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Energy transduction and genome function – an evolutionary synthesis

Event

Starts:

November
122012

09:00

Ends:

November
132012

17:00

Location

The Royal Society, London, 6-9 Carlton House Terrace, London, SW1Y 5AG

Overview

© Odra Noel

Organised by Dr Nick Lane, Professor John Allen, Professor William Martin and Professor John Raven FRS

Event details

Living organisms are self-replicating, self-sustaining dynamic systems. Newly emerging insights into the interdependence of bioenergetics and genome function have far-reaching implications for diverse fields, from the origin of life to genomic complexity, from multicellular differentiation to ageing. This meeting brings together major contributors from diverse disciplines, with the objective of driving an evolutionary synthesis that is rooted in thermodynamics.

Biographies of the organisers and speakers are available below and you can also download the programme (PDF). Recorded audio of the presentations are available by clicking on the speakers names below and papers will be published in a future issue of Philosophical Transactions B.

Enquiries: Contact the events team.

Event organisers

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Schedule of talks

Session 1

4 talks Show detail Hide detail

On the inevitable journey to being

Dr Michael Russell, JPL, California Institute of Technology

Abstract

Life is the evolutionary culmination of emergent symmetry-breaking, macroscopically organized dynamic structures in the universe. Members of this cascading series of autocatalytic energy converting systems, or engines in Cottrell’s terminology, become ever more complex—more chemical and less physical—as each engine extracts, exploits and generates ever lower grades of energy and resources in the service of entropy generation. Each one of these engines emerges spontaneously from order created by a particular mother engine or engines as the disequilibrated potential daughter is driven beyond a critical point, as in e.g., the transition to thermonuclear reactions during gravitationally-driven star formation; the transition to convective flow in systems driven beyond the Rayleigh limit by thermal gradients (such as those responsible for the tectonic dynamics of our planet); and the onset of Mohr-Coulomb failure and fracture propagation due to differential mechanical stress exceeding rock strength (as occurs in the planet's tectonically-strained ocean floor rock). Importantly, it is these fractures in the ocean floor, acting themselves as engines of dissipation, that allow ocean water access to the crust which in turn drives the onset of exothermic serpentinization, alkaline hydrothermal convection and thereby the spontaneous production of precipitated submarine hydrothermal mounds. It is at such mounds finally that, we argue, the two chemical disequilibria directly causative in the emergence of life spontaneously arose across the mineral precipitate membranes separating the acidulous, nitrate-bearing CO2-rich, Hadean sea from the alkaline and CH4/H2-rich serpentine-generated effluents. The first and foremost of these great geochemical gifts was the imposition of essential redox gradients involving hydrothermal CH4 and H2 as electron donors, and CO2 and nitrate, nitrite, and ferric iron from the ambient ocean as acceptors; which gradients, we propose, functioned as the original “carbon-fixing engine”. The second gift, also imposed across the inorganic membrane, was a post-critical-point (milli)voltage pH potential (proton concentration gradient) that, we hypothesize, drove the condensation of orthophosphate to produce a high energy currency:- “the pyrophosphatase engine”. Notably, of course, this specific ionic gradient, there available for the taking, is one upon which all extant cellular systems now depend even though they must constantly recreate it on their own through the harnessing of redox gradients, or the catabolism of biomolecules such as glucose, to recondense ADP to ATP. Once metabolizing cells emerged and evolved in this submarine mound, the call for constant and far-from-equilibrium free energy sources presumably diminished somewhat due to the relative stability, and “templating effect” of the relatively stable organized states of matter mediating the key steps of proto-life free energy conversion. Thus the metabolic engines could sustain themselves by merely “ticking over” during times of deprivation and in this way more robustly survive for the long periods that life occupied the ocean floor and deep biosphere before its escape to the wider and more free-energy rich world and, ultimately, its “discovery” of photosynthesis.

