Attractor analysis of asynchronous Boolean models of signal transduction networks

Prior work on the dynamics of Boolean networks, including analysis of the state space attractors and the basin of attraction of each attractor, has mainly focused on synchronous update of the nodes’ states. Although the simplicity of synchronous updating makes it very attractive, it fails to take into account the variety of time scales associated with different types of biological processes. Several different asynchronous update methods have been proposed to overcome this limitation, but there have not been any systematic comparisons of the dynamic behaviors displayed by the same system under different update methods. Here we fill this gap by combining theoretical analysis such as solution of scalar equations and Markov chain techniques, as well as numerical simulations to carry out a thorough comparative study on the dynamic behavior of a previously proposed Boolean model of a signal transduction network in plants. Prior evidence suggests that this network admits oscillations, but it is not known whether these oscillations are sustained. We perform an attractor analysis of this system using synchronous and three different asynchronous updating schemes both in the case of the unperturbed (wild-type) and perturbed (node-disrupted) systems. This analysis reveals that while the wild-type system possesses an update-independent fixed point, any oscillations eventually disappear unless strict constraints regarding the timing of certain processes and the initial state of the system are satisfied. Interestingly, in the case of disruption of a particular node all models lead to an extended attractor. Overall, our work provides a roadmap on how Boolean network modeling can be used as a predictive tool to uncover the dynamic patterns of a biological system under various internal and environmental perturbations.     

Individuality,subjectivity, and minimal cognition

The paper links discussions of two topics: biological individuality and the simplest forms of mentality. I discuss several attempts to locate the boundary between metabolic activity and ‘minimal cognition.’ I then look at differences between the kinds of individuality present in unicellular life, multicellular life in general, and animals of several kinds. Nervous systems, which are clearly relevant to cognition and subjectivity, also play an important role in the form of individuality seen in animals. The last part of the paper links these biological transitions to the evolutionary history of subjective experience.     

Shifting to structures in physics and biology: a prophylactic for promiscuous realism

Within the philosophy of science, the realism debate has been revitalised by the development of forms of structural realism. These urge a shift in focus from the object oriented ontologies that come and go through the history of science to the structures that remain through theory change. Such views have typically been elaborated in the context of theories of physics and are motivated by, first of all, the presence within such theories of mathematical equations that allow straightforward representation of the relevant structures; and secondly, the implications of such theories for the individuality and identity of putative objects. My aim in this paper is to explore the possibility of extending such views to biological theories. An obvious concern is that within the context of the latter it is typically insisted that we cannot find the kinds of highly mathematised structures that structural realism can point to in physics. I shall indicate how the model-theoretic approach to theories might help allay such concerns. Furthermore, issues of identity and individuality also arise within biology. Thus Dupré has recently noted that there exists a 'General Problem of Biological Individuality' which relates to the issue of how one divides 'massively integrated and interconnected' systems into discrete components. In response Dupré advocates a form of 'Promiscuous Realism' that holds, for example, that there is no unique way of dividing the phylogenetic tree into kinds. Instead I shall urge serious consideration of those aspects of the work of Dupré and others that lean towards a structuralist interpretation. By doing so I hope to suggest possible ways in which a structuralist stance might be extended to biology.     

A polyethnic London carnival as a contested cultural performance*

This article argues that the theoretical problem of the new racism thesis, as originally formulated in the 1980s, was the account of the discursive change it proposed and the role and significance of Powellism in this process. In offering a modification of the thesis I highlight the significance of the use of anecdotal accounts of the plight of ordinary English people in areas of black settlement as central to the re-articulation of racialized common sense in Powellism. I go on to argue that the particular discursive form of the racialized anecdote is one that is developed within Parliamentary debates from at least the mid-1950s onwards and that Enoch Powell is not the author but the elite beneficiary of this ideological work. I suggest that this Commons' sense informs and makes possible the success of the campaign for exclusion of black Commonwealth migrants prior to Powellism, and that Powell fashions his own elite/populist version of such narratives in 1968. Offering an account of racism as a discursive fiction, I argue that the anecdotal form of political racism in post-war Britain is a political and ideological response to the public prohibition on 'race' talk in public space. In offering a tentative theory of post-'race' signification which is consistent with empirical evidence, I argue that the 'moment' of re-articulation of racism in post-war politics is one consistent with the evacuated space of the prohibited notion of 'old' racism.     

