A critical review of the statisticalist debate

Over the past decade philosophers of biology have discussed whether evolutionary theory is a causal theory or a phenomenological study of evolution based solely on the statistical features of a population. This article reviews this controversy from three aspects, respectively concerning the assumptions, applications, and explanations of evolutionary theory, with a view to arriving at a definite conclusion in each contention. In so doing I also argue that an implicit methodological assumption shared by both sides of the debate, namely the overconfidence in conceptual analysis as a tool to understand the scientific theory, is the real culprit that has both generated the problem and precluded its solution for such a long time.     

Life-history evolution and the origin of multicellularity

The fitness of an evolutionary individual can be understood in terms of its two basic components: survival and reproduction. As embodied in current theory, trade-offs between these fitness components drive the evolution of life-history traits in extant multicellular organisms. Here, we argue that the evolution of germ-soma specialization and the emergence of individuality at a new higher level during the transition from unicellular to multicellular organisms are also consequences of trade-offs between the two components of fitness-survival and reproduction. The models presented here explore fitness trade-offs at both the cell and group levels during the unicellular-multicellular transition. When the two components of fitness negatively covary at the lower level there is an enhanced fitness at the group level equal to the covariance of components at the lower level. We show that the group fitness trade-offs are initially determined by the cell level trade-offs. However, as the transition proceeds to multicellularity, the group level trade-offs depart from the cell level ones, because certain fitness advantages of cell specialization may be realized only by the group. The curvature of the trade-off between fitness components is a basic issue in life-history theory and we predict that this curvature is concave in single-celled organisms but becomes increasingly convex as group size increases in multicellular organisms. We argue that the increasingly convex curvature of the trade-off function is driven by the initial cost of reproduction to survival which increases as group size increases. To illustrate the principles and conclusions of the model, we consider aspects of the biology of the volvocine green algae, which contain both unicellular and multicellular members.     

Moral Philosophy,Moral Expertise,and the Argument from Disagreement

Several recent articles have weighed in on the question of whether moral philosophers can be counted as moral experts. One argument denying this has been rejected by both sides of the debate. According to this argument, the extent of disagreement in modern moral philosophy prevents moral philosophers from being classified as moral experts. Call this the Argument From Disagreement (AD). In this article, I defend a version of AD. Insofar as practical issues in moral philosophy are characterized by disagreement between moral philosophers who are more or less equally well credentialed on the issue, non‐philosophers have no good reasons to defer to their views.     

Fundamental issues in systems biology

In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call 'pragmatic systems biology', emphasises large-scale molecular interactions; the other, which we shall refer to as 'systems-theoretic biology', emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers.     

On the assignment of fitness to parents and offspring: whose fitness is it and when does it matter?

There has been a long‐standing conceptual debate over the legitimacy of assigning components of offspring fitness to parents for purposes of evolutionary analysis. The benefits and risks inherent in assigning fitness of offspring to parents have been given primarily as verbal arguments and no explicit theoretical analyses have examined quantitatively how the assignment of fitness can affect evolutionary inferences. Using a simple quantitative genetic model, we contrast the conclusions drawn about how selection acts on a maternal character when components of offspring fitness (such as early survival) are assigned to parents vs. when they are assigned directly to the individual offspring. We find that there are potential shortcomings of both possible assignments of fitness. In general, whenever there is a genetic correlation between the parental and direct effects on offspring fitness, assigning components of offspring fitness to parents yields incorrect dynamical equations and may even lead to incorrect conclusions about the direction of evolution. Assignment of offspring fitness to parents may also produce incorrect estimates of selection whenever environmental variation contributes to variance of the maternal trait. Whereas assignment of offspring fitness to the offspring avoids these potential problems, it introduces the possible problem of missing components of kin selection provided by the mother, which may not be detected in selection analyses. There are also certain conditions where either model can be appropriate because assignment of offspring fitness to parents may yield the same dynamical equations as assigning offspring fitness directly to offspring. We discuss these implications of the alternative assignments of fitness for modelling, selection analysis and experimentation in evolutionary biology.     

Fitness of three Fusarium pathogens of wheat

Crown rot and head blight of wheat are caused by the same Fusarium species. To better understand their biology, this study has compared 30 isolates of the three dominant species using 13 pathogenic and saprophytic fitness measures including aggressiveness for the two diseases, saprophytic growth and fecundity and deoxynivalenol (DON) production from saprophytic colonization of grain and straw. Pathogenic fitness was generally linked to DON production in infected tissue. The superior crown rot fitness of Fusarium pseudograminearum was linked to high DON production in the stem base tissue, while Fusarium culmorum and Fusarium graminearum had superior head blight fitness with high DON production in grains. Within each species, some isolates had similar aggressiveness for both diseases but differed in DON production in infected tissue to indicate that more than one mechanism controlled aggressiveness. All three species produced more DON when infecting living host tissue compared with saprophytic colonization of grain or straw, but there were significant links between these saprophytic fitness components and aggressiveness. As necrotrophic pathogens spend a part of their life cycle on dead organic matter, saprophytic fitness is an important component of their overall fitness. Any management strategy must target weaknesses in both pathogenic fitness and saprophytic fitness.     

