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Biological Boundaries and Biological Age.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The chronologic age classically used in demography is often unable to give useful information about which exact stage in development or aging processes has reached an organism. Hence, we propose here to explain in some applications for what reason the chronologic age fails in explaining totally the observed state of an organism, which leads to propose a new notion, the biological age. This biological age is essentially determined by the number of divisions before the Hayflick's limit the tissue or mitochondrion in a critical organ (in the sense where its loss causes the death of the whole organism) has already used for...
Source: Acta Biotheoretica - November 12, 2009 Category: Biomedical Science Authors: Demongeot J Tags: Acta Biotheor Source Type: journals

Application of Change-Point Problem to the Detection of Plant Patches.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In ecology, if the considered area or space is large, the spatial distribution of individuals of a given plant species is never homogeneous; plants form different patches. The homogeneity change in space or in time (in particular, the related change-point problem) is an important research subject in mathematical statistics. In the paper, for a given data system along a straight line, two areas are considered, where the data of each area come from different discrete distributions, with unknown parameters. In the paper a method is presented for the estimation of the distribution change-point between both areas and an est...
Source: Acta Biotheoretica - November 6, 2009 Category: Biomedical Science Authors: López I, Gámez M, Garay J, Standovár T, Varga Z Tags: Acta Biotheor Source Type: journals

A Tissue-Level Electromechanical Model of the Left Ventricle: Application to the Analysis of Intraventricular Pressure.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The ventricular pressure profile is characteristic of the cardiac contraction progress and is useful to evaluate the cardiac performance. In this contribution, a tissue-level electromechanical model of the left ventricle is proposed, to assist the interpretation of left ventricular pressure waveforms. The left ventricle has been modeled as an ellipsoid composed of twelve mechano-hydraulic sub-systems. The asynchronous contraction of these twelve myocardial segments has been represented in order to reproduce a realistic pressure profiles. To take into account the different energy domains involved, the tissue-level scale...
Source: Acta Biotheoretica - October 29, 2009 Category: Biomedical Science Authors: Le Rolle V, Carrault G, Richard PY, Pibarot P, Durand LG, Hernández AI Tags: Acta Biotheor Source Type: journals

Editorial : Proceedings of the Second International Conference of the French-speaking Society for Theoretical Biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19855929 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - October 24, 2009 Category: Biomedical Science Authors: Arino J, Portet S Tags: Acta Biotheor Source Type: journals

Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Ins and Outs of Systems Biology vis-à-vis Molecular Biology: Continuation or Clear Cut? Acta Biotheor. 2009 Oct 24; Authors: De Backer P, De Waele D, Van Speybroeck L The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether...
Source: Acta Biotheoretica - October 24, 2009 Category: Biomedical Science Authors: De Backer P, De Waele D, Van Speybroeck L Tags: Acta Biotheor Source Type: journals

Multiregional Periodic Matrix for Modeling the Population Dynamics of Sardine (Sardina pilchardus) Along the Moroccan Atlantic Coast: Management Elements for Fisheries.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, we present a deterministic time discrete mathematical model based on multiregional periodic matrices to describe the dynamics of Sardina pilchardus in the Central Atlantic area of the Moroccan coast. This model deals with two stages (immature and mature) and three spatial zones where sardines are supposed to migrate from one zone to another. The population dynamics is described by an autonomous recurrence equation N(t + 1) = A.N(t), where A is a positive matrix whose entries are estimated using data collected during biannual acoustic surveys carried out from 2001 to 2003 onboard the Norwegian research ve...
Source: Acta Biotheoretica - October 19, 2009 Category: Biomedical Science Authors: Serghini M, Boutayeb A, Auger P, Charouki N, Ramzi A, Ettahiri O, Tchuente M Tags: Acta Biotheor Source Type: journals

Periodic Solutions of Piecewise Affine Gene Network Models with Non Uniform Decay Rates: The Case of a Negative Feedback Loop.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper concerns periodic solutions of a class of equations that model gene regulatory networks. Unlike the vast majority of previous studies, it is not assumed that all decay rates are identical. To handle this more general situation, we rely on monotonicity properties of these systems. Under an alternative assumption, it is shown that a classical fixed point theorem for monotone, concave operators can be applied to these systems. The required assumption is expressed in geometrical terms as an alignment condition on so-called focal points. As an application, we show the existence and uniqueness of a stable periodic...
Source: Acta Biotheoretica - October 7, 2009 Category: Biomedical Science Authors: Farcot E, Gouzé JL Tags: Acta Biotheor Source Type: journals

