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.     

Beyond Paradise—Meeting the Challenges in Tropical Biology in the 21st Century

Tropical ecosystems support a diversity of species and ecological processes that are unparalleled anywhere else on Earth. Despite their tremendous social and scientific importance, tropical ecosystems are rapidly disappearing. To usher tropical ecosystems and the human communities dependent upon them through the environmental transformations of the 21st century, tropical biologists must provide critical knowledge in three areas: 1) the structure and function of tropical ecosystems; 2) the nature and magnitude of anthropogenic effects on tropical ecosystems; and 3) the socio‐economic drivers of these anthropogenic effects. To develop effective strategies for conservation, restoration, and sustainable management of tropical ecosystems, scientific perspectives must be integrated with social necessities. A new set of principles built on a framework for pursuing relevant tropical biological research will facilitate interdisciplinary approaches, integrate biological knowledge with the social sciences, and link science with policy. We propose four broad recommendations for immediate action in tropical biology and conservation that are fundamental to all biological and social disciplines in the tropics: 1) assemble and disseminate information on life's diversity in the tropics; 2) enhance tropical field stations and build a worldwide network to link them with tropical field biologists at their field sites; 3) bring the field of tropical biology to the tropics by strengthening institutions in tropical countries through novel partnerships between tropical and temperate zone institutions and scientists; and 4) create concrete mechanisms to increase interactions between tropical biologists, social scientists, and policy makers.     

The Conservation and Management of Tunas and Their Relatives: Setting Life History Research Priorities

Scombrids (tunas, bonitos, Spanish mackerels and mackerels) support important fisheries in tropical, subtropical and temperate waters around the world, being one of the most economically- and socially-important marine species globally. Their sustainable exploitation, management and conservation depend on accurate life history information for the development of quantitative fisheries stock assessments, and in the fishery data-poor situations for the identification of vulnerable species. Here, we assemble life history traits (maximum size, growth, longevity, maturity, fecundity, spawning duration and spawning interval) for the 51 species of scombrids globally. We identify major biological gaps in knowledge and prioritize life history research needs in scombrids based on their biological gaps in knowledge, the importance of their fisheries and their current conservation status according to the International Union for Conservation of Nature Red List. We find that the growth and reproductive biology of tunas and mackerel species have been more extensively studied than for Spanish mackerels and bonitos, although there are notable exceptions in all groups. We also reveal that reproductive biology of species, particular fecundity, is the least studied biological aspect in scombrids. We identify two priority groups, including 32 species of scombrids, and several populations of principal market tunas, for which life history research should be prioritized following the species-specific life history gaps identified in this study in the coming decades. By highlighting the important gaps in biological knowledge and providing a priority setting for life history research in scombrid species this study provides guidance for management and conservation and serves as a guide for biologists and resource managers interested in the biology, ecology, and management of scombrid species.     

The philosophy of modelling or does the philosophy of biology have any use?

Biologists in search of answers to real-world issues such as the ecological consequences of global warming, the design of species'' conservation plans, understanding landscape dynamics and understanding gene expression make decisions constantly that are based on a ‘philosophical’ stance as to how to create and test explanations of an observed phenomenon. For better or for worse, some kind of philosophy is an integral part of the doing of biology. Given this, it is more important than ever to undertake a practical assessment of what philosophy does mean and should mean to biologists. Here, I address three questions: should biologists pay any attention to ‘philosophy’; should biologists pay any attention to ‘philosophy of biology’; and should biologists pay any attention to the philosophy of biology literature on modelling? I describe why the last question is easily answered affirmatively, with the proviso that the practical benefits to be gained by biologists from this literature will be directly proportional to the extent to which biologists understand ‘philosophy’ to be a part of biology, not apart from biology.     

Use of macroecology to integrate social justice and conservation

Both conservation biology and macroecology are synthetic, and macroecological research consistently has informed the theory and practice of biological conservation. Explicit integration of the macroecology of human systems and natural systems has been rare, but can advance the incorporation of social justice, environmental justice and environmental equity into conservation biology and participatory conservation (inclusion in decision‐making of those who are affected by, or can affect, that decision). The basis of this strong link is the focus of macroecology on the relations of a given biota to environmental patterns and processes, and these patterns and processes can affect humans differentially. Macroecological integration of social justice and conservation generally requires spatial and temporal representation of all variables at resolutions and extents that allow meaningful analyses. This requirement may facilitate clarity about social metrics and norms. To illustrate, we examine applications of macroecology to analysis of the effects of climate change on social justice and biological conservation; relations among climate, violence among humans and conservation; and the response of the spread of disease to social and ecological factors. We believe that macroecology is a means of providing transparent inferences that can inform conservation, health and social policies.     

