Fisher Lecture: the 2002 R. A. Fisher lecture: dedicated to the memory of Shanti S. Gupta. Variances are not always nuisance parameters

In classical problems, e.g., comparing two populations, fitting a regression surface, etc., variability is a nuisance parameter. The term "nuisance parameter" is meant here in both the technical and the practical sense. However, there are many instances where understanding the structure of variability is just as central as understanding the mean structure. The purpose of this article is to review a few of these problems. I focus in particular on two issues: (a) the determination of the validity of an assay; and (b) the issue of the power for detecting health effects from nutrient intakes when the latter are measured by food frequency questionnaires. I will also briefly mention the problems of variance structure in generalized linear mixed models, robust parameter design in quality technology, and the signal in microarrays. In these and other problems, treating variance structure as a nuisance instead of a central part of the modeling effort not only leads to inefficient estimation of means, but also to misleading conclusions.     

顺式和反式-AT型聚酮合酶研究进展及应用

聚酮类化合物因广泛应用于医药等方面而被大家所熟知,Ⅰ型聚酮合酶（Polyketide Synthase,PKS）在催化聚酮类化合物的生物合成中起着重要的作用。根据不同的酰基转移酶（Acyltransferase,AT）结构域,I型PKS可分为顺式-AT （cis-Acyltransferase,cis-AT）型PKS和反式-AT （trans-Acyltransferase,trans-AT）型PKS,目前cis-AT型PKS研究得比较透彻,trans-AT型PKS相关研究成为当今热点。本文总结了cis-AT型PKS和trans-AT型PKS的联系与区别、工程进展、相关应用以及目前存在的问题,以期为了解cis-AT型PKS和trans-AT型PKS在聚酮化合物合成中的作用提供参考。     

The emergence of the chordate body plan: some puzzles and problems

Lacalli, T.C. 2010. The emergence of the chordate body plan: some puzzles and problems. —Acta Zoologica (Stockholm) 91 : 4–10 Rather than being sessile filter feeders, ancestral chordates are now thought to have evolved from more active benthic animals, possibly hemichordate‐like, that took to swimming, to generate something resembling modern amphioxus. This general picture conceals a number of specific problems that underline how little we understand the transition in detail. I will address three. First, and closest to resolution is the issue of dorsoventral inversion, which has implications for understanding how an internalized brain evolved. This is because the mouth, dorsal after inversion, has first to be moved out of the way. Its migration down the left side of the head during amphioxus development may be a recapitulation of this event. Two other puzzles, both further from resolution are: (1) the significance, if any, of the neurenteric canal, which may be telling us something important about the true nature of deuterostomy, specifically whether hemichordates and echinoderms are deuterostomes for a different reason than chordates, and (2) whether the functional digestive tract of chordates is a secondary replacement of an earlier structure whose fate remains unexplained. Resolving these latter two issues will require a better understanding of molecular level events during development in protochordates and their immediate invertebrate relatives.     

Populations under microevolutionary scrutiny: what will we gain?

Understanding the evolution of biodiversity and the function of biological systems are burning and linked questions in biology. Evolution of biodiversity begins at the level of microevolution, with the differentiation of individuals in populations. The study of this process splits into two conceptually different approaches (1) the concept of functional biology of testing hypothesis by precisely controlled and forward-directed experiments (digital and experimental evolution), and (2) the concept of a theory-based historical narrative (testing hypothesis on events in the past for their suitability to best explain the present). Here, I discuss and emphasize the benefits of the study of natural bacterial populations for a deeper understanding of prokaryotic biology. Also, I adress current problems in taxonomy at the ‘species’ level which obviously need discussion and clarification. I exemplify this with a natural model population for such studies, Bacillus simplex from “Evolution Canyon”, Israel.     

