Arbuscular mycorrhiza (AM), a type of plant‐fungal endosymbiosis, and nodulation, a bacterial‐plant endosymbiosis, are the most ubiquitous symbioses on earth. Recent findings have established part of a shared genetic basis underlying these interactions. Here, we approach root endosymbioses through the lens of the homology and modularity concepts aiming at further clarifying the proximate and ultimate causes for the establishment of these biological systems. We review the genetics that underlie interspecific signaling and its concomitant shift in genetic programs for either partner. (...) Also, through the comparative analysis of genetic modules shared by AM and nodulation symbioses, we identify fundamental nodes in these networks, suggesting the elemental steps that may have permitted symbiotic adaptation. Here, we show that this approach, allied to recent technical advances in the study of genetic systems architecture, can provide clear testable hypotheses for the advancement of our understanding on the evolution and development of symbiotic systems. (shrink)

No single theory so far proposed gives a wholly satisfactory account of the origin and maintenance of bird-song dialects. This failure is the consequence of a weak comparative literature that precludes careful comparisons among species or studies, and of the complexity of the issues involved. Complexity arises because dialects seem to bear upon a wide range of features in the life history of bird species. We give an account of the principal issues in bird-song dialects: evolution of vocal learning, experimental (...) findings on song ontogeny, dialect descriptions, female and male reactions to differences in dialect, and population genetics and dispersal.We present a synthetic theory of the origin and maintenance of song dialects, one that accommodates most of the different systems reported in the literature. The few data available suggest that large, regional dialect populations are genetically differentiated; this pattern is correlated with reduced dispersal between dialects, assortative mating by females, and male-male exclusion. At the same time, “subdialects” may be formed within regional dialects. Subdialect clusters are usually small and may represent vocal mimicry among a few adjacent territorial males. The relative importance of genetic and social adaptation may contribute to the emergence of subdialects; their distinctiveness may be correlated with the degree of polygyny, for example. Thus, subdialect formation is linked to one theory of the evolution of repertoire size, but data are too fragmentary to examine this idea critically. (shrink)

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution (...) are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification. (shrink)

Although “theory” has been the prevalent unit of analysis in the meta-study of science throughout most of the twentieth century, the concept remains elusive. I further explore the leitmotiv of several authors in this issue: that we should deal with theorizing (rather than theory) in biology as a cognitive activity that is to be investigated naturalistically. I first contrast how philosophers and biologists have tended to think about theory in the last century or so, and consider recent calls to upgrade (...) the role of theory in the life sciences against the background of the recent “data deluge” in molecular biology, systems biology, etc. I then review thinking about theory in biology in relation to physical theory as a positive or negative exemplar. I conclude by discussing various aspects of a positive program for “naturalizing theorizing.”. (shrink)

Using the Burgess Shale controversies as a case-study, this paper argues that controversies within different domains may interact as to create a situation of "complicated intricacies," where the practicing scientist has to navigate through a context of multiple thought collectives. To some extent each of these collectives has its own dynamic complete with fairly negotiated standards for investigation and explanation, theoretical background assumptions and certain peculiarities of practice. But the intellectual development in one of these collectives may "spill over" having (...) far reaching consequences for the treatment of apparently independent epistemic problems that are subject of investigation in other thought collectives. For the practicing scientist it is necessary to take this complex web of interactions into account in order to be able to navigate in such a situation. So far most studies of academic science have had a tendency to treat the practicing scientist as members of a single (enclosed) thought collective that stands intellectually isolated from other similar entities unless the discipline was in a state of crisis of paradigmatic proportions. The richness and complexity of Burgess Shale debate shows that this encapsulated kind of analysis is not enough. (shrink)

This article traces my attempts to come to grips with the problem of change. Systems science deals with general principles, but, as with science in general, is wedded to mechanistic models. Natural systems are not machines, are generative, and can change unpredictably. An example is given showing that explicit dynamical models are subverted by the present moment, which is non-existent in them. This moment can be modeled by a compositional hierarchy, but no change happens therein. Subsumptive hierarchies can serve as (...) metaperspectives on change, modeling stages of development. The Second Law of thermodynamics provides the motivation for development, which can be modeled generally using thermodynamic and information theoretic (infodynamic) concepts. Development is progressive change, constitutive of different systems, and goes from vagueness toward increasingly more definite embodiment, ending up in senescence, which derives from information overload. While becoming increasingly burdened with information, the present moment, as such, still evades this developmental systematicity. Internalist thinking has emerged as an attempt to further come to grips with it. (shrink)