Prediction of butterfly diversity hotspots in Belgium: a comparison of statistically focused and land use-focused models

Aim We evaluate differences between and the applicability of three linear predictive models to determine butterfly hotspots in Belgium for nature conservation purposes. Location The study is carried out in Belgium for records located to Universal Transverse Mercator (UTM) grid cells of 5 × 5 km. Methods We first determine the relationship between factors correlated to butterfly diversity by means of modified t‐tests and principal components analysis; subsequently, we predict hotspots using linear models based on land use, climate and topographical variables of well‐surveyed UTM grid cells (n = 197). The well‐surveyed squares are divided into a training set and an evaluation set to test the model predictions. We apply three different models: (1) a ‘statistically focused’ model where variables are entered in descending order of statistical significance, (2) a ‘land use‐focused’ model where land use variables known to be related to butterfly diversity are forced into the model and (3) a ‘hybrid’ model where the variables of the ‘land use‐focused model’ are entered first and subsequently complemented by the remaining variables entered in descending order of statistical significance. Results A principal components analyses reveals that climate, and to a large extent, land use are locked into topography, and that topography and climate are the variables most strongly correlated with butterfly diversity in Belgium. In the statistically focused model, biogeographical region alone explains 65% of the variability; other variables entering the statistically focused model are the area of coniferous and deciduous woodland, elevation and the number of frost days; the statistically focused model explains 77% of the variability in the training set and 66% in the evaluation set. In the land use‐focused model, biogeographical region, deciduous and mixed woodland, natural grassland, heathland and bog, woodland edge, urban and agricultural area and biotope diversity are forced into the model; the land use‐focused model explains 68% of the variability in the training set and 57% in the evaluation set. In the hybrid model, all variables from the land use‐focused model are entered first and the covariates elevation, number of frost days and natural grassland area are added on statistical grounds; the hybrid model explains 78% of the variability in the training set and 67% in the evaluation set. Applying the different models to determine butterfly diversity hotspots resulted in the delimitation of spatially different areas. Main conclusions The best predictions of butterfly diversity in Belgium are obtained by the hybrid model in which land use variables relevant to butterfly richness are entered first after which climatic and topographic variables were added on strictly statistical grounds. The land use‐focused model does not predict butterfly diversity in a satisfactory manner. When using predictive models to determine butterfly diversity, conservation biologists need to be aware of the consequences of applying such models. Although, in conservation biology, land use‐focused models are preferable to statistically focused models, one should always check whether the applied model makes sense on the ground. Predictive models can target mapping efforts towards potentially species‐rich sites and permits the incorporation of un‐surveyed sites into nature conservancy policies. Species richness distribution maps produced by predictive modelling should therefore be used as pro‐active conservation tools.     

Evolution of the capacity to evolve

Abstract During the past two decades, the fields of molecular biology and genetics have enabled study of far broader and more detailed aspects of evolutionary change than were possible when the evolutionary synthesis was elaborated in the mid‐twentieth century. The capacity for complete sequencing of both genes and proteins of all groups of organisms provide, simultaneously, the means to determine both the patterns and processes of evolution throughout the history of life. Increased knowledge of the genome documents the changing nature of its composition, mode of transmission, and the nature of the units of selection. Advances in evolutionary developmental biology demonstrate the conservation of genetic elements throughout multicellular organisms, and explain how control of the timing, position and nature of their expression has produced the extraordinary diversity of living plants and animals. The next generation of evolutionary biologists will benefit greatly from the increased integration of these new fields of research with those that are currently emphasized in the standard textbooks and journals.     

