Acta Biotheoretica最新文献

{"title":"Phylogenetic Inference and the Misplaced Premise of Substitution Rates","authors":"Kirk Fitzhugh","doi":"10.1007/s10441-021-09412-4","DOIUrl":"10.1007/s10441-021-09412-4","url":null,"abstract":"<div><p>Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 4","pages":"799 - 819"},"PeriodicalIF":1.3,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09412-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38955494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Mathematical Model of the Tuberculosis Epidemic","authors":"Ally Yeketi Ayinla,&nbsp;Wan Ainun Mior Othman,&nbsp;Musa Rabiu","doi":"10.1007/s10441-020-09406-8","DOIUrl":"10.1007/s10441-020-09406-8","url":null,"abstract":"<div><p>Tuberculosis has continued to retain its title as “the captain among these men of death”. This is evident as it is the leading cause of death globally from a single infectious agent. TB as it is fondly called has become a major threat to the achievement of the sustainable development goals (SDG) and hence require inputs from different research disciplines. This work presents a mathematical model of tuberculosis. A compartmental model of seven classes was used in the model formulation comprising of the susceptible S, vaccinated V, exposed E, undiagnosed infectious <i>I</i>₁, diagnosed infectious <i>I</i>₂, treated <i>T</i> and recovered R. The stability analysis of the model was established as well as the condition for the model to undergo backward bifurcation. With the existence of backward bifurcation, keeping the basic reproduction number less than unity <span>(({R_{0}}&lt;1))</span> is no more sufficient to keep TB out of the community. Hence, it is shown by the analysis that vaccination program, diagnosis and treatment helps to control the TB dynamics. In furtherance to that, it is shown that preference should be given to diagnosis over treatment as diagnosis precedes treatment. It is as well shown that at lower vaccination rate (0–20%), TB would still be endemic in the population. As such, high vaccination rate is required to send TB out of the community.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 3","pages":"225 - 255"},"PeriodicalIF":1.3,"publicationDate":"2021-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-020-09406-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38891053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary Processes Transpiring in the Stages of Lithopanspermia","authors":"Ian von Hegner","doi":"10.1007/s10441-021-09411-5","DOIUrl":"10.1007/s10441-021-09411-5","url":null,"abstract":"<div><p>Lithopanspermia is a theory proposing a natural exchange of organisms between solar system bodies as a result of asteroidal or cometary impactors. Research has examined not only the physics of the stages themselves but also the survival probabilities for life in each stage. However, although life is the primary factor of interest in lithopanspermia, this life is mainly treated as a passive cargo. Life, however, does not merely passively receive an onslaught of stress from surroundings; instead, it reacts. Thus, planetary ejection, interplanetary transport, and planetary entry are only the first three factors in the equation. The other factors are the quality, quantity, and evolutionary strategy of the transported organisms. Thus, a reduction in organism quantity in stage 1 might increase organism quality towards a second stress challenge in stage 3. Thus, robustness towards a stressor might in fact be higher in the bacterial population surviving after transport in stage 3 than at the beginning in stage 1. Therefore, the stages of lithopanspermia can themselves facilitate evolutionary processes that enhance the ability of the collected organisms to survive stresses such as pressure and heat shock. Thus, the multiple abiotic pressures that the population encounters through the three stages can potentially lead to very robust bacteria with survival capacities considerably higher than might otherwise be expected. This analysis details an outcome that is possible but probably rare. However, in addition to lithopanspermia, spacecraft mediated panspermia may also exist. The analogous stages in a spacecraft would result in a greater likelihood of increasing the stress tolerance of hitchhiking organisms. Furthermore, missions seeking life elsewhere will frequently be sent to places where the possibility of life as we know it is assumed to exist. Thus, we not only can transport terrestrial organisms to places where they are potentially more likely to survive but also may increase their invasive potential along the way. This analysis highlights further requirements that planetary protection protocols must implement and also provides a framework for analyses of ecological scenarios regarding the transmission of life, natural or artificial, between worlds in a solar system.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 4","pages":"783 - 798"},"PeriodicalIF":1.3,"publicationDate":"2021-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09411-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25588994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biology and Pragmatism: The Organism-Environment Bond","authors":"David Depew","doi":"10.1007/s10441-021-09410-6","DOIUrl":"10.1007/s10441-021-09410-6","url":null,"abstract":"<div><p>This review essay provides an analysis of the context and content of Trevor Pearce’s <i>Pragmatism’s Evolution</i>. The work highlights the bond between organisms and their environments.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 4","pages":"875 - 885"},"PeriodicalIF":1.3,"publicationDate":"2021-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09410-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43083643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cooperative Equilibrium in Biosphere Evolution: Reconciling Competition and Cooperation in Evolutionary Ecology","authors":"John Herring","doi":"10.1007/s10441-021-09409-z","DOIUrl":"10.1007/s10441-021-09409-z","url":null,"abstract":"<div><p>As our understanding of biological evolution continues to deepen, tension still surrounds the relationship between competition and cooperation in the evolution of the biosphere, with rival viewpoints often associated with the Red Queen and Black Queen hypotheses respectively. This essay seeks to reconcile these viewpoints by integrating observations of some general trends in biosphere evolution with concepts from game theory. It is here argued that biodiversity and ecological cooperation are intimately related, and that both tend to cyclically increase over biological history; this is likely due to the greater relative stability of cooperation over competition as a means of long-term conflict resolution within ecosystems. By integrating this view of the biosphere with existing models such as Niche Game Theory, it may be argued that competition and cooperation in ecosystems coexist at equilibria which shift preferentially towards increasing cooperation over biological history. This potentially points to a state of “cooperative equilibrium” as a limit or endpoint in long-term biosphere evolution, such that Black Queen and Red Queen behavior dominate different phases in an evolutionary movement towards optimal cooperative stability in ecological networks. This concept, if accepted, may also bear implications for developing future mathematical models in evolutionary biology, as well as for resolving the perennial debate regarding the relative roles of conflict and harmony in nature.