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.

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.

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.

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.

Forty Years of ‘The Strategy’: Levins on Model Building and Idealization

This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is concerned, at its core, with justifying the use of multiple, idealized models in population biology.

The strategy of “The strategy of model building in population biology”

In this essay, I argue for four related claims. First, Richard Levins’ classic “The Strategy of Model Building in Population Biology” was a statement and defense of theoretical population biology growing out of collaborations between Robert MacArthur, Richard Lewontin, E. O. Wilson, and others. Second, I argue that the essay served as a response to the rise of systems ecology especially as pioneered by Kenneth Watt. Third, the arguments offered by Levins against systems ecology and in favor of his own methodological program are best construed as “pragmatic”. Fourth, I consider limitations of Levins’ arguments given contemporary population biology.

Reconsidering the Placebo Response from a Broad Anthropological Perspective

This paper considers how the full range of human experience may catalyze a placebo response. The placebo effect has been characterized as something to control in clinical research, something to cultivate in clinical practice and something present in all healing encounters. We examine domains in which the term ‘placebo’ is used in discourse: clinical research, clinical practice, media representations of treatment efficacy and lay interpretations of placebo—an underresearched topic. We briefly review major theoretical frameworks proposed to explain the placebo effect: classical conditioning, expectancy, the therapeutic relationship and sociocultural ‘meaning.’ As a corrective to what we see as an overemphasis on conscious cognitive approaches to understanding placebo, we reorient the discussion to argue that direct embodied experience may take precedence over meaning-making in the healing encounter. As an example, we examine the neurobiology of rehearsing or visualizing wellness as a mode of directly (performatively) producing an outcome often dismissed as a ‘placebo response.’ Given body/mind/emotional resonance, we suggest that the placebo response is an evolutionarily adaptive trait and part of healing mechanisms operating across many levels—from genetic and cellular to social and cultural.

Spandrels and a pervasive problem of evidence

Evolutionary biology, indeed any science that attempts to reconstruct prehistory, faces practical limitations on available data. These limitations create the problem of contrast failure: specific observations may fail to discriminate between rival evolutionary hypotheses. Assessing the risk of contrast failure provides a way to evaluate testing protocols in evolutionary science. Here I will argue that part of the methodological critique in the Spandrels paper involves diagnosing contrast failure problems. I then distinguish the problem of contrast failure from the more familiar philosophical problem of underdetermination, and demonstrate how contrast failure arises in scientific practice with an investigation into Lewontin and White’s (Evolution 14:116–129, 1960) estimation of an adaptive landscape.

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.

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.

Blogging Evolution

A weblog (“blog”) is an publication on the WorldWideWeb in which brief entries are displayed in date order, much like a diary or journal. I describe the general characteristics of blogs, contrasting blogs with other of WWW formats for self-publishing. I describe four categories for blogs about evolutionary biology: “professional,” “amateur,” “apostolic,” and “imaginative.” I also discuss blog networks. I identify paradigms of each category. Throughout, I aim to illuminate blogs about evolutionary biology from the point of view of a user looking for information about the topic. I conclude that blogs are not the best type of source for systematic and authoritative information about evolution, and that they are best used by the information-seeker as a way of identifying what issues are of interest in the community of evolutionists and for generating research leads or fresh insights on one’s own work.

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.

Morphological, anatomical and chemical characterization of white spruce ( Picea glauca ‘Conica’) differently aged needles and hypotheses on their influence on Oligonychus ununguis infestation

Our investigations suggest that the usually observed avoidance by O. ununguis of current year’s twigs of P. glauca ‘Conica’ as a place for feeding and development may be connected with their morphological and anatomical structure as well their biochemical composition. Needles of the current year’s twigs were covered with a thicker layer of wax and formed more extensive epidermis cell walls, in comparison with needles of 1-year-old twigs. Young needles also showed lower concentration of reducing sugars and soluble proteins, which might additionally reduce their nutritional suitability for mite development. Differences were also found between the 1-year-old growth and current growth in contribution of essential oils and a range of other compounds. Further analyses of the effect of these compounds on mite behavior may provide additional explanation of the feeding preferences of the mite.

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.

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.

Mastery of Mothering Skills and Satisfaction with Associated Health Services: An Ethnocultural Comparison

In this paper, I examine the mastery of mothering skills and satisfaction with associated health services in women who had recently given birth in Montreal (n = 33). I compare experience between women of two distinct ethnocultural groups: Anglophone Euro-Canadian and Anglophone Afro-Caribbean. The overall aim is to discern differentials in the mastery of mothering skills and associated satisfaction with maternal and child health services. The study is framed by neo-Weberian social theory suggesting that modernization and bureaucratization increasingly eviscerate everyday skills and knowledge. These processes also lead to changes regarding what is considered credible ‘authoritative knowledge.’ I found that older Anglophone Euro-Canadians expressed the greatest skill deficits. They attempted to redress these deficits through consultation of professionally authored books, medical Web sites and health professionals. Older Anglophone Euro-Canadians saw these resources as sources of ‘authoritative knowledge.’ They also expressed dissatisfaction with related health services. In contrast, Anglophone Afro-Caribbeans and younger lower-income Anglophone Euro-Canadians expressed satisfaction with their skills. This derived from widespread previous experience with children and more extensive and readily available kith and kin networks. These were considered sources of ‘authoritative knowledge’ in this group. This group expressed less dissatisfaction with health services, as they did not need, or expect, these services to redress skill deficits.

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.

Fitness “kinematics”: biological function,altruism, and organism–environment development

It’s recently been argued that biological fitness can’t change over the course of an organism’s life as a result of organisms’ behaviors. However, some characterizations of biological function and biological altruism tacitly or explicitly assume that an effect of a trait can change an organism’s fitness. In the first part of the paper, I explain that the core idea of changing fitness can be understood in terms of conditional probabilities defined over sequences of events in an organism’s life. The result is a notion of “conditional fitness” which is static but which captures intuitions about apparent behavioral effects on fitness. The second part of the paper investigates the possibility of providing a systematic foundation for conditional fitness in terms of spaces of sequences of states of an organism and its environment. I argue that the resulting “organism–environment history conception” helps unify diverse biological perspectives, and may provide part of a metaphysics of natural selection.

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’.