Commentary: statistics for biomarkers

This short commentary discusses Biomarkers' requirements for the reporting of statistical analyses in submitted papers. It is expected that submitters will follow the general instructions of the journal, the more detailed guidance given by the International Committee of Medical Journal Editors, the specific guidelines developed by the EQUATOR network, and those of various specialist groups. Biomarkers expects that the study design and subsequent statistical analyses are clearly reported and that the data reported can be made available for independent assessment. The journal recognizes that there is continuing debate about different approaches to statistical science. Biomarkers appreciates that the field continues to develop rapidly and encourages the use of new methodologies.     

A systematic assessment of normalization approaches for the Infinium 450K methylation platform

The Illumina Infinium HumanMethylation450 BeadChip has emerged as one of the most popular platforms for genome wide profiling of DNA methylation. While the technology is wide-spread, systematic technical biases are believed to be present in the data. For example, this array incorporates two different chemical assays, i.e., Type I and Type II probes, which exhibit different technical characteristics and potentially complicate the computational and statistical analysis. Several normalization methods have been introduced recently to adjust for possible biases. However, there is considerable debate within the field on which normalization procedure should be used and indeed whether normalization is even necessary. Yet despite the importance of the question, there has been little comprehensive comparison of normalization methods. We sought to systematically compare several popular normalization approaches using the Norwegian Mother and Child Cohort Study (MoBa) methylation data set and the technical replicates analyzed with it as a case study. We assessed both the reproducibility between technical replicates following normalization and the effect of normalization on association analysis. Results indicate that the raw data are already highly reproducible, some normalization approaches can slightly improve reproducibility, but other normalization approaches may introduce more variability into the data. Results also suggest that differences in association analysis after applying different normalizations are not large when the signal is strong, but when the signal is more modest, different normalizations can yield very different numbers of findings that meet a weaker statistical significance threshold. Overall, our work provides useful, objective assessment of the effectiveness of key normalization methods.     

Consolidated strategy for the analysis of microarray spike-in data

As the number of users of microarray technology continues to grow, so does the importance of platform assessments and comparisons. Spike-in experiments have been successfully used for internal technology assessments by microarray manufacturers and for comparisons of competing data analysis approaches. The microarray literature is saturated with statistical assessments based on spike-in experiment data. Unfortunately, the statistical assessments vary widely and are applicable only in specific cases. This has introduced confusion into the debate over best practices with regards to which platform, protocols and data analysis tools are best. Furthermore, cross-platform comparisons have proven difficult because reported concentrations are not comparable. In this article, we introduce two new spike-in experiments, present a novel statistical solution that enables cross-platform comparisons, and propose a comprehensive procedure for assessments based on spike-in experiments. The ideas are implemented in a user friendly Bioconductor package: spkTools. We demonstrated the utility of our tools by presenting the first spike-in-based comparison of the three major platforms–Affymetrix, Agilent and Illumina.     

A systematic assessment of normalization approaches for the Infinium 450K methylation platform

The Illumina Infinium HumanMethylation450 BeadChip has emerged as one of the most popular platforms for genome wide profiling of DNA methylation. While the technology is wide-spread, systematic technical biases are believed to be present in the data. For example, this array incorporates two different chemical assays, i.e., Type I and Type II probes, which exhibit different technical characteristics and potentially complicate the computational and statistical analysis. Several normalization methods have been introduced recently to adjust for possible biases. However, there is considerable debate within the field on which normalization procedure should be used and indeed whether normalization is even necessary. Yet despite the importance of the question, there has been little comprehensive comparison of normalization methods. We sought to systematically compare several popular normalization approaches using the Norwegian Mother and Child Cohort Study (MoBa) methylation data set and the technical replicates analyzed with it as a case study. We assessed both the reproducibility between technical replicates following normalization and the effect of normalization on association analysis. Results indicate that the raw data are already highly reproducible, some normalization approaches can slightly improve reproducibility, but other normalization approaches may introduce more variability into the data. Results also suggest that differences in association analysis after applying different normalizations are not large when the signal is strong, but when the signal is more modest, different normalizations can yield very different numbers of findings that meet a weaker statistical significance threshold. Overall, our work provides useful, objective assessment of the effectiveness of key normalization methods.     

