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Philosophy of Biology

Edited by John Wilkins (University of Sydney, University of Melbourne)
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  1. M. D. Akhundov (1991). An American Looks at Soviet Science. A Review of Loren R. Graham, "Science, Philosophy and Human Behavior in the Soviet Union". [REVIEW] Biology and Philosophy 6 (3):363.
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    Developmental Biology
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  2. Gerard Jagers op Akkerhuis (2001). Extrapolating a Hierarchy of Building Block Systems Towards Future Neural Network Organisms. Acta Biotheoretica 49 (3):171-189.
    It is possible to predict future life forms? In this paper it is argued that the answer to this question may well be positive. As a basis for predictions a rationale is used that is derived from historical data, e.g. from a hierarchical classification that ranks all building block systems, that have evolved so far. This classification is based on specific emergent properties that allow stepwise transitions, from low level building blocks to higher level ones. This paper shows how this (...)
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  3. Jesus Artalejo (2014). On the Markovian Approach for Modeling the Dynamics of Nosocomial Infections. Acta Biotheoretica 62 (1):15-34.
    We analyze the dynamics of nosocomial infections in intensive care units by using a Markov chain model. Since population size in the ICU is small, in contrast to previous studies, we concentrate on the analytical solution rather than using simulation. We investigate how changes in the system parameters affect to some important behavioral indicators of the spread of the pathogen. We also present an exact measure of the number of secondary cases of infection produced by one colonized patient.
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  4. Jean-Pierre Aubin (2013). Tychastic Viability. Acta Biotheoretica 61 (3):329-340.
    Tychastic viability is defined in an uncertain dynamical framework and used for providing a “viability risk eradication measure”, first, by delineating the set of initial conditions from which all evolutions satisfy viability constraints, second, for the other “risky” initial states, by introducing their duration index. This approach provides an alternative to the stochastic representation of chance and these two measures replace the statistical measures.
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  5. John Beatty (1988). The Wright Stuff: William Provine, "Sewall Wright and Evolutionary Biology". [REVIEW] Biology and Philosophy 3 (2):275.
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  6. Ismail Belgacem & Jean-luc Gouzé (2013). Global Stability of Enzymatic Chains of Full Reversible Michaelis-Menten Reactions. Acta Biotheoretica 61 (3):425-436.
    We consider a chain of metabolic reactions catalyzed by enzymes, of reversible Michaelis-Menten type with full dynamics, i.e. not reduced with any quasi-steady state approximations. We study the corresponding dynamical system and show its global stability if the equilibrium exists. If the system is open, the equilibrium may not exist. The main tool is monotone systems theory. Finally we study the implications of these results for the study of coupled genetic-metabolic systems.
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  7. Andre Bergholz, Stephan Heymann, Jörg Schenk & Johann Freytag (2001). Biological Sequences Integrated: A Relational Database Approach. Acta Biotheoretica 49 (3):145-159.
    Over the last decade the modeling and the storage of biological data has been a topic of wide interest for scientists dealing with biological and biomedical research. Currently most data is still stored in text files which leads to data redundancies and file chaos.In this paper we show how to use relational modeling techniques and relational database technology for modeling and storing biological sequence data, i.e. for data maintained in collections like EMBL or SWISS-PROT to better serve the needs for (...)
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  8. Samuel Bernard (2013). How to Build a Multiscale Model in Biology. Acta Biotheoretica 61 (3):291-303.
    Biological processes span several scales in space, from the single molecules to organisms and ecosystems. Multiscale modelling approaches in biology are useful to take into account the complex interactions between different organisation levels in those systems. We review several single- and multiscale models, from the most simple to the complex ones, and discuss their properties from a multiscale point of view. Approaches based on master equations for stochastic processes, individual-based models, hybrid continuous-discrete models and structured PDE models are presented.
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  9. H. Bettermann & P. Van Leeuwen (1992). Dimensional Analysis of RR Dynamic in 24 Hour Electrocardiograms. Acta Biotheoretica 40 (4):297-312.
