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Theoretical Biology Forum

Sergio Pennazio
The dawn of photosynthesis, characterized by the research of Priestley, Ingen- Housz and Senebier, culminated in 1804 with a historical essay of Théodore De Saussure. According to the historians, during the first half of the nineteenth century in which the genesis of the cell theory started off, the research on photosynthesis met a phase of stagnation. Indeed, the literature review of the period does not report particular innovation; however, several scientists (botanists, physiologists, and chemists) supported the thesis of De Saussure with a series of analyses that, in our opinion, deserve to be known...
January 1, 2017: Theoretical Biology Forum
Elisa Guidi, Patrizia Meringolo, Andrea Guazzini, Franco Bagnoli
Intimate partner violence (IPV) has been a well-studied problem in the past psychological literature, especially through its classical methodology such as qualitative, quantitative and mixed methods. This article introduces two basic stochastic models as an alternative approach to simulate the short and long-term dynamics of a couple at risk of IPV. In both models, the members of the couple may assume a finite number of states, updating them in a probabilistic way at discrete time steps. After defining the transition probabilities, we first analyze the evolution of the couple in isolation and then we consider the case in which the individuals modify their behavior depending on the perceived violence from other couples in their environment or based on the perceived informal social support...
January 1, 2017: Theoretical Biology Forum
Michael A Flannery
This essay responds to Peter T. Saunders's call to go Beyond the neo-Darwinist Paradigm. While there is much to commend in his analysis, especially his suggestion that the extended evolutionary synthesis (EES) may not go far enough, he leaves the question of whether this should involve mere revision or total replacement open. A historiographical review reveals significant problems stemming from certain positivist assumptions and commitments within neo-Darwinian orthodoxy and the EES over and above any scientific considerations...
January 1, 2017: Theoretical Biology Forum
Roberto Cazzolla Gatti
Nowadays, the idea that life affects the development of the planetary environment, and can, in turn, affect the future evolution of itself (in a coevolutionary way) is well-accepted. However, since the proposal of the Gaia hypothesis, there has been widespread criticism. Most of it is related to teleology, the absence of natural selection at a universal scale, and the lack of planetary reproduction. Some of the problems concerning the 'internal' logic of the idea have been resolved. Nevertheless, it is not sure whether Earth can be considered a unit of selection and (therefore) Gaia can adapt according to Darwinian evolution...
January 1, 2017: Theoretical Biology Forum
Silvana Balzan, Laura Sabatino, Valter Lubrano
Angiogenesis is a physiological process required for embryonic vascular development and involved in the pathophysiological progress of diseases such as atherosclerosis. In fact, hypoxia, ischemia and oxidative stress are common events in atherosclerotic plaque that stimulate angiogenesis, leading to the formation of a neovascularization in the intima of atherosclerotic lesions. The presence of these capillaries favours the progression of the plaque instability. Several studies indicate oxidized low-density lipoprotein (ox-LDL) and its endothelial receptor lectin-like oxidized low-density lipoprotein (LOX-1) as the major responsible for the occurrence and progression of atherosclerosis through apoptosis...
January 1, 2017: Theoretical Biology Forum
David Lambert
No abstract text is available yet for this article.
January 1, 2017: Theoretical Biology Forum
David Lambert
No abstract text is available yet for this article.
December 1, 2016: Theoretical Biology Forum
Mesut Tez M D, Selda Tez M D
Cancer may be the most important global public health problem. The effort of understanding carcinogenesis has been accelerating over the last years on account of its high incidence and impact on the lives of individuals' affected. There are a number of theories of carcinogenesis and these theories may be used to justify various alternative cancer treatments. The small variations in cancer mortality observed during the previous years indicate that the clinical applications of these theories have been very limited...
January 1, 2016: Theoretical Biology Forum
Masomeh Taherian, Megerdich Toomanian, Mohammadreza Molaei
In this essay the researcher modeled contagious cholera illness by geometrical dynamic methods in two forms, seasonal variables and without seasonal variables. In modeling the illness without seasonal variables geometric points and dynamical results are acquired. Disease free equilibrium of this model is considered. The model which is made by seasonal variables is a complicated model from geometrical point of view. So it is considered numerically. The numerical results are given in six figures and the figures are studied biologically...
January 1, 2016: Theoretical Biology Forum
Peter T Saunders
Ever since Darwin, there have been challenges to the claim that the natural selection of small random variations is a sufficient explanation of evolution. Even mainstream evolutionists are now beginning to accept that something more is required. The question is whether this will be merely a few add-ons that leave the paradigm unaltered, or whether the whole framework of explanation, including its application to other disciplines, will be changed.
January 1, 2016: Theoretical Biology Forum
Michael Ruse
I reflect on my fifty-year history as a philosopher of biology, showing how it has taken me from rather narrow analytic studies, through the history of ideas, and now on to issues to do with science and religion. I argue that moral concerns were and still are a major motivation behind what I do and write.