Importance versus intensity of ecological effects: why context matters

In any ecological study, target organisms are usually impacted by multiple environmental drivers. In plant interaction research, recent debate has focussed on the importance of competition; that is, its role in regulating plant success relative to other environmental drivers. Despite being clearly and specifically defined, the apparently simple concept of the importance of competition has been commonly overlooked, and its recognition has helped reconcile long-running debates about the dependence of competition on environmental severity. In this review, we argue that extending this formalised concept of importance to other aspects of ecology would be beneficial. We discuss approaches for measuring importance, and provide examples where explicit acknowledgement of this simple concept might promote understanding and resolve debate.     

Stochastic processes play more important roles in driving the dynamics of rarer species

Aims One major goal of modern community ecology is to understand how deterministic and stochastic processes combine to drive community assembly. However, little empirical knowledge is known about how their relative importance varies between common and rare species.Methods We exploited two 30-year data sets of plant communities in a temperate steppe using two different methods. One is a null model method, and the other is a recently developed direct-calculation method.Important findings We found that stochastic processes tended to be more important in influencing rare than common species. This finding suggests that stochastic forces may play a more important role in structuring communities with more rare species, providing a possible solution to the debate on the varied importance of deterministic and stochastic processes among different communities.     

Intensity and Importance of Competition for a Grass (Festuca rubra) and a Legume (Trifolium pratense) Vary with Environmental Changes

How plant competition varies across environmental gradients has been a long debate among ecologists. We conducted a growth chamber experiment to determine the intensity and importance of competition for plants grown in changed environmental conditions. Festuca rubra and Trifolium pratense were grown in monoculturs and in two- and/or three-species mixtures under three environmental treatments. The measured competitive variations in terms of growth (height and biomass) were species-dependent. Competition intensity for Festuca increased with decreased productivity, whilst competition importance displayed a humpback response. However, significant response was detected in neither competition intensity nor importance for Trifolium. Intensity and importance of competition followed different response patterns, suggesting that they may not be correlated along an environmental gradient. The biological and physiological variables of plants play an important role to determine the interspecific competition associated with competition intensity and importance. However, the competitive feature can be modified by multiple environmental changes which may increase or hinder how competitive a plant is.     

Reproductive clonality in protozoan pathogens—truth or artefact?

The debate around the frequency and importance of genetic exchange in parasitic protozoa is now several decades old. Recently, fresh assertions have been made that predominant clonal evolution explains the population structures of several key protozoan pathogens. Here, we present an alternative perspective. On the assumption that much apparent clonality may be an artefact of inadequate sampling and study design, we review current research to define why sex might be so difficult to detect in protozoan parasite populations. In doing so, we contrast laboratory models of genetic exchange in parasitic protozoa with natural patterns of genetic diversity and consider the fitness advantage of sex at different evolutionary scales. We discuss approaches to improve the accuracy of efforts to characterize genetic exchange in the field. We also examine the implications of the first population genomic studies for the debate around sex and clonality in parasitic protozoa and discuss caveats for the future.     

Sending proteins to dense core secretory granules: still a lot to sort out

The intracellular sorting of peptide hormone precursors to the dense core secretory granules (DCSGs) is essential for their bioactivation. Despite the fundamental importance of this cellular process, the nature of the sorting signals for entry of proteins into DCSGs remains a source of vigorous debate. This review highlights recent discoveries that are consistent with a model in which several protein domains, acting in a cell-specific fashion and at different steps in the sorting process, act in concert to regulate the entry of proteins into DCSGs.     

