Small Research Project: Natural information and Epigenetics.


"Today,the notion of genes sending signals to other genes is as central as the notion of a genetic code was forty years ago. (Maynard-Smith 2000, 187–88. Also 2010 see number 42 in bibliography at bottom)

When evolution (or learning) leads to a signaling system, information is created. (Skyrms 2010, 40) "

(Source: Introduction to Calcott, B. (2014). The Creation and Reuse of Information in Gene Regulatory Networks. Philosophy of Science, 81 (5), 879–890. https://doi.org/10.1086/677687 )

Announcing a new research initiative and small project.


For a long time the central dogma of molecular biology - that information cannot pass from the phenotype to the genotype - held rigid influence over the molecular biosciences. While the central dogma still has a place, the challenge to its scope from the field of epigenetics has now taken hold in the biosciences worldwide.

It's well understood that methylation effects in the cytoplasm during certain stages of development can be transmitted (Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes & Development, 16(1), 6–21. https://doi.org/10.1101/gad.947102 ). Another well known example of epigenetic information transmission is prions, or proteinaceous infectious particles. These are the kind of non-viral and non-bacterial pathogens that cause such diseases as Creutzfeldt–Jakob disease/syndrome. Because the disease agents are fragments of protein, and not genetic information like that which viruses advantage, the transmission of information in the disease is from Protein fragments to cellular DNA (Chakravarty, A. K., & Jarosz, D. F. (2018). More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. Journal of Molecular Biology, 430(23), 4607–4618. https://doi.org/10.1016/j.jmb.2018.07.017 .)

This IIMx research project, initiated and being undertaken by research director Dr Bruce Long, is aimed at identifying the best conception(s) of causation and naturalised information for application to epigenetic information transmission.

If you would like to participate by way of funding (and have IP and publishing/copyright rights at certain funding levels) please contact research.director@iimx.info or visit our Patreon funding page:




Bibliography


Beebee, H., Hitchcock, C., & Menzies, P. (2010). The Oxford Handbook of Causation. Oxford University Press.

Beebee, H., Hitchcock, C., Menzies, P., & Carroll, J. W. (2010). Anti‐Reductionism. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0014

Beebee, H., Hitchcock, C., Menzies, P., & Dowe, P. (2010). Causal Process Theories. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0011

Beebee, H., Hitchcock, C., Menzies, P., & Glennan, S. (2010). Mechanisms. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0016

Beebee, H., Hitchcock, C., Menzies, P., & Godfrey‐Smith, P. (2010). Causal Pluralism. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0017

Beebee, H., Hitchcock, C., Menzies, P., & Healey, R. (2010). Causation in Quantum Mechanics. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0034

Beebee, H., Hitchcock, C., Menzies, P., & Hitchcock, C. (2010). Causal Modelling. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0015

Beebee, H., Hitchcock, C., Menzies, P., & Hitchcock, C. (2010). Causal Modelling. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0015

Beebee, H., Hitchcock, C., Menzies, P., & Humphreys, P. (2010). Causation and Reduction. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0031

Beebee, H., Hitchcock, C., Menzies, P., & Jackson, F. (2010). Causation and Semantic Content. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0029

Beebee, H., Hitchcock, C., Menzies, P., Maslen, C., Horgan, T., & Daly, H. (2010). Mental Causation. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0025

Beebee, H., Hitchcock, C., Menzies, P., & Menzies, P. (2010). Platitudes and Counterexamples. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0018

Beebee, H., Hitchcock, C., Menzies, P., & Mumford, S. (2010). Causal Powers and Capacities. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0013

Beebee, H., Hitchcock, C., Menzies, P., & Paul, L. A. (2010). Counterfactual Theories. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0009

Beebee, H., Hitchcock, C., Menzies, P., Price, H., & Weslake, B. (2010). The Time‐Asymmetry of Causation. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0021

Beebee, H., Hitchcock, C., Menzies, P., & Sklar, L. (2010). Causation in Statistical Mechanics. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0033

Beebee, H., Hitchcock, C., Menzies, P., & Tooley, M. (2010). Causes, Laws, and Ontology. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0019