Microclimatic challenges in global change biology

Despite decades of work on climate change biology, the scientific community remains uncertain about where and when most species distributions will respond to altered climates. A major barrier is the spatial mismatch between the size of organisms and the scale at which climate data are collected and modeled. Using a meta‐analysis of published literature, we show that grid lengths in species distribution models are, on average, ca. 10 000‐fold larger than the animals they study, and ca. 1000‐fold larger than the plants they study. And the gap is even worse than these ratios indicate, as most work has focused on organisms that are significantly biased toward large size. This mismatch is problematic because organisms do not experience climate on coarse scales. Rather, they live in microclimates, which can be highly heterogeneous and strongly divergent from surrounding macroclimates. Bridging the spatial gap should be a high priority for research and will require gathering climate data at finer scales, developing better methods for downscaling environmental data to microclimates, and improving our statistical understanding of variation at finer scales. Interdisciplinary collaborations (including ecologists, engineers, climatologists, meteorologists, statisticians, and geographers) will be key to bridging the gap, and ultimately to providing scientifically grounded data and recommendations to conservation biologists and policy makers.     

Möbius: an integrated discrete-event modeling environment

M?bius has found numerous applications in computational biology to build and solve stochastic models of biological processes. It provides the user with a modeling workflow and several sophisticated features that are not available in the simulation tools commonly used by computational biologists. AVAILABILITY: M?bius is free for academic users. It can be downloaded from www.mobius.uiuc.edu     

Calculating life? Duelling discourses in interdisciplinary systems biology

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.     

Topographic determinants of mobile vertebrate predator hotspots: current knowledge and future directions

Despite being identified as a driver of mobile predator aggregations (hotspots) in both marine and terrestrial environments, topographic complexity has long remained a challenging concept for scientists to visualise and a difficult parameter to estimate. It is only with the advent of high‐speed computers and the recent popularisation of geographical information systems (GIS) that terrain attributes have begun to be quantitatively measured in three‐dimensional space and related to wildlife dynamics, making the well‐established field of geomorphometry (or ‘digital terrain modelling’) a discipline of growing appeal to biologists. Although a diverse array of numerical metrics is now available to describe the shape, geometry and physical properties of natural habitats, few of these are known to, or adequately used by, ecologists. In this review, we examine the nature and usage of 56 geomorphometrics extracted from the ecological modelling literature over a period of 32 years (1979–2011). We show that, in studies of mobile predators, numerous topographic variables have largely been overlooked in favour of single basic metrics that do not, on their own, fully capture the complexity of continuous landscapes. Based on a simulation approach, we assess the redundancy and correlation structure of these metrics and demonstrate that a majority are highly collinear. We highlight a suite of 7–8 complementary metrics which best explain topographic patterns across a bathymetric grid of the west Australian seafloor, and contend that field and analytical protocols should prioritise variables of these types, particularly when the responses of predator populations to physical habitat features are of interest. We suggest that prominent structures such as canyons, seamounts or mountain chains can serve as useful proxies for predator hotspots, especially in remote locations where access to high‐resolution biological data is often limited.     

Marine molecular biology: an emerging field of biological sciences

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.     

AREA RELATIONS BETWEEN LABELING INDEX CURVES FROM MULTICOMPARTMENT CELL KINETICS MODELS.

The study of the multicompartment models in cell kinetics can be simplified by the use of a conservation law relating the integrals, with respect to time, of labeling index in various compartments. We present a proof of the conservation law directed to the nonmathematician, as well as four applications from biology. The first demonstrates a contradiction, which biologists have yet to resolve, between a certain biological model and experimental results. The second and third are simpler proofs of results already proven by other techniques in the literature. The fourth is a result which appears to be new.     

Perceptions of nature conservation by future biologists attending private universities in São Paulo State,Brazil

As conservation agents, biologists play a central role in nature preservation as information-gatherers, promoters of environmental education, lobbyists, and members of societies. Consequently, it is important to understand what factors determine their attitudes towards conservation. We aimed to assess which taxa and recovery measures students from biology core courses consider priorities for conservation and to determine the value students associate with conservation compared to other topics. We asked students (n?=?122) from two private universities in São Paulo State, Brazil to fill out an anonymous questionnaire. They highlighted rarity, vanishing habitats and endemism as important criteria in prioritizing species. Carnivores were identified as the most threatened mammals and habitat recovery was deemed to be the most efficient conservation action. Students valued healthcare, cultural heritage and science over conservation. Our results reveal a two-sided perspective of conservation among students from biology core courses; they possess knowledge of conservation issues but are greatly influenced by anthropocentric and utilitarian views of nature.     

