Subdiscipline Of Biology Research Articles

Do Christians Need to Reconcile Evolutionary Theory and Doctrines of Divine Providence and Creation?

Many Christian scholars have argued that standard versions of evolutionary theory and orthodox theological commitments can be reconciled. Some theistic evolutionists or “evolutionary creationists” have argued that evolutionary mechanisms such as random mutation and natural selection are nothing less than God’s way of creating. Though I dispute the logical coherence of these attempted reconciliations elsewhere, I argue here that there is little reason for Christians to attempt them, since an accumulating body of evidence from multiple subdisciplines of biology casts doubt on the creative power of the main evolutionary mechanisms. Thus, rather than addressing the question, “Can a meaningful doctrine of divine providence or creation be reconciled with mainstream evolutionary theory?” this essay will address the question of whether Christians should, or need to, attempt such a reconciliation at all.

Ecological networks: Pursuing the shortest path, however narrow and crooked

Representing data as networks cuts across all sub-disciplines in ecology and evolutionary biology. Besides providing a compact representation of the interconnections between agents, network analysis allows the identification of especially important nodes, according to various metrics that often rely on the calculation of the shortest paths connecting any two nodes. While the interpretation of a shortest paths is straightforward in binary, unweighted networks, whenever weights are reported, the calculation could yield unexpected results. We analyzed 129 studies of ecological networks published in the last decade that use shortest paths, and discovered a methodological inaccuracy related to the edge weights used to calculate shortest paths (and related centrality measures), particularly in interaction networks. Specifically, 49% of the studies do not report sufficient information on the calculation to allow their replication, and 61% of the studies on weighted networks may contain errors in how shortest paths are calculated. Using toy models and empirical ecological data, we show how to transform the data prior to calculation and illustrate the pitfalls that need to be avoided. We conclude by proposing a five-point check-list to foster best-practices in the calculation and reporting of centrality measures in ecology and evolution studies.

The Genetic Basis of Plant Functional Traits and the Evolution of Plant-Environment Interactions

Leaves are the most conspicuous organs of plants, and their form and function are key determinants of plant ecology. Moreover, energy captured by leaves through photosynthetic carbon reduction forms the base of nearly every terrestrial ecosystem. As such, the morphology and physiology of leaves have been a central focus of research on plant ecophysiology, development, and evolution. We review recent research on the genetic basis of leaf structure and nutrient profile, as well as stomatal patterning, as exemplar traits for understanding the evolution of plant functional traits. We discuss available and emerging methods for determining the genetic basis of plant traits and then present a synthetic assessment of the molecular basis of each trait and the extent to which patterns of natural diversity are relevant to ecoevolutionary analysis. Overall, we find that research on these three traits has emerged from different subdisciplines in biology. We have a deep understanding of the developmental genetics of leaf size and stomatal patterning and, to a lesser degree, leaf shape, though research on these has been limited to a small number of plant species. By contrast, there is a deep literature describing natural genetic diversity of leaf nitrogen content due, in part, to the ease of measuring this trait in large genetic mapping populations. The molecular control of leaf phosphorus concentration, on the other hand, has been severely understudied. For all three traits, there are few examples of studies that have empirically linked molecular genetic variation in specific genes with phenotypic diversity observed in natural populations of plants. We conclude by discussing present challenges with synthesizing different traditions in genetics, physiology, development, and evolution and prospects for progress in the coming years.

Less photoprotection can be good in some genetic and environmental contexts.

Antioxidant systems modulate oxidant-based signaling networks and excessive removal of oxidants can prevent beneficial acclimation responses. Evidence from mutant, transgenic, and locally adapted natural plant systems is used to interpret differences in the capacity for antioxidation and formulate hypotheses for future inquiry. We focus on the first line of chloroplast antioxidant defense, pre-emptive thermal dissipation of excess absorbed light (monitored as nonphotochemical fluorescence quenching, NPQ) as well as on tocopherol-based antioxidation. Findings from NPQ-deficient and tocopherol-deficient mutants that exhibited enhanced biomass production and/or enhanced foliar water-transport capacity are reviewed and discussed in the context of the impact of lower levels of antioxidation on plant performance in hot/dry conditions, under cool temperature, and in the presence of biotic stress. The complexity of cellular redox-signaling networks is related to the complexity of environmental and endogenous inputs as well as to the need for intensified training and collaboration in the study of plant-environment interactions across biological sub-disciplines.

