Procedural understanding in biology: the ‘thinking behind the doing’

Several developments in science education aim to improve pupils' ability to ‘think scientifically’. This paper argues for the explicit teaching of the ideas that pupils need to ‘think about’ to do this; ideas related to the design of investigations and the collection, presentation, analysis, and evaluation of the resulting evidence — ideas which are important both for pupils who continue to study or work with biology and for all pupils to become biologically literate. This paper considers some of the concepts of evidence which are particularly important to biology, and discusses how and why the ideas could be taught.     

Technological speculations and science

Scientific advance is driven more by technological advance than by any other factor. But there is a lack of opportunities to publish ideas about new technology that could advance understanding of science. In part this is because technological speculation can be unlimited, and so is worthless, without physical proof that the idea can work. But new technological ideas rarely arise in a single mind, or discipline, so communication of incomplete technological ideas has a valuable place in their development. This Journal embraces not just scientific hypotheses but technological ones as well, to help spread half-formed technological ideas into the community where they can be finished as concepts and turned into prototypes.     

Intellectual property law: a primer for scientists

“Intellectual property” (IP) is a generic legal term for patents, copyrights, and trademarks, which provide legal rights to protect ideas, the expression of ideas, and the inventors and creators of such ideas. A patent provides legal protection for a new invention, an application of a new idea, discovery, or concept that is useful. Copyright provides legal protection from copying for any creative work, as well as business and scientific publications, computer software, and compilations of information. A trademark provides rights to use symbols, particular words, logos, or other markings that indicate the source of a product or service. A further method of benefiting from an invention is simply to keep it secret, rather than to disclose it—a “trade secret.” IP impinges on almost everything scientists do. As scientists are paid to come up with ideas and aspire to patent and/or publish their work, the protection of ideas and of written works especially should be of interest and concern to all.     

Scientific Bases for Enuring Productive Longevity of Agrolandscapes in Russia

Biology Bulletin - V.V. Dokuchaev’s ideas are the foundation of modern ideas about rational nature-usage methods in our steppes in order to ensure productive longevity of agro-ecosystems and...     

Toward an adequate mathematical model of mental space: conscious/unconscious dynamics on m-adic trees

We try to perform geometrization of cognitive science and psychology by representing information states of cognitive systems by points of mental space given by a hierarchic m-adic tree. Associations are represented by balls and ideas by collections of balls. We consider dynamics of ideas based on lifting of dynamics of mental points. We apply our dynamical model for modeling of flows of unconscious and conscious information in the human brain. In a series of models, Models 1–3, we consider cognitive systems with increasing complexity of psychological behavior determined by structure of flows of associations and ideas.     

A p-Adic model for the process of thinking disturbed by physiological and information noise

We develop a model of the process of thinking in the presence of noise (which is produced by the simultaneous action of a huge number of neurons in the brain as well as by external information and internal cognitive processes). Our model is based on Freud's idea on the splitting of cognitive processes into two (closely connected) domains: consciousness and subconsciousness. We represent the process of thinking as a random dynamical process in a space of ideas endowed with a non-Euclidean geometry (which differs extremely from the ordinary Euclidean geometry of spatial location of neurons in the brain). The so-called p-adic geometry on a space of ideas describes the ability of cognitive systems to form associations. We show that random dynamical thinking systems on a p -adic space of ideas still generate only deterministic ideas. We also study positive and negative effects of noise (in particular, creativeness and stress).     

Process, structure and context in relation to integrative biology.

This paper seeks to provide some integrative tools of thought regarding biological function related to ideas of process, structure, and context. The incorporation of linguistic and mathematical thinking is discussed within the context of managing thinking about natural systems as described by Robert Rosen. Examples from ecology, protein networks, and liver function are introduced to illustrate key ideas. It is hoped that these tools of thought, and the further work needed to mobilise such ideas, will continue to address a number of issues raised and pursued by Michael Conrad, such as the seed-germination model and vertical information processing.     

