Darwinian Data Structure Selection

Data structure selection and tuning is laborious but can vastly improve an application's performance and memory footprint. Some data structures share a common interface and enjoy multiple implementations. We call them Darwinian Data Structures (DDS), since we can subject their implementations to survival of the fittest. We introduce ARTEMIS a multi-objective, cloud-based search-based optimisation framework that automatically finds optimal, tuned DDS modulo a test suite, then changes an application to use that DDS. ARTEMIS achieves substantial performance improvements for \emph{every} project in $5$ Java projects from DaCapo benchmark, $8$ popular projects and $30$ uniformly sampled projects from GitHub. For execution time, CPU usage, and memory consumption, ARTEMIS finds at least one solution that improves \emph{all} measures for $86\%$ ($37/43$) of the projects. The median improvement across the best solutions is $4.8\%$, $10.1\%$, $5.1\%$ for runtime, memory and CPU usage. These aggregate results understate ARTEMIS's potential impact. Some of the benchmarks it improves are libraries or utility functions. Two examples are gson, a ubiquitous Java serialization framework, and xalan, Apache's XML transformation tool. ARTEMIS improves gson by $16.5$\%, $1\%$ and $2.2\%$ for memory, runtime, and CPU; ARTEMIS improves xalan's memory consumption by $23.5$\%. \emph{Every} client of these projects will benefit from these performance improvements.Comment: 11 page

Inventing an arsenal: adaptive evolution and neofunctionalization of snake venom phospholipase A(2 )genes

BACKGROUND: Gene duplication followed by functional divergence has long been hypothesized to be the main source of molecular novelty. Convincing examples of neofunctionalization, however, remain rare. Snake venom phospholipase A(2 )genes are members of large multigene families with many diverse functions, thus they are excellent models to study the emergence of novel functions after gene duplications. RESULTS: Here, I show that positive Darwinian selection and neofunctionalization is common in snake venom phospholipase A(2 )genes. The pattern of gene duplication and positive selection indicates that adaptive molecular evolution occurs immediately after duplication events as novel functions emerge and continues as gene families diversify and are refined. Surprisingly, adaptive evolution of group-I phospholipases in elapids is also associated with speciation events, suggesting adaptation of the phospholipase arsenal to novel prey species after niche shifts. Mapping the location of sites under positive selection onto the crystal structure of phospholipase A(2 )identified regions evolving under diversifying selection are located on the molecular surface and are likely protein-protein interactions sites essential for toxin functions. CONCLUSION: These data show that increases in genomic complexity (through gene duplications) can lead to phenotypic complexity (venom composition) and that positive Darwinian selection is a common evolutionary force in snake venoms. Finally, regions identified under selection on the surface of phospholipase A(2 )enzymes are potential candidate sites for structure based antivenin design

The Extended (Evolutionary) Synthesis Debate: Where Science Meets Philosophy

Recent debates between proponents of the modern evolutionary synthesis (the standard model in evolutionary biology) and those of a possible extended synthesis are a good example of the fascinating tangle among empirical, theoretical, and conceptual or philosophical matters that is the practice of evolutionary biology. In this essay, we briefly discuss two case studies from this debate, highlighting the relevance of philosophical thinking to evolutionary biologists in the hope of spurring further constructive cross-pollination between the two fields

‘The uses of ethnography in the science of cultural evolution’. Commentary on Mesoudi, A., Whiten, A. and K. Laland ‘Toward a unified science of cultural evolution’

There is considerable scope for developing a more explicit role for ethnography within the research program proposed in the article. Ethnographic studies of cultural micro-evolution would complement experimental approaches by providing insights into the “natural” settings in which cultural behaviours occur. Ethnography can also contribute to the study of cultural macro-evolution by shedding light on the conditions that generate and maintain cultural lineages

Simple model for the Darwinian transition in early evolution

It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and led to the emergence of vertical descent and the first well-defined species in early evolution. A nonlinear analysis of a stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable route from early collective evolution to the start of individuality and vertical Darwinian evolution, enabling the emergence of the first species.Comment: 9 pages, 5 figures, under review at Physical Review

Evolution and complexity: the double-edged sword

We attempt to provide a comprehensive answer to the question of whether, and when, an arrow of complexity emerges in Darwinian evolution. We note that this expression can be interpreted in different ways, including a passive, incidental growth, or a pervasive bias towards complexification. We argue at length that an arrow of complexity does indeed occur in evolution, which can be most reasonably interpreted as the result of a passive trend rather than a driven one. What, then, is the role of evolution in the creation of this trend, and under which conditions will it emerge? In the later sections of this article we point out that when certain proper conditions (which we attempt to formulate in a concise form) are met, Darwinian evolution predictably creates a sustained trend of increase in maximum complexity (that is, an arrow of complexity) that would not be possible without it; but if they are not, evolution will not only fail to produce an arrow of complexity, but may actually prevent any increase in complexity altogether. We conclude that, with regard to the growth of complexity, evolution is very much a double-edged sword