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The energetics of organic synthesis inside and outside the cell

Professor Jan Amend, University of Southern California

Abstract

Thermodynamic modeling of organic synthesis has largely been focused on deep-sea hydrothermal systems. When seawater mixes with hydrothermal fluids, redox gradients are established that serve as potential energy sources for the formation of organic compounds and biomolecules from inorganic starting materials. This energetic drive, which varies substantially depending on the type of host rock, is present and available both for abiotic (outside the cell) and biotic (inside the cell) processes. Here, we review and synthesize a library of theoretical studies that target organic synthesis energetics. The biogeochemical scenarios evaluated include those in present-day hydrothermal systems and in putative early Earth environments. It is consistently and repeatedly shown in these studies that the formation of relatively simple organic compounds and biomolecules can be energy-yielding (exergonic) at conditions that occur in hydrothermal systems. Expanding on our ability to calculate biomass synthesis energetics, we also present here a new approach for estimating the energetics of polymerization reactions, specifically those associated with polypeptide formation from the requisite amino acids.

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The early evolution of biological energy conservation: hydrogen, metals, gradients and electron bifurcation

Professor William Martin, Heinrich Heine University, Germany

Abstract

In very early chemical evolution, the forerunners of carbon and energy metabolism were the processes of generating reduced carbon compounds from carbon dioxide and the mechanisms of harnessing energy as compounds capable of doing some chemical work. New insights into energy conservation in methanogens and acetogens — cells that fuel both their carbon and energy metabolism through the CO2/H2 redox couple — suggest that reduced ferredoxin is the most ancient biological energy currency. Those anaerobic autotrophs generate reduced ferredoxin from H2 via a mechanism called electron bifurcation, a process that in turn links ferredoxin reduction to exergonic reactions and the generation of transmembrane ion gradients. Overall carbon and energy metabolsm in methanogens and acetogens that lack cytochromes and quinones (or the quinone analogue methanophenazine) involves Ech and Rnf complexes that pump ions while reducing protons and NAD+, respectively, with electrons from ferredoxin. This has some similarity to serpentinization, a geochemical process in which electons from Fe2+ generate H2 and reduced carbon compounds such as methane. The new findings from microbial physiology are remarkably congruent with the independently derived idea that life evolved in submarine alkaline hydrothermal vents and underscore evolutionarily significant similarities as well as differences in acetogen and methanogen physiology.

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A reassessment of autotrophy at the emergence of life

Professor Wolfgang Nitschke, CNRS Marseilles

Abstract

An empirical way to study the origin of life is through extrapolating the evolutionary history of extant life back towards its very beginning while respecting geochemical boundary conditions and fundamental physical laws. This approach has in the past identified the Wood-Ljungdahl (WL) pathway of aceto- and methanogens as a promising candidate for primordial energy and carbon metabolism. However, a number of problems with this scenario have recently been pointed out (Schoepp et al., 2012, Biochim.Biophys.Acta, doi: 10.1016/j.bbabio.2012.09.005) suggesting that the original model may require amendments and reinterpretations. Here we present a scenario which stipulates that methane and nitrogen oxyanions ought to be considered in addition to the canonical WL-substrates, H2 and CO2. The recently described denitrifying methanotrophs represent an extant example for a corresponding metabolism. We will present arguments suggesting that denitrifying methanotrophy may pre-date aceto- and methanogenesis. Extant methanotrophic pathways suggest that the earliest carbon-fixing and energy harvesting metabolism may have condensed CO (delivered by the Ni/Fe-catalysed reduction of CO2) and a second C1-body represented by formaldehyde (or a sulphur-associated methyl group) produced by monooxygenation of methane to methanol (at a diiron centre) followed by further oxidation to formaldehyde (possibly catalysed by a molybdenum/tungsten-sulphide). In both half-reactions, redox bifurcations play crucial roles.

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Session 2

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Discovering the electronic circuit diagram of life

Professor Paul Falkowski, Rutgers University

Abstract

Life is far from thermodynamic equilibrium. Over the past decade, together with his collaborators, Professor Falkowski has been analyzing the biochemical reactions responsible for energy generation in all organisms, and they have identified a set of ~1500 “core” genes which encode for the energy transduction systems on a planetary scale. He will examine the evolutionary trajectory of these core reactions, culminating in the splitting of water by light and the use of oxygen as a terminal electron acceptor by aerobic microbes. These two, and fifteen other processes, form a global electronic circuit, where individual organisms essentially are transistors on a planetary circuit board. The wires are the two primary geophysical fluids: the ocean and the atmosphere. The primary power supply is solar energy. The output is a self-replicating system that decreases entropy at the cost of increased energy dissipation; a condition that is not amenable to classical Boltzmann functions. The system has a limited number of transistor designs. They have identified 35 basic structural elements, which appear to have a single common ancestor with a core Fe4S4 motif. They are attempting to develop a phylogeny of the core motifs in an effort to understand the evolution of biologically catalyzed redox reactions.

