Is there a special conservation biology?

Conservation biology is special to the extent that it fills useful roles in the scientific and conservation fields that are not being filled by practitioners of other disciplines. The emergence of the “new conservation biology” in the late 1970's and its blossoming in the 1980's and 1990's reflect, to a large degree, a failure of traditional academic ecology and the natural resource disciplines to address modern conservation problems adequately. Yet, to be successful conservation biology, as an interdisciplinary field, must build on the strengths of other disciplines both basic and applied. The new conservation biology grew out of concern over extinction of species, although the field has expanded to include issues about management of several levels of biological organization. I examine four controversial questions of importance to conservation biologists today: 1) are there any robust principles of conservation biology? 2) Is advocacy an appropriate activity of conservation biologists? 3) Are we educating conservation biologists properly? 4) Is conservation biology distinct from other biological and resource management disciplines? I answer three of these questions with a tentative “yes” and one (3) with a regretful “in most cases, no.” I see a need for broader Training for students of conservation biology, more emphasis on collecting basic field data, compelling applications of conservation biology to real problems, increased influence on policy, and expansion of the international scope of the discipline. If all these occur, conservation biology will by truly special.     

Parts and Theories in Compositional Biology

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict.     

Taking the Relational Turn: Biosemiotics and Some New Trends in Biology

A cluster of similar trends emerging in separate fields of science and philosophy points to new opportunities to apply biosemiotic ideas as tools for conceptual integration in theoretical biology. I characterize these developments as the outcome of a “relational turn” in these disciplines. They signal a shift of attention away from objects and things and towards relational structures and processes. Increasingly sophisticated research technologies of molecular biology have generated an enormous quantity of experimental data, sparking a need for relational approaches that could help to find recurrent patterns in the mass of data. Earlier conceptions of relational biology and cybernetics, once deemed too abstract and speculative, are now resurrected and applied by means of new computational and simulation tools. I think this receptivity should be extended to incorporate nets of semiotic relations as heuristic guides for discerning global patterns of interactions in living systems. In this article I review aspects of systems biology and new directions in evolutionary theory, focusing on the role of circular and downward causation in relational structures and dynamical networks. I also indicate promising avenues of integration of some ideas of biosemiotics with those emerging from these new currents in biology. Relational developments in biology bear a telling similarity to a parallel relational turn presently manifest in the philosophy of science, rooted in the philosophy of physics and mathematics and in different varieties of structural and informational realism. The recognition of the relational nature of reality within these disciplines entails a tacit repudiation of nominalistic biases in science that have hindered the reception of semitiotic conceptions in biology. In previous investigations I explored connections between two kinds of relational structures: the networks of self-referential circular loops that appear pervasively in living systems, and the triadic relational structures that Peircean semiotics places at the basis of all semiotic transactions. Current relational views in the sciences seem oblivious to the difference between dyadic and triadic relations. Incorporating this essential distinction from biosemiotics into other fields could be a first step in seizing the opportunities opened by the relational turn for a renewal of biology and of natural philosophy in general, across disciplinary boundaries.     

Didactics of molecular ecology

Summary Molecular biology conferred enormous progresses in biosciences during the past few years. This paradigm permutation in biological research certainly challenges biological education. Nevertheless, this is no reason to fundamentally reorganise biological education at the universities. A most entire view of the matter should remain a central request which meets the capacity and imagination of students. Selected biological phenomena taken from the traditional treasury remain suitable in the future too to mediate basic biological ways ot thinking. Forthcoming syllabuses, however, will necessitate the expansion of this concept. The scope of the present contribution is to show, how the integration of molecular biology in the teaching of classical disciplines of biology may be reached. Choosing ecology and environmental biology as examples, molecular biology will not only strengthen explanation models of cause-effect relationships in these disciplines, but also will facilitate the interconnections to interdisciplinary fields such as health education, social, and political education. This may result in an entire structural concept of classical and molecular biology.     

Ecological modelling in an evolutionary context

I argue that one of the strong features in disciplines like molecular biology and cosmology is the extent ot which they use a powerful theoretical framework to generate and test quantitative predictions. Studies of biological evolution can exploit a similar advantage by integrating our current understanding of physiological and sociobiological processes to generate models of much greater sophistication than has commonly been the practice hitherto. I illustrate this with a number of examples drawn from the evolutionary biology of human and nonhuman primates.     