Demystifying computer science for molecular ecologists

In this age of data‐driven science and high‐throughput biology, computational thinking is becoming an increasingly important skill for tackling both new and long‐standing biological questions. However, despite its obvious importance and conspicuous integration into many areas of biology, computer science is still viewed as an obscure field that has, thus far, permeated into only a few of the biology curricula across the nation. A national survey has shown that lack of computational literacy in environmental sciences is the norm rather than the exception [Valle & Berdanier (2012) Bulletin of the Ecological Society of America, 93, 373–389]. In this article, we seek to introduce a few important concepts in computer science with the aim of providing a context‐specific introduction aimed at research biologists. Our goal was to help biologists understand some of the most important mainstream computational concepts to better appreciate bioinformatics methods and trade‐offs that are not obvious to the uninitiated.     

Using Protistan Examples to Dispel the Myths of Intelligent Design

ABSTRACT. In recent years the teaching of the religiously based philosophy of intelligent design (ID) has been proposed as an alternative to modern evolutionary theory. Advocates of ID are largely motivated by their opposition to naturalistic explanations of biological diversity, in accordance with their goal of challenging the philosophy of scientific materialism. Intelligent design has been embraced by a wide variety of creationists who promote highly questionable claims that purport to show the inadequacy of evolutionary theory, which they consider to be a threat to a theistic worldview. We find that examples from protistan biology are well suited for providing evidence of many key evolutionary concepts, and have often been misrepresented or roundly ignored by ID advocates. These include examples of adaptations and radiations that are said to be statistically impossible, as well as examples of speciation both in the laboratory and as documented in the fossil record. Because many biologists may not be familiar with the richness of the protist evolution dataset or with ID‐based criticisms of evolution, we provide examples of current ID arguments and specific protistan counter‐examples.     

Redefining plant systems biology: from cell to ecosystem

Molecular biologists typically restrict systems biology to cellular levels. By contrast, ecologists define biological systems as communities of interacting individuals at different trophic levels that process energy, nutrient and information flows. Modern plant breeding needs to increase agricultural productivity while decreasing the ecological footprint. This requires a holistic systems biology approach that couples different aggregation levels while considering the variables that affect these biological systems from cell to community. The challenge is to generate accurate experimental data that can be used together with modelling concepts and techniques that allow experimentally verifying in silico predictions. The coupling of aggregation levels in plant sciences, termed Integral Quantification of Biological Organization (IQ(BiO)), might enhance our abilities to generate new desired plant phenotypes.     

Discrepancies in occupancy and abundance approaches to identifying and protecting habitat for an at‐risk species

Predicting how environmental factors affect the distribution of species is a fundamental goal of conservation biology. Conservation biologists rely on species distribution and abundance models to identify key habitat characteristics for species. Occupancy modeling is frequently promoted as a practical alternative to use of abundance in identifying habitat quality. While occupancy and abundance are potentially governed by different limiting factors operating at different scales, few studies have directly compared predictive models for these approaches in the same system. We evaluated how much occupancy and abundance are driven by the same environmental factors for a species of conservation concern, the greater short‐horned lizard (Phrynosoma hernandesi). Occupancy was most strongly dictated by precipitation, temperature, and density of ant mounds. While these factors were also in the best‐supported predictive models for lizard abundance, the magnitude of the effects varied, with the sign of the effect changing for temperature and precipitation. These discrepancies show that while occupancy modeling can be an efficient approach for conservation planning, predictors of occupancy probability should not automatically be equated with predictors of population abundance. Understanding the differences in factors that control occupancy versus abundance can help us to identify habitat requirements and mitigate the loss of threatened species.     

Recent philosophy of biology: a review

Academia is subdivided into separate disciplines, most of which are quite discrete. In this review I trace the interactions between two of these disciplines: biology and philosophy of biology. I concentrate on those topics that have the most extensive biological content: function, species, systematics, selection, reduction and development. In the final section of this paper I touch briefly on those issues that biologists and philosophers have addressed that do not have much in the way of biological content.