The modern synthesis and "Progress" in evolution: a view from the journal literature.

The concept of "progress" in evolutionary theory and its relationship to a putative notion of "Progress" in a global, normatively loaded sense of "change for the better" have been the subject of debate since Darwin admonished himself in a marginal note to avoid using the terms 'higher' and 'lower.' While an increase in some kind of complexity in the natural world might seem self-evident, efforts to explicate this trend meet notorious philosophical difficulties. Numerous historians pin the Modern Synthesis as a pivotal moment in this history; Michael Ruse even provocatively hypothesizes that Ernst Mayr and other "architects" of the Synthesis worked actively to eliminate Progress from evolutionary biology's scientific purview.

Gain-of-function research and model organisms in biology.

So-called 'gain-of-function' (GOF) research is virological research that results in a virus substantially more virulent or transmissible than its wild antecedent. GOF research has been subject to ethical analysis in the past, but the methods of GOF research have to date been underexamined by philosophers in these analyses. Here, we examine the typical animal used in influenza GOF experiments, the ferret, and show how despite its longstanding use, it does not easily satisfy the desirable criteria for an We then discuss the limitations of the ferret model, and how those epistemic limitations bear on ethical and policy questions around the risks and benefits of GOF research.

Of stirps and chromosomes: Generality through detail.

One claim found in the received historiography of the biometrical school (comprised primarily of Francis Galton, Karl Pearson, and W. F. R.

Whatever happened to reversion?

The idea of 'reversion' or 'atavism' has a peculiar history. For many authors in the late-nineteenth and early-twentieth centuries - including Darwin, Galton, Pearson, Weismann, and Spencer, among others - reversion was one of the central phenomena which a theory of heredity ought to explain. By only a few decades later, however, Fisher and others could look back upon reversion as a historical curiosity, a non-problem, or even an impediment to clear theorizing.

Cognitive Phenotypes and the Evolution of Animal Decisions.

Despite the clear fitness consequences of animal decisions, the science of animal decision making in evolutionary biology is underdeveloped compared with decision science in human psychology. Specifically, the field lacks a conceptual framework that defines and describes the relevant components of a decision, leading to imprecise language and concepts. The 'judgment and decision-making' (JDM) framework in human psychology is a powerful tool for framing and understanding human decisions, and we apply it here to components of animal decisions, which we refer to as 'cognitive phenotypes'.

evoText: A new tool for analyzing the biological sciences.

We introduce here evoText, a new tool for automated analysis of the literature in the biological sciences. evoText contains a database of hundreds of thousands of journal articles and an array of analysis tools for generating quantitative data on the nature and history of life science, especially ecology and evolutionary biology. This article describes the features of evoText, presents a variety of examples of the kinds of analyses that evoText can run, and offers a brief tutorial describing how to use it.

RLetters: A Web-Based Application for Text Analysis of Journal Articles.

While textual analysis of the journal literature is a burgeoning field, there is still a profound lack of user-friendly software for accomplishing this task. RLetters is a free, open-source web application which provides researchers with an environment in which they can select sets of journal articles and analyze them with cutting-edge textual analysis tools. RLetters allows users without prior expertise in textual analysis to analyze word frequency, collocations, cooccurrences, term networks, and more.

The early history of chance in evolution.

Work throughout the history and philosophy of biology frequently employs 'chance', 'unpredictability', 'probability', and many similar terms. One common way of understanding how these concepts were introduced in evolution focuses on two central issues: the first use of statistical methods in evolution (Galton), and the first use of the concept of "objective chance" in evolution (Wright). I argue that while this approach has merit, it fails to fully capture interesting philosophical reflections on the role of chance expounded by two of Galton's students, Karl Pearson and W.

Military genomic testing: proportionality, expected benefits, and the connection between genotypes and phenotypes.

Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternalism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize.

Nietzsche's aesthetic critique of Darwin.

Despite his position as one of the first philosophers to write in the "post-Darwinian" world, the critique of Darwin by Friedrich Nietzsche is often ignored for a host of unsatisfactory reasons. I argue that Nietzsche's critique of Darwin is important to the study of both Nietzsche's and Darwin's impact on philosophy. Further, I show that the central claims of Nietzsche's critique have been broadly misunderstood.

MTBindingSim: simulate protein binding to microtubules.

Summary: Many protein-protein interactions are more complex than can be accounted for by 1:1 binding models. However, biochemists have few tools available to help them recognize and predict the behaviors of these more complicated systems, making it difficult to design experiments that distinguish between possible binding models. MTBindingSim provides researchers with an environment in which they can rapidly compare different models of binding for a given scenario.

"Describing our whole experience": the statistical philosophies of W. F. R. Weldon and Karl Pearson.

There are two motivations commonly ascribed to historical actors for taking up statistics: to reduce complicated data to a mean value (e.g., Quetelet), and to take account of diversity (e.