Stress response and population dynamics: Is Allee effect hormesis?

Hormesis is a fundamental notion in ecotoxicology while competition between organisms is an essential notion in population ecology and species adaptation and evolution. Both sub-disciplines of ecology deal with the response of organisms to abiotic and biotic stresses. In ecotoxicology, the Linear-non-Threshold (LNT), Threshold and Hormetic models are used to describe the dominant responses of a plethora of endpoints to abiotic stress. In population ecology, the logistic, theta-logistic and the Allee effect models are used to describe the growth of populations under different responses to (biotic) stress induced by population density. The per capita rate of population increase (r) measures species fitness. When it is used as endpoint, the responses to population density seem to perfectly correspond to LNT, Threshold and Hormetic responses to abiotic stress, respectively. Our analysis suggests the Allee effect is a hormetic-like response of r to population density, an ultimate biotic stress. This biphasic dose-response model appears across different systems and situations (from molecules to tumor growth to population dynamics), is highly supported by ecological and evolutionary theory, and has important implications in most sub-disciplines of biology as well as in environmental and earth sciences. Joined multi-disciplinary efforts would facilitate the development and application of advanced research approaches for better understanding potential planetary-scale implications.

Wave-Particle Duality in Complex Quantum Systems.

Stunning progress in the experimental resolution and control of natural or man-made complex systems at the level of their quantum mechanical constituents raises the question, across diverse subdisciplines of physics, chemistry, and biology, whether the fundamental quantum nature may condition the dynamical and functional system properties on mesoscopic if not macroscopic scales. However, which are the distinctive signatures of quantum properties in complex systems, notably when modulated by environmental stochasticity and dynamical instabilities? It appears that, to settle this question across the above communities, a shared understanding is needed of the central feature of quantum mechanics: wave-particle duality. In this Perspective, we elaborate how randomness induced by this very quantum property can be discerned from the stochasticity ubiquitous in complex systems already on the classical level. We argue that in the study of increasingly complex systems, such distinction requires the analysis of single incidents of quantum dynamical processes.

Conservation metagenomics: a new branch of conservation biology.

Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.

How frequency-dependent selection affects population fitness, maladaptation and evolutionary rescue.

Frequency‐dependent (FD) selection is a central process maintaining genetic variation and mediating evolution of population fitness. FD selection has attracted interest from researchers in a wide range of biological subdisciplines, including evolutionary genetics, behavioural ecology and, more recently, community ecology. However, the implications of frequency dependence for applied biological problems, particularly maladaptation, biological conservation and evolutionary rescue remain underexplored. The neglect of FD selection in conservation is particularly unfortunate. Classical theory, dating back to the 1940s, demonstrated that frequency dependence can either increase or decrease population fitness. These evolutionary consequences of FD selection are relevant to modern concerns about population persistence and the capacity of evolution to alleviate extinction risks. But exactly when should we expect FD selection to increase versus decrease absolute fitness and population growth? And how much of an impact is FD selection expected to have on population persistence versus extinction in changing environments? The answers to these questions have implications for evolutionary rescue under climate change and may inform strategies for managing threatened populations. Here, we revisit the core theory of FD selection, reviewing classical single‐locus models of population genetic change and outlining short‐ and long‐run consequences of FD selection for the evolution of population fitness. We then develop a quantitative genetic model of evolutionary rescue in a deteriorating environment, with population persistence hinging upon the evolution of a quantitative trait subject to both frequency‐dependent and frequency‐independent natural selection. We discuss the empirical literature pertinent to this theory, which supports key assumptions of our model. We show that FD selection can promote population persistence when it aligns with the direction of frequency‐independent selection imposed by abiotic environmental conditions. However, under most scenarios of environmental change, FD selection limits a population's evolutionary responsiveness to changing conditions and narrows the rate of environmental change that is evolutionarily tolerable.

