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Theory in Biosciences, Theorie in Den Biowissenschaften

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https://www.readbyqxmd.com/read/30132255/the-emerging-structure-of-the-extended-evolutionary-synthesis-where-does-evo-devo-fit-in
#1
Alejandro Fábregas-Tejeda, Francisco Vergara-Silva
The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses...
August 21, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/30066215/some-theoretical-insights-into-the-hologenome-theory-of-evolution-and-the-role-of-microbes-in-speciation
#2
Adrian Stencel, Dominika M Wloch-Salamon
Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated...
July 31, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29992378/bioenergetics-of-life-disease-and-death-phenomena
#3
Andrzej Kasperski, Renata Kasperska
In this article, some new aspects of unified cell bioenergetics are presented. From the perspective of unified cell bioenergetics certain subsequent stages of cancer development, from initiation stage, through transformation to metastasis, are analyzed. Here we show that after transformation, cancer cells are permanently exposed to reactive oxygen species, that causes continual random DNA mutations and as a result genome and chromosomal destabilizations. The modern cancer attractor hypothesis has been extended in explaining cancer development...
July 10, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29978435/tetz-s-theory-and-law-of-longevity
#4
George Tetz, Victor Tetz
Here, we present new theory and law of longevity intended to evaluate fundamental factors that control lifespan. This theory is based on the fact that genes affecting host organism longevity are represented by subpopulations: genes of host eukaryotic cells, commensal microbiota, and non-living genetic elements. Based on Tetz's theory of longevity, we propose that lifespan and aging are defined by the accumulation of alterations over all genes of macroorganism and microbiome and the non-living genetic elements associated with them...
July 5, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29931521/phylogenetics-beyond-biology
#5
Nancy Retzlaff, Peter F Stadler
Evolutionary processes have been described not only in biology but also for a wide range of human cultural activities including languages and law. In contrast to the evolution of DNA or protein sequences, the detailed mechanisms giving rise to the observed evolution-like processes are not or only partially known. The absence of a mechanistic model of evolution implies that it remains unknown how the distances between different taxa have to be quantified. Considering distortions of metric distances, we first show that poor choices of the distance measure can lead to incorrect phylogenetic trees...
June 21, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29948922/systems-biology-of-eukaryotic-superorganisms-and-the-holobiont-concept
#6
Ulrich Kutschera
The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this "holistic view" of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype...
June 14, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29721787/an-optimal-stopping-approach-for-onset-of-fish-migration
#7
Hidekazu Yoshioka, Yuta Yaegashi
Comprehending life history of migratory fish, onset of migration in particular, is a key biological and ecological research topic that still has not been clarified. In this paper, we propose a simple mathematical model for the onset of fish migration in the context of a stochastic optimal stopping theory, which is a new attempt to our knowledge. Finding the criteria of the onset of migration reduces to solving a variational inequality of a degenerate elliptic type. As a first step of the new mathematical modeling, mathematical and numerical analyses with particular emphasis on whether the model is consistent with the past observation results of fish migration are examined, demonstrating reasonable agreement between the theory and observation results...
May 2, 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29616406/georgy-gause-s-shift-from-ecology-and-evolutionary-biology-to-antibiotics-research-reasons-objectives-circumstances
#8
Nataliia Kodash, Martin Fischer
Georgy Gause (1910-1986) is best known for his contribution to ecology and evolutionary theory. His book "The Struggle for Existence" (1934) inspired generations of ecologists. Yet his scientific interests were diverse, embracing many aspects of the life sciences and medicine. The most notable shift in his research took place in the early 1940s when he began to study antibiotics and discovered Gramicidin S. Superficially, this shift looked like an attempt to switch from purely theoretical to applied research during the years of World War II, but Gause's decision may also have been seriously affected by the "Great Purge" and the growth of Lysenkoism...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29572780/mathematical-modeling-of-cancer-immune-system-considering-the-role-of-antibodies
#9
Sumana Ghosh, Sandip Banerjee
A mathematical model for the quantitative analysis of cancer-immune interaction, considering the role of antibodies has been proposed in this paper. The model is based on the clinical evidence, which states that antibodies can directly kill cancerous cells (Ivano et al. in J Clin Investig 119(8):2143-2159, 2009). The existence of transcritical bifurcation, which has been proved using Sotomayor theorem, provides strong biological implications. Through numerical simulations, it has been illustrated that under certain therapy (like monoclonal antibody therapy), which is capable of altering the parameters of the system, cancer-free state can be obtained...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29532441/self-complementary-circular-codes-in-coding-theory
#10
Elena Fimmel, Christian J Michel, Martin Starman, Lutz Strüngmann
Self-complementary circular codes are involved in pairing genetic processes. A maximal [Formula: see text] self-complementary circular code X of trinucleotides was identified in genes of bacteria, archaea, eukaryotes, plasmids and viruses (Michel in Life 7(20):1-16 2017, J Theor Biol 380:156-177, 2015; Arquès and Michel in J Theor Biol 182:45-58 1996). In this paper, self-complementary circular codes are investigated using the graph theory approach recently formulated in Fimmel et al. (Philos Trans R Soc A 374:20150058, 2016)...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29488055/the-evolutionary-origin-of-chordate-segmentation-revisiting-the-enterocoel-theory
#11
REVIEW
Takayuki Onai
