Online research in philosophy

Abstract Many apparently complex mechanisms in biology, especially in embryology and molecular biology, can be explained easily by reasoning at the level of the “efficient cause” of the observed phenomenology: the mechanism can then be explained by a simple geometrical argument or a variational principle, leading to the solution of an optimization problem, for example, via the co-existence of a minimization and a maximization problem (a min–max principle). Passing from a microscopic (or cellular) level (optimal min–max solution of the simple (...) mechanistic system) to the macroscopic level often involves an averaging effect (linked to the repetition of a large number of such microscopic systems with possible random choice of the parameters of each of them) that gives birth to a global functional feature (e.g. at the tissue level). We will illustrate these general principles by building in four different domains of application “a minima” models and showing the main properties of their solutions: (1) extraction of a minimal RNA structure functioning as the first “peptidic machine,” a kind of ancestral ribosome; (2) study of a genetic regulatory network of Drosophila centred on Engrailed gene and expressing successively two genes inside a limit cycle; (3) study of a genetic network regulating neural activity and proliferation in mammals; and (4) study of a simple geometric model of epiboly in zebrafish. Content Type Journal Article Category Regular Article Pages 1-17 DOI 10.1007/s10441-012-9146-4 Authors L. Almeida, AGIM, FRE CNRS 3405, Faculty of Medicine of Grenoble, University J. Fourier, 38 700 La Tronche, France J. Demongeot, AGIM, FRE CNRS 3405, Faculty of Medicine of Grenoble, University J. Fourier, 38 700 La Tronche, France Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Several key areas in modeling the cardiovascular and respiratory control systems are reviewed and examples are given which reflect the research state of the art in these areas. Attention is given to the interrelated issues of data collection, experimental design, and model application including model development and analysis. Examples are given of current clinical problems which can be examined via modeling, and important issues related to model adaptation to the clinical setting.

Abstract Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for (...) revisions and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance. Content Type Journal Article Category Regular Article Pages 1-17 DOI 10.1007/s10441-011-9143-z Authors Tudor M. Baetu, Department of Philosophy, University of Maryland, 1125D Skinner Building, College Park, MD 20742, USA Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

How can an incomplete and uncertain model of the environment be used to perceive, infer, decide and act efficiently? This is the challenge that both living and artificial cognitive systems have to face. Symbolic logic is, by its nature, unable to deal with this question. The subjectivist approach to probability is an extension to logic that is designed specifically to face this challenge. In this paper, we review a number of frequently encountered cognitive issues and cast them into a common (...) Bayesian formalism. The concepts we review are ambiguities, fusion, multimodality, conflicts, modularity, hierarchies and loops. First, each of these concepts is introduced briefly using some examples from the neuroscience, psychophysics or robotics literature. Then, the concept is formalized using a template Bayesian model. The assumptions and common features of these models, as well as their major differences, are outlined and discussed. (shrink)

