IUPS President’s Lecture (Sponsored by Wiley) 17:30 - 18:30, Sunday 21 July Hall 1 (The ICC) Physiology moves back onto

1. IUPS President’s Lecture (Sponsored by Wiley) 17:30 - 18:30, Sunday 21 July Hall 1 (The ICC) Physiology moves back onto centre stage: a new synthesis with evolutionary biology Denis Noble University of Oxford, United Kingdom

2. Evolution: a brief history 1809 Jean-Baptiste Lamarck published ZoologiePhilosophique. Established transformation of species; assumed inheritance of acquired characteristics 1859 Charles Darwin published The Origin of Species. Proposed theory of natural selection, but had no theory of heredity. Also assumed inheritance of acquired characteristics 1900 approx. Neo-Darwinism: incorporation of Mendelian discrete inheritance. Weismann barrier: exclusion of inheritance of acquired characteristics 1940 approx. The Modern Synthesis: Julian Huxley, R A Fisher, J B S Haldane, Sewell Wright

3. Evolution: the Modern Synthesis often called Neo-Darwinism Popularised by The Selfish Gene (1976) Gene-centred view of natural selection (slow accumulation of ‘random’ mutations, followed by selection) Impossibility of inheritance of acquired characteristics (mis-called ‘Larmarckism’) Distinction between replicator (genes) and vehicle (phenotype) Buttressed by [mis-interpretations of] The Central Dogma of Molecular Biology (Crick) All these rules have been broken !

4. Shapiro, 2011: Evolution. A view from the 21st Century • “It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works. All careful studies of mutagenesis find statistically significant non-random patterns of change.” (page 82) • Are mutations random?

5. Random? • The question is not just whether changes are random, but whether they are functionally relevant. • “I will use the definition that the changes are assumed to be random with respect to physiological function and could not therefore be influenced by such function or by functional changes in response to the environment. This is the assumption that excludes the phenotype from in any way influencing or guiding genetic change.” (Noble 2013) • That assumption is now insecure since some genome changes are related to physiological function.

6. Example of targeted genome insertion • P element homing in fruit flies. These are DNA transposons that insert into the genome in a functionally significant way, depending on the added DNA. There is up to 50% greater insertion into regions of the genome that are related functionally. • Possible explanation: donor element and target site may be brought close together in the nucleus, i.e. organisation of the genome is important. This kind of information is also therefore ‘genetic’. Hama, Ali, and Kornberg 1990 Genes Dev4: 1079–1093

7. Are mutations random? Are gradual accumulations of mutations the cause of speciation? “The 2001 Nature report of the draft human genome contained two important figures illustrating what genome sequencing had taught us about protein evolution. Using transcription factors and chromatin binding proteins as examples, the figures showed that these classes of protein did not evolve one amino acid at a time. Instead, the two classes of protein “shuffled” and “accreted” copies of functional protein segments called domains…...” Shapiro, 2011, page 95

8. Initial sequencing and analysis of the human genome International Human Genome Sequencing Consortium Nature 2001, 409, 860-921 Domain accretion in chromatin proteins * * * * * * * * * * * Domain accretion in yeast (Y), worm (W), fly (F), vertebrates, (V) Human (H) shown by stars,

9. First conclusion Proteins did not all evolve via gradual accumulation of mutations Some other forms of genome reorganisation must have occurred

10. What was wrong with neo-darwinism? The errors are both philosophical (conceptual and linguistic) and scientific (empirical, experimental)

11. Selfish gene: Metaphor or empirical science? in reply to Midgley (1979): “that was no metaphor. I believe it is the literal truth, provided certain key words are defined in the particular ways favoured by biologists” (Dawkins, 1981). But a metaphor does not cease to be a metaphor simply because one defines a word to mean something other than its normal meaning. Indeed, it is the function of metaphor to do precisely this. (Noble, J Physiol, 2011) Noble D. (2011). Neo-Darwinism, the Modern Synthesis, and Selfish Genes: are they of use in physiology? Journal of Physiology589, 1007-1015.

