Showing papers in "Biological Theory in 2009"

Theses on Biosemiotics: Prolegomena to a Theoretical Biology

Abstract: Theses on the semiotic study of life as presented here provide a collectively formulated set of statements on what biology needs to be focused on in order to describe life as a process based on semiosis, or signaction. An aim of the biosemiotic approach is to explain how life evolves through all varieties of forms of communication and signification (including cellular adaptive behavior, animal communication, and human intellect) and to provide tools for grounding sign theories. We introduce the concept of semiotic threshold zone and analyze the concepts of semiosis, function, umwelt, and the like as the basic concepts for theoretical biology.

The Concept of Morphospaces in Evolutionary and Developmental Biology: Mathematics and Metaphors

Abstract: Formal spaces have become commonplace conceptual and computational tools in a large array of scientific disciplines, including both the natural and the social sciences. Morphological spaces (morphospaces) are spaces describing and relating organismal phenotypes. They play a central role in morphometrics, the statistical description of biological forms, but also underlie the notion of adaptive landscapes that drives many theoretical considerations in evolutionary biology. We briefly review the topological and geometrical properties of the most common morphospaces in the biological literature. In contemporarygeometricmorphometrics,thenotionofamorphospace is based on the Euclidean tangent space to Kendall’s shape space, which is a Riemannian manifold. Many more classical morphospaces, such as Raup’s space of coiled shells, lack these metric properties, e.g., due to incommensurably scaled variables, so that these morphospaces typically are affine vector spaces. Other notions of a morphospace, like Thomas and Reif’s (1993) skeleton space, may not give rise to a quantitative measure of similarity at all. Such spaces can often be characterized in terms of topological or pretopological spaces. The typical language of theoretical and evolutionary biology, comprising statements about the “distance” among phenotypes in an according space or about different “directions” of evolution, is not warranted for all types of morphospaces. Graphical visualizations of morphospaces or adaptive landscapes may tempt the reader to apply “Euclidean intuitions” to a morphospace, whatever its actual topology might be. We discuss the limits of metaphors such as the developmental hourglass and adaptive landscapes that ensue from the geometric properties of the underlying morphospace.

Biology Clearly Needs Morphometrics. Does Morphometrics Need Biology

Abstract: It is now well documented that biology needs morphometrics. Morphometrics can provide useful and often unexpected information about development and growth, functional—especially mechanical—adaptation, and evolutionary difference and relationship. Such studies often apply coordinate data from anatomical landmarks. Recently semi-landmarks and sliding landmarks increase information content, especially of apparently featureless regions (e.g., skull vault). Yet, how we landmark our materials limits the results we get and the questions we ask. Here we show different landmarking schemes leading to different equivalences between specimens and different results. Geometric morphometric methods often treat landmarks as points on rubber sheets. Distortions of the sheets are often visualized by techniques like thin plate splines showing changes or differences as stretches or contractions. The statistics of morphometrics can handle these. Further consideration of anatomical landmarks, however, implies that real biologies are sometimes more complex. Sometimes two-dimensional rubber sheets of anatomies contain cusps or holes representing appearances or disappearances of structures. In three dimensions, equivalent rubber blocks may show not only appearances or disappearances but also reversals of positions of structures. Such phenomena are generally ignored in landmarks and analyses. We show that in some cases morphometrics can take account of such matters. But we also suggest that sometimes these modifications from elastic analogues are so complex that new methods may be required for our morphometric packages. It is in this sense that improvement of morphometrics needs deeper understanding of biology.

Making Knowledge in Synthetic Biology: Design Meets Kludge

Abstract: Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custombuilt kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational design. Nor do they straightforwardly embody Richard Feynman’s “last blackboard” statement (1988) that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice.