Innateness as an explanatory concept

Although many of the issues surrounding innateness have received a good deal of attention lately, the basic concept of token innateness has been largely ignored. In the present paper, I try to correct this imbalance by offering an account of the innateness of token traits. I begin by explaining Stephen Stich's account of token innateness and offering a counterexample to that account. I then clarify why the contemporary biological approaches to innateness will not be able to resolve the problems that beset Stich's account. From there, I develop an alternative understanding of the innateness of token traits, what I call a causal/explanatory account. The argument to be made is that token innateness is both a causal, and an explanatory, concept. After clarifying this understanding of innateness, and showing how it handles several counterexamples to other accounts, I end with some comments on what the causal/explanatory account suggests for our understanding of innateness in general.     

Links between ecology and ecophilosophy,ethics and the requirements of environmental management

Abstract This paper concerns the ways that our philosophical attitudes to the environment can influence the appropriateness of methodologies for solving environmental problems. Sometimes a public perception is expressed that science takes scant regard of the concerns of the people affected. Is it possible for scientists and managers to respond to such concerns and still fulfil the logical and methodological rigour that their discipline demands? I believe we have to address fundamental issues of definitions and meaning before useful debate can occur among parties interested in environmental decision-making. Delving into the ideas behind our everyday practices of environmental management should promote re-evaluation of our beliefs, attitudes and concerns about nature. I examine environmental science from both ethical and managerial perspectives. I explore how our assumptions and attitudes might influence ecology, in particular issues raised by environmental impacts and conservation. The major points argued here are:

• 1 Any legal requirements of environmental investigations must be met, but perhaps we should act more in line with the spirit of legislation.
• 2 The managerial imperatives of environmental investigations need to be examined closely because of widely perceived problems with the use of science in impact assessment. We must change either our methods of assessment or the regulations and administration of environmental impact assessment (EIA).
• 3 Science is not paramount in the processes of environmental decision-making. We need to be aware of how psychosocial factors affect the ultimately political decisions about environmental problems.
• 4 Philosophy and ethics offer a range of perspectives that may benefit ecology. Scientists need to be aware of these just as they should be of their own leanings about how we treat nature.
• 5 Scientists need to translate social concerns or demands about the environment into properly defined scientific questions, and then study them as a matter of urgency.
• 6 Ecology needs to guide ecophilosophers and environmental ethicists as to how nature works, why we expect variability in ecosystems, what is naturalness, and other issues where a scientific understanding of nature has progressed beyond the point where these observers of ecology have so far taken inspiration.

     

1.688 g/cm3 satellite‐related repeats: a missing link to dosage compensation and speciation

Despite the important progress that has been made on dosage compensation (DC), a critical link in our understanding of the X chromosome recognition mechanisms is still missing. Recent studies in Drosophila indicate that the missing link could be a family of DNA repeats populating the euchromatin of the X chromosome. In this opinion article, I discuss how these findings add a new fresh twist on the DC problem. In the following sections, I first summarize our understanding of DC in Drosophila and integrate these recent discoveries into our knowledge of the X chromosome recognition problem. Next, I introduce a model according to which, 1.688 g/cm³ satellite‐related (SR) repeats would be the primary recognition elements for the dosage compensation complex. Contrary to the current belief, I suggest that the DC system in Drosophila is not conserved and static, but it is continuously co‐evolving with the target SR repeats. The potential role of the SR repeats in hybrid incompatibilities and speciation is also discussed.     

Mycobacterium marinum: the generalization and specialization of a pathogenic mycobacterium

Mycobacterium marinum is being used increasingly as a model for understanding pathogenic mycobacteria. However, recently discovered differences between M. marinum and M. tuberculosis suggest that adaptation to specialized niches is reflected in unique strategies of pathogenesis. This review emphasizes the areas in which studying M. marinum has made contributions to the understanding of tuberculosis, as well as the potential for using characteristics unique to M. marinum for understanding general issues of host–pathogen interactions.     