Publication Rates of Molecular Versus Non-Molecular Biologists: A Case Study of Seven Primarily Undergraduate Institutions

At many primarily undergraduate institutions, biology faculty members mentor student research collaborators. If publication is required for tenure and promotion, this research is expected to result in periodic publications; and publication rates are a common metric used to assess faculty productivity. However, we have uncovered a highly significant difference in the time required to publish articles based on biological sub-discipline. It takes, on average, twice as long for molecular biologists to publish articles than scholars from other sub-disciplines in biology. We believe that this analysis can be used to assess whether this phenomenon generalizes to other disciplines and/or other categories of institutions.

Curricula Influence College Student Knowledge and Attitudes Regarding Invasive Species

Negative impacts from invasive species present a global problem. Consequently, invasive species biology has emerged as an important subdiscipline of conservation biology. One of the goals of invasive species biology is to educate the public about impacts and potential control of invasive species. The purpose of this study was to determine if a lecture, a lecture and laboratory learning model, or both influence college student learning gains and whether increase in knowledge results in changes in attitudes about invasive species. A pre- and posttest instrument that measured knowledge and attitudes of invasive species was administered to several different classes of students at a university and community college. One group of students received a lecture and laboratory curriculum between the pre- and posttest (the lecture and laboratory treatment group). A second group of students received a lecture between the pre- and posttest (the lecture-only treatment group) and a third group received no instruction between tests (the control group). The lecture was in the form of an electronic presentation, whereas the laboratory curriculum included a case study, a visual aid, and a scavenger hunt to educate students about examples of invasive plant and animal species. In all classes and groups, there were at least 2 weeks between administering the pre- and posttest. Results showed that the control group scores were not different between the pre- and posttest. However, both the lecture-only and the lecture and laboratory treatment groups had scores that changed after receiving the curricula. In addition, there was an effect of curricula on student learning for the three conditions. The differences between the group that received no curricula vs. the two that did indicated that the curricula were effective teaching interventions to help students become more educated about invasive species.

Artificial Light Regulation of an Allosteric Bienzyme Complex by a Photosensitive Ligand.

The artificial regulation of proteins by light is an emerging subdiscipline of synthetic biology. Here, we used this concept to photocontrol both catalysis and allostery within the heterodimeric enzyme complex imidazole glycerol phosphate synthase (ImGP-S). ImGP-S consists of the cyclase subunit HisF and the glutaminase subunit HisH, which is allosterically stimulated by substrate binding to HisF. We show that a light-sensitive diarylethene (1,2-dithienylethene, DTE)-based competitive inhibitor in its ring-open state binds with low micromolar affinity to the cyclase subunit and displaces its substrate from the active site. As a consequence, catalysis by HisF and allosteric stimulation of HisH are impaired. Following UV-light irradiation, the DTE ligand adopts its ring-closed state and loses affinity for HisF, restoring activity and allostery. Our approach allows for the switching of ImGP-S activity and allostery during catalysis and appears to be generally applicable for the light regulation of other multienzyme complexes.

Management, Archiving, and Sharing for Biologists and the Role of Research Institutions in the Technology-Oriented Age

Data are one of the primary outputs of science. Although certain subdisciplines of biology have pioneered efforts to ensure their long-term preservation and facilitate collaborations, data continue to disappear, owing mostly to technological, regulatory, and ideological hurdles. In this article, we describe the important steps toward proper data management and archiving and provide a critical discussion on the importance of long-term data conservation. We then illustrate the rise in data archiving through the Joint Data Archiving Policy and the Dryad Digital Repository. In particular, we discuss data integration and how the limited availability of large-scale data sets can hinder new discoveries. Finally, we propose solutions to increase the rate of data preservation, for example by generating mechanisms insuring proper data management and archiving, by providing training in data management, and by transforming the traditional role of research institutions and libraries as data generators toward managers and archivers.