Reduction of Supercritical Multiregional Stochastic Models with Fast Migration.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a multitype global model that incorporates the effect of both processes and, making use of the existence of different time scales for demography and migration, build a reduced model in which the variables correspond to the total population in each age class. We extend previous results that relate the behavior of the original and the reduced model showing that, given a large enough separation of time scales between demography and migration, we can obtain information about the behavior of the multitype global model through the study of the simpler reduced model. We concentrate on the case where the two systems are...
Source: Acta Biotheoretica - October 6, 2009 Category: Biomedical Science Authors: Rincón A, Alonso JA, Sanz L Tags: Acta Biotheor Source Type: journals

Computational Modelling of Protein Interactions: Energy Minimization for the Refinement and Scoring of Association Decoys.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The prediction of protein-protein interactions based on independently obtained structural information for each interacting partner remains an important challenge in computational chemistry. Procedures where hypothetical interaction models (or decoys) are generated, then ranked using a biochemically relevant scoring function have been garnering interest as an avenue for addressing such challenges. The program PatchDock has been shown to produce reasonable decoys for modeling the association between pig alpha-amylase and the VH-domains of camelide antibody raised against it. We designed a biochemically relevant method by...
Source: Acta Biotheoretica - September 22, 2009 Category: Biomedical Science Authors: Dibrov A, Myal Y, Leygue E Tags: Acta Biotheor Source Type: journals

The alkaline solution to the emergence of life: energy, entropy and early evolution.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19653128 [PubMed - in process] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - August 6, 2009 Category: Biomedical Science Authors: Russell MJ Tags: Acta Biotheor Source Type: journals

An S-Curve-Based Approach of Identifying Biological Sequences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The main idea of S-curve diagram is to assign different angle values (from 0 degrees to 180 degrees ) to different nucleotide acid residues or to different protein amino acids, and then according to cos alpha ( j ) and sin alpha ( j ), the values are accumulated to construct an S-curve diagram, which is in strict one-to-one correspondence with the biological sequence. In addition, the S-curve diagram proves to be without the degeneracy phenomenon, so that both the degeneracy problem represented by diagrams and the problem of visualization for biological sequence data are solved. Meanwhile, a new approach to differentia...
Source: Acta Biotheoretica - June 15, 2009 Category: Biomedical Science Authors: Zhao LP, Lv YH, Li C, Yao MH, Jin XZ Tags: Acta Biotheor Source Type: journals

Pattern cladistics and the 'realism-antirealism debate' in the philosophy of biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 'ne...
Source: Acta Biotheoretica - May 31, 2009 Category: Biomedical Science Authors: Vergara-Silva F Tags: Acta Biotheor Source Type: journals

Editorial: from a biological point of view.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19507041 [PubMed - in process] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - May 31, 2009 Category: Biomedical Science Authors: Vergara-Silva F Tags: Acta Biotheor Source Type: journals

Mathematical Analysis of a Two Strain HIV/AIDS Model with Antiretroviral Treatment.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A two strain HIV/AIDS model with treatment which allows AIDS patients with sensitive HIV-strain to undergo amelioration is presented as a system of non-linear ordinary differential equations. The disease-free equilibrium is shown to be globally asymptotically stable when the associated epidemic threshold known as the basic reproduction number for the model is less than unity. The centre manifold theory is used to show that the sensitive HIV-strain only and resistant HIV-strain only endemic equilibria are locally asymptotically stable when the associated reproduction numbers are greater than unity. Qualitative analysis ...
Source: Acta Biotheoretica - April 9, 2009 Category: Biomedical Science Authors: Bhunu CP, Garira W, Magombedze G Tags: Acta Biotheor Source Type: journals

Reflections on Systematics and Phylogenetic Reconstruction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 19350210 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - April 7, 2009 Category: Biomedical Science Authors: Schwartz JH Tags: Acta Biotheor Source Type: journals

Editorial: Systematics, Darwinism, and the Philosophy of Science.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19343507 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - April 3, 2009 Category: Biomedical Science Authors: Vergara-Silva F, Winther RG Tags: Acta Biotheor Source Type: journals

Introduction: From a Philosophical Point of View.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19259623 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - March 4, 2009 Category: Biomedical Science Authors: Winther RG Tags: Acta Biotheor Source Type: journals

Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19229636 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - February 20, 2009 Category: Biomedical Science Authors: Winther RG Tags: Acta Biotheor Source Type: journals

Rational Disagreements in Phylogenetics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Acta Biotheoretica - February 20, 2009 Category: Biomedical Science Authors: Mc Manus FG Tags: Acta Biotheor Source Type: journals