    Using dimensional analysis, we demonstrate that it is possible to quantify changes in the topological structure of cardiac dynamics over long periods of time. A method was developed to calculate a dimension-like measure from a correlation algorithm within a data window of 500 heart beats which is moved in equidistant steps over the time series of the RR intervals over 24 hours. The correspondence between the apparent dimension and the correlation dimension was tested using artificial data sequences. Furthermore 24 hour (...)
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  10. Liliane Bodson (2000). Edited Volumes-Ces Animaux Que l'Homme Choisit D'Inhumer. Contribution a l'Etude de la Place Et du Role de l'Animal Dans Les Rites Funeraires. History and Philosophy of the Life Sciences 22 (3):454.
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  11. J. Bogaert (2003). Chance in Biology - Using Probability to Explore Nature. [REVIEW] Acta Biotheoretica 51 (1):55-57.
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  12. J. Bogaert (2002). Landscape Ecology — A Top-Down Approach. [REVIEW] Acta Biotheoretica 50 (2):129-131.
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  13. Jan Bogaert (2001). Multivariate Statistics for Wildlife and Ecology Research. [REVIEW] Acta Biotheoretica 49 (2):141-143.
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  14. Fanta Bouba, Alassane Bah, Christophe Cambier, Samba Ndiaye & Jacques-André Ndione (2014). Decision Making Environment on Rift Valley Fever in Ferlo. Acta Biotheoretica 62 (3):405-415.
    The Rift Valley fever , which first appeared in Kenya in 1912, is an anthropozoonosis widespread in tropical areas. In Senegal, it is particularly felt in the Ferlo area where a strong presence of ponds shared by humans, cattle and vectors is noted. As part of the studies carried out on the environmental factors which favour its start and propagation, the focus of this paper is put on the decision making process to evaluate the impacts, the interactions and to make (...)
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  15. Sandy C. Boucher (forthcoming). Functionalism and Structuralism as Philosophical Stances: Van Fraassen Meets the Philosophy of Biology. Biology and Philosophy:1-21.
    I consider the broad perspectives in biology known as ‘functionalism’ and ‘structuralism’, as well as a modern version of functionalism, ‘adaptationism’. I do not take a position on which of these perspectives is preferable; my concern is with the prior question, how should they be understood? Adapting van Fraassen’s argument for treating materialism as a stance, rather than a factual belief with propositional content, in the first part of the paper I offer an argument for construing functionalism and structuralism as (...)
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  16. Michael Bradie (1992). Darwin's Legacy. A Review of Robert J. Richards, "Darwin and the Emergence of Evolutionary Theories of Mind and Behavior". [REVIEW] Biology and Philosophy 7 (1):111.
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  17. Lindell Bromham (forthcoming). What is a Gene For? Biology and Philosophy:1-21.
    The word “gene” means different things to different people, and can even be used in multiple ways by the same individual. In this review, I follow a particular thread running through Griffith and Stotz’s “Genetics and Philosophy: an introduction”, which is the way that methods of investigation influence the way we define the concept of “gene”, from nineteen century breeding experiments to twenty-first century big data bioinformatics. These different views lead to a set of gene concepts, which only partially overlap (...)
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  18. Tjard De Cock Buning (1985). Qualitative and Quantitative Explanation of the Forms of Heat Sensitive Organs in Snakes. Acta Biotheoretica 34 (2-4):193-205.
    Heat sensitive pit organs in different species of snakes show various shapes. The relation between form characters and functions were analysed by means of two different research programs. This paper presents the methodological steps involved in these research programs. The first approach is called a qualitative explanation because it connects experimental data by means of qualitative statements in order to give a functional morphological explanation for the construction of the pits in respect to the behaviour of the snake. The second (...)
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  19. Lars Bygren, Gunnar Kaati & Sören Edvinsson (2001). Longevity Determined by Paternal Ancestors' Nutrition During Their Slow Growth Period. Acta Biotheoretica 49 (1):53-59.