On the transfer of fitness from the cell to the multicellular organism

The fitness of any evolutionary unit can be understood in terms of its two basic components: fecundity (reproduction) and viability (survival). Trade-offs between these fitness components drive the evolution of life-history traits in extant multicellular organisms. We argue that these trade-offs gain special significance during the transition from unicellular to multicellular life. In particular, the evolution of germ–soma specialization and the emergence of individuality at the cell group (or organism) level are also consequences of trade-offs between the two basic fitness components, or so we argue using a multilevel selection approach. During the origin of multicellularity, we study how the group trade-offs between viability and fecundity are initially determined by the cell level trade-offs, but as the transition proceeds, the fitness trade-offs at the group level depart from those at the cell level. We predict that these trade-offs begin with concave curvature in single-celled organisms but become increasingly convex as group size increases in multicellular organisms. We argue that the increasingly convex curvature of the trade-off function is driven by the cost of reproduction which increases as group size increases. We consider aspects of the biology of the volvocine green algae – which contain both unicellular and multicellular members – to illustrate the principles and conclusions discussed.     

Synthesizing insight: artificial life as thought experimentation in biology

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow up with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists.     

The indirect benefits of mating with attractive males outweigh the direct costs

The fitness consequences of mate choice are a source of ongoing debate in evolutionary biology. Recent theory predicts that indirect benefits of female choice due to offspring inheriting superior genes are likely to be negated when there are direct costs associated with choice, including any costs of mating with attractive males. To estimate the fitness consequences of mating with males of varying attractiveness, we housed female house crickets, Acheta domesticus, with either attractive or unattractive males and measured a variety of direct and indirect fitness components. These fitness components were combined to give relative estimates of the number of grandchildren produced and the intrinsic rate of increase (relative net fitness). We found that females mated to attractive males incur a substantial survival cost. However, these costs are cancelled out and may be outweighed by the benefits of having offspring with elevated fitness. This benefit is due predominantly, but not exclusively, to the effect of an increase in sons' attractiveness. Our results suggest that the direct costs that females experience when mating with attractive males can be outweighed by indirect benefits. They also reveal the value of estimating the net fitness consequences of a mating strategy by including measures of offspring quality in estimates of fitness.     

Hamilton goes empirical: estimation of inclusive fitness from life-history data

Hamilton's theory of kin selection is one of the most important advances in evolutionary biology since Darwin. Central to the kin-selection theory is the concept of inclusive fitness. However, despite the importance of inclusive fitness in evolutionary theory, empirical estimation of inclusive fitness has remained an elusive task. Using the concept of individual fitness, I present a method for estimating inclusive fitness and its components for diploid organisms with age-structured life histories. The method presented here: (i) allows empirical estimation of inclusive fitness from life-history data; (ii) simultaneously considers all components of fitness, including timing and magnitude of reproduction; (iii) is consistent with Hamilton's definition of inclusive fitness; and (iv) adequately addresses shortcomings of existing methods of estimating inclusive fitness. I also demonstrate the application of this new method for testing Hamilton's rule.     

Testing for epistasis between deleterious mutations in a parasitoid wasp

Abstract.— Determining the way in which deleterious mutations interact to effect fitness is crucial to numerous areas in evolutionary biology. For example, if each additional mutation leads to a greater decrease in log fitness than the last, termed synergistic epistasis, then sex and recombination provide an advantage because they enable deleterious mutations to be eliminated more efficiently. However, there is a severe shortage of relevant empirical data, especially of the form that can help test mutational explanations for the widespread occurrence of sex. Here, we test for epistasis in the parasitic wasp Nasonia vitripennis , examining the fitness consequences of chemically induced deleterious mutations. We examine two components of fitness, both of which are thought to be important in natural populations of parasitic wasps: longevity and egg production. Our results show synergistic epistasis for longevity, but not for egg production.     

Defining the landscape of adaptive genetic diversity

Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.).     

