecology and Evolution 24 157165.

G. Longo and P. E. Tendero (2007) The Differential Method and the Causal Incompleteness of Programming Theory in Molecular Biology. Foundations of Science 12 337366.

K. Maeda et al. (2008) Chemical compass model of avian magnetoreception. Nature 453 387390.

A. Madlung and L. Comai (2004) The Effect of Stress on Genome regulation and Structure. Annals of Botany 94 481495.

I. Martincorena , A. S. N. Seshasayee and N. M. Luscombe (2012) Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature 485 9598.

E. Mayr (1961) Cause and effect in biology. Science 134 15011506.

H. H. McAdams and A. Arkin (1997) Stochastic mechanisms in gene expression. Proceedings of the National Academy of Sciences of the United States of America 94 814819.

H. H. McAdams and A. Arkin (1999) It's a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics 15 6569.

J. T. Mettetal and A. van Oudenaarden (2007) Necessary noise. Science 317 463464.

T. Mikeladze-Dvali et al. (2005) The growth regulators warts/lats and melted interact in a bistable loop to specify opposite fates in Drosophila R8 photoreceptors. Cell 122 775787.

K. F. Murphy , R. M. Adams , X. Wang , G. Balázsi and J. J. Collins (2010) Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Research 38 27122726.

S. Newlands et al. (1998) Transcription occurs in pulses in muscle fibers. Genes and Development 12 27482758.

L. A. Parada , J. J. Roix and T. Misteli (2003) An uncertainty principle in chromosome positioning. Trends in Cell Biology 13 393396.

Y. Pilpel (2011) Noise in biological systems: pros, cons, and mechanisms of control. Methods in Molecular Biology 759 407425.

D. Polev (2012) Transcriptional noise as a driver of gene evolution. Journal of Theoretical Biology 293 2733.

A. Raj and A. van Oudenaarden (2008) Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135 216226.

J. M. Raser and E. K. O'Shea (2005) Noise in gene expression: origins, consequences, and control. Science 309 20102013.

T. Ritz , P. Thalau , J. B. Phillips , R. Wiltschko and W. Wiltschko (2004) Resonance effects indicate a radical-pair mechanism for avian magnetic compass. Nature 429 177180.

D. K. Ro et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440 940943.

D. R. Rojo et al. (2011) Influence of stochastic gene expression on the cell survival rheostat after traumatic brain injury. PLoS One 6 e23111.

A. Rosenberg (2001) Discussion note: Indeterminism, probability, and randomness in evolutionary theory. Philosophy of Science 68 (4) 536544.

I. L. Ross , C. M. Browne and D. A. Hume (1994) Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. Immunology and Cell Biology 72 177185.

W. Roux (1881) Der Kampf der Teile im Organismus. Ein Beitrag zur Vervollständigung der mechanischen Zweckmäß igkeitslehre, Engelmann, Leipzig.

A. Ruvinsky (2009) Genetics and Randomness, CRC Press.

M. Springer and J. Paulsson (2006) Biological physics: harmonies from noise. Nature 439 2728.

J. L. Spudich and D. E. Koshland Jr. (1976) Non-genetic individuality: chance in the single cell. Nature 262 467471.

D. Stockholm et al. (2007) The origin of phenotypic heterogeneity in a clonal cell population in vitro. PLoS One 2 e394.

F. M. Szczebara et al. (2003) Total biosynthesis of hydrocortisone from a simple carbon source in yeast. Nature Biotechnology 21 143149.

J. Tamames , R. Gil , A. Latorre , J. Peretó , F. J. Silva and A. Moya (2007) The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evolutionary Biology 7 181.

M. Thattai and A. van Oudenaarden (2001) Intrinsic noise in gene regulatory networks. Proceedings of the National Academy of Sciences of the United States of America 98 86148619.

J. E. Till , E. A. Mc Culloch and L. Siminovitch (1964) A stochastic model of stem cell proliferation, based on the growth of spleen colony-forming. Proceedings of the National Academy of Sciences of the United States of America 51 2936.

S. Tonegawa (1976) Reiteration frequency of immunoglobulin light chain genes: further evidence for somatic generation of antibody diversity. Proceedings of the National Academy of Sciences of the United States of America 73 203207.

V. N. Uversky (2011) Intrinsically disordered proteins from A to Z. International Journal of Biochemistry and Cell Biology 43 10901103.

J. D. Velasco (2012) Objective and subjective probability in gene expression. Progress in Biophysics and Molecular Biology 110 (1) 510.

J. D. Watson and F. H. Crick (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171 737738.

C. Werndl (2012) Probability, Indeterminism and Biological Processes. In: D. Dieks , J. G. Wenceslao , S. Hartmann , M. Stoeltzner and M. Weber (eds.) Probabilities, Laws and Structures, The Philosophy of Science in a European Perspective, Volume 3, Springer-Verlag263277.

M. F. Wernet , E. O. Mazzoni , A. Celik , D. M. Duncan , I. Duncan and C. Desplan (2006) Stochastic spineless expression creates the retinal mosaic for colour vision. Nature 440 (7081) 174180.

M. Wijgerde , F. Grosveld and P. Fraser (1995) Transcription complex stability and chromatin dynamics in vivo. Nature 377 209213.

T. Zhou , L. Chen and K. Aihara (2005) Molecular communication through stochastic synchronization induced by extracellular fluctuations. Physical Review Letters 95 178103.

W. Zurek (2009) Quantum Darwinism. Nature Physics 5 181188.

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