Biological networks 101: Computational modeling for molecular biologists

Computational modeling of biological networks permits the comprehensive analysis of cells and tissues to define molecular phenotypes and novel hypotheses. Although a large number of software tools have been developed, the versatility of these tools is limited by mathematical complexities that prevent their broad adoption and effective use by molecular biologists. This study clarifies the basic aspects of molecular modeling, how to convert data into useful input, as well as the number of time points and molecular parameters that should be considered for molecular regulatory models with both explanatory and predictive potential. We illustrate the necessary experimental preconditions for converting data into a computational model of network dynamics. This model requires neither a thorough background in mathematics nor precise data on intracellular concentrations, binding affinities or reaction kinetics. Finally, we show how an interactive model of crosstalk between signal transduction pathways in primary human articular chondrocytes allows insight into processes that regulate gene expression.     

Biological Sciences Curriculum Study

In order to name an animal they see, children use their existing mental models to provide the animal with a name. In this study, pupils of a range of ages (4, 8, 11, and 14 years old) were presented with preserved specimens of six different animals and asked a series of questions about them. The results indicate that pupils of all ages mainly recognize and use anatomical features when naming the animals and explaining why they are what they are. However, older pupils are more likely to also use behavioural and habitat attributes. For both girls and boys, the home and direct observation are more important as sources of knowledge than school or books, although books seem more important for boys than for girls. As pupils age, their reasons for grouping animals become more complicated: in addition to relying on shared anatomical features, they begin to show evidence of an embedded taxonomic knowledge, knowing, for instance, what a mammal is and using this knowledge to group animals.     

The American Society of Zoologists, 1889-1989: A Century of Integrating the Biological Sciences

The growth and development of the American Society of Zoologists(ASZ) came in an era of rapid expansion among the life sciences,as well as during a period when biologists were seeking to providethemselves with a united and effective voice. In ASZ's earlyyears it usually remained subsidiary, overshadowed by largerorganizations like the American Society of Naturalists or theAmerican Association for the Advancement of Science, and constrainedby its small enrollment to hold meetings in conjunction withthese larger societies. As ASZ's numbers increased, however,new members entered from many specialized fields, and it becamea focal organization for associations dedicated to such studiesas ecology, genetics, animal behavior, or systematic zoology.Much of ASZ's success in achieving its integrative status canbe attributed to the formation of divisions within the Society,each dedicating itself to the specialized interests of its ownmembers under the larger umbrella of zoology. This development,of course, paralleled the interaction between ASZ and the largersocial issues that have arisen during the century of the Society'shistory. ASZ has consistently concerned itself with just treatmentfor all, regardless of race or sex; with government supportof science; with the education of science teachers and of youngand talented biologists; and with all those issues that improvethe productivity of zoologists and enhance their capacity forreaching an ever deeper understanding of animal biology.     

The Formation of the Theory of Homology in Biological Sciences

Homology is among the most important comparative concepts in biology. Today, the evolutionary reinterpretation of homology is usually conceived of as the most important event in the development of the concept. This paradigmatic turning point, however important for the historical explanation of life, is not of crucial importance for the development of the concept of homology itself. In the broadest sense, homology can be understood as sameness in reference to the universal guarantor so that in this sense the different concepts of homology show a certain kind of "metahomology". This holds in the old morphological conception, as well as in the evolutionary usage of homology. Depending on what is (or was) taken as a guarantor, different types of homology may be distinguished (as idealistic, historical, developmental etc.). This study represents a historical overview of the development of the homology concept followed by some clues on how to navigate the pluralistic terminology of modern approaches to homology.     

The second Conceptual Assessment in the Biological Sciences workshop

A second National Science Foundation-sponsored workshop on Conceptual Assessment in Biology was held in January 2008. Reports prepared for the workshop revealed that research groups working in a variety of biological sciences are continuing to develop conceptual assessment instruments for use in the classroom. Discussions at this meeting largely focused on two issues: 1) the utility of the backwards design approach of Wiggins and McTighe (11), in which identification of learning outcomes (determining what to assess) lies at the beginning of course design; and 2) the utility of defining expected learning outcomes as the building of runable mental models (and designing conceptual assessments that would test the correctness of these mental models). A third meeting is being planned that will focus on the processes involved in writing and validating conceptual assessment instruments.