Creating parts that allow for rational design: Synthetic biology and the problem of context-sensitivity

The parts-based engineering approach in synthetic biology aims to create pre-characterised biological parts that can be used for the rational design of novel functional systems. Given the context-sensitivity of biological entities, a key question synthetic biologists have to address is what properties these parts should have so that they give a predictable output even when they are used in different contexts. In the first part of this paper I will analyse some of the answers that synthetic biologists have given to this question and claim that the focus of these answers on parts and their properties does not allow us to tackle the problem of context-sensitivity. In the second part of the paper, I will argue that we might have to abandon the notions of parts and their properties in order to understand how independence in biology could be achieved. Using Robert Cummins’ account of functional analysis, I will then develop the notion of a capacity and its condition space and show how these notions can help to tackle the problem of context-sensitivity in biology.     

Vector NTI Suite在分子生物学领域的应用

有许多软件可以帮助分子生物学工作者解决一些他们日常实验室工作中遇到的问题.Vector NTI Suite是一种高度集成、功能齐全的分子生物学应用软件,它可以对核酸、蛋白质等分子进行大量的操作和分析,以及建立和管理生物数据库.重点对Vector NTI Suite软件的概况、应用现状及其在分子生物学领域的应用进行综述与探讨.     

How to fail in advertising: The potential of marketing theory to predict the community-level selection of defended prey

Economics and ecology both present us with a key challenge: scaling up from individual behaviour to community-level effects. As a result, biologists have frequently utilized theories and frameworks from economics in their attempt to better understand animal behaviour. In the study of predator–prey interactions, we face a particularly difficult task—understanding how predator choices and strategies will impact the ecology and evolution not just of individual prey species, but whole communities. However, a similar challenge has been encountered, and largely solved, in Marketing, which has created frameworks that successfully predict human consumer behaviour at the community level. We argue that by applying these frameworks to non-human consumers, we can leverage this predictive power to understand the behaviour of these key ecological actors in shaping the communities they act upon. We here use predator–prey interactions, as a case study, to demonstrate and discuss the potential of marketing and human-consumer theory in helping us bridge the gap from laboratory experiments to complex community dynamics.     

Effects of environmental variables on fish feeding ecology: implications for the performance of baited fishing gear and stock assessment

The effectiveness of baited fishing gear ultimately depends upon behaviour of the target species – activity rhythms, feeding motivation, and sensory and locomotory abilities. While any environmental parameter that mediates feeding or locomotion can have an important influence on the active space presented by the bait and fish catchability, few biologists have considered how such variation in behaviour might affect catch per unit effort (CPUE) and the resultant stock abundance estimates or population parameters. This review reveals that environment‐related variation in feeding behaviour can act through four different mechanisms: metabolic processes, sensory limitations, social interactions and direct impacts. Water temperature, light level, current velocity and ambient prey density are likely to have largest effects on fish catchability, potentially affecting variation in CPUE by a factor of ten. Feeding behaviour is also density‐dependent, with both positive and negative effects. Over time and geographic space a target species can occupy wide ranges of environmental conditions, and in certain cases, spatial and temporal variation in feeding biology could have a larger impact on CPUE than patterns of abundance. Temperature, light and current can be measured with relative facility and corrections to stock assessment models are feasible. Making corrections for biological variables such as prey density and bait competitors will be more difficult because the measurements are often not practical and relationships to feeding catchability are more complex and poorly understood. There is a critical need for greater understanding of how environmental variables affect feeding‐related performance of baited fishing gear. A combination of field observations and laboratory experiments will be necessary to parameterize stock assessment models that are improved to accommodate variation in fish behaviour. Otherwise, survey data could reveal more about variation in behaviour than abundance trends.     

Costing reproduction

The placing of animal behaviour in an evolutionary context is one of the great achievements of biologists in the last century. Life history theory has been a powerful tool in explaining both adaptation and constraint in phenotypic evolution, but rarely addresses the mechanistic bases of the traits it discusses. Recent advances in molecular biology have begun to uncover these mechanisms, and provide a challenge to the traditional view that life history trade-offs are the result of the differential allocation of limiting resources. In particular, costs of reproduction in Caenorhabditis elegans appear to arise from molecular signals, which have been claimed to be arbitrary with respect to fitness. We review the evidence that costs of reproduction in C. elegans are not resource based, and find that this is not necessarily the case. However, we welcome the challenge to traditional thinking, and suggest that integrating an understanding of mechanisms into life history theory will be one of the most exciting tasks facing evolutionary biologists in the 21st century. Copyright 2003 Published by Elsevier Science Ltd on behalf of The Association for the Study of Animal Behaviour.      

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.     

