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.     

Research program for a search of the origin of Darwinian evolution

The search for origin of ‘life’ is made even more complicated by differing definitions of the subject matter, although a general consensus is that an appropriate definition should center on Darwinian evolution (Cleland and Chyba 2002). Within a physical approach which has been defined as a level-4 evolution (Tessera and Hoelzer 2013), one mechanism could be described showing that only three conditions are required to allow natural selection to apply to populations of different system lineages. This approach leads to a vesicle- based model with the necessary properties. Of course such a model has to be tested. Thus, after a brief presentation of the model an experimental program is proposed that implements the different steps able to show whether this new direction of the research in the field is valid and workable.     

Hitchhiking under positive Darwinian selection

Positive selection can be inferred from its effect on linked neutral variation. In the restrictive case when there is no recombination, all linked variation is removed. If recombination is present but rare, both deterministic and stochastic models of positive selection show that linked variation hitchhikes to either low or high frequencies. While the frequency distribution of variation can be influenced by a number of evolutionary processes, an excess of derived variants at high frequency is a unique pattern produced by hitchhiking (derived refers to the nonancestral state as determined from an outgroup). We adopt a statistic, H, to measure an excess of high compared to intermediate frequency variants. Only a few high-frequency variants are needed to detect hitchhiking since not many are expected under neutrality. This is of particular utility in regions of low recombination where there is not much variation and in regions of normal or high recombination, where the hitchhiking effect can be limited to a small (<1 kb) region. Application of the H test to published surveys of Drosophila variation reveals an excess of high frequency variants that are likely to have been influenced by positive selection.     

Revisiting the Darwinian shortfall in biodiversity conservation

Among the seven shortfalls of biodiversity knowledge, the one that makes direct reference to phylogenetic information is the Darwinian shortfall, which embraces three components: “(1) the lack of fully resolved phylogenies for most groups of organisms; (2) the limited knowledge of branch lengths and difficulties in absolute time calibrations; and (3) unknown evolutionary models linking those phylogenies to ecological traits and the life-history variation” (Diniz-Filho et al. in Trends Ecol Evol 28:689–694, 2013). In order to overcome them, Diniz-Filho et al. (Trends Ecol Evol 28:689–694, 2013) emphasized the need to know the problems relative to phylogeny reconstruction, but they did not provide a clear comprehension of these problems. In the present article, I aim to comment on these problems in the context of the five epistemic stages of phylogenetic analysis. These are: (1) taxon sampling; (2) evidence; (3) homology assessment; (4) optimization methods; and (5) hypotheses formulation. A brief review of these stages is necessary to comprehend how complex is the use of phylogenetic hypotheses in ecology and conservation. I also provide additional and balanced solutions in an attempt to overcome the evolutionary shortfall.     

Ruse's Darwinian meta-ethics: A critique

Michael Ruse, in Taking Darwin Seriously seeks to establish that taking Darwin seriously requires us to treat morality as subjective and naturalistic. I argue that, if morality is not objective, then we have no good reason for being moral if we can avoid detection and punishment. As a consequence, we will only continue to behave morally as long as we remain ignorant of Ruse's theory, that is, as long as the cat is not let out of the bag. Ruse offers a number of arguments to show that his theory can overcome such problems. I argue that they all fail. Ruse also argues that he can offer a naturalistic account of ethics which steps around the naturalistic fallacy and avoids the confusion of reasons with causes. His principal argument for this view is an analogy between spiritualism and morality. I argue that this analogy fails.     

Darwinian psychiatry and the concept of mental disorder

In this paper, we discuss the concept of mental disorder from the perspective of Darwinian psychiatry. Using this perspective does not resolve all of the quandaries which philosophers of medicine face when trying to provide a general definition of disease. However, it does take an important step toward clarifying why current methods of psychiatric diagnosis are criticizable and how clinicians can improve the identification of true mental disorders. According to Darwinian psychiatry, the validity of the conventional criteria of psychiatric morbidity is dependent on their association with functional impairment. Suffering, statistical deviance, and physical lesion are frequent correlates of mental disorders but, in absence of dysfunctional consequences, none of these criteria is sufficient for considering a psychological or behavioral condition as a psychiatric disorder. The Darwinian concept of mental disorder builds from two basic ideas: (1) the capacity to achieve biological goals is the best single attribute that characterizes mental health; and (2), the assessment of functional capacities cannot be properly made without consideration of the environment in which the individual lives. These two ideas reflect a concept of mental disorder that is both functional and ecological. A correct application of evolutionary knowledge should not necessarily lead to the conclusion that therapeutic intervention should be limited to conditions that jeopardize biological adaptation. Because one of the basic aims of medicine is to alleviate human suffering, an understanding of the evolutionary foundations of the concept of mental disorder should translate into more effective ways for promoting individual and social well-being, not into the search for natural laws determining what is therapeutically right or wrong.     

Bit by bit: the Darwinian basis of life

All known examples of life belong to the same biology, but there is increasing enthusiasm among astronomers, astrobiologists, and synthetic biologists that other forms of life may soon be discovered or synthesized. This enthusiasm should be tempered by the fact that the probability for life to originate is not known. As a guiding principle in parsing potential examples of alternative life, one should ask: How many heritable “bits” of information are involved, and where did they come from? A genetic system that contains more bits than the number that were required to initiate its operation might reasonably be considered a new form of life.Thanks to a combination of ground- and space-based astronomical observations, the number of confirmed extrasolar planets will soon exceed 1,000. An increasing number of these will be said to lie within the “habitable zone” and even be pronounced as “Earth-like.” Within a decade there will be observational data regarding the atmospheric composition of some of those planets, and just maybe those data will indicate something funny going on—something well outside the state of chemical equilibrium—on a potentially hospitable planet. Perhaps our astronomy colleagues should be forgiven for their enthusiasm in declaring that humanity is on the brink of discovering alien life.But haven''t we heard this before? Didn''t President Clinton announce in 1996 that a Martian meteorite recovered in Antarctica [1] “speaks of the possibility of life” on Mars? (No, it turned out to be mineralic artifacts.) Wasn''t some “alien” arsenic-based life discovered recently in Mono Lake, California [2]? (No, it''s a familiar proteobacterium struggling to survive in a toxic environment.) Didn''t Craig Venter and his colleagues recently create a synthetic bacterial cell [3], “the first self-replicating species we''ve had on the planet whose parent is a computer”? (No, its parent is Mycoplasma mycoides and its genome was dutifully reconstructed through DNA synthesis and PCR amplification.)Why are we so confused (or so lonely) that we have such trouble distinguishing life from non-life and distinguishing our biology from another? A key limitation is that we know of only one life form, causing us to regard life from that singular perspective (Figure 1). We see life as cellular, with a nucleic acid genome that is translated to a protein machinery. Life self-reproduces, transmits heritable information to its progeny, and undergoes Darwinian evolution based on natural selection. Life captures high-energy starting materials and converts them to lower-energy products to drive metabolic processes. Life exists on at least one temperate, rocky planet, where it has persisted for about four billion years. There are likely to be tens of thousands of “habitable” planets within a thousand light years of Earth, and more than a billion such planets in our galaxy, so surely (say the astronomers) we are not alone.Open in a separate windowFigure 1Phylogenetic tree of life based on small-subunit ribosomal RNA sequences, showing representative species from each of the three kingdoms (compiled by Pace [11]).The root of the tree is indicated by a horizontal line. The locations on the tree of Halomonas sp. (GFAJ-1) [2] and Mycoplasma mycoides (JCVI-syn1.0) [3] are indicated by black circles adjacent to Escherichia and Bacillus, respectively.     

Darwinian evolution does not rule out the gaia hypothesis

This study explores so-called Darwinian Daisyworlds mathematically rigorously in detail. The original Daisyworld was introduced by Watson & Lovelock (1983) to demonstrate how two species of daisies regulate the global temperature of their planet through competition among these species against the rising solar luminosity, i.e. the Gaia hypothesis. Its variants are Darwinian Daisyworlds in which daisies can adapt themselves to the local temperature. Robertson & Robinson (1998) insist their Darwinian daisies lose the ability for temperature regulation on the basis of their spreadsheet simulations. Lenton & Lovelock (2000) point out that the constraints on adaptation recovers Darwinian daisies' ability of temperature regulation on the basis of their Euler-code simulations. The present study shows there exist the exact and closed-form solutions to these two Daisyworlds. The results contradict the former studies: Robertson and Robinson's daisies do regulate the global temperature even longer than non-adaptive daisies; Lenton and Lovelock's daisies are less adaptive than Robertson and Robinson's daisies because of the constraints on adaptation; the introduction of weak adaptability drives species into a dead end of evolution. Thus, the present results confirm that the Gaia hypothesis and Darwinian evolution can coexist.     

Elder abuse--an ethical dilemma for caregivers

The mistreatment of elders by their adult children, spouses, or other caregivers is a problem of increasing magnitude. We have few laws and even fewer policies to help caregivers identify and prevent abuse, partly because it has no common pattern, and partly because it so often goes unreported. Abuse can be intentional or unintentional, and as often results from failing to act, as from acts of anger or cruelty. Therefore, we must do a better job of enforcing mandatory reporting and educating and supporting our caregivers to prevent stress and burnout. Above all, we must seek an ethical course of action, knowing that there are legal, personal, and professional ethical ideals and standards that can guide us, whether the elderly are being cared for in their own home or in nursing homes.     

The relativity of Darwinian populations and the ecology of endosymbiosis

If there is a single discipline of science calling the basic concepts of biology into question, it is without doubt microbiology. Indeed, developments in microbiology have recently forced us to rethink such fundamental concepts as the organism, individual, and genome. In this paper I show how microorganisms are changing our understanding of natural aggregations and develop the concept of a Darwinian population to embrace these discoveries. I start by showing that it is hard to set the boundaries of a Darwinian population, and I suggest thinking of a Darwinian population as a relative property of a Darwinian individual. Then I argue, in contrast to the commonly held view, that Darwinian populations are multispecies units, and that in order to accept the multispecies account of Darwinian populations we have to separate fitness from natural selection. Finally, I show how all these ideas provide a theoretical framework leading to a more precise understanding of the ecology of endosymbiosis than is afforded by poetic metaphors such as ‘slavery’.     

Labs and slabs: Television crime drama and the quest for forensic realism

This essay examines how crime dramas produced during, and since, the 1990s became marked by the quest for ‘forensic realism’. In particular, the essay traces a landmark shift in the development of forensic realism in the form of the ground-breaking British police drama Prime Suspect in 1991. It is argued that this television series not only represents a turning point in television history, but that it also constitutes a key text in the broader cultural turn towards forensic fascination. Prime Suspect vividly revealed and displayed corpses, crime scenes and post-mortem photos in an unprecedented fashion for television. This essay shows how in the process it established new standards and expectations regarding the aesthetics and thematic content of the perceived ‘realism’ of the crime genre. Through an analysis of the reception and impact of Prime Suspect the essay also demonstrates how crime drama’s increasing fascination with forensic realism has driven debate over just what kinds of stories and images constitute acceptable or appropriate subject matter for popular entertainment, and for the medium of television itself.