Populations as Individuals

Abstract: Biologists studying ecology and evolution use the term “population” in many different ways. Yet little philosophical analysis of the concept has been done, either by biologists or philosophers, in contrast to the voluminous literature on the concept of “species.” This is in spite of the fact that “population” is arguably a far more central concept in ecological and evolutionary studies than “species” is. The fact that such a central concept has been employed in so many different ways is potentially problematic for the reason that inconsistent usages (especially when the usage has not been made explicit) might lead to false controversies in which disputants are simply talking past one another. However, the inconsistent usages are not the only, or even the most important reason to examine the concept. If any set of organisms is legitimately called a “population,” selection and drift processes become purely arbitrary, too. Moreover, key ecological variables, such as abundance and distribution, depend on a nonarbitrary way of identifying populations. I sketch the beginnings of a population concept, drawing inspiration from the Ghiselin-Hull individuality thesis, and show why some alternative approaches are nonstarters.

Numbers and Arithmetic: Neither Hardwired Nor Out There

Abstract: What is the nature of number systems and arithmetic that we use in science for quantification, analysis, and modeling? I argue that number concepts and arithmetic are neither hardwired in the brain, nor do they exist out there in the universe. Innate subitizing and early cognitive preconditions for number— which we share with many other species—cannot provide the foundations for the precision, richness, and range of number concepts and simple arithmetic, let alone that of more complex mathematical concepts. Numbers and arithmetic, and mathematics in general, have unique features—precision, objectivity, rigor, generalizability, stability, symbolizability, and applicability to the real world—that must be accounted for. They are sophisticated concepts that developed culturally only in recent human history. I suggest that numbers and arithmetic are realized through precise combinations of non-mathematical everyday cognitive mechanisms that make human imagination and abstraction possible. One such mechanism, conceptual metaphor, is a neurally instantiated inference-preserving cross-domain mapping that allows the conceptualization of abstract entities in terms of grounded bodily experience. I analyze how the inferential organization of the properties and “laws” of arithmetic emerge metaphorically from everyday meaningful actions. Numbers and arithmetic are thus—outside of natural selection—the product of the biologically constrained interaction of individuals with the appropriate cultural and historical phenotypic variation supported by language, writing systems, and education.

Synthetic Biology: A Bridge Between Functional and Evolutionary Biology

Abstract: The interests of synthetic biologists may appear to differ greatly from those of evolutionary biologists. The engineering of organisms must be distinguished from the tinkering action of evolution; the ambition of synthetic biologists is to overcome the limits of natural evolution. But the relations between synthetic biology and evolutionary biology are more complex than this abrupt opposition: Synthetic biology may play an important role in the increasing interactions between functional and evolutionary biology. In practice, synthetic biologists have learnt to submit the proteins and modules they construct to a Darwinian process of selection that optimizes their functioning. More importantly, synthetic biology can provide evolutionary biologists with decisive tools to test the scenarios they have elaborated by resurrecting some of the postulated intermediates in the evolutionary process, characterizing their properties, and experimentally testing the genetic changes supposed to be the source of new morphologies and functions. This synthetic, experimental evolution will renew and clarify many debates in evolutionary biology: It will lead to the explosion of some vague concepts as constraints, parallel evolution, and convergence, and replace them with precise mechanistic descriptions. In this way, synthetic biology resurrects the old philosophical debate about the relations between the real and the possible.

Knowing As Making, Making As Knowing: The Many Lives of Synthetic Biology

Abstract: The ways in which the various activities of synthetic biology connect to those of conventional biology display both a multiplicity and variety that reflect the multiplicity and variety of meanings for which the term synthetic biology has been invoked, today as in the past. Central to this variety, as well as to the connection itself, is the complex relationship between knowing (understanding, representing) and making (constructing, intervening) that has prevailed in the life sciences. That relationship is the focus of this article. More specifically, my aim is to explore the different assumptions about how knowing is related to making that have prevailed, implicitly or explicitly in the various activities—now or in the past—subsumed under the name synthetic biology.