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Energy, ecology, and the distribution of microbial life

Professor Jennifer Macalady, Penn State University

Abstract

We are fundamentally interested in what controls the distribution of microbial life in space and time. In ecological terms, this amounts to understanding the relationship between microbial populations and environmental conditions (niches). Understood quantitatively, niches unlock our ability to interpret the signatures of life recorded in rocks and empower the use of microbial genetic potential for engineering applications of all types. In this contribution we will focus on niches related to energy metabolism because of direct links to elemental cycling, engineering, and astrobiology. To what degree does niche differentiation related to energy metabolism drive microbial diversity and evolution? Although microbiologists are well aware of large-scale taxonomic patterns in energy-harvesting metabolisms (e.g. oxygenic phototrophy in cyanobacteria, sulfate reduction in deltaproteobacteria), we live in profound ignorance of the quantitative niches inhabited by most microorganisms alive today. Our recent work suggests that relatively subtle variations in the concentration ratios of external electron donors and acceptors are sufficient to select for new populations, and that quantitative knowledge of microbial niches can be used to predict the abundance of specific microbial taxa in a landscape of environmental variations. These results are reviewed in the context of resource ratio theory, which predicts the outcome of competition among plant species sharing limiting resources. We then identify challenges to the view that niches related to energy transduction organise microbial populations in space and time. Lastly, we evaluate the prospect that a focus on testing ecological theory will transform our awe-struck collective gaze at the microbial constellations into a predictive science in time to participate in the grand challenges we face as planetary engineers.

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The influence of photosynthesis on genome function

Professor John A Raven FRS, University of Dundee, UK

Abstract

Photolithotrophic organisms may be divided into those which use an electron donor other than water (the anoxygenic photolithotrophs, all of which are bacteria) and those which use water as the electron donor (including the cyanobacteria and the photosynthetic eukaryotes). Those photolithotrophic organisms with the most reduced genomes have more genes than do the chemoorganotrophs with the most reduced genomes, and the fastest-growing chemoorganotrophs have significantly higher specific growth rates than the fastest-growing photolithotrophs. This slower growth of photosynthetic organisms apparently results from diversion of resources into the photosynthetic apparatus which account for half of the cell protein. The inherent dangers in photosynthesis (and especially oxygenic photosynthesis), including the formation of reactive oxygen species, can damage the cell and especially the photosynthetic apparatus. The extent to which protective measures in photolithotrophs fail and involve greater DNA damage and repair and faster protein turnover, with implications for energetics and rRNA expression, than in chemoorganotrophs, will be discussed, as will possible implications for the location of genes within the eukaryotic cell. A related source of environmental damage is UVB radiation, whose flux at the Earth’s surface decreased as oxygen (and ozone) increased in the atmosphere; possible relict UV avoidance and repair mechanisms from the times of higher UV fluxes will be discussed. Local, and then global, oxygenation led to the much discussed requirements of defence against reactive oxygen species and the opportunity for aerobic respiration for organisms in the oxygenated habitats. However, there are also effects on the nitrogen, phosphorus and iron cycles which decrease the availability to organisms of combined (non-dinitrogen) nitrogen, phosphorus and ferrous iron in the oxygenated biosphere. The implications of the decreased availability of nutrient elements for evolution of novel pathways related to enhancing the availability of these elements, and/or decreasing the requirement for them, will be discussed. Finally, we consider evidence from codon usage of economies in the use of potentially growth-limiting elements in the genome and, especially, the proteome.