12. Conclusion The selfish gene idea is not falsifiable Further details in Noble D. (2011). Neo-Darwinism, the Modern Synthesis, and Selfish Genes: are they of use in physiology? Journal of Physiology589, 1007-1015. “selfishness cannot be defined as an intrinsic property of nucleotide sequences independently of gene frequency. It is a strange hypothesis that uses its own definition of its postulated entity as its only prediction”.

13. Are mutations random? Are gradual accumulations of mutations the cause of speciation? “It is important to note that selection has never led to formation of a new species. Selection operates as a purifying but not creative force.” (Shapiro, 2011, page 144) Thousands of years of domestic selection produced new varieties not new species By contrast, hybridisation in plants does achieve speciation

14. Second conclusion ‘Selfishness’ is not a testable hypothesis Question Has the concept of a gene changed?

15. Phenotype Biological Networks signalling pathways, filters, conditioners incubators that enable and restrict reactions X X Environment ‘determinants of phenotype’ ≡ original concept of ‘gene’ molecular biology notion: gene = DNA sequence DNA Kohl P, Crampin E, Quinn TA & Noble D. (2010). Systems Biology: an approach. Clinical Pharmacology and Therapeutics 88, 25-33.

16. Phenotype Biological Networks signalling pathways, filters, conditioners incubators that enable and restrict reactions X Environment ‘determinants of phenotype’ ≡ original concept of ‘gene’ molecular biology notion: gene = DNA sequence DNA Most knock-outs and mutations are buffered by the networks

17. Most knock-outs and mutations are buffered by the networks Some examples

18. Em If IbNa Model of sinus node – ibNa & if Example of ‘gene knock-out’ Hyperpolarization Activates if 80% 100% 40% 60% 20% Noble, D., J. C. Denyer, H.F. Brown. & D DiFrancesco (1992). Proc Royal SocietyB 250: 199-207.

19. Genetic buffering: How extensive is it? Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, Lee W, Proctor M, St Onge RP, Tyers M, Koller D, Altman RB, Davis RW, Nislow C & Giaever G. (2008). The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320, 362-365. 80% of knockouts are silent!

20. Why should a physiologist be concerned about evolutionary theory? The modern synthesis is a gene-centred theory of evolution Yet organisms are very good at ‘immunising’ themselves from their genomes Noble D, Differential and integral views of genetics in computational systems Biology, 2011,Interface Focus 1, 7-15

21. Conclusion: Knockouts do not reveal regulators Davies, J. 2009 Regulation, necessity, and the misinterpretation of knockouts. Bioessays31, 826–830.

22. Origin of the problem: Downward causation

23. The reductionist causal chain I know one approach that will fail, which is to start with genes, make proteins from them and to try to build things bottom-up Sydney Brenner, 2001 They [genes] created us, body and mind Richard Dawkins, 1976 organism organ tissue cellular sub-cellular pathways protein gene

24. NOBLE, D (2002) Nature Reviews Molecular Cell Biology3, 460-463. Unravelling complexity Need to work in an integrative way at all levels: organism organ tissue cellular sub-cellular pathways protein gene Systems level triggers of cell signalling Systems level controls of gene expression Epigenetic marking by all levels Protein machinery reads and corrects genes There are feed-downs as well as upward between all these levels

25. Origin of the problem: Downward causation Royal Society journal Interface Focus Focused issue, 2012 (Editors: Ellis, Noble, O’Connor)

26. Some principles of Systems Biology Second principle Transmission of information is NOT one-way So, the ‘central dogma’ of biology is insufficient or even incorrect! (Shapiro, J. A. 2009 Revisiting the Central Dogma in the 21st Century. Annals of the New York Academy of Sciences 1178, 6-28 Shapiro, J.A. 2011 Evolution. Aview from the 21st Century, FT Press Science) There is ‘downward causation’ from all levels This influences gene expression, and gene marking (epigenetic inheritance) “Lamarckism is not so obviously false as is sometimes made out” (John Maynard Smith, Evolutionary Genetics, OUP, 1998)

