The new biology: beyond the Modern Synthesis

Building, Maintaining, and (re-)Deploying Genetic Toolkits during Convergent Evolution

A surprising insight from the advent of genomic sequencing was that many genes are deeply conserved during evolution. With a particular focus on genes that interact with light in animals, I explore the metaphor of genetic toolkits, which can be operationalized as lists of genes involved in a trait of interest. A fascinating observation is that genes of a toolkit are often used again and again during convergent evolution, sometimes across vast phylogenetic distances. Such a pattern in the evolution of toolkits requires three different stages: (i) origin, (ii) maintenance, and (iii) redeployment of the genes. The functional origins of toolkit genes might often be rooted in interactions with external environments. The origins of light interacting genes in particular may be tied to ancient responses to photo-oxidative stress, inspiring questions about the extent to which the evolution of other toolkits was also impacted by stress. Maintenance of genetic toolkits over long evolutionary timescales requires gene multifunctionality to prevent gene loss when a trait of interest is absent. Finally, the deployment of toolkit genes in convergently evolved traits like eyes sometimes involves the repeated use of similar, ancient genes yet other times involves different genes, specific to each convergent origin. How often a particular gene family is used time and again for the same function may depend on how many possible biological solutions are available. When few solutions exist and the genes are maintained, evolution may be constrained to use the same genes over and over. However, when many different solutions are possible, convergent evolution often takes multiple different paths. Therefore, a focus on genetic toolkits highlights the combination of legacy-plus-innovation that drives the evolution of biological diversity.

Similar enzymatic functions in distinct bioluminescence systems: evolutionary recruitment of sulfotransferases in ostracod light organs

Genes from ancient families are sometimes involved in the convergent evolutionary origins of similar traits, even across vast phylogenetic distances. Sulfotransferases are an ancient family of enzymes that transfer sulfate from a donor to a wide variety of substrates, including probable roles in some bioluminescence systems. Here, we demonstrate multiple sulfotransferases, highly expressed in light organs of the bioluminescent ostracod Vargula tsujii, transfer sulfate in vitro to the luciferin substrate, vargulin. We find luciferin sulfotransferases (LSTs) of ostracods are not orthologous to known LSTs of fireflies or sea pansies; animals with distinct and convergently evolved bioluminescence systems compared to ostracods. Therefore, distantly related sulfotransferases were independently recruited at least three times, leading to parallel evolution of luciferin metabolism in three highly diverged organisms. Reuse of homologous genes is surprising in these bioluminescence systems because the other components, including luciferins and luciferases, are completely distinct. Whether convergently evolved traits incorporate ancient genes with similar functions or instead use distinct, often newer, genes may be constrained by how many genetic solutions exist for a particular function. When fewer solutions exist, as in genetic sulfation of small molecules, evolution may be more constrained to use the same genes time and again.

Beyond the modern synthesis: A framework for a more inclusive biological synthesis

Many theorists in recent years have been calling for evolutionary biology to move beyond the Modern Synthesis - the paradigm that has long provided the theoretical backbone for the discipline. Terms like "postmodern synthesis," "integrative synthesis," and "extended evolutionary synthesis" have been invoked by various critics in connection with the many recent developments that pose deep challenges - even contradictions - to the traditional model and underscore the need for an update, or a makeover. However, none of these critics, to this author's knowledge, has to date offered an explicit alternative that could provide a unifying theoretical paradigm for our vastly increased knowledge about living systems and the history of life on Earth (but see Noble 2015, 2017). This paper briefly summarizes the case against the Modern Synthesis and its many amendments over the years, and a new paradigm is proposed, called an "Inclusive Biological Synthesis," which, it is argued, can provide a more general framework for the biological sciences. The focus of this framework is the fundamental nature of life as a contingent dynamic process - an always at-risk "survival enterprise." The ongoing, inescapable challenge of earning a living in a given environmental context - biological survival and reproduction - presents an existential problem to which all biological phenomena can be related and comprehended. They and their "parts" can be analyzed in relation to ethologist Niko Tinbergen's four key questions. Some basic properties and guiding assumptions related to this alternative paradigm are also identified.

