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. Sun, 21 Mar 2010 17:01:14 +0100 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 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 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 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 underlying notion of function, and whether this c... 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 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. Schmalhausen (1884-1963) and the parallelisms between them and E. Haeckel (1834-1919), V. Franz (1883-1950), and C. ... 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 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-phylogenetic classification system for living organisms based on structurally explicable characters. Thus, typology, as a non-phylogenetic foundation of idealistic morpholog... 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 http://www.medworm.com/index.php?rid=851710&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%3D17046366%26dopt%3DAbstract This article focuses on the interphyletic comparison of gene expression patterns. By means of the hypothesis of the inversion of the dorsoventral axis during the evolution of the Bilateria, it is demonstrated, that evolutionary developmental biologists use similarities in spatial and temporal gene expression patterns as evidence for the formulation of hypotheses of homology concerning either developing structures or body regions. The molecular genetic and morphogenetic evidence used is discussed within the framework of a cladistic-phylogenetic analysis based on the phylogenetic tree of the Bilateria. I argue that similarity of spatial and temporal gene expression patterns is not a sufficient criterion for homology inference. Therefore, gene expression patterns should be coded as characters... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851710 Wed, 01 Mar 2006 05:00:00 +0100 851710 http://www.medworm.com/index.php?rid=851709&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%3D17046367%26dopt%3DAbstract Authors: Wissemann V Johannes Reinke (1839-1931) was one of the most eminent and influential botanists, politician, philosopher and "anti-Haeckelist" of the 19th century. Educated in the mid 19th century he had faced revolutionary changes in the scientific understanding of the origin and evolution of life. Working mainly at the phenotypic level, Reinke was interested in the basic mechanisms and the guiding idea behind all processes which coordinated gene regulation and morphogenesis. What drove Reinke in his search of regulatory mechanisms for evolutionary patterns and processes was his religious belief. For the origin of the very first life, Reinke believed in creation but once life was established, evolution followed natural laws. This led to his early concept of "Dominanten" entitie... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851709 Wed, 01 Mar 2006 05:00:00 +0100 851709 http://www.medworm.com/index.php?rid=851708&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%3D17046368%26dopt%3DAbstract This article examines the origin of life on Earth and its connection to the Superstring Theory, that attempts to explain all phenomena in the universe (Theory of Everything) and unify the four known forces and relativity and quantum theory. The four forces of gravity, electro-magnetism, strong and weak nuclear were all present and necessary for the origin of life on the Earth. It was the separation of the unified force into four singular forces that allowed the origin of life. PMID: 17046368 [PubMed - indexed for MEDLINE] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851708 Wed, 01 Mar 2006 05:00:00 +0100 851708 http://www.medworm.com/index.php?rid=851707&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%3D17046369%26dopt%3DAbstract Authors: Ahmed E, Hashish AH We argued that immune system is an adaptive complex system. It is shown that it has emergent properties. Its network structure is of the small world network type. The network is of the threshold type, which helps in avoiding autoimmunity. It has the property that every antigen (e.g. virus or bacteria) is typically attacked by more than one effector. This stabilizes the equilibrium state. Modelling complex systems is discussed. Cellular automata (CA)-type models are successful, but there are much less analytic results about CA than about other less successful models e.g. partial differential equations (PDE). A compromise is proposed. PMID: 17046369 [PubMed - indexed for MEDLINE] (Source: Theory in Biosciences) Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851707 Wed, 01 Mar 2006 05:00:00 +0100 851707 http://www.medworm.com/index.php?rid=851725&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%3D17046350%26dopt%3DAbstract Authors: Ghiselin MT The recognition of correspondences has long been a fundamental activity among systematists. Advocates of Naturphilosophie, such as Lorenz Oken, drew far-fetched analogies between taxonomic groups and all sorts of other things, including the Persons of the Trinity. They treated change through time either as analogous to an ontogeny or as the product of divinely instituted laws of nature. Darwin changed things by making the taxonomic units strictly historical, implying that they are not classes but rather individuals in a broad metaphysical sense. That means that taxa are concrete, particular things, or wholes made up of parts which are themselves individuals, and that there are no laws of nature for them. Homology is a relationship of correspondence between parts of... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851725 Tue, 01 Nov 2005 05:00:00 +0100 851725 http://www.medworm.com/index.php?rid=851724&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%3D17046351%26dopt%3DAbstract Authors: Richter S Analyzing morphological characters in a phylogenetic context comprises two steps, character analysis and cladistic analysis, which are equivalent to two independent tests for hypotheses on homology. The concept of homology concerns comparable parts of the same or different organisms if their correspondences are the consequence of the same genetic or epigenetic information, and consequently of the same origin. The concept of homology is more inclusive than the character concept. Characters are seen as parts of transformation series. In the first step of morphological character analyses correspondences and non-correspondences between two characters are analyzed. A range of different examination methods and accurate study contribute to the severity of test. The hypothes... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851724 Tue, 01 Nov 2005 05:00:00 +0100 851724 http://www.medworm.com/index.php?rid=851723&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%3D17046352%26dopt%3DAbstract Authors: Scholtz G In this article the interface between development and homology is discussed. Development is here interpreted as a sequence of evolutionarily independent stages. Any approach stressing the importance of specific developmental stages is rejected. A homology definition is favoured which includes similarity, and complexity serves as a test for homology. Complexity is seen as the possibility of subdividing a character into evolutionarily independent corresponding substructures. Topology as a test for homology is critically discussed because corresponding positions are not necessarily indicative of homology. Complexity can be used twofold for homology assessments of development: either stages or processes of development are homologized. These two approaches must not be con... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851723 Tue, 01 Nov 2005 05:00:00 +0100 851723 http://www.medworm.com/index.php?rid=851722&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%3D17046353%26dopt%3DAbstract Authors: Olsson L, Ericsson R, Cerny R Vertebrate head development is a classical topic lately invigorated by methodological as well as conceptual advances. In contrast to the classical segmentalist views going back to idealistic morphology, the head is now seen not as simply an extension of the trunk, but as a structure patterned by different mechanisms and tissues. Whereas the trunk paraxial mesoderm imposes its segmental pattern on adjacent tissues such as the neural crest derivatives, in the head the neural crest cells carry pattern information needed for proper morphogenesis of mesodermal derivatives, such as the cranial muscles. Neural crest cells make connective tissue components which attach the muscle fiber to the skeletal elements. These crest cells take their origin from the... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851722 Tue, 01 Nov 2005 05:00:00 +0100 851722 http://www.medworm.com/index.php?rid=851721&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%3D17046354%26dopt%3DAbstract Authors: Wagner GP The identity of avian digits has been unresolved since the beginning of evolutionary morphology in the mid-19th century, i.e. as soon as questions of phylogenetic homology have been raised. The main source of concern is the persistent discrepancy between anatomical/paleontological and embryological evidence over the identity of avian digits. In this paper, recent evidence pertaining to the question of avian digit homology is reviewed and the various ideas of how to resolve the disagreement among developmental and phylogenetic evidence are evaluated. Paleontological evidence unequivocally supports the hypothesis that the fully formed digits of maniraptoran theropods are digits DI, DII, and DIII, because the phylogenetic position of Herrerasaurus is resolved, even when... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851721 Tue, 01 Nov 2005 05:00:00 +0100 851721 http://www.medworm.com/index.php?rid=851720&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%3D17046355%26dopt%3DAbstract Authors: Arendt D The evolution of the nervous system is one of the most fascinating, but also most nebulous fields of homology research. We do not know for example whether the last common ancestors of human, squid, and fly already possessed an elaborate brain and eyes, or rather had a simple, diffuse nervous system. Nevertheless, in the past decade molecular data has greatly advanced our understanding of bilaterian nervous system evolution. In this methodological review, I explain the four levels on which molecular genetic studies advance the quest for homologies between animal nervous systems. (I) Bioinformatic homology research elucidates the evolutionary history of gene families relevant for nervous system evolution such as the opsin superfamily. It tells us when and in what order ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851720 Tue, 01 Nov 2005 05:00:00 +0100 851720 http://www.medworm.com/index.php?rid=851719&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%3D17046356%26dopt%3DAbstract Authors: Theissen G Understanding the interrelationship between the phylogeny of developmental control genes and the evolution of morphological features is a central goal of evolutionary developmental biology (evo-devo). It requires that one distinguishes properly between gene genealogy and function. Gene duplication, gene loss and speciation in combination with differential changes in gene function can generate complex evolutionary scenarios that require additional terms beyond homology for a proper description. Use and possible misuse of these terms, including "orthology", "paralogy" and "subfunctionalization", is exemplified with AGAMOUS-like genes encoding transcription factors involved in flower and fruit development. This MADS-box gene subfamily demonstrates that homologous genes... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851719 Tue, 01 Nov 2005 05:00:00 +0100 851719 http://www.medworm.com/index.php?rid=851718&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%3D17046357%26dopt%3DAbstract Authors: Rutishauser R, Moline P Developmental biology and evolutionary studies have merged into evolutionary developmental biology ("evo-devo"). This synthesis already influenced and still continues to change the conceptual framework of structural biology. One of the cornerstones of structural biology is the concept of homology. But the search for homology ("sameness") of biological structures depends on our favourite perspectives (axioms, paradigms). Five levels of homology ("sameness") can be identified in the literature, although they overlap to some degree: (i) serial homology (homonomy) within modular organisms, (ii) historical homology (synapomorphy), which is taken as the only acceptable homology by many biologists, (iii) underlying homology (i.e., parallelism) in closely relat... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851718 Tue, 01 Nov 2005 05:00:00 +0100 851718 http://www.medworm.com/index.php?rid=851717&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%3D17046358%26dopt%3DAbstract Authors: Hossfeld U, Olsson L The homology concept has had a long and varied history, starting out as a geometrical term in ancient Greece. Here we describe briefly how a typological use of homology to designate organs and body parts in the same position anatomically in different organisms was changed by Darwin's theory of evolution into a phylogenetic concept. We try to indicate the diversity of opinions on how to define and test for homology that has prevailed historically, before the important books by Hennig (1950. Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin) and Remane (1952. Die Grundlagen des Natürlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Geest & Portig, Leipzig) brought more rigor into both the d... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851717 Tue, 01 Nov 2005 05:00:00 +0100 851717 http://www.medworm.com/index.php?rid=851730&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%3D17046345%26dopt%3DAbstract Authors: Kutschera U, Niklas KJ In 1905, the Russian biologist C. Mereschkowsky postulated that plastids (e.g., chloroplasts) are the evolutionary descendants of endosymbiotic cyanobacteria-like organisms. In 1927, I. Wallin explicitly postulated that mitochondria likewise evolved from once free-living bacteria. Here, we summarize the history of these endosymbiotic concepts to their modern-day derivative, the "serial endosymbiosis theory", which collectively expound on the origin of eukaryotic cell organelles (plastids, mitochondria) and subsequent endosymbiotic events. Additionally, we review recent hypotheses about the origin of the nucleus. Model systems for the study of "endosymbiosis in action" are also described, and the hypothesis that symbiogenesis may contribute to the generat... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851730 Mon, 01 Aug 2005 04:00:00 +0100 851730 http://www.medworm.com/index.php?rid=851729&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%3D17046346%26dopt%3DAbstract Authors: Lee SH, Wolpoff MH The problem of whether the hominid fossil sample of habiline specimens is comprised of more than one species has received much attention in paleoanthropology. The core of this debate has critical implications about when and how variation can be explained by taxonomy. In this paper, we examine the problem of whether the observed variation in habiline samples reflects species differences. We test the null hypothesis of no difference by examining the degree of variability in habiline sample in comparison with other single-species early hominid fossil samples from Sterkfontein and Swartkrans (Sterkfontein is earlier than the habiline sample, Swartkrans may be within the habiline time span). We developed a new method for this examination, which we call STandard E... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851729 Mon, 01 Aug 2005 04:00:00 +0100 851729 http://www.medworm.com/index.php?rid=851728&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%3D17046347%26dopt%3DAbstract Authors: Schetinin V, Schult J A new technique is presented developed to learn multi-class concepts from clinical electroencephalograms (EEGs). A desired concept is represented as a neuronal computational model consisting of the input, hidden, and output neurons. In this model the hidden neurons learn independently to classify the EEG segments presented by spectral and statistical features. This technique has been applied to the EEG data recorded from 65 sleeping healthy newborns in order to learn a brain maturation concept of newborns aged between 35 and 51 weeks. The 39,399 and 19,670 segments from these data have been used for learning and testing the concept, respectively. As a result, the concept has correctly classified 80.1% of the testing segments or 87.7% of the 65 records. ... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851728 Mon, 01 Aug 2005 04:00:00 +0100 851728 http://www.medworm.com/index.php?rid=851727&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%3D17046348%26dopt%3DAbstract Authors: Pfeiffer I, Brenig B, Kutschera U The phylogenetic relationships of erpobdellid leeches collected throughout Europe were investigated using newly obtained mitochondrial cytochrome c oxidase subunit I (CO-I) gene sequence data from 10 taxa. Monophyly of the five European Erpobdella species (sub-family Erpobdellinae) was supported, but a newly discovered leech, E. wuttkei Kutschera, 2004 (the smallest member of its genus, discovered in an aquarium) was only distantly related to this clade. Three members of the semiaquatic Trochetinae were included in this study. The largest European leech species discovered so far, Trocheta haskonis Grosser, 2000, was found to be a terrestrial predator that feeds on earthworms. The rare species T. haskonis is the sister taxon of T. bykowskii Ged... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851727 Mon, 01 Aug 2005 04:00:00 +0100 851727 http://www.medworm.com/index.php?rid=851726&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%3D17046349%26dopt%3DAbstract Authors: Shpak M It was shown by Gillespie [1974. Am. Nat. 108, 145-151], that if two genotypes produce the same average number of offspring on but have a different variance associated within each generation, the genotype with a lower variance will have a higher effective fitness. Specifically, the effective fitness is w(e)=w-sigma(2)/N, where w is the mean fitness, sigma(2) is the variance in offspring number, and N is the total population size. The model also predicts that if a strategy has a higher arithmetic mean fitness and a higher variance than the competitor, the outcome of selection will depend on the population size (with larger population sizes favoring the high-variance, high-mean genotype). This suggests that for metapopulations with large numbers of (relatively) small dem... Theory in Biosciences journals http://www.medworm.com/rss/comments.php?id=851726 Mon, 01 Aug 2005 04:00:00 +0100 851726