Citation Metrics and Impact Factors Fail as Measures of Scientific Quality, in Particular in Taxonomy, and are Biased by Biological Discipline and by Geographic and Taxonomic Factors

Based on my experience and analyses of citation frequencies of papers published in various biological journals, I discuss the use of citation counts and journal Impact Factors as measures of scientific quality. I conclude that citation frequency differs not only among biological sub-disciplines such as ecology and taxonomy, but also among taxonomic papers on highly similar topics, and that these latter differences largely depend on the organismal group (cryptogams vs. vascular plants and species-rich vs small genera and families) and the geographic region concerned. As a result, journals with a broad biological scope face difficulties in competing in terms of Impact Factors, and thus in competing for the best manuscripts, with journals specialized on particular sub-disciplines that attract many citations. However, since papers on “hot” topics also tend to be short-lived, these differences, at least in part, would be much reduced if citations were counted for longer periods of time or were compensated based on the average age of cited papers in the particular field. In particular in taxonomy, factors such as originality and innovativeness, generally regarded as measures of scientific quality, appear to be inversely correlated with citation frequency. I, therefore, conclude that scientific editors would be able to significantly increase the Impact Factors of taxonomic journals, not by choosing for publication the most scientifically valuable and supreme articles, but by picking manuscripts based the taxonomic position and geographic distribution of the organisms concerned. Still, the author sincerely hopes that no editor will ever take such measures!

Biodiversity is a chimera, and chimeras aren’t real

A recent article by Burch-Brown and Archer (Biol Philos, 2017) provides compelling arguments that biodiversity is either a natural kind or a pragmatically-valid scientific entity. I call into question three of these arguments. The first argument contends that biodiversity is a Homeostatic Property Cluster (HPC). I respond that there is no plausible homeostatic mechanism that would make biodiversity an HPC natural kind. The second argument proposes that biodiversity is a multiply-realizable functional kind. I respond that there is no shared function to ground this account. The final, and strongest, argument, is that biodiversity is an ineliminable explanans and explanandum in various subdisciplines of biology. I argue that once we look at the details of the relevant research, not only does biodiversity in a broad sense not function in explanatory roles, but we must eliminate biodiversity in favor of more specific concepts in order to make sense of the leading explanations in contemporary ecology and conservation science.

Virtual virus, a semester-long interdisciplinary project on the crossroads of creativity and knowledge integration.

Virtual virus is a semester-long interdisciplinary project offered as part of upper level elective course in virology. Students are challenged to apply key concepts from multiple biological sub-disciplines to 'synthesize' a plausible virtual virus. The project is executed as a scaffolded series of hands-on sessions and mini-projects that are integrated into continuous story leading to mock conference presentation and comprehensive report modeling article publication. It complements classroom instruction helping students to meet overarching learning targets traditionally associated undergraduate virology courses such as viral structure and function, mode of viral propagation and flow of genetic information and virus/host interactions on the cellular and organismal level. Formal instructor and informal peer feedback were used as tools to prompt reflection and guide revisions of the final report. Student learning gains and attitudes toward the approach were studied by evaluating project work product and end of the semester survey. Outcome analysis demonstrated that students exit the course with elaborated conceptual understanding of viruses and ownership of their work. The project can be viewed as an approach to model the process of scientific discovery in fast-forward mode by combining active learning, creativity and problem solving to assemble and communicate a virtual virus story.

