Addy Pross Department of Chemistry, Ben Gurion University of the Negev Be’er Sheva , Israel

1. Seeking the Evolutionary Roots of Horizontal Gene Transfer (HGT) AddyPross Department of Chemistry, Ben GurionUniversity of the Negev Be’erSheva, Israel HGT & LUCA Conference, The Open University, Milton Keynes, Sept. 4-6, 2013

2. Despite 60 yrs mol. Biol, where we discovered life’s molecular mechanisms, we do not understand chem-bio connection Biologyin Crisis Carl Woese “Biology today is no more fully understood in principle than physics was a century ago…. the guiding vision has reached its end …. a new, deeper, representation of reality is called for” Bottom line: 150 years after Darwin, we still don’t adequately understand biology’s essence and the nature of the evolutionary process

3. Central HGT & LUCA Questions a loosely coupled network of cellular components? • How fundamental is HGT to the evolutionary process? • What was the nature of LUCA? • What does Woese’s‘Darwinian threshold’ actually represent? • Is the evolutionary process best represented by a tree or a web? • Is HGT Lamarckian or Darwinian?

4. Systems Chemistry A new area of chemistry Systems Biology -‘top-down’ Systems Chemistry -‘bottom-up’ Deals with simple replicating chemical systems and the networks they establish G. von Kiedrowski, S. Otto, P. Herdewijn, J. Syst. Chem. 2010 Regular Chemistry Systems Chemistry Biology Complex replicative Non-replicative Simple replicative

5. To understand how something works, look at a simple version Biology Systems chemistry

6. Systems Chemistry: Merging Chemistry and Biology Chemical phase Biological phase Simple Life Complex Life Non-Life ? Darwinian theory One singlephysicochemical process Lets begin by looking at molecular roots of replication Replication reaction -the underlying connection A. Pross, J. Syst. Chem. 2011

7. Molecular Replication T Molecular Replication T A + B + C + ….. e.g., nucleic acids, peptides, synthetic molecules Template mechanism S. Spiegelman, 1967 G. von Kiedrowski, 1986 L. Orgel, 1987 J. Rebek, 1994 M.R. Ghadiri, 1996 G. F. Joyce, 1997

8. Replication Reaction is Autocatalytic Autocatalysis -can exhibit exponential growth • 79 replication cycles would convert a single molecule to a mole (279 ~ 6. 1023). • a further 83 cycles would generatea mass equal to that of the earth, 1027g! Replication is unsustainable T. Malthus, An Essay on the Principle of Population, 1798

9. Stability A system is stable if it is persistent, unchanging over time. Scientifically important concept - can be quantified. Thermodynamic Stability – an inherent property of a chemical system, one that is quantifiable. Second Law of Thermodynamics: All systems tend from less stable to more stable

10. An Alternative Stability Kind DynamicKinetic Stability (DKS) A stability kind associated with replicating systems (chemical or biological) that display persistence Can underpin a general theory of evolution and help identify the driving force for the evolutionary process Remarkably this stability kind also has fundamental math basis Pross et al. 2004-2013

11. Dynamic Kinetic Stability (DKS) Replication is unsustainable, therefore for stability rate of replicator formation rate of decay ~ = dX/dt = kXM - gX X = replicator conc. M = monomer conc. k,g = rate constants. A. Lotka, 1910 dX/dt = 0 would define a steady state population If a replicating system is stable then its stability is of a dynamic kinetic kind

12. Stability in ‘Regular’ and Replicative Worlds • ‘Regular’ chemical systems are stable because they DO NOT react. • Replicating chemical systems are stable (persistent) because they DO react – to make more of themselves! DKS would apply to all stable replicating systems, biological and chemical. A.Pross, Pure Appl. Chem. 2005

13. Selection Rules in ‘Regular’ Chemical and Replicator Worlds ‘Regular’ Chemical World: Thermodynamically Thermodynamically Less Stable More Stable Replicator World: Dynamic kinetically Dynamic kinetically Less Stable More Stable A. Pross, J. Syst. Chem. 2011 A. Pross, Pure Appl. Chem. 2005

14. Example of Replicator Selection Rule activated nucleotides Mutant RNA QbRNA 74 replication cycles (220 b) (4500 b) S. Spiegelman, 1967 Sequence of events: Replication Mutation Selection Evolution Faster RNA drive slower RNA into extinction In stability terms: From DK less stable to DK more stable

15. v. Important One process – one set of principles Identifying the Driving Force for Evolution Chemical phase Biological phase Simple replicating entity Simple Life Complex Life Driving force not NS, NS selects, not drive. But for what?Stability Drive toward greater DKS One single physicochemical process What actually takes place during evolutionary process? A. Pross, J. Syst. Chem. 2011

16. Evolutionary Process Characterized by Complexification A clear tendency toward complexification during evolution – both chemical and biological Chemical(molecular) level: Molecular replicating system simple life Biological level: prokaryotes eukaryotes multicellorganisms ecological networks

