From Formation to Ecosystem: Tansley’s Response to Clements’ Climax

Arthur G. Tansley never accepted Frederic E. Clements’ view that succession is a developmental process whose final stage, the climax formation, is determined primarily by regional climate and that all other types of vegetation are some kind of successional stage or arrested successional stage. Tansley was convinced that in a given region a variety of environmental factors could produce different kinds of climax formations. At the heart of their dispute was Clements’ organicist view of succession, i.e., the formation was a complex organism with an ontogeny and phylogeny. As early as 1905, Tansley offered an alternative to Clements’ complex organism, the quasi-organism, but Clements in private and public rejected this compromise. Tansley and other plant ecologists continued to criticize Clements’ theories for the next 20 years, but with no impact on Clements. John Phillips, a South African plant ecologist who was a follower of Clements, published a series of papers in 1934 and 1935 defending Clementsian ecology. These papers were triggered by the publication of a letter by another ecologist working in Africa who claimed that there was a strong correlation between soils and various kinds of climax vegetation, which was contrary to what was predicted by Phillips and Clements. In 1935, Tansley published an attack on Phillips and Clements and their developmental theory of succession. In it, he proposed the concept of the ecosystem as a way to get around Clements’ monoclimax theory by making the physical environment (e.g., soil chemistry, soil texture, soil moisture) as important a factor as climate, plants and other organisms in determining the composition and characteristics of ecological entities, i.e., ecosystems. Tansley’s ecosystem concept quickly replaced Clements’ monoclimax theory as a dominant paradigm in ecology.     

From Peirce’s Semiotics to Information-Sign-Symbol

Peirce is the father of semiotics. However, his theory was developed long before the developments in information theory. The codification procedures studied by the latter turn out to be crucial also for biology. At the root of both information and semiosis there are equivalence classes. In the case of biological systems, we speak of functional equivalence classes. Equivalence classes represent the grid that organism impose on biochemical processes and signals of the external or internal environment. The whole feedback circuit that is built in this way allows information control. Symbolic systems represent another kind of dealing-with-information as far as they deal with the matching of our concepts with the world.     

The Controversy on Fish Pain: A Veterinarian’s Perspective

Fish welfare is still a relatively new field. As such, regulations and protocols to ensure fish welfare are currently limited and vary considerably in different jurisdictions. This is in part because of the ongoing controversy as to whether or not fish feel pain. This controversy has persisted for several years, yet veterinarians have been mostly absent from the discussion so far. This essay aims to address this issue. Here, it is argued that while this controversy has its place, it is unlikely to be resolved in the near future. Fish welfare could instead be improved by pursuing more clinically applicable research to increase knowledge of fishes’ behavior and physiology. Such research would assist in learning the optimal environment for their specific needs, as well as compiling some verified indicators of pain in fish. This would then lead to improved studies that could help to determine if and when analgesic drugs can be beneficial in fish, as they are in many other species.     

Testing Someone Else’s Intelligence: From Regimentation to Freedom1

This article discusses the trend in the development of testing from maximum regimentation of the test-takers’ activity (where they solve problems clearly formulated by the creator with a single correct answer) to diagnostic problematic situations that are very new and indefinite with an open beginning and an open end. With increasing frequency, the open beginning used in testing presupposes a freedom of independent formulation of one’s own research questions of the reality being studied and a search for answers while interacting with that reality. The emergence of mass testing of exploratory behavior is a reflection of the conviction that one of the key abilities that will be required in the very near future is the ability to cope with uncertainty and novelty, including by actively investigating them.

The discussion deals with the problems of testing intelligence and creativity in conditions of novelty and uncertainty, including the “judging problem.” It is pointed out that any thinking test, especially a test of creative thinking, is also an implicit (albeit perhaps not conscious) claim by its developers that their wisdom is virtually unsurpassed. After all, it is assumed that any person’s intelligence and creativity that unfold in a new situation may be described in the context of the model produced by the creative intellect of the test’s developer and, hence, by a more powerful “superintellect.” The errors that are practically inevitable with such an approach can be corrected in a dialog among various groups of researchers or, to the contrary, may be deepened if criticism is shut off.

The article analyzes a fundamental methodological error of creativity testing—the “standard list of creative answers” drawn up by the test-maker in advance, against which the participants’ solutions are checked. This error is explored in the case of an invention-oriented task in the international scholastic test PISA 2012, based on which the education ratings of countries are constructed.

An optimistic thesis is offered: no matter how successful testing is, humankind will never be fully prepared to determine its creative potential, due to its forward development. Without diagnostic tools, however, it will be far less prepared; they are a new and important part of that potential.     

The NCBI Databases: an Evolutionist’s Perspective

The National Center for Biotechnology Information (NCBI) organizes information resources for life scientists on an evolutionary scheme. This facilitates research about present-day organisms. The recent discovery of a new arenavirus, the LUJO virus, illustrates the utility of adopting evolution as a central architectural principle for life sciences databases: using the NCBI’s resources, clinicians were able to classify the new virus in real time—soon enough to aid in the diagnosis and treatment of a hemorrhagic fever caused by the LUJO virus. Topics fundamental to the study of evolution, often thought of as useless, are indeed vital because they inform how life science information ought to be organized.     

Pituitary Adenoma: A Clinician’S Perspective

ObjectiveTo review the underlying causes of pituitary lesions, a rational approach to their diagnosis, and therapeutic options.MethodsThe types of pituitary lesions and their clinical manifestations are reviewed, and treatment strategies and long-term follow-up are discussed.ResultsA pituitary adenoma is quite common and poses a challenge to the clinician to determine the clinical significance, the appropriate diagnosis, the need for treatment, and the appropriate therapy or therapies. The treatment of a pituitary adenoma depends on the type of tumor; a prolactinoma is treated medically with a dopamine agonist drug, and other lesions are usually treated by transsphenoidal surgical removal. Replacement of a deficient hormone or hormones is necessary for optimal functioning. Some patients require more than one treatment, including surgical intervention, replacement of a hormone or hormones, medications to lower hormone hypersecretion to normal (for prolactinoma, acromegaly, or Cushing disease), pituitary radiation therapy (optimally with focused irradiation such as the Gamma Knife or LINEAC), and, in the situation of persistent Cushing disease, bilateral adrenalectomy as a last resort. Lifelong monitoring is necessary for all these patients.ConclusionThe goal is to decrease the mass effect of the adenoma, to restore normal pituitary function, and to suppress hormone hypersecretion. Achievement of this goal necessitates the cooperation and interdisciplinary efforts of several medical specialties. (Endocr Pract. 2008;14:757-763)     

A Beginner’s Guide to Phylogenetics

Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet’s inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which exist in this rapidly expanding field of evolutionary biology.     

From Goethe’s plant archetype via Haeckel’s biogenetic law to plant evo-devo 2016

In 1790, the German poet Johann W. v. Goethe (1749–1832) proposed the concept of a hypothetical sessile organism known as the ‘Plant Archetype,’ which was subsequently reconstructed and depicted by 19th-century botanists, such as Franz Unger (1800–1870) and Julius Sachs (1832–1897), and can be considered one of the first expressions of Evo-Devo thinking. Here, we present the history of this concept in the context of Ernst Haeckel’s (1834–1919) biogenetic law espoused in his Generelle Morphologie der Organismen of 1866. We show that Haeckel’s idea of biological recapitulation may help to explain why various phenomena, such as the ontogenetic transformations in the stellar anatomy of lycopods and ferns, the transition from primary to secondary anatomy of seed plants, the presence of unfused juvenile cone scale segments in the Japanese cedar (Cryptomeria japonica), and the transition of C3- to C4-photosynthesis in the ontogeny of maize (Zea mays), appear to support his theories. In addition, we outline the current status of plant evolutionary developmental biology (Evo-Devo), which can be traced back to Haeckel's (1866) biogenetic law, with a focus on the model plant thale cress (Arabidopsis thaliana).     

A New Insight into Sanger’s Development of Sequencing: From Proteins to DNA, 1943–1977

Fred Sanger, the inventor of the first protein, RNA and DNA sequencing methods, has traditionally been seen as a technical scientist, engaged in laboratory bench work and not interested at all in intellectual debates in biology. In his autobiography and commentaries by fellow researchers, he is portrayed as having a trajectory exclusively dependent on technological progress. The scarce historical scholarship on Sanger partially challenges these accounts by highlighting the importance of professional contacts, institutional and disciplinary moves in his career, spanning from 1940 to 1983. This paper will complement such literature by focusing, for the first time, on the transition of Sanger’s sequencing strategies from degrading to copying the target molecule, which occurred in the late 1960s as he was shifting from protein and RNA to DNA sequencing, shortly after his move from the Department of Biochemistry to the Laboratory of Molecular Biology, both based in Cambridge (UK). Through a reinterpretation of Sanger’s papers and retrospective accounts and a pioneering investigation of his laboratory notebooks, I will claim that sequencing shifted from the working procedures of organic chemistry to those of the emergent molecular biology. I will also argue that sequencing deserves a history in its own right as a practice and not as a technique subordinated to the development of molecular biology or genomics. My proposed history of sequencing leads to a reappraisal of current STS debates on bioinformatics, biotechnology and biomedicine.     

From the editor’s desk

Improving cotton fibre quality is a major breeding goal for Upland cotton in China. To investigate the genetic mechanisms of fibre quality, a diverse panel of 403 Upland cotton accessions was grown, and the fibre quality traits were measured in six different environments. Genotyping was performed with genomewide simple sequence repeats. A total of 201 markers were polymorphic and generated 394 allele loci, and 403 accessions were arranged into two subgroups using Structure software. Of the marker loci, 18.94% showed significant linkage disequilibrium (\(P< 0.05\)). A mixed linear model in association mapping showed that 51 associations were significant between 39 polymorphic loci and five fibre quality traits, according to best linear unbiased prediction, and in at least three of six environments. Of the 39 associated marker loci, 12 were coincident with previous studies. There were 41 typical accessions identified as containing favourable allele loci related to fibre quality traits. The identified favourable QTL alleles and typical accessions for fibre quality are excellent genetic resources for future cotton breeding in China.     

From Membrane Pores to Aquaporins: 50 Years Measuring Water Fluxes

This review focuses on studies of water movement across biological membranes performed over the last 50 years. Different scientific approaches had tried to elucidate such intriguing mechanism, from hypotheses emphasizing the role of the lipid bilayer to the cloning of aquaporins, the ubiquitous proteins described as specific water channels. Pioneering and clarifying biophysical work are reviewed beside results obtained with the help of recent sophisticated techniques, to conclude that great advances in the subject live together with old questions without definitive answers.     

A Comprehensive,Simulation-Based Approach to Teaching Clinical Skills: The Medical Students’ Perspective

The purpose of this study was to determine if third-year medical students participating in a mandatory 12-week simulation course perceived improvement in decision-making, communication, and teamwork skills. Students participated in or observed 24 acute emergency scenarios. At 4-week intervals, students completed 0-10 point Likert scale questionnaires evaluating the curriculum and role of team leader. Linear contrasts were used to examine changes in outcomes. P-values were Bonferroni-corrected for multiple pairwise comparisons. Student evaluations (n = 96) demonstrated increases from week 4 to 12 in educational value (p = 0.006), decision-making (p < 0.001), communication (p = 0.02), teamwork (p = 0.01), confidence in management (p < 0.001), and translation to clinical experience (p < 0.001). Regarding the team leader role, students reported a decrease in stress (p = 0.001) and increase in ability to facilitate team function (p < 0.001) and awareness of team building (p = <0.001). Ratings demonstrate a positive impact of simulation on both clinical management skills and team leadership skills. A simulation curriculum can enhance the ability to manage acute clinical problems and translates well to the clinical experience. These positive perceptions increase as the exposure to simulation increases.     

Epigenetics in Alzheimer’s Disease: Perspective of DNA Methylation

Research over the years has shown that causes of Alzheimer’s disease are not well understood, but over the past years, the involvement of epigenetic mechanisms in the developing memory formation either under pathological or physiological conditions has become clear. The term epigenetics represents the heredity of changes in phenotype that are independent of altered DNA sequences. Different studies validated that cytosine methylation of genomic DNA decreases with age in different tissues of mammals, and therefore, the role of epigenetic factors in developing neurological disorders in aging has been under focus. In this review, we summarized and reviewed the involvement of different epigenetic mechanisms especially the DNA methylation in Alzheimer’s disease (AD), late-onset Alzheimer’s disease (LOAD), familial Alzheimer’s disease (FAD), and autosomal dominant Alzheimer’s disease (ADAD). Down to the minutest of details, we tried to discuss the methylation patterns like mitochondrial DNA methylation and ribosomal DNA (rDNA) methylation. Additionally, we mentioned some therapeutic approaches related to epigenetics, which could provide a potential cure for AD. Moreover, we reviewed some recent studies that validate DNA methylation as a potential biomarker and its role in AD. We hope that this review will provide new insights into the understanding of AD pathogenesis from the epigenetic perspective especially from the perspective of DNA methylation.     

