GMOD for Evolutionary Biology

The Generic Model Organism Database (GMOD, "http://gmod.org":http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data. GMOD is also a community of people addressing common challenges with biological data. Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.

This talk will focus on three areas of particular interest to iEvoBio participants. 
1) GBrowse_syn comparative genomics viewer
2) Natural Diversity Module of the Chado database schema
3) GMOD evolutionary biology hackathon 

The GBrowse_syn comparative genomics viewer displays synteny between a reference and any number of related species. It shows inversions, duplications, and indels, and can show synteny across non-contiguous regions. It is built on the widely used GBrowse genome viewer. The Natural Diversity Module is an extension to GMOD’s Chado database schema to enable Chado to support natural diversity, population genomics, individuals, breeding, phenotypes and geolocation information. This module is the first extension to Chado to be designed by the community, rather than at one institution. We will close by soliciting nominations and ideas for a GMOD Evolutionary Biology Hackathon. This hackathon will be held November 8-12, at NESCent, which is sponsoring the event. There will be an open call for participation in August.
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Evolutionary Biology and Rape

This article queries whether an evolutionary analysis of rape may be more compelling in explaining a rape victim\u27s fear than a defendant\u27s sexual aggression. Such a victim-oriented approach could help legal decisionmakers assess the reasonableness of the victim\u27s fear when determining whether sex was forced or threatened. These ideas are explored in the context of two well-known rape trials, State v. Rusk and State v. Smith. This article concludes that evolutionary biology can contribute to an understanding of rape. However, the supposed evolutionary underpinnings of male sexual aggression should not justify such behavior or render it acceptable as a criminal defense. Moreover, evolutionary research must be evaluated in a social frame so that generalizations do not unfairly or inaccurately bias plaintiffs or defendants

Evolutionary biology for the 21st century

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.Molecular and Cellular BiologyOrganismic and Evolutionary Biolog

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 evolutionary biology of dance without frills

Recently psychologists have taken up the question of whether dance is reliant on unique human adaptations, or whether it is rooted in neural and cognitive mechanisms shared with other species 1, 2. In its full cultural complexity, human dance clearly has no direct analog in animal behavior. Most definitions of dance include the consistent production of movement sequences timed to an external rhythm. While not sufficient for dance, modes of auditory-motor timing, such as synchronization and entrainment, are experimentally tractable constructs that may be analyzed and compared between species. In an effort to assess the evolutionary precursors to entrainment and social features of human dance, Laland and colleagues [2] have suggested that dance may be an incidental byproduct of adaptations supporting vocal or motor imitation — referred to here as the ‘imitation and sequencing’ hypothesis. In support of this hypothesis, Laland and colleagues rely on four convergent lines of evidence drawn from behavioral and neurobiological research on dance behavior in humans and rhythmic behavior in other animals. Here, we propose a less cognitive, more parsimonious account for the evolution of dance. Our ‘timing and interaction’ hypothesis suggests that dance is scaffolded off of broadly conserved timing mechanisms allowing both cooperative and antagonistic social coordination

The relationship between evolutionary biology and religion

Belief in creationism and intelligent design is widespread and gaining in significance in a number of countries. This article examines the characteristics of science and of religions and the possible relationship between science and religion. I argue that creationism is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with creationist beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant a creationist one for students who are firm creationists. We can help students to find their evolutionary biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can not only help students learn about the theory of evolution but better to appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science and the ways in which scientific knowledge differs from other forms of knowledge