17. Extent of Complexification During Evolution Chemical phase Biologicalphase Simple Replicating System Simple Life Complex Life low complexity highcomplexity One continuous process Drive toward greater DKS low complexity – low stability high complexity – highstability A. Pross, J. Syst. Chem. 2011

18. General Theory of Evolution All stable (persistent) replicating systems will tend to evolve (primarily by complexification) toward systems of greater DKS. Extended theory embraces both biological and chemical systems A. Pross, J. Syst. Chem. 2011

19. Darwinian concepts-Particular applications of broader chemical concepts Darwinian ConceptsChemical Concepts dynamic kinetic stability (DKS) survival of the fittest drive toward greater DKS Darwinian concepts firmly rooted in chemistry Biology – a complex manifestation of replicative chemistry natural selection kinetic selection fitness A.Pross, J. Syst. Chem. 2011 A.Pross, Chem. Eur. J. 2009

20. Global Characteristics of Living Systems Explained by DKS • Diversity • Functional complexity • Dynamic character • Far-from-equilibrium state • Teleonomy (purposeful nature) • Homochiral character This DKS view explains many characteristics but I want to discuss diversity as it’s relevant to HGT issue

21. Origin of Diversity Darwin’s Two Principles Diversity – a central element of Darwinian theory - many become few - few become many Principle of Natural Selection Principle of Divergence

22. Topology of ‘Regular’ Chemical and Replicator Spaces Thermodynamic sink ‘Regular’ (thermodynamic) Space Replicator (kinetic) Space Convergent Divergent Replicator Space – Open, circumstantial Topology of replicator space explains diversity Clarifies Darwin’s Principle of Divergence A. Pross, J. Syst. Chem. 2011

23. Regular systems: History inaccessible Futurepredictable Implications of Different Topologies Replicators: History accessible Future unpredictable N. Wagner, A. Pross, Entropy 2011 A. Pross, Pure Appl. Chem. 2005

24. Diversification at Chemical Level 1) Replication (VGT) + mutation activated nucleotides QbRNA Mutant RNA 74 replication cycles (4500 b) (220 b) S. Spiegelman et al., PNAS, 1967 2) HGT – mechanism for diversification that is notdirectly connected to replication step. HGT already evident at chemical level.

25. Molecular HGT in Action N. Lehman et al., Nature 2012 (fig: Attwater & Holliger, Nature 2012) Recall concluded earlier moleccomplexif enhances DKS Cooperative cycle out-replicates individual cycles. An expression of HGT at molecular level! HGT – not just mechanism for variation but for complexification

26. Complexification during Evolutionn Chemical phase Biologicalphase Simple Replicating System Simple Life Complex Life low complexity high complexity One continuous process Drive toward greater DKS low complexity – low stability high complexity – highstability A. Pross, J. Syst. Chem. 2011

27. Answers to Central HGT Questions How general is HGT in evolution? HGT crucially important as a major mechanism for diversity and complexification. Operates along the entire evolutionary process. Simple replicators – simple HGT molecular level: transformation More complex replicators – more complex HGT prokaryotic level: conjugation, transduction eukaryotic level: sexual selection HGT lesson - variation is not restricted to the replicative step. Nature is opportunistic! Lamarckiancharacter

28. Nature of LUCA Woese says LUCA communal before phase change to organismal when Darwinian evol begins. But before answering let’s address more general questn: Was LUCA organismal or communal? Is extant life organismal or communal? Plants cannot fix nitrogen without bacterial assistance Humans are 90% bacterial by cell count Bacteria live in colonies (communicate chemically and coordinate actions eg, in biofilm formation) Animals seem to be individual, but actually network dependent, replicatively incomplete Conclusion: life is a network phenomenon, intrinsically communal

29. Systems Chemistry Viewpoint Having said that, degree of individuality appears to have increased during evolution Systems chemistry studies indicate that network formation (complexification) is the primary mechanism for increasing DKS Central mechanism of abiogenesiswould have been network formation. Conclusion: LUCA was communal because evolution is fundamentally a networking process – right from its origins. Biology overemphasizes life’s individuality.

30. Dynamic Kinetic Stability (DKS) Stability in replicative world (DKS) is not associated with individuals, only with populations. Individual replicators have no DKS. Individuals don’t evolve, populations do!

31. Is LUCA a meaningful concept? LUCA - associated with Darwinian Threshold Woese saw D-T as transition from communal to individual Primal speciation: the point at which replicative networks physically separated, began to utilize available resources differentially, and began to evolve independently Darwinian Threshold = Speciation Threshold LUCA – diverse population of replicatively coupled entities that preceded speciation

32. Key Conclusions • DKS - the conceptual bridge between Chemistry and Biology. • Unifies abiogenesis and biological evolution • Integrates Darwinian theory into general chemical theory • DKS – the driving force for evolution • Systems Chemistry – the road to greater biological understanding. HGT and LUCA can be better understood by seeking their roots in chemistry • Scientific reduction in biology is alive and well! • Carl Woese’s prophesy of revolution in biology may be realised - through Systems Chemistry.

34. Thank you for your attention!