One of the definitive characteristics of chordates (cephalochordates, vertebrates) is the somites, which are a series of paraxial mesodermal blocks exhibiting segmentation. The presence of somites in the basal chordate amphioxus and in vertebrates, but not in tunicates (the sister group of vertebrates), suggests that the tunicates lost the somites secondarily. Somites are patterned from anterior to posterior during embryogenesis. How such a segmental pattern evolved from deuterostome ancestors is mysterious...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29159683/interaction-rates-vital-rates-background-fitness-and-replicator-dynamics-how-to-embed-evolutionary-game-structure-into-realistic-population-dynamics
#12
K Argasinski, M Broom
In this paper we are concerned with how aggregated outcomes of individual behaviours, during interactions with other individuals (games) or with environmental factors, determine the vital rates constituting the growth rate of the population. This approach needs additional elements, namely the rates of event occurrence (interaction rates). Interaction rates describe the distribution of the interaction events in time, which seriously affects the population dynamics, as is shown in this paper. This leads to the model of a population of individuals playing different games, where focal game affected by the considered trait can be extracted from the general model, and the impact on the dynamics of other events (which is not neutral) can be described by an average background fertility and mortality...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29147851/bijective-codon-transformations-show-genetic-code-symmetries-centered-on-cytosine-s-coding-properties
#13
Hervé Seligmann
Homology of some RNAs with template DNA requires systematic exchanges between nucleotides. Such exchanges produce 'swinger' RNA along 23 bijective transformations (nine symmetric, X ↔ Y; and 14 asymmetric, X → Y → Z → X, for example A ↔ C and A → C → G → A, respectively). Here, analyses compare amino acids coded by swinger-transformed codons to those coded by untransformed codons, defining coding invariance after transformations. Swinger transformations cluster according to coding invariance in four groups characterized by transformations into cytosine (C = C, T → C, A → C, and G → C)...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/29086163/process-analysis-of-carcinogenesis-concept-derivation-of-the-tissue-function-preservation-of-a-homogeneous-gene-expression
#14
Thomas Löser
A new system for maintaining homogeneous gene expression in tissue and for destroying through apoptosis nonconforming cells is introduced. This functionality is called the "similarity comparison." Accordingly, the survival of mutated cells is hindered due to reduced gene expression. That, in turn, maintains the homogeneity of the tissue and prevents tumors from developing. The concept of the similarity comparison is that every stationary cell in every tissue constantly screens the gene expression of its neighbors...
April 2018: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28963715/addition-to-special-issue-in-commemoration-of-olaf-breidbach-part-ii
#15
EDITORIAL
Sabine Schwarz
No abstract text is available yet for this article.
December 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28776127/on-the-global-stability-of-an-epidemic-model-of-computer-viruses
#16
Mohammad Reza Parsaei, Reza Javidan, Narges Shayegh Kargar, Hassan Saberi Nik
In this paper, we study the global properties of a computer virus propagation model. It is, interesting to note that the classical method of Lyapunov functions combined with the Volterra-Lyapunov matrix properties, can lead to the proof of the endemic global stability of the dynamical model characterizing the spread of computer viruses over the Internet. The analysis and results presented in this paper make building blocks towards a comprehensive study and deeper understanding of the fundamental mechanism in computer virus propagation model...
December 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28721495/diversity-and-survival-of-artificial-lifeforms-under-sedimentation-and-random-motion
#17
Nicolas Glade, Olivier Bastien, Pascal Ballet
Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures...
December 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28631149/vigor-of-survival-determinism-subtle-evolutionary-gradualism-interspersed-with-robust-phylogenetic-leaping
#18
Pavle Krsmanovic
Discussions of the survival determinism concept have previously focused on its primary role in the evolution of early unicellular organisms in the light of findings which have been reported on a number of diseases. The rationale for such parallel was in the view according to which multicellular organisms could be regarded as sophisticated colonies of semi-autonomous, single-celled entities, whereby various diseases were described as conditions arising upon the activation of the respective survival mechanisms in a milieu unsuitable for such robust stress response...
December 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28612184/autopolyploidy-leads-to-rapid-genomic-changes-in-arabidopsis-thaliana
#19
Shihong Liu, Yan Yang, Fang Wei, Jifa Duan, Janeen Braynen, Baoming Tian, Gangqiang Cao, Gongyao Shi, Jiachen Yuan
Polyploidy is a widespread feature of plant genomes. As a typical model of polyploidy, autopolyploidy has been postulated evolutionary dead ends and received little attention compared with allopolyploidy. For the limited data available so far, the evolutionary outcome of genome diversity in autopolyploids remains controversial in comparison with its diploid ancestors. In the present study, the effects of autopolyploidy on genome diversity were revealed at a genome-wide scale by comparative analyses of polymorphism between Arabidopsis autopolyploids (autotetraploids and autotriploids) and related diploids within the first ten successive inbred generations using amplified fragment length polymorphism...
December 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
https://www.readbyqxmd.com/read/28597395/correlates-and-catalysts-of-hominin-evolution-in-africa
#20
Jeffrey K McKee
Hominin evolution in the African Pliocene and Pleistocene was accompanied and mediated by changes in the abiotic and biotic spheres. It has been hypothesized that such environmental changes were catalysts of hominin morphological evolution and speciations. Whereas there is little doubt that ecological changes were relevant to shaping the trajectories of mammalian evolution, testing specific hypotheses with data from the fossil record has yielded ambiguous results regarding environmental disruption as a primary catalyst...
December 2017: Theory in Biosciences, Theorie in Den Biowissenschaften
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