27. Some principles of Systems Biology Third principle DNA is NOT the sole transmitter of inheritance We all inherit a complete egg cell DNA marking – methylation, histone marking and other processes (maternal factors can transmit through generations) Epigenetic marking can also be transmitted through sperm line (via RNAs) We should invert the usual question: What prevents inheritance of acquired characteristics? Jablonka& Lamb (1995) Epigenetic inheritance and Evolution (OUP)

28. Examples of Inheritance of epigenetic information Weaver, I. C. G.,. 2009 Life at the interface between a dynamic environment and a fixed genome Mammalian Brain Development (Ed Janigro) 17-40. Anway, M. D., Leathers, C. & Skinner, M. K. 2006 Endocrine disruptor vinclozolin induced epigenetic transgenerational adult-onset disease. Endocrinology147, 5515-5523. Pembrey ME, Bygren LO, Kaati G, Edvinsson S, Northstone K, Sjostrom M, Golding J & ALSPAC_study_team. (2006). Sex-specific, male-line transgenerational responses in humans. European Journal of Human Genetics 14, 159-166. Sun, Y. H., Chen, S. P., Wang, Y. P., Hu, W. & Zhu, Z. Y. 2005 Cytoplasmic Impact on Cross-Genus Cloned Fish Derived from Transgenic Common Carp (Cyprinuscarpio) Nuclei and Goldfish (Carassiusauratus) Enucleated Eggs. Biology of Reproduction72, 510-515. Rechavi, O, Minevish, G, Hobert, O. 2011 TransgenerationalInheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans. Cell, 147, 1248-1256.

29. The Guardian, 14 February 2007 ARE Weaver et al The Journal of Neuroscience, February 14, 2007 • 27(7):1756 –1768

30. Inheritance of epigenetic information Anway, M. D., Leathers, C. & Skinner, M. K. 2006 Endocrine disruptor vinclozolin induced epigenetic transgenerational adult-onset disease. Endocrinology147, 5515-5523. An endocrine disruptor) can induce transgenerational (four generations were followed) disease states or abnormalities, and this suggests a potential epigenetic etiology and molecular basis of adult onset disease. Sharma, A. & Singh, Priyanka. 2006 Detection of transgenerationalspermatogenic inheritance of adult male acquired CNS gene expression characteristics using a Drosophila systems model. PLoS one4, e5763. Chronic PTZ treatment of adult males changes CNS transcriptome. This is inherited. First demonstration of spermatogenic inheritance of an adult-induced characteristic.

31. Third conclusion Environmentally-induced changes can be inherited Question What happens in cross-species clones?

32. Sun, Y. H., Chen, S. P., Wang, Y. P., Hu, W. & Zhu, Z. Y. (2005)

33. Inheritance of epigenetic (cytoplasmic) information Goldfish 26 Sun, Y. H., Chen, S. P., Wang, Y. P., Hu, W. & Zhu, Z. Y. (2005) Cytoplasmic Impact on Cross-Genus Cloned Fish Derived from Transgenic Common Carp (Cyprinuscarpio) Nuclei and Goldfish (Carassiusauratus) Enucleated Eggs. Biology of Reproduction72, 510-515. Carp nucleus in Goldfish egg ? 28 Carp 33

34. Inheritance of epigenetic (cytoplasmic) information Sun, Y. H., Chen, S. P., Wang, Y. P., Hu, W. & Zhu, Z. Y. (2005) Cytoplasmic Impact on Cross-Genus Cloned Fish Derived from Transgenic Common Carp (Cyprinuscarpio) Nuclei and Goldfish (Carassiusauratus) Enucleated Eggs. Biology of Reproduction72, 510-515. Goldfish 26 Carp nucleus in Goldfish egg 28 Carp 33 X-ray photographs showed that the vertebral number of six cloned fish was of the enucleated egg providing goldfish type, ranging from 26 to 28. In contrast, the vertebral number of nuclear-donor common carp was 33–36. These data suggest that the goldfish egg cytoplasm plays an important role in regulating the somite development and vertebral number in the nuclear transplants.