Characterisation of the Context-Dependence of the Gene Concept in Research Articles

The purpose of this study is to interpret and qualitatively characterise the content in some research articles and evaluate cases of possible difference in meanings of the gene concept used. Using a reformulation of Hirst’s criteria of forms of knowledge, articles from five different sub-disciplines in biology (transmission genetic, molecular biology, genomics, developmental biology and population genetics) were characterised according to knowledge project, methods used and conceptual contexts. Depending on knowledge project, the gene may be used as a location of recombination, a target of regulatory proteins, a carrier of regulatory sequences, a cause in organ formation or a basis for a genetic map. Methods used range from catching wild birds and dissecting beetle larvae to growing yeast cells in 94 small wells as well as mapping of recombinants, doing statistical calculations, immunoblotting analysis of protein levels, analysis of gene expression with PCR, immunostaining of embryos and automated constructions of multi-locus linkage maps. The succeeding conceptual contexts focused around concepts as meiosis and chromosome, DNA and regulation, cell fitness and production, development and organ formation, conservation and evolution. These contextual differences lead to certain content leaps in relation to different conceptual schemes. The analysis of the various uses of the gene concept shows how differences in methodologies and questions entail a concept that escapes single definitions and “drift around” in meanings. These findings make it important to ask how science might use concepts as tools of specific inquiries and to discuss possible consequences for biology education.

A Student-Centered Framework for Teaching Undergraduate Parasitology

Many biology subdisciplines are re-evaluating their undergraduate curriculum amid changing student attitudes towards education. However, a modern framework for undergraduate parasitology has yet to be formally outlined. We present a student-centered approach to teaching parasitology, which diminishes the power of the lectern and emphasizes the use of active learning techniques.

Differences in Collaboration Patterns across Discipline, Career Stage, and Gender.

Collaboration plays an increasingly important role in promoting research productivity and impact. What remains unclear is whether female and male researchers in science, technology, engineering, and mathematical (STEM) disciplines differ in their collaboration propensity. Here, we report on an empirical analysis of the complete publication records of 3,980 faculty members in six STEM disciplines at select U.S. research universities. We find that female faculty have significantly fewer distinct co-authors over their careers than males, but that this difference can be fully accounted for by females’ lower publication rate and shorter career lengths. Next, we find that female scientists have a lower probability of repeating previous co-authors than males, an intriguing result because prior research shows that teams involving new collaborations produce work with higher impact. Finally, we find evidence for gender segregation in some sub-disciplines in molecular biology, in particular in genomics where we find female faculty to be clearly under-represented.

The Biologically-Based Bias of Personality Disorder Diagnosis.

The Biologically-Based Bias of Personality Disorder Diagnosis.

A Survey of Bioinformatics Database and Software Usage through Mining the Literature.

Computer-based resources are central to much, if not most, biological and medical research. However, while there is an ever expanding choice of bioinformatics resources to use, described within the biomedical literature, little work to date has provided an evaluation of the full range of availability or levels of usage of database and software resources. Here we use text mining to process the PubMed Central full-text corpus, identifying mentions of databases or software within the scientific literature. We provide an audit of the resources contained within the biomedical literature, and a comparison of their relative usage, both over time and between the sub-disciplines of bioinformatics, biology and medicine. We find that trends in resource usage differs between these domains. The bioinformatics literature emphasises novel resource development, while database and software usage within biology and medicine is more stable and conservative. Many resources are only mentioned in the bioinformatics literature, with a relatively small number making it out into general biology, and fewer still into the medical literature. In addition, many resources are seeing a steady decline in their usage (e.g., BLAST, SWISS-PROT), though some are instead seeing rapid growth (e.g., the GO, R). We find a striking imbalance in resource usage with the top 5% of resource names (133 names) accounting for 47% of total usage, and over 70% of resources extracted being only mentioned once each. While these results highlight the dynamic and creative nature of bioinformatics research they raise questions about software reuse, choice and the sharing of bioinformatics practice. Is it acceptable that so many resources are apparently never reused? Finally, our work is a step towards automated extraction of scientific method from text. We make the dataset generated by our study available under the CC0 license here: http://dx.doi.org/10.6084/m9.figshare.1281371.