Psychomorphospace—From Biology to Perception, and Back: Towards an Integrated Quantification of Facial Form Variation

Abstract: Several disciplines share an interest in the evolutionary selection pressures that shaped human physical functioning and appearance, psyche, and behavior. The methodologies invoked from the disciplines studying these domains are often based on different rhetorics, and hence may conflict. Progress in one field is thereby hampered from effective transfer to others. Topics at the intersection of anthropometry and psychometry, such as the impact of sexual selection on the hominin face, are a typical example. Since the underlying (evolutionary) theory explicitly places facial form in the middle of a causal chain as the mediating variable between biological causes and psychological effects, a particularly convenient conceptual and analytic scenario arises as follows. Modern morphometrics allows analysis of shape both “backwards” (by regressions on biology) and “forwards” (via predictions of psychology). The two computations are commensurate, hence the two kinds of effects can be compared and evaluated as directions in the same morphospace. We suggest translating the morphometric methodology of “Darwinian aesthetics” into this space, where psychological and other processes of interest can be coded commensurately. Such a translation permits researchers to relate the effects of biological processes on form to the perceptions of the same processes in one unified “psychomorphospace.”

The Unreasonable Ineffectiveness of Fisherian “Tests” in Biology, and Especially in Medicine

Abstract: Biometrics has done damage with levels of R or p or Student’s t. The damage widened with Ronald A. Fisher’s victory in the 1920s and 1930s in devising mechanical methods of “testing,” against methods of common sense and scientific impact, “oomph.” The scale along which one would measure oomph is particularly clear in biomedical sciences: life or death. Cardiovascular epidemiology, to take one example, combines with gusto the “fallacy of the transposed conditional” and what we call the “sizeless stare” of statistical significance. Some medical editors have battled against the 5% philosophy, as did, for example, Kenneth Rothman, the founder of Epidemiology. And decades ago a sensible few in education, ecology, and sociology initiated a “significance test controversy.” But, grantors, journal referees, and tenure committees in the statistical sciences had faith that probability spaces can substitute for scientific judgment. A finding of p< .05 is deemed to be “better” for variable X than p< .11 for variable Y .I t is not. It depends on the oomph of X and Y —the effect size, size judged in the light of how much it matters for scientific or clinical purposes. In 1995 a Cancer Trialists’ Collaborative Group, for example, came to a rare consensus on effect size: 10 different studies had agreed that a certain drug for treating prostate cancer can increase patient survival by 12%. An 11th study published in the New England Journal in 1998 dismissed the drug. The dismissal was based on a t-test, not on what William Gosset (the “Student” of Student’s t) had called, against Ronald A. Fisher’s machinery, “real” error. 1

Understanding Colonial Traits Using Symbiosis Research and Ecosystem Ecology

Abstract: E. O. Wilson (1974: 54) describes the problem that social organisms pose: “On what bases do we distinguish the extremely modified members of an invertebrate colony from the organs of a metazoan animal?” This framing of the issue has inspired many to look more closely at how groups of organisms form and behave as emergent individuals. The possible existence of “superorganisms” test our best intuitions about what can count and act as genuine biological individuals and how we should study them. As we will discuss, colonies of certain organisms display many of the properties that we usually reserve only to individual organisms. Although there is good reason to believe that many social insects form genuine emergent biological individuals, the conclusion offered here is of a slightly different sort. I will argue that to understand some social insects’ interactions and the emergent traits they give rise to, it may be helpful to shift our understanding from a community-level approach to an ecosystem-level approach. I will argue that viewing certain insect colonies (termites) as parts of ecosystems allows us to better understand some of the adaptations that have emerged from their evolution.

Synthetic Biology and the Emergence of a Dual Meaning of Noise

Abstract: The question is discussed how noise gained a functional meaning in the context of biology. According to the common view, noise is considered a disturbance or perturbation. I analyze how this understanding changed and what kind of developments during the last 10 years contributed to the emergence of a new understanding of noise. Results gained during a field study in a synthetic biology laboratory show that the emergence of this new research discipline—its highly interdisciplinary character, its new technologies and novel modeling strategies—provided essential impulses, which led to the observed change in the concept of noise. The laboratory study is combined with a historical analysis, which explores the general question as to how concepts travel between disciplines and, specifically, how noise was transferred from engineering and physics into biology. In the past, scientists, such as Lotka and Goodwin, tried to introduce a statistical mechanics into biology and discussed the problem of “unfitting” concepts. The change in the meaning of the concept can be interpreted as a way of making it fit to the novel context in which it is applied.