Abstract Vision substitution by electro-stimulation has been studied since the 60s beginning with P. Bach-y-Rita. Camera pictures or movies encoded in gray levels are displayed using an electro-stimulation display device on the surface of a body part, such as the skin or the tongue. Medical-technical devices have been developed on this principle to compensate for sensory-motor disabilities such as blindness or loss of balance, or to guide specific actions, such as surgery. However, the electrical signals of stationary or moving slowly (...) moving objects, displayed on a Tongue display unit (TDU), are quickly lost due to saturation of receptors undergoing electrostimulation. We propose to add random saccades or sparkle to the displayed visual scene to increase the quality of pattern recognition by the subjects. In the present experimental trimodal study (normal vision, TDU vision substitution, or both), we show that the presence of a moderate sparkle level enhances the perception of the direction of lines drawn on a TDU and reduces the response time. Content Type Journal Article Category Regular Article Pages 1-13 DOI 10.1007/s10441-012-9148-2 Authors Abdessalem Chekhchoukh, AGIM Laboratory (Laboratory of AGeing Imaging and Modeling), University of Grenoble, CNRS FRE 3405, Domaine de la Merci, 38700 La Tronche, France Nicolas Glade, AGIM Laboratory (Laboratory of AGeing Imaging and Modeling), University of Grenoble, CNRS FRE 3405, Domaine de la Merci, 38700 La Tronche, France Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Abstract Angiogenesis is a complex morphogenetic process regulated by growth factors, but also by the force balance between endothelial cells (EC) traction stresses and extracellular matrix (ECM) viscoelastic resistance. Studies conducted with in vitro angiogenesis assays demonstrated that decreasing ECM stiffness triggers an angiogenic switch that promotes organization of EC into tubular cords or pseudo-capillaries. Thus, mechano-sensitivity of EC with regard to proteases secretion, and notably matrix metalloproteinases (MMPs), should likely play a pivotal role in this switching mechanism. While most (...) studies analysing strain regulation of MMPs used cell cultured on stretched membranes, this work focuses on MMP expression during self-assembly of EC into capillary-like structures within fibrin gels, i.e. on conditions that mimics more closely the in vivo cellular mechanical microenvironment. The activity of MMP-2 and MMP-9, two MMPs that have a pivotal role in capillaries formation, has been monitored in pace with the progressive elongation of EAhy926 cells that takes place during the emergence of cellular cords. We found an increase of the zymogen proMMP-2 that correlates with the initial stages of EC cords formation. However, MMP-2 was not detected. ProMMP-9 secretion decreased, with levels of MMP-9 kept at a rather low value. In order to analyse more precisely the observed differences of EAhy926 response on fibrin and plastic substrates, we proposed a theoretical model of the mechano-regulation of proMMP-2 activation in the presence of type 2 tissue inhibitor of MMPs (TIMP-2). Using association/dissociation rates experimentally reported for this enzymatic network, the model adequately describes the synergism of proMMP-2 and TIMP-2 strain activation during pseudo-capillary morphogenesis. All together, these results provide a first step toward a systems biology approach of angiogenesis mechano-regulation by cell-generated extracellular stresses and strains. Content Type Journal Article Category Regular Article Pages 1-20 DOI 10.1007/s10441-012-9147-3 Authors Minh-Uyen Dao Thi, Faculté de Médecine de Grenoble, DyCTiM team, UJF-Grenoble 1, CNRS, Laboratoire TIMC-IMAG UMR 5525, 38041 Grenoble, France Candice Trocmé, BEP/DBTP, CHU Albert Michallon, BP 217, 38043 Grenoble Cedex 9, France Marie-Paule Montmasson, Faculté de Médecine de Grenoble, DyCTiM team, UJF-Grenoble 1, CNRS, Laboratoire TIMC-IMAG UMR 5525, 38041 Grenoble, France Eric Fanchon, Faculté de Médecine de Grenoble, BCM team, UJF-Grenoble 1, CNRS, Laboratoire TIMC-IMAG UMR 5525, 38041 Grenoble, France Bertrand Toussaint, BEP/DBTP, CHU Albert Michallon, BP 217, 38043 Grenoble Cedex 9, France Philippe Tracqui, Faculté de Médecine de Grenoble, DyCTiM team, UJF-Grenoble 1, CNRS, Laboratoire TIMC-IMAG UMR 5525, 38041 Grenoble, France Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Limit cycles, because they are constituted of a periodic succession of states (discrete or continuous) constitute a good manner to store information. From any points of the state space reached after a perturbation or stimulation of the cognitive system storing this information, one can aim to join through a more or less long return trajectory a precise neighbourhood of the asymptotic trajectory at a specific moment (or a specific place) on the limit cycle, i.e. where the information of interest stands. (...) We propose that the isochronal fibration, initially imagined and described by A. T. Winfree may be an excellent way to connect directly those two locations. Each isochron is indeed the set of points in temporal phase with one single point of the attractor. The characterisation of the isochronal fibration of various dynamical systems is not easy and until now has principally only been done numerically but not analytically. By integrating the homogeneous solutions of the dynamical system we can solve this fibration in the case of the well known anharmonic pendulum. Other isochronal fibration on classical examples such as the van der Pol system and the non-symmetrical PFK limit cycle are obtained numerically and we also provide the first numerical study on 3-dimentional systems like the anharmonic pendulum with a linear relaxation on its third variable and the Lorenz attractor. The empirical approach seems us useful for dealing with the isochronal fibration which could constitute a powerful tool for understanding and controlling the dynamics of biological or biological-inspired systems. (shrink)

We give in this paper indications about the dynamical impact (as phenotypic changes) coming from the main sources of perturbation in biological regulatory networks. First, we define the boundary of the interaction graph expressing the regulations between the main elements of the network (genes, proteins, metabolites, ...). Then, we search what changes in the state values on the boundary could cause some changes of states in the core of the system (robustness to boundary conditions). After, we analyse the role of (...) the mode of updating (sequential, block sequential or parallel) on the asymptotics of the network, essentially on the occurrence of limit cycles (robustness to updating methods). Finally, we show the influence of some topological changes (e.g. suppression or addition of interactions) on the dynamical behaviour of the system (robustness to topology perturbations). (shrink)

The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only (...) one codon by synonymy class as solutions of a combinatory variational problem. We compare these solutions to sequences of present RNAs considered as relics, with a high interspecific invariance, like invariant parts of tRNAs and micro-RNAs. We conclude by emphasizing some optimal properties of the genetic code. (shrink)