    Social circumstances often impinge on later generations in a socio-economic manner, giving children an uneven start in life. Overfeeding and overeating might not be an exception. The pathways might be complex but one direct mechanism could be genomic imprinting and loss of imprinting. An intergenerational "feedforward" control loop has been proposed, that links grandparental nutrition with the grandchild's growth. The mechanism has been speculated to be a specific response, e.g. to their nutritional state, directly modifying the setting of the gametic (...)
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  20. Brett Calcott (2009). Modeling Biology: Structures, Behaviors, Evolution. [REVIEW] Acta Biotheoretica 57 (3):383-387.
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  21. Jorge da Fonseca Cancela & Kimon Hadjibiros (1977). Le modele matriciel deterministe de Leslie et ses applications en dynamique des populations. Acta Biotheoretica 26 (4):239-261.
    The Leslie matrix model for discrete population growth has been modified and used several times in population dynamics. A review is given of the basic model and of its principal modifications. The modifications relating to the influences of ‘internal’ or ‘external’ factors to the population are studied with greater detail. The same applies to models where the population is divided in stages rather than in age classes.In the same line, Hadjibiros studied a more general model, where the transition matrix corresponds (...)
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  22. T. M. Caro (1989). Making a Dent in Speciesism. A Review of Paul W. Taylor, "Respect for Nature: A Theory of Environmental Ethics". [REVIEW] Biology and Philosophy 4 (3):353.
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  23. Kunal Chakraborty & Sankha Das (2014). Biological Conservation of a Prey–Predator System Incorporating Constant Prey Refuge Through Provision of Alternative Food to Predators: A Theoretical Study. Acta Biotheoretica 62 (2):183-205.
    We describe a prey–predator system incorporating constant prey refuge through provision of alternative food to predators. The proposed model deals with a problem of non-selective harvesting of a prey–predator system in which both the prey and the predator species obey logistic law of growth. The long-run sustainability of an exploited system is discussed through provision of alternative food to predators. We have analyzed the variability of the system in presence of constant prey refuge and examined the stabilizing effect on predator–prey (...)
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  24. Deborah J. Coon (1990). Of Gold and Pyrite. An Essay Review of Daniel W. Bjork, "William James: The Center of His Vision". [REVIEW] Biology and Philosophy 5 (4):493.
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  25. Michael C. Corballis (1988). Psychology's Place in the Science of the Mind/Brain? A Review of Patricia Smith Churchland, "Neurophilosophy: Toward a Unified Science of the Mind/Brain". [REVIEW] Biology and Philosophy 3 (3):363.
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  26. Adrian Currie (forthcoming). Marsupial Lions and Methodological Omnivory: Function, Success and Reconstruction in Paleobiology. Biology and Philosophy:1-23.
    Historical scientists frequently face incomplete data, and lack direct experimental access to their targets. This has led some philosophers and scientists to be pessimistic about the epistemic potential of the historical sciences. And yet, historical science often produces plausible, sophisticated hypotheses. I explain this capacity to generate knowledge in the face of apparent evidential scarcity by examining recent work on Thylacoleo carnifex, the ‘marsupial lion’. Here, we see two important methodological features. First, historical scientists are methodological omnivores, that is, they (...)
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  27. Zoubeida R. Dagher & Sibel Erduran (2014). Laws and Explanations in Biology and Chemistry: Philosophical Perspectives and Educational Implications. In Michael R. Matthews (ed.), International Handbook of Research in History, Philosophy and Science Teaching. Springer. 1203-1233.
    This chapter utilises scholarship in philosophy of biology and philosophy of chemistry to produce meaningful implications for biology and chemistry education. The primary purpose for studying philosophical literature is to identify different perspectives on the nature of laws and explanations within these disciplines. The goal is not to resolve ongoing debates about the nature of laws and explanations but to consider their multiple forms and purposes in ways that promote deep and practical understanding of biological and chemical knowledge in educational (...)
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  28. J. Dankmeljer, J. Gloor & P. H. Van Laer (1975). Differentiation in Biology. Acta Biotheoretica 24 (1-2):35-57.
