Objects limit human comprehension

This paper demonstrates that the human visual system, the primary sensory conduit for primates, processes ambient energy in a way that obligatorily constructs the objects that we ineluctably perceive. And since our perceptual apparatus processes information only in terms of objects (along with the properties and movements of objects), we are limited in our ability to comprehend ‘what is’ when we move beyond our ordinary world of midsize objects—as, for example, when we address the micro microworld of quantum physics.

Adaptationism and the adaptive landscape

Debates over adaptationism can be clarified and partially resolved by careful consideration of the ‘grain’ at which evolutionary processes are described. The framework of ‘adaptive landscapes’ can be used to illustrate and facilitate this investigation. We argue that natural selection may have special status at an intermediate grain of analysis of evolutionary processes. The cases of sickle-cell disease and genomic imprinting are used as case studies.

Making Sense in Time: Remote Sensing and the Challenges of Temporal Heterogeneity in Social Analysis of Environmental Change—cases from Malawi

This article contributes to the encouraging recent trend toward more critical examination of the linkages between remote sensing and social analysis of environmental change. Using two case studies from Malawi, we explain the importance of thinking about temporal scale when using remote sensing data. Specifically, from our on-the-ground research, we came to appreciate three important issues: (1) multiple causation and multiple temporal scales operating simultaneously—making inference of casual relations between particular social factors and observed land use changes difficult; (2) ‘visible’ vs. ‘invisible’ processes and events; and (3) ‘continuous’ vs. ‘punctuated’ social and environmental processes. We observe that in each case, social differentiation is key to understanding which temporal frames are most relevant in understanding observed land use dynamics. We conclude that, while these are not entirely new observations, research on the applications of remote sensing in social analysis of environmental change could be enriched by more rigorous examination of linkages between environmental change, temporal scale, and the social relations (including social differentiation) that can help to explain how and why particular temporal frames are most salient.

Is it a revolution?

Jablonka and Lamb's claim that evolutionary biology is undergoing a ‘revolution’ is queried. But the very concept of revolutionary change has uncertain application to a field organized in the manner of contemporary biology. The explanatory primacy of sequence properties is also discussed.

Functional homology and homology of function: biological concepts and philosophical consequences

“Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme of hierarchy in homology. I situate ‘homology of function’ within existing definitions and criteria for structural assessments of homology, and introduce a criterion of ‘organization’ for judging function homologues, which focuses on hierarchically interconnected interdependencies (similar to relative position and connection for skeletal elements in structural homology). This analysis of biological concepts has at least three broad philosophical consequences: (1) it provides the grounds for the study of behavior and psychological categories as homologues; (2) it demonstrates that philosophers who take selected effect function as primary effectively ignore large portions of comparative, structural, and experimental research, thereby misconstruing biological reasoning and knowledge; and, (3) it underwrites causal generalizations, which illuminates inferences made from model organisms in experimental biology.

Seven types of adaptationism

Godfrey-Smith (2001) has distinguished three types of adaptationism. This article builds on his analysis, and revises it in places, by distinguishing seven varieties of adaptationism. This taxonomy allows us to clarify what is at stake in debates over adaptationism, and it also helps to cement the importance of Gould and Lewontin’s ‘Spandrels’ essay. Some adaptationists have suggested that their essay does not offer any coherent alternative to the adaptationist programme: it consists only in an exhortation to test adaptationist hypotheses more thoroughly than was usual in the 1970s. Here it is argued that the ‘Spandrels’ paper points towards a genuinely non-adaptationist methodology implicit in much evolutionary developmental biology. This conclusion helps to expose the links between older debates over adaptationism and more recent questions about the property of evolvability.

Biological Levers and Extended Adaptationism

Two critiques of simple adaptationism are distinguished: anti-adaptationism and extended adaptationism. Adaptationists and anti-adaptationists share the presumption that an evolutionary explanation should identify the dominant simple cause of the evolutionary outcome to be explained. A consideration of extended-adaptationist models such as coevolution, niche construction and extended phenotypes reveals the inappropriateness of this presumption in explaining the evolution of certain important kinds of features—those that play particular roles in the regulation of organic processes, especially behavior. These biological or behavioral ‘levers’ are distinctively available for adaptation and exaptation by their possessors and for co-optation by other organisms. As a result they are likely to result from a distinctive and complex type of evolutionary process that conforms neither to simple adaptationist nor to anti-adaptationist styles of explanation. Many of the human features whose evolutionary explanation is most controversial belong to this category, including the female orgasm.

