Adaptation and Moral Realism

Conventional wisdom has it that evolution makes a sham of morality, even if morality is an adaptation. I disagree. I argue that our best current adaptationist theory of meaning offers objective truth conditionsfor signaling systems of all sorts. The objectivity is, however, relative to species – specifically to the adaptive history of the signaling system in question. While evolution may not provide the kind of species independent objective standards that (e.g.) Kantians desire, this should be enough for the practical work of justifying our confidence in the objectivity of moral standards. If you believe morality is an adaptation, you should be a moral realist.     

What Does it Take to Produce Interpretation? Informational, Peircean and Code-Semiotic Views on Biosemiotics

This paper presents a critical analysis of code-semiotics, which we see as the latest attempt to create paradigmatic foundation for solving the question of the emergence of life and consciousness. We view code semiotics as a an attempt to revise the empirical scientific Darwinian paradigm, and to go beyond the complex systems, emergence, self-organization, and informational paradigms, and also the selfish gene theory of Dawkins and the Peircean pragmaticist semiotic theory built on the simultaneous types of evolution. As such it is a new and bold attempt to use semiotics to solve the problems created by the evolutionary paradigm’s commitment to produce a theory of how to connect the two sides of the Cartesian dualistic view of physical reality and consciousness in a consistent way.     

Reports of the Death of Extrinsic Mortality Moulding Senescence Have Been Greatly Exaggerated

The classic evolutionary theory of aging posits that senescence evolves because the weakening of selection with age allows mutations with late-acting deleterious effects to accumulate. Because extrinsic mortality is an important cause of weakening selection, the central prediction of the theory has been that higher extrinsic mortality should lead to the evolution of a higher rate of senescence. However, the validity of this prediction has been questioned, even to the extent of suggesting that it is not a prediction of the theory at all, primarily on the basis that changes in population growth rate will compensate for changes in extrinsic mortality. The implication is that empiricists have been using the wrong prediction to test the theory. This claim is misleading, however, because it does not apply on an evolutionary timescale, when population size must be roughly constant. With a constant population size, Hamilton’s fitness sensitivities show that extrinsic mortality determines the rate at which the strength of selection declines with age, and thus determines the rate of senescence. The central prediction has been confirmed in the few controlled experiments with model organisms that have been conducted, but clearly this is an area ripe for further investigation.     

Waddington redux: models and explanation in stem cell and systems biology

Stem cell biology and systems biology are two prominent new approaches to studying cell development. In stem cell biology, the predominant method is experimental manipulation of concrete cells and tissues. Systems biology, in contrast, emphasizes mathematical modeling of cellular systems. For scientists and philosophers interested in development, an important question arises: how should the two approaches relate? This essay proposes an answer, using the model of Waddington’s landscape to triangulate between stem cell and systems approaches. This simple abstract model represents development as an undulating surface of hills and valleys. Originally constructed by C. H. Waddington to visually explicate an integrated theory of genetics, development and evolution, the landscape model can play an updated unificatory role. I examine this model’s structure, representational assumptions, and uses in all three contexts, and argue that explanations of cell development require both mathematical models and concrete experiments. On this view, the two approaches are interdependent, with mathematical models playing a crucial but circumscribed role in explanations of cell development.     

An international study ofyoung peoples' drawings of what is inside themselves

This paper reviews the question of why the presentation of evolution in class frequently does not achieve acceptance of the evolutionary theory. In general, problems are twofold. Firstly, students may come to this particular topic with strong preconceptions, often based on specific religious teachings. Secondly, teachers may or may not bring an informed and/or dedicated approach to the teaching of evolution, relating to what they themselves were taught. Additional to our review of this topic and its problems, we suggest the use of a simple ‘test’ formulated, not on trying to impose knowledge and belief of evolution on the student, but on directing students towards the application of information on evolution to material already familiar to them. In this process, it is hoped that students will naturally incorporate at least some of the ideas of evolution into their own belief systems. Students are thus encouraged to assess or reassess evolution in terms of what they already consider to be true from their own experiences. Preliminary results (two trial runs) using this questionnaire indicate that students readily apply information with which they are familiar to Darwinian principles, and vice versa. These results, including verbal and written comments, also suggest that this ‘test’ may be meaningful as a first step towards acceptance of evolutionary theory. Teachers may find our questionnaire useful in determining a student's ability to understand evolutionary theory, and in exploring connections between understanding of and belief in evolution. Reviewed by Will H. Blackwell     