Playing 'hide-and-seek' with factor H: game-theoretical analysis of a single nucleotide polymorphism

As a part of the complement system, factor H regulates phagocytosis and helps differentiate between a body's own and foreign cells. Owing to mimicry efforts, some pathogenic microorganisms such as Candida albicans are able to bind factor H on their cell surfaces and, thus, become similar to host cells. This implies that the decision between self and foreign is not clear-cut, which leads to a classification problem for the immune system. Here, two different alleles determining the binding affinity of factor H are relevant. Those alleles differ in the SNP Y402H; they are known to be associated with susceptibility to certain diseases. Interestingly, the fraction of both alleles differs in ethnic groups. The game-theoretical model proposed in this article explains the coexistence of both alleles by a battle of the sexes game and investigates the trade-off between pathogen detection and protection of host cells. Further, we discuss the ethnicity-dependent frequencies of the alleles. Moreover, the model elucidates the mimicry efforts by pathogenic microorganisms.

Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation

Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.

How to talk about genome editing

Background

Human genome editing is an area of growing prominence, with many potential therapeutic applications.

Sources of data

A project by two UK charities, whose participants included fertility sector patients and practitioners and also people affected by genetic disease and rare disease. Scientific research into, and wider discussion of, genomics and genome editing.

Areas of agreement

There is a need for improved public and professional understanding of genome editing.

Areas of controversy

The way genome editing is discussed is often inconsistent and confusing. Simply defining and explaining the term 'genome' can present challenges.

Growing points

There are approaches that lend themselves to achieving greater clarity and coherence in discussion of genome editing.

Areas timely for developing research

People's understanding should ideally be able to withstand and evolve alongside current developments in genome editing, rather than being tied firmly to specific aspects of genome editing (which may in future be supplanted).

Hacia una epistemología evolutiva extendida: la retroalimentación entre variación y selección

Este artículo se sitúa en la perspectiva de la naturalización del conocimiento científico, toda vez que es un intento por caracterizar y describir la evolución del conocimiento a partir de nociones de la biología. El objetivo principal es responder si es posible sostener la analogía que propone la epistemología evolutiva (EE): que la evolución del conocimiento científico (ECC) es similar a la evolución orgánica (EO). La pregunta surge tras las críticas que han atacado el núcleo de la analogía. La respuesta es que la analogía sí se sostiene si se tienen en cuenta las relaciones de retroalimentación que es posible proponer a la luz de la síntesis extendida (SE), una teoría posterior que complementa la síntesis moderna (SM). Así, este trabajo comienza con una descripción del estado de la “epistemología evolutiva”, prosigue señalando por qué la síntesis moderna, que sirvió de base para su formulación, no es suficiente para fundamentar la epistemología evolutiva y finaliza proponiendo que es pertinente una modificación que puede describirse como “epistemología evolutiva extendida”.

Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow

As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses.

Anticipatory gene regulation driven by maternal effects in an insect-host system

Adaptive mechanisms involved in the prediction of future environments are common in organisms experiencing temporally variable environments. One of these is AGR (anticipatory gene regulation); in which differential gene expression occur in an individual, triggered by the experience of an ancestor. In this study, we explored the existence of AGR driven by a maternal effect, in an insect–host system. We analyzed gene expression of detoxifying systems in aphids across two generations, by shifting mothers and offspring from chemically defended to nondefended hosts, and vice versa. Then, we measured fitness (intrinsic rate of increase) and the relative abundance of transcripts from certain candidate genes in daughters, using RT‐qPCR (quantitative reverse‐transcription PCR). We found AGR in most cases, but responses varied according to the system being analyzed. For some pathways (e.g., cathepsins), the experience of both mothers and offsprings affected the response (i.e., when both, mother and daughter grew in the defended host, the maximum response was elicited; when only the mother grew in the defended host, an intermediate response was elicited; and when both, mother and daughter grew in a nondefended host, the response was undetectable). In other cases (esterases and GSTs), gene over‐expression was maintained even if the daughter was transferred to the nondefended host. In spite of these changes at the gene‐regulatory level, fitness was constant across hosts, suggesting that insects keep adapted thanks to this fluctuating gene expression. Also, it seems that that telescopic reproduction permits aphids to anticipate stressful environments, by minute changes in the timing of differential gene expression.