How race becomes biology: Embodiment of social inequality

The current debate over racial inequalities in health is arguably the most important venue for advancing both scientific and public understanding of race, racism, and human biological variation. In the United States and elsewhere, there are well-defined inequalities between racially defined groups for a range of biological outcomes—cardiovascular disease, diabetes, stroke, certain cancers, low birth weight, preterm delivery, and others. Among biomedical researchers, these patterns are often taken as evidence of fundamental genetic differences between alleged races. However, a growing body of evidence establishes the primacy of social inequalities in the origin and persistence of racial health disparities. Here, I summarize this evidence and argue that the debate over racial inequalities in health presents an opportunity to refine the critique of race in three ways: 1) to reiterate why the race concept is inconsistent with patterns of global human genetic diversity; 2) to refocus attention on the complex, environmental influences on human biology at multiple levels of analysis and across the lifecourse; and 3) to revise the claim that race is a cultural construct and expand research on the sociocultural reality of race and racism. Drawing on recent developments in neighboring disciplines, I present a model for explaining how racial inequality becomes embodied—literally—in the biological well-being of racialized groups and individuals. This model requires a shift in the way we articulate the critique of race as bad biology. Am J Phys Anthropol 2009. © 2009 Wiley-Liss, Inc.     

Pragmatism, Patronage and Politics in English Biology: The Rise and Fall of Economic Biology 1904–1920

The rise of applied biology was one of the most striking feature of the biological sciences in the early 20th century. Strongly oriented toward agriculture, this was closely associated with the growth of a number of disciplines, notably, entomology and mycology. This period also saw a market expansion of the English University system, and biology departments in the newly inaugurated civic universities took an early and leading role in the development of applied biology through their support of Economic Biology. This sought explicitly to promote the application of biological knowledge to economically important problems and especially to agriculture. The impact of Economic Biology was felt most strongly within Zoology, where it became synonymous with entomology. The transience of Economic Biology belies its significance, for example, in providing a means for the expansion of biology at the civic universities. More broadly, it opened up new research and employment opportunities within the life sciences. In late Edwardian Britain, newly available state funds for agriculturally relevant biological disciplines transformed the life sciences. This paper examines the impact of these funds - mobilized either under the 1909 Development Act, or under the auspices of colonial interests - on Economic Biology and the institutionalization of applied biology. The rise and fall of Economic Biology casts new light on the way in which institutional and political alignments profoundly shaped the development of British biology.     

Prebiotic world, macroevolution, and Darwin’s theory: a new insight

Darwin’s main contribution to modern biology was to make clear that all history of life on earth is dominated by a simple principle, which is usually summarised as 'descent with modification'. However, interpretations about how this modification is produced have been controversial. In light of the data provided by recent studies on molecular biology, developmental biology, genomics, and other biological disciplines we discuss, in this paper, how Darwin's theory may apply to two main 'types' of evolution: that occurring in the prebiotic world and that regarding the acquisition of major key-innovations differentiating higher-taxa, which makes up part of the so-called macroevolution. We argue that these studies show that evolution is a fascinating, complex and multifaceted process, with different mechanisms drivin it on different occasions and in different places.     

Why Are Computational Neuroscience and Systems Biology So Separate?

Despite similar computational approaches, there is surprisingly little interaction between the computational neuroscience and the systems biology research communities. In this review I reconstruct the history of the two disciplines and show that this may explain why they grew up apart. The separation is a pity, as both fields can learn quite a bit from each other. Several examples are given, covering sociological, software technical, and methodological aspects. Systems biology is a better organized community which is very effective at sharing resources, while computational neuroscience has more experience in multiscale modeling and the analysis of information processing by biological systems. Finally, I speculate about how the relationship between the two fields may evolve in the near future.     

Seeing the forest for the trees: the limitations of phylogenies in comparative biology. (American Society of Naturalists Address)

The past 30 years have seen a revolution in comparative biology. Before that time, systematics was not at the forefront of the biological sciences, and few scientists considered phylogenetic relationships when investigating evolutionary questions. By contrast, systematic biology is now one of the most vigorous disciplines in biology, and the use of phylogenies not only is requisite in macroevolutionary studies but also has been applied to a wide range of topics and fields that no one could possibly have envisioned 30 years ago. My message is simple: phylogenies are fundamental to comparative biology, but they are not the be-all and end-all. Phylogenies are powerful tools for understanding the past, but like any tool, they have their limitations. In addition, phylogenies are much more informative about pattern than they are about process. The best way to fully understand the past-both pattern and process-is to integrate phylogenies with other types of historical data as well as with direct studies of evolutionary process.     

Mechanical misconceptions: Have we lost the “mechanics” in “sports biomechanics”?

Biomechanics principally stems from two disciplines, mechanics and biology. However, both the application and language of the mechanical constructs are not always adhered to when applied to biological systems, which can lead to errors and misunderstandings within the scientific literature. Here we address three topics that seem to be common points of confusion and misconception, with a specific focus on sports biomechanics applications: (1) joint reaction forces as they pertain to loads actually experienced by biological joints; (2) the partitioning of scalar quantities into directional components; and (3) weight and gravity alteration. For each topic, we discuss how mechanical concepts have been commonly misapplied in peer-reviewed publications, the consequences of those misapplications, and how biomechanics, exercise science, and other related disciplines can collectively benefit by more carefully adhering to and applying concepts of classical mechanics.     