Helping in cooperatively breeding long-tailed tits: a test of Hamilton's rule

Inclusive fitness theory provides the conceptual framework for our current understanding of social evolution, and empirical studies suggest that kin selection is a critical process in the evolution of animal sociality. A key prediction of inclusive fitness theory is that altruistic behaviour evolves when the costs incurred by an altruist (c) are outweighed by the benefit to the recipient (b), weighted by the relatedness of altruist to recipient (r), i.e. Hamilton''s rule rb > c. Despite its central importance in social evolution theory, there have been relatively few empirical tests of Hamilton''s rule, and hardly any among cooperatively breeding vertebrates, leading some authors to question its utility. Here, we use data from a long-term study of cooperatively breeding long-tailed tits Aegithalos caudatus to examine whether helping behaviour satisfies Hamilton''s condition for the evolution of altruism. We show that helpers are altruistic because they incur survival costs through the provision of alloparental care for offspring. However, they also accrue substantial benefits through increased survival of related breeders and offspring, and despite the low average relatedness of helpers to recipients, these benefits of helping outweigh the costs incurred. We conclude that Hamilton''s rule for the evolution of altruistic helping behaviour is satisfied in this species.     

Evolution of biological information

How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon defined information as a decrease in the uncertainty of a receiver. For molecular systems, uncertainty is closely related to entropy and hence has clear connections to the Second Law of Thermodynamics. These aspects of information theory have allowed the development of a straightforward and practical method of measuring information in genetic control systems. Here this method is used to observe information gain in the binding sites for an artificial ‘protein’ in a computer simulation of evolution. The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium.     

Negotiation of mutualism: rhizobia and legumes

The evolution and persistence of biological cooperation have been an important puzzle in evolutionary theory. Here, we suggest a new approach based on bargaining theory to tackle the question. We present a mechanistic model for negotiation of benefits between a nitrogen-fixing nodule and a legume plant. To that end, we first derive growth rates for the nodule and plant from metabolic models of each as a function of material fluxes between them. We use these growth rates as pay-off functions in the negotiation process, which is analogous to collective bargaining between a firm and a workers' union. Our model predicts that negotiations lead to the Nash bargaining solution, maximizing the product of players' pay-offs. This work introduces elements of cooperative game theory into the field of mutualistic interactions. In the discussion of the paper, we argue for the benefits of such an approach in studying the question of biological cooperation.     

Virulence evolution via host exploitation and toxin production in spore-producing pathogens

Many pathogens produce resilient free-living propagules that allow their dissemination in the absence of direct contact between susceptible and infected hosts. One might expect pathogens capable of producing such long-lived propagules to evolve high levels of virulence because their reproductive success is de-coupled from the survival of their host. Despite some comparative data supporting this prediction, theory has questioned its general validity. I present theoretical results that incorporate two transmission routes neglected by previous theory: death-mediated propagule production and direct host-host transmission. This theory predicts that spore-producing pathogens should evolve high levels of virulence under quite broad conditions. Moreover, a novel prediction of this theory is that the production of propagules can generate selection for the evolution of pathogen characteristics such as toxins whose sole function is to kill the host. This latter result reveals an unanticipated mechanism through which virulence is expected to evolve in spore-producing pathogens.     

What is an organism? An immunological answer

The question, "What is an organism?," formerly considered as essential in biology, has now been increasingly replaced by a larger question, "What is a biological individual?" On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection that tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory that makes possible a biological individuation based on physiological grounds. I give a new answer to the question of the individuation of an organism by linking together the evolutionary and the immunological approaches to biological individuation.     

From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses

Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are identified as major determinants of these rates. Furthermore, a quantitative analysis reveals that, as expected, evolution rates increase linearly with mutation rates for slowly mutating viruses. However, this relationship plateaus for fast mutating viruses. A model is proposed in which deleterious mutations impose an evolutionary speed limit and set an extinction threshold in nature. The model is consistent with data from replication kinetics, selection strength and chemical mutagenesis studies.     

Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory

The nearly neutral theory of molecular evolution predicts larger generation-time effects for synonymous than for nonsynonymous substitutions. This prediction is tested using the sequences of 49 single-copy genes by calculating the average and variance of synonymous and nonsynonymous substitutions in mammalian star phylogenies (rodentia, artiodactyla, and primates). The average pattern of the 49 genes supports the prediction of the nearly neutral theory, with some notable exceptions.The nearly neutral theory also predicts that the variance of the evolutionary rate is larger than the value predicted by the completely neutral theory. This prediction is tested by examining the dispersion index (ratio of the variance to the mean), which is positively correlated with the average substitution number. After weighting by the lineage effects, this correlation almost disappears for nonsynonymous substitutions, but not quite so for synonymous substitutions. After weighting, the dispersion indices of both synonymous and nonsynonymous substitutions still exceed values expected under the simple Poisson process. The results indicate that both the systematic bias in evolutionary rate among the lineages and the episodic type of rate variation are contributing to the large variance. The former is more significant to synonymous substitutions than to nonsynonymous substitutions. Isochore evolution may be similar to synonymous substitutions. The rate and pattern found here are consistent with the nearly neutral theory, such that the relative contributions of drift and selection differ between the two types of substitutions. The results are also consistent with Gillespie's episodic selection theory.     

Origins for Everyone

The origin of life on Earth remains a mystery, but the question can still be approached with scientific rigor. Identifying life??s origins requires the definition of life itself, which has been described as a self-sustaining system capable of Darwinian evolution, although it's also possible that there is no good scientific definition. All known living systems contain linear strings of information based on DNA, a molecule that makes Darwinian evolution possible through replication and mutation. This review explains the scientific concepts and issues underlying the origin of life, possible mechanisms of origins, and the features of living systems that can arguably be viewed as an inevitable consequence of the earliest molecules.     

Coherent phenomena in photosynthetic light harvesting: part two—observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or “quantum beats” via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.     

Cross-talk and information transfer in mammalian and bacterial signaling

In mammalian and bacterial cells simple phosphorylation circuits play an important role in signaling. Bacteria have hundreds of two-component signaling systems that involve phosphotransfer between a receptor and a response regulator. In mammalian cells a similar pathway is the TGF-beta pathway, where extracellular TGF-beta ligands activate cell surface receptors that phosphorylate Smad proteins, which in turn activate many genes. In TGF-beta signaling the multiplicity of ligands begs the question as to whether cells can distinguish signals coming from different ligands, but transduced through a small set of Smads. Here we use information theory with stochastic simulations of networks to address this question. We find that when signals are transduced through only one Smad, the cell cannot distinguish between different levels of the external ligands. Increasing the number of Smads from one to two significantly improves information transmission as well as the ability to discriminate between ligands. Surprisingly, both total information transmitted and the capacity to discriminate between ligands are quite insensitive to high levels of cross-talk between the two Smads. Robustness against cross-talk requires that the average amplitude of the signals are large. We find that smaller systems, as exemplified by some two-component systems in bacteria, are significantly much less robust against cross-talk. For such system sizes phosphotransfer is also less robust against cross-talk than phosphorylation. This suggests that mammalian signal transduction can tolerate a high amount of cross-talk without degrading information content. This may have played a role in the evolution of new functionalities from small mutations in signaling pathways, allowed for the development of cross-regulation and led to increased overall robustness due to redundancy in signaling pathways. On the other hand the lack of cross-regulation observed in many bacterial two-component systems may partly be due to the loss of information content due to cross-talk.     

Kin selection does not explain male aggregation at leks of 4 manakin species

In lek-mating systems, males aggregate at display arenas andfemales visit solely for the purpose of mating. This breedingsystem is characterized by high variance in male mating successwith one male often receiving most copulations. High reproductiveskew among males has led to question why males join leks whentheir chances of reproductive success are so low. Kin selectionhas been invoked as a mechanism to explain the evolution oflekking behavior, whereby nonreproducing but genetically relatedmales gain indirect inclusive-fitness benefits. Evidence forkin selection among lek-mating birds is, however, mixed. Here,we show that kin selection is unlikely to be an important explanationfor evolution of lekking behavior in manakins (Aves: Pipridae).We found that for 4 species chosen from several major cladeswithin Pipridae, males within leks were not significantly morerelated than expected from random assortment of males in thepopulation. This means that nonreproducing males do not gainindirect inclusive-fitness benefits by joining leks. This resultsuggests alternative mechanisms must be invoked to explain theevolution of lek-mating systems in manakins.     

What is complexity?

Arguments for or against a trend in the evolution of complexity are weakened by the lack of an unambiguous definition of complexity. Such definitions abound for both dynamical systems and biological organisms, but have drawbacks of either a conceptual or a practical nature. Physical complexity, a measure based on automata theory and information theory, is a simple and intuitive measure of the amount of information that an organism stores, in its genome, about the environment in which it evolves. It is argued that physical complexity must increase in molecular evolution of asexual organisms in a single niche if the environment does not change, due to natural selection. It is possible that complexity decreases in co-evolving systems as well as at high mutation rates, in sexual populations, and in time-dependent landscapes. However, it is reasoned that these factors usually help, rather than hinder, the evolution of complexity, and that a theory of physical complexity for co-evolving species will reveal an overall trend towards higher complexity in biological evolution.