    In this paper the authors give a survey of biological phenomena , for which the term ‘differentiation’, used in the widest sense, has a meaningful application. The last chapter deals with some general aspects of differentiation and connected phenomena, such as polarity, symmetry, loss of potencies, dedifferentiation, redifferentiation, adifferentiation, regulation and integration.To prevent this article becoming too voluminous, the authors had to refrain from extending the treatment of differentiation to non-living matter and to human society.
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  29. Geert Jan De Klerk (1979). Mechanism and Vitalism. A History of the Controversy. Acta Biotheoretica 28 (1):1-10.
    This is an attempt to interpret the history of mechanism vs. vitalism in relation to the changing framework of culture and to show the interrelation between both these views and experimental science. After the scientific revolution of the seventeenth century, causal mechanism of classical physics provided the framework for the study of nature. The teleological and holistic properties of life, however, which are incompatible with this theory yielded — as a result both of internal developments within biology and of a (...)
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  30. Ph de Reffye, E. Elguero & E. Costes (1991). Growth Units Construction in Trees: A Stochastic Approach. Acta Biotheoretica 39 (3-4):325-342.
    Trees architectural study shows gradients in the meristematic activity. This activity is described by the number of internodes per growth unit, which is considered as the output of a dynamic random process. Several species were observed, which led us to propose and then estimate some mathematical models. Computing the functioning of a tree in a given environment therefore involves finding the probability function of the meristems and following the evolution of the parameters of this law along the botanical gradients within (...)
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  31. Ronald De Sousa (1992). Applying Sociobiology. [REVIEW] Biology and Philosophy 7 (2):237.
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  32. J. Demongeot, O. Hansen, H. Hessami, A. S. Jannot & J. Mintsa (2013). Random Modelling of Contagious Diseases. Acta Biotheoretica 61 (1):141-172.
    Modelling contagious diseases needs to include a mechanistic knowledge about contacts between hosts and pathogens as specific as possible, e.g., by incorporating in the model information about social networks through which the disease spreads. The unknown part concerning the contact mechanism can be modelled using a stochastic approach. For that purpose, we revisit SIR models by introducing first a microscopic stochastic version of the contacts between individuals of different populations , then by adding a random perturbation in the vicinity of (...)
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  33. J. Demongeot, H. Hazgui, H. Ben Amor & J. Waku (2014). Stability, Complexity and Robustness in Population Dynamics. Acta Biotheoretica 62 (3):243-284.
    The problem of stability in population dynamics concerns many domains of application in demography, biology, mechanics and mathematics. The problem is highly generic and independent of the population considered . We give in this paper some examples of population dynamics concerning nucleic acids interacting through direct nucleic binding with small or cyclic RNAs acting on mRNAs or tRNAs as translation factors or through protein complexes expressed by genes and linked to DNA as transcription factors. The networks made of these interactions (...)
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  34. J. Demongeot, H. Hazgui, S. Bandiera, O. Cohen & A. Henrion-Caude (2013). MitomiRs, ChloromiRs and Modelling of the microRNA Inhibition. Acta Biotheoretica 61 (3):367-383.
    MicroRNAs are non-coding parts of nuclear and mitochondrial genomes, preventing the weakest part of the genetic regulatory networks from being expressed and preventing the appearance of a too many attractors in these networks. They have also a great influence on the chromatin clock, which ensures the updating of the genetic regulatory networks. The post-transcriptional inhibitory activity by the microRNAs, which is partly unspecific, is due firstly to their possibly direct negative action during translation by hybridizing tRNAs, especially those inside the (...)
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  35. P. Den Boer (1968). Spreading of Risk and Stabilization of Animal Numbers. Acta Biotheoretica 18 (1-4):165-194.
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  36. U. An der Heiden & G. Roth (1987). Mathematical Model and Simulation of Retina and Tectum Opticum of Lower Vertebrates. Acta Biotheoretica 36 (3):179-212.