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 4","pages":"629 - 641"},"PeriodicalIF":1.3,"publicationDate":"2021-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09409-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25375971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Can a More Variable Species Win Interspecific Competition?","authors":"Janusz Uchmański","doi":"10.1007/s10441-021-09408-0","DOIUrl":"10.1007/s10441-021-09408-0","url":null,"abstract":"<div><p>An individual-based approach is used to describe population dynamics. Two kinds of models have been constructed with different distributions illustrating individual variability. In both models, the growth rate of an individual and its final body weight at the end of the growth period, which determines the number of offspring, are functions of the amount of resources assimilated by an individual. In the model with a symmetric distribution, the half saturation constant in the Michaelis–Menten function describing the relationship between the growth of individuals and the amount of resources has a normal distribution. In the model with an asymmetric distribution, resources are not equally partitioned among individuals. The individual who acquired more resources in the past, will acquire more resources in the future. A single population comprising identical individuals has a very short extinction time. If individuals differ in the amount of food assimilated, this time significantly increases irrespectively of the type of model describing population dynamics. Individuals of two populations of competing species use common resources. For larger differences in individual variability, the more variable species will have a longer extinction time and will exclude less variable species. Both populations can also coexist when their variabilities are equal or even when they are slightly different, in the latter case under the condition of high variability of both species. These conclusions have a deterministic nature in the case of the model with the asymmetric distribution—repeated simulations give the same results. In the case of the model with the symmetric distribution, these conclusions are of a statistical nature—if we repeat the simulation many times, then the more variable species will have a longer extinction time more frequently, but some results will happen (although less often) when the less variable species has a longer extinction time. Additionally, in the model with the asymmetric distribution, the result of competition will depend on the way of the introduction of variability into the model. If the higher variability is due to an increase in the proportion of individuals with a low assimilation of resources, it can produce a longer extinction time of the less variable species.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 4","pages":"591 - 628"},"PeriodicalIF":1.3,"publicationDate":"2021-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-021-09408-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25365198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical Analysis of an Industrial HIV/AIDS Model that Incorporates Carefree Attitude Towards Sex","authors":"Baba Seidu,&nbsp;O. D. Makinde,&nbsp;Christopher S. Bornaa","doi":"10.1007/s10441-020-09407-7","DOIUrl":"10.1007/s10441-020-09407-7","url":null,"abstract":"<div><p>A nonlinear differential equation model is proposed to study the dynamics of HIV/AIDS and its effects on workforce productivity. The disease-free equilibrium point of the model is shown to be locally asymptotically stable when the associated basic reproduction number <span>(mathcal{{R}}_{0})</span> is less than unity. The model is also shown to exhibit multiple endemic states for some parameter values when <span>(mathcal{{R}}_{0}&lt;1)</span> and <span>(mathcal{{R}}_{0}&gt;1)</span>. Global asymptotic stability of the disease-free equilibrium is guaranteed only when the fractions of the Susceptible subclass populations are within some bounds. Optimal control analysis of the model revealed that the most cost effective strategy that should be adopted in the fight against HIV/AIDS spread within the workforce is one that seeks to prevent infections and the treatment of infected individuals.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 3","pages":"257 - 276"},"PeriodicalIF":1.3,"publicationDate":"2021-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-020-09407-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38865700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The comparative and the experimental revisited","authors":"Miguel García-Sancho","doi":"10.1007/s10441-020-09403-x","DOIUrl":"10.1007/s10441-020-09403-x","url":null,"abstract":"","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 3","pages":"493 - 495"},"PeriodicalIF":1.3,"publicationDate":"2021-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-020-09403-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50048640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Teaching Biologists the Philosophy of Their Time","authors":"Sophie Juliane Veigl","doi":"10.1007/s10441-020-09404-w","DOIUrl":"10.1007/s10441-020-09404-w","url":null,"abstract":"","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 3","pages":"483 - 491"},"PeriodicalIF":1.3,"publicationDate":"2021-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-020-09404-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50025396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Structure of Causal Explanations in Population Biology","authors":"Erik Weber,&nbsp;Roxan Degeyter","doi":"10.1007/s10441-020-09405-9","DOIUrl":"10.1007/s10441-020-09405-9","url":null,"abstract":"<div><p>The scope of this paper can be clarified by means of a well-known phenomenon that is usually called ‘industrial melanism’: the fact that the melanic form of the peppered moth became dominant in industrial areas in England in the second half of the nineteenth century. Such changes in relative phenotype frequencies are important explananda for population biologists. Apart from trying to explain such changes over time, population biologists also often try to explain differences between populations, e.g. why yellow shell colour is dominant in certain colonies of land snails and almost absent in other colonies. The causal explanations that are given to address such explananda are the objects of analysis in this paper. Our primary aim is to explicate their structure: we want to capture the typical ingredients of causal explanations in population biology, and their organisation. Based on this explication, we discuss how natural selection fits into recent mechanical philosophy of science, and engage in the debate on the nature of evolutionary theory.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"69 3","pages":"449 - 476"},"PeriodicalIF":1.3,"publicationDate":"2021-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10441-020-09405-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38820919","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}