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Seeking the Evolutionary Roots of Horizontal Gene Transfer (HGT). Addy Pross Department of Chemistry, Ben Gurion University of the Negev Be’er Sheva , Israel. HGT & LUCA Conference, The Open University, Milton Keynes, Sept. 4-6, 2013. - PowerPoint PPT Presentation
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Addy Pross
Department of Chemistry, Ben Gurion University of the NegevBe’er Sheva, Israel
HGT & LUCA Conference, The Open University, Milton Keynes, Sept. 4-6, 2013
Seeking the Evolutionary Roots of Horizontal Gene Transfer (HGT)
Biology in Crisis
“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”
Carl Woese
Bottom line: 150 years after Darwin, we still don’t adequately understand biology’s essence and the nature of the evolutionary process
Central HGT & LUCA Questions
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?
Regular Chemistry BiologySystems
Chemistry
Systems Chemistry
Systems Biology -‘top-down’ Systems Chemistry -‘bottom-up’Deals with simple replicating chemical systems and the networks they establish
A new area of chemistry
Non-replicative Simple replicative
Complex replicative
G. von Kiedrowski, S. Otto, P. Herdewijn, J. Syst. Chem. 2010
Biology Systems chemistry
To understand how something works, look at a simple version
Simple Life
Complex Life
Biological phase Non-Life
Systems Chemistry:Merging Chemistry and Biology
Chemicalphase
One single physicochemical process
Replication reaction - the underlying connection
A. Pross, J. Syst. Chem. 2011
Darwinian theory?
Molecular Replication
A + B + C + ….. T T Molecular
Replication
Template mechanismS. Spiegelman, 1967
G. von Kiedrowski, 1986 L. Orgel, 1987
J. Rebek, 1994 M.R. Ghadiri, 1996
G. F. Joyce, 1997
e.g., nucleic acids, peptides, synthetic molecules
Replication Reaction is Autocatalytic
79 replication cycles would convert a single molecule to a mole (279 ~ 6. 1023).
a further 83 cycles would generate a mass equal to that of the earth, 1027g!
Replication is unsustainable
Autocatalysis - can exhibit exponential growth
T. Malthus, An Essay on the Principle of Population, 1798
StabilityA system is stable if it is persistent, unchanging
over time.
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
An Alternative Stability Kind
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
Dynamic Kinetic Stability (DKS)
Pross et al. 2004-2013
Dynamic Kinetic Stability (DKS)
dX/dt = kXM - gXX = 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
Replication is unsustainable, therefore for stability rate of replicator formation rate of decay ~=
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
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. 2011A. Pross, Pure Appl. Chem. 2005
Example of Replicator Selection Rule
Qb RNAnucleotides
S. Spiegelman, 1967
(4500 b)Mutant RNA
(220 b)74 replication cycles
Faster RNA drive slower RNA into extinction
In stability terms:
From DK less stable to DK more stable
activated
Replication Mutation Selection Evolution
Sequence of events:
Identifying the Driving Force for Evolution
Simple Life
Complex Life
Simple replicating
entity Drive toward greater DKS
One single physicochemical process
A. Pross, J. Syst. Chem. 2011
Chemicalphase
Biological phase
What actually takes place during evolutionary process?
Chemical (molecular) level:Molecular replicating system simple life
A clear tendency toward complexification during evolution – both chemical and biological
prokaryotes eukaryotes
multicell organisms
Biological level:
ecological networks
Evolutionary Process Characterized by Complexification
Extent of Complexification During Evolution
Simple Life
Complex Life
Chemical phase
Simple Replicating
System
One continuous process
Biological phase
low complexity high complexity
Drive toward greater DKSlow complexity – low stabilityhigh complexity – high stability
A. Pross, J. Syst. Chem. 2011
General Theory of Evolution
A. Pross, J. Syst. Chem. 2011
Extended theory embraces both biological and chemical systems
All stable (persistent) replicating systems will tend to evolve (primarily by complexification) toward systems of greater DKS.
Darwinian Concepts Chemical 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
A.Pross, J. Syst. Chem. 2011A.Pross, Chem. Eur. J. 2009
Darwinian concepts - Particular applications of broader chemical concepts
kinetic selection
fitness
natural selection
Global Characteristics of Living Systems Explained by DKS
Diversity Functional complexity Dynamic character Far-from-equilibrium state Teleonomy (purposeful nature) Homochiral character
Principle of Natural Selection Principle of Divergence
Darwin’s Two Principles
Origin of DiversityDiversity – a central element of Darwinian theory
- many become few- few become many
‘Regular’ (thermodynamic) Space
Topology of ‘Regular’ Chemical and Replicator Spaces
Thermodynamic sink
Replicator (kinetic) Space
Convergent Divergent
Replicator Space – Open, circumstantial
A. Pross, J. Syst. Chem. 2011Clarifies Darwin’s Principle of Divergence
Topology of replicator space explains diversity
Implications of Different Topologies
Regular systems: History inaccessible
Future predictable
Replicators:History accessible
Future unpredictable
N. Wagner, A. Pross, Entropy 2011A. Pross, Pure Appl. Chem. 2005
Diversification at Chemical Level
nucleotides
(4500 b)Mutant RNA
(220 b)74 replication cycles
activated
1) Replication (VGT) + mutation
Qb RNA
2) HGT – mechanism for diversification that is not directly connected to replication step.
S. Spiegelman et al., PNAS, 1967
HGT already evident at chemical level.
Molecular HGT in Action
N. Lehman et al., Nature 2012 (fig: Attwater & Holliger, Nature 2012)
Cooperative cycle out-replicates individual cycles.An expression of HGT at molecular level!
HGT – not just mechanism for variation but for complexification
Complexification during Evolutionn
Simple Life
Complex Life
Chemical phase
Simple Replicating
System
One continuous process
Biological phase
low complexity high complexity
Drive toward greater DKSlow complexity – low stabilityhigh complexity – high stability
A. Pross, J. Syst. Chem. 2011
Answers to Central HGT QuestionsHow 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 selectionHGT lesson - variation is not restricted to the replicative step. Nature is opportunistic! Lamarckian character
Nature of LUCAWas LUCA organismal or communal?Is extant life organismal or communal?
Plants cannot fix nitrogen without bacterial assistanceHumans are 90% bacterial by cell countBacteria 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
Systems Chemistry ViewpointSystems chemistry studies indicate that network formation (complexification) is the primary mechanism for increasing DKS
Central mechanism of abiogenesis would have been network formation.
Conclusion: LUCA was communal because evolution is fundamentally a networking process – right from its origins.
Biology overemphasizes life’s individuality.
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!
Is LUCA a meaningful concept?
Darwinian Threshold = Speciation Threshold
LUCA – diverse population of replicatively coupled entities that preceded speciation
LUCA - associated with Darwinian Threshold
Primal speciation: the point at which replicative networks physically separated, began to utilize available resources differentially, and began to evolve independently
Key ConclusionsDKS - the conceptual bridge between Chemistry and
Biology.
32
• 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.
Thank you for your attention!