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How evolutionary tinkering rewires chloroplast gene regulation

Dr Sujith Puthiyaveetil, Washington State University

Abstract

Chloroplasts are the sites of photosynthesis in plants and algae. True to their symbiotic origin from cyanobacteria, chloroplasts contain genes encoding some of the core proteins of the two photosystems. The expression of these chloroplast genes is regulated by photosynthetic electron transport through a bacterial-type sensor kinase known as Chloroplast Sensor Kinase (CSK). CSK represses the transcription of photosystem I (PS I) genes in PS I light condition, thus explaining the acclimatory process of photosystem stoichiometry adjustment. Here we show that overexpression of CSK induces a shade avoidance phenotype, consistent with its function in low light acclimation. In cyanobacteria and in non-green algae, CSK homologues co-exist with their response regulator partners in canonical bacterial two-component systems. In green algae and plants, however, no response regulator partner of CSK is found. Yeast two-hybrid analysis reveals interaction of CSK with the sigma factor subunit (SIG1) of the eubacterial chloroplast RNA polymerase. Here we present further evidence for the interactions of CSK and SIG1, using in vitro pull-down assays. We also show that CSK interacts with quinone. SIG1 becomes phosphorylated in PS I light, and then specifically represses transcription of PS I genes. In view of the identical signalling properties of CSK and SIG1 and of their interaction, we suggest that CSK is the SIG1 kinase. Here we also propose that the selective repression of PS I genes arises from the operation of a gene-regulatory phosphoswitch in SIG1. Evolution has rewired a two-component regulatory system into a novel chloroplast signalling pathway by tinkering with a sensor histidine kinase and a sigma factor, with phosphorylation still kept as the basis of signal transduction. The CSK-SIG1 regulatory system strongly supports a proposal for the selection pressure behind the evolutionary stasis of chloroplast genes.

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Session 3

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Dr Leonid Sazanov, MRC Mitochondrial Biology Unit

Abstract

NADH-ubiquinone oxidoreductase (complex I) is the first and the largest enzyme in the respiratory chain of mitochondria and most bacteria. Complex I is central to bioenergetics and is implicated in many human neurodegenerative diseases, as well as in aging. It couples electron transfer between NADH and ubiquinone to proton translocation across the membrane. It is an L-shaped assembly, with the hydrophobic arm embedded in the membrane and the hydrophilic arm protruding into the bacterial cytoplasm or mitochondrial matrix. Bacterial enzyme usually consists of 14 conserved core subunits, whilst mitochondrial complex contains also about 30 “accessory” subunits, bringing its total molecular mass to 1 MDa. We have recently shown that, unexpectedly, complex I from the alpha-proteobacterium Paracoccus denitrificans, a close relative of the “proto-mitochondrion”, contains three “accessory” subunits. This suggests that evolution of complex I via addition of subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. We study bacterial complex I as a “minimal” structural model of human enzyme. We have determined the crystal structure of the hydrophilic domain of complex I from Thermus thermophilus, revealing the arrangement of NADH, flavin and nine Fe-S clusters. The structure shows how eight different subunits, related to various smaller redox proteins, were combined during evolution to provide a uniquely long (95 angstrom) electron transfer chain. 
Recently, we have determined the structure of the membrane domain of complex I from E. coli. We have also described the low-resolution architecture of the entire complex I from T. thermophilus. Three largest subunits of the membrane domain are related to each other and to the family of Mrp Na+/H+ antiporters. The structures show that each antiporter-like subunit contains a single proton translocation channel formed by two connected half-channels. Complex I-like family of enzymes includes membrane-bound hydrogenases and probably originated from the unification of soluble hydrogenases and Mrp-type antiporters. The mechanism of coupling between the electron transfer in the hydrophilic domain and proton translocation in the membrane domain of complex I is not yet established. The antiporter-like subunits are well separated from the quinone-binding site, implying that long-range conformational changes must play a role in coupling. The structures suggest that two coupling elements, including the unusual long amphipathic alpha-helix, likely help coordinate conformational changes in the membrane domain, driven by redox reactions near the quinone-binding site.

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Evolutionary and regulatory aspects of tetrapyrrole biosynthesis

Professor Carl Bauer, Indiana University

Abstract

The tetrapyrrole biosynthetic pathway is responsible for synthesizing heme, cobalamin (vitamin B12) and chlorophyll. These cofactors are responsible many important biological processes such as photosynthesis, respiration and enzyme substrate modification. Chlorophyll synthesis provides photosynthetic organisms the ability to convert solar energy into cellular energy and to produce atmospheric oxygen as a byproduct of this energy conversion. Life on Earth would be vastly different without this capability. Heme synthesis is responsible for the ability of cells to shuttle electrons from energy generating to energy utilizing processes as well as to function as a gas carrier and a gas sensor. Respiration is clearly dependent on these features of heme. Cobalamin is an essential vitamin in many organisms and is used by enzymes to provide a facile way of performing methylationreactions. Over the years our laboratory has investigated many properties of tetrapyrrole biosynthesis, from the discovery of the genes involved in synthesis of chlorophyll, to transcriptional control of enzyme involved in all three branches of this biosynthetic pathway. This later feature, transcriptional control of tetrapyrrole biosynthesis with transcription factors that utilize tetrapyrrols as cofactors will be discussed.