Evolutionary perspectives on learning: conceptual and methodological issues in the study of adaptive specializations

Inquiry into evolutionary adaptations has flourished since the modern synthesis of evolutionary biology. Comparative methods, genetic techniques, and various experimental and modeling approaches are used to test adaptive hypotheses. In psychology, the concept of adaptation is broadly applied and is central to comparative psychology and cognition. The concept of an adaptive specialization of learning is a proposed account for exceptions to general learning processes, as seen in studies of Pavlovian conditioning of taste aversions, sexual responses, and fear. The evidence generally consists of selective associations forming between biologically relevant conditioned and unconditioned stimuli, with conditioned responses differing in magnitude, persistence, or other measures relative to non-biologically relevant stimuli. Selective associations for biologically relevant stimuli may suggest adaptive specializations of learning, but do not necessarily confirm adaptive hypotheses as conceived of in evolutionary biology. Exceptions to general learning processes do not necessarily default to an adaptive specialization explanation, even if experimental results "make biological sense". This paper examines the degree to which hypotheses of adaptive specializations of learning in sexual and fear response systems have been tested using methodologies developed in evolutionary biology (e.g., comparative methods, quantitative and molecular genetics, survival experiments). A broader aim is to offer perspectives from evolutionary biology for testing adaptive hypotheses in psychological science.

The inheritance of process: a dynamical systems approach

A central unresolved problem of evolutionary biology concerns the way in which evolution at the genotypic level relates to the evolution of phenotypes. This genotype-phenotype map involves developmental and physiological processes, which are complex and not well understood. These processes co-determine the rate and direction of adaptive change by shaping the distribution of phenotypic variability on which selection can act. In this study, we argue-expanding on earlier ideas by Goodwin, Oster, and Alberch-that an explicit treatment of this map in terms of dynamical systems theory can provide an integrated understanding of evolution and development. We describe a conceptual framework, which demonstrates how development determines the probability of possible phenotypic transitions-and hence the evolvability of a biological system. We use a simple conceptual model to illustrate how the regulatory dynamics of the genotype-phenotype map can be passed on from generation to generation, and how heredity itself can be treated as a dynamic process. Our model yields explanations for punctuated evolutionary dynamics, the difference between micro- and macroevolution, and for the role of the environment in major phenotypic transitions. We propose a quantitative research program in evolutionary developmental systems biology-combining experimental methods with mathematical modeling-which aims at elaborating our conceptual framework by applying it to a wide range of evolving developmental systems. This requires a large and sustained effort, which we believe is justified by the significant potential benefits of an extended evolutionary theory that uses dynamic molecular genetic data to reintegrate development and evolution.

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

When Charles Darwin formulated the central principles of evolutionary biology in the Origin of Species in 1859 and the architects of the Modern Synthesis integrated these principles with population genetics almost a century later, the principal if not the sole objects of evolutionary biology were multicellular eukaryotes, primarily animals and plants. Before the advent of efficient gene sequencing, all attempts to extend evolutionary studies to bacteria have been futile. Sequencing of the rRNA genes in thousands of microbes allowed the construction of the three- domain “ribosomal Tree of Life” that was widely thought to have resolved the evolutionary relationships between the cellular life forms. However, subsequent massive sequencing of numerous, complete microbial genomes revealed novel evolutionary phenomena, the most fundamental of these being: (1) pervasive horizontal gene transfer (HGT), in large part mediated by viruses and plasmids, that shapes the genomes of archaea and bacteria and call for a radical revision (if not abandonment) of the Tree of Life concept, (2) Lamarckian-type inheritance that appears to be critical for antivirus defense and other forms of adaptation in prokaryotes, and (3) evolution of evolvability, i.e., dedicated mechanisms for evolution such as vehicles for HGT and stress-induced mutagenesis systems. In the non-cellular part of the microbial world, phylogenomics and metagenomics of viruses and related selfish genetic elements revealed enormous genetic and molecular diversity and extremely high abundance of viruses that come across as the dominant biological entities on earth. Furthermore, the perennial arms race between viruses and their hosts is one of the defining factors of evolution. Thus, microbial phylogenomics adds new dimensions to the fundamental picture of evolution even as the principle of descent with modification discovered by Darwin and the laws of population genetics remain at the core of evolutionary biology.