Measurement, Explanation, and Biology: Lessons From a Long Century

Abstract: It is far from obvious that outside of highly specialized domains such as commercial agriculture, the methodology of biometrics—quantitative comparisons over groups of organisms—should be of any use in today’s bioinformatically informed biological sciences. The methods in our biometric textbooks, such as regressions and principal components analysis, make assumptions of homogeneity that are incompatible with current understandings of the origins of developmental or evolutionary data in historically contingent processes, processes that might have come out otherwise; the appropriate statistical methods are those suited to random walks, not normal distributions. A valid methodology would further require that especially close attention be paid to the difference between aspects of processes that are plastic, those that encode their own histories or biographies, and the very small fraction of quantifications that can usefully and realistically be modeled as varying by colored noise around a central tendency that itself has some quantitative meaning. This point of view—that only a vanishingly small fraction of the quantitative information borne by any living organism is worth quantifying—is illustrated by some data on a human birth defect, namely, fetal alcohol syndrome. In a suggestive metaphor, the biometrician is like the pilgrim in Friedrich’s painting Der Wanderer uber dem Nebelmeer, uncertain as to whether to measure the mountains or the clouds. The mountains stand for contingent history, the clouds for the subset of the data most closely matching controlled experiments suitable for quantitative biometric summary. Biometrics applies to the clouds, not the mountains. The success of statistical methods comes at the expense of all the theories that we simultaneously hold to be true about the biological materials to which they both pertain. Biometrics is thus complementary to all of the emerging reductionist sciences of biological structure.

On Systematists’ Single Objective Tree of Ancestors and Descendants

Abstract: It is often said that there is just one “objective” tree of life: a single accurate branching hierarchy of species reflecting order of descent. For any two species there is a single correct answer as to whether one is a “daughter” of the other, whether the two are “sister species” by virtue of their descent from a common parental species, whether they belong to a family line that excludes any given third species, and so on. This position is not right. We may whittle a tree of life, paring troublesome branches, in order to portray an ordering that admits of no legitimate dissent. But the history of life can sustain many legitimate arrangements of the same branches of species. The same can be said about other taxonomically relevant groups besides species, such as “Least Inclusive Taxonomic Units” (LITUs), so the basic claim survives even if we abandon traditional species. Similarly, the claim survives even if we distinguish between synchronic and diachronic groups, even if we consider polytomies, even if we distinguish between models and the world modeled, and even if we recognize an objective world. Nor is the claim merely an epistemic one.

Google Embryo for Building Quantitative Understanding of an Embryo As It Builds Itself. I. Lessons from Ganymede and Google Earth

Abstract: Google Earth allows us to obtain a new vision of the planet we live on, with an ability to zoom in from space to ground level detail at any point on Earth. As it is only recently that we have been able to look toward the Earth from space, we review instead the history of imaging of the Jupiter moon Ganymede, another globe, first seen by Galileo. Observations of Ganymede are mined for lessons on the importance and impact of improving imaging technology. Similarly, new insights may await us when we have proper tools for quantitatively looking at another unexplored globe, the embryo, in a sense for the first time.

Google Embryo for Building Quantitative Understanding of an Embryo As It Builds Itself. II. Progress Toward an Embryo Surface Microscope

Abstract: Embryos start out as tiny globes, on which many important events occur, including cell divisions, shape changes and changes of neighbors, waves of contraction and expansion, motion of cell sheets, extension of filopodia, shearing of cell connections, and differentiation and morphogenesis of tissues such as skin and brain. I propose to build a robotic microscope that would enable a new way to look at embryos: Google Embryo. This is akin to sending a space probe to Jupiter and its moons, sending back spectacular new visions of their complexity, activity, and beauty.