Racial identity and nationalism: a theoretical view from Latin America

The empirical intersection of ideas about race and nation are well-established, but theoretical explanations for this are less developed. Some ideas are advanced about how and why ideologies of race, nation, gender and sexuality intertwine. This leads on to a consideration of the tensions between sameness and difference that are argued to be constitutive of national identities. From here, an argument is developed about dynamics of appropriation and the maintenance of hegemony in racially diverse and multicultural nations. These theoretical ideas are illustrated with material from Latin America, particularly Colombia, with reference to Colombian popular music as an important cultural form in nationalist expression.     

Categorizing Ideas about Trees: A Tree of Trees

The aim of this study is to explore whether matrices and MP trees used to produce systematic categories of organisms could be useful to produce categories of ideas in history of science. We study the history of the use of trees in systematics to represent the diversity of life from 1766 to 1991. We apply to those ideas a method inspired from coding homologous parts of organisms. We discretize conceptual parts of ideas, writings and drawings about trees contained in 41 main writings; we detect shared parts among authors and code them into a 91-characters matrix and use a tree representation to show who shares what with whom. In other words, we propose a hierarchical representation of the shared ideas about trees among authors: this produces a “tree of trees.” Then, we categorize schools of tree-representations. Classical schools like “cladists” and “pheneticists” are recovered but others are not: “gradists” are separated into two blocks, one of them being called here “grade theoreticians.” We propose new interesting categories like the “buffonian school,” the “metaphoricians,” and those using “strictly genealogical classifications.” We consider that networks are not useful to represent shared ideas at the present step of the study. A cladogram is made for showing who is sharing what with whom, but also heterobathmy and homoplasy of characters. The present cladogram is not modelling processes of transmission of ideas about trees, and here it is mostly used to test for proximity of ideas of the same age and for categorization.     

The mechanisms of athermal microwave biological effects

A brief survey of current ideas about the physical mechanisms of low-level millimeter/microwave-biological effects is given, and the experimental evidence supporting these ideas is reviewed. The conjectural models do not yet represent a complete physical theory, but they do counter the idea that low-level effects are physically impossible and suggest experiments.     

Separating ‘Inquiry Questions’ and ‘Techniques’ to Help Learners Move between the How and the Why of Biology Practical Work

School science practical activities have been criticised for exposing learners to a series of phenomena disconnected from the conceptual frameworks needed to understand them. Such activities are successful in the ‘domain of observables’ but not the ‘domain of ideas’. Few resources exist for classroom teachers wishing to improve the effectiveness of practical activities in the domain of ideas. This report describes an action research project to develop a scaffold for biology practical lessons. This scaffold separates inquiry questions and the techniques needed to address them, and thus combines two approaches to scaffolding in a single tool (‘problematising’ and ‘reducing the degrees of freedom’). Analysis of the speech of 16–17 year olds in the study class (n = 23) was used to assess their engagement in the domain of ideas. Following the scaffold’s introduction, the learners were found to speak more about relevant ideas and concepts during practical activities. When the scaffold was partially faded, the learners continued to demonstrate engagement with the domain of ideas. The approach reported here would seem to have much potential for supporting learning from ‘minds-on’ biology practical work in a variety of contexts.     

Collegiality and careerism trump critical questions and bold new ideas: a student's perspective and solution. The structure of scientific funding limits bold new ideas

Funding agencies (and journals) seem to be discriminating against ideas that are contrary to the mainstream, leading to leading to the preferential funding of predictable and safe research over radically new ideas. To remedy this problem a restructuring of the scientific funding system is needed, e.g. by utilizing laymen--together with scientists--to evaluate grant proposals.     

Toward an adequate mathematical model of mental space: Conscious/unconscious dynamics on m-adic trees

We try to perform geometrization of cognitive science and psychology by representing information states of cognitive systems by points of mental space given by a hierarchic m-adic tree. Associations are represented by balls and ideas by collections of balls. We consider dynamics of ideas based on lifting of dynamics of mental points. We apply our dynamical model for modeling of flows of unconscious and conscious information in the human brain. In a series of models, Models 1–3, we consider cognitive systems with increasing complexity of psychological behavior determined by structure of flows of associations and ideas.     