The wealth of species: ecological communities, complex systems and the legacy of Frank Preston

General statistical patterns in community ecology have attracted considerable recent debate. Difficulties in discriminating among mathematical models and the ecological mechanisms underlying them are likely related to a phenomenon first described by Frank Preston. He noted that the frequency distribution of abundances among species was uncannily similar to the Boltzmann distribution of kinetic energies among gas molecules and the Pareto distribution of incomes among wage earners. We provide additional examples to show that four different 'distributions of wealth' (species abundance distributions, species–area and species–time relations, and distance decay of compositional similarity) are not unique to ecology, but have analogues in other physical, geological, economic and cultural systems. Because these appear to be general statistical patterns characteristic of many complex dynamical systems they are likely not generated by uniquely ecological mechanistic processes.     

The intensity of competition versus its importance: an overlooked distinction and some implications

The intensity of competition is a physiological concept, related directly to the well-being of individual organisms but only indirectly and conditionally to their fitness, and even more indirectly to the evolution of populations and the structure of communities. The importance of competition is primarily an ecological and evolutionary concept, related directly to the ecology and fitness of individuals but only indirectly to their physiological states. The intensity of competition is not necessarily correlated with the intensities of predation, disturbance, abiotic stress, or other ecological processes. The importance of competition is necessarily relative to the importances of other processes. Intensity refers primarily to the process of present competition, whereas importance refers primarily to the products of past competition. The distinction between the intensity and the importance of competition clarifies two long-standing ecological debates. Some ecologists have proposed that competition is greater in more stressful habitats, others the opposite, and still others that no such relationship exists. Evidence cited to refute or support these positions often confuses intensity and importance. Distinguishing between them focuses questions more sharply and indicates what sorts of new evidence should be sought. The more widely known debate over the prevalence of competition as an agent of community structure is a debate about the importance of competition, but evidence about the intensity of competition has often been used by both sides. We argue that intensity and importance need not be correlated, and so measurements of the intensity of competition are not directly relevant to this debate. This distinction also generates testable hypotheses and suggests directions for research. For example, we hypothesize that competition can be unimportant even if it is very intense: no such hypothesis is possible unless importance is distinguished from intensity. We discuss the application of these ideas to methods and theories used to study competition, ecological communities, and the evolution of competitive ability. We advocate a research approach that presumes multiple, interacting causes, including competition, affecting community structure, and we show how the distinction between intensity and importance helps to make this feasible.     

Trophic cascades: the primacy of trait-mediated indirect interactions

Trophic cascades are textbook examples of predator indirect effects on ecological systems. Yet there is considerable debate about their nature, strength and overall importance. This debate stems in part from continued uncertainty about the ultimate mechanisms driving cascading effects. We present a synthesis of empirical evidence in support of one possible ultimate mechanism: the foraging‐predation risk trade‐offs undertaken by intermediary species. We show that simple trade‐off behaviour can lead to both positive and negative indirect effects of predators on plant resources and hence can explain considerable contingency on the nature and strength of cascading effects among systems. Thus, predicting the sign and strength of indirect effect simply requires knowledge of habitat and resource use by prey with regard to predators’ presence, habitat use and hunting mode. The synthesis allows us to postulate a hypothesis for new conceptualization of trophic cascades which is to be viewed as an ultimate trade‐off between intervening species. In this context, different predators apply different rules of engagement based on their hunting mode and habitat use. These different rules then determine whether behavioural effects persist or attenuate at the level of the food chain.     

Individualist and Multi-level Perspectives on Selection in Structured Populations

Recent years have seen a renewed debate over the importance of groupselection, especially as it relates to the evolution of altruism. Onefeature of this debate has been disagreement over which kinds ofprocesses should be described in terms of selection at multiple levels,within and between groups. Adapting some earlier discussions, we presenta mathematical framework that can be used to explore the exactrelationships between evolutionary models that do, and those that donot, explicitly recognize biological groups as fitness-bearing entities.We show a fundamental set of mathematical equivalences between these twokinds of models, one of which applies a form of multi-level selectiontheory and the other being a form of ``individualism.' However, we alsoargue that each type of model can have heuristic advantages over theother. Indeed, it can be positively useful to engage in a kind ofback-and-forth switching between two different perspectives on theevolutionary role of groups. So the position we defend is a``gestalt-switching pluralism.'     