Species as Explanatory Hypotheses: Refinements and Implications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Acta Biotheoretica - February 18, 2009 Category: Biomedical Science Authors: Fitzhugh K Tags: Acta Biotheor Source Type: journals

Explanation and Falsification in Phylogenetic Inference: Exercises in Popperian Philosophy.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 whic...
Source: Acta Biotheoretica - February 4, 2009 Category: Biomedical Science Authors: Kluge AG Tags: Acta Biotheor Source Type: journals

Explicitly Accounting for Pixel Dimension in Calculating Classical and Fractal Landscape Shape Metrics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Different summarized shape indices, like mean shape index (MSI) and area weighted mean shape index (AWMSI) can change over multiple size scales. This variation is important to describe scale heterogeneity of landscapes, but the exact mathematical form of the dependence is rarely known. In this paper, the use of fractal geometry (by the perimeter and area Hausdorff dimensions) made us able to describe the scale dependence of these indices. Moreover, we showed how fractal dimensions can be deducted from existing MSI and AWMSI data. In this way, the equality of a multiscale tabulated MSI and AWMSI dataset and two scale-in...
Source: Acta Biotheoretica - January 29, 2009 Category: Biomedical Science Authors: Imre AR, Rocchini D Tags: Acta Biotheor Source Type: journals

Mathematical Modeling of Intrusive Growth of Fusiform Initials in Relation to Radial Growth and Expanding Cambial Circumference in Pinus sylvestris L.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study on the cambium of Pinus sylvestris L. examines the intrusive growth of fusiform cambial initials and its possible contribution to the tangential and radial expansions of the cambial cylinder. The location and extent of intrusive growth of the fusiform initials were determined by microscopic observations and by mathematical modeling. In order to meet the required circumferential expansion of the cambial cylinder, the fusiform initials grow in groups by means of a symplastic rather than intrusive growth, leaving no room for the assumption that intrusive growth of the initials takes place between radial walls and h...
Source: Acta Biotheoretica - January 29, 2009 Category: Biomedical Science Authors: Karczewska D, Karczewski J, Włoch W, Jura-Morawiec J, Kojs P, Iqbal M, Krawczyszyn J Tags: Acta Biotheor Source Type: journals

Prediction of Subcellular Localization of Apoptosis Protein Using Chou's Pseudo Amino Acid Composition.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 previ...
Source: Acta Biotheoretica - January 24, 2009 Category: Biomedical Science Authors: Lin H, Wang H, Ding H, Chen YL, Li QZ Tags: Acta Biotheor Source Type: journals

Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction-there is no theory-free "view from nowhere." Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each with examples. Ultimately, it is importa...
Source: Acta Biotheoretica - January 7, 2009 Category: Biomedical Science Authors: Winther RG Tags: Acta Biotheor Source Type: journals

Evidence, Content and Corroboration and the Tree of Life.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Discussion of this "total evidence" approach leads to several interesting conclusions about generating ToL hypotheses. PMID: 19015816 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - November 18, 2008 Category: Biomedical Science Authors: Kurt Lienau E, Desalle R Tags: Acta Biotheor Source Type: journals

Egg Distributions of Insect Parasitoids: Modelling and Analysis of Temporal Data with Host Density Dependence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 mixe...
Source: Acta Biotheoretica - October 25, 2008 Category: Biomedical Science Authors: Fenlon JS, Faddy MJ, Toussidou M, de Courcy Williams ME Tags: Acta Biotheor Source Type: journals

Study and Simulation of Reaction-Diffusion Systems Affected by Interacting Signaling Pathways.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Possible effects of interaction (cross-talk) between signaling pathways is studied in a system of Reaction-Diffusion (RD) equations. Furthermore, the relevance of spontaneous neurite symmetry breaking and Turing instability has been examined through numerical simulations. The interaction between Retinoic Acid (RA) and Notch signaling pathways is considered as a perturbation to RD system of axon-forming potential for N2a neuroblastoma cells. The present work suggests that large increases to the level of RA-Notch interaction can possibly have substantial impacts on neurite outgrowth and on the process of axon formation. ...
Source: Acta Biotheoretica - October 22, 2008 Category: Biomedical Science Authors: Bani-Yaghoub M, Amundsen DE Tags: Acta Biotheor Source Type: journals

