Homology and the hierarchy of biological systems

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.     

When is a cladist not a cladist?

The term “cladist” has distinct meanings in distinct contexts. Communication between philosophers, historians, and biologists has been hindered by different understandings of the term in various contexts. In this paper I trace historical and conceptual connections between several broadly distinct senses of the term “cladist”. I propose seven specific definitions that capture distinct contemporary uses. This serves to disambiguate some cases where the meaning is unclear, and will help resolve apparent disagreements that in fact result from conflicting understandings of the term.     

Levels of organization in biology: on the nature and nomenclature of ecology's fourth level

Viewing the universe as being composed of hierarchically arranged systems is widely accepted as a useful model of reality. In ecology, three levels of organization are generally recognized: organisms, populations, and communities (biocoenoses). For half a century increasing numbers of ecologists have concluded that recognition of a fourth level would facilitate increased understanding of ecological phenomena. Sometimes the word "ecosystem" is used for this level, but this is arguably inappropriate. Since 1986, I and others have argued that the term "landscape" would be a suitable term for a level of organization defined as an ecological system containing more than one community type. However, "landscape" and "landscape level" continue to be used extensively by ecologists in the popular sense of a large expanse of space. I therefore now propose that the term "ecoscape" be used instead for this fourth level of organization. A clearly defined fourth level for ecology would focus attention on the emergent properties of this level, and maintain the spatial and temporal scale-free nature inherent in this hierarchy of organizational levels for living entities.     

T.H. Morgan,neither an epistemological empiricist nor a “Methodological” empiricist

T. H. Morgan (1866–1945), the founder of the Drosophila research group in genetics that established the chromosome theory of Mendelian inheritance, has been described as a radical empiricist in the historical literature. His empiricism, furthermore, is supposed to have prejudiced him against certain scientific conclusions. This paper aims to show two things: first, that the sense in which the term empiricism has been used by scholars is too weak to be illuminating. It is necessary to distinguish between empiricism as an epistemological position and the so-called methodological empiricism. I will argue that the way the latter has been presented cannot distinguish an empiricist methodology from a non-empiricist one. Second, I will show that T. H. Morgan was not an epistemological empiricist as this term is usually defined in philosophy. The reason is that he believed in the existence of genes as material entities when they were unobservable entities when they were unobservable entities introduced to account for the phenotypic ratios found in breeding experiments. These two points, of course, are interrelated. If we were to water down the meaning of empiricis, perhaps we could call Morgan an empiricist. But then we would also fail to distinguish empiricism from realism.     

Chance: From metaphysical principle to explanatory concept. The idea of uncertainty in a natural history of knowledge

The term "chance" has been given varied and different meanings in the history of occidental thought, carrying metaphysical connotations and controversial power. Despite the obscurity implied by this polysemy, this term is still frequently used without undergoing the conceptual clarifications that could locate its precise meaning and its original function in a theory. Here I propose a brief genealogical draft of this term and of its conceptual forms, from Aristotle to Darwin, to demonstrate the necessity of specifying what function it is fulfilling in each precise theoretical framework, in order not to be overwhelmed by the wide spectrum of the word.     

Darwinism without populations: a more inclusive understanding of the "Survival of the Fittest"

Following Wallace's suggestion, Darwin framed his theory using Spencer's expression "survival of the fittest". Since then, fitness occupies a significant place in the conventional understanding of Darwinism, even though the explicit meaning of the term 'fitness' is rarely stated. In this paper I examine some of the different roles that fitness has played in the development of the theory. Whereas the meaning of fitness was originally understood in ecological terms, it took a statistical turn in terms of reproductive success throughout the 20th Century. This has lead to the ever-increasing importance of sexually reproducing organisms and the populations they compose in evolutionary explanations. I will argue that, moving forward, evolutionary theory should look back at its ecological roots in order to be more inclusive in the type of systems it examines. Many biological systems (e.g. clonal species, colonial species, multi-species communities) can only be satisfactorily accounted for by offering a non-reproductive account of fitness. This argument will be made by examining biological systems with very small or transient population structures. I argue this has significant consequences for how we define Darwinism, increasing the significance of survival (or persistence) over that of reproduction.     