Can Synthetic Biology Shed Light on the Origins of Life

Abstract: It is a most commonly accepted hypothesis that life originated from inanimate matter, somehow being a synthetic product of organic aggregates, and as such a result of some sort of prebiotic synthetic biology. In the past decades, the newly formed scientific discipline of synthetic biology has set ambitious goals by pursuing the complete design and production of genetic circuits, entire genomes, or even whole organisms. I argue that synthetic biology might also shed some novel and interesting perspectives on the question of the origins of life, and that, in addition, it might challenge our most commonly accepted definitions of life, thereby changing the ways we might think about life and its origins.

Chemistry and the Engineering of Life Around 1900: Research and Reflections by Jacques Loeb

Abstract: Dissatisfied with the descriptive and speculative methods of evolutionary biology of his time, the physiologist Jacques Loeb (1859–1924), best known for his “engineering” approach to biology, reflected on the possibilities of artificially creating life in the laboratory. With the objective of experimentally tackling one of the crucial questions of organic evolution, i.e., the origin of life from inanimate matter, he rejected claims made by contemporary scientists of having produced artificial life through osmotic growth processes in inorganic salt solutions. According to Loeb, the answer to the question of whether or not life could be created artificially had to come from macro-molecular chemistry, in particular from the research on the recently discovered DNA. He was convinced that a prerequisite for making living matter from inanimate substances was the chemical synthesis of nuclear material capable of self-replication. Moreover, Loeb, experimentally refuting some vitalistic explanations as well as colloidal chemists’ far-reaching claims that biologically relevant macromolecules follow colloidal rather than chemical laws, pioneered research on the physical and chemical explanations of biological phenomena.

Rethinking the Meaning of Biological Information

Abstract: Throughout the history of molecular biology, the primary meaning of biological information has been taken from the image of a word-based linguistic code. I want to argue that the metaphor of such a code does not begin to capture either the variety or the richness of the processes by which nucleotide sequences inform biological processes. Current research demonstrates that nucleotide sequences inform not only development but also heredity and evolution, and they do so in all sorts of ways. Even though they do not exhaust the varieties of biological information employed in these processes, I claim that the power of DNA sequences to inform these processes is richer and perhaps far greater than the conventional understanding of genetic information permits, indeed richer than what any of our images of simple linguistic codes or of senders and receivers permits. Rather than a tape in a Turing machine or a message or signal sent through the generations, DNA is first and foremost a physicochemical structure with a range of potential uses by the physicochemical arsenal of biological cells that is so large as to expose the poverty of our most familiar metaphors. Recognition of this fact leads us to conclude that DNA is both more and less than we thought—more because it carries both symbolic and non-symbolic information and less because accepting that fact undermines its radical distinction from other biological molecules.

Specialty Boundaries, Compound Problems, and Collaborative Complexity

Abstract: Donald T. Campbell (1969) argued that the organization of university departments shaped the boundaries among specialties. This article extends his argument in two ways. First, specialties are also shaped by other institutions, such as sponsors and learned societies. Second, the intersection among specialties is shaped by the complexity of the problems that research addresses. Specialization of research is a way to deal with the complexity of nature. One way of doing this is to erect specialties that focus on different aspects of nature, and which do not overlap in subject matter. This view is the basis of Campbell’s “fish-scale” model of relations among specialties, and assumes that nature is descriptively complex in the sense of William C. Wimsatt (1974). But specialties often overlap and are thus interactively complex as well. Here I argue that a kind of interactive complexity—collaborative complexity—arises when research on a problem must take the not-yet-established contents of multiple specialties into account. Such compound problems are exemplified by attempts to explain historical particulars, such as particular adaptations in single species, e.g., masculinization in Spotted Hyenas (Crocuta crocuta).

