Nine Quick Tips for Analyzing Network Data

These tips provide a quick and concentrated guide for beginners in the analysis of network data

NEXUS/Physics: An interdisciplinary repurposing of physics for biologists

In response to increasing calls for the reform of the undergraduate science curriculum for life science majors and pre-medical students (Bio2010, Scientific Foundations for Future Physicians, Vision & Change), an interdisciplinary team has created NEXUS/Physics: a repurposing of an introductory physics curriculum for the life sciences. The curriculum interacts strongly and supportively with introductory biology and chemistry courses taken by life sciences students, with the goal of helping students build general, multi-discipline scientific competencies. In order to do this, our two-semester NEXUS/Physics course sequence is positioned as a second year course so students will have had some exposure to basic concepts in biology and chemistry. NEXUS/Physics stresses interdisciplinary examples and the content differs markedly from traditional introductory physics to facilitate this. It extends the discussion of energy to include interatomic potentials and chemical reactions, the discussion of thermodynamics to include enthalpy and Gibbs free energy, and includes a serious discussion of random vs. coherent motion including diffusion. The development of instructional materials is coordinated with careful education research. Both the new content and the results of the research are described in a series of papers for which this paper serves as an overview and context.Comment: 12 page

Automatic document classification of biological literature

Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept

Reinventing College Physics for Biologists: Explicating an epistemological curriculum

The University of Maryland Physics Education Research Group (UMd-PERG) carried out a five-year research project to rethink, observe, and reform introductory algebra-based (college) physics. This class is one of the Maryland Physics Department's large service courses, serving primarily life-science majors. After consultation with biologists, we re-focused the class on helping the students learn to think scientifically -- to build coherence, think in terms of mechanism, and to follow the implications of assumptions. We designed the course to tap into students' productive conceptual and epistemological resources, based on a theoretical framework from research on learning. The reformed class retains its traditional structure in terms of time and instructional personnel, but we modified existing best-practices curricular materials, including Peer Instruction, Interactive Lecture Demonstrations, and Tutorials. We provided class-controlled spaces for student collaboration, which allowed us to observe and record students learning directly. We also scanned all written homework and examinations, and we administered pre-post conceptual and epistemological surveys. The reformed class enhanced the strong gains on pre-post conceptual tests produced by the best-practices materials while obtaining unprecedented pre-post gains on epistemological surveys instead of the traditional losses.Comment: 35 pages including a 15 page appendix of supplementary material

‘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

The view from elsewhere: perspectives on ALife Modeling

Many artificial life researchers stress the interdisciplinary character of the field. Against such a backdrop, this report reviews and discusses artificial life, as it is depicted in, and as it interfaces with, adjacent disciplines (in particular, philosophy, biology, and linguistics), and in the light of a specific historical example of interdisciplinary research (namely cybernetics) with which artificial life shares many features. This report grew out of a workshop held at the Sixth European Conference on Artificial Life in Prague and features individual contributions from the workshop's eight speakers, plus a section designed to reflect the debates that took place during the workshop's discussion sessions. The major theme that emerged during these sessions was the identity and status of artificial life as a scientific endeavor

Evaluating Reproducibility in Computational Biology Research

For my Honors Senior Project, I read five research papers in the field of computational biology and attempted to reproduce the results. However, for the most part, this proved a challenge, as many details vital to utilizing relevant software and data had been excluded. Using Geir Kjetil Sandve\u27s paper Ten Simple Rules for Reproducible Computational Research as a guide, I discuss how authors of these five papers did and did not obey these rules of reproducibility and how this affected my ability to reproduce their results

The Semantic Web: Apotheosis of annotation, but what are its semantics?

This article discusses what kind of entity the proposed Semantic Web (SW) is, principally by reference to the relationship of natural language structure to knowledge representation (KR). There are three distinct views on this issue. The first is that the SW is basically a renaming of the traditional AI KR task, with all its problems and challenges. The second view is that the SW will be, at a minimum, the World Wide Web with its constituent documents annotated so as to yield their content, or meaning structure, more directly. This view makes natural language processing central as the procedural bridge from texts to KR, usually via some form of automated information extraction. The third view is that the SW is about trusted databases as the foundation of a system of Web processes and services. There's also a fourth view, which is much more difficult to define and discuss: If the SW just keeps moving as an engineering development and is lucky, then real problems won't arise. This article is part of a special issue called Semantic Web Update

Peacemaking among inconsistent rationalities?

Kacelnik, Schuck-Paim and Pompilio (this volume, p. 377) show that rationality axioms from economics are neither necessary nor sufficient to guarantee that animal behavior is biologically adaptive. To illustrate that biological adaptiveness does not imply conformity with the consistency axioms of economics, Kacelnik et al describe animals that sensibly experiment with actions yielding sub-maximum levels of short-term energy intake to monitor their environments for change, leading to apparently intransitive patterns of choice that are nevertheless biologically adaptive. Invalidating the converse claim that economic rationality implies biological adaptiveness is Kacelnik et al’s example of female ruffs that are worse off when they conform to the constant-ratio rule, frequently interpreted as a normative consistency requirement of economic rationality. Together, the two examples demonstrate that axiomatic norms are both unnecessary and insufficient for determining whether a particular behavior is biologically adaptive. Additionally, Kacelnik et al call into question what has been reported in the animal behavior literature as preference reversals, such as risk attitudes among wild rufous hummingbirds or the food-hoarding propensities of grey jays. Kacelnik et al attribute apparent reversals to state-dependent fitness functions modulated by subtle differences in the training phase of animal experiments. For example, animals trained on menus that include a strictly dominated option will tend to have lower accumulated energy reserves and therefore exhibit systematically different patterns of choice––not because they fail to maximize, but because their training has induced systematically different nutritional states. Another possible explanation for preference reversals in animal studies with strictly dominated, or “decoy” options is that menus containing dominated items may convey valid information about future opportunities (Houston and McNamara, 1999). If menus are correlated through time, then menus with inferior options today predict scarcity in the future and imply a distinct optimal course of action, in violation of regularity assumptions that posit invariance with respect to the inclusion of strictly dominated alternatives. In environments with payoff structures that can be modeled as cooperative games, a family’s best response sometimes requires individual family members to behave suboptimally as part of a diversification strategy that reduces the risk of reproductive failure (Hutchinson, 1996). Futhermore, theoretical biologists have documented the fragility of expected fitness maximizing behaviour with respect to the assumption of stable environments. Once the model allows for shocks to the environment’s stochastic structure, simple behavior rules that are suboptimal (in terms of expected fitness) when viewed narrowly from the perspective of unchanging payoffs in a fixed environment may outperform rules based on maximazation within a static small world (Bookstaber and Langsam, 1985).Rationality, rationalities, irrationality, bounded rationality, biology, biological rationality