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The role of mitochondria in the maintenance of nuclear DNA

Dr Janneke Balk, University of East Anglia

Abstract

An important function of mitochondria and chloroplasts, two types of organelles from endosymbiotic origin, is the assembly of iron-sulphur (Fe-S) clusters. These metal cofactors function as versatile catalysts in many essential enzymes. In our studies using the model plant Arabidopsis thaliana, we have found that mitochondria, but not the chloroplasts, contribute to the maturation of Fe-S proteins in the cytosol and nucleus. The proteins involved in this process are highly conserved from yeast to mammals to plants, and include an ATP binding cassette (ABC) transporter of the mitochondria, as well as 7 – 8 proteins of the Cytosolic Iron-sulphur cluster Assembly (CIA) pathway. Recently we found that Arabidopsis mutants in the ABC transporter or in one of the CIA genes have increased DNA breakage and recombination. Together with similar findings in yeast and mammals, the results link mitochondria to nuclear genome integrity through assembly of Fe-S proteins.

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Energy, fidelity and sex. Oocyte mitochondrial DNA as a protected genetic template

Professor John F Allen, Queen Mary, University of London, UK

Abstract

Oxidative phosphorylation couples ATP synthesis to respiratory electron transport. In eukaryotes, this coupling occurs in mitochondria, which carry DNA. Respiratory electron transport in the presence of molecular oxygen generates mutagenic free radicals at a frequency that is itself increased by mutation. Damage to mitochondrial DNA therefore accumulates within the life-span of individual organisms. Syngamy requires motility of one gamete, and this motility requires ATP. We propose that oxidative phosphorylation is absent in the special case of quiescent, template mitochondria, and that these remain sequestered in oocytes and female germ lines. Oocyte mitochondrial DNA is thus protected from damage. Here we present evidence that female gametes, which are immotile, repress mitochondrial DNA transcription, electron transport, and free radical production. In contrast, somatic cells and male gametes are seen actively to transcribe mitochondrial genes for respiratory electron carriers, and to produce oxygen free radicals. We find that this functional division of labour between sperm and egg is widely distributed within the animal kingdom, and characterised by contrasting mitochondrial size and morphology. We suggest that mitochondrial anisogamy explains the occurrence of two sexes. If quiescent oocyte mitochondria alone retain the capacity for an indefinite number of accurate replications of mitochondrial DNA, then "female" can be defined as that sex which transmits genetic template mitochondria. Template mitochondria then give rise to mitochondria that perform oxidative phosphorylation in somatic cells and in male gametes of each new generation. Template mitochondria also persist within the female germ line, to populate the oocytes of daughters. Thus mitochondria are maternally inherited.

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Session 4

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On the singular origin of eukaryotes

Dr Nick Lane, University College London, UK

Abstract

The eukaryotes are monophyletic and share a common ancestor that by definition only arose once. But singularities are common in evolution and do not necessarily imply an improbable event. I shall argue that the origin of eukaryotes was genuinely improbable, for bioenergetic reasons. Prokaryotes depend on plasma membrane potential for ATP synthesis. Membrane bioenergetics limits energy availability per gene in prokaryotes, which show no tendency to evolve genomic or morphological complexity. On the contrary: genomic and morphological streamlining maximises prokaryotic energy per gene and replication speed. Eukaryotes almost certainly arose in a rare endosymbiosis between two prokaryotes, an archaeal host cell and a bacterial endosymbiont, the ancestor of mitochondria. The genetic configuration of bioenergetic membranes in eukaryotes with mitochondria differs from that in prokaryotes with invaginated plasma membranes in that mitochondrial membranes are associated only with the genes specifically required for ATP synthesis. Loss of other endosymbiont genes and bioenergetic specialization supported, energetically, orders of magnitude more DNA in the host cell. This allowed gene families to expand and explore sequence space in a manner that cannot be realized in prokaryotes. While rare in prokaryotes, endosymbiosis is not rare enough to account for a genuinely singular event over four billion years of evolution. Yet the integration of prokaryotic host with endosymbiont is fraught with difficulties, producing a restrictive bottleneck. Many basal eukaryotic traits might be explained in terms of the dynamics of a prokaryote with endosymbionts, including the nucleus, sex, two sexes, sensescence and speciation. A requirement for sex and recombination on a genome-wide scale in eukaryotes may have acted as a restrictive bottleneck preceding the big-bang radiation of eukaryotic supergroups.