The Edges and Boundaries of Biological Objects

Abstract: There are many different kinds of biological objects: species, organisms, genes, ecosystems, developmental systems, populations, colonies, higher taxa, microbes, monophyletic groups, etc. Some of these objects are nested one within another, like lineages—though this nesting may be complex (Wimsatt 1976). Other objects cut across these hierarchies in interesting and informative ways, sometimes producing surprising functional patterns, e.g., niches, guilds, ecosystems, and units of conservation. Moreover, some of these hierarchies are genealogical while others not. Objects may also change from one into another, or even overlap by sharing parts, spatially or temporally. Making matters more complicated, the edges and boundaries of biological objects are rarely, if ever, sharp. It is often unclear when and where one biological object ends and another one begins in space and time. Biologists need to be able to individuate each kind of object from one another, and particular objects from others of the same kind. This task is ongoing, demanding revisions as new evidence and hypotheses are discovered or adopted. Furthermore, delimiting biological objects is often not determined by empirical facts alone; which facts are salient may depend on theoretical and conceptual context. This problem of individuation cannot be avoided for any researcher working in the biological sciences; it permeates the discipline. A dynamic conceptualization of the edges and boundaries of these objects is needed—one in which common problems are recognized across these sciences. A central problem in identifying biological objects is that which empirical facts are relevant in determining where and when a biological object begins and ends, or what its parts are is very opaque; conceptual or theoretical frameworks are typically used for guidance in making these determinations. The upshot is that disputes over individuating biological objects are often over conceptual issues. This can take many shapes, e.g., how a conceptual debate plays out may determine which facts count as relevant, or even what counts as a fact of matter at all. The concepts in dispute may be biological or may concern deep ontological commitments, e.g., over the nature of object-hood or vagueness. Regardless of the specifics, it should come as no surprise that the disciplinary boundaries separating biology and philosophy are themselves blurred in these matters. We would further argue that these conditions give rise to excellent philosophical work on and in biology, and so should be encouraged. It was in this spirit that we proposed the workshop “The Edges and Boundaries of Biological Objects.” Though delimitation of biological objects is a problem that cuts across the disciplines, there is no field of study, professional societies, journals, or regular meetings dedicated to its study (more on this below with regard to Elihu Gerson’s contribution). Nonetheless, our conviction has been that much might be learned from gathering researchers to examine this suite of issues as a central research task. One of our goals was to facilitate collaboration between researchers across disciplinary boundaries both in biology and philosophy, by highlighting shared conceptual issues across a range of biological cases— hopefully encouraging novel applications of techniques common in one field of study to similar problems in other fields. To that end, we designed the workshop around cases and objects, inviting at least one philosopher and one biologist in each instance. Topics included characters, character states, and homologies; microbes; immunology and infectious disease; taxa; DNA barcoding; origins, major evolutionary transitions and cultural evolution; ecosystems; paleontology and fossil birds; and populations. Bookending these sessions were a keynote address by Michael Ghiselin on the metaphysics of taxonomy and a session on Scientific Perspectives and the Value of Boundaries. Together, these topics comprised a useful way of approaching the individuation problem. Though within each field of biology particular problems and historically important examples may drive discussion, by extending the topics covered beyond a single field or kind of biological object, more general conceptual problems in individuation could be extracted. For example, background metaphysical commitments matter, and genuine disagreement over ontology is not uncommon— but this should not be confused with a straightforward

Whose Boundary? An Individual Species Perspectival Approach to Borders

Abstract: Understanding ecological boundaries is recognized by ecologists as important for understanding ecosystem dynamics. All borders are borders in relation to some organism. However, much of the literature on habitat change ignores this basic ecological fact. In addition, borders are highly influenced by accidental or historical features of ecosystems, and researchers have in many cases defined them only in terms of convenience. Several viewpoints explored in this article reflect this skepticism about identifying ecosystems as real structured entities. I draw on Ghiselin’s (1974) hypothesis that species are not natural kinds but individuals, to develop a relational approach to ecological boundaries. I argue that with regard to ecology a border is always a border for a specific organism, and is a border in a specific manner for that organism. I draw on studies of two species of tsetse fly found in the Mauhoun river basin in Burkina Faso to illustrate why this relational approach is important. This approach may also help identify weaknesses in conservation efforts that have not properly asked the question, “Boundary for what?”