Drought and drought tolerance

Drought tolerance is a nebulous term that becomes more nebulous the more closely we look at it, much as a newspaper photograph does when viewed through a magnifying glass. From the vantage point of an ecologist the features that distinguish xerophytic from mesophytic vegetation are clear. We can all tell that a cactus is more drought tolerant than a carnation. But when we look at crop plants, the features that confer drought tolerance are far from clear. The main reason for the contrast is that the traits we associate with xerophytes typically concern survival during drought, whereas with crops we are concerned with production—and insofar as the term drought tolerance has any useful meaning in an agricultural context, it must be defined in terms of yield in relation to a limiting water supply.Further, with the well-developed major crop plants, those of us trying to increase water-limited yield would be pleased to achieve improvements of just a few percent in environments that are highly variable in their water supply. This variability often means that several seasons are required to demonstrate the advantages of an allegedly improved cultivar. Traits that confer drought tolerance in such circumstances are subtle, and may manifest themselves in some types of drought but not in others. Indeed the most influential characters often have no direct connection to plant water relations at all, as I elaborate on below.I will concentrate on the agricultural rather than the natural environment (although there are no doubt lessons for us still to learn from analysing the behaviour of natural vegetation—see Monneveux, this volume), and will argue that drought tolerance is best viewed at an ontogenetic time scale—i.e. at the time scale of the development of the crop—weeks to months for an annual crop. The timing of the main developmental changes, like floral initiation and flowering, and the rate of development of leaf area in relation to the seasonal water supply, are the most important variables at this time scale. Occasionally though, rapid changes in the environment, such as a sudden large rise in air temperature and humidity deficit, perhaps associated with hot dry winds, make appropriate short-term physiological and biochemical responses essential for the survival of the crop. These short term responses may be amenable to cellular and sub-cellular manipulation, especially if the sudden environmental deterioration occurs at especially sensitive stages in development such as pollen meiosis or anthesis.Purists insist that drought is a meteorological term that refers only substantial to periods in which rainfall fails to keep up with potential evaporation. Within the spirit of this meeting it is appropriate to interpret the term more loosely than this definition, and to define it as circumstances in which plants suffer reduced growth or yield because of insufficient water supply, or because of too large a humidity deficit despite there being seemingly adequate water in the soil.     

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.     

Darwin's artificial selection as an experiment

Darwin used artificial selection (ASN) extensively and variedly in his theorizing. Darwin used ASN as an analogy to natural selection; he compared artificial to natural varieties, hereditary variation in nature to that in the breeding farm; and he also compared the overall effectiveness of the two processes. Most historians and philosophers of biology have argued that ASN worked as an analogical field in Darwin's theorizing. I will argue rather that this provides a limited and somewhat muddled view of Darwinian science. I say "limited" because I will show that Darwin also used ASN as a complex experimental field. And I say "muddled" because, if we concentrate on the analogical role exclusively, we conceive Darwinian science as rather disconnected from contemporary conceptions of "good science". I will argue that ASN should be conceived as a multifaceted experiment. As a traditional experiment, ASN established the efficacy of Darwin's preferred cause: natural selection. As a non-traditional experiment, ASN disclosed the nature of a crucial element in Darwin's evolutionary mechanics: the nature of hereditary variation. Finally, I will argue that the experiment conception should help us make sense of Darwin's comments regarding the "monstrous" nature of domestic breeds traditionally considered to be problematic.     

GENETIC HARM: BITTEN BY THE BODY THAT KEEPS YOU?

... We must attempt to explain, how, if ever, our existence may harm us. To address this and the other questions raised, I propose to examine what constitutes harm and whether it makes sense to say that our genetic makeup may harm us. To do this I will describe three approaches to the problem of describing the status of negative effects our genes have upon us, which I have named the "technical harm" view, the "constitutive" view, and the "harmful conditions" view. On the technical harm view, the standard definitions of harm are applied to genetic disposition in an attempt to couch genetic defects or flaws in terms of harming. The constitutive view rejects applying the concept of harm to genetic disposition on the grounds that it is impossible to separate genetic disposition from individual identity. Lastly, the harmful conditions view, which I conclude is the most successful of the three, focuses on the tendency of certain genetic dispositions to cause harm in the future and thus avoids what I will argue are the "context" shortcomings of the other two approaches. To conclude the discussion I will very briefly analyze the ramifications of a harmful conditions view for the concept of genetic disease and the prospects for genetic counseling, gene therapy, and reproductive decision making.     