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Why did eukaryotes evolve only once? - genetic and energetic aspects of conflict and conflict mediation

Professor Neil Blackstone, Northern Illinois University

Abstract

According to multi-level theory, evolutionary transitions require mediating conflicts between lower-level units in favor of the higher-level unit. By this view, the origin of eukaryotes and the origin of multicellularity would seem largely equivalent. Yet eukaryotes evolved only once in the history of life, while multicellular eukaryotes have evolved many times. Examining conflicts between evolutionary units and mechanisms that mediate these conflicts can illuminate these differences. Energy-converting endosymbionts that allow eukaryotes to transcend surface-to-volume constraints also can allocate energy into their own selfish replication. This principal conflict in the origin of eukaryotes can be mediated by genetic or energetic mechanisms. Genome transfer diminishes the heritable variation of the symbiont, but requires the de novo evolution of protein-import apparatus and was opposed by selection for selfish symbionts. In contrast, metabolic signaling is a shared primitive feature of all cells. Redox state of the cytosol is an emergent feature that cannot be subverted by an individual symbiont. Hypothetical scenarios illustrate how metabolic regulation may have mediated the conflicts inherent at different stages in the origin of eukaryotes. Aspects of metabolic regulation may have subsequently been co-opted from within-cell to between-cell pathways, allowing multicellularity to emerge repeatedly.

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Mitochondria, not just for energy

Sir Salvador Moncada FRS, University College London

Abstract

Mitochondria play an important role in cell proliferation by ensuring that substrates are provided for macromolecular synthesis via acceleration of the TCA cycle.  We have shown that the activity of key metabolic enzymes is regulated by the ubiquitin ligases that control the function of the cyclins. Thus, anaphase-promoting complex/cyclosome (APC/C)-Cdh1, which controls G1- to-S-phase transition by targeting specific degradation motifs in cell cycle proteins, also regulates the glycolysis-promoting enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isoform 3 (PFKFB3) and glutaminase 1 (GLS1), a critical enzyme in glycolysis.  A decrease in the activity of APC/C-Cdh1 in mid-to-late G1 releases both proteins, thus explaining the simultaneous increase in the utilization of glucose and glutamine during cell proliferation. A second ubiquitin ligase (SCF(Skp1/CUL-1/F-box protein)-b-TrCP) degrades PFKFB3 during late G1/S so that the upregulation of glycolysis is tightly controlled at a specific point in G1 whereas the activity of GLSI remains high throughout S-phase.

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A bioenergetic theory of evolution and disease

Professor Douglas Wallace, Children’s Hospital of Philadelphia and University of Pennsylvania

Abstract

Western biomedical philosophy has been dominated by a structural paradigm of evolution, an anatomical paradigm of medicine, and a Mendelian paradigm of genetics. While these have been a powerful combination for addressing many previous biomedical questions, they have proven inadequate to understand the biology and genetics of the common metabolic and degenerative diseases, cancer, and aging. Life is the interplay between structure (anatomy), energy (vital force), and information (inheritance, Mendelian and otherwise). By switching our perspective from anatomy to energy and from the Mendelian genetics of anatomy to the non-Mendelian inheritance of energy we can generate a comprehensive paradigm of evolution, a coherent paradigm of complex diseases, and an integrated paradigm of inheritance. These three new paradigms provide straight forward explanations to the enigma of the selectionist-neutralist debate in evolutionary genetics as well as to the biology and inheritance of the common “complex” diseases.

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Energy transduction and genome function – an evolutionary synthesis The Royal Society, London 6-9 Carlton House Terrace London SW1Y 5AG UK