Felsbilder im Lang‐Shan

In a recent polemic, Leda Cosmides and John Tooby offer new proposals to bridge the gulf between biological and cultural explanations of human behaviour. By focussing on the evolved architecture of the human mind, they seek specific psychological mechanisms by which genes may influence human social institutions. A major challenge for this approach is how to trace precisely which psychological endowments, formed by the Pleistocene age, have shaped which aspect of our contemporary cultures. Here it is suggested that the temporal framework of individual human lives may provide one means of establishing clearer connections between brain structure and social institutions. For biologists this will involve extending conventional views of human ontogeny to include the phases of aging and death, which have been so important for the genesis of culture. This image of the lifespan may in turn help anthropologists come to terms with the physical bases of intergenerational transfers on which the perpetuation of culture depends.     

Factors Influencing Membership of Federal Wildlife Biologists in The Wildlife Society

ABSTRACT Membership in scientific societies is an avenue wildlife professionals may use to maintain and enhance their professional capabilities. We studied factors influencing United States Fish and Wildlife Service (USFWS) and United States Geological Survey (USGS) biologists’ membership in scientific societies in general and The Wildlife Society (TWS) in particular. We conducted an internet census survey of 3,755 USFWS professionals and 932 USGS Biological Resource Division professionals. The survey collected data on membership and participation in scientific societies as well as other variables that we theorized could influence membership. We used logistic regressions to identify factors correlated with the membership of wildlife biologists in TWS. A greater proportion of USGS biologists (90.2%) than USFWS biologists (51.8%) were members of scientific societies, and the likelihood of wildlife biologists belonging to TWS was higher in USGS. Factors most consistently correlated with membership in TWS included minimal external constraints (e.g., family responsibilities and costs), supervisor support for membership, and membership of friends, peers, and supervisors in scientific societies. Our results suggest that membership in scientific societies is heavily influenced by the organizational culture of employing agencies. Agencies seeking to increase their employees’ membership, and thus benefits from participation, in scientific societies will be most successful if they create a culture in which involvement in scientific societies is expected and in which peers and supervisors also participate.     

What the Peritrichs Have Taught Us*†

SYNOPSIS. The peritrichs have taught naturalists, biologists, zoologists, and other kinds of scientists many of their secrets. Consequently, we know many details regarding their gross structure, ultrastructure, ecology, and life history. Their sexual phenomena are rather clearly understood. While general agreement has been attained as regards the forementioned topics, the taxonomic position of peritrichs is still vigorously debated. In this address representative examples of advances in our knowledge of peritrichs will be reviewed … representative instead of all-inclusive examples. A plea for the restoration of peritrichs to a taxonomic position above spirotrichs will be made. The Society's members will be assured that all protozoologists will have the opportunity to help design a completely International Commission on Protozoology in the International Union of Biological Sciences and they will be assured that such a Commission can and should be planned at the 1969 International Conference in Leningrad.     

Behavioural models of population growth rates: implications for conservation and prediction

Conservation biologists often wish to predict how vertebrate populations will respond to local or global changes in conditions such as those resulting from sea-level rise, deforestation, exploitation, genetically modified crops, global warming, human disturbance or from conservation activities. Predicting the consequences of such changes almost always requires understanding the population growth rate and the density dependence. Traditional means of directly measuring density dependence are often extremely difficult and have the problem that if the environment changes then it is necessary to remeasure the density dependence. We describe an alternative approach that does not require such long datasets and can be used to predict the density dependence under novel conditions. Game theory can be used to describe behavioural decisions that individuals make in response to interference, prey depletion, territorial behaviour or social dominance, and the resultant fitness consequences. It is then possible to predict how survival or reproductive output changes with population size. From this we can then make predictions about the responses of populations to environmental changes. We will illustrate how this can be applied to a range of species and a range of applied problems.     

Towards mechanistic models of plant organ growth

Modelling and simulation are increasingly used as tools in the study of plant growth and developmental processes. By formulating experimentally obtained knowledge as a system of interacting mathematical equations, it becomes feasible for biologists to gain a mechanistic understanding of the complex behaviour of biological systems. In this review, the modelling tools that are currently available and the progress that has been made to model plant development, based on experimental knowledge, are described. In terms of implementation, it is argued that, for the modelling of plant organ growth, the cellular level should form the cornerstone. It integrates the output of molecular regulatory networks to two processes, cell division and cell expansion, that drive growth and development of the organ. In turn, these cellular processes are controlled at the molecular level by hormone signalling. Therefore, combining a cellular modelling framework with regulatory modules for the regulation of cell division, expansion, and hormone signalling could form the basis of a functional organ growth simulation model. The current state of progress towards this aim is that the regulation of the cell cycle and hormone transport have been modelled extensively and these modules could be integrated. However, much less progress has been made on the modelling of cell expansion, which urgently needs to be addressed. A limitation of the current generation models is that they are largely qualitative. The possibilities to characterize existing and future models more quantitatively will be discussed. Together with experimental methods to measure crucial model parameters, these modelling techniques provide a basis to develop a Systems Biology approach to gain a fundamental insight into the relationship between gene function and whole organ behaviour.     

