Digital Genesis: Computers, Evolution and Artificial Life

The application of evolution in the digital realm, with the goal of creating artificial intelligence and artificial life, has a history as long as that of the digital computer itself. We illustrate the intertwined history of these ideas, starting with the early theoretical work of John von Neumann and the pioneering experimental work of Nils Aall Barricelli. We argue that evolutionary thinking and artificial life will continue to play an integral role in the future development of the digital world.Comment: Extended abstract of talk presented at the 7th Munich-Sydney-Tilburg Philosophy of Science Conference: Evolutionary Thinking, University of Sydney, 20-22 March 2014. Presentation slides from talk available at http://www.tim-taylor.com/papers/digital-genesis-presentation.pd

Plio-Pleistocene climatic change had a major impact on the assembly and disassembly processes of Iberian rodent communities

Comprehension of changes in community composition through multiple spatio-temporal scales is a prime challenge in ecology and palaeobiology. However, assembly, structuring and disassembly of biotic metacommunities in deep-time is insufficiently known. To address this, we used the extensively sampled Iberian Plio-Pleistocene fossil record of rodent faunas as our model system to explore how global climatic events may alter metacommunity structure. Through factor analysis, we found five sets of genera, called faunal components, which co-vary in proportional diversity over time. These faunal components had different spatio-temporal distributions throughout the Plio-Pleistocene, resulting in non-random changes in species assemblages, particularly in response to the development of the Pleistocene glaciations. Three successive metacommunities with distinctive taxonomic structures were identified as a consequence of the differential responses of their members to global climatic change: (1) Ruscinian subtropical faunas (5.3–3.4 Ma) dominated by a faunal component that can be considered as a Miocene legacy; (2) transition faunas during the Villafranchian–Biharian (3.4–0.8 Ma) with a mixture of different faunal components; and (3) final dominance of the temperate Toringian faunas (0.8–0.01 Ma) that would lead to the modern Iberian assemblage. The influence of the cooling global temperature drove the reorganisation of these rodent metacommunities. Selective extinction processes due to this large-scale environmental disturbance progressively eliminated the subtropical specialist species from the early Pliocene metacommunity. This disassembly process was accompanied by the organisation of a diversified metacommunity with an increased importance of biome generalist species, and finally followed by the assembly during the middle–late Pleistocene of a new set of species specialised in the novel environments developed as a consequence of the glaciations

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach

The origins of the Acheulean: past and present perspectives on a major transition in human evolution

The emergence of the Acheulean from the earlier Oldowan constitutes a major transition in human evolution, the theme of this special issue. This paper discusses the evidence for the origins of the Acheulean, a cornerstone in the history of human technology, from two perspectives; firstly, a review of the history of investigations on Acheulean research is presented. This approach introduces the evolution of theories throughout the development of the discipline, and reviews the way in which cumulative knowledge led to the prevalent explanatory framework for the emergence of the Acheulean. The second part presents the current state of the art in Acheulean origins research, and reviews the hard evidence for the appearance of this technology in Africa around 1.7 Ma, and its significance for the evolutionary history of Homo erectus. This article is part of the themed issue ‘Major transitions in human evolution’

Reflections on language evolution

This essay reflects on the fact that as we learn more about the biological underpinnings of our language faculty, the dominant evolutionary narrative coming out of the linguistic tradition most explicitly oriented towards biology ("biolinguistics") appears increasingly implausible. This text offers ways of opening up linguistic inquiry and fostering interdisciplinarity, taking advantage of new opportunities to provide quantitative, testable hypotheses concerning the complex evolutionary path that led to the modern human language faculty. The essay is structured around three main themes: (i) renewed appreciation for the comparative method applied to cognitive questions, leading to the identification of elementary but fundamental abstractions in non-linguistic species relevant to language; (ii) awareness of the conceptual gaps between disciplines, and the need to carefully link genotype and phenotype without bypassing any "intermediate" levels of description (certainly not the brain); and (iii) adoption of a "philosophical" outlook that puts the complexity of biological entities front and center

3D Computer Modeling Offers New Insights Into Diatom Ecology

Algae supply over half of the Earth’s global primary production and form the base of almost all aquatic food networks. Thus, changes in algal productivity or composition will induce profound shifts in many ecosystems. This research is guided by two questions. Herein I ask if 3D models of algae can be created accurately enough to use for research applications? If they can be accurately created, then how can these models be used to advance our understanding of functional trait evolution and paleoecology? Herein, I develop 3D computer models for estimating the volume of individual algae and their parts. I also examine pressures that influence algae biomass, resource requirements, and trait evolution. Further, I apply these to an annually resolved sediment records to reveal paleontological applications that can be used to reconstruct past ecosystems and evolutionary events. This dissertation provides the means improve historical ecological reconstructions, advance predictions of ecological changes that will occur under global climate change and allow for evolutionary cost benefit analysis of traits of microscopic organisms. For this study I exploit the sedimentary record from Herd Lake Idaho USA (44.089428, -114.173921). because it contains large (~0.5 cm) annual layers. These layers are extraordinarily abundant in the remains of the diatom Stephanodiscus niagarae. These qualities present an ideal setting to produce accurate 3D computer models of a diatom that influences a large portion of the nutrient cycles in an aquatic system. The abundance of individuals provides ample data and diversity for strong statistical interpretations of the diatom populations while the annual resolution of the sediment provides a means to compare the novel methods to weather and climate data that inform us of the ecological significance of these new methods. The bounds of this study are within the years 1927 – 2011 and pertain to aquatic environments on Earth. Although these works are constrained to the recent past and local ecosystems, future applications are bound only by the geological time frame in which algae have existed and are limited in space to wherever algae are found in the universe

Reflections on language evolution

This essay reflects on the fact that as we learn more about the biological underpinnings of our language faculty, the dominant evolutionary narrative coming out of the linguistic tradition most explicitly oriented towards biology ("biolinguistics") appears increasingly implausible. This text offers ways of opening up linguistic inquiry and fostering interdisciplinarity, taking advantage of new opportunities to provide quantitative, testable hypotheses concerning the complex evolutionary path that led to the modern human language faculty. The essay is structured around three main themes: (i) renewed appreciation for the comparative method applied to cognitive questions, leading to the identification of elementary but fundamental abstractions in non-linguistic species relevant to language; (ii) awareness of the conceptual gaps between disciplines, and the need to carefully link genotype and phenotype without bypassing any "intermediate" levels of description (certainly not the brain); and (iii) adoption of a "philosophical" outlook that puts the complexity of biological entities front and center