Complexity and the reductionism-holism debate in systems biology

Reductionism has largely influenced the development of science, culminating in its application to molecular biology. An increasing number of novel research findings have, however, shattered this view, showing how the molecular-reductionist approach cannot entirely handle the complexity of biological systems. Within this framework, the advent of systems biology as a new and more integrative field of research is described, along with the form which has taken on the debate of reductionism versus holism. Such an issue occupies a central position in systems biology, and nonetheless it is not always clearly delineated. This partly occurs because different dimensions (ontological, epistemological, methodological) are involved, and yet the concerned ones often remain unspecified. Besides, within systems biology different streams can be distinguished depending on the degree of commitment to embrace genuine systemic principles. Some useful insights into the future development of this discipline might be gained from the tradition of complexity and self-organization. This is especially true with regards the idea of self-reference, which incorporated into the organizational scheme is able to generate autonomy as an emergent property of the biological whole.

Evolutionary molecular medicine

Evolution has long provided a foundation for population genetics, but some major advances in evolutionary biology from the twentieth century that provide foundations for evolutionary medicine are only now being applied in molecular medicine. They include the need for both proximate and evolutionary explanations, kin selection, evolutionary models for cooperation, competition between alleles, co-evolution, and new strategies for tracing phylogenies and identifying signals of selection. Recent advances in genomics are transforming evolutionary biology in ways that create even more opportunities for progress at its interfaces with genetics, medicine, and public health. This article reviews 15 evolutionary principles and their applications in molecular medicine in hopes that readers will use them and related principles to speed the development of evolutionary molecular medicine.

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

Organisms that live in variable environments must adjust their physiology to compensate for environmental change. Modern functional genomics technologies offer global top-down discovery-based tools for identifying and exploring the mechanistic basis by which organisms respond physiologically to a detected change in the environment. Given that populations and species from different niches may exhibit different acclimation abilities, comparative genomic approaches may offer more nuanced understanding of acclimation responses, and provide insight into the mechanistic and genomic basis of variable acclimation. The physiological genomics literature is large and growing, as is the comparative evolutionary genomics literature. Yet, expansion of physiological genomics experiments to exploit taxonomic variation remains relatively undeveloped. Here, recent advances in the emerging field of comparative physiological genomics are considered, including examples of plants, bees and fish, and opportunities for further development are outlined particularly in the context of climate change research. Elements of robust experimental design are discussed with emphasis on the phylogenetic comparative approach. Understanding how acclimation ability is partitioned among populations and species in nature, and knowledge of the relevant genes and mechanisms, will be important for characterizing and predicting the ecological and evolutionary consequences of human-accelerated environmental change.

Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis

Systems biology (SB) is at least a decade old now and maturing rapidly. A more recent field, evolutionary systems biology (ESB), is in the process of further developing system-level approaches through the expansion of their explanatory and potentially predictive scope. This chapter will outline the varieties of ESB existing today by tracing the diverse roots and fusions that make up this integrative project. My approach is philosophical and historical. As well as examining the recent origins of ESB, I will reflect on its central features and the different clusters of research it comprises. In its broadest interpretation, ESB consists of five overlapping approaches: comparative and correlational ESB; network architecture ESB; network property ESB; population genetics ESB; and finally, standard evolutionary questions answered with SB methods. After outlining each approach with examples, I will examine some strong general claims about ESB, particularly that it can be viewed as the next step toward a fuller modern synthesis of evolutionary biology (EB), and that it is also the way forward for evolutionary and systems medicine. I will conclude with a discussion of whether the emerging field of ESB has the capacity to combine an even broader scope of research aims and efforts than it presently does.

New experiments for an undivided genetics

There used to be a broad split within the experimental genetics research community between those who did mechanistic research using homozygous laboratory strains and those who studied patterns of genetic variation in wild populations. The former benefited from the advantage of reproducible experiments, but faced difficulties of interpretation given possible genomic and evolutionary complexities. The latter research approach featured readily interpreted evolutionary and genomic contexts, particularly phylogeny, but was poor at determining functional significance. Such burgeoning experimental strategies as genome-wide analysis of quantitative trait loci, genotype-phenotype associations, and the products of experimental evolution are now fostering a unification of experimental genetic research that strengthens its scientific power.