The strategy concept and John Maynard Smith’s influence on theoretical biology

Here we argue that the concept of strategies, as it was introduced into biology by John Maynard Smith, is a prime illustration of the four dimensions of theoretical biology in the post-genomic era. These four dimensions are: data analysis and management, mathematical and computational model building and simulation, concept formation and analysis, and theory integration. We argue that all four dimensions of theoretical biology are crucial to future interactions between theoretical and empirical biologists as well as with philosophers of biology.     

Epistemology of living organisms in Aristotle’s philosophy

Summary For Aristotle, living entities are exemplars of substance being. This means that they show a unity of matter and form on the one hand and of potency and act on the other, in contrast to the duality shown in these respects by accidental beings, exemplified by artefacts. An animal, although composed of the same elements (arche) considered by presocratic philosophers, is defined as an individual unity, generated and maintained by an organisation which relates its parts in a hierarchical and functional way. Crucial to his understanding of the living is the hierarchy in which each part is defined by fitness to a function, as an instrument (organon), performing within the whole. The whole being is also an instrument (an organism) for a specific kind of life, which actualises an internal and specific principle (psuche). Both the regularity of appearance of each organism and its fitness to a specific function justify the introduction, in addition to the study of necessary causes, of an additional way of analysis in terms of hypothetical necessities, or necessary conditions for a goal to be attained. Fitness to a function and regularity of appearance make necessary the analysis not just of the elementary components, but of another principle (eidos, form) which defines a structure directed to a goal. While for accidental beings matter can survive their destruction, the corruption (pthora) of living entities causes the disruption of the entire unity of matter and form. Living entities, both as matter and form, show therefore a temporal limitation in being generated and corrupted, although they persist as specific forms since they generate offspring which regularly share their differential characteristics defined in their form. After reviewing recent interpretations of Aristotle’s biological writings, I will suggest the usefulness of this conceptual framework to analyse some problems approached by current developmental biology.     

Estimating selection on neonatal traits in red deer using elasticity path analysis

Van Tienderen recently published a method that links selection gradients between a phenotypic trait and multiple fitness components with the effects of these fitness components on the population growth rate (mean absolute fitness). The method allows selection to be simultaneously estimated across multiple fitness components in a population dynamic framework. In this paper we apply the method to a population of red deer living in the North Block of the Isle of Rum, Scotland. We show that (1) selection on birth date and birth weight can operate through multiple fitness components simultaneously; (2) our estimates of the response to selection are consistent with the observed change in trait values that we cannot explain with environmental and phenotypic covariates; (3) selection on both traits has fluctuated over the course of the study; (4) selection operates through different fitness components in different years; and (5) no environmental covariates correlate with selection because different fitness components respond to density and climatic variation in contrasting ways.     

Measuring quality of life in theory and in practice: a dialogue between philosophical and psychological approaches

Measuring quality of life is of concern to both philosophers and psychologists, yet the two disciplines typically approach the question in very different ways, ways so diverse that it may look as if they are engaged in such disparate activities that no dialogue between them is possible. In this paper we aim to construct the beginnings of a dialogue between the two disciplines which will show how they could serve each other and yet also show how, from the dialogue, difficult and previously unconsidered issues emerge for both sides.     

Environmental uncertainty, autocorrelation and the evolution of survival

Survival is a key fitness component and the evolution of age- and stage-specific patterns in survival is a central question in evolutionary biology. In variable environments, favouring chances of survival at the expense of other fitness components could increase fitness by spreading risk across uncertain conditions, especially if environmental conditions improve in the future. Both the magnitude of environmental variation and temporal autocorrelation in the environment might therefore affect the evolution of survival patterns. Despite this, the influence of temporal autocorrelation on the evolution of survival patterns has not been addressed. Here, we use a trade-off structure which reflects the empirically inspired paradigm of acquisition and allocation of resources to investigate how the evolutionarily stable survival probability is shaped in variable, density-dependent environments. We show that temporal autocorrelation is likely to be an important aspect of environmental variability that contributes to shaping age- and stage-specific patterns of survival probabilities in nature.     

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.     

Individual essentialism in biology

A few philosophers of biology have recently explicitly rejected Essential Membership, the doctrine that if an individual organism belongs to a taxon, particularly a species, it does so essentially. But philosophers of biology have not addressed the broader issue, much discussed by metaphysicians on the basis of modal intuitions, of what is essential to the organism. In this paper, I address that issue from a biological basis, arguing for the Kripkean view that an organism has a partly intrinsic, partly historical, essence. The arguments appeal to the demands of biological explanation and are analogous to arguments that I have given elsewhere that a taxon has a partly intrinsic, partly historical, essence. These conclusions about the essences of individuals and taxa yield an argument for Essential Membership. Finally, I cast doubt on LaPorte’s objection to that doctrine arising from the view that a species cannot survive having a daughter.