    The processing of information within the retino-tectal visual system of amphibians is decomposed into five major operational stages, three of them taking place in the retina and two in the optic tectum. The stages in the retina involve a spatially local high-pass filtering in connection to the perception of moving objects, separation of the receptor activity into ON- and OFF-channels regarding the distinction of objects on both light and dark backgrounds, spatial integration via near excitation and far-reaching inhibition. Variation of (...)
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  37. U. An Der Heiden, G. Roth & H. Schwegler (1985). Principles of Self-Generation and Self-Maintenance. Acta Biotheoretica 34 (2-4):125-137.
    Living systems are characterized as self-generating and self-maintaining systems. This type of characterization allows integration of a wide variety of detailed knowledge in biology.The paper clarifies general notions such as processes, systems, and interactions. Basic properties of self-generating systems, i.e. systems which produce their own parts and hence themselves, are discussed and exemplified. This makes possible a clear distinction between living beings and ordinary machines. Stronger conditions are summarized under the concept of self-maintenance as an almost unique character of living (...)
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  38. Tomasz Downarowicz, Dante Travisany, Martin Montecino & Alejandro Maass (2014). Symbolic Extensions Applied to Multiscale Structure of Genomes. Acta Biotheoretica 62 (2):145-169.
    A genome of a living organism consists of a long string of symbols over a finite alphabet carrying critical information for the organism. This includes its ability to control post natal growth, homeostasis, adaptation to changes in the surrounding environment, or to biochemically respond at the cellular level to various specific regulatory signals. In this sense, a genome represents a symbolic encoding of a highly organized system of information whose functioning may be revealed as a natural multilayer structure in terms (...)
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  39. John Drake (2004). Stochastic Population Dynamics in Ecology and Conservation. [REVIEW] Acta Biotheoretica 52 (3):219-220.
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  40. E. Dulos, J. Boissonade, J. J. Perraud, B. Rudovics & P. De Kepper (1996). Chemical Morphogenesis: Turing Patterns in an Experimental Chemical System. Acta Biotheoretica 44 (3-4):249-261.
    Patterns resulting from the sole interplay between reaction and diffusion are probably involved in certain stages of morphogenesis in biological systems, as initially proposed by Alan Turing. Self-organization phenomena of this type can only develop in nonlinear systems maintained far from equilibrium. We present Turing patterns experimentally observed in a chemical system. An oscillating chemical reaction, the CIMA reaction, is operated in an open spatial reactor designed in order to obtain a pure reaction-diffusion system. The two types of Turing patterns (...)
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  41. Yonge Feng, Hao Lin & Liaofu Luo (2014). Prediction of Protein Secondary Structure Using Feature Selection and Analysis Approach. Acta Biotheoretica 62 (1):1-14.
    The prediction of the secondary structure of a protein from its amino acid sequence is an important step towards the prediction of its three-dimensional structure. However, the accuracy of ab initio secondary structure prediction from sequence is about 80 % currently, which is still far from satisfactory. In this study, we proposed a novel method that uses binomial distribution to optimize tetrapeptide structural words and increment of diversity with quadratic discriminant to perform prediction for protein three-state secondary structure. A benchmark (...)
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  42. John Fenlon, Malcolm Faddy, Menia Toussidou & Michael de Courcy Williams (2009). Egg Distributions of Insect Parasitoids: Modelling and Analysis of Temporal Data with Host Density Dependence. Acta Biotheoretica 57 (3):309-320.
    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, (...)
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  43. A. Ferchichi, M. Jerry & S. Ben Miled (2014). Viability Analysis of Fisheries Management on Hermaphrodite Population. Acta Biotheoretica 62 (3):355-369.
    We study the viability domains of bio-economic constraints for fishing model of hermaphrodite population, displaying three stages, juvenile, female and male. The dynamic of this model is subject to two constraints: an ecological constraint ensuring the stock perennity, and an economic constraint ensuring a minimum revenue for fishermen. Using viability kernel, we find out a viability domain which simultaneously guarantees a minimum stock level and a minimum income for fleets.
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    Developmental Biology
     Developmental Constraints