MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Theory in Biosciences' source. Thu, 09 Feb 2012 14:32:18 +0100 http://www.medworm.com/index.php?rid=5576660&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22222764%26dopt%3DAbstract This study shows that adding periodicity to the autonomous quarantine/isolation model developed in Safi and Gumel (Discret Contin Dyn Syst Ser B 14:209-231, 2010) does not alter the threshold dynamics of the autonomous system with respect to the elimination or persistence of the disease in the population. PMID: 22222764 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5576660 Fri, 06 Jan 2012 05:00:00 +0100 5576660 http://www.medworm.com/index.php?rid=5557923&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22209953%26dopt%3DAbstract Authors: Mackiewicz P, Bodył A, Gagat P Abstract The rhizarian amoeba Paulinella chromatophora harbors two photosynthetically active and deeply integrated cyanobacterial endosymbionts acquired ~60 million years ago. Recent genomic analyses of P. chromatophora have revealed the loss of many essential genes from the endosymbiont's genome, and have identified more than 30 genes that have been transferred to the host cell's nucleus through endosymbiotic gene transfer (EGT). This indicates that, similar to classical primary plastids, Paulinella endosymbionts have evolved a transport system to import their nuclear-encoded proteins. To deduce how these proteins are transported, we searched for potential targeting signals in genes for 10 EGT-derived proteins. Our analyses indicate that f... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5557923 Sat, 31 Dec 2011 05:00:00 +0100 5557923 http://www.medworm.com/index.php?rid=5488933&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22147531%26dopt%3DAbstract Authors: Ay N, Der R, Prokopenko M PMID: 22147531 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488933 Wed, 07 Dec 2011 05:00:00 +0100 5488933 http://www.medworm.com/index.php?rid=5488932&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22147532%26dopt%3DAbstract Authors: Boedecker J, Obst O, Lizier JT, Mayer NM, Asada M Abstract We investigate information processing in randomly connected recurrent neural networks. It has been shown previously that the computational capabilities of these networks are maximized when the recurrent layer is close to the border between a stable and an unstable dynamics regime, the so called edge of chaos. The reasons, however, for this maximized performance are not completely understood. We adopt an information-theoretical framework and are for the first time able to quantify the computational capabilities between elements of these networks directly as they undergo the phase transition to chaos. Specifically, we present evidence that both information transfer and storage in the recurrent layer are maximized clo... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488932 Wed, 07 Dec 2011 05:00:00 +0100 5488932 http://www.medworm.com/index.php?rid=5488934&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22135038%26dopt%3DAbstract Authors: Nebel ME, Scheid A Abstract Predicting secondary structures of RNA molecules is one of the fundamental problems of and thus a challenging task in computational structural biology. Over the past decades, mainly two different approaches have been considered to compute predictions of RNA secondary structures from a single sequence: the first one relies on physics-based and the other on probabilistic RNA models. Particularly, the free energy minimization (MFE) approach is usually considered the most popular and successful method. Moreover, based on the paradigm-shifting work by McCaskill which proposes the computation of partition functions (PFs) and base pair probabilities based on thermodynamics, several extended partition function algorithms, statistical sampling methods an... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488934 Thu, 01 Dec 2011 05:00:00 +0100 5488934 http://www.medworm.com/index.php?rid=5488936&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22127955%26dopt%3DAbstract This article reviews eight different methods for guiding the self-organization of RBNs. In particular, the article is focused on guiding RBNs toward the critical dynamical regime, which is near the phase transition between the ordered and dynamical phases. The properties and advantages of the critical regime for life, computation, adaptability, evolvability, and robustness are reviewed. The guidance methods of RBNs can be used for engineering systems with the features of the critical regime, as well as for studying how natural selection evolved living systems, which are also critical. PMID: 22127955 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488936 Wed, 30 Nov 2011 05:00:00 +0100 5488936 http://www.medworm.com/index.php?rid=5488935&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22127956%26dopt%3DAbstract We present a methodology for studying coherent information structure, consisting of state-space diagrams of the local information dynamics and a measure of structure in these diagrams. The methodology identifies both clear and "hidden" coherent structure in complex computation, most notably reconciling conflicting interpretations of the complexity of the Elementary Cellular Automata rule 22. PMID: 22127956 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488935 Wed, 30 Nov 2011 05:00:00 +0100 5488935 http://www.medworm.com/index.php?rid=5488937&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22125233%26dopt%3DAbstract This article studies in some detail the use of the predictive information (PI), also called excess entropy or effective measure complexity, of the sensorimotor process. The PI of a process quantifies the total information of past experience that can be used for predicting future events. However, the application of information theoretic measures in robotics mostly is restricted to the case of a finite, discrete state-action space. This article aims at applying the PI in the dynamical systems approach to robot control. We study linear systems as a first step and derive exact results for the PI together with explicit learning rules for the parameters of the controller. Interestingly, these learning rules are of Hebbian nature and local in the sense that the synaptic update is given by the pro... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488937 Tue, 29 Nov 2011 05:00:00 +0100 5488937 http://www.medworm.com/index.php?rid=5488938&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22120547%26dopt%3DAbstract This article extends the perception-action loop formalism to multiple agents. The multiple-access channel model is presented and used to identify the relationships between informational quantities of two agents interacting in the same environment. The central question investigated in this article is the impact of coordination. Information-theoretic limits on what can be achieved with and without coordination are identified. For this purpose, different abstract channels are studied, along with a concrete example of agents interacting in space. It is shown that, under some conditions, self-organizing systems based on information-theoretic quantities have a tendency to spontaneously generate coordinated behavior. Moreover, in the perspective of engineering such systems to achieve specific tas... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5488938 Sat, 26 Nov 2011 05:00:00 +0100 5488938 http://www.medworm.com/index.php?rid=5453158&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22116784%26dopt%3DAbstract This article critically analyzes the arguments of the 'generalized Darwinism' recently proposed for the analysis of social-economical systems. We argue that 'generalized Darwinism' is both restrictive and empty. It is restrictive because it excludes alternative (non-selectionist) evolutionary mechanisms such as orthogenesis, saltationism and mutationism without any examination of their suitability for modeling socio-economic processes and ignoring their important roles in the development of contemporary evolutionary theory. It is empty, because it reduces Darwinism to an abstract triple-principle scheme (variation, selection and inheritance) thus ignoring the actual structure of Darwinism as a complex and dynamic theoretical structure inseparable from a very detailed system of theoretical ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5453158 Fri, 25 Nov 2011 05:00:00 +0100 5453158 http://www.medworm.com/index.php?rid=5453157&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22116785%26dopt%3DAbstract We present three strategies for guided self-organization, namely by using external rewards, a problem-specific error function, or assumptions about the symmetries of the desired behavior. The strategies are analyzed for two different robots in a physically realistic simulation. PMID: 22116785 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5453157 Fri, 25 Nov 2011 05:00:00 +0100 5453157 http://www.medworm.com/index.php?rid=5309396&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21979857%26dopt%3DAbstract In this study, we describe the model and present results concerning the effect on the overall dynamics of varying (a) the average residence time of the elements in the reactor, (b) both the composition of the firing disk and the concentration of the molecules belonging to it, (c) the composition of the incoming flux. PMID: 21979857 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5309396 Fri, 07 Oct 2011 04:00:00 +0100 5309396 http://www.medworm.com/index.php?rid=5272959&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21948188%26dopt%3DAbstract Authors: Khor S Abstract A protein residue network or PRN is a network induced by spatial contacts between amino acid residues of a protein. Studies of the structure of PRNs have revealed a list of network characteristics common to a diverse class of proteins. Explanations for the observed network characteristics for protein folding have been suggested but not tested in an integrated way. In this article, in silico experiments are performed to understand how structural characteristics of PRNs influence protein folding as modeled by a search problem. We find that the blend of structural characteristics PRNs possess help to place them in a sweet spot within the space of all network configurations tested. PRNs are plausible 3D structures and yield competitive search performances. Henc... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5272959 Tue, 27 Sep 2011 04:00:00 +0100 5272959 http://www.medworm.com/index.php?rid=5272961&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21948152%26dopt%3DAbstract Authors: Sîrbu A, Ruskin HJ, Crane M Abstract Gene regulatory networks (GRNs) are complex biological systems that have a large impact on protein levels, so that discovering network interactions is a major objective of systems biology. Quantitative GRN models have been inferred, to date, from time series measurements of gene expression, but at small scale, and with limited application to real data. Time series experiments are typically short (number of time points of the order of ten), whereas regulatory networks can be very large (containing hundreds of genes). This creates an under-determination problem, which negatively influences the results of any inferential algorithm. Presented here is an integrative approach to model inference, which has not been previously discussed to the... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5272961 Sat, 24 Sep 2011 04:00:00 +0100 5272961 http://www.medworm.com/index.php?rid=5272960&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21948153%26dopt%3DAbstract Authors: Lindo AM, Faria BF, de Abreu FV Abstract In complex systems, feedback loops can build intricate emergent phenomena, so that a description of the whole system cannot be easily derived from the properties of the individual parts. Here, we propose that inter-molecular frustration mechanisms can provide non-trivial feedback loops which can develop non-trivial specificity amplification. We show that this mechanism can be seen as a more general form of a kinetic proofreading (KP) mechanism, with an interesting new property, namely the ability to tune the specificity amplification by changing the reactants concentrations. This contrasts with the classical KP mechanism in which specificity is a function of only the reaction rate constants involved in a chemical pathway. These resu... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5272960 Sat, 24 Sep 2011 04:00:00 +0100 5272960 http://www.medworm.com/index.php?rid=5147409&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21842439%26dopt%3DAbstract Authors: Bhunu CP, Mushayabasa S Mathematical models have long been used to better understand disease transmission dynamics and how to effectively control them. Here, a chancroid infection model is presented and analyzed. The disease-free equilibrium is shown to be globally asymptotically stable when the reproduction number is less than unity. High levels of treatment are shown to reduce the reproduction number suggesting that treatment has the potential to control chancroid infections in any given community. This result is also supported by numerical simulations which show a decline in chancroid cases whenever the reproduction number is less than unity. PMID: 21842439 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5147409 Sat, 13 Aug 2011 23:00:00 +0100 5147409 http://www.medworm.com/index.php?rid=5089936&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21785867%26dopt%3DAbstract Authors: Freire MA Polymer formation is arguably one of the essential factors that allowed the emergence, stabilisation and spread of life on Earth. Consequently, studies concerning biopolymers could shed light on the origins of life itself. Of particular interest are RNA and polysaccharide polymers, the archetypes of the contrasting proposed evolutionary scenarios and their respective polymerases. Nucleic acid polymerases were hypothesised, before their discovery, to have a functional similarity with glycogen phosphorylase. Further identification and characterisation of nucleic acid polymerases; particularly of polynucleotide phosphorylase (PNPase), provided experimental evidence for the initial premise. Once discovered, frequent similarities were found between PNPase and glycogen pho... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=5089936 Thu, 21 Jul 2011 23:00:00 +0100 5089936 http://www.medworm.com/index.php?rid=4997052&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21706186%26dopt%3DAbstract Authors: Gigliotta O, Pezzulo G, Nolfi S PMID: 21706186 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4997052 Fri, 24 Jun 2011 23:00:00 +0100 4997052 http://www.medworm.com/index.php?rid=4946913&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21604186%26dopt%3DAbstract Authors: Gigliotta O, Pezzulo G, Nolfi S We show how simulated robots evolved for the ability to display a context-dependent periodic behavior can spontaneously develop an internal model and rely on it to fulfill their task when sensory stimulation is temporarily unavailable. The analysis of some of the best evolved agents indicates that their internal model operates by anticipating sensory stimuli. More precisely, it anticipates functional properties of the next sensory state rather than the exact state that sensors will assume. The characteristics of the states that are anticipated and of the sensorimotor rules that determine how the agents react to the experienced states, however, ensure that they produce very similar behaviour during normal and blind phases in which sensory stimula... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4946913 Sat, 21 May 2011 23:00:00 +0100 4946913 http://www.medworm.com/index.php?rid=4798181&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21509695%26dopt%3DAbstract Authors: Kirkilionis M, Janus U, Sbano L We model in detail a simple synthetic genetic clock that was engineered in Atkinson et al. (Cell 113(5):597-607, 2003) using Escherichia coli as a host organism. Based on this engineered clock its theoretical description uses the modelling framework presented in Kirkilionis et al. (Theory Biosci. doi: 10.1007/s12064-011-0125-0 , 2011, this volume). The main goal of this accompanying article was to illustrate that parts of the modelling process can be algorithmically automatised once the model framework we called 'average dynamics' is accepted (Sbano and Kirkilionis, WMI Preprint 7/2007, 2008c; Kirkilionis and Sbano, Adv Complex Syst 13(3):293-326, 2010). The advantage of the 'average dynamics' framework is that system components (especially in ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4798181 Wed, 20 Apr 2011 23:00:00 +0100 4798181 http://www.medworm.com/index.php?rid=4798183&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21487823%26dopt%3DAbstract We present a new approach or framework to model dynamic regulatory genetic activity. The framework is using a multi-scale analysis based upon generic assumptions on the relative time scales attached to the different transitions of molecular states defining the genetic system. At micro-level such systems are regulated by the interaction of two kinds of molecular players: macro-molecules like DNA or polymerases, and smaller molecules acting as transcription factors. The proposed genetic model then represents the larger less abundant molecules with a finite discrete state space, for example describing different conformations of these molecules. This is in contrast to the representations of the transcription factors which are-like in classical reaction kinetics-represented by their particle nu... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4798183 Tue, 12 Apr 2011 23:00:00 +0100 4798183 http://www.medworm.com/index.php?rid=4798182&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21487824%26dopt%3DAbstract This article presents the results of the wavelet analysis applied to the a-wave component of the human electroretinogram. In order to deepen and improve our knowledge about the behavior of the early photoreceptoral response, including the possible activation of interactions and correlations among the photoreceptors, we have detected and identified the stable time-frequency components of the a-wave, using six representative values of luminance. The results indicate the occurrence of three frequencies lying in the range 20-200 Hz. The lowest one is attributed to the summed activities of the photoreceptors. The others are weaker and at low luminance one of them does not occur. We relate them to the response of the rods and the cones whose aggregate activities are non-linear and typically exh... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4798182 Tue, 12 Apr 2011 23:00:00 +0100 4798182 http://www.medworm.com/index.php?rid=4798184&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21479663%26dopt%3DAbstract In this study, we simulate an imatinib-like treatment of CML by modifying the fitness and the death rate of cancerous cells and describe the several scenarios in the evolutionary dynamics of white blood cells as a consequence of the efficacy of the different modeled therapies. The patient response to the therapy is investigated by simulating a drug administration following a continuous or pulsed time scheduling. A permanent disappearance of leukemic clones is achieved with a continuous therapy. This theoretical behavior is in a good agreement with that observed in previous clinical investigations. However, these findings demonstrate that an intermittent therapy could represent a valid alternative in patients with high risk of toxicity. A suitable tuned pulsed therapy can also reduce the pr... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4798184 Fri, 08 Apr 2011 23:00:00 +0100 4798184 http://www.medworm.com/index.php?rid=4693448&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21451965%26dopt%3DAbstract Authors: Kirkilionis M, Kepes F PMID: 21451965 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4693448 Wed, 30 Mar 2011 23:00:00 +0100 4693448 http://www.medworm.com/index.php?rid=4572090&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21384168%26dopt%3DAbstract Authors: Norris V, Zemirline A, Amar P, Audinot JN, Ballet P, Ben-Jacob E, Bernot G, Beslon G, Cabin A, Fanchon E, Giavitto JL, Glade N, Greussay P, Grondin Y, Foster JA, Hutzler G, Jost J, Kepes F, Michel O, Molina F, Signorini J, Stano P, Thierry AR The relevance of biological materials and processes to computing-alias bioputing-has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4572090 Tue, 08 Mar 2011 00:00:00 +0100 4572090 http://www.medworm.com/index.php?rid=4517680&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21293950%26dopt%3DAbstract Authors: Osei BM, Ellingwood CD, Hoffmann JP, Bentil DE We use a reaction diffusion equation, together with a genetic algorithm approach for model selection to develop a general modeling framework for biological invasions. The diffusion component of the reaction diffusion model is generalized to include dispersal and advection. The reaction component is generalized to include both linear and non-linear density dependence, and Allee effect. A combination of the reaction diffusion and genetic algorithm is able to evolve the most parsimonious model for invasive species spread. Zebra mussel data obtained from Lake Champlain, which demarcates the states of New York and Vermont, is used to test the appropriateness of the model. We estimate the minimum wave spread rate of Zebra mussels to be ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4517680 Fri, 04 Feb 2011 00:00:00 +0100 4517680 http://www.medworm.com/index.php?rid=4517679&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21293951%26dopt%3DAbstract Authors: Cebrat S, Stauffer D, Sá Martins JS, de Oliveira SM, de Oliveira PM We have simulated the evolution of sexually reproducing populations composed of individuals represented by diploid genomes. A series of eight bits formed an allele occupying one of 128 loci of one haploid genome (chromosome). The environment required a specific activity of each locus, this being the sum of the activities of both alleles located at the corresponding loci on two chromosomes. This activity is represented by the number of bits set to zero. In a constant environment the best fitted individuals were homozygous with alleles' activities corresponding to half of the environment requirement for a locus (in diploid genome two alleles at corresponding loci produced a proper activity). Changing the enviro... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4517679 Fri, 04 Feb 2011 00:00:00 +0100 4517679 http://www.medworm.com/index.php?rid=4517681&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21287293%26dopt%3DAbstract This article assumes a specific intuitive notion of complexity as a difficulty to generate and/or assess the plausibility of models. Based on this intuitive understanding of complexity, it identifies two main causes of complexity, namely, radical openness and contextuality. The former is the idea that there are no natural systems. The modeler always needs to draw artificial boundaries around phenomena to generate feasible models. Contextuality is intimately connected to the requirement to simplify models and to leave out most aspects. Complexity occurs when contextuality and radical openness cannot be contained that is when it is not clear where the boundaries of the system are and which abstractions are the correct ones. This concept of complexity is illustrated using a number of example ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4517681 Wed, 02 Feb 2011 00:00:00 +0100 4517681 http://www.medworm.com/index.php?rid=4517682&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21279471%26dopt%3DAbstract Authors: Zintzaras E, Kowald A Recently, an enzyme (Cre recombinase) has been developed by directed evolution that successfully removes the HIV genome from the nuclear DNA of infected cells. To explore this idea further, we hypothesized that a replication deficient virus (called "police virus"), added externally, can deliver such a recombinase which excises the integrated HIV DNA from the genome of infected cells. Such a "police virus" could attack and remove the integrated provirus which is not possible using contemporary strategies. The hypothesis was tested by developing a mathematical model that describes the dynamics of virus-host cell interaction and the consequences of introducing the "police virus". The simulations show that such a therapeutic vector may eradicate all HIV virus... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4517682 Sat, 29 Jan 2011 00:00:00 +0100 4517682 http://www.medworm.com/index.php?rid=4313517&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21174233%26dopt%3DAbstract Authors: Ma W, Yu C, Zhang W, Zhou P, Hu J Self-replication, an important concept abstracted from reproduction, the key feature of life, remains vague in definition and lacking in clear interpretation in terms of its chemical mechanism. Mentioned frequently in discussions concerning the essence of life and its origin, the vague concept has caused a lot of uncertain statements, confusable references, and malposed debates, and has seriously held back efforts in this field. In this article, we try to improve the situation by a conceptual analysis in a more fundamental and clearer background. Self-replication in the substantial world could not mean anything but that "an entity favors the production of its own." The major chemical mechanism for such favoring is catalysis, which can be class... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4313517 Tue, 21 Dec 2010 00:00:00 +0100 4313517 http://www.medworm.com/index.php?rid=4246895&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21116873%26dopt%3DAbstract This article proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called "extended present" as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the abstract notion of "biological inertia". PMID: 21116873 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4246895 Tue, 30 Nov 2010 00:00:00 +0100 4246895 http://www.medworm.com/index.php?rid=4214904&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21104341%26dopt%3DAbstract Authors: Piñol CM, Banzon R The catastrophic senescence of the Pacific salmon is among the initial tests used to validate the Penna aging model. Based on the mutation accumulation theory, the sudden decrease in fitness following reproduction may be solely attributed to the semelparity of the species. In this work, we report other consequences of mutation accumulation. Contrary to earlier findings, such dramatic manifestation of aging depends not only on the choice of breeding strategy but also on the value of the reproduction age, R, and the mutation threshold, T. Senescence is catastrophic when [Formula: see text] As the organism's tolerance for harmful genetic mutations increases, the aging process becomes more gradual. We observe senescence that is threshold dependent whenever T &... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4214904 Tue, 23 Nov 2010 00:00:00 +0100 4214904 http://www.medworm.com/index.php?rid=4135072&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21046474%26dopt%3DAbstract Authors: Lin H, Li QZ Promoters are modular DNA structures containing complex regulatory elements required for gene transcription initiation. Hence, the identification of promoters using machine learning approach is very important for improving genome annotation and understanding transcriptional regulation. In recent years, many methods have been proposed for the prediction of eukaryotic and prokaryotic promoters. However, the performances of these methods are still far from being satisfactory. In this article, we develop a hybrid approach (called IPMD) that combines position correlation score function and increment of diversity with modified Mahalanobis Discriminant to predict eukaryotic and prokaryotic promoters. By applying the proposed method to Drosophila melanogaster, Homo sapien... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4135072 Wed, 03 Nov 2010 00:00:00 +0100 4135072 http://www.medworm.com/index.php?rid=4061157&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20936375%26dopt%3DAbstract Authors: Sreedharan V, Shpak M In most sexually reproducing species, including humans, mitochondria and other cytoplasmic elements are uniparentally (usually maternally) inherited. This phenomenon is of broad interest as a mechanism for countering the proliferation of selfish mitochondria. Uniparental inheritance can be enforced either by the female gametes excluding male cytoplasm or male gametes excluding their own from the zygote. Previous studies have shown that male-enforced uniparental inheritance is unlikely to evolve as a primary mechanism, because unlike female enforcement, the positive linkage disequilibrium between the modifier for eliminating the gamete's own mitochondria and a wild-type mitochondrial complement is broken from one generation to the next. However, it has bee... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4061157 Fri, 08 Oct 2010 23:00:00 +0100 4061157 http://www.medworm.com/index.php?rid=4040836&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20922578%26dopt%3DAbstract We present the first sensitivity analysis of the equations defining the Th model, showing that the qualitative dynamical behavior of the model is very robust against changes in three out of four tested parameters. The robustness of the model is in agreement with our claim that the qualitative behavior of the system is to a large extent independent of the methodological framework used for modeling. PMID: 20922578 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=4040836 Mon, 04 Oct 2010 23:00:00 +0100 4040836 http://www.medworm.com/index.php?rid=3961596&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20824512%26dopt%3DAbstract Authors: Macmillan HR, McConnell MJ We develop a family of branching process models to study cerebral cortical development at the level of individual neural stem and progenitor cells (NS/PCs) and the neurons they produce. Population-level data about "the average NS/PC" is incorporated as constraints for exploring (i) heterogeneity in the proliferative neural cell types and (ii) variability in daughter cell fate decision making. Preliminary studies demonstrate this variability, generate testable hypotheses about heterogeneity, and motivate new experiments moving forward. PMID: 20824512 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3961596 Tue, 07 Sep 2010 23:00:00 +0100 3961596 http://www.medworm.com/index.php?rid=3961597&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20821275%26dopt%3DAbstract Authors: Mahajan G, Mehta A A competitive learning model was introduced in Mehta and Luck (Phys Rev E 60, 5:5218-5230, 1999), in which the learning is outcome-related. Every individual chooses between a pair of existing strategies or types, guided by a combination of two factors: tendency to conform to the local majority, and a preference for the type with higher perceived success among its neighbors, based on their relative outcomes. Here, an extension of the interfacial model of Mehta and Luck (Phys Rev E 60, 5:5218-5230, 1999) is proposed, in which individuals additionally take into account their own outcomes in arriving at their outcome-based choices. Three possible update rules for handling bulk sites are considered. The corresponding phase diagrams, obtained at coexistence, show ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3961597 Mon, 06 Sep 2010 23:00:00 +0100 3961597 http://www.medworm.com/index.php?rid=3933815&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20809365%26dopt%3DAbstract Authors: Schuster P Evolution is a highly complex multilevel process and mathematical modeling of evolutionary phenomenon requires proper abstraction and radical reduction to essential features. Examples are natural selection, Mendel's laws of inheritance, optimization by mutation and selection, and neutral evolution. An attempt is made to describe the roots of evolutionary theory in mathematical terms. Evolution can be studied in vitro outside cells with polynucleotide molecules. Replication and mutation are visualized as chemical reactions that can be resolved, analyzed, and modeled at the molecular level, and straightforward extension eventually results in a theory of evolution based upon biochemical kinetics. Error propagation in replication commonly results in an error threshold t... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3933815 Tue, 31 Aug 2010 23:00:00 +0100 3933815 http://www.medworm.com/index.php?rid=3933814&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20809366%26dopt%3DAbstract Authors: Nikolov S, Vera J, Schmitz U, Wolkenhauer O In this paper we present and discuss a model-based approach to link miRNA translational control with cell signalling networks. MicroRNAs are small regulatory RNAs that are able to regulate the activity and the stability of specific messenger RNA and have been implicated in tumour progression due to their ability to translationally regulate critical oncogenes and tumour suppressors. In our approach, data on protein-protein interactions and miRNA regulation, obtained from bioinformatics databases, are integrated with quantitative experimental data using mathematical modelling. Predictive computational simulations and qualitative (bifurcation) analyses of those mathematical models are employed to further support the investigation of suc... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3933814 Mon, 30 Aug 2010 23:00:00 +0100 3933814 http://www.medworm.com/index.php?rid=3933813&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20809367%26dopt%3DAbstract Authors: McCaig C, Begon M, Norman R, Shankland C Changing scale, for example, the ability to move seamlessly from an individual-based model to a population-based model, is an important problem in many fields. In this paper, we introduce process algebra as a novel solution to this problem in the context of models of infectious disease spread. Process algebra allows us to describe a system in terms of the stochastic behaviour of individuals, and is a technique from computer science. We review the use of process algebra in biological systems, and the variety of quantitative and qualitative analysis techniques available. The analysis illustrated here solves the changing scale problem: from the individual behaviour we can rigorously derive equations to describe the mean behaviour of the sy... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3933813 Mon, 30 Aug 2010 23:00:00 +0100 3933813 http://www.medworm.com/index.php?rid=3899774&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20734159%26dopt%3DAbstract Authors: Göbel B, Langemann D The regulation of the human energy metabolism is crucial to ensure the functionality of the entire organism. Deregulations may lead to severe pathologies such as diabetes mellitus and obesity. The decisive role of the brain as active controller and heavy consumer in the complex whole-body energy metabolism is the object of recent research. Latest studies suggest the priority of the brain energy supply in the competition between brain and body periphery for the available energy resources. In this paper, a systemic investigation of the human energy metabolism is presented which consists of a compartment model including periphery, blood, and brain as well as signaling paths via insulin, appetite, and ingestion. The presented dynamical system particularly c... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3899774 Mon, 23 Aug 2010 23:00:00 +0100 3899774 http://www.medworm.com/index.php?rid=3899775&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20730508%26dopt%3DAbstract Authors: Ruebenacker O, Blinov M A large and growing network ("cloud") of interlinked terms and records of items of Systems Biology knowledge is available from the web. These items include pathways, reactions, substances, literature references, organisms, and anatomy, all described in different data sets. Here, we discuss how the knowledge from the cloud can be molded into representations (views) useful for data visualization and modeling. We discuss methods to create and use various views relevant for visualization, modeling, and model annotations, while hiding irrelevant details without unacceptable loss or distortion. We show that views are compatible with understanding substances and processes as sets of microscopic compounds and events respectively, which allows the representation... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3899775 Fri, 20 Aug 2010 23:00:00 +0100 3899775 http://www.medworm.com/index.php?rid=3823495&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20676941%26dopt%3DAbstract Authors: Presnov E, Isaeva V, Kasyanov N This paper presents a topological interpretation of some developmental events through the use of well-known concepts and theorems of combinatorial geometry. The organization of early embryo using a simulation of cleavage considering only blastomere contacts is examined. Each blastomere is modeled as a topological cell and whole embryo-as cell packing. The egg cleavage results in a pattern of cellular contacts on the surface of each blastomere and whole embryo, a discrete morphogenetic field. We find topological distinctions between different types of early egg cleavage and suggest a topological classification of cleavage. Blastulation and gastrulation may be related to an inevitable emergence of discrete curvature that directs development in thr... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3823495 Thu, 29 Jul 2010 23:00:00 +0100 3823495 http://www.medworm.com/index.php?rid=3733434&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20607621%26dopt%3DAbstract Authors: Wissemann V Ever since existence of sexuality in plants was accepted in around 1700, questions centred about the role and maintenance of sexual reproduction in general, leading to a number of hypotheses like the Vicar of Bray, the Ratchet or the Hitch-hiker theory. Bell (The masterpiece of nature. The evolution and genetics of sexuality. University of California Press, Berkeley, LA, 1982) formulated the Red Queen Hypothesis (RQH) which explains the persistence of sexual reproduction as an outcome of a coevolutionary arms race between hosts and parasites. By sexual recombination and genetic diversification hosts minimize the risk of pathogen infection. Since virulence of pathogens is genetically determined and often species specific, parasites are mostly adapted to common host ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3733434 Tue, 06 Jul 2010 23:00:00 +0100 3733434 http://www.medworm.com/index.php?rid=3691191&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20571938%26dopt%3DAbstract Authors: Lewis O, Steinmo S In this essay, we explore the epistemological and ontological assumptions that have been made to make political science "scientific." We show how political science has generally adopted an ontologically reductionist philosophy of science derived from Newtonian physics and mechanics. This mechanical framework has encountered problems and constraints on its explanatory power, because an emphasis on equilibrium analysis is ill-suited for the study of political change. We outline the primary differences between an evolutionary ontology of social science and the physics-based philosophy commonly employed. Finally, we show how evolutionary thinking adds insight into the study of political phenomena and research questions that are of central importance to the field... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3691191 Tue, 22 Jun 2010 23:00:00 +0100 3691191 http://www.medworm.com/index.php?rid=3672818&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20556544%26dopt%3DAbstract Authors: Pincheira-Donoso D Geographical variation in environmental temperatures is expected to impose clinal phenotypic selection that results in the expression of large-scale gradients of body mass variation within animal clades. Body size is predicted to increase with increasing latitude and elevation, and hence, with decreasing temperature, a pattern broadly known as Bergmann's rule. However, empirical observations are highly conflicting. Whilst most studies support this prediction in endotherms (birds and mammals), analyses conducted on ectotherms often fail to report this pattern. Does it reduce the validity of this macroecological rule? Since the original formulation of Bergmann's rule only involved endothermic organisms, I argue that the controversy is not a consequence of its ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3672818 Wed, 16 Jun 2010 23:00:00 +0100 3672818 http://www.medworm.com/index.php?rid=3672819&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20556543%26dopt%3DAbstract Authors: Verpooten J, Nelissen M Iconic representations (i.e., figurative imagery and realistic art) only started to appear consistently some 45,000 years ago, although humans have been anatomically modern since 200,000-160,000 years ago. What explains this? Some authors have suggested a neurocognitive change took place, leading to a creative explosion, although this has been contested. Here, we examine the hypothesis that demographic changes caused cultural "cumulative adaptive evolution" and as such the emergence of modern symbolic behavior. This approach usefully explains the evolution of utilitarian skills and tools, and the creation of symbols to identify groups. However, it does not equally effectively explain the evolution of behaviors that may not be directly adaptive, such as ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3672819 Tue, 15 Jun 2010 23:00:00 +0100 3672819 http://www.medworm.com/index.php?rid=3672820&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20549382%26dopt%3DAbstract Authors: Carrapiço F When new entities are formed by the integration of individual organisms, these new entities possess characteristics which go beyond the sum of the individual properties of each element of the association, resulting in the development of new attributes and capacities as an integrated whole. In this process, these new entities also agglutinate and dynamize synergies not present in the individual organisms. In this sense, evolution is a dynamic process that evolves not in the way of perfection or progress, but in the way of adaptation to new conditions. Symbiogenesis, as an evolutionary mechanism, allows a coherent conceptual rupture with some evolutionary ideas of the past and, at the same time, shows and builds a new approach to life, based on solid evolutionary ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3672820 Mon, 14 Jun 2010 23:00:00 +0100 3672820 http://www.medworm.com/index.php?rid=3659629&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20532997%26dopt%3DAbstract Authors: Correia L Evolution has, for a long time, inspired computer scientists to produce computer models mimicking its behavior. Evolutionary algorithm (EA) is one of the areas where this approach has flourished. EAs have been used to model and study evolution, but they have been especially developed for their aptitude as optimization tools for engineering. Developed models are quite simple in comparison with their natural sources of inspiration. However, since EAs run on computers, we have the freedom, especially in optimization models, to test approaches both realistic and outright speculative, from the biological point of view. In this article, we discuss different common evolutionary algorithm models, and then present some alternatives of interest. These include biologically insp... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3659629 Tue, 08 Jun 2010 23:00:00 +0100 3659629 http://www.medworm.com/index.php?rid=3659628&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20532998%26dopt%3DAbstract Authors: Steele J, Kandler A Darwin saw similarities between the evolution of species and the evolution of languages, and it is now widely accepted that similarities between related languages can often be interpreted in terms of a bifurcating descent history ('phylogenesis'). Such interpretations are supported when the distributions of shared and unshared traits (for example, in terms of etymological roots for elements of basic vocabulary) are analysed using tree-building techniques and found to be well-explained by a phylogenetic model. In this article, we question the demographic assumption which is sometimes made when a tree-building approach has been taken to a set of cultures or languages, namely that the resulting tree is also representative of a bifurcating population history. U... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3659628 Tue, 08 Jun 2010 23:00:00 +0100 3659628 http://www.medworm.com/index.php?rid=3659630&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20532673%26dopt%3DAbstract Authors: Santos M, Fragata I, Santos J, Simões P, Marques A, Lima M, Matos M Adaptation to a new environment (as well as its underlying mechanisms) is one of the most important topics in Evolutionary Biology. Understanding the adaptive process of natural populations to captivity is essential not only in general evolutionary studies but also in conservation programmes. Since 1990, the Group of Experimental Evolution (CBA/FCUL) has been performing long-term, real-time evolutionary studies, with the characterization of laboratory adaptation in populations of Drosophila subobscura founded in different times and from different locations. Initially, these experiments involved phenotypic assays and more recently were expanded to studies at the molecular level (microsatellite and chromosoma... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3659630 Mon, 07 Jun 2010 23:00:00 +0100 3659630 http://www.medworm.com/index.php?rid=3633652&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20524078%26dopt%3DAbstract Authors: Wilkins JS Arguments against essentialism in biology rely strongly on a claim that modern biology abandoned Aristotle's notion of a species as a class of necessary and sufficient properties. However, neither his theory of essentialism, nor his logical definition of species and genus (eidos and genos) play much of a role in biological research and taxonomy, including his own. The objections to natural kinds thinking by early twentieth century biologists wrestling with the new genetics overlooked the fact that species have typical developmental cycles and most have a large shared genetic component. These are the "what-it-is-to-be" members of that species. An intrinsic biological essentialism does not commit us to Aristotelian notions, nor even modern notions, of essence. There i... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3633652 Thu, 03 Jun 2010 23:00:00 +0100 3633652 http://www.medworm.com/index.php?rid=3626079&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20514523%26dopt%3DAbstract Authors: Monroe MJ, Bokma F The theory of punctuated equilibrium, which proposes that biological species evolve rapidly when they originate rather than gradually over time, has sparked intense debate between palaeontologists and evolutionary biologists about the mode of character evolution and the importance of natural selection. Difficulty in interpreting the fossil record prevented consensus, and it remains disputed as to what extent gradual change in established species is responsible for phenotypic differences between species. Against the historical background of the concept of evolution concentrated in speciation events, we review attempts to investigate tempo and mode of evolution using present-day species since the introduction of the theory of punctuated equilibrium in 1972. We... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3626079 Mon, 31 May 2010 23:00:00 +0100 3626079 http://www.medworm.com/index.php?rid=3626080&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20512429%26dopt%3DAbstract Authors: Stella M, Kleisner K The concept of Umwelt, in particular the interpretation originally developed by Jakob von Uexküll, played an important role in the development of biological thought of the first half of the twentieth century. The theory of Umwelt (Umweltlehre) was one of the most original ideas that appeared in German biology at that time. It was the first attempt to introduce subjectivity into a science about organisms; it laid down the foundations of behavioural research and inspired the development of ethology. However, the theory of Umwelt has also been used to support more sinister activities and even some dangerous ideologies. The concept of Umwelt is of interest not only to historians: within some intellectual circles, it is still broadly used today. Our aim was ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3626080 Fri, 28 May 2010 23:00:00 +0100 3626080 http://www.medworm.com/index.php?rid=3614920&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20509011%26dopt%3DAbstract Authors: Tattersall I Human beings are distinguished from all other organisms by their symbolic way of processing information about the world. This unique cognitive style is qualitatively different from all the earlier hominid cognitive styles, and is not simply an improved version of them. The hominid fossil and archaeological records show clearly that biological and technological innovations have typically been highly sporadic, and totally out of phase, since the invention of stone tools some 2.5 million years ago. They also confirm that this pattern applied in the arrival of modern cognition: the anatomically recognizable species Homo sapiens was well established long before any population of it began to show indications of behaving symbolically. This places the origin of symbolic t... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3614920 Thu, 27 May 2010 23:00:00 +0100 3614920 http://www.medworm.com/index.php?rid=3614919&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20509012%26dopt%3DAbstract Authors: Levy A Many of the fundamental concepts of biology lack consensual, precise definitions. Partly, this is due to a contrast between our discrete language and the continuous character of nature. Some debates over these concepts are confounded by the use of the same terms with different specific meanings, indicating a possible need for an expanded scientific lexicon. Words have their own histories, and frequently scientific terms with a vernacular origin retain associated vestigial meanings. Even terms newly coined within science have histories and changing meanings, which can lead to confusion among debaters. Debates over concepts are further confounded when the same terms are used in different fields of biology, with distinct (even conflicting) objectives, and by biologists wit... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3614919 Thu, 27 May 2010 23:00:00 +0100 3614919 http://www.medworm.com/index.php?rid=3608326&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502978%26dopt%3DAbstract Authors: Gontier N PMID: 20502978 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608326 Tue, 25 May 2010 23:00:00 +0100 3608326 http://www.medworm.com/index.php?rid=3608325&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502979%26dopt%3DAbstract Authors: Vieira AB In this article, language is considered as a behavioural trait evolving by means of natural selection, in co-evolution with the Palaeolithic tool industries. This perspective enables an analysis of the grammatical and syntactic equivalents of the multiple abilities and effects of lithic tools across the successive modes of their development and consider their influence in intra-group communication and the social biology of the hominine species concerned. The hypothesis is that grammatical equivalents inherent to stone tool work guide the evolution of language. PMID: 20502979 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608325 Tue, 25 May 2010 23:00:00 +0100 3608325 http://www.medworm.com/index.php?rid=3608324&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502980%26dopt%3DAbstract Authors: Costa FO, Carvalho GR Geographic and temporal patterns of morphological and behavioral diversifications among species stimulated Darwin to propose a mechanism for evolutionary change through natural selection. Scientific developments have revealed an even more fundamental level of biological complexity: sequence variation in DNA. While genome projects yield spectacular insights into molecular evolution, they have targeted only a few species. In contrast, the Barcode of Life Initiative (BOLI) proposes a horizontal approach to genomics, examining short, standardized genome segments across the sweep of eukaryotic life, all 10 million species. BOLI will extend our understanding of evolution and speciation in varied ways. It will facilitate quantification of biological diversity by... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608324 Tue, 25 May 2010 23:00:00 +0100 3608324 http://www.medworm.com/index.php?rid=3608323&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502981%26dopt%3DAbstract This article explores the relationship between punctuated equilibrium (PE) and species selection in the light of this philosophical debate about the nature of theoretical fertility, or suggestiveness. I argue that (1) PE suggests, but does not imply, that species selection is a mechanism of evolution; (2) the suggestiveness in this case is not reducible to predictive novelty; (3) species selection is not a metaphorical extension of PE; and (4) getting clear about the way in which PE suggests species selection can help solve a puzzle about punctuated equilibrium. The puzzle is that Eldredge and Gould's initial presentation of PE seems to presuppose a minimalist or extrapolationist view of macroevolution, even though many scientists take PE to challenge that minimalist view. PMID: 205029... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608323 Tue, 25 May 2010 23:00:00 +0100 3608323 http://www.medworm.com/index.php?rid=3608322&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502982%26dopt%3DAbstract Authors: Gontier N Evolutionary epistemology can provide a unified scientific methodology that enables scholars to study the evolution of life as well as the evolution of cognition, science, culture and any other phenomenon displayed by living organisms. In this article, three heuristics are provided that allow for a thorough search for the units, levels and mechanisms of evolution. Contrary to previous approaches, units, levels and mechanisms are not identified by pointing out essential features, but rather ostensive definitions are preferred. That is, units are considered as such if a level of evolution and a mechanism of evolution is identifiable. Levels are levels if one can point out units that evolve at that level according to evolutionary mechanisms, and mechanisms are considere... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608322 Tue, 25 May 2010 23:00:00 +0100 3608322 http://www.medworm.com/index.php?rid=3608321&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502983%26dopt%3DAbstract Authors: Matos M In 2009 we celebrate Charles Darwin's second centenary, and 150 years since the publication of 'The Origin of Species'. After so many years, what has changed in the way we understand Evolution? Obviously we have now a full understanding of the mechanisms underlying heritability. Many molecular tools are available, allowing among other things to reconstruct more accurately the evolutionary history of species and use a comparative approach to infer evolutionary processes. But we can also study evolution in action. Such studies-Experimental Evolution-help us to characterize in detail the evolutionary processes and patterns as a function of environmental challenges, the previous history and present state of populations, and the interactions between such factors. We have no... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608321 Tue, 25 May 2010 23:00:00 +0100 3608321 http://www.medworm.com/index.php?rid=3608320&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20502984%26dopt%3DAbstract Authors: Krebs P, Pezzatti GB, Mazzoleni S, Talbot LM, Conedera M "Fire regime" has become, in recent decades, a key concept in many scientific domains. In spite of its wide spread use, the concept still lacks a clear and wide established definition. Many believe that it was first discussed in a famous report on national park management in the United States, and that it may be simply defined as a selection of a few measurable parameters that summarize the fire occurrence patterns in an area. This view has been uncritically perpetuated in the scientific community in the last decades. In this paper we attempt a historical reconstruction of the origin, the evolution and the current meaning of "fire regime" as a concept. Its roots go back to the 19th century in France and to the first half... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3608320 Tue, 25 May 2010 23:00:00 +0100 3608320 http://www.medworm.com/index.php?rid=3589692&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20490712%26dopt%3DAbstract Authors: Castro L, Toro MA Cooperation based in mutual benefit provides a perfect scenario to start selfish behaviors aimed to obtain greater benefit at the expense of the partner. Here we investigate if mutual benefit cooperation can be stable between individuals that cooperate with kindness (good partners) or if they will be displaced by other individuals that try to obtain more benefit with less cost (bad partners). Our model assumes an asymmetry between partners in such a way that one of them (actor) proposes the cooperation whereas the other (receiver) always accepts the offer. It also assumes that actors can choose the partner on the basis of their past experiences with the potential partners. With the help of a simple two-locus mathematical model we show that not only the gene t... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3589692 Wed, 19 May 2010 23:00:00 +0100 3589692 http://www.medworm.com/index.php?rid=3284560&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20157853%26dopt%3DAbstract Authors: Knoke B, Bodenstein C, Marhl M, Perc M, Schuster S It has often been asked which physiological advantages calcium (Ca(2+)) oscillations in non-excitable cells may have as compared to an adjustable stationary Ca(2+) signal. One of the proposed answers is that an oscillatory regime allows a lowering of the average Ca(2+) concentration, which is likely to be advantageous because Ca(2+) is harmful to the cell in high concentrations. To check this hypothesis, we apply Jensen's inequality to study the relation between the average Ca(2+) concentration during oscillations and the Ca(2+) concentration at the (unstable) steady state. Jensen's inequality states that for a (strictly) convex function, the function value of the average of a set of argument values is lower than the average o... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3284560 Tue, 16 Feb 2010 00:00:00 +0100 3284560 http://www.medworm.com/index.php?rid=3072345&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19997788%26dopt%3DAbstract We describe the life cycle of the myxomycetes, present new observations on the myxamoebae and propose a higher-order phylogeny based on elongation factor-1 alpha gene sequences. Our results document the congruence between the morphology-based taxonomy of the myxomycetes and molecular data. In addition, we show that free-living amoebae, common protists in the soil, are among the closest living relatives of the myxomycetes and conclude that de Bary's 'Amoeba-hypothesis' on the evolutionary origin of the plasmodial slime molds may have been correct. PMID: 19997788 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3072345 Tue, 08 Dec 2009 00:00:00 +0100 3072345 http://www.medworm.com/index.php?rid=3048957&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19946800%26dopt%3DAbstract Authors: Mabrouk N, Deffuant G, Tolker-Nielsen T, Lobry C Recent experimental observations of Pseudomonas aeruginosa, a model bacterium in biofilm research, reveal that, under specific growth conditions, bacterial cells form patterns of interconnected microcolonies. In the present work, we use an individual-based model to assess the involvement of bacteria motility and self-produced extracellular substance in the formation of these patterns. In our simulations, the pattern of interconnected microcolonies appears only when bacteria motility is reduced by excreted extracellular macromolecules. Immotile bacteria form isolated microcolonies and constantly motile bacteria form flat biofilms. Based on experimental data and computer simulations, we suggest a mechanism that could be responsibl... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=3048957 Sat, 28 Nov 2009 00:00:00 +0100 3048957 http://www.medworm.com/index.php?rid=2984798&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19902285%26dopt%3DAbstract This article develops mathematical models describing the evolutionary dynamics of both asexually and sexually reproducing populations of diploid unicellular organisms. The asexual and sexual life cycles are based on the asexual and sexual life cycles in Saccharomyces cerevisiae, Baker's yeast, which normally reproduces by asexual budding, but switches to sexual reproduction when stressed. The mathematical models consider three reproduction pathways: (1) Asexual reproduction, (2) self-fertilization, and (3) sexual reproduction. We also consider two forms of genome organization. In the first case, we assume that the genome consists of two multi-gene chromosomes, whereas in the second case, we consider the opposite extreme and assume that each gene defines a separate chromosome, which we call... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2984798 Tue, 10 Nov 2009 00:00:00 +0100 2984798 http://www.medworm.com/index.php?rid=2968030&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19890672%26dopt%3DAbstract In conclusion, humans showed a surprising ability to classify milk snake patterns; they repeatedly formed the same distinct groups of species, thus completing a process that resembles unsupervised categorization. PMID: 19890672 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2968030 Thu, 05 Nov 2009 00:00:00 +0100 2968030 http://www.medworm.com/index.php?rid=2909688&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19841958%26dopt%3DAbstract From molecules to the biosphere: Nikolai V. Timoféeff-Ressovsky's (1900-1981) research program within a totalitarian landscape. Theory Biosci. 2009 Oct 16; Authors: Levit GS, Hoßfeld U Nikolai Vladimirovich Timoféeff-Ressovsky was one of the key figures in the Synthetic Theory of Evolution. Living and researching under what was arguably the two most powerful and cruel totalitarian regimes in human history, the Third Reich and the Soviet Union, Timoféeff-Ressovsky succeeded in developing an ambitious research program aiming to explain evolution on all major levels, from the molecular-genetic, the populational, and the biogeocenotic to the level of the entire Biosphere. Yet his scientific biography remains largely unwritten and his role under totalitarianism, ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2909688 Thu, 15 Oct 2009 23:00:00 +0100 2909688 http://www.medworm.com/index.php?rid=2847074&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19784686%26dopt%3DAbstract Authors: Scherrer K, Jost J PMID: 19784686 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2847074 Fri, 25 Sep 2009 23:00:00 +0100 2847074 http://www.medworm.com/index.php?rid=2834914&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19779755%26dopt%3DAbstract Comments on "Gene and genon concept" by K. Scherrer and J. Jost. Theory Biosci. 2009 Sep 25; Authors: Billeter MA PMID: 19779755 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2834914 Thu, 24 Sep 2009 23:00:00 +0100 2834914 http://www.medworm.com/index.php?rid=2804759&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19756808%26dopt%3DAbstract Authors: Nebel ME, Scheid A Over the last few decades, much effort has been taken to develop approaches for identifying good predictions of RNA secondary structure. This is due to the fact that most computational prediction methods based on free energy minimization compute a number of suboptimal foldings and we have to identify the native folding among all these possible secondary structures. Using the abstract shapes approach as introduced by Giegerich et al. (Nucleic Acids Res 32(16):4843-4851, 2004), each class of similar secondary structures is represented by one shape and the native structures can be found among the top shape representatives. In this article, we derive some interesting results answering enumeration problems for abstract shapes and secondary structures of RNA. We c... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2804759 Mon, 14 Sep 2009 23:00:00 +0100 2804759 http://www.medworm.com/index.php?rid=2770449&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19730918%26dopt%3DAbstract Comments on the paper by K. Scherrer and J. Jost "Gene and genon" concept: coding versus regulation. Theory Biosci. 2009 Sep 3; Authors: Gros F PMID: 19730918 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2770449 Wed, 02 Sep 2009 23:00:00 +0100 2770449 http://www.medworm.com/index.php?rid=2741972&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19707809%26dopt%3DAbstract Authors: Breidbach O PMID: 19707809 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2741972 Tue, 25 Aug 2009 23:00:00 +0100 2741972 http://www.medworm.com/index.php?rid=2723566&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19697074%26dopt%3DAbstract Authors: Noble D PMID: 19697074 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2723566 Thu, 20 Aug 2009 23:00:00 +0100 2723566 http://www.medworm.com/index.php?rid=2723565&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19697075%26dopt%3DAbstract Authors: Forsdyke DR Reconsideration of the term "gene" should take into account (a) the potential clash between hierarchical levels of information discussed in the 1970s by Gregory Bateson, (b) the contrast between conventional and genome phenotypes discussed in the 1980s by Richard Grantham, and (c) the emergence in the 1990s of a new science-Evolutionary Bioinformatics-that views genomes as channels conveying multiple forms of information through the generations. From this perspective, there is conceptual continuity between the functional "gene" of Mendel and today's GenBank sequences. If the function attributed to a gene can change specifically as the result of a DNA mutation, then the mutated part of DNA can be considered as part of the gene. Conversely, even if appearing to locat... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2723565 Thu, 20 Aug 2009 23:00:00 +0100 2723565 http://www.medworm.com/index.php?rid=2547153&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19557452%26dopt%3DAbstract Authors: Stadler PF, Prohaska SJ, Forst CV, Krakauer DC The precise elucidation of the gene concept has become the subject of intense discussion in light of results from several, large high-throughput surveys of transcriptomes and proteomes. In previous work, we proposed an approach for constructing gene concepts that combines genomic heritability with elements of function. Here, we introduce a definition of the gene within a computational framework of cellular interactions. The definition seeks to satisfy the practical requirements imposed by annotation, capture logical aspects of regulation, and encompass the evolutionary property of homology. PMID: 19557452 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2547153 Thu, 25 Jun 2009 23:00:00 +0100 2547153 http://www.medworm.com/index.php?rid=2547155&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19424735%26dopt%3DAbstract Authors: Barbosa LA, Fontanari JF Axelrod's model for culture dissemination offers a nontrivial answer to the question of why there is cultural diversity given that people's beliefs have a tendency to become more similar to each other's as they interact repeatedly. The answer depends on the two control parameters of the model, namely, the number F of cultural features that characterize each agent, and the number q of traits that each feature can take on, as well as on the size A of the territory or, equivalently, on the number of interacting agents. Here, we investigate the dependence of the number C of distinct coexisting cultures on the area A in Axelrod's model, the culture-area relationship, through extensive Monte Carlo simulations. We find a non-monotonous culture-area relation, ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2547155 Thu, 07 May 2009 23:00:00 +0100 2547155 http://www.medworm.com/index.php?rid=2547157&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19399544%26dopt%3DAbstract Authors: Kutschera U One century ago, Constantin S. Mereschkowsky introduced the symbiogenesis theory for the origin of chloroplasts from ancient cyanobacteria which was later supplemented by Ivan E. Wallin's proposal that mitochondria evolved from once free-living bacteria. Today, this Mereschkowsky-Wallin principle of symbiogenesis, which is also known as the serial primary endosymbiosis theory, explains the evolutionary origin of eukaryotic cells and hence the emergence of all eukaryotes (protists, fungi, animals and plants). In 1858, the concept of natural selection was described independently by Charles Darwin and Alfred R. Wallace. In the same year, Antonio Snider-Pellegrini proposed the idea of shifting continents, which was later expanded by Alfred Wegener, who published his th... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2547157 Mon, 27 Apr 2009 23:00:00 +0100 2547157 http://www.medworm.com/index.php?rid=2547159&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19381704%26dopt%3DAbstract In conclusion, the association approach to an analysis of the distribution of trait variation over populations resolves problems that are frequently encountered with the apportionment perspective and its commonly applied measures in both population genetics and ecology, suggesting new and more comprehensive methods of analysis that include patterns of differentiation and apportionment. PMID: 19381704 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2547159 Fri, 17 Apr 2009 23:00:00 +0100 2547159 http://www.medworm.com/index.php?rid=2283219&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19290561%26dopt%3DAbstract Authors: Mendoza Meza ME, Bhaya A This paper introduces a threshold policy with hysteresis (TPH) for the control of one-predator one-prey models. The models studied are the Lotka-Volterra and Rosenzweig-MacArthur two species density-dependent predator-prey models and the Arditi-Ginzburg nondimensional ratio-dependent model. The proposed policy (TPH) changes the dynamics of the system in such a way that a bounded oscillation is achieved confined to a region that does not allow extinction of either species. The policy can be designed by a suitable choice of so called virtual equilibrium points in a simple and intuitive manner. PMID: 19290561 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2283219 Tue, 17 Mar 2009 04:00:00 +0100 2283219 http://www.medworm.com/index.php?rid=2241570&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19263105%26dopt%3DAbstract Authors: Talent N Gametophytic apomixis, asexual reproduction involving megagametophytes, occurs in many flowering-plant families and as several variant mechanisms. Developmental destabilization of sexual reproduction as a result of hybridization and/or polyploidy appears to be a general trigger for its evolution, but the evidence is complicated by ploidy-level changes and hybridization occurring with facultative apomixis. The repeated origins of polyploid apomictic complexes in the palaeopolyploid Maloid Rosaceae suggest a new model of evolutionary transitions that may have wider applicability. Two conjectures are fundamental to this model: (1) that as previously suggested by Rutishauser, like many sexual flowering plants the polyploid apomicts require maternal-paternal balance in the... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2241570 Thu, 05 Mar 2009 05:00:00 +0100 2241570 http://www.medworm.com/index.php?rid=2217157&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19241099%26dopt%3DAbstract Authors: Love AC A central reason that undergirds the significance of evo-devo is the claim that development was left out of the Modern synthesis. This claim turns out to be quite complicated, both in terms of whether development was genuinely excluded and how to understand the different kinds of embryological research that might have contributed. The present paper reevaluates this central claim by focusing on the practice of model organism choice. Through a survey of examples utilized in the literature of the Modern synthesis, I identify a previously overlooked feature: exclusion of research on marine invertebrates. Understanding the import of this pattern requires interpreting it in terms of two epistemic values operating in biological research: theoretical generality and explanatory... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2217157 Wed, 25 Feb 2009 05:00:00 +0100 2217157 http://www.medworm.com/index.php?rid=2201216&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19225820%26dopt%3DAbstract Authors: Chambers KE, McDaniell R, Raincrow JD, Deshmukh M, Stadler PF, Chiu CH Large-scale-even genome-wide-duplications have repeatedly been invoked as an explanation for major radiations. Teleosts, the most species-rich vertebrate clade, underwent a "fish-specific genome duplication" (FSGD) that is shared by most ray-finned fish lineages. We investigate here the Hox complement of the goldeye (Hiodon alosoides), a representative of Osteoglossomorpha, the most basal teleostean clade. An extensive PCR survey reveals that goldeye has at least eight Hox clusters, indicating a duplicated genome compared to basal actinopterygians. The possession of duplicated Hox clusters is uncoupled to species richness. The Hox system of the goldeye is substantially different from that of other teleost l... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2201216 Thu, 19 Feb 2009 05:00:00 +0100 2201216 http://www.medworm.com/index.php?rid=2201217&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19224263%26dopt%3DAbstract In conclusion I argue that the complete dismissal of saltational evolution is a major historical error of evolutionary biology tracing back to Darwin that needs to be rectified. PMID: 19224263 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2201217 Wed, 18 Feb 2009 05:00:00 +0100 2201217 http://www.medworm.com/index.php?rid=2195264&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19221824%26dopt%3DAbstract Authors: Raineri M The concept of chordates arose from the alliance between embryology and evolution in the second half of the nineteenth century, as a result of a theoretical elaboration on Kowalevsky's discoveries about some fundamental similarities between the ontogeny of the lancelet, a putative primitive fish, and that of ascidians, then classified as molluscs. Carrying out his embryological studies in the light of Darwin's theory and von Baer's account of the germ layers, Kowalevsky was influenced by the German tradition of idealistic morphology that was concerned with transformations driven by laws of form, rather than with a gradual evolution occurring by means of variation, selection and adaptation. In agreement with this tradition, Kowalevsky interpreted the vertebrate-like s... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2195264 Tue, 17 Feb 2009 05:00:00 +0100 2195264 http://www.medworm.com/index.php?rid=2188391&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19214616%26dopt%3DAbstract Authors: Hall BK Eighteen seventy-four was a high point in evolutionary embryology. Thanks to Charles Darwin, the theory of evolution by natural selection provided a revolutionary new way of viewing the relationships and origins of organisms on Earth. Thanks to Ernst Haeckel, embryos were the way to study evolution (Haeckel in Generelle morphologie der organismen, vols 1, 2. Verlag Georg Reimer, Berlin, 1866)-it really was embryos in evolution-and recapitulation was in the air. Thanks to Anton Dohrn, a new research facility was on the ground, designed, located and structured to facilitate the study of embryos in evolution. Anton Dohrn devised, designed, financed, supervised the construction and then administered the Naples Zoological Station specifically so that researchers from all na... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2188391 Fri, 13 Feb 2009 05:00:00 +0100 2188391 http://www.medworm.com/index.php?rid=2188392&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19214615%26dopt%3DAbstract Authors: Olsson L, Hoßfeld U, Breidbach O PMID: 19214615 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2188392 Thu, 12 Feb 2009 05:00:00 +0100 2188392 http://www.medworm.com/index.php?rid=2093017&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19130112%26dopt%3DAbstract Authors: Gianinetti A During malting, barley germinates and produces hydrolytic enzymes that de-structure the endosperm, making the grains soft and friable. This process starts close to the embryo and spreads throughout the whole grain. It is leaded by the degradation of cell walls, which are mainly constituted of beta-glucans. Fast and extended breakdown of beta-glucans occurs by means of an expanding reaction front driven by beta-glucanase, and appears to follow pseudo-first-order kinetics. Endosperm permeabilization to macromolecules is closely linked to the dismantling of cell walls, thus that access to beta-glucans by beta-glucanase itself is limited. It is shown that the kinetics of beta-glucan degradation during malting are consequent to this condition, and can be explained acco... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2093017 Thu, 08 Jan 2009 05:00:00 +0100 2093017 http://www.medworm.com/index.php?rid=2061720&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19101746%26dopt%3DAbstract Authors: Bornholdt S, Sneppen K, Westphal H Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime (Van Valen in Evol Theory 1:1-30, 1973). Using the fossil marine animal genera database (Sepkoski in Bull Am Paleontol 363, pp 563, 2002) we here examine the relationship between longevity of a higher taxonomic group (orders) and the longevity of its lower taxonomic groups (genera). We find insignificant correlation between the size of an order and its longevity, whereas we observe large correlation between the lifetime of an order and the lifetime of its constituent genera. These observations suggest that longevity of taxono... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2061720 Sat, 20 Dec 2008 05:00:00 +0100 2061720 http://www.medworm.com/index.php?rid=2018255&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19057935%26dopt%3DAbstract This article develops a simplified set of models describing asexual and sexual replication in unicellular diploid organisms. The models assume organisms whose genomes consist of two chromosomes, where each chromosome is assumed to be functional if it is equal to some master sequence sigma(0), and non-functional otherwise. We review the previously studied case of selective mating, where it is assumed that only haploids with functional chromosomes can fuse, and also consider the case of random haploid fusion. When the cost for sex is small, as measured by the ratio of the characteristic haploid fusion time to the characteristic growth time, we find that sexual replication with random haploid fusion leads to a greater mean fitness for the population than a purely asexual strategy. However, in... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=2018255 Fri, 05 Dec 2008 05:00:00 +0100 2018255 http://www.medworm.com/index.php?rid=1902248&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18946696%26dopt%3DAbstract This article presents the thesis that this conception is too restrictive and that evolution can occur in systems in which there is no copy of information between generations. For that purpose, this article introduces a new set of concepts and a theoretical framework that is designed to be equally applicable to the study of the evolution of biological and nonbiological systems. In contrast to some theoretical approaches in evolution, like neo-Darwinism, the approach presented here is not focused on the transmission and change of hereditary information that can be copied (like in the case of DNA). Instead, multiple mechanisms by which a system can generate offspring (with and without copying) and by which information in it affects the structure and evolution of its offspring are considered. ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1902248 Thu, 23 Oct 2008 04:00:00 +0100 1902248 http://www.medworm.com/index.php?rid=1902249&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18941823%26dopt%3DAbstract Authors: Magdoń-Maksymowicz MS There are some analytical solutions of the Penna model of biological aging; here, we discuss the approach by Coe et al. (Phys. Rev. Lett. 89, 288103, 2002), based on the concept of self-consistent solution of a master equation representing the Penna model. The equation describes transition of the population distribution at time t to next time step (t + 1). For the steady state, the population n(a, l, t) at age a and for given genome length l becomes time-independent. In this paper we discuss the stability of the analytical solution at various ranges of the model parameters-the birth rate b or mutation rate m. The map for the transition from n(a, l, t) to the next time step population distribution n(a + 1, l, t + 1) is constructed. Then the fix point... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1902249 Wed, 22 Oct 2008 04:00:00 +0100 1902249 http://www.medworm.com/index.php?rid=1794785&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18791761%26dopt%3DAbstract Authors: Jaffe K Hymenoptera have haploid males, which produce sperm by cloning. Sperm selection theory predicts that because termites have diploid males that produce genetically diverse sperm, they may profit from a high sperm surplus (large K), whereas Hymenoptera (ants, bees and wasps) should produce few sperm per fertilization (low Kappa). Male reproductive "kings", which continuously provide spermatozoa during the whole life of the queen, allow for a large K. Available empirical evidence confirms the existence of a large difference in K between diploid insects, especially Blattodea (Isoptera) (K > 1,000), and haplo-diploids such as Hymenoptera (K < 10). The available data suggest that sperm selection may be an important evolutionary force for species with diploid, but not ha... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1794785 Sat, 13 Sep 2008 04:00:00 +0100 1794785 http://www.medworm.com/index.php?rid=1726639&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18716819%26dopt%3DAbstract Authors: Tannenbaum E This paper develops simplified mathematical models describing the mutation-selection balance for the asexual and sexual replication pathways in Saccharomyces cerevisiae, or Baker's yeast. The simplified models are based on the single-fitness-peak approximation in quasispecies theory. We assume diploid genomes consisting of two chromosomes, and we assume that each chromosome is functional if and only if its base sequence is identical to some master sequence. The growth and replication of the yeast cells is modeled as a first-order process, with first-order growth rate constants that are determined by whether a given genome consists of zero, one, or two functional chromosomes. In the asexual pathway, we assume that a given diploid cell divides into two diploids. For... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1726639 Thu, 21 Aug 2008 04:00:00 +0100 1726639 http://www.medworm.com/index.php?rid=1709822&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18704538%26dopt%3DAbstract Authors: Levit GS, Simunek M, Hoßfeld U Toward the end of the 1930s, Bernhard Rensch (1900-1990) turned from Lamarckism and orthogenesis to selectionism and became one of the key figures in the making of the Synthetic Theory of Evolution (STE). He contributed to the Darwinization of biological systematics, the criticism of various anti-Darwinian movements in the German lands, but more importantly founded a macroevolutionary theory based on Darwinian gradualism. In the course of time, Rensch's version of the STE developed into an all-embracing metaphysical conception based on a kind of Spinozism. Here we approach Rensch's "selectionist turn" by outlining its context, and by analyzing his theoretical transformation. We try to reconstruct the immanent logic of Rensch's evolution from... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1709822 Wed, 13 Aug 2008 04:00:00 +0100 1709822 http://www.medworm.com/index.php?rid=1577533&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18597134%26dopt%3DAbstract Authors: Gilbert SF The American precursors of evo-devo have numerous phenotypes. Fritz Müller, a German émigré living in Brazil, was one of the first post-Darwin evolutionary biologists to look seriously at the roles of larvae in constraining and permitting evolutionary change. His book, Für Darwin, contains the germs of numerous ideas concerning recapitulation, larval ecology, punctuated equilibrium, and canalization. William Keith Brooks was interested in larval ecology and the mechanisms that promoted selectable variation. One of his students, E. B. Wilson, followed one of Mülller's paths and brought the notion of embryonic homologies into the area of developmental biology and animal classification. Frank R. Lillie took a different page out of Müller a... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1577533 Thu, 03 Jul 2008 04:00:00 +0100 1577533 http://www.medworm.com/index.php?rid=1552045&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18581157%26dopt%3DAbstract Authors: Kutschera U, Niklas KJ Seventy-five years ago, the geneticist Richard Goldschmidt hypothesized that single mutations affecting development could result in major phenotypic changes in a single generation to produce unique organisms within animal populations that he called "hopeful monsters". Three decades ago, Sarah P. Gibbs proposed that photosynthetic unicellular micro-organisms like euglenoids and dinoflagellates are the products of a process now called "secondary endosymbiosis" (i.e., the evolution of a chloroplast surrounded by three or four membranes resulting from the incorporation of a eukaryotic alga by a eukaryotic heterotrophic host cell). In this article, we explore the evidence for Goldschmidt's "hopeful monster" concept and expand the scope of this theory to inclu... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1552045 Thu, 26 Jun 2008 04:00:00 +0100 1552045 http://www.medworm.com/index.php?rid=1531902&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18563466%26dopt%3DAbstract Authors: Biswas D, Das SK, Roy S The growth process of a living organism is studied with the help of a mathematical model where a part of the surplus power is assumed to be used for growth. In the present study, the basic mathematical framework of the growth process is based on a pioneering theory proposed by von Bertalanffy and his work is the main intellectual driving force behind the present analysis. Considering the existence of an optimum size for which the surplus power becomes maximum, it has been found that the scaling exponent for the intake rate must be smaller than the exponent for the metabolic cost. A relationship among the empirical constants in allometric scaling has also been established on the basis of the fact that an organism never ceases to generate surplus energy. ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1531902 Thu, 19 Jun 2008 04:00:00 +0100 1531902 http://www.medworm.com/index.php?rid=1531903&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18561366%26dopt%3DAbstract Authors: PMID: 18561366 [PubMed - indexed for MEDLINE] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1531903 Sun, 01 Jun 2008 04:00:00 +0100 1531903 http://www.medworm.com/index.php?rid=1461330&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18493811%26dopt%3DAbstract Authors: Guimarães RC, Moreira CH, de Farias ST A model for the formation of the genetic code is presented where protein synthesis is directed initially by tRNA dimers. Proteins that are resistant to degradation and efficient RNA-binders protect the RNAs. Replication becomes elongational producing poly-tRNAs from which the mRNAs and ribosomes are derived. Attributions are successively fixed to tRNAs paired through the perfect palindromic anticodons, with the same bases at the extremities (5'ANA: UNU 3'; GNG: CNC; principal dinucleotides, pDiN). The 5' degeneracy is then developed. The first pairs to be encoded correspond to the hydropathy correlation outliers (Gly-CC: Pro-GG and Ser-GA: Ser-CU) and to the sector of homogeneous pDiN, composed by two pyrimidines or two purines. Thes... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1461330 Wed, 21 May 2008 04:00:00 +0100 1461330 http://www.medworm.com/index.php?rid=1426913&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18458976%26dopt%3DAbstract Authors: Sumpter D, Buhl J, Biro D, Couzin I Moving animal groups provide some of the most intriguing and difficult to characterise examples of collective behaviour. We review some recent (and not so recent) empirical research on the motion of animal groups, including fish, locusts and homing pigeons. An important concept which unifies our understanding of these groups is that of transfer of directional information. Individuals which change their direction of travel in response to the direction taken by their near neighbours can quickly transfer information about the presence of a predatory threat or food source. We show that such information transfer is optimised when the density of individuals in a group is close to that at which a phase transition occurs between random and ordered m... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1426913 Tue, 06 May 2008 04:00:00 +0100 1426913 http://www.medworm.com/index.php?rid=1426912&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18458977%26dopt%3DAbstract Authors: Poudret M, Arnould A, Comet JP, Le Gall P, Meseure P, Képès F Many complex cellular processes involve major changes in topology and geometry. We have developed a method using topology-based geometric modelling in which the edge labels of an n-dimensional generalized map (a subclass of graphs) represent the relations between neighbouring biological compartments. We illustrate our method using two topological models of the Golgi apparatus. These models can be animated using transformation rules, which depend on geometric and/or biochemical data and which modify both these data and the topology. Both models constitute plausible topological representations of the Golgi apparatus, but only the model based on a recent hypothesis about the Golgi apparatus is fully compatibl... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1426912 Tue, 06 May 2008 04:00:00 +0100 1426912 http://www.medworm.com/index.php?rid=1416561&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18449590%26dopt%3DAbstract Authors: Gutkin B, Jost J, Tuckwell HC We examine the effects of stochastic input currents on the firing behaviour of two coupled Type 1 or Type 2 neurons. In Hodgkin-Huxley model neurons with standard parameters, which are Type 2, in the bistable regime, synaptic transmission can initiate oscillatory joint spiking, but white noise can terminate it. In Type 1 cells (models), typified by a quadratic integrate and fire model, synaptic coupling can cause oscillatory behaviour in excitatory cells, but Gaussian white noise can again terminate it. We locally determine an approximate basin of attraction, [Formula: see text] of the periodic orbit and explain the firing behaviour in terms of the effects of noise on the probability of escape of trajectories from [Formula: see text]. PMID: 18... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1416561 Thu, 01 May 2008 04:00:00 +0100 1416561 http://www.medworm.com/index.php?rid=1413643&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18446398%26dopt%3DAbstract Authors: Sbano L, Kirkilionis M In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the different abilities to form bonds between different types of atoms and molecules create much of the properties we experience in our everyday life, especially in all biological activity. There are essentially two types of processes related to biochemical reaction networks, the interactions among molecules and interactions involving their conformational changes, so in a sense, their internal state. The first type of processes can be conveniently approximated by the so-called mass-action kinetics, but this is not necessarily so f... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1413643 Wed, 30 Apr 2008 04:00:00 +0100 1413643 http://www.medworm.com/index.php?rid=1410019&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18443838%26dopt%3DAbstract Authors: Jost J, Helbing D, Lörincz A, Middendorf M PMID: 18443838 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1410019 Tue, 29 Apr 2008 04:00:00 +0100 1410019 http://www.medworm.com/index.php?rid=1410018&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18443839%26dopt%3DAbstract Authors: Scheidler A, Merkle D, Middendorf M In this paper, we consider computing systems that have autonomous helper components which fulfill support functions and that possess reconfigurable hardware so that they can specialize to different types of service tasks. Several self-organized task partitioning methods are proposed that can be used by the helper components to decide how to reconfigure and which service tasks to execute. The proposed task partitioning methods are inspired by the so-called ant queue system that can be found in real ants for partitioning tasks between the individuals. The aim of this study is to investigate basic properties of the task partitioning methods, like stability and efficiency, in order to obtain basic insights into the design of task partitioning me... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1410018 Tue, 29 Apr 2008 04:00:00 +0100 1410018 http://www.medworm.com/index.php?rid=1410017&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18443840%26dopt%3DAbstract Authors: Sadovsky MG, Putintseva JA, Shchepanovsky AS Information capacity of nucleotide sequences measures the unexpectedness of a continuation of a given string of nucleotides, thus having a sound relation to a variety of biological issues. A continuation is defined in a way maximizing the entropy of the ensemble of such continuations. The capacity is defined as a mutual entropy of real frequency dictionary of a sequence with respect to the one bearing the most expected continuations; it does not depend on the length of strings contained in a dictionary. Various genomes exhibit a multi-minima pattern of the dependence of information capacity on the string length, thus reflecting an order within a sequence. The strings with significant deviation of an expected frequency from the real ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1410017 Tue, 29 Apr 2008 04:00:00 +0100 1410017 http://www.medworm.com/index.php?rid=1407399&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18438693%26dopt%3DAbstract Authors: Barat A, Ruskin HJ, Crane M In order to better understand and predict the release of proteins from bioerodible microspheres or nanospheres, it is important to know the influences of different initial factors on the release mechanisms, though often it is difficult to assess what exactly is at the origin of a certain dissolution profile. We propose here a new class of fine-grained multi-agent models built to incorporate increasing complexity, permitting the exploration of the role of different parameters, especially that of the internal morphology of the spheres, in the exhibited release profile. This approach, based on Monte Carlo (MC) and cellular automata (CA) techniques, has permitted the testing of various assumptions and hypotheses about several experimental systems of nan... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1407399 Sat, 26 Apr 2008 04:00:00 +0100 1407399 http://www.medworm.com/index.php?rid=1401510&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18437441%26dopt%3DAbstract Authors: Tournier L, Gouzé JL A key point in the analysis of dynamical models of biological systems is to handle systems of relatively high dimensions. In the present paper we propose a method to hierarchically organize a certain type of piecewise affine (PWA) differential systems. This specific class of systems has been extensively studied for the past few years, as it provides a good framework to model gene regulatory networks. The method, shown on several examples, allows a qualitative analysis of the asymptotic behavior of a PWA system, decomposing it into several smaller subsystems. This technique, based on the well-known strongly connected components decomposition, is not new. However, its adaptation to the non-smooth PWA differential equations turns out to be quite relevant... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1401510 Fri, 25 Apr 2008 04:00:00 +0100 1401510 http://www.medworm.com/index.php?rid=1394017&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18427853%26dopt%3DAbstract Authors: Bernardet U, Bermúdez I Badia S, Verschure PF Returning to the point of departure after exploring the environment is a key capability for most animals. In the absence of landmarks, this task will be solved by integrating direction and distance traveled over time. This is referred to as path integration or dead reckoning. An important question is how the nervous systems of navigating animals such as the 1 mm(3) brain of ants can integrate local information in order to make global decision. In this article we propose a neurobiologically plausible system of storing and retrieving direction and distance information. The path memory of our model builds on the well established concept of population codes, moreover our system does not rely on trigonometric functions or other com... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1394017 Tue, 22 Apr 2008 04:00:00 +0100 1394017 http://www.medworm.com/index.php?rid=1394016&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18427854%26dopt%3DAbstract Authors: Kaneko K, Furusawa C We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are derived and confirmed experimentally. They include a power law distribution of gene expressions, a lognormal distribution of cellular chemical abundances over cells, and embedding of the power law into the network connectivity distribution. Second, given a consistency between genotype and phenotype, a general relationship between phenotype fluctuations by genetic variation and isogenic phenotypic fluctuation by developmental noise is derived. Third, we discuss the chaos mechanism for stem cell differentiation with autonomous r... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1394016 Tue, 22 Apr 2008 04:00:00 +0100 1394016 http://www.medworm.com/index.php?rid=1387003&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18421492%26dopt%3DAbstract Authors: Marco D The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1387003 Fri, 18 Apr 2008 04:00:00 +0100 1387003 http://www.medworm.com/index.php?rid=1379626&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18415133%26dopt%3DAbstract This study examined how Physarum amoebae compute these solutions. The mechanism involves the adaptation of the tubular body, which appears to be similar to a network, based on cell dynamics. Our model describes how the network of tubes expands and contracts depending on the flux of protoplasmic streaming, and reproduces experimental observations of the behavior of the organism. The proposed algorithm based on Physarum is simple and powerful. PMID: 18415133 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1379626 Wed, 16 Apr 2008 04:00:00 +0100 1379626 http://www.medworm.com/index.php?rid=1379625&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18415134%26dopt%3DAbstract Authors: Inden B The way genes are interpreted biases an artificial evolutionary system towards some phenotypes. When evolving artificial neural networks, methods using direct encoding have genes representing neurons and synapses, while methods employing artificial ontogeny interpret genomes as recipes for the construction of phenotypes. Here, a neuroevolution system (neuroevolution with ontogeny or NEON) is presented that can emulate a well-known neuroevolution method using direct encoding (neuroevolution of augmenting topologies or NEAT), and therefore, can solve the same kinds of tasks. Performance on challenging control and memory benchmark tasks is reported. However, the encoding used by NEON is indirect, and it is shown how characteristics of artificial ontogeny can be introduced... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1379625 Wed, 16 Apr 2008 04:00:00 +0100 1379625 http://www.medworm.com/index.php?rid=1379627&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18414915%26dopt%3DAbstract Authors: Baptista T, Costa E The synchronisation phenomena in biological systems is a current and recurring subject of scientific study. This topic, namely that of circadian clocks, served as inspiration to develop an agent-based simulation that serves the main purpose of being a proof-of-concept of the model used in the BitBang framework, that implements a modern autonomous agent model. Despite having been extensively studied, circadian clocks still have much to be investigated. Rather than wanting to learn more about the internals of this biological process, we look to study the emergence of this kind of adaptation to a daily cycle. To that end we implemented a world with a day/night cycle, and analyse the ways the agents adapt to that cycle. The results show the evolution of the age... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1379627 Tue, 15 Apr 2008 04:00:00 +0100 1379627 http://www.medworm.com/index.php?rid=1332809&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18368432%26dopt%3DAbstract We present some of these uncertainties not as impediments, but as challenges to be recognized and managed. PMID: 18368432 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1332809 Thu, 27 Mar 2008 04:00:00 +0100 1332809 http://www.medworm.com/index.php?rid=1321296&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18357481%26dopt%3DAbstract Authors: Mesoudi A, Danielson P Recent work in the fields of evolutionary ethics and moral psychology appears to be converging on a single empirically- and evolutionary-based science of morality or ethics. To date, however, these fields have failed to provide an adequate conceptualisation of how culture affects the content and distribution of moral norms. This is particularly important for a large class of moral norms relating to rapidly changing technological or social environments, such as norms regarding the acceptability of genetically modified organisms. Here we suggest that a science of morality/ethics can benefit from adopting a cultural evolution or gene-culture coevolution approach, which treats culture as a second, separate evolutionary system that acts in parallel to biologi... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1321296 Fri, 21 Mar 2008 04:00:00 +0100 1321296 http://www.medworm.com/index.php?rid=1288626&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18324433%26dopt%3DAbstract Authors: Fontanari JF, Perlovsky LI Structured meaning-signal mappings, i.e., mappings that preserve neighborhood relationships by associating similar signals with similar meanings, are advantageous in an environment where signals are corrupted by noise and sub-optimal meaning inferences are rewarded as well. The evolution of these mappings, however, cannot be explained within a traditional language evolutionary game scenario in which individuals meet randomly because the evolutionary dynamics is trapped in local maxima that do not reflect the structure of the meaning and signal spaces. Here we use a simple game theoretical model to show analytically that when individuals adopting the same communication code meet more frequently than individuals using different codes-a result of the sp... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1288626 Fri, 07 Mar 2008 05:00:00 +0100 1288626 http://www.medworm.com/index.php?rid=1283687&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18320253%26dopt%3DAbstract "Genes" Theory Biosci. 2008 Mar 5; Authors: Prohaska SJ, Stadler PF In order to describe a cell at molecular level, a notion of a "gene" is neither necessary nor helpful. It is sufficient to consider the molecules (i.e., chromosomes, transcripts, proteins) and their interactions to describe cellular processes. The downside of the resulting high resolution is that it becomes very tedious to address features on the organismal and phenotypic levels with a language based on molecular terms. Looking for the missing link between biological disciplines dealing with different levels of biological organization, we suggest to return to the original intent behind the term "gene". To this end, we propose to investigate whether a useful notion of "gene" can be constructed based on an underl... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1283687 Wed, 05 Mar 2008 05:00:00 +0100 1283687 http://www.medworm.com/index.php?rid=1248071&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18286313%26dopt%3DAbstract This study develops a simplified model describing the evolutionary dynamics of a population composed of obligate sexually and asexually reproducing, unicellular organisms. The model assumes that the organisms have diploid genomes consisting of two chromosomes, and that the sexual organisms replicate by first dividing into haploid intermediates, which then combine with other haploids, followed by the normal mitotic division of the resulting diploid into two new daughter cells. We assume that the fitness landscape of the diploids is analogous to the single-fitness-peak approach often used in single-chromosome studies. That is, we assume a master chromosome that becomes defective with just one point mutation. The diploid fitness then depends on whether the genome has zero, one, or two copies ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1248071 Wed, 20 Feb 2008 05:00:00 +0100 1248071 http://www.medworm.com/index.php?rid=1212356&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18247075%26dopt%3DAbstract Authors: Sandvik H Tree thinking is an integral part of modern evolutionary biology, and a necessary precondition for phylogenetics and comparative analyses. Tree thinking has during the 20th century largely replaced group thinking, developmental thinking and anthropocentricism in biology. Unfortunately, however, this does not imply that tree thinking can be taken for granted. The findings reported here indicate that tree thinking is very much an acquired ability which needs extensive training. I tested a sample of undergraduate and graduate students of biology by means of questionnaires. Not a single student was able to correctly interpret a simple tree drawing. Several other findings demonstrate that tree thinking is virtually absent in students unless they are explicitly taught how ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1212356 Tue, 05 Feb 2008 05:00:00 +0100 1212356 http://www.medworm.com/index.php?rid=1158510&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18197448%26dopt%3DAbstract Authors: Knoke B, Marhl M, Perc M, Schuster S Nonlinear oscillatory systems, playing a major role in biology, do not exhibit harmonic oscillations. Therefore, one might assume that the average value of any of their oscillating variables is unequal to the steady-state value. For a number of mathematical models of calcium oscillations (e.g. the Somogyi-Stucki model and several models developed by Goldbeter and co-workers), the average value of the cytosolic calcium concentration (not, however, of the concentration in the intracellular store) does equal its value at the corresponding unstable steady state at the same parameter values. The average value for parameter values in the unstable region is even equal to the level at the stable steady state for other parameter values, which allow ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1158510 Tue, 15 Jan 2008 05:00:00 +0100 1158510 http://www.medworm.com/index.php?rid=1152947&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18193313%26dopt%3DAbstract Authors: Jost J, Pepper J We develop a formal framework for the optimal allocation of limited resources that includes and clarifies the interplay between individual optimization and the resulting effects at the population level. As an example, in regard to the evolution of sexual recombination, the paradox of the twofold cost of sex is avoided by distinguishing between the evolution of recombination and the subsequent emergence and stability of different mating types as a result of individual optimization within a population that benefits from recombination. PMID: 18193313 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1152947 Sat, 12 Jan 2008 05:00:00 +0100 1152947 http://www.medworm.com/index.php?rid=1152946&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18193314%26dopt%3DAbstract In this study we analyzed these surface-dwelling pink-pigmented epiphytes in three contrasting habitats of field-grown sunflower plants (Helianthus annuus). Using the methanol-ammonium salts agar surface impression method and a polymerase chain reaction (PCR)-based assay, we document the occurrence and characterize the composition of the methylobacteria in these epiphytic habitats. In both the sun-exposed phylloplane (yellow ligulate florets; green leaves) and the moist, dark rhizoplane pink-pigmented methylobacteria were detected that are assigned to the taxa M. mesophilicum, M. extorquens, M. radiotolerans and M. sp. (un-identifiable by our methods). Considerable differences in relative species compositions were found. These data are discussed with respect to a biogeographic model of the... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1152946 Fri, 11 Jan 2008 05:00:00 +0100 1152946 http://www.medworm.com/index.php?rid=1140243&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18180970%26dopt%3DAbstract Authors: Kleisner K Independent phenotypic emergence of superficially similar traits is a phenomenon frequently reported from investigations in the whole biota. Superficial similarity (including mimicry) is frequently explained as results of selective forces (predation or external environment). However, the mechanisms underlying independent (polyphyletic) emergence of similar phenotypic features remain largely unknown. A part of superficial similarity may emerge due to the occasional re-activation of latent genetic and/or developmental precursors. A specific kind of superficial similarity is represented by the phenomenon of mimicry that presupposes the attendance of a particular animal-interpreter. Despite diversity of ways how mimetic patterns are generated, they are structurally simi... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1140243 Tue, 08 Jan 2008 05:00:00 +0100 1140243 http://www.medworm.com/index.php?rid=1033692&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18008099%26dopt%3DAbstract A clash of traditions: the history of comparative and experimental embryology in Sweden as exemplified by the research of Gösta Jägersten and Sven Hörstadius. Theory Biosci. 2007 Dec;126(4):117-129 Authors: Olsson L Until the 1940s research traditions were often imported from Germany to Sweden, and young scientists went to German universities to learn new techniques and get in touch with the latest ideas. In developmental biology, the comparative, phylogenetic embryology advocated most forcefully by Ernst Haeckel co-existed with the "Entwickelungsmechanik" tradition developed by Wilhelm His, Wilheln Roux and others partly as a reaction to Haeckel's ideas. I use the zoology department at Uppsala University as a microcosmos to reflect the tensions between these tra... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1033692 Sat, 17 Nov 2007 14:29:08 +0100 1033692 http://www.medworm.com/index.php?rid=1015945&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17990017%26dopt%3DAbstract Authors: Gilbert SF, Levit GS PMID: 17990017 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1015945 Thu, 08 Nov 2007 05:00:00 +0100 1015945 http://www.medworm.com/index.php?rid=1015944&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17990018%26dopt%3DAbstract Authors: Reiß C, Springer S, Hoßfeld U, Olsson L, Levit GS PMID: 17990018 [PubMed - as supplied by publisher] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1015944 Thu, 08 Nov 2007 05:00:00 +0100 1015944 http://www.medworm.com/index.php?rid=1015943&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17990019%26dopt%3DAbstract Authors: Morange M The limited value most French biologists attributed to Darwinism and Mendelism in the first half of the twentieth century, and their conviction that these theories were at best insufficient to explain evolution and development, probably created conditions propitious to the development of Evo-devo at the end of the century. The separation between embryology and evolution did not exist in French biology as it did in American genetics: explanations for these two phenomena were sought equally in the "organization" of the egg. The major contribution of French biologists to Evo-devo was clearly the invention of the notion of the regulatory gene by Jacob and Monod; not the operon model per se, but the introduction of a hierarchy between two different kinds of genes. The con... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1015943 Thu, 08 Nov 2007 05:00:00 +0100 1015943 http://www.medworm.com/index.php?rid=1010704&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17985173%26dopt%3DAbstract The roots of Evo-Devo in Russia: Is there a characteristic "Russian Tradition"? Theory Biosci. 2007 Nov 6; Authors: Levit GS This paper raises the general question of whether there are any national peculiarities that characterize the scientific and philosophical roots of Russian-language evolutionary developmental biology. The researchers and theories are surveyed which, with hindsight, have been crucial for the Russian tradition when it comes to general methodological principles and constituting concepts. Based on published works and archival documents the main concepts of the "founding fathers" of the Russian tradition with their "Western analogues" are compared. The focus is on A. O. Kowalevsky (1840-1901), I. I. Metschnikov (1945-1916), A. N. Sewertzoff (1866-1936), I. I. S... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=1010704 Tue, 06 Nov 2007 05:00:00 +0100 1010704 http://www.medworm.com/index.php?rid=851695&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17472902%26dopt%3DAbstract Authors: Breidbach O, Ghiselin MT According to Anton Dohrn, evolutionary development was performed in a single progressive lineage where some proto-annelid initiated an evolutionary development that went straight on via annelids and lower vertebrates to man. From that line, a kind of metamorphosing nature, certain branches were derived, like protists or worms or even tunicates, which Dohrn thought off as degenerating groups. With that concept Dohrn came close to typological ideas of his time. Nevertheless, recent evo-devo literature seems to be influenced by Dohrn's outline of evolution. PMID: 17472902 [PubMed - in process] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851695 Tue, 01 May 2007 04:00:00 +0100 851695 http://www.medworm.com/index.php?rid=851701&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17412289%26dopt%3DAbstract Authors: Kutschera U, Niklas KJ The vast majority of angiosperms, including most of the agronomically important crop plants (wheat, etc.), assimilate CO(2) through the inefficient C(3) pathway of photosynthesis. Under ambient conditions these organisms loose about 1/3 of fixed carbon via photorespiration, an energetically wasteful process. Plants with C(4) photosynthesis (such as maize) eliminate photorespiration via a biochemical CO(2)-pump and thus have a larger rate of carbon gain. The genus Flaveria (yellowtops, Asteraceae) contains not only C(3) and C(4) species, but also many C(3)-C(4) intermediates, which have been interpreted as evolving from C(3) to fully expressed C(4) metabolism. However, the evolutionary significance of C(3)-C(4)Flaveria-intermediates has long been a matter... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851701 Sun, 01 Apr 2007 04:00:00 +0100 851701 http://www.medworm.com/index.php?rid=851700&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17412290%26dopt%3DAbstract Authors: Ay N, Krakauer DC We provide a geometric framework for investigating the robustness of information flows over biological networks. We use information measures to quantify the impact of knockout perturbations on simple networks. Robustness has two components, a measure of the causal contribution of a node or nodes, and a measure of the change or exclusion dependence, of the network following node removal. Causality is measured as statistical contribution of a node to network function, whereas exclusion dependence measures a distance between unperturbed network and reconfigured network function.We explore the role that redundancy plays in increasing robustness, and how redundacy can be exploited through error-correcting codes implemented by networks. We provide examples of the r... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851700 Sun, 01 Apr 2007 04:00:00 +0100 851700 http://www.medworm.com/index.php?rid=851699&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17412291%26dopt%3DAbstract Authors: Zawierta M, Biecek P, Waga W, Cebrat S In a simple computer model of population evolution, we have shown that frequency of recombination between haplotypes during the gamete production influences the effectiveness of the reproduction strategy. High recombination rates keeps the fraction of defective alleles low while low recombination rate or uneven distributed recombination spots change the strategy of genomes' evolution and result in the accumulation of heterozygous loci in the genomes. Even short fragment of chromosome with restricted recombination influences the genetic structure of neighboring regions. PMID: 17412291 [PubMed - in process] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851699 Sun, 01 Apr 2007 04:00:00 +0100 851699 http://www.medworm.com/index.php?rid=851698&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17412292%26dopt%3DAbstract Authors: Som A In this article, a new approach is presented for estimating the efficiencies of the nucleotide substitution models in a four-taxon case and then this approach is used to estimate the relative efficiencies of six substitution models under a wide variety of conditions. In this approach, efficiencies of the models are estimated by using a simple probability distribution theory. To assess the accuracy of the new approach, efficiencies of the models are also estimated by using the direct estimation method. Simulation results from the direct estimation method confirmed that the new approach is highly accurate. The success of the new approach opens a unique opportunity to develop analytical methods for estimating the relative efficiencies of the substitution models in a straigh... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851698 Sun, 01 Apr 2007 04:00:00 +0100 851698 http://www.medworm.com/index.php?rid=851697&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17412293%26dopt%3DAbstract Authors: Malarz K The phase diagrams survival-extinction for the Penna model with parameters: (mutations rate)-(birth rate), (mutation rate)-(harmful mutations threshold), (harmful mutation threshold)-(minimal reproduction age) are presented. The extinction phase may be caused by either mutational meltdown or overpopulation. When the Verhulst factor is responsible for removing only newly born babies and does not act on adults the overpopulation is avoided and only genetic factors may lead to species extinction. PMID: 17412293 [PubMed - in process] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851697 Sun, 01 Apr 2007 04:00:00 +0100 851697 http://www.medworm.com/index.php?rid=851696&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17412294%26dopt%3DAbstract Authors: Breidbach O, Ghiselin MT The paper tries to set right certain ideas about the history of evolutionary developmental biology. The main point is, that we had to enface the dominance of a comparative approach towards evolutionary developmental biology before 1900, which even later on was effective in Russia, for example, till the 1930s. The problem of the experimentalist approach set against this tradition was and is that there is no concept of gestalt that may allow to integrate the former comparative views and the modern mechanistic interpretations. We argue, that it would be wrong just to describe the comparative tradition as being outdated, as it may allow to get the framework for a dynamical concept of Gestalt that may integrate the ideas of morphogenesis and pattern formati... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851696 Sun, 01 Apr 2007 04:00:00 +0100 851696 http://www.medworm.com/index.php?rid=851706&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046370%26dopt%3DAbstract This article deals with the relationship between vocabulary (total number of distinct oligomers or "words") and text-length (total number of oligomers or "words") for a coding DNA sequence (CDS). For natural human languages, Heaps established a mathematical formula known as Heaps' law, which relates vocabulary to text-length. Our analysis shows that Heaps' law fails to model this relationship for CDSs. Here we develop a mathematical model to establish the relationship between the number of type of words (vocabulary) and the number of words sampled (text-length) for CDSs, when non-overlapping nucleotide strings with the same length are treated as words. We use tangent-hyperbolic function, which captures the saturation property of vocabulary. Based on the parameters of the model, we formulat... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851706 Tue, 01 Aug 2006 04:00:00 +0100 851706 http://www.medworm.com/index.php?rid=851705&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046371%26dopt%3DAbstract Authors: Breidbach O, Jost J We define a gestalt as the invariants of a collection of patterns that can mutually be transformed into each other through a class of transformations encoded by, or conversely, determining that gestalt. The class of these transformations needs to satisfy structural regularities like the ones of the mathematical structure of a group. This makes an analysis of a gestalt possible in terms of relations between its representing patterns. While the gestalt concept has its origins in cognitive psychology, it has also important implications for morphology. PMID: 17046371 [PubMed - indexed for MEDLINE] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851705 Tue, 01 Aug 2006 04:00:00 +0100 851705 http://www.medworm.com/index.php?rid=851704&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046372%26dopt%3DAbstract Authors: Jost J We study a learning rule based upon the temporal correlation (weighted by a learning kernel) between incoming spikes and the internal state of the postsynaptic neuron, building upon previous studies of spike timing dependent synaptic plasticity (Kempter, R., Gerstner, W., van Hemmen, J.L., Wagner, H., 1998. Extracting Oscillations: Neuronal coincidence detection with noisy periodic spike input. Neural computation 10, 1987-2017; Kempter, R., Gerstner, W., van Hemmen, J.L., 1999. Hebbian learning and spiking neurons. Physical Reviewm E59, 4498-4514; van Hemmen, J.L., 2001. Theory of synaptic plasticity. In: Moss, F., Gielen, S. (Eds.), Handbook of biological physics. vol. 4, Neuro Informatics, neural modelling, Elsevier, Amsterdam, pp. 771-823. Our learning rule for the s... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851704 Tue, 01 Aug 2006 04:00:00 +0100 851704 http://www.medworm.com/index.php?rid=851703&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046373%26dopt%3DAbstract Authors: Stauffer D, Rohde K Rapoport's rule claims that latitudinal ranges of plant and animal species are generally smaller at low than at high latitudes. However, doubts as to the generality of the rule have been expressed, because studies providing evidence against the rule are more numerous than those in support of it. In groups for which support has been provided, the trend of increasing latitudinal ranges with latitude is restricted to or at least most distinct at high latitudes, suggesting that the effect may be a local phenomenon, for example the result of glaciations. Here we test the rule using two models, a simple one-dimensional one with a fixed number of animals expanding in a northern or southerly direction only, and the evolutionary/ecological Chowdhury model using birt... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851703 Tue, 01 Aug 2006 04:00:00 +0100 851703 http://www.medworm.com/index.php?rid=851702&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046374%26dopt%3DAbstract Authors: Lipowski A, Lipowska D Twenty years ago, after analysing palaeontological data, Raup and Sepkoski suggested that mass extinctions on Earth appear cyclically in time with a period of approximately 26 million years (My). To explain the 26My period, a number of proposals were made involving, e.g., astronomical effects, increased volcanic activity, or the Earth's magnetic field reversal, none of which, however, has been confirmed. Here we study a spatially extended discrete model of an ecosystem and show that the periodicity of mass extinctions might be a natural feature of the ecosystem's dynamics and not the result of a periodic external perturbation. In our model, periodic changes of the diversity of an ecosystem and some of its other characteristics are induced by the coevolut... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851702 Tue, 01 Aug 2006 04:00:00 +0100 851702 http://www.medworm.com/index.php?rid=851716&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046360%26dopt%3DAbstract The conceptual framework of evolutionary morphology in the studies of Ernst Haeckel and Fritz Müller. Theory Biosci. 2006 Mar;124(3-4):265-80 Authors: Breidbach O In his Gastraea studies Ernst Haeckel characterized the initial stages of the animal embryo, describing complete and incomplete cleavages in various groups, until the gastrula stage. Thereby, he was able to point out various degrees of developmental diversification in these initial stages of development. As the functional meaning of such cleavages was not clear however, it was difficult to argue about putative functional adaptations. Information about the consequences for tissue formation initiated in this primary phase of development was simply lacking. Haeckel could only provide a vague picture of a highly dive... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851716 Wed, 01 Mar 2006 05:00:00 +0100 851716 http://www.medworm.com/index.php?rid=851715&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046361%26dopt%3DAbstract The history of essentialism vs. Ernst Mayr's "Essentialism Story": a case study of German idealistic morphology. Theory Biosci. 2006 Mar;124(3-4):281-307 Authors: Levit GS, Meister K Idealistic morphology as perhaps the most important historical manifestation of typology is very suitable for a historical analysis of Ernst Mayr's "Essentialism Story", which postulates an antagonism between "typological thinking" and "population thinking". We show that German-language idealistic-morphological theories consisted of two clearly distinguishable parts. The cornerstone of these theories was the concept of the type as an abstract pattern representing a certain class of phenomena and embodying the norm of this class. The primary objective of pure typology was to create a non-phylogeneti... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851715 Wed, 01 Mar 2006 05:00:00 +0100 851715 http://www.medworm.com/index.php?rid=851714&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046362%26dopt%3DAbstract Authors: Ghiselin MT How much, if anything, morphology contributed to the modern synthesis is partly a matter of how one defines that term. In the strict sense, morphology is a purely formal discipline and had very little to contribute. Morphology may also be considered a kind of data, and when it becomes functional a better case can be made for its role in evolutionary studies. Be that as it may, the incorporation of morphology into the synthesis was a later development. The initial focus was at the populational level, including the problems of speciation, which makes sense because that was where the opportunities seemed to be. As the synthesis evolved and matured it expanded its horizons and incorporated a larger range of topics. Very little discussion of morphology occurs in the can... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851714 Wed, 01 Mar 2006 05:00:00 +0100 851714 http://www.medworm.com/index.php?rid=851713&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046363%26dopt%3DAbstract Authors: Love AC Although the role of morphology in evolutionary theory remains a subject of debate, assessing the contributions of morphological investigation to evolutionary developmental biology (Evo-devo) is a more circumscribed issue of direct relevance to ongoing research. Historical studies of morphologically oriented researchers and the formation of the Modern Synthesis in the Anglo-American context identify a recurring theme: the synthetic theory of evolution did not capture multiple levels of biological organization. When this feature is incorporated into a philosophical framework for explaining the origin of evolutionary innovations and novelties (a core domain of inquiry in Evo-devo) two specific roles for morphology can be described: (1) the conceptualization and operation... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851713 Wed, 01 Mar 2006 05:00:00 +0100 851713 http://www.medworm.com/index.php?rid=851712&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046364%26dopt%3DAbstract Authors: Zachos FE, Hossfeld U Adolf Remane was primarily a morphologist and systematist. In 1952, he published an influential book on the foundations of systematics and phylogenetics in which he advocated homology as the central concept of morphology and the basis of the natural system and discussed criteria serving to discriminate homology from homoplasy in great detail. During the decades when the Modern Synthesis of evolution was created, he repeatedly commented on and criticised the synthetic theory of evolution, which he never fully accepted. Remane disapproved of idealistic morphology and was strongly opposed to Lamarckian, saltationist and orthogenetic theories of evolution. Yet, while appreciating the synthetic theory's validity in the realm of speciation and microevolution, h... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851712 Wed, 01 Mar 2006 05:00:00 +0100 851712 http://www.medworm.com/index.php?rid=851711&cid=s_36105_62_f&fid=36105&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17046365%26dopt%3DAbstract Authors: Theissen G Hopeful monsters are organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage. The Synthetic Theory of evolutionary biology has rejected the evolutionary relevance of hopeful monsters, but could not fully explain the mechanism and mode of macroevolution. On the other hand, several lines of evidence suggest that hopeful monsters played an important role during the origin of key innovations and novel body plans by saltational rather than gradual evolution. Homeotic mutants are identified as an especially promising class of hopeful monsters. Examples for animal and plant lineages that may have originated as hopeful monsters are given. Nevertheless, a brief review of the history of the concept of hopeful monsters reveals... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851711 Wed, 01 Mar 2006 05:00:00 +0100 851711