On the relationship between evolutionary and psychological definitions of altruism and selfishness

I examine the relationship between evolutionary definitions of altruism that are based on fitness effects and psychological definitions that are based on the motives of the actor. I show that evolutionary altruism can be motivated by proximate mechanisms that are psychologically either altruistic or selfish. I also show that evolutionary definitions do rely upon motives as a metaphor in which the outcome of natural selection is compared to the decisions of a psychologically selfish (or altruistic) individual. Ignoring the precise nature of both psychological and evolutionary definitions has obscured many important issues, including the biological roots of psychological altruism.     

Framing the Loss of Solace: Issues and Challenges in Researching Indigenous Compensation Claims

The 2016 judgment in the ‘Timber Creek’ compensation case (Griffiths v Northern Territory of Australia (no. 3) (2016) FCA 900) signals an end to an era of extinguishment-related injustice and inequality, representing, as it does, the first litigated Federal Court award of compensation for the loss or impairment of rights and interests, under the 1993 Native Title Act. In this paper, I explore some of the methodological challenges and conceptual issues confronting anthropologists involved in researching compensation claims. In drawing upon my experience in researching two such claims, I discuss how the issues of gender, resource development, environmental transformation, the Stolen Generation, and the history of Indigenous-European relations in remote and rural Australia impact upon investigations into the loss or diminution of traditional attachments to land. In conceptualising this loss of connection, I discuss material relating to the ‘anthropology of emotions’, and I point to some of the obstacles encountered when talking about emotions cross-culturally. In conclusion, I explore research undertaken into the social and psychological impacts of ecosystem distress, loss of place, and environmental change, and I posit the value of Glenn Albrecht’s concept of ‘solastalgia’ (2005. “Solastalgia, a New Concept in Human Health and Identity.” Philosophy Activism Nature 3: 41–44) in framing research into the loss of solace, and in expanding upon the legal notion of this loss as ‘inconvenience’ and ‘injured feelings’.     

Commentary on Ditch,Stitch and Pitch: the niche is here to stay

A recent set of discussion papers in the Journal of Biogeography by McInerny and Etienne (henceforth M&E) questions the value of niche concepts in relation to a diverse group of practices collectively labelled species distribution modelling (SDM), and specifically the usefulness of the idea of a fundamental niche. In this Correspondence, I argue that certain types of SDM may indeed dispense with niche concepts, but that such is not the case for an important class of SDM‐based activities, including transferring predictions in space and time. Using a single term (SDM) to denote diverse objectives and practices does not help to clarify issues; I discuss this point. I also review several criticisms raised by M&E about the use of the concept of fundamental niche in the context of modelling species' distributions and their environments.     

Possibility,legitimacy, and the new ontologies of choice: a comment on Brubaker

In Trans, Rogers Brubaker makes a major argument about the contentious politics of the contemporary self. In this commentary, I first lay out what is think is the solidity of the book’s contrasting tableau of the functioning of race and gender in American society and beyond. I then point to Brubaker’s bundling together of issues of legitimacy and issues of ontology and begin to imagine what alternative analyses can come out of their unbundling – suggesting that race and gender are perhaps more analogous social formations than Trans argues. Finally, I bring attention to the role of ontological hierarchy in the formulation and policing of identity claims and conclude that the return of biology and the new empire of choice may not be two parallel, independent developments but one and the same process. Theoretically, I amplify one of the book’s epistemological contributions by calling for a reflexive turn in social-constructionist thought.     

Racial categories as resources and constraints in everyday interactions: Implications for racialism and non-racialism in post-apartheid South Africa

The anti-apartheid struggle was characterized by tensions between the opposing ideologies of non-racialism (exemplified by the Freedom Charter) and racialism (exemplified by Black Consciousness). These tensions have remained prevalent in public policies and discourse, and in the writings of social scientists, in the post-apartheid period. In this paper I examine some ways in which issues of whether, when, and how race matters become visible in everyday interactions in South Africa, and what insights this may offer with respect to these ongoing tensions. Specifically, I employ an ethnomethodological, conversation analytic approach to examine some ways in which racial categories are treated as resources for action or constraints on action. I conclude by arguing that these findings point to the contingent and situational operation of a practical non-racialism (as well as practical racialism), and thus to the achievement of these ideologies in the moment-by-moment unfolding of interactions.     