Mathematics and Measurements for High-throughput Quantitative Biology

Abstract: Bioscientists generate far more data than their minds can handle, and this trend is likely to continue. With the aid of a small set of versatile tools for mathematical modeling and statistical assessment, bioscientists can explore their real-world systems without experiencing data overflow. This article outlines an approach for combining modern high-throughput, low-cost, but non-selective biospectroscopy measurements with soft, multivariate biochemometrics data modeling to overview complex systems, test hypotheses, and making new discoveries. From preliminary, broad hypotheses and goals, many relevant samples are selected and measured with respect to many informative variables. The resulting tables represent a “cacophony” of data. From these, the most relevant and reliable “underlying harmonies and rhythms” are extracted and tested statistically, displayed for interpretation, and used for prediction. Outliers are detected automatically. Interesting subsets of samples can then be chosen for in-depth analyses in subsequent research cycles. This pragmatic, top-down approach takes advantage of developments in both “soft,” data-driven modeling and “hard,” knowledge-driven cultures. Data analytical examples show how information-rich biospectroscopy can be used for characterizing and quantifying known and unknown chemical constituents and physical phenomena in intact biosamples. This is based on a combination of deductive “hard” and inductive “soft” modeling. The examples represent NIR spectra of biochemical mixtures, FTIR spectra of a microbiological fermentation process, and FTIR analysis of fatty acids in milk for functional genomics.

Megavariate Genetics: What You Find Is What You Go Looking For

Abstract: The subjectivity or “purpose dependency” of measurement in biology is discussed using examples from high-dimensional medical genetic research The human observer and study designer tacitly determine the numerical and graphical representation of biological simplicity or complexity via choice of ascertainment (sampling frame), numbers to measure, referential basis, statistical learning formalism and feature search, and also via the selection of display styles (cognitive analogies) for all these quantifications

Metaphysics and Classification: Update and Overview

Abstract: The differences between classes and individuals are profound and the fact that biological species are individuals rather than classes provides the basis for organizing knowledge on a causal basis. The class of species is a natural kind and there are laws of nature for this and other classes of natural kinds such as the organism and the molecule. Particular species, like other individuals, function in historical narratives by virtue of laws of nature applying to them. The notion that species can evolve by changing their members is a category mistake. Darwin believed that there is no “essential” difference between species and subspecies in the sense that there is only a quantitative difference between them. The concept of biological species is defined on the basis of a qualitative difference. The rank of taxa can be used to distinguish between important natural kinds. Without such kinds language would become purely referential, and have no “sense” as Frege had put it.

Marjorie, Matriarchy, and “Wretched Reflection”: A Personal Remembrance of Marjorie Grene