At the beginning of this special issue of Acta Biotheoretica carrying the above title, we present a brief overview on currently important topics that have been brought up during the last “European Conference on Mathematical and Theoretical Biology” in Edinburgh. After emphasizing the need for a “synthetic biology” also from the side of theory, model building and analysis, we survey most plenary talks of this Conference and a selected series of eigth review articles, which are mainly related to corresponding minisymposia, (...) reflecting the current state of the art and the lively discussion within this interdisciplinary field. (shrink)

When we perceive the external world, our brain has to deal with the incompleteness and uncertainty associated with sensory inputs, memory and prior knowledge. In theoretical neuroscience probabilistic approaches have received a growing interest recently, as they account for the ability to reason with incomplete knowledge and to efficiently describe perceptive and behavioral tasks. How can the probability distributions that need to be estimated in these models be represented and processed in the brain, in particular at the single cell level? (...) We consider the basic function carried out by photoreceptor cells which consists in detecting the presence or absence of light. We give a system-level understanding of the process of phototransduction based on a bayesian formalism: we show that the process of phototransduction is equivalent to a temporal probabilistic inference in a Hidden Markov Model (HMM), for estimating the presence or absence of light. Thus, the biochemical mechanisms of phototransduction underlie the estimation of the current state probability distribution of the presence of light. A classical descriptive model describes the interactions between the different molecular messengers, ions, enzymes and channel proteins occurring within the photoreceptor by a set of nonlinear coupled differential equations. In contrast, the probabilistic HMM model is described by a discrete recurrence equation. It appears that the binary HMM has a general solution in the case of constant input. This allows a detailed analysis of the dynamics of the system. The biochemical system and the HMM behave similarly under steady-state conditions. Consequently a formal equivalence can be found between the biochemical system and the HMM. Numerical simulations further extend the results to the dynamic case and to noisy input. All in all, we have derived a probabilistic model equivalent to a classical descriptive model of phototransduction, which has the additional advantage of assigning a function to phototransduction. The example of phototransduction shows how simple biochemical interactions underlie simple probabilistic inferences. (shrink)

A simple numerical procedure is presented for the problem of estimating the parameters of models for the distribution of eggs oviposited in a host. The modelling is extended to incorporate both host density and time dependence to produce a remarkably parsimonious structure with only seven parameters to describe a data set of over 3,000 observations. This is further refined using a mixed model to accommodate several large outliers. Both models show that the level of superparasitism declines with increasing host density, (...) and the rate declines over time. It is proposed that the differing behaviours represented by the mixed model may reflect a balance between behavioural strategies of different selective benefit. (shrink)

The formal definition of species as explanatory hypotheses presented by Fitzhugh (Marine Biol 26:155–165, 2005a , b ) is emended. A species is an explanatory account of the occurrences of the same character(s) among gonochoristic or cross-fertilizing hermaphroditic individuals by way of character origin and subsequent fixation during tokogeny. In addition to species, biological systematics also employs hypotheses that are ontogenetic, tokogenetic, intraspecific, and phylogenetic, each of which provides explanatory hypotheses for distinctly different classes of causal questions. It is suggested (...) that species hypotheses can not be applied to organisms with obligate asexual, parthenogenetic, and self-fertilizing modes of reproduction. Hypotheses explaining shared characters among such organisms are, instead, strictly phylogenetic. Several implications of this emended definition are examined, especially the relations between species, intraspecific, and phylogenetic hypotheses, as well as the limitations of species names to be applied to temporally different characters within populations. (shrink)

Morphogenesis is a key process in developmental biology. An important issue is the understanding of the generation of shape and cellular organisation in tissues. Despite of their great diversity, morphogenetic processes share common features. This work is an attempt to describe this diversity using the same formalism based on a cellular description. Tissue is seen as a multi-cellular system whose behaviour is the result of all constitutive cells dynamics. Morphogenesis is then considered as a spatiotemporal organization of cells activities. We (...) show how this formalism relies on Reaction–Diffusion/Positional Information approach and how it permits to generalize its modelling possibilities. Three quite different applications for concrete morphogenetic processes are presented. The first one is a model for epithelial invagination, the second is a model of cellular differentiation by local cell–cell signalling. The last example is the secondary radial growth of conifer trees. From the mathematical point of view, different modelling tools are used according to the specificity of each process. (shrink)

Multi-level discrete models of genetic networks, or the more general piecewise affine differential models, provide qualitative information on the dynamics of the system, based on a small number of parameters (such as synthesis and degradation rates). Boolean models also provide qualitative information, but are based simply on the structure of interconnections. To explore the relationship between the two formalisms, a piecewise affine differential model and a Boolean model are compared, for the carbon starvation response network in E. coli . The (...) asymptotic dynamics of both models are shown to be quite similar. This study suggests new tools for analysis and reduction of biological networks. (shrink)