Network biology: a direct approach to study biological function

In this paper we discuss the dualism of gene networks and their role in systems biology. We argue that gene networks (1) can serve as a conceptual framework, forming a fundamental level of a phenomenological description, and (2) are a means to represent and analyze data. The latter point does not only allow a systems analysis but is even amenable for a direct approach to study biological function. Here we focus on the clarity of our main arguments and conceptual meaning of gene networks, rather than the causal inference of gene networks from data. WIREs Syst Biol Med 2011 3 379-391 DOI: 10.1002/wsbm.134 For further resources related to this article, please visit the WIREs website.

Playing Darwin. Part A. Experimental evolution in Drosophila

In 2009 we celebrate Charles Darwin's second centenary, and 150 years since the publication of 'The Origin of Species'. After so many years, what has changed in the way we understand Evolution? Obviously we have now a full understanding of the mechanisms underlying heritability. Many molecular tools are available, allowing among other things to reconstruct more accurately the evolutionary history of species and use a comparative approach to infer evolutionary processes. But we can also study evolution in action. Such studies-Experimental Evolution-help us to characterize in detail the evolutionary processes and patterns as a function of environmental challenges, the previous history and present state of populations, and the interactions between such factors. We have now a wide variety of organisms that have been studied with this approach, exploring a diversity of potentialities, in biological characteristics and genetic tools, and covering a variety of evolutionary questions. In this short article I will illustrate the potentialities of Experimental Evolution, focusing in three studies in Drosophila. These and other studies of Experimental Evolution illustrate that Evolution is often local, involving complex patterns and processes, which lead both to specific adaptations and to biological diversity, as Darwin already stated clearly in 'The Origin of Species'.

So what do we really mean when we say that systems biology is holistic?

BACKGROUND

An old debate has undergone a resurgence in systems biology: that of reductionism versus holism. At least 35 articles in the systems biology literature since 2003 have touched on this issue. The histories of holism and reductionism in the philosophy of biology are reviewed, and the current debate in systems biology is placed in context.

RESULTS

Inter-theoretic reductionism in the strict sense envisaged by its creators from the 1930s to the 1960s is largely impractical in biology, and was effectively abandoned by the early 1970s in favour of a more piecemeal approach using individual reductive explanations. Classical holism was a stillborn theory of the 1920s, but the term survived in several fields as a loose umbrella designation for various kinds of anti-reductionism which often differ markedly. Several of these different anti-reductionisms are on display in the holistic rhetoric of the recent systems biology literature. This debate also coincides with a time when interesting arguments are being proposed within the philosophy of biology for a new kind of reductionism.

CONCLUSIONS

Engaging more deeply with these issues should sharpen our ideas concerning the philosophy of systems biology and its future best methodology. As with previous decisive moments in the history of biology, only those theories that immediately suggest relatively easy experiments will be winners.

Atomic force microscopy comes of age

AFM (atomic force microscopy) analysis, both of fixed cells, and live cells in physiological environments, is set to offer a step change in the research of cellular function. With the ability to map cell topography and morphology, provide structural details of surface proteins and their expression patterns and to detect pico-Newton force interactions, AFM represents an exciting addition to the arsenal of the cell biologist. With the explosion of new applications, and the advent of combined instrumentation such as AFM-confocal systems, the biological application of AFM has come of age. The use of AFM in the area of biomedical research has been proposed for some time, and is one where a significant impact could be made. Fixed cell analysis provides qualitative and quantitative subcellular and surface data capable of revealing new biomarkers in medical pathologies. Image height and contrast, surface roughness, fractal, volume and force analysis provide a platform for the multiparameter analysis of cell and protein functions. Here, we review the current status of AFM in the field and discuss the important contribution AFM is poised to make in the understanding of biological systems.