Beebee, H., Hitchcock, C., Menzies, P., & Williamson, J. (2010). Probabilistic Theories. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0010

Beebee, H., Hitchcock, C., Menzies, P., & Woodward, J. F. (2010). Agency and Interventionist Theories. Oxford University Press. Retrieved from http://www.oxfordhandbooks.com/view/10.1093/oxfordhb/9780199279739.001.0001/oxfordhb-9780199279739-e-0012

Bergstrom, C. T., & Rosvall, M. (2011a). Response to commentaries on “The Transmission Sense of Information.” Biology & Philosophy, 26(2), 195–200. 

Bergstrom, C. T., & Rosvall, M. (2011b). The transmission sense of information. Biology & Philosophy, 26(2), 159–176. 

Blanco, E., & Corominas, M. (2012). CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. BMC Genomics, 13(1), 688–688. https://doi.org/10.1186/1471-2164-13-688

Calcott, B. (2014). The Creation and Reuse of Information in Gene Regulatory Networks. Philosophy of Science, 81(5), 879–890. https://doi.org/10.1086/677687

Causal Democracy and Causal Contributions in Developmental Systems Theory. (2000). The Oxford Handbook of Philosophy of Science /, 67(s1), S332,S347. 

Causation in Biology. (2009). Oxford : Oxford University Press. 

Chergui, M. (2012). Ultrafast Structural Dynamics of Biological Systems. In E. H. Egelman (Ed.), Comprehensive Biophysics (pp. 398 – 424). Amsterdam: Elsevier. 

Couch, M., & Pfeifer, J. (2016). The philosophy of Philip Kitcher. New York, NY: Oxford University Press. 

Donaldson-Matasci, M. C., Bergstrom, C. T., & Lachmann, M. (2010). The fitness value of information. Oikos, 119(2), 219–230. 

English, S., Pen, I., Shea, N., & Uller, T. (2015). The Information Value of Non-Genetic Inheritance in Plants and Animals. PLOS ONE, 10(1), e0116996. 

Linquist, Stephan. Exploring the Folkbiological Conception of Human Nature. (2011). Philosophical Transactions., 366, 444,453. 

Godfrey-Smith, P. (2011). Senders, receivers, and genetic information: comments on Bergstrom and Rosvall. Biology & Philosophy, 26(2), 177–181. 

González, G. L. (2013). Beyond Developmental Compatibility A Note On Generative Linguistics and the Developmentalist Challenge. Teorema: Revista Internacional de Filosofía, 32(2), 29–44. 

Griffiths, P. E. (2016). Proximate and Ultimate Information in Biology. In The Philosophy of Philip Kitcher. New York: Oxford University Press. https://doi.org/10.1093/acprof:oso/9780199381357.003.0004

Griffiths, P. E., & Knight, R. D. (1998). What is the developmentalist challenge? (response to article by Kenneth C. Schaffner in this issue, p. 209). Philosophy of Science, 65(2), 253–258. https://doi.org/10.1086/392636

Harris, Z. S. (1989). The Form of information in science: analysis of an immunology sublanguage (Vol. 104). Dordrecht [Netherlands];Boston; Kluwer Academic Publishers. 

Huneman, P. (2010). Assessing the Prospects for a Return of Organisms in Evolutionary Biology. History and Philosophy of the Life Sciences, 32(2/3), 341–371. https://doi.org/10.2307/23335078

Information and Epigenetics. (2018). John Wiley & Sons, Inc. 

Konermann, S., Brigham, M., Trevino, A., Hsu, P., Heidenreich, M., Cong, R., … Zhang, S. (2013). Optical control of mammalian endogenous transcription and epigenetic states. Nature, 500(7463), 472–476. https://doi.org/10.1038/nature12466

Liu, T., Zheng, X., & Wang, J. (2010). Prediction of protein structural class using a complexity-based distance measure. Amino Acids, 38(3), 721–728. https://doi.org/10.1007/s00726-009-0276-1

Mayer, C., Mcinroy, G. R., Murat, P., Van Delft, P., & Balasubramanian, S. (2016). An Epigenetics‐Inspired DNA‐Based Data Storage System. Angewandte Chemie International Edition, 55(37), 11144–11148. https://doi.org/10.1002/anie.201605531

Smith, J. M. (2010). The concept of information in biology. In P. Davies & N. H. Gregersen (Eds.), Information and the Nature of Reality: From Physics to Metaphysics (pp. 123–145). Cambridge University Press. 

