From the Academy: Colloquium Perspective: In the light of evolution I: Adaptation and complex design

On Citing Dobzhansky about the Significance of Evolution to Biology

Evolutionary thinking illuminates biology. Dobzhansky advocated this view in two distinct papers. The earliest paper (1964) is a discussion of the relationship between distinct biological disciplines, and one of the key ideas is that evolution is an integrative principle of biology. The later paper (1973) is a long argument to the effect that evolution makes more sense of the living than some creationist doctrines. The first paper should then be the primary reference for those biologists who cite Dobzhansky to champion among their peers the added value of evolutionary thinking in a specific scientific problem. Here, looking at citation data, we find evidence that this expected referencing practice does not coincide with the actual referencing practice in the scientific literature.

Probabilistic causation and the explanatory role of natural selection

The explanatory role of natural selection is one of the long-term debates in evolutionary biology. Nevertheless, the consensus has been slippery because conceptual confusions and the absence of a unified, formal causal model that integrates different explanatory scopes of natural selection. In this study we attempt to examine two questions: (i) What can the theory of natural selection explain? and (ii) Is there a causal or explanatory model that integrates all natural selection explananda? For the first question, we argue that five explananda have been assigned to the theory of natural selection and that four of them may be actually considered explananda of natural selection. For the second question, we claim that a probabilistic conception of causality and the statistical relevance concept of explanation are both good models for understanding the explanatory role of natural selection. We review the biological and philosophical disputes about the explanatory role of natural selection and formalize some explananda in probabilistic terms using classical results from population genetics. Most of these explananda have been discussed in philosophical terms but some of them have been mixed up and confused. We analyze and set the limits of these problems.

The challenges and scope of theoretical biology

Scientific theories seek to provide simple explanations for significant empirical regularities based on fundamental physical and mechanistic constraints. Biological theories have rarely reached a level of generality and predictive power comparable to physical theories. This discrepancy is explained through a combination of frozen accidents, environmental heterogeneity, and widespread non-linearities observed in adaptive processes. At the same time, model building has proven to be very successful when it comes to explaining and predicting the behavior of particular biological systems. In this respect biology resembles alternative model-rich frameworks, such as economics and engineering. In this paper we explore the prospects for general theories in biology, and suggest that these take inspiration not only from physics, but also from the information sciences. Future theoretical biology is likely to represent a hybrid of parsimonious reasoning and algorithmic or rule-based explanation. An open question is whether these new frameworks will remain transparent to human reason. In this context, we discuss the role of machine learning in the early stages of scientific discovery. We argue that evolutionary history is not only a source of uncertainty, but also provides the basis, through conserved traits, for very general explanations for biological regularities, and the prospect of unified theories of life.

Colloquium paper: three ambitious (and rather unorthodox) assignments for the field of biodiversity genetics

The field of molecular genetics has many roles in biodiversity assessment and conservation. I summarize three of those standard roles and propose logical extensions of each. First, many biologists suppose that a comprehensive picture of the Tree of Life will soon emerge from multilocus DNA sequence data interpreted in concert with fossils and other evidence. If nonreticulate trees are indeed valid metaphors for life's history, then a well dated global phylogeny will offer an opportunity to erect a universally standardized scheme of biological classification. If life's history proves to be somewhat reticulate, a web-like phylogenetic pattern should become evident and will offer opportunities to reevaluate the fundamental nature of evolutionary processes. Second, extensive networks of wildlife sanctuaries offer some hope for shepherding appreciable biodiversity through the ongoing extinction crisis, and molecular genetics can assist in park design by helping to identify key species, historically important biotic areas, and biodiversity hotspots. An opportunity centers on the concept of Pleistocene Parks that could protect "legacy biotas" in much the same way that traditional national parks preserve special geological features and historical landmarks honor legacy events in human affairs. Third, genetic perspectives have become an integral part of many focused conservation efforts by unveiling ecological, behavioral, or evolutionary phenomena relevant to population management. They also can open opportunities to educate the public about the many intellectual gifts and aesthetic marvels of the natural world.

Historical and contingent factors affect re-evolution of a complex feature lost during mass extinction in communities of digital organisms

Re-evolution of complex biological features following the extinction of taxa bearing them remains one of evolution's most interesting phenomena, but is not amenable to study in fossil taxa. We used communities of digital organisms (computer programs that self-replicate, mutate and evolve), subjected to periods of low resource availability, to study the evolution, loss and re-evolution of a complex computational trait, the function EQU (bit-wise logical equals). We focused our analysis on cases where the pre-extinction EQU clade had surviving descendents at the end of the extinction episode. To see if these clades retained the capacity to re-evolve EQU, we seeded one set of multiple subreplicate 'replay' populations using the most abundant survivor of the pre-extinction EQU clade, and another set with the actual end-extinction ancestor of the organism in which EQU re-evolved following the extinction episode. Our results demonstrate that stochastic, historical, genomic and ecological factors can lead to constraints on further adaptation, and facilitate or hinder re-evolution of a complex feature.