A Model for Short- and Long-range Interactions of Migrating Tumour Cell.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We examine the consequences of long-range effects on tumour cell migration. Our starting point are previous results of ours where we have shown that the migration patterns of glioma cells are best interpreted if one assumes attractive interactions between cells. Here we complement the cellular automaton model previously introduced by the assumption of the existence of a chemorepellent produced by the main bulk of large spheroids (in the hypoxic/necrotic areas). Visible effects due to the presence of such a substance can be found in the density profiles of cells migrating out of a single spheroid as well as in the angul...
Source: Acta Biotheoretica - October 9, 2008 Category: Biomedical Science Authors: Aubert M, Badoual M, Grammaticos B Tags: Acta Biotheor Source Type: journals

Typology Reconfigured: From the Metaphysics of Essentialism to the Epistemology of Representation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 tac...
Source: Acta Biotheoretica - September 30, 2008 Category: Biomedical Science Authors: Love AC Tags: Acta Biotheor Source Type: journals

What, Exactly, is Cladistics? Re-writing the History of Systematics and Biogeography.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18825502 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - September 30, 2008 Category: Biomedical Science Authors: Williams DM, Ebach MC Tags: Acta Biotheor Source Type: journals

Species as a Process.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 unders...
Source: Acta Biotheoretica - September 24, 2008 Category: Biomedical Science Authors: Rieppel O Tags: Acta Biotheor Source Type: journals

Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering homologues as another example of natural kinds, comparing them with ...
Source: Acta Biotheoretica - September 19, 2008 Category: Biomedical Science Authors: Brigandt I Tags: Acta Biotheor Source Type: journals

DNA Computing, Computation Complexity and Problem of Biological Evolution Rate.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An analogy between the evolution of organisms and some complex computational problems (cryptosystem cracking, determination of the shortest path in a graph) is considered. It is shown that in the absence of a priori information about possible species of organisms such a problem is complex (is rated in the class NP) and cannot be solved in a polynomial number of steps. This conclusion suggests the need for re-examination of evolution mechanisms. Ideas of a deterministic approach to the evolution are discussed. PMID: 18787960 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - September 12, 2008 Category: Biomedical Science Authors: Melkikh AV Tags: Acta Biotheor Source Type: journals

In What Sense Does 'Nothing Make Sense Except in the Light of Evolution'?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 tha...
Source: Acta Biotheoretica - September 6, 2008 Category: Biomedical Science Authors: Griffiths PE Tags: Acta Biotheor Source Type: journals

Revisiting the Relation Between Species Diversity and Information Theory.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The Shannon information function (H) has been extensively used in ecology as a statistic of species diversity. Yet, the use of Shannon diversity index has also been criticized, mainly because of its ambiguous ecological interpretation and because of its relatively great sensitivity to the relative abundances of species in the community. In my opinion, the major shortcoming of the traditional perspective (on the possible relation of species diversity with information theory) is that species need for an external receiver (the scientist or ecologist) to exist and transmit information. Because organisms are self-catalized ...
Source: Acta Biotheoretica - July 11, 2008 Category: Biomedical Science Authors: Camargo JA Tags: Acta Biotheor Source Type: journals

On physicalism and Downward Causation in Developmental and Cancer Biology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The dominant position in Philosophy of Science contends that downward causation is an illusion. Instead, we argue that downward causation doesn't introduce vicious circles either in physics or in biology. We also question the metaphysical claim that "physical facts fix all the facts." Downward causation does not imply any contradiction if we reject the assumption of the completeness and the causal closure of the physical world that this assertion contains. We provide an argument for rejecting this assumption. Furthermore, this allows us to reconsider the concept of diachronic emergence. PMID: 18542843 [PubMed - as ...
Source: Acta Biotheoretica - June 10, 2008 Category: Biomedical Science Authors: Soto AM, Sonnenschein C, Miquel PA Tags: Acta Biotheor Source Type: journals

DNA Codes and Information: Formal Structures and Relational Causes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Recently the terms "codes" and "information" as used in the context of molecular biology have been the subject of much discussion. Here I propose that a variety of structural realism can assist us in rethinking the concepts of DNA codes and information apart from semantic criteria. Using the genetic code as a theoretical backdrop, a necessary distinction is made between codes qua symbolic representations and information qua structure that accords with data. Structural attractors are also shown to be entailed by the mapping relation that any DNA code is a part of (as the domain). In this framework, these attractors are ...
Source: Acta Biotheoretica - May 9, 2008 Category: Biomedical Science Authors: Sternberg RV Tags: Acta Biotheor Source Type: journals