Measuring Causal Specificity. (2015). The Oxford Handbook of Philosophy of Science /, 82, 529,555. 

Millikan, R. G. (2007). An Input Condition for Teleosemantics? Reply to Shea (And Godfrey-Smith). Philosophy and Phenomenological Research, 75(2), 436–455. 

Oyama, S. (2000). The ontogeny of information : developmental systems and evolution /. Cambridge ; Cambridge University Press. 


Richters, J. E. (1997). The Hubble hypothesis and the developmentalists dilemma. Development and Psychopathology, 9(2), 193–229. https://doi.org/10.1017/S0954579497002022

Rosvall, M., Bergstrom, C. T., fysik, I. för, fakulteten, T., & universitet, U. (2011). Response to commentaries on “The transmission sense of information”: discussion note. Biology & Philosophy, 26(2), 195. 

Schaffner, K. F. (1998). Genes, Behavior, and Developmental Emergentism: One Process, Indivisible? Philosophy of Science, 65(2), 209–252. https://doi.org/10.1086/392635

Schaffner, K. F. (2016). Genes, Behavior, and the Developmentalist Challenge: One Process, Indivisible? Oxford University Press. 

Shea, N. (2007a). Consumers Need Information: Supplementing Teleosemantics with an Input Condition. Philosophy and Phenomenological Research, 75(2), 404–435. 

Shea, N. (2007b). Representation in the genome and in other inheritance systems. Biology & Philosophy, 22(3), 313. 

Shea, N. (2011a). Developmental Systems Theory Formulated as a Claim about Inherited Representations. Philosophy of Science, 78(1), 60–82. 

Shea, N. (2011b). What’s transmitted? Inherited information. Biology and Philosophy, 26(2), 183–189. 

Shea, N. (2011c). What’s transmitted? Inherited information. Biology & Philosophy, 26(2), 183–189. 

Shea, N. (2011d). What’s transmitted? Inherited information.(DISCUSSION NOTE). Biology & Philosophy, 26(2), 183. 

Shea, N. (2013a). Inherited representations are read in development. British Journal for the Philosophy of Science, 64(1), 1–31. 

Shea, N. (2013b). Naturalising Representational Content. Philosophy Compass, 8(5), 496–509. 


Shea, N. (2014a). Neural Signaling of Probabilistic Vectors. Philosophy of Science, 81(5), 902–913. 

Shea, N. (2014b). Reward Prediction Error Signals are Meta‐Representational. Noûs, 48(2), 314–341. 

Solving the Circularity Problem for Functions: A Response to Nanay. (2012). The Journal of Philosophy., 109(10), 613,622. 

Studies from University of Bordeaux Have Provided New Information about Botany (Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues).(Report). (2017). Life Science Weekly, 3171. 

Sukhoverkhov, A. (2010). Memory, Sign Systems, and Self-Reproductive Processes. Biological Theory, 5(2), 161–166. 

Sukhoverkhov, A. (2012). Natural Signs and the Origin of Language. Biosemiotics, 5(2), 153–159. 

Sukhoverkhov, A. V., & Fowler, C. A. (2015). Why Language Evolution Needs Memory: Systems and Ecological Approaches. Biosemiotics, 8(1), 47–65. 



The Organism as the Subject and Object of Evolution. (1983). Scientia (Rivista Di Scienza) Rivista Internazionale Di Sintesi Scientifica., 118, 65,82. 

The Oxford Handbook of Causation. (2009). Oxford University Press. https://doi.org/10.1093/oxfordhb/9780199279739.001.0001


Walker, S. I., Davies, P. C. W., & Ellis, G. F. R. (2017). From matter to life: information and causality. Cambridge, United Kingdom: Cambridge University Press. 