The Ethics of Birth and Death: Gender Infanticide in India

This paper discusses the persistent devaluation of the girl child in India and the link between the entrenched perception of female valuelessness and the actual practice of infanticide of girl babies or foetuses. It seeks to place female infanticide, or ‘gendercide,’ within the context of Western-derived conceptions of ethics, justice and rights. To date, current ethical theories and internationally purveyed moral frameworks, as well as legal and political declarations, have fallen short of an adequate moral appraisal of infanticide. This paper seeks to rethink the issue.

Honeybees, Communicative Order, and the Collapse of Ecosystems

The paper examines the sudden disappearance in the United States of millions of honeybees in managed bee colonies. The major research undertaken in the U.S. concentrates on finding the pathogens responsible. This paper suggests an alternative avenue of research a) that as a result of global warming there is a disjunction between bees pollinating cycles and the life cycle of plants b) that understanding changes in “timing cycles” as a result of global warming is the key to understanding the disappearance of the bees. It notes that Gregory Bateson argued that any condition of ecosystem collapse would be characterized first by a collapse in its communicative order rather, than from changed physical states. The collapse of bee colonies and demise of other pollinators is a seeming confirmation of Gregory Bateson argument. Honeybees are ‘go betweens’ in ecosystemic order. It also argues that an appropriate topology of timing cycles and their recursions would enable better visual comprehension of the heterarchical ‘pattern which connects’, in Bateson’s phrase, and prompt awareness of possible catastrophe in human food supplies.

Assessing the fitness landscape revolution

According to Pigliucci and Kaplan, there is a revolution underway in how we understand fitness landscapes. Recent models suggest that a perennial problem in these landscapes—how to get from one peak across a fitness valley to another peak—is, in fact, non-existent. In this paper I assess the structure and the extent of Pigliucci and Kaplan’s proposed revolution and argue for two points. First, I provide an alternative interpretation of what underwrites this revolution, motivated by some recent work on model-based science. Second, I show that the implications of this revolution need to carefully assessed depending on question being asked, for peak-shifting is not central to all evolutionary questions that fitness landscapes have been used to explore.

Spiking neural network simulation: numerical integration with the Parker-Sochacki method

Mathematical neuronal models are normally expressed using differential equations. The Parker-Sochacki method is a new technique for the numerical integration of differential equations applicable to many neuronal models. Using this method, the solution order can be adapted according to the local conditions at each time step, enabling adaptive error control without changing the integration timestep. The method has been limited to polynomial equations, but we present division and power operations that expand its scope. We apply the Parker-Sochacki method to the Izhikevich ‘simple’ model and a Hodgkin-Huxley type neuron, comparing the results with those obtained using the Runge-Kutta and Bulirsch-Stoer methods. Benchmark simulations demonstrate an improved speed/accuracy trade-off for the method relative to these established techniques.

Enabling conditions for ‘open-ended evolution’

In this paper we review and argue for the relevance of the concept of open-ended evolution in biological theory. Defining it as a process in which a set of chemical systems bring about an unlimited variety of equivalent systems that are not subject to any pre-determined upper bound of organizational complexity, we explain why only a special type of self-constructing, autonomous systems can actually implement it. We further argue that this capacity derives from the ‘dynamic decoupling’ (in its minimal or most basic sense: the phenotype–genotype decoupling) by means of which a radically new way of material organization (minimal living organization) is achieved, allowing for the long-term sustenance of systems whose individual-metabolic and collective-historical pathways become thereafter deeply intertwined.