Dobzhansky argued that biology only makes sense if life on earth has a shared history. But his dictum is often reinterpreted to mean that biology only makes sense in the light of adaptation. Some philosophers of science have argued in this spirit that all work in ‘proximal’ biosciences such as anatomy, physiology and molecular biology must be framed, at least implicitly, by the selection histories of the organisms under study. Others have denied this and have proposed non-evolutionary ways in which (...) biologists can frame these investigations. This paper argues that an evolutionary perspective is indeed necessary, but that it must be a forward-looking perspective informed by a general understanding of the evolutionary process, not a backward-looking perspective informed by the specific evolutionary history of the species being studied. Interestingly, it turns out that there are aspects of proximal biology that even a creationist cannot study except in the light of a theory of their effect on future evolution. (shrink)

Hypoxia hampers ATP production and threatens cell survival. Since cellular energetics tightly controls cell responses and fate, ATP levels and dynamics are of utmost importance. An integrated mathematical model of ATP synthesis by the mitochondrial oxidative phosphorylation/electron transfer chain system has been recently published (Beard, PLoS Comput Biol 1(4):e36, 2005). This model was validated under static conditions. To evaluate its performance under dynamical situations, we implemented and simulated it (Simulink®, The Mathworks). Inner membrane potential (ΔΨ) and [NADH] (feeding the electron (...) transfer chain) were used as indicators of mitochondrial function. Root mean squared error (rmse) was used to compare simulations and experiments (isolated cardiac mitochondria, Bose et al. J Biol Chem 278(40):39155–39165, 2003). Steady-state experimental data were reproduced within 2–6%. Model dynamics were evaluated under: (i) baseline, (ii) activation of NADH production, (iii) addition of ADP, (iv) addition of inorganic phosphate, (v) oxygen exhaustion. In all phases, except the last one, ΔΨ and [NADH] as well as oxygen consumption, were reproduced (within 10, 7 and 12%, respectively). Under anoxia, simulated ΔΨ markedly depolarized (no change in experiments). In conclusion, the model reproduces dynamic data as long as oxygen is present. Anticipated improvement by the inclusion of ATP consumption and explicit Krebs cycle are under evaluation. (shrink)

Cancer is a complex disease, necessitating research on many different levels; at the subcellular level to identify genes, proteins and signaling pathways associated with the disease; at the cellular level to identify, for example, cell-cell adhesion and communication mechanisms; at the tissue level to investigate disruption of homeostasis and interaction with the tissue of origin or settlement of metastasis; and finally at the systems level to explore its global impact, e.g. through the mechanism of cachexia. Mathematical models have been proposed (...) to identify key mechanisms that underlie dynamics and events at every scale of interest, and increasing effort is now being paid to multi-scale models that bridge the different scales. With more biological data becoming available and with increased interdisciplinary efforts, theoretical models are rendering suitable tools to predict the origin and course of the disease. The ultimate aims of cancer models, however, are to enlighten our concept of the carcinogenesis process and to assist in the designing of treatment protocols that can reduce mortality and improve patient quality of life. Conventional treatment of cancer is surgery combined with radiotherapy or chemotherapy for localized tumors or systemic treatment of advanced cancers, respectively. Although radiation is widely used as treatment, most scheduling is based on empirical knowledge and less on the predictions of sophisticated growth dynamical models of treatment response. Part of the failure to translate modeling research to the clinic may stem from language barriers, exacerbated by often esoteric model renderings with inaccessible parameterization. Here we discuss some ideas for combining tractable dynamical tumor growth models with radiation response models using biologically accessible parameters to provide a more intuitive and exploitable framework for understanding the complexity of radiotherapy treatment and failure. (shrink)

Dusky groupers ( Epinephelus marginatus ) are characterized by a complex sex allocation strategies and overexploitation of bigger individuals. We developed an individual based model to investigate the long-term effects of density dependence on grouper population dynamics and to analyze the variabilities of extinction probabilities as a result of interacting mortalities at different life stages. We conduct several simulations with different forms of sex allocation functions and different combinations of mortality rates. The model was parametrized using data on dusky grouper (...) populations from the literature. The most important insights produced by this simulation study are that density dependence of sex allocation is an evolutionarily stable strategy, increases the population biomass, mitigates the effect of the removal of large male and indicates a need for protection of females and flexible stages. (shrink)