Three kinds of new mechanism

I distinguish three theses associated with the new mechanistic philosophy—concerning causation, explanation and scientific methodology. Advocates of each thesis are identified and relationships among them are outlined. I then look at some recent work on natural selection and mechanisms. Framing that debate in terms of different kinds of New Mechanism significantly affects what is at stake.     

Organisms in evolution

Organisms constitute one of the most remarkable features of our living world. However, they have not yet received any accepted characterization within the framework of the evolutionary theory. The reasons for this contrast between the saliency of organisms in the biological landscape and their theoretical status are multiple and they are analyzed in the first part of this paper. Starting from this contrast, I argue for a theoretically grounded concept of organism within the framework of evolutionary theory itself. To this effect I argue that the theory of major transitions in evolution (Maynard Smith and Szathmáry 1995; Michod 1999) provides us with the theoretical basis for an understanding of the individuality of organisms and I propose a first characterization of organisms as evolutionary units structured by a division of reproductive labor among their parts. I also discuss one of the most important implications of this definition, namely that some colonial entities are to be counted as superorganisms. Finally, I show that though theoretically satisfying, this definition does not suffice in order fully to individuate the organisms and superorganisms in practice. To this end, physiology is needed, because it offers us some criteria for their individuation in ecological space. These criteria, however, are not immune to errors through misidentification and their shortcomings are discussed in the last section. In conclusion, I emphasize the positive implications of these criteria concerning the ecological significance of organisms.     

Foundational issues concerning taxa and taxon names

In a series of articles, Rieppel (2005, Biol. Philos. 20:465-487; 2006a, Cladistics 22:186-197; 2006b, Systematist 26:5-9), Keller et al. (2003, Bot. Rev. 69:93-110), and Nixon and Carpenter (2000, Cladistics 16:298-318) criticize the philosophical foundations of the PhyloCode. They argue that species and higher taxa are not individuals, and they reject the view that taxon names are rigid designators. Furthermore, they charge supporters of the individuality thesis and rigid designator theory with assuming essentialism, committing logical inconsistencies, and offering proposals that render taxonomy untestable. These charges are unsound. Such charges turn on confusions over rigid designator theory and the distinction between kinds and individuals. In addition, Rieppel's, Keller et al.'s, and Nixon and Carpenter's proposed alternatives are no better and have their own problems. The individuality thesis and rigid designator theory should not be quickly abandoned.     

A levels-of-selection approach to evolutionary individuality

What changes when an evolutionary transition in individuality takes place? Many different answers have been given, in respect of different cases of actual transition, but some have suggested a general answer: that a major transition is a change in the extent to which selection acts at one hierarchical level rather than another. The current paper evaluates some different ways to develop this general answer as a way to characterise the property ‘evolutionary individuality’; and offers a justification of the option taken in Clarke (J Philos 110(8):413–435, 2013)—to define evolutionary individuality in terms of an object’s capacity to undergo selection at its own level. In addition, I suggest a method by which the property can be measured and argue that a problem which is often considered to be fatal to that method—the problem of ‘cross-level by-products’—can be avoided.     

Genes,genomes and identity. Projections on matter

This paper aims to show that references to genes and genomes are counterproductive in legal and political understandings of what it is to be human and a unique individual. To support this claim, I will give a brief overview of the many incompatible meanings the term ‘identity’ has gathered in reference to genes or genome in the contexts of biology and family ancestry, personal identity, species identity. One finds various and incompatible understandings of these expressions. While genetics is usually considered to deliver definitive knowledge about history and the future, genomics seems to work with more complicated relations between DNA, inheritance and phenotype. In genomics, ‘identity’ is no longer about identification and status markers but about individualization. Regulatory and legal documents project from traits to genomes, implying that the individuality is at least represented, if not created, in a unique genome. Boundaries between humans and other animals, between different ‘kinds’ of humans, and between all individual humans are re‐established via reference to the chemical matter of DNA. My analysis will show how this trend is a reactionary response to modern understandings of identities as social products and that it ignores new biomedical understandings of human bodies.     