The Biosemiotic Turn

With the publication of this inaugural issue of the internationally peer-reviewed journal Biosemiotics, our still-developing young interdiscipline marks yet another milestone in its journey towards adulthood. For this occasion, the editors of Biosemiotics have asked me to provide for those readers who may be newcomers to our field a very brief overview of the history of biosemiotics, contextualizing it within and against the larger currents of philosophical and scientific thinking from which it has emerged. To explain the origins of this most twenty-first century endeavour effectively, however, will require tracing—at least to the level of a thumbnail sketch—how the ‘sign’ concept appeared, was lost, and now must be painstakingly rediscovered and refined in science. To relate this long history, this article will appear in Biosemiotics in three instalments, examining, respectively: (1) The History of the Sign Concept in Pre-Modernist Science, (2) The History of the Sign Concept in Modernist Science, and (3) The Biosemiotic Attempt to Develop a More Useful Sign Concept for Contemporary Science. In this instalment, we begin our introductory ‘stroll through the woods of sciences and signs’ by following the development of the sign concept within the context of scientific inquiry, in necessarily broad outline, from the beginnings of such inquiry in sixth century BCE, through its long development in the Middle Ages, and up unto the onset of modernity. For only within this larger historical context can our contemporary attempt to develop a naturalistic understanding of sign relations be understood.

Amazon Forestry Tranformed: Integrating Knowledge for Smallholder Timber Managemet in Eastern Brazil

Recent discussions of local knowledge emphasize its dynamic nature invoking local peoples’ ability to effectively integrate traditional or local with science-based or “modern” knowledges. The smallholder timber industry of the Amazon’s estuarine floodplain provides an outstanding example of local patterns of resource management and economic activities transformed from within by smallholder farmers who participated in the industrial timber boom of the 1970s and 1980s. These farmers of eastern Amazonia have developed a vertically integrated local industry based on expertise reflecting profound locally developed knowledge of specific forests and management of ecological processes, individual observation and experimentation, as well as concepts and practices derived from temporary employment by large-scale industrial timber firms. At each stage of the smallholder forestry process—from managing natural regeneration to running small sawmills and marketing lumber—local managers apply an innovative set of practices reflecting their diverse experiences. This combination of technical, market, and ecological knowledge results in forests, timber markets, and economic patterns that do not correspond to many of the widely-held generalizations concerning either local or industrial tropical timber exploitation. This article uses data from 7 years of research in the Amazon floodplain.

Social Learning Processes in Swiss Soil Protection—The ‘From Farmer - To Farmer’ Project

Social learning approaches have become a prominent focus in studies related to sustainable agriculture. In order to better understand the potential of social learning for more sustainable development, the present study assessed the processes, effects and facilitating elements of interaction related to social learning in the context of Swiss soil protection and the innovative ‘From Farmer - To Farmer’ project. The study reveals that social learning contributes to fundamental transformations of patterns of interactions. However, the study also demonstrates that a learning-oriented understanding of sustainable development implies including analysis of the institutional environments in which the organizations of the individual representatives of face-to-face-based social learning processes are operating. This has shown to be a decisive element when face-to-face-based learning processes of the organisations’ representatives are translated into organisational learning. Moreover, the study revealed that this was achieved not directly through formalisation of new lines of institutionalised cooperation but by establishing links in a ‘boundary space’ trying out new forms of collaboration, aiming at social learning and co-production of knowledge. It is argued that further research on social learning processes should give greater emphasis to this intermediary level of ‘boundary spaces’.

Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

The end of the adaptive landscape metaphor?

The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology; the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms.

Advances in concepts and methods for the marine environment: implications for policy

Science-based indicators aimed at measuring the sustainability of human activities on the environment have become of prime importance in the policy arena. At the international level, the Commission on Sustainable Development and the Convention on Biological Diversity and other Multilateral Environmental Agreements have recognised the need to develop a set of scientific indicators related to changes in biodiversity and other environmental issues able to direct policy decisions. In the marine realm, the study of the effects of both ‘top-down’ extractive activities such as fishing is more and more dealt with, in conjunction with ‘bottom-up’ activities such as nutrient loading and the effects on biogeochemical cycles, marine geochemistry and ecosystem structure and functioning of other pollutants and contaminants. ‘Conventional’ approaches such as the identification of taxa, model organisms and related methodologies will continue playing a key role for the monitoring of human-induced changes in the marine environment. On the other hand, newly developed disciplines such as genomics, proteomics and biodiversity informatics are increasingly looked at as a source of information and applications that can respond to questions and concerns by the policy community such as the need to adapt to global and climate change in the marine environment so as to mitigate its societal implications.