Infertility affects 15 per cent of the world's couples. Research at Edinburgh University has been directed at transplanting fetal ovarian tissue into infertile women, thus enabling them to bear children. Fetal ovary transplantation (FOT) has generated substantial controversy; in fact, one ethicist deemed the procedure 'so grotesque as to be unbelievable' (1). Some have suggested that fetal eggs may harbour unknown chromosomal abnormalities: however, there is no evidence that these eggs possess a higher incidence of genetic anomaly than ova found (...) in a healthy adult female. There is also concern that fetal egg children will be psychologically harmed by the knowledge of their special conceptual status. It will be demonstrated that special conceptual status in and of itself does not determine developmental success. Rather, psychological well-being is dependent upon how the family and child cope with the unique challenges inherent in FOT. Lastly, though considering FOT a legitimate method of family building, given the global population crisis the wisdom of procreational rights will be challenged. Inherent to this challenge is a re-evaluation of the treatment of infertility as a significant disease necessitating remedy. (shrink)

For several decades, economists have been preoccupied with an attempt to place their entire subject on the ‘sound microfoundations’ of general equilibrium theory, with its individualistic premises. However, this project has run into seemingly intractable problems. This essay examines underlying questions such as the appropriate building block of analysis and the structure of explanation in economics. The examination of biology is found to be instructive, due to debates concerning the limitations of reductionism within that discipline. The final part of the (...) paper argues for the autonomy of a non‐reductionist macroeconomics, based on the institution as the unit of analysis. (shrink)

The primary method by which science endeavors to order the world is the analytic approach, consistent with Cartesian principles of dividing the problem in as many sections as required for an optimal solution, and progressing from the simplest to the most complex reasoning. When the interactions among the various elements of the system being studied are minimal, such a procedure indeed makes it possible to formulate laws that describe chains of causality. However, when the variables are interdependent and linked by (...) non-linear equations, the atomistic method cannot account for the phenomenon in its entirety. Spurred by this inadequacy, scientists sought to discover synthetic methods which, early in the twentieth century, led to the conceptualization of holistic theories in a number of disciplines. The most highly developed fields are the psychology of form, structural anthropology (1), and the various systems theories (2). More recently, the development of epigenetic concepts in biology has corresponded to the appearance of different theories of pattern in physics and mathematics (3, 4) and to the progressive emergence of the concept of self-organization (5, 6, 7). The objective is to explain the production of complex structures on the basis of interacting elements, none of which contains a guiding scheme that dictates these structures. In biology, the challenge is to locate the constraints that are expressed in a space of possibilities (8) in order to develop a theory of organization that is capable of predicting the finite number of forms that living creatures can assume (9). This school of thought can be described as structuralist, emergentist, self-organizational, or epigeneticist, depending on the theoretical version that is emphasized. (shrink)

Terminology within the biological sciences gets its import not just from semantic meaning, but also from the way it functions within the rhetorics of the various disciplinary practices. The ‘sociobiology’ of human behavior inherits three distinct rhetorics from the genetic disciplines. Sociobiologists use population genetic, biometrical genetic, and molecular genetic rhetorics, without acknowledging the conceptual and experimental constraints that are assumed by geneticists. The eclectic blending of these three rhetorics obscures important differences of context and meaning. Sociobiologists use foundational terms (...) in genetics, such as ‘gene’, ‘fitness’, ‘evolution’, ‘heritability’, ‘trait’ and ‘polygenic inheritance’, in starkly different ways from geneticists, while basing their analysis of human behavior on the implied authority of genetics. As a free‐floating ‘gene talk’ moves across different disciplinary contexts, and before different audiences, it takes the form of an over‐simplified and misleading arch‐determinism. The result is widespread application of vague, incomplete, and distorted biological theory. If most sociobiologists, do not deliberately promote biological determinism, still less a political agenda, there is ample evidence that they misconstrue the implications of the genetic language that they borrow. (shrink)

Systems involving many interacting variables are at the heart of the natural and social sciences. Causal language is pervasive in the analysis of such systems, especially when insight into their behavior is translated into policy decisions. This is exemplified by economics, but to an increasing extent also by biology, due to the advent of sophisticated tools to identify the genetic basis of many diseases. It is argued here that a regularity notion of causality can only be meaningfully defined for systems (...) with linear interactions among their variables. For the vastly more important class of nonlinear systems, no such notion is likely to exist. This thesis is developed with examples of dynamical systems taken mostly from mathematical biology. It is discussed with particular reference to the problem of causal inference in complex genetic systems, systems for which often only statistical characterizations exist. (shrink)

Quine has developed two reasons for thinking that our ontology should not include the ontological category of properties. His first point is that the criterion for individuating properties is unclear, and the second is that postulating the existence of properties would not explain anything. In what follows I critically examine these two themes, which I will call the clarity argument and the parsimony argument. Although I will suggest that these two arguments are defective, I also will try to show that (...) certain related arguments on behalf of the existence of properties are likewise flawed. This will set the stage for the discussion in the fourth section of the perspective provided by evolutionary theory on the question of the ontological status of properties. It will emerge that evolutionary theory provides reason for thinking that properties exist, and, additionally, gives an interesting point of view on the epistemological and metaphysical issues that Quine has addressed. (shrink)

