Stefan Linquist

This paper considers whether the available evidence from archeology, biological anthropology, primatology, and comparative gene-sequencing, can test evolutionary game theory models of cooperation as historical hypotheses about the actual course of human prehistory. The examination proceeds on the assumption that cooperation is the product of cultural selection and is not a genetically encoded trait. Nevertheless, we conclude that gene sequence data may yet shed signi cant light on the evolution of cooperation

As conservation biology has developed as a distinct discipline from ecology, conservation guidelines based on ecological theory have been largely cast aside in favor of theory-independent decision procedures for designing conservation reserves. I argue that this transition has failed to advance the field toward its aim of preserving biodiversity. The abandonment of island biogeography theory in favor of complementarity-based algorithms is a case in point. In what follows, I consider the four central objections raised against island biogeographic conservation guidelines, arguing that they fail to undermine the credibility of this framework as a conservation tool. At best, these objections call for a more careful application of this framework to conservation problems, not its wholesale abandonment. At the same time, complementarily-based algorithms are biased in favor of networks of small reserves containing non-overlapping species. These conditions threaten to promote inbreeding depression, genetic drift and other factors that increase a population’s risk of extinction. Therefore, recent developments in the field of conservation biology have arguably not contributed to its ultimate aim of preserving the maximum amount of biodiversity in the long run.

The media attention and subsequent scientific backlash engendered by the claim, announced by spokespeople for the Encyclopedia of DNA Elements project, that 80% of the human genome has a “biochemical function” highlights the need for a clearer understanding of function concepts in biology. This article provides an overview of two major function concepts that have been developed in the philosophy of science – the “causal role” concept and the “selected effects” concept – and their relevance to ENCODE. Unlike some previous critiques, the ENCODE project is not considered problematic because it employed a causal role definition of function, but because of how this concept was misused. In addition, several unique challenges that arise when dealing with transposable elements, but which were ignored by ENCODE, are highlighted. These include issues surrounding TE-level versus organism-level selection, the origins versus the persistence of elements, and accidental versus functional organism-level benefits. Finally, some key questions are presented that should be addressed in any studies aiming to ascribe functions to major portions of large eukaryotic genomes, the majority of which is made up of transposable elements.