Long-term functional side-effects of stimulants and sedatives in Drosophila melanogaster

BACKGROUND

Small invertebrate animals, such as nematodes and fruit flies, are increasingly being used to test candidate drugs both for specific therapeutic purposes and for long-term health effects. Some of the protocols used in these experiments feature such experimental design features as lifelong virginity and very low densities. By contrast, the ability of both fruit flies and nematodes to resist stress is frequently correlated with their longevity and other functional measures, suggesting that low-stress assays are not necessarily the only useful protocol for testing the long-term effects of drugs.

METHODOLOGY/PRINCIPAL FINDINGS

Here we report an alternative protocol for fruit fly drug-testing that maximizes reproductive opportunities and other types of interaction, with moderately high population densities. We validate this protocol using two types of experimental tests: 1. We show that this protocol detects previously well-established genetic differences between outbred fruit fly populations. 2. We show that this protocol is able to distinguish among the long-term effects of similar types of drugs within two broad categories, stimulants and tranquilizers.

CONCLUSIONS

Large-scale fly drug testing can be conducted using mixed-sex high-density cage assays. We find that the commonly-used stimulants caffeine and theobromine differ dramatically in their chronic functional effects, theobromine being more benign. Likewise, we find that two generic pharmaceutical tranquilizers, lithium carbonate and valproic acid, differ dramatically in their chronic effects, lithium being more benign. However, these findings do not necessarily apply to human subjects, and we thus do not recommend the use of any one substance over any other.

Adaptation, aging, and genomic information

Aging is not simply an accumulation of damage or inappropriate higher-order signaling, though it does secondarily involve both of these subsidiary mechanisms. Rather, aging occurs because of the extensive absence of adaptive genomic information required for survival to, and function at, later adult ages, due to the declining forces of natural selection during adult life. This absence of information then secondarily leads to misallocations and damage at every level of biological organization. But the primary problem is a failure of adaptation at later ages. Contemporary proposals concerning means by which human aging can be ended or cured which are based on simple signaling or damage theories will thus reliably fail. Strategies based on reverse-engineering age-extended adaptation using experimental evolution and genomics offer the prospect of systematically greater success.

Towards a postmodern synthesis of evolutionary biology

In 2009, we are celebrating the 200th anniversary of Charles Darwin and the 150th jubilee of his masterpiece, the Origin of Species. Darwin developed the first coherent and compelling narrative of biological evolution and thus founded evolutionary biology-and modern biology in general, remembering the famous dictum of Dobzhansky. It is, however, counter-productive, and ultimately, a disservice to Darwin's legacy, to define modern evolutionary biology as neo-Darwinism. The current picture of evolution, informed, in particular, by results of comparative genomics and systems biology, is by far more complex than that presented in the Origin of Species, so that Darwinian principles, including natural selection, are incorporated into the evolving new synthesis as important but certainly not all-embracing tenets. This expansion of evolutionary biology does not denigrate Darwin in the least but rather emphasizes the fertility of his ideas.

Darwinian evolution in the light of genomics

Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or ‘forest’ of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

Making SENSE: strategies for engineering negligible senescence evolutionarily

Thirty years ago, in 1977, few biologists thought that it would be possible to increase the maximum life span characteristic of each species over the variety of environmental conditions in which they live, whether in nature or in the laboratory. But the evolutionary theory of aging suggested otherwise. Accordingly, experiments were performed with fruit flies, Drosophila melanogaster, which showed that manipulation of the forces of natural selection over a number of generations could substantially slow the rate of aging, both demographically and physiologically. After this first transgression of the supposedly absolute limits to life extension, it was suggested that mammals too could be experimentally evolved to have greater life spans and slower aging. And further, it was argued that such postponed-aging mammals could be used to reverse-engineer a slowing of human aging. The subsequent discovery and theoretical explanation of mortality-rate plateaus revealed that aging was not due to the progressive physiological accumulation of damage. Instead, aging is now understood by evolutionary biologists to arise from a transient fall in age-specific adaptation, a fall that does not necessarily proceed toward ineluctable death. This implies that SENS must be based on re-tuning adaptation, not repairing damage. As evolutionary manipulation of model organisms shows us how adaptation can be focused on engineering negligible senescence, there are thus both scientific and practical reasons for making SENS evolutionary; that is making SENSE.