Ischemic stroke involves numerous and complex pathophysiological mechanisms including blood flow reduction, ionic exchanges, spreading depressions and cell death through necrosis or apoptosis. We used a mathematical model based on these phenomena to study the influences of intensity and duration of ischemia on the final size of the infarcted area. This model relies on a set of ordinary and partial differential equations. After a sensibility study, the model was used to carry out in silico experiments in various ischemic conditions. The (...) simulation results show that the proportion of apoptotic cells increases when the intensity of ischemia decreases, which contributes to the model validation. The simulation results also show that the influence of ischemia duration on the infarct size is more complicated. They suggest that reperfusion is beneficial when performed in the early stroke but may be either inefficacious or even deleterious when performed later after the stroke onset. This aggravation could be explained by the depolarisation waves which might continue to spread ischemic damage and by the speeding up of the apoptotic process leading to cell death. The effect of reperfusion on cell death through these two phenomena needs to be further studied in order to develop new therapeutic strategies for stroke patients. (shrink)

Abstract In this paper we introduce a stochastic model for a population living and migrating between s sites without distinction in the states between residents and immigrants. The evolutionary stable strategies (ESS) is characterized by the maximization of a stochastic growth rate. We obtain that the expectation of reproductive values, normalized by some random quantity, are constant on all sites and that the expectation of the normalized vector population structure is proportional to eigenvector of the dispersion matrix associated to eigenvalue (...) one, which are, in some way, analogous to the results obtained in the deterministic case. Content Type Journal Article Category Regular Article Pages 1-11 DOI 10.1007/s10441-011-9142-0 Authors Mohamed Khaladi, Department of Mathematics, Faculty of Sciences, LMPDP and UMI UMMISCO, IRD-UPMC, 40001 Marrakesh, Morocco Jean-Dominique Lebreton, CEFE/CNRS, 1919 Route de Mende, 34293 Montpellier cedex 5, France Abdelaziz Khermjioui, Department of Mathematics, Faculty of Sciences, LMPDP and UMI UMMISCO, IRD-UPMC, 40001 Marrakesh, Morocco Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction (the classes defined in terms of similarity relations) into a thing (such as an historical individual). The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

We consider a two-patch epidemiological system where individuals can move from one patch to another, and local interactions between the individuals within a patch are governed by the classical SIRS model. When the time-scale associated with migration is much smaller than the time-scale associated with infection, aggregation methods can be used to simplify the initial complete model formulated as a system of ordinary differential equations. Analysis of the aggregated model then shows that the two-patch basic reproduction rate is smaller than (...) the 1 patch one. We extend this result to a linear chain of P patches (P > 2). These results are illustrated by some examples for which numerical integration of the system of ordinary differential equations is performed. Simulations of an individual based model implemented with a multi-agent system are also carried out. (shrink)

In this work a mechanistic explanation of the classical algae growth model built by M. R. Droop in the late sixties is proposed. We first recall the history of the construction of the “predictive” variable yield Droop model as well as the meaning of the introduced cell quota. We then introduce some theoretical hypotheses on the biological phenomena involved in nutrient storage by the algae that lead us to a “conceptual” model. Though more complex than Droop’s one, our model remains (...) accessible to a complete mathematical study: its confrontation to the Droop model shows both have the same asymptotic behavior. However, while Droop’s cell quota comes from experimental bio-chemical measurements not related to intra-cellular biological phenomena, its analogous in our model directly follows our theoretical hypotheses. This new model should then be looked at as a re-interpretation of Droop’s work from a theoretical biologist’s point of view. (shrink)

We examine three critical aspects of Popper’s formulation of the ‘ Logic of Scientific Discovery ’—evidence, content and degree of corroboration—and place these concepts in the context of the Tree of Life (ToL) problem with particular reference to molecular systematics. Content, in the sense discussed by Popper, refers to the breadth and scope of existence that a hypothesis purports to explain. Content, in conjunction with the amount of available and relevant evidence, determines the testability, or potential degree of corroboration, of (...) a statement; content distinguishes scientific hypotheses from metaphysical assertions. Degree of corroboration refers to the relative and tentative confidence assigned to one hypothesis over another, based upon the performance of each under critical tests. Here we suggest that systematists attempt to maximize content and evidence to increase the potential degree of corroboration in all phylogenetic endeavors. Discussion of this “total evidence” approach leads to several interesting conclusions about generating ToL hypotheses. (shrink)

Apoptosis proteins play an essential role in regulating a balance between cell proliferation and death. The successful prediction of subcellular localization of apoptosis proteins directly from primary sequence is much benefited to understand programmed cell death and drug discovery. In this paper, by use of Chou’s pseudo amino acid composition (PseAAC), a total of 317 apoptosis proteins are predicted by support vector machine (SVM). The jackknife cross-validation is applied to test predictive capability of (...) proposed method. The predictive results show that overall prediction accuracy is 91.1% which is higher than previous methods. Furthermore, another dataset containing 98 apoptosis proteins is examined by proposed method. The overall predicted successful rate is 92.9%. (shrink)