Semiotes: a semantics for sharing

MOTIVATION: Reliable, automated communication of biological information requires methods to declare the information's semantics. In this paper I describe an approach to semantic declaration intended to permit independent, distributed databases, algorithms, and servers to exchange and process requests for information and computations without requiring coordination or agreement among them on universe of discourse, data model, schema, or implementation. RESULTS: This approach uses Glossa, a formal language defining the semantics of biological ideas, information, and algorithms, to executably define the semantics of complex ideas and computations by constructs of semiotes, terms which axiomatically define very simple notions. A database or algorithm wishing to exchange information or computations maintains a set of mappings between its particular notions and semiotes, and a parser to translate between its indigenous ideas and implementation and the semiotes. Requests from other databases or algorithms are issued as semiotic messages, locally interpreted and processed, and the results returned as semiotes to the requesting entity. Thus, semiotes serve as a shared, abstract layer of definitions which can be computably combined by each database or algorithm according to its own needs and ideas. By combining the explicit declaration of semantics with the computation of the semantics of complex ideas, Glossa and its semiotes permit independent computational entities to lightly federate their capabilities as desired while maintaining their unique perspectives on both scientific and technical questions.     

Exploring the influence of plant and animal item contexts on student response patterns to natural selection multiple choice items

Background

Research has shown that students have a variety of ideas about natural selection that may be context dependent. Prior analyses of student responses to open-ended evolution items have demonstrated that students apply more core ideas about natural selection when asked about animals, but respond with the same number of naive ideas for plant and animal items. Other research has shown that changing an item to ask about trait loss or gain shifted the types of naive ideas applied by students in their responses. In this paper, we take up both of these findings to determine if differences exist in the types of ideas students apply to similar items with either a plant or an animal in the item stem.

Results

In order to understand if students applied different ideas to plants or animals in distractor-driven multiple-choice questions, we analyzed high school biology students’ responses to matched-item pairs. Dichotomous scoring revealed that students chose the correct response more often for the animal items as compared to the plant items. Chi squared analyses revealed significant differences in the distribution of student responses to matched items. For example, more students chose responses that defined animal fitness as related to their strength and plants’ fitness related to its longevity.

Conclusions

These results suggest that varied context of plants or animals in item stems on diagnostic assessments can provide teachers with a more complete picture of their students’ ideas about natural selection prior to instruction. This is particularly important in assessments used prior to instruction; as teachers will gain greater insight into the variety of ways students think about natural selection across different types of plants and animals.

     

Restoration and the Origins of Ecology

Ernst Haeckel is well known for originating the science of ecology to describe the study of the relationships among organisms and their environment. This short article reflects on some of Ernst Haeckel’s ideas on the role of humans in nature and the relation between art and nature to point out affinities of Haeckel’s ideas to tighten the connection between today’s science and practice of ecological restoration.     

Alcide d’Orbigny entre Cuvier et Lamarck

In the History of Science, Alcide d’Orbigny has the distinctive characteristic to be placed, between Cuvier and Lamarck, who were the two masters of Natural Science for most of the 19th century. It is in this historical context that Alcide d’Orbigny lived. Of Cuvier, he remembered ideas on disasters and species fixedness without using the same evidence, for he was not a vertebrist. Of Lamarck, he rejected the ideas on life continuity and species transformation while using the research field opened by the Zoology and Invertebrate Palaeontology founder. Alcide d’Orbigny’s originality was to use Lamarck’s Invertebrate fossils as evidence of the ideas that Cuvier had based on Vertebrate fossils.     

Hempelian and Kuhnian approaches in the philosophy of medicine: the Semmelweis case

Semmelweis's investigations of puerperal fever are some of the most interesting in the history of medicine. This paper considers analysis of the Semmelweis case. It argues that this analysis is inadequate and needs to be supplemented by some Kuhnian ideas. Kuhn's notion of paradigm needs to be modified to apply to medicine in order to take account of the classification schemes involved in medical theorising. However with a suitable modification it provides an explanation of Semmelweis's failure which is argued to be superior to some of the external reasons often given. Despite this success in applying Kuhn's ideas to medicine, it is argued that these ideas must be further modified to take account of the fact that medicine is not a natural science but primarily a practice designed to prevent and cure diseases.