Abstract: In biological terms, the word “matriarch” is associated with a particular kind of social organization, one where the female serves as leader of the group. For those keen on the natural world, it oftentimes conjures up a huge, lumbering elephant, gently guiding and protecting her progeny with her trunk, followed by a group of female relatives and adolescents (while all the while, the males are off being “rogue”). But the word in its Greek origination holds a deeper meaning, devoid of elephants or even of the social organization of any animals. It comes from the word mater, for mother, and archein, a difficult word to define that can mean origin, beginning, or even rule or principle, as in first principle. Immediately translated, the word matriarch means a mother—a woman—who serves simultaneously as originator, ruler, guide, or perhaps the source of being or point of origination. It is gendered to be sure, but that makes it even more appropriate for my remembrance of Marjorie. For many of us at the International Society for History, Philosophy, and Social Studies of Biology (ISHPSSB), Marjorie Grene served as a matriarch—a guide, a leader, the inspiration, the beginnings of our society. She was in fact in it from the start, not just in her intellectual efforts (more about that later) but also in organizing the first set of meetings at Cornell University with Dick Burian in the early 1980s that eventually paved the way for the creation of ISHPSSB. She, incidentally, called it the “multi-lettered, multi-presidented society” because of its awkward name and because so many people were honored as presidents (including Marjorie) at its inception. I attended the summer meetings organized by Marjorie and Dick, mostly because of the stunning list of luminaries. As a graduate student in ecology and evolutionary biology, keen on paleobotany, I was just too dazzled by the likes of Stephen J. Gould and Niles Eldredge to remember much else (this was at the peak of “punk eek” mania), but I do vaguely recall Marjorie and Dick sitting together in rickety wooden chairs near the front row in a room absolutely crowded with bodies. It was later, in the winter months, that I finally met Marjorie, face to face, in Karl Niklas’s office. They were meeting regularly to read Willi Hennig’s work—then all the rage—in German. As my doctoral advisor, Karl wanted me to meet someone he described as a “legend in her own time.” I vividly remember that meeting—she was seated in a chair immediately opposite him looking like a caricature of the eternal Radcliffe graduate, or a character out of an Iris Murdoch novel from the 1950s: short hair, plaid pleated skirt, black turtleneck, sensible shoes. So small, that she had to raise her arms to pick up their reading material from his desk, Marjorie seemed to disappear into her chair. This was deceptive, I quickly realized, as her voice boomed in fake indignation at hearing herself described in such an unimaginative cliché. She railed at him for some time, all with affection, of course, but then just as quickly focused her attention on me, asking about my research interests. She took an avid interest in younger people, especially women, a characteristic that has benefited many of us who were lucky enough to know Marjorie as young people. Her real interest became even more apparent, when a year or so later, I told her that I had turned to the history of science, and that I had chosen to work on the subject of botany and the evolutionary synthesis, thanks to the tutelage of Will Provine. A campus visit by George Ledyard Stebbins in 1986 practically sealed our friendship, since he was Marjorie’s close friend (her description, not mine). Visiting Cornell for some three weeks to deliver a series of lectures, Ledyard sought out Marjorie for good company. As his appointed “guide” (I was put in

A Bio-Logical Theory of Animal Learning

Abstract: Thisarticleprovidesthefoundationforanewpredictivetheory of animal learning that is based upon a simple logical model. The knowledge of experimental subjects at a given time is described using logical equations. These logical equations are thenusedtopredictasubject’sresponsewhenpresentedwitha knownorapreviouslyunknownsituation.Thisnewtheorysuccessfully anticipates phenomena that existing theories predict, aswellasphenomenathattheycannot.Itprovidesatheoretical account for phenomena that are beyond the domain of existing models, such as extinction and the detection of novelty, from which “external inhibition” can be explained. Examples of the methods applied to make predictions are given using previously published results. The present theory proposes a new way to envision the minimal functions of the nervous system, and provides possible new insights into the way that brains ultimately create and use knowledge about the world.

How Quantification Persuades When It Persuades

Abstract: Although Harry Woolf’s great collective volume Quantification (1961) mostly overlooked biology, Thomas Kuhn’s chapter there on the role of quantitative measurement within the physical sciences maps quite well onto the forms of reasoning that actually persuade us as biologists 50 years later. Kuhn distinguished between two contexts, that of producing quantitative anomalies (instead of “reasonable agreement” between data and theory) and that of resolving them. The implied form of reasoning is actually C. S. Peirce’s abduction or inference to the best explanation: “The surprising fact C is observed; but if A were true, C would be a matter of course; hence there is reason to suspect that A is true.” This article reviews abduction and the Kuhnian dichotomy in a range of classic examples where quantitative reasoning has ended arguments in the natural sciences. Included are John Snow’s discovery of the cause of cholera, Jean Perrin’s proof that atoms exist, the discovery of the double helix, the Alvarezes’ explanation of the extraterrestrial origin of the Cretaceous-Tertiary extinction, and current examples in passive smoking, ulcers, and the anthropogenicity of global warming. Modern biology is a quantitative science to the extent that we operate by “strong inference,” the insistence that our data are surprising on everybody else’s hypotheses but follow as a matter of course from our own, and that we demand numerical consilience whenever we infer across levels of analysis or across disciplines.