The goal of this paper is to encourage a reconfiguration of the discussion about typology in biology away from the metaphysics of essentialism and toward the epistemology of classifying natural phenomena for the purposes of empirical inquiry. First, I briefly review arguments concerning ‘typological thinking’, essentialism, species, and natural kinds, highlighting their predominantly metaphysical nature. Second, I use a distinction between the aims, strategies, and tactics of science to suggest how a shift from metaphysics to epistemology might be accomplished. Typological (...) thinking can be understood as a scientific tactic that involves representing natural phenomena using idealizations and approximations, which facilitates explanation, investigation, and theorizing via abstraction and generalization. Third, a variety of typologies from different areas of biology are introduced to emphasize the diversity of this representational reasoning. One particular example is used to examine how there can be epistemological conflict between typology and evolutionary analysis. This demonstrates that alternative strategies of typological thinking arise due to the divergent explanatory goals of researchers working in different disciplines with disparate methodologies. I conclude with several research questions that emerge from an epistemological reconfiguration of typology. (shrink)

This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...) confirming evolutionary trees or cladograms. The identification and investigation of styles is useful for exploring sociological and epistemological issues such as individuating scientific communities and assessing the rationality of algorithm choice. Regarding the last point, this paper suggests that the values motivating ML and MP perspectives are justified but only contextually; these algorithms also have normative force because they can be therapeutic by allowing us to rationally choose among several competing trees, nonetheless this force is limited and cannot be used in order to decide the controversy tout court. (shrink)

Abstract In this work we deal with a general class of spatially distributed periodic SIS epidemic models with two time scales. We let susceptible and infected individuals migrate between patches with periodic time dependent migration rates. The existence of two time scales in the system allows to describe certain features of the asymptotic behavior of its solutions with the help of a less dimensional, aggregated , system. We derive global reproduction numbers governing the general spatially distributed nonautonomous system through the (...) aggregated system. We apply this result when the mass action law and the frequency dependent transmission law are considered. Comparing these global reproductive numbers to their non spatially distributed counterparts yields the following: adequate periodic migration rates allow global persistence or eradication of epidemics where locally, in absence of migrations, the contrary is expected. Content Type Journal Article Category Regular Article Pages 1-16 DOI 10.1007/s10441-011-9141-1 Authors M. Marvá, Dpto Matemáticas, Universidad de Alcalá, 28871 Madrid, Spain R. Bravo de la Parra, Dpto Matemáticas, Universidad de Alcalá, 28871 Madrid, Spain P. Auger, UR UMMISCO, IRD France Nord, 93143 Bondy, France Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Sickle cell haemoglobin (HbS) polymerization reduces erythrocyte deformability, causing deleterous vaso-occlusions. The double-nucleation model states that polymers grow from HbS aggregates, the nuclei, (i) in solution (homogeneous nucleation), (ii) onto existing polymers (heterogeneous nucleation). When linearized at initial HbS concentration, this model predicts early polymerization and its characteristic delay-time (Ferrone et al. J Mol Biol 183(4):591–610, 611–631, 1985). Addressing its relevance for describing complete polymerization, we constructed the full, non-linearized model (Simulink®, The MathWorks). Here, we compare the simulated outputs to (...) experimental progress curves (n = 6–8 different [HbS], 3–6 mM range, from Ferrone’s group). Within 10% from start, average root mean square (rms) deviation between simulated and experimental curves is 0.04 ± 0.01 (25°C, n = 8; mean ± standard error). Conversely, for complete progress curves, averaged rms is 0.48 ± 0.04. This figure is improved to 0.13 ± 0.01 by adjusting heterogeneous pathway parameters (p 2 μ cc : + 40%), and the fraction of polymer surface available for nucleation (ϕ), from 5e−7, (3 mM) to 13 (6 mM). Similar results are obtained at 37°C. We conclude that the physico-chemical description of heterogeneous nucleation warrants refinements in order to capture the whole HbS polymerization process. (shrink)

Secretion is a fundamental cellular process involving the regulated release of intracellular products from cells. Physiological functions such as neurotransmission, or the release of hormones and digestive enzymes, are all governed by cell secretion. Anomalies in the processes involved in secretion contribute to the development and progression of diseases such as diabetes and other hormonal disorders. To unravel the mechanisms that govern such diseases, it is essential to understand how hormones, growth factors and neurotransmitters are synthesized and processed, and how (...) their signals are recognized, amplified and transmitted by intracellular signaling pathways in the target cells. Here, we discuss diverse aspects of the detailed mechanisms involved in secretion based on mathematical models. The models range from stochastic ones describing the trafficking of secretory vesicles to deterministic ones investigating the regulation of cellular processes that underlie hormonal secretion. In all cases, the models are closely related to experimental results and suggest theoretical predictions for the secretion mechanisms. (shrink)