Low Risks,High Public Concern? The Cases of Persistent Organic Pollutants (POPs), Heavy Metals,and Nanotech Particles

Risk is an ancient, historic concept; almost everybody has some subjective understanding of what is meant by it. However, there are different types of knowledge, notions, interests, and processes involved both in science-based risk assessment and subjective risk perception. In the present article, we show how risk assessment and risk perception are intricately intertwined. This is exemplified by introducing the state-of-the-art risk assessments applied to three cases (i.e., heavy metals, POPs, and nanotech particles), each with their own unique history and degree of scientific understanding. We elaborate that, when dealing with risk, actors employ different notions (e.g., pure vs. speculative risk), processes (e.g., affective involvement in case) and relations (e.g., trust depending on benefiting from risk) depending on their knowledge, concern, and interests. Finally, we argue that it is important to combine studies on risk perception and risk assessment at an early stage of technology development. The issues and problems of public risk perception are discussed.     

Cytolethal distending toxins

The cytolethal distending toxins (CDTs) constitute the most recently discovered family of bacterial protein toxins. CDTs are unique among bacterial toxins as they have the ability to induce DNA double strand breaks (DSBs) in both proliferating and nonproliferating cells, thereby causing irreversible cell cycle arrest or death of the target cells. CDTs are encoded by three linked genes (cdtA, cdtB and cdtC) which have been identified among a variety of Gram-negative pathogenic bacteria. All three of these gene products are required to constitute the fully active holotoxin, and this is in agreement with the recently determined crystal structure of CDT. The CdtB component has functional homology with mammalian deoxyribonuclease I (DNase I). Mutation of the conserved sites necessary for this catalytic activity prevents the induction of DSBs as well as all subsequent intoxication responses of target cells. CDT is endocytosed via clathrin-coated pits and requires an intact Golgi complex to exert the cytotoxic activity. Several issues remain to be elucidated regarding CDT biology, such as the detailed function(s) of the CdtA and CdtC subunits, the identity of the cell surface receptor(s) for CDT, the final steps in the cellular internalization pathway, and a molecular understanding of how CDT interacts with DNA. Moreover, the role of CDTs in the pathogenesis of diseases still remains unclear.     

The cell biology of human hair follicle pigmentation

Although we have made significant progress in understanding the regulation of the UVR‐exposed epidermal‐melanin unit, we know relatively little about how human hair follicle pigmentation is regulated. Progress has been hampered by gaps in our knowledge of the hair growth cycle’s controls, to which hair pigmentation appears tightly coupled. However, pigment cell researchers may have overly focused on the follicular melanocytes of the nocturnal and UVR‐shy mouse as a proxy for human epidermal melanocytes. Here, I emphasize the epidermis‐follicular melanocyte pluralism of human skin, as research models for vitiligo, alopecia areata and melanoma, personal care/cosmetics innovation. Further motivation could be in finding answers to why hair follicle and epidermal pigmentary units remain broadly distinct? Why melanomas tend to originate from epidermal rather than follicular melanocytes? Why multiple follicular melanocyte sub‐populations exist? Why follicular melanocytes are more sensitive to aging influences? In this perspective, I attempt to raise the status of the human hair follicle melanocyte and highlight some species‐specific issues involved which the general reader of the pigmentation literature (with its substantial mouse‐based data) may not fully appreciate.     