This paper considers recent heated debates led by Jerry A. Coyne andMichael J. Wade on issues stemming from the 1929–1962 R.A. Fisher-Sewall Wrightcontroversy in population genetics. William B. Provine once remarked that theFisher-Wright controversy is central, fundamental, and very influential.Indeed,it is also persistent. The argumentative structure of therecent (1997–2000) debates is analyzed with the aim of eliminating a logicalconflict in them, viz., that the two sides in the debates havedifferent aims and that, as such, they are talking past each other. (...) Given aphilosophical analysis of the argumentative structure of the debates,suggestions supportive of Wade's work on the debate are made that areaimed, modestly, at putting the persistent Fisher-Wright controversy on thecourse to resolution. (shrink)

Edward O. Wilson's forays into human sociobiology have been the target of persistent, vehement attack by his Harvard colleague in evolutionary biology, Richard C. Lewontin. Through examination of existing documents in the case, together with in-depth personal interviews of Wilson, Lewontin, and other biologists, the reasons for Wilson's stance and Lewontin's criticisms are uncovered. It is argued that the dispute is not primarily personally or politically motivated, but involves a conflict between long-term scientific-cum-moral agendas, with the reductionist program as a (...) key issue. It is concluded that it is in the interest of both disputants to keep the controversy alive. (shrink)

In this paper I trace Michael Ruse's Booknotes from the first volumeof Biology and Philosophy in 1986 to the present. I deal withboth the style and the content of these booknotes. Ruse paid specialattention to authors outside of the traditional English axis as wellas to feminist writers. He complained that too much attention wasbeing paid to certain topics (e.g., evolutionary ethics, evolutionaryepistemology, the species problem and reduction) while other, moreimportant topics were all but ignored (e.g., natural selection,population genetics, levels of (...) selection and extraterrestrial life).He also dealt with the Darwin Industry. Creationism, his love-haterelationships with several authors and his undiluted love of CharlesDickens. (shrink)

The beanbag genetics controversy can be traced from the dispute between Fisher and Wright, through Mayr''s influential promotion of the issue, to the contemporary units of selection debate. It centers on the claim that genic models of natural selection break down in the face of epistatic interactions among genes during phenotypic development. This claim is explored from both a conceptual and a quantitative point of view, and is shown to be defective on both counts.Firstly, an analysis of the controversy''s theoretical (...) origins demonstrates that this claim derives from a misinterpretation of the conceptual foundations of Fisher''s genetical theory of natural selection, and confounds his fundamentally different concepts of the average excess and average effect of a gene. Secondly, an extension of the genic approach is proposed which models the dynamics of selection among epistatically interacting complexes of many genes. Paradoxically, this preliminary, but fundamentally genic model provides quantitative support for some controversial qualitative claims regarding the evolutionary consequences of strong gene interactions made by opponents of genic selectionism, including Mayr''s theory of peripartric speciation. These findings foster hope that the proposed approach may eventually nudge the beanbag controversy out of its conceptual trenches into a more empirically oriented dialogue. (shrink)

There is a long history of controversy in ecology over the role of competition in determining patterns of distribution and abundance, and over the significance of the mathematical modeling of competitive interactions. This paper examines the controversy. Three kinds of considerations have been involved at one time or another during the history of this debate. There has been dispute about the kinds of regularities ecologists can expect to find, about the significance of evolutionary considerations for ecological inquiry, and about the (...) empirical credentials of theoretical studies of competition. Each of these elements is examined with an eye toward gaining philosophical clarification of the issues involved. In the process, certain shortcomings of contemporary philosophical theories are revealed. In particular, I argue that plausibility arguments based on background considerations are an important part of the model building tradition, but that current accounts of the structure and evaluation of scientific theories do little to illuminate this side of theoretical ecology. (shrink)

Biology cannot accommodate all aspects of culture. Aspects of culture that a biological approach can take into account can be covered by the biological categories of phenotype and environment. There is no need to treat culture as a separate category. Attempts to elaborate biological explanations of cultural variation will meet with success only if biologists expand theories of development, and integrate them in evolutionary biology. The alternative — elaborating the idea of so-called cultural inheritance — makes little sense from a (...) biological point of view. (shrink)

Implications of variance in the time at which sibs become mature are considered, particularly with respect to the fragmentation of a parental genome over time. It is concluded that regardless of the adaptive derivation of various intra-sibship maturation schedules, they each have important genetic consequences.

Maynard Smith’s defenses of adaptationism and of the value of optimization theory in evolutionary biology are both criticized. His defense does not adequately respond to the criticism of adaptationism by Gould and Lewontin. It is also argued here that natural selection cannot be interpreted as an optimization process if the objective function to be optimized is either (i) interpretable as a fitness, or (ii) correlated with the mean population fitness. This result holds even if fitnesses are frequency-independent; the problem is (...) further exacerbated in the frequency-dependent context modeled by evolutionary game theory. However, Eshel and Feldman’s new results on “long-term” evolution may provide some hope for the continuing relevance of the game-theoretic framework. These arguments also demonstrate the irrelevance of attempts by Intelligent Design creationists to use computational limits on optimization algorithms as evidence against evolutionary theory. It is pointed out that adaptation, natural selection, and optimization are not equivalent processes in the context of biological evolution. (shrink)