Modelling of Cells Bioenergetics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This paper presents an integrated model describing the control of Saccharomyces cerevisiae yeast cells bioenergetics. This model describes the oxidative and respirofermentative metabolism. The model assumes that the mitochondria of the Saccharomyces cerevisiae cells are charged with NADH during the tricarboxylic acid cycle, and NADH is discharged from mitochondria later in the electron transport system. Selected effects observed in the Saccharomyces cerevisiae eucaryotic cells, including the Pasteur's and Crabtree effects, are also modeled. PMID: 18379882 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - April 1, 2008 Category: Biomedical Science Authors: Kasperski A Tags: Acta Biotheor Source Type: journals

Robustness in Regulatory Networks: A Multi-Disciplinary Approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, essential...
Source: Acta Biotheoretica - April 1, 2008 Category: Biomedical Science Authors: Demongeot J, Elena A, Sené S Tags: Acta Biotheor Source Type: journals

Asymptotic Distribution of Density-Dependent Stage-Grouped Population Dynamics Models.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18373070 [Pub...
Source: Acta Biotheoretica - March 29, 2008 Category: Biomedical Science Authors: Zetlaoui M, Picard N, Bar-Hen A Tags: Acta Biotheor Source Type: journals

Species Richness and the Analytic Geometry of Latitudinal and Altitudinal Gradients.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Extensive empirical work has shown that species richness decreases roughly exponentially or quadratically with latitude. What appears to be a latitudinal gradient in fact may simply be a negative correlation of latitude with area at that latitude, due to convergence of lines of meridian at the poles. There is simply less area at high latitudes, which means fewer niches and fewer opportunities for speciation, hence diminished biodiversity at high latitudes. Similarly, analytic geometry of a cone shows that species number should decrease linearly with altitude on a conical mountain. Here, I provide an explicit mathematic...
Source: Acta Biotheoretica - March 18, 2008 Category: Biomedical Science Authors: Gorelick R Tags: Acta Biotheor Source Type: journals

Beyond the Oncogene Paradigm: Understanding Complexity in Cancerogenesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In the past decades, an enormous amount of precious information has been collected about molecular and genetic characteristics of cancer. This knowledge is mainly based on a reductionistic approach, meanwhile cancer is widely recognized to be a 'system biology disease'. The behavior of complex physiological processes cannot be understood simply by knowing how the parts work in isolation. There is not solely a matter how to integrate all available knowledge in such a way that we can still deal with complexity, but we must be aware that a deeply transformation of the currently accepted oncologic paradigm is urgently need...
Source: Acta Biotheoretica - February 21, 2008 Category: Biomedical Science Authors: Bizzarri M, Cucina A, Conti F, D'Anselmi F Tags: Acta Biotheor Source Type: journals

A General Formalism for Tissue Morphogenesis Based on Cellular Dynamics and Control System Interactions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Acta Biotheoretica - February 15, 2008 Category: Biomedical Science Authors: Forest L, Demongeot J Tags: Acta Biotheor Source Type: journals

Effect of the Number of Patches in a Multi-patch SIRS Model with Fast Migration on the Basic Reproduction Rate.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Acta Biotheoretica - February 14, 2008 Category: Biomedical Science Authors: Kouokam E, Auger P, Hbid H, Tchuente M Tags: Acta Biotheor Source Type: journals

Evolution and RNA Relics. A Systems Biology View.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 s...
Source: Acta Biotheoretica - February 14, 2008 Category: Biomedical Science Authors: Demongeot J, Glade N, Moreira A Tags: Acta Biotheor Source Type: journals

Imaging Oxygen Distribution in Marine Sediments. The Importance of Bioturbation and Sediment Heterogeneity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Acta Biotheoretica - February 5, 2008 Category: Biomedical Science Authors: Pischedda L, Poggiale JC, Cuny P, Gilbert F Tags: Acta Biotheor Source Type: journals

The Double Nucleation Model for Sickle Cell Haemoglobin Polymerization: Full Integration and Comparison with Experimental Data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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((R)), The MathWorks). He...
Source: Acta Biotheoretica - February 5, 2008 Category: Biomedical Science Authors: Medkour T, Ferrone F, Galactéros F, Hannaert P Tags: Acta Biotheor Source Type: journals

A Mechanistic Investigation of the Algae Growth "Droop" Model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, wh...
Source: Acta Biotheoretica - February 5, 2008 Category: Biomedical Science Authors: Lemesle V, Mailleret L Tags: Acta Biotheor Source Type: journals

Dynamic Simulation of Mitochondrial Respiration and Oxidative Phosphorylation: Comparison with Experimental Results.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. PMID: 18231864 [PubMed - as supplied by publisher] (Source: Acta Biotheoretica)
Source: Acta Biotheoretica - January 30, 2008 Category: Biomedical Science Authors: Guillaud F, Hannaert P Tags: Acta Biotheor Source Type: journals