35. McClintock, Barbara. 1984 The significance of responses of the genome to challenge. Science226, 792-801. And Nobel Prize Lecture, 1983 In the future attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them,often by restructuring the genome. We know about the components of genomes that could be made available for such restructuring. We know nothing, however, about how the cell senses danger and instigates responses to it. A genome consists largely of semistablegenetic elements that may be rearranged or even moved around in the genome thus modifying the information content of DNA. (Beurton et al 2008)

36. Fourth conclusion Cytoplasmic changes can be inherited Question Possible mechanisms?

37. Rechavi, O, Minevish, G, Hobert, O. 2011 Transgenerational • Inheritance of an Acquired Small RNA-Based Antiviral Response • in C. elegans. Cell, 147, 1248-1256. • Viral replication triggers an RNAi-dependent viral silencing response • The acquired silencing response is transgenerationallytransmitted • Transgenerational transmittance is non-Mendelian • involves small antiviral RNAs • Inheritance is robust • for over 100 generations

38. Stop press: from Joe Nadeau’s lab Nelson, V. R., Heaney, J. D., Tesar, P. J., Davidson, N. O., & Nadeau, J. H. (2012). Transgenerationalepigenetic effects of Apobec1 deficiency on testicular germ cell tumor susceptibility and embryonic viability. Proceedings of the National Academy of Sciences, 109, E2766–E2773 these [epigenetic] effects persist for many generations and are as strong as conventional genetic inheritance The heritable epigenetic changes persisted for multiple generations and were fully reversed after consecutive crosses through the alternative germ-lineage “the belief that the soma and germline do not communicate is patently incorrect.” PNAS Commentary article

39. Sixth conclusion Environmentally-induced changes can be inherited The inheritance is robust, can carry through many generations and the molecular mechanisms are known in some cases Question If gradual mutations is not the answer, what is responsible for re-organisation of genomes?

40. THE NETWORK OF LIFE • “Contrary to traditional theories, it is now well documented that all prokaryotes and many eukaryotes acquire novel genomic segments and biochemical functions from other, often unrelated cells rather than exclusively by vertical inheritance from progenitors” Shapiro: Evolution. A view from the 21stCentury p 91

41. Beurton PJ, Falk R & Rheinberger H-J, ed. (2008). The Concept of the Gene in Development and Evolution: Historical and Epistemological Perspectives. Cambridge University Press, Cambridge. “it seems that a cell’s enzymes are capable of actively manipulating DNA to do this or that. A genome consists largely of semistable genetic elements that may be rearranged or even moved around in the genome thus modifying the information content of DNA.” Genes “begin to look like hardly definable temporary products of a cell’s physiology”

42. Final conclusion If functional changes in the adult can be inherited, and therefore a target for natural selection, then physiology – the analysis of function – IS highly relevant to evolution. “It is hard to think of a more fundamental change for physiology and for the conceptual foundations of biology in general” (Noble ExpPhysiol2013)

43. Evolution & physiology: towards a new Synthesis Gene-centred view of natural selection Selection is multi-level Impossibility of inheritance of acquired characteristics Acquired characters can be inherited Distinction between replicator (genes) and vehicle (phenotype) The genome is an ‘organ of the cell’ not its dictator. Control is distributed. The Central Dogma of Molecular Biology Genomes are not isolated from organism & environment

44. Evolution & physiology: towards a new Synthesis

45. Evolution & physiology: towards a new Synthesis Questions page http://musicoflife.co.uk/pdfs/Answers.pdf

46. Further reading Does the Modern Synthesis need extending or replacing? Pigliucci, M., & Müller, GB. (2010). Evolution - The extended synthesis. Cambridge, Mass: MIT Press. Gissis, SB., & Jablonka, E. (Eds.). (2011). Transformations of Lamarckism. From Subtle Fluids to Molecular Biology. Cambridge, Mass: MIT Press Shapiro, J. (2011) Evolution: a view from the 21st Century FT Press Beurton, PJ, Falk, R. & Rheinberger, H-J. (2008) The concept of the gene in development and evolution: historical and epistemological perspectives. CUP. Noble, D. (2006) The Music of Life, OUP.