The Origin of Homo sapiens in the Light of Different Research Methods

The origins of Homo sapiens is a central issue of modern paleoanthropology. The available fossil material serves as a basis for postulating different hypotheses and models, but as is widely appreciated, anthropologists have yet to reach a consensus about human origins. It seems possible that the main reasons behind such an irreducible divergence of opinions are different methodological approaches rather than the analyses of fossil material. Some scientists would say that it is the fragmentary nature of fossil material which accounts for the debates about the origins of H. sapiens. Had the debate been only a matter of the empirical considerations many disagreements concerning H. sapiens would have probably disappeared long ago. But since the controversies are imbued in methodological reality the closure of the debate is not to be expected soon. There are three research methods: morphological, archaeological and genetic. Each approach has a specific definition of H. sapiens at its disposal, which largely accounts for the different scenarios for the origin of our species. Any debate concerning this problem must therefore begin with a discussion about the research methods. The controversy about our origins thus appears to be of secondary importance. The present paper aims at presenting the methodological controversy in relation to the origins of H. sapiens. The discussion about the genealogy of H. sapiens certainly is in urgent need of a new, more integrated way of approaching the past.     

The DNA Sequence-dependence of Nucleosome Positioning in vivo and in vitro

Abstract

The contribution of histone-DNA interactions to nucleosome positioning in vivo is currently a matter of debate. We argue here that certain nucleosome positions, often in promoter regions, in yeast may be, at least in part, specified by the DNA sequence. In contrast other positions may be poorly specified. Positioning thus has both statistical and DNA-determined components. We further argue that the relative affinity of the octamer for different DNA sequences can vary and therefore the interaction of histones with the DNA is a ‘tunable’ property.     

Statistical Confusion Among Graduate Students: Sickness or Symptom?

Abstract: Statistics is one of the most important yet difficult subjects for many ecology and wildlife graduate students to learn. Insufficient knowledge about how to conduct quality science and the ongoing debate about the relative value of competing statistical ideologies contribute to uncertainties among graduate students regarding which statistical tests are most appropriate. Herein, we argue that increased education of the available statistical tests alone is unlikely to ameliorate the problem. Instead, we suggest that statistical uncertainties among graduate students are a secondary symptom of a larger problem. We believe the root cause lies in the lack of education on how to conduct science as an integrated process from hypothesis creation through statistical analysis. We argue that if students are taught to think about how each step of the process will affect all other steps, many statistical uncertainties will be avoided.     

The meaning of genetic research results: reflections from individuals with and without a known genetic disorder

In the debate about whether to return individual genetic results to research participants, consideration of the nature of results has taken precedence over contextual factors associated with different study designs and populations. We conducted in-depth interviews with 24 individuals who participated in a genotype-driven study of cystic fibrosis: 9 of the individuals had cystic fibrosis, 15 had participated as healthy volunteers, and all had gene variants of interest to the researchers. These interviews revealed that the two groups had different ideas about the meaningfulness of genetic results. Our findings point to the importance of understanding research context, such as participants' relationship with the researcher and whether they have the disease condition under study, when considering whether to return individual results.     

Adaptation and the comparative method

Over the past two decades, it has become widely accepted that phylogenies need to be incorporated into statistical analyses of interspecific data. However, recent debate has focused on whether it is appropriate to apply phylogenetic comparative methods (PCMs) to the study of adaptation. Although some of the criticisms are serious, it is premature to stop applying PCMs altogether. New statistical methods designed explicitly for the comparative study of adaptation overcome these criticisms and offer fresh insights into the evolution of phenotypes.     

Victorian gardeners and botanical nomenclature

ELLIOTT, B., 1992. Victorian gardeners and botanical nomenclature. A review of the debate over the relative importance of English over Latin names for plants is presented.