Optimal foraging theory has been criticized for underestimating patch exploitation time. However, proper modeling of costs not only answers these criticisms, but it also explains apparently irrational behaviors like the sunk-cost effect. When a forager is sure to experience high initial costs repeatedly, the forager should devote more time to exploitation than searching in order to minimize the accumulation of said costs. Thus, increased recognition or reconnaissance costs lead to increased exploitation times in order to reduce the frequency of future (...) costs, and this result can be used to explain paradoxical human preference for higher costs. In fact, this result also provides an explanation for how continuing a very costly task indefinitely provides the optimal long-term rate of gain; the entry cost of each new task is so great that the forager avoids ever returning to search. In general, apparently irrational decisions may be optimal when considering the lifetime of a forager within a larger system. (shrink)

The influence of sediment oxygen heterogeneity, due to bioturbation, on diffusive oxygen flux was investigated. Laboratory experiments were carried out with 3 macrobenthic species presenting different bioturbation behaviour patterns: the polychaetes Nereis diversicolor and Nereis virens, both constructing ventilated galleries in the sediment column, and the gastropod Cyclope neritea, a burrowing species which does not build any structure. Oxygen two-dimensional distribution in sediments was quantified by means of the optical planar optode technique. Diffusive oxygen fluxes (mean and integrated) and a (...) variability index were calculated on the captured oxygen images. All species increased sediment oxygen heterogeneity compared to the controls without animals. This was particularly noticeable with the polychaetes because of the construction of more or less complex burrows. Integrated diffusive oxygen flux increased with oxygen heterogeneity due to the production of interface available for solute exchanges between overlying water and sediments. This work shows that sediment heterogeneity is an important feature of the control of oxygen exchanges at the sediment–water interface. (shrink)

Species are generally considered to be the basic units of evolution, and hence to constitute spatio-temporally bounded entities. In addition, it has been argued that species also instantiate a natural kind. Evolution is fundamentally about change. The question then is how species can remain the same through evolutionary change. Proponents of the species qua individuals thesis individuate species through their unique evolutionary origin. Individuals, or spatio-temporally located particulars in general, can be bodies, objects, events, or processes, or a combination of (...) these. It is here argued that species are best understood as open or closed, causally integrated processual systems that also instantiate an historically conditioned homeostatic property cluster natural kind. (shrink)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between (neo)Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

We study the SIS and SIRI epidemic models discussing different approaches to compute the thresholds that determine the appearance of an epidemic disease. The stochastic SIS model is a well known mathematical model, studied in several contexts. Here, we present recursively derivations of the dynamic equations for all the moments and we derive the stationary states of the state variables using the moment closure method. We observe that the steady states give a good approximation of the quasi-stationary states of the (...) SIS model. We present the relation between the SIS stochastic model and the contact process introducing creation and annihilation operators. For the spatial stochastic epidemic reinfection model SIRI, where susceptibles S can become infected I, then recover and remain only partial immune against reinfection R, we present the phase transition lines using the mean field and the pair approximation for the moments. We use a scaling argument that allow us to determine analytically an explicit formula for the phase transition lines in pair approximation. (shrink)

Abstract The presence of gene–environment statistical interaction ( G x E ) and correlation ( rGE ) in biological development has led both practitioners and philosophers of science to question the legitimacy of heritability estimates. The paper offers a novel approach to assess the impact of G x E and rGE on the way genetic and environmental causation can be partitioned. A probabilistic framework is developed, based on a quantitative genetic model that incorporates G x E and rGE , offering (...) a rigorous way of interpreting heritability estimates. Specifically, given an estimate of heritability and the variance components associated with estimates of G x E and rGE , I arrive at a probabilistic account of the relative effect of genes and environment. Content Type Journal Article Category Regular Article Pages 1-13 DOI 10.1007/s10441-011-9139-8 Authors Omri Tal, School of Philosophy and The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv, 69978 Israel Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Toxic plants have been used for years in agriculture to control major crop pests. However, the continuous exposure of targeted pests to toxins dramatically increases the rate of resistance evolution (Gassman et al. in Annu Rev Entomol 54:147–163, 2009a ; Tabashnik et al. Nat Biotechnol 26:199–202, 2008 ). To prevent or delay resistance, non toxic host plants can be used as refuges. Our study considers spatial and temporal refuges that are respectively implemented concurrently or alternatively a toxic crop. A conceptual (...) model based on impulsive differential equations is proposed to describe the dynamics of the susceptible and resistant pest populations over time. The mathematical study enlightens threshold values of the proportion of the spatial refuge and key parameters that should help to understand evolution of pest resistance to toxic crop. (shrink)