Unburdening evo-devo: ancestral attractions, model organisms, and basal baloney

Although flourishing, I argue that evo-devo is not yet a mature scientific discipline. Its philosophical foundation exhibits an internal inconsistency that results from a metaphysical confusion. In modern evolutionary biology, species and other taxa are most commonly considered as individuals. I accept this thesis to be the best available foundation for modern evolutionary biology. However, evo-devo is characterized by a remarkable degree of typological thinking, which instead treats taxa as classes. This metaphysical incompatibility causes much distorted thinking. In this paper, I will discuss the logical implications of accepting the individuality thesis for evo-devo. First, I will illustrate the degree to which typological thinking pervades evo-devo. This ranges from the relatively innocent use of typologically tainted language to the more serious misuse of differences between taxa as evidence against homology and monophyly, and the logically flawed concept of partial homology. Second, I will illustrate how, in a context of typological thinking, evo-devo's harmless preoccupation with distant ancestors has become transformed into a pernicious problem afflicting the choice of model organisms. I will expose the logical flaws underlying the common assumption that model organisms can be expected to represent the clades they are a part of in an unambiguous way. I will expose the logical flaws underlying the general assumption that basal taxa are the best available stand-ins for ancestors and that they best represent the clade of which they are a part, while also allowing for optimal extrapolation of results.     

Leibnizian organisms,nested individuals,and units of selection

Summary Leibniz developed a new notion of individuality, according to which individuals are nested one within another, thereby abandoning the Aristotelian formula at the heart of substantialist metaphysics, ‘one body, one substance’. On this model, the level of individuality is determined by the degree of activity, and partly defined by its relations with other individuals. In this article, we show the importance of this new notion of individuality for some persisting questions in theoretical biology. Many evolutionary theorists presuppose a model of individuality that will eventually reduce to spatiotemporal mechanisms, and some still look for an exclusive level or function to determine a unit of selection. In recent years, a number of alternatives to these exclusive approaches have emereged, and no consensus can be foreseen. It is for this reason that we propose the model of nested individuals. This model supports pluralistic multi-level selection and rejects an exclusive level or function for a unit of selection. Since activity is essential to the unity of an individual, this model focuses on integrating processes of interaction and replication instead of choosing between them. In addition, the model of nested individuals may also be seen as a distinct perspective among the various alternative models for the unit of selection. This model stresses activity and pluralism: it accepts simultaneuous co-existence of individuals at different levels, nested one within the other. Our aim in this article is to show now a chapter of the history of metaphysics may be fruitfully brought to bear on the current debate over the unit of selection in evolutionary biology.     

Is there such a thing as landscape genetics?

For a scientific discipline to be interdisciplinary, it must satisfy two conditions; it must consist of contributions from at least two existing disciplines, and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this study, I examine the complete body of peer‐reviewed literature self‐identified as landscape genetics (LG) using the statistical approaches of text mining and natural language processing. The goal here was to quantify the kinds of questions being addressed in LG studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published LG studies examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual‐ and population‐based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if LGs is to serve as a real bridge connecting evolution and ecology sensu lato.     

Quality prevails over identity in the sexually selected vocalisations of an ageing mammal

Background

Male sexually selected vocalisations generally contain both individuality and quality cues that are crucial in intra- as well as inter-sexual communication. As individuality is a fixed feature whereas male phenotypic quality changes with age, individuality and quality cues may be subjected to different selection pressures over time. Individuality (for example, morphology of the vocal apparatus) and quality (for example, body size and dominance status) can both affect the vocal production mechanism, inducing the same components of vocalisations to convey both kinds of information. In this case, do quality-related changes to the acoustic structure of calls induce a modification of vocal cues to identity from year to year? We investigated this question in fallow deer (Dama dama), in which some acoustic parameters of vocalisations (groans) code for both individuality and quality.

Results

We carried out a longitudinal analysis of groan individuality, examining the effects of age and dominance rank on the acoustic structure of groans of the same males recorded during consecutive years. We found both age- and rank-related changes to groans; the minimum values of the highest formant frequencies and the fundamental frequency increased with the age of males and they decreased when males became more dominant. Both age- and rank-related acoustic parameters contributed to individuality. Male quality changed with age, inducing a change in quality-related parameters and thus, a modification of vocal cues to male individuality between years.

Conclusions

The encoding of individuality and quality information in the same components of vocalisations induces a tradeoff between these two kinds of signals over time. Fallow deer vocalisations are honest signals of quality that are not fixed over time but are modified dynamically according to male quality. As they are more reliable cues to quality than to individuality, they may not be used by conspecifics to recognize a given male from one year to another, but potentially used by both sexes to assess male quality during each breeding season.

     

Are humans disturbing conditions in ecology?