Elusive locus of control in biological development: genetic versus developmental programs.

Taken as a composite, the meaning of the composite term "genetic program"-widely taken to suggest an explanation of biological development - simultaneously depends upon and underwrites the particular presumption that a "plan of procedure" for development is itself written in the sequence of nucleotide bases. Is this presumption correct? I want to argue that, at best, it must be said to be misleading, and at worst, simply false: To the extent that we may speak at all of a developmental program, or of a set of instructions for development, in contra-distinction to the data or resources for such a program, current research obliges us to acknowledge that these "instructions" are not written into the DNA itself (or at least, are not all written in the DNA), but rather are distributed throughout the fertilized egg. I will argue that the notion of genetic program depends upon, and sustains, a fundamental category error in which two independent distinctions, one between "genetic" and "epigenetic," and the other, between program and data, are pulled into mistaken alignment. The net effect of such alignment is to reinforce two outmoded associations: on the one hand, between "genetic" and active, and, on the other, between "epigenetic" and passive. J. Exp. Zool. (Mol. Dev. Evol.) 285:283-290, 1999.     

The Limits of Authenticity in Vietnamese Consumer Markets

In this article, I address the saliency of the concept of "authenticity" in contexts of international law and anthropological inquiry. Using my research findings in Ho Chi Minh City (HCMC), Vietnam, I show that although Vietnamese shoppers distinguish between what they term real and fake goods, they do not share with foreign corporations and international trade organizations a preoccupation with product and brand authenticity. To make this point, I describe four types of goods—model goods, mimic goods, real goods, and fake goods—employed by shoppers in HCMC, and discuss why they have little in common with notions of "authenticity" and "ownership" inherent in international standards of intellectual property. I argue that these conceptual differences in the commercial sphere challenge claims about the universal applicability of intellectual property rights laws and also encourage anthropologists to ask whether authenticity is always a useful tool of cross-cultural understanding.     

Why Katrina's Victims Aren't Refugees: Musings on a "Dirty" Word

In the aftermath of Hurricane Katrina, a controversy emerged in the U.S. public sphere over the use of the word refugee to characterize the displaced residents of New Orleans. In this article, I explore the significance of the concept of "the refugee" for U.S. citizens, and I discuss what the failure to find an appropriate term to describe stranded New Orleanians reveals about the experience of poverty. I argue that the conceptual void uncovered by the crisis reflects the larger social void in which poor New Orleanians have long been confined and I examine the role of public discourse in defining and helping justify the inequalities uncovered by Katrina.     

Aspects of plant intelligence

Intelligence is not a term commonly used when plants are discussed. However, I believe that this is an omission based not on a true assessment of the ability of plants to compute complex aspects of their environment, but solely a reflection of a sessile lifestyle. This article, which is admittedly controversial, attempts to raise many issues that surround this area. To commence use of the term intelligence with regard to plant behaviour will lead to a better understanding of the complexity of plant signal transduction and the discrimination and sensitivity with which plants construct images of their environment, and raises critical questions concerning how plants compute responses at the whole-plant level. Approaches to investigating learning and memory in plants will also be considered.     