What will result from the interaction between functional and evolutionary biology?

The modern synthesis has been considered to be wrongly called a "synthesis", since it had completely excluded embryology, and many other disciplines. The recent developments of Evo-Devo have been seen as a step in the right direction, as complementing the modern synthesis, and probably leading to a "new synthesis". My argument is that the absence of embryology from the modern synthesis was the visible sign of a more profound lack: the absence of functional biology in the evolutionary synthesis. I will consider the reasons for this absence, as well as the recent transformations which favoured a closer interaction between these two branches of biology. Then I will describe two examples of recent work in which functional and evolutionary questioning were tightly linked. The most significant part of the paper will be devoted to the transformation of evolutionary theory that can be expected from this encounter: a deep transformation, or simply an experimental confirmation of this theory? I will not choose between these two different possibilities, but will discuss some of the difficulties which make the choice problematic.     

Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept

The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary developmental biology. It is shown that the concept or variant of homology preferred by a particular biological field is used to bring about items of biological knowledge that are characteristic for this field. A particular branch of biology uses its homology concept to pursue its specific theoretical goals.     

Biodiversity Realism: Preserving the tree of life

Biodiversity is a key concept in the biological sciences. While it has its origin in conservation biology, it has become useful across multiple biological disciplines as a means to describe biological variation. It remains, however, unclear what particular biological units the concept refers to. There are currently multiple accounts of which biological features constitute biodiversity and how these are to be measured. In this paper, I draw from the species concept debate to argue for a set of desiderata for the concept of “biodiversity” that is both principled and coheres with the concept’s use. Given these desiderata, this concept should be understood as referring to difference quantified in terms of the phylogenetic structure of lineages, also known as the ‘tree of life’.     

A proposal for the classification of biological weapons sensu lato

Due to historical and legislation reasons, the category of bioweapons is rather poorly defined. Authors often disagree on involving or excluding agents like hormones, psychochemicals, certain plants and animals (such as weeds or pests) or synthetic organisms. Applying a wide definition apparently threatens by eroding the regime of international legislation, while narrow definitions abandon several important issues. Therefore, I propose a category of ‘biological weapons sensu lato’ (BWsl) that is defined here as any tool of human aggression whose acting principle is based on disciplines of biology including particularly microbiology, epidemiology, medical biology, physiology, psychology, pharmacology and ecology, but excluding those based on inorganic agents. Synthetically produced equivalents (not necessarily exact copies) and mock weapons are also included. This definition does not involve any claim to subject all these weapons to international legislation but serves a purely scholarly purpose. BWsl may be properly categorized on the base of the magnitude of the human population potentially targeted (4 levels: individuals, towns, countries, global) and the biological nature of the weapons’ intended effects (4 levels: agricultural-ecological agents, and non-pathogenic, pathogenic, or lethal agents against humans).     

The application of atomic force microscopy to the study of living vertebrate cells in culture

Atomic force microscopy (AFM), a relatively new variant of scanning probe microscopy developed for the material sciences, is becoming an increasingly important tool in other disciplines. In this review I describe in nontechnical terms some of the basic aspects of using AFM to study living vertebrate cells. Although AFM has some unusual attributes such as an ability to be used with living cells, AFM also has attributes that make its use in cell biology a real challenge. This review was written to encourage researchers in the biological and biomedical sciences to consider AFM as a potential (and potent) tool for their cell biological research.     

The Professionalization of Science Studies: Cutting Some Slack

During the past hundred years or so, those scholars studying science have isolated themselves as much as possible from scientists as well as from workers in other disciplines who study science. The result of this effort is history of science, philosophy of science and sociology of science as separate disciplines. I argue in this paper that now is the time for these disciplinary boundaries to be lowered or at least made more permeable so that a unified discipline of Science Studies might emerge. I discuss representative problems that stand in the way of such an integration. These problems may seem so formidable in the abstract that no one in their right mind would waste their time trying to bring about a unified field of Science Studies. However, those of us who limit ourselves to the study of the biological sciences have already formed a society in which workers from all disciplines can share their expertise -- the International Society for the History, Philosophy and Social Studies of Science.     

Landscape evolutionary genomics

Tremendous advances in genetic and genomic techniques have resulted in the capacity to identify genes involved in adaptive evolution across numerous biological systems. One of the next major steps in evolutionary biology will be to determine how landscape-level geographical and environmental features are involved in the distribution of this functional adaptive genetic variation. Here, I outline how an emerging synthesis of multiple disciplines has and will continue to facilitate a deeper understanding of the ways in which heterogeneity of the natural landscapes mould the genomes of organisms.     

Object-oriented biological system integration: a SARS coronavirus example

MOTIVATION: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary. RESULTS: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems. AVAILABILITY: A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm