The ‘requirement of total evidence’ and its role in phylogenetic systematics

The question of whether or not to partition data for the purposes of inferring phylogenetic hypotheses remains controversial. Opinions have been especially divided since Kluge's (1989, Systematic Zoology 38, 7–25) claim that data partitioning violates the requirement of total evidence (RTE). Unfortunately, advocacy for or against the RTE has not been based on accurate portrayals of the requirement. The RTE is a basic maxim for non-deductive inference, stipulating that evidence must be considered if it has relevance to an inference. Evidence is relevant if it has a positive or negative effect on a given conclusion. In the case of ℈partitioned’ phylogenetic inferences, the RTE is violated, and the basis for rational belief in any conclusion is compromised, unless it is shown that the partitions are evidentially irrelevant to one another. The goal of phylogenetic systematics is to hypothesize past causal conditions to account for observed shared similarities among two or more species. Such inferences are non-deductive, necessitating consideration of the RTE. Some phylogeneticists claim the parsimony criterion as justification for the RTE. There is no relation between the two – parsimony is a relation between a hypothesis and causal question(s). Parsimony does not dictate the content of premises prior to an inference. ℈Taxonomic congruence,’ ℈supertrees,’ and ℈conditional combination’ methods violate the RTE. Taxonomic congruence and supertree methods also fail to achieve the intended goal of phylogenetic inference, such that ℈consensus trees’ and ℈supertrees’ lack an empirical basis. ℈Conditional combination’ is problematic because hypotheses derived from partitioned data cannot be compared – a causal hypothesis inferred to account for a set of effects only has relevance to those effects, not any comparative relevance to other causal hypotheses. A similar problem arises in the comparisons of hypotheses derived from different causal theories.     

Measuring salinity by conductivity

The simple conductivity method described here uses a home-made electrode for determining the salinity of estuarine waters     

The Importance of Type II Error and Falsifiability

Aim. Before intergovernmental consensus under the Rio Declaration in 1992, ignorance of type I errors had been disfavoured in science. However, the Precautionary Principle (PP) counsels the avoidance of type II errors, rather than of type I errors. We need a new academic code for the PP. Material and methods. The risk of extinction has usually been evaluated based on conservative estimates of the present population size. I define the weight of evidence as the extinction risk of Japanese vascular plants based on unbiased estimates. Catch quotas in the fisheries are usually decided by precautionary approach. I calculate the long-term yield and risk of stock collapse under a simple stock dynamics model. Results. The weight of evidence depends on the frequency of grids with size unknown. In a few plant species, rankings based on conservative estimates have differed from rankings based on unbiased estimates. In fishery management, a catch quota based on a precautionary approach proved neither sufficient nor necessary to avoid stock collapse. The precautionary approach is one of the reasons that prevent us from maximizing a sustainable yield. Conclusions. We need to clarify the endpoint of risks, and check whether it is necessary to adopt a PP. We can obtain the weight of evidence that is measured under unbiased estimates, while the risk based on a PP is measured under conservative estimates.     

Predictors of Species Sensitivity to Fragmentation

We reviewed empirical data and hypotheses derived from demographic, optimal foraging, life-history, community, and biogeographic theory for predicting the sensitivity of species to habitat fragmentation. We found 12 traits or trait groups that have been suggested as predictors of species sensitivity: population size; population fluctuation and storage effect; dispersal power; reproductive potential; annual survival; sociality; body size; trophic position; ecological specialisation, microhabitat and matrix use; disturbance and competition sensitive traits; rarity; and biogeographic position. For each trait we discuss the theoretical justification for its sensitivity to fragmentation and empirical evidence for and against the suitability of the trait as a predictor of fragmentation sensitivity. Where relevant, we also discuss experimental design problems for testing the underlying hypotheses. There is good empirical support for 6 of the 12 traits as sensitivity predictors: population size; population fluctuation and storage effects; traits associated with competitive ability and disturbance sensitivity in plants; microhabitat specialisation and matrix use; rarity in the form of low abundance within a habitat; and relative biogeographic position. Few clear patterns emerge for the remaining traits from empirical studies if examined in isolation. Consequently, interactions of species traits and environmental conditions must be considered if we want to be able to predict species sensitivity to fragmentation. We develop a classification of fragmentation sensitivity based on specific trait combinations and discuss the implications of the results for ecological theory.     

Transforming scientific evidence into better consumer choices

Translational research using evidence-based and comparative effectiveness research continues to evolve, becoming a useful tool in improving informed consent and decision-making in the clinical setting. While in development, emerging technologies, including cellular and molecular biology, are leading to establishing evidence-based dental practices. One emerging technology, which conjoins bench proteomic findings to clinical decision-making for treatment intervention, is the Translational Evidence Mechanism. This mechanism was developed to be a foundation for a compact between researcher, translational researcher, clinician, and patient. The output of such a mechanism is the clinical practice guideline (CPG), an interactive tool for dentists and patients to game evidence in reaching optimum clinical decisions that correspond to individual patient preferences and values. As such, the clinical practice guideline requires the vesting of decision, utility, and cost best evidence. Evidence-based research provides decision data, a first attempt at supporting decision-making by providing best outcome data. Since then comparative effectiveness research has emerged, using systematic review analysis to compare similar treatments or procedures in maximizing the choice of the most effective cost/benefit option within the context of best evidence. With innovation in the clinical practice guideline for optimizing efficacy and comparative effectiveness research, evidence-based practices will shape a new approach to health-based systems that adhere to shared decision-making between bench scientists, healthcare providers and patients.     

Assessment of biology investigations

The restricted range of biology investigations submitted for assessment in England and Wales, almost exclusively laboratory-based and with very little fieldwork, can be seen as a consequence of Sc1 being perceived as a skills-based performance model. An alternative approach to procedural understanding conceptualises investigations as the process of utilising a knowledge base, the Concepts of Evidence. Four biology investigations set in different contexts are analysed in this paper and the Concepts of Evidence used are shown to be very similar for each. However, the sequence in which ideas are used and actions occur differs between lab-based investigations and fieldwork. A case is made for the assessment of investigations against the Concepts of Evidence in written tests as being potentially a more reliable and valid way of assessing the ideas used in all types of biology investigations, thus reducing the distorting effect of assessment on the curriculum.     

A weight of evidence approach for selecting exposure biomarkers for biomonitoring

Context: It is known that there are usually several biomarkers and/or medium combinations that can be applied to answer a specific exposure question. To help determine an appropriate combination for the specific question, we have developed a weight-of-evidence Framework that provides a relative appropriateness score for competing combinations.

Methods: The Framework is based on an expert assessor’s evaluation of the relevance and suitability of the biomarker and medium for the question based on a set of criteria. We provide a computer based modeling tool to guide the researcher through the process.

Results: We present an example with six biomarkers of benzene exposure in one matrix; the six are either the most commonly used biomarkers and/or have recent widespread usage. The example clearly demonstrates the usefulness of the Framework for scoring the choices, as well as the transparency of the method that provides the basis for discussion.

Conclusions: The Framework provides for the first time a method to transparently document the rationale behind selecting, from among a set of alternatives, the most scientifically supportable exposure biomarker to address a specific biomonitoring question, thus providing a reproducible account of expert opinions on the suitability of a biomarker.     

The Weight of Evidence Does Not Support the Listing of Styrene as “Reasonably Anticipated to be a Human Carcinogen” in NTP's Twelfth Report on Carcinogens

Styrene was listed as “reasonably anticipated to be a human carcinogen” in the twelfth edition of the National Toxicology Program's Report on Carcinogens based on what we contend are erroneous findings of limited evidence of carcinogenicity in humans, sufficient evidence of carcinogenicity in experimental animals, and supporting mechanistic data. The epidemiology studies show no consistent increased incidence of, or mortality from, any type of cancer. In animal studies, increased incidence rates of mostly benign tumors have been observed only in certain strains of one species (mice) and at one tissue site (lung). The lack of concordance of tumor incidence and tumor type among animals (even within the same species) and humans indicates that there has been no particular cancer consistently observed among all available studies. The only plausible mechanism for styrene-induced carcinogenesis—a non-genotoxic mode of action that is specific to the mouse lung—is not relevant to humans. As a whole, the evidence does not support the characterization of styrene as “reasonably anticipated to be a human carcinogen,” and styrene should not be listed in the Report on Carcinogens.     

Biochemical evidence accumulates across neurons to drive a network-level eruption

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Restoration Ecology's silver jubilee: innovation,debate, and creating a future for restoration ecology

At a time when the science and practice of restoration ecology is adapting to ongoing environmental and social change, innovations in both methods and concepts are essential. Encouraging innovation means allowing open debate about alternative approaches that may add to the toolbox available for restoration. Such approaches are usually being examined as additions to, rather than substitutes for, traditional restoration practices. Recent debate has focused on the scope and intent of restoration as defined in documents such as the Society for Ecological Restoration Standards. There is a mismatch between the default aim in the standards of full restoration to a native reference system and the goals of international restoration efforts that have a broader and more functional focus. The next generation of restoration scientists and practitioners will need to navigate these issues to ensure that restoration remains effective and relevant. This will require, amongst other things, ongoing learning, sharing information and insights, humility, objectivity, continuous examination of assumptions, and questioning current practices and perspectives.