Revolutionizing medicine in the 21(st) century through systems approaches

Personalized medicine is a term for a revolution in medicine that envisions the individual patient as the central focus of healthcare in the future. The term "personalized medicine", however, fails to reflect the enormous dimensionality of this new medicine that will be predictive, preventive, personalized, and participatory-a vision of medicine we have termed P4 medicine. This reflects a paradigm change in how medicine will be practiced that is revolutionary rather than evolutionary. P4 medicine arises from the confluence of a systems approach to medicine and from the digitalization of medicine that creates the large data sets necessary to deal with the complexities of disease. We predict that systems approaches will empower the transition from conventional reactive medical practice to a more proactive P4 medicine focused on wellness, and will reverse the escalating costs of drug development an will have enormous social and economic benefits. Our vision for P4 medicine in 10 years is that each patient will be associated with a virtual data cloud of billions of data points and that we will have the information technology for healthcare to reduce this enormous data dimensionality to simple hypotheses about health and/or disease for each individual. These data will be multi-scale across all levels of biological organization and extremely heterogeneous in type - this enormous amount of data represents a striking signal-to-noise (S/N) challenge. The key to dealing with this S/N challenge is to take a "holistic systems approach" to disease as we will discuss in this article.     

Precarious Subjects: Anticipating Neoliberalism in Northern Italy's Workplace

ABSTRACT  In Italy, the term precarizzazione (precarious-ization) refers to the process of implementing neoliberal policies to transition toward a semipermanent and privatized labor regime but also to the normalization of psychic uncertainty and hypervigilance of worker-citizens. In this article, I examine "precarious workers" and a psychological harassment called "mobbing," specifically, and suggest that these practices of labor exclusion of a transitional work regime produce emergent subjectivities through an analytics of anticipation. I illustrate the social, political, and psychic effects of imagining neoliberalism, as Italians do in this context, not as complete but, rather, as a metadiscursive object of emotionally charged apprehension and anticipation.     

Ethics consultation as moral engagement

I will begin by presenting some doubts about what might be called the "received view" of the role of the moral expert as a health care consultant. Then I will review the literature on moral experts and moral expertise and proceed to apply the results of that review to the notion that there are some who are expert in ethical decision making in health care. I will try to show that certain conclusions that can be drawn from this rather circumscribed topic have implications for the very conception of the relationship between moral theory and clinical ethics.     

Species,sets, and the derivative nature of Philosophy

Concepts and methods originating in one discipline can distort the structure of another when they are applied to the latter. I exemplify this mostly with reference to systematic biology, especially problems which have arisen in relation to the nature of species. Thus the received views of classes, individuals (which term I suggest be replaced by units to avoid misunderstandings), and sets are all inapplicable, but each can be suitably modified. The concept of fuzzy set was developed to deal with species and I defend its applicability. Taxa at all levels are real and participate in biological processes. Analysis of cause and pattern provides the deep structure in which metabiology is grounded; violation of this principle has led to diverse errors in biology.     

Teaching "Species"

A clear understanding of the term "species" is fundamental to the subject of evolution. However, introductory textbooks often fail to address this topic until one of the later chapters, after having used the term species in all preceding chapters. Furthermore, definitions of terms critical to a clear understanding of this subject are often vague or absent in chapters on species concepts. We feel the popular notion of a "species problem" has been unnecessarily inflated by this less-than-effective educational approach. Clearly addressing this essential subject at the beginning of a course on evolution will prepare students to learn the details and complexities of evolution. Here we provide the background for an alternative approach to this foundational topic, followed by an outlined lesson plan. We emphasize early introduction of this subject in texts and courses using unambiguous terminology and including the historical development of species concepts.     

Identifying and evaluating layers of vulnerability – a way forward

“Vulnerability” is a key concept for research ethics and public health ethics. This term can be discussed from either a conceptual or a practical perspective. I previously proposed the metaphor of layers to understand how this concept functions from the conceptual perspective in human research. In this paper I will clarify how my analysis includes other definitions of vulnerability. Then, I will take the practical‐ethical perspective, rejecting the usefulness of taxonomies to analyze vulnerabilities. My proposal specifies two steps and provides a procedural guide to help rank layers. I introduce the notion of cascade vulnerability and outline the dispositional nature of layers of vulnerability to underscore the importance of identifying their stimulus condition. In addition, I identify three kinds of obligations and some strategies to implement them. This strategy outlines the normative force of harmful layers of vulnerability. It offers concrete guidance. It contributes substantial content to the practical sphere but it does not simplify or idealize research subjects, research context or public health challenges.