From Carlquist’s ecological wood anatomy to Carlquist’s Law: why comparative anatomy is crucial for functional xylem biology

All students of xylem structure–function relations need to be familiar with the work of Sherwin Carlquist. He studies xylem through the lens of the comparative method, which uses the appearance of similar anatomical features under similar conditions of natural selection to infer function. “Function” in biology implies adaptation; maximally supported adaptation inferences require experimental and comparative xylem scientists to work with one another. Engaging with comparative inferences of xylem function will, more likely sooner rather than later, bring one to the work of Sherwin Carlquist. To mark his 90th birthday, I highlight just a few examples of his extraordinarily perceptive and general comparative insights. One is “Carlquist’s Law”, the pervasive tendency for vessels to be solitary when background cells are conductive. I cover his pioneering of “ecological” wood anatomy, viewing xylem variation as reflecting the effects of selection across climate and habit variation. Another is the embolism vulnerability–conduit diameter relationship, one of the most widely invoked structure–function relationships in xylem biology. I discuss the inferential richness within the notion of Carlquistian paedomorphosis, including detailed functional inferences regarding ray cell orientation. My final example comes from his very recent work offering the first satisfactory hypothesis accounting for the geographical and histological distribution of scalariform perforation plates as an adaptation, including “Carlquist’s Ratchet”, why scalariform plates are adaptive but do not re-evolve once lost. This extraordinarily rich production over six decades is filled with comparative inferences that should keep students of xylem function busy testing for decades to come.     

A Quantitative Approach to the Prioritization of Zoonotic Diseases in North America: A Health Professionals’ Perspective

Background

Currently, zoonoses account for 58% to 61% of all communicable diseases causing illness in humans globally and up to 75% of emerging human pathogens. Although the impact of zoonoses on animal health and public health in North America is significant, there has been no published research involving health professionals on the prioritization of zoonoses in this region.

Methodology/Principal Findings

We used conjoint analysis (CA), a well-established quantitative method in market research, to identify the relative importance of 21 key characteristics of zoonotic diseases for their prioritization in Canada and the US. Relative importance weights from the CA were used to develop a point-scoring system to derive a recommended list of zoonoses for prioritization in Canada and the US. Study participants with a background in epidemiology, public health, medical sciences, veterinary sciences and infectious disease research were recruited to complete the online survey (707 from Canada and 764 from the US). Hierarchical Bayes models were fitted to the survey data to derive CA-weighted scores for disease criteria. Scores were applied to 62 zoonotic diseases to rank diseases in order of priority.

Conclusions/Significance

We present the first zoonoses prioritization exercise involving health professionals in North America. Our previous study indicated individuals with no prior knowledge in infectious diseases were capable of producing meaningful results with acceptable model fits (79.4%). This study suggests health professionals with some knowledge in infectious diseases were capable of producing meaningful results with better-fitted models than the general public (83.7% and 84.2%). Despite more similarities in demographics and model fit between the combined public and combined professional groups, there was more uniformity across priority lists between the Canadian public and Canadian professionals and between the US public and US professionals. Our study suggests that CA can be used as a potential tool for the prioritization of zoonoses.     

Alzheimer’s Disease and Epilepsy: A Perspective on the Opportunities for Overlapping Therapeutic Innovation

Early-onset Alzheimer’s disease (AD) is associated with variants in amyloid precursor protein (APP) and presenilin (PSEN) 1 and 2. It is increasingly recognized that patients with AD experience undiagnosed focal seizures. These AD patients with reported seizures may have worsened disease trajectory. Seizures in epilepsy can also lead to cognitive deficits, neuroinflammation, and neurodegeneration. Epilepsy is roughly three times more common in individuals aged 65 and older. Due to the numerous available antiseizure drugs (ASDs), treatment of seizures has been proposed to reduce the burden of AD. More work is needed to establish the functional impact of seizures in AD to determine whether ASDs could be a rational therapeutic strategy. The efficacy of ASDs in aged animals is not routinely studied, despite the fact that the elderly represents the fastest growing demographic with epilepsy. This leaves a particular gap in understanding the discrete pathophysiological overlap between hyperexcitability and aging, and AD more specifically. Most of our preclinical knowledge of hyperexcitability in AD has come from mouse models that overexpress APP. While these studies have been invaluable, other drivers underlie AD, e.g. PSEN2. A diversity of animal models should be more frequently integrated into the study of hyperexcitability in AD, which could be particularly beneficial to identify novel therapies. Specifically, AD-associated risk genes, in particular PSENs, altogether represent underexplored contributors to hyperexcitability. This review assesses the available studies of ASDs administration in clinical AD populations and preclinical studies with AD-associated models and offers a perspective on the opportunities for further therapeutic innovation.