January 1, 2016: Theoretical Biology Forum
Antonio Lima-de-Faria
It may sound as a truism but it may be necessary to recall that science is not made by instruments, or by well equipped laboratories, but by the unique personalities that use them. As a consequence their intellect, their emotional experiences and their physical ability, cannot be separated from their achievements - being they minor or profound.
January 1, 2016: Theoretical Biology Forum
Paolo Freguglia
The aim of this paper is a free interpretation and reconstruction of a part of Giovanni Virginio Schiaparelli's essay (1898) where the author presents some ideas about a correspondence between living organisms and geometrical curves. From our analysis we derive a new approach to the ago-antagonist conception of the Darwinian evolution theory which is a continuation of [2].
January 1, 2016: Theoretical Biology Forum
Fred W Cummings
A number of common features can be observed in the earliest developing embryos of all animal phyla. A simple extant model of morphogenesis is outlined here, with the aim of giving a model of the relatively rapid appearance of Cambrian animals, 541-515 mya. Developmental patterning, elucidated by a simple linear model with only short-range diffusion of ligands, is given as the origin of the most primitive animals. The key aspect of the model involves the interaction between the emergence of the Wnt and Hedgehog (Hh) signaling pathways...
January 1, 2016: Theoretical Biology Forum
Balasubramanian Chandramouli, Giordano Mancini
Classical Molecular Dynamics (MD) simulations can provide insights at the nanoscopic scale into protein dynamics. Currently, simulations of large proteins and complexes can be routinely carried out in the ns-μs time regime. Clustering of MD trajectories is often performed to identify selective conformations and to compare simulation and experimental data coming from different sources on closely related systems. However, clustering techniques are usually applied without a careful validation of results and benchmark studies involving the application of different algorithms to MD data often deal with relatively small peptides instead of average or large proteins; finally clustering is often applied as a means to analyze refined data and also as a way to simplify further analysis of trajectories...
January 1, 2016: Theoretical Biology Forum
Armando Bazzani, Claudia Sala, Enrico Giampieri, Gastone Castellani
Understanding the factors that control the dynamics of interacting species is a fundamental problem in ecology. The nature of the interactions among different species is usually not completely understood, but it is assumed that the species interaction plays an important role in the ecosystem properties as predicted by the niches models for an ecosystem. However, recent studies point out as the neutral hypothesis proposed by Hubbell of non-interacting species with an external source from the surrounding environment, allows to explain the relative species abundance distribution when the ecosystem has reached a stationary situation...
January 1, 2016: Theoretical Biology Forum
Massimiliano Aschi, Andrea Amadei
The understanding of the factors governing the enzyme catalysis is one of the most important goals of biochemistry and biophysics. In this context the contribution of theoretical research might be of high relevance. However, despite the huge amount of proposed approaches, the modelling of enzyme reactions still represents a very difficult task and a definitive and conclusive theoretical-computational strategy is still far from being available. In this study, after a presentation of the main difficulties associated to a coherent and possibly rigorous modelling of these processes, we present a computational theoretical method specifically designed for addressing complex molecular systems eventually applied to a benchmark reaction: the initial proton transfer in Triosephosphate Isomerase...
January 1, 2016: Theoretical Biology Forum
Franco Spirito
The probability of fixation of a mutant that causes assortative mating according to the 'mass action model' has been studied. A gene of this kind represents one of the simplest hypothetical mechanisms of prezygotic isolation. Computer analysis by Monte Carlo simulations revealed that the fixation of the mutant is very unlikely unless the population is very small in size and/or the degree of partial assortative mating is very low. The introduction into the biological model of pleiotropic effects of the gene on fitness (viability) can facilitate the process of fixation (even to a very large extent in the case of strong selection in favor of the mutant allele)...
2015: Theoretical Biology Forum
Sergio Pennazio
An elementary but correct concept of plant life has come to us in writings of Theophrastus who divided the plant life in its three basic stages: generation, sprouting, growth. This image of plants remained practically unchanged until the seventeenth-century, when the scientific method based on experimentation was introduced by Bacon. The invention of the microscope and the change of the traditional alchemy for an embryonic chemistry allowed some penetrating minds to look upon plants as highly complex living structures, to which had to correspond some specific functions...
2015: Theoretical Biology Forum
Aisha Munawar, Ahmed Akrem, Ashiq Hussain, Patrick Spencer, Christian Betzel
Snake venom is a myriad of biologically active proteins and peptides. Three finger toxins are highly conserved in their molecular structure, but interestingly possess diverse biological functions. During the course of evolution the introduction of subtle mutations in loop regions and slight variations in the three dimensional structure, has resulted in their functional versatility. Cytotoxin-1 (UniProt ID: P01467), isolated from Naja mossambica mossambica, showed the potential to inhibit chymotrypsin and the chymotryptic activity of the 20S proteasome...
2015: Theoretical Biology Forum
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