Honeybee colony drone production and maintenance in accordance with environmental factors: an interplay of queen and worker decisions

Social insect colonies display a remarkable ability to adjust investment in reproduction (i.e., production of sexuals) in accordance with environmental conditions such as season and food availability. How this feat is accomplished by the colony’s queen(s) and workers remains a puzzle. Here, I review what we have learned about this subject in the European honeybee (Apis mellifera), specifically with regard to a colony’s production of males (drones). I identify five environmental conditions that influence colony-level patterns of drone production and then define five stages of drone rearing that are accomplished by the queen and workers. Using this framework, I detail our current understanding of how the queen or workers adjust their actions at each stage of drone rearing in response to each of the environmental conditions. Future investigations of this topic in honeybees and other social insect societies will lead to a better understanding of how colonies manage to flexibly and efficiently allocate their resources under changing environmental conditions.     

Environmental migrants,structural injustice,and moral responsibility

Climate change and environmental problems will force or induce millions of people to migrate. In this article, I describe environmental migration and articulate some of the ethical issues. To begin, I give an account of these migrants that overcomes misleading dichotomies. Then, I focus attention on two important ethical issues: justice and responsibility. Although we are all at risk of becoming environmental migrants, we are not equally at risk. Our risk depends on our temporal position, geographical location, social position, and the kind of society in which we live. We all contribute to environmental problems, but we do not contribute equally. About 11% of the world population is responsible for 50% of carbon emissions. These inequalities raise issues of justice because many of the people who are at high risk have contributed little to the problems. Since the issues of justice are relatively clear and compelling, I focus more attention on issues of responsibility. I use Iris Marion Young’s account of responsibility for structural injustice to address four key questions about moral responsibility and environmental migration.     

Design and analysis of multiple-choice feeding-preference experiments

Summary A serious omission in ecological methodology is the absence of a rigorous statistical procedure to analyse multiple-choice feeding-preference experiments. A sample of 21 studies in the littoral marine context shows that results from such experiments are used to study a variety of conceptual issues, ranging from nutritional biology to ecosystem dynamics. A majority of such studies have been incorrectly analysed. The analytical problem has two facets: (1) lack of independence in the simultaneous offer of food types and (2) the existence of autogenic changes particular to each food type. Problem (2) requires the use of control arenas without the consumer. A recent advance allows the rigorous analysis of experiments with two food types offered simultaneously. Here I propose a method for the multiple-choice case. For the first problem I suggest the use of multivariate statistical analysis, providing both a parametric and a nonparametric procedure. The second problem is solved using basic statistical theory. I analyse data from an experiment with the sea urchin Tetrapygus niger feeding on three species of algae: Ulva nematoidea, Gymnogongrus furcellatus, and Macrocystis pyrifera. The parametric and nonparametric procedures yielded similar results, and showed that when offered the three species of algae T. niger does not feed at random but shows a preference for U. nematoidea. The method requires that the number of replicates in the treatment and control arenas be the same, and greater than the number of food types. The method is useful for other kinds of multiple-choice experiments.     

More on the genetical theory of multilevel selection

In my article The genetical theory of multilevel selection, I provided a synthesis of the theory of multilevel selection (MLS) and the theory of natural selection in class‐structured populations. I framed this synthesis within Fisher's genetical paradigm, taking a strictly genetical approach to traits and fitness. I showed that this resolves a number of long‐standing conceptual problems that have plagued the MLS literature, including the issues of ‘aggregate’ vs. ‘emergent’ group traits, ‘collective fitness₁’ vs. ‘collective fitness₂’ and ‘MLS1’ vs. ‘MLS2 ‘. In his commentary, Goodnight suggests this theoretical and conceptual synthesis is flawed in several respects. Here, I show this is incorrect, by: reiterating the theoretical and conceptual goals of my synthesis; clarifying that my genetical approach to traits is necessary for a proper analysis of the action of MLS independently of non‐Darwinian factors; emphasizing that the Price–Hamilton approach to MLS provides a consistent, useful and conceptually superior theoretical framework; and explaining the role of reproductive value in the study of natural selection in class‐structured populations. I also show that Goodnight's contextual analysis treatment of MLS in a class‐structured population is mathematically, biologically and conceptually inadequate.