Conservation of migrants on their wintering grounds: an overview

Most research on the behaviour and ecology of wintering migrants has been undertaken in the Neotropics. In Africa, conservation biologists are faced with a comparative paucity of baseline data to assess the significance of environmental change, in contrast to the comparatively well-developed monitoring programmes in place on the breeding grounds. A programme of monitoring, established through international collaboration and matched with further ecological research, is required. Given the 'dispersed' distribution of most passerine migrants, determination of the significance of apparent detrimental effects can be hard to ascertain. However, migrants may provide conservationists with an effective vehicle for the provision of input into region-wide development policy. It is only through influencing regional development policies within the continent that large-scale and long-term conservation of important bird habitats will be achieved.     

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.     

State-of-the-art in membrane protein prediction

Membrane proteins are crucial for many biological functions and have become attractive targets for pharmacological agents. About 10%-30% of all proteins contain membrane-spanning helices. Despite recent successes, high-resolution structures for membrane proteins remain exceptional. The gap between known sequences and known structures calls for finding solutions through bioinformatics. While many methods predict membrane helices, very few predict membrane strands. The good news is that most methods for helical membrane proteins are available and are more often right than wrong. The best current prediction methods appear to correctly predict all membrane helices for about 50%-70% of all proteins, and to falsely predict membrane helices for about 10% of all globular proteins. The bad news is that developers have seriously overestimated the accuracy of their methods. In particular, while simple hydrophobicity scales identify many membrane helices, they frequently and incorrectly predict membrane helices in globular proteins. Additionally, all methods tend to confuse signal peptides with membrane helices. Nonetheless, wet-lab biologists can reach into an impressive toolbox for membrane protein predictions. However, the computational biologists will have to improve their methods considerably before they reach the levels of accuracy they claim.     

The case for developmental ecology

We call for renewed emphasis on the tasks confronting animals as they develop and learn. We are extending the use of the term ‘developmental ecology’ employed by plant biologists who have studied how fitness can be influenced by the ecological context present during development (Watson et al. 2001, Evolutionary Ecology,15, 425-442). We seek an expanded venue for the term, arguing that for animal behaviourists to understand some of the traits so familiar in behavioural ecology, they must consider the fundamental phenomena of development. Not doing so runs the risk of misidentifying both the proximal and functional causes of traits. For example, without a developmental view, macrogeographical variation in species-typical behaviour may be viewed as evidence of genotypic differences when, in fact, the variation is being produced by developmental contexts. Detailed below are some general issues about how development can be studied if it is to contribute to our knowledge of the adaptive value of behavioural systems. We argue for a prospective and longitudinal orientation, with an emphasis on relatively continuous observation and measurement. Both behaviours and contexts that may only occur during ontogeny are examined, as well as the reproductive outcome of the traits of interest. We present examples from our work on courtship and communication in brown-headed cowbirds, Molothrus ater, to show that a prospective and ecological view of development reveals pronounced variation in patterns of reproductive behaviour that cannot be understood without taking into account developmental ecology.     

Awareness and use of biodiversity collections by fish biologists

A survey of 280 fish biologists from a diverse pool of disciplines was conducted in order to assess the use made of biodiversity collections and how collections can better collect, curate and share the data they have. From the responses, data for how fish biologists use collections, what data they find the most useful, what factors influence the decisions to use collections, how they access the data and explore why some fish biologists make the decision to not use biodiversity collections is collated and reported. The results of which could be used to formulate sustainability plans for collections administrators and staff who curate fish biodiversity collections, while also highlighting the diversity of data and uses to researchers.     

Chemokine oligomerization and interactions with receptors and glycosaminoglycans: the role of structural dynamics in function

The first chemokine structure, that of IL-8/CXCL8, was determined in 1990. Since then, many chemokine structures have emerged. To the initial disappointment of structural biologists, the tertiary structures of these small proteins were found to be highly conserved. However, they have since proven to be much more interesting and diverse than originally expected. Somewhat like lego blocks, many chemokines oligomerize and there is significant diversity in their oligomeric forms and propensity to oligomerize. Chemokines not only interact with receptors where different oligomeric forms can induce different signaling responses, they also interact with glycosaminoglycans which can stabilize oligomers and other structures that would not otherwise form in solution. Although chemokine monomers and dimers yielded quickly to structure determination, structural information about larger chemokine oligomers, chemokines receptors, and complexes of chemokines with glycosaminoglycans and receptors has been more difficult to obtain, but recent breakthroughs suggest that this information will be forthcoming, especially with receptor structures. Equally important and challenging, will be efforts to correlate the structural information with function.     

瓢虫性选择行为及进化机制研究

昆虫性选择行为一直是行为生物学家和进化生物学家所关注的热点。早期对瓢虫性选择行为研究主要集中在非随机性交配模式,随着研究的深入,近些年对瓢虫性选择行为研究取得了许多新成果,包括多次交配的行为机制、性选择的识别机制、精子传送及竞争等。为全面地了解瓢虫性选择行为研究现状,本文总结了瓢虫非随机性交配模式,综述了近十余年对瓢虫性行为及进化的研究成果,同时对瓢虫性选择行为未来的研究方向进行了展望。