Abstract Flax seedlings grown in the absence of environmental stimuli, stresses and injuries do not form epidermal meristems in their hypocotyls. Such meristems do form when the stimuli are combined with a transient depletion of calcium. These stimuli include the “manipulation stimulus” resulting from transferring the seedlings from germination to growth conditions. If, after a stimulus, calcium depletion is delayed, meristem production is also delayed; in other words, the meristem-production instruction can be memorised. Memorisation includes both storage and recall of (...) information. Here, we focus on information recall. We show that if the first transient calcium depletion is followed by a second transient depletion there is a new round of meristem production. We also show that if an excess of calcium follows calcium depletion, meristem production is blocked; but if the excess of calcium is in turn followed by another calcium depletion, again there is a new round of meristem production. The same stored information can thus be recalled repeatedly (at least twice). We describe a conceptual model that takes into account these findings. Content Type Journal Article Category Regular Article Pages 1-15 DOI 10.1007/s10441-012-9145-5 Authors Marie-Claire Verdus, Laboratoire AMMIS (Assemblages Moléculaires, Modélisation et Imagerie SIMS), CNRS (GDR DYCOEC), Faculté des Sciences et Techniques, Université de Rouen, 76821 Mont-Saint-Aignan Cedex, France Camille Ripoll, Laboratoire AMMIS (Assemblages Moléculaires, Modélisation et Imagerie SIMS), CNRS (GDR DYCOEC), Faculté des Sciences et Techniques, Université de Rouen, 76821 Mont-Saint-Aignan Cedex, France Vic Norris, Laboratoire AMMIS (Assemblages Moléculaires, Modélisation et Imagerie SIMS), CNRS (GDR DYCOEC), Faculté des Sciences et Techniques, Université de Rouen, 76821 Mont-Saint-Aignan Cedex, France Michel Thellier, Laboratoire AMMIS (Assemblages Moléculaires, Modélisation et Imagerie SIMS), CNRS (GDR DYCOEC), Faculté des Sciences et Techniques, Université de Rouen, 76821 Mont-Saint-Aignan Cedex, France Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters ( sensu Olivier Rieppel) in modern developmental biology’s (...) (mechanistic) theories, I arrive at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists (mainly, Colin Patterson), which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology. (shrink)

In this work, we compare two global approaches which are usually considered as completely unconnected one with the other. The former is Thom’s topology and the latter is Jung’s psychology. More precisely, it seemed to us interesting to adapt some morphologies of Thom’s catastrophe theory to some Jung’s notions. Thus, we showed that the swallowtail, which is one of these morphologies, was able to describe geometrically the structural organisation of the psyche according to Jung, with its collective unconscious, personal unconscious (...) and conscious. Moreover, we have correlated this morphology with Jung’s evolutive processes like individualisation and individuation. These comparisons incited us to think that some morphologies of Thom’s catastrophe theory are the geometrical dealing of Jung’s archetypes. (shrink)

Abstract Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of (...) biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns. Content Type Journal Article Category Regular Article Pages 1-15 DOI 10.1007/s10441-012-9144-6 Authors Paul L. Wennekes, Community and Conservation Ecology Group, University of Groningen, Groningen, The Netherlands James Rosindell, Institute of Integrative and Comparative Biology, University of Leeds, Leeds, UK Rampal S. Etienne, Community and Conservation Ecology Group, University of Groningen, Groningen, The Netherlands Journal Acta Biotheoretica Online ISSN 1572-8358 Print ISSN 0001-5342. (shrink)

The development of comparative biology (systematics) has been of interest to philosophers and historians. Particular attention has been placed on the ‘war’ of the 1970s and 1980s, the apparent dispute among those who preferred this or that methodology. In this contribution we examine the history of comparative biology from the perspective of fundamentals rather than methodologies. Our examination is framed within the artificial—natural classification dichotomy, a viewpoint currently lost from view but (...) worth resurrecting. (shrink)

Matrix models are widely used in biology to predict the temporal evolution of stage-structured populations. One issue related to matrix models that is often disregarded is the sampling variability. As the sample used to estimate the vital rates of the models are of finite size, a sampling error is attached to parameter estimation, which has in turn repercussions on all the predictions of the model. In this study, we address the question of building confidence bounds around the predictions of matrix (...) models due to sampling variability. We focus on a density-dependent Usher model, the maximum likelihood estimator of parameters, and the predicted stationary stage vector. The asymptotic distribution of the stationary stage vector is specified, assuming that the parameters of the model remain in a set of the parameter space where the model admits one unique equilibrium point. Tests for density-dependence are also incidentally provided. The model is applied to a tropical rain forest in French Guiana. (shrink)