In this paper I argue, first, that ecologists have routinely treated humans—or more specifically, anthropogenic causal factors—as disturbing conditions. I define disturbing conditions as exogenous variables, variables “outside” a model, that when present in a target system, inhibit the applicability or accuracy of the model. This treatment is surprising given that (1) humans play a dominant role in many ecosystems and (2) definitions of ecology contain no fundamental distinction between human and natural. Second, I argue that the treatment of humans as disturbing conditions is an idealization: since it is, and has long been, known that humans are pervasive, this treatment amounts to an intentionally introduced theoretical distortion. Finally, characterizing this treatment as idealization forces us to confront the question of its justification, and so, drawing on three different kinds of idealization, I evaluate how this treatment may be justified.     

African communal basis for autonomy and life choices

I argue that the metaphysical capacity of autonomy is not intrinsically valuable; it is valuable only when used in relation to a community's values and instrumentally for making the proper choices that will promote one's own and the community's well‐being. I use the example of the choice to take one's life by suicide to illuminate this view. I articulate a plausible African conception of personhood as a basis for the idea of relational autonomy. I argue that this conception is better understood as a social‐moral thesis, and not a metaphysical thesis. A metaphysical thesis gives an account of the abstract nature of an atomic individual, his agency, and rational choice. The social‐moral thesis indicates that personhood and autonomy are positive and relational to the life plans, well‐being, material conditions, and the best means for achieving them that are made available and possible by harmonious living in a community. This idea of autonomy is not just having the capacity of freewill; it also involves how such freewill is used, in terms of how an individual's choices are guided by internalized communal values.     

On the double social life of failure

What might it mean to follow failure ‘out into the world’ (Alexander, introduction to this volume) in a way that is attentive both to its contingent and diffuse effects, and to the work involved in making it socially legible? This essay follows a moment of social breakdown, its reverberations in social life, and the forms of diagnosis it elicited as a way of exploring the double social life of failure. Focusing on the aftermath of Kyrgyzstan's 2010 ‘Osh events’ (Oshskie sobytiia) as they took hold in a multi-tenant and ethnically mixed dormitory apartment for migrant workers in Moscow, I follow failure forwards, exploring how a period of intercommunal violence reverberated in a context of protracted work migration, legal non-recognition, and the digital circulation of blame. I also track it backwards, attending to my interlocutors’ practices of diagnosis and excavation. Among Kyrgyz and Uzbeks in Moscow, the Osh events figured as indexical of different kinds of failure – whether of protection, recognition, or proper state care. I take vernacular diagnoses of bardak – normative breakdown – as an ethnographic entry point for thinking about the spatial and temporal afterlives of violence, their articulation in an age of digital mediation, and the ethics of naming and diagnosing failure.     

The logical priority of the tree over characters and some of its consequences for taxonomy

The aim of the present paper is to explore the role of the character in phylogenetic systematics. I argue that too much emphasis is put on particular characters rather than congruence both in the choice of phylogenetic hypotheses and in taxonomic decisions. This means that the logical priority of the tree over the characters is neglected. To a large extent, this is a result of not paying enough attention to the individuality thesis which states that clades are historical individuals and hence contingent in nature.     

Prefigured Features: A view from the New Guinea Highlands

Stimulated by a conference on Portraiture and the Problematics of Representation, which aimed to address portraiture as a set of cultural practices under the rubric of ‘any body-representation that stands for an individual’, in this paper I ask some questions raised by materials from Papua New Guinea. I begin with an investigation of the notion of individuation in relation to the heads which are taken in Asmat and Marind-Anim headhunting. I argue that if anyone's individuality is represented by a captured head it is that of the new owner, not his deceased victim. I then turn to Hagen feather plaques and suggest that they are best understood as assemblages of material resulting from mobilising relations, and hence not as portraits embodying notions of likeness.     

Loving recognition: a proposal for the practical efficacy of love as a public virtue

The anthropology of love has tended to focus on the romantic, and to explore its universality. In this article I ask a different kind of question of love. How might love be recruited as a moral force and deployed as a public virtue? I conceive of love not solely or principally as a private and domestic virtue but as a public and civil practice: a structuring of social interaction by means of affective appreciation of individual others. I understand love as the human capacity and the human practice of respecting the individuality of other lives. The desirous appreciation and affirmation of another ‘I’ – the loving attention – serves to surmount the customary ‘category‐thinking’ by which the world is normally apprehended: the generalizing, homogenizing, and stereotyping that characterize a culture's symbolic identification of the world. Loving recognition is such that the individuality of another life, its precious integrity and uniqueness, may be socially accommodated.