Working in a New World: Kuhn, Constructivism and Mind-Dependence. (2015). Studies in History and Philosophy of Science., 50, 83,89.
Epigenetics and Methylation

Arney, K. L., Bao, S., Bannister, A. J., Kouzarides, T., & Surani, M. A. (2002). Histone methylation defines epigenetic asymmetry in the mouse zygote. The International Journal of Developmental Biology, 46(3), 317–320. https://doi.org/10.1387/ijdb.12068953

Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes & Development, 16(1), 6–21. https://doi.org/10.1101/gad.947102

Bosviel, R., Durif, J., Déchelotte, P., Bignon, Y., & Bernard-gallon, D. (2012). Epigenetic modulation of BRCA1 and BRCA2 gene expression by equol in breast cancer cell lines. British Journal of Nutrition, 108(7), 1187–1193. https://doi.org/10.1017/S000711451100657X

de Waal, E., Yamazaki, Y., Ingale, P., Bartolomei, M., Yanagimachi, R., & Mccarrey, J. (2012). Primary epimutations introduced during intracytoplasmic sperm injection (ICSI) are corrected by germline-specific epigenetic reprogramming. Proceedings of the National Academy of Sciences of the United States of America, 109(11), 4163–4168. https://doi.org/10.1073/pnas.1201990109

Shin, H.-J. R., Kim, H., Kim, K. I., & Baek, S. H. (2016). Epigenetic and transcriptional regulation of autophagy. Autophagy, 12(11), 2248–2249. 

Prions and Epigenetics

Chakravarty, A. K., & Jarosz, D. F. (2018). More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. Journal of Molecular Biology, 430(23), 4607–4618. https://doi.org/10.1016/j.jmb.2018.07.017

Chen, B., Bruce, K. L., Newnam, G. P., Gyoneva, S., Romanyuk, A. V., & Chernoff, Y. O. (2010). Genetic and epigenetic control of the efficiency and fidelity of cross‐species prion transmission. Molecular Microbiology, 76(6), 1483–1499. https://doi.org/10.1111/j.1365-2958.2010.07177.x

Halfmann, R., Jarosz, D. F., Jones, S. K., Chang, A., Lancaster, A. K., & Lindquist, S. (2012). Prions are a common mechanism for phenotypic inheritance in wild yeasts.(RESEARCH ARTICLE)(Report). Nature, 482(7385), 363–368. https://doi.org/10.1038/naturel0875

Halfmann, R., & Lindquist, S. (2010). Epigenetics in the extreme: prions and the inheritance of environmentally acquired traits. Science (New York, N.Y.), 330(6004), 629–632. https://doi.org/10.1126/science.1191081

Harvey, Z. H., Chen, Y., & Jarosz, D. F. (2018). Protein-Based Inheritance: Epigenetics beyond the Chromosome. Molecular Cell, 69(2), 195–202. https://doi.org/10.1016/j.molcel.2017.10.030

Launer, J. (2016). Epigenetics for dummies. Postgraduate Medical Journal, 92(1085), 183–184. https://doi.org/10.1136/postgradmedj-2016-133993

Manjrekar, J. (2017). Epigenetic inheritance, prions and evolution. Journal of Genetics, 96(3), 445–456. https://doi.org/10.1007/s12041-017-0798-3

Nizhnikov, A., Ryzhova, T., Volkov, K., Zadorsky, S., Sopova, J., Inge-Vechtomov, S., & Galkin, A. (2016). Interaction of Prions Causes Heritable Traits in Saccharomyces cerevisiae. PLoS Genetics, 12(12), e1006504. https://doi.org/10.1371/journal.pgen.1006504

Rédei, G. P. (2008). Encyclopedia of Genetics, Genomics, Proteomics and Informatics. Dordrecht: Springer Netherlands. 

Schmeets, M. G. J. (2014). About epigenetics and the central dogma of molecular biology. Neuropsychoanalysis, 16(1), 1–4. https://doi.org/10.1080/15294145.2014.900936