Certain species of fish have recently become important model systems in comparative genomics and in developmental biology, in certain instances because of their small genome sizes (e.g., in the pufferfish) and, in other cases, because of the opportunity they provide to combine an easily accessible and experimentally manipulable embryology with the power of genetic approaches (e.g., in the zebrafish). The resulting accumulation of genomic information indicates that, surprisingly, many gene families of fish consist of more members than in mammals. Most (...) modern fish, including the zebrafish and medakka, are diploid organisms; however, the greater number of genes in fish was possibly caused by additional ancient genome duplications which happened in the lineage leading to modern ray-finned fishes but not along the lineage leading to tetrapods. Since these two lineages shared their last common ancestor (in the Devonian about 360 million years ago) individual duplicated members of gene families were later lost in fish. Interestingly, comparative data indicate that, in some cases, genes in mammals even serve somewhat different functions than their homologues in fish, highlighting that the degree of evolutionary relatedness of genes is not always a reliable predictor of their evolutionary conservation and their similarity of function. Since fish are phenotypically probably not more complex than mammals, it is possible that evolution took alternative paths to the “economics of genomics” through alternative solutions to gene regulation. It is suggested that the more complex genomic architecture of fish permitted them to adapt and speciate quickly in response to changing selective regimes. BioEssays 20:511–515, 1998. © 1998 John Wiley & Sons, Inc. (shrink)

The biological species (biospecies) concept applies only to sexually reproducing species, which means that until sexual reproduction evolved, there were no biospecies. On the universal tree of life, biospecies concepts therefore apply only to a relatively small number of clades, notably plants andanimals. I argue that it is useful to treat the various ways of being a species (species modes) as traits of clades. By extension from biospecies to the other concepts intended to capture the natural realities of what keeps (...) taxa distinct, we can treat other modes as traits also, and so come to understand that theplurality of species concepts reflects the biological realities of monophyletic groups.We should expect that specialists in different organisms will tend to favour those concepts that best represent the intrinsic mechanisms that keep taxa distinct in their clades. I will address the question whether modes ofreproduction such as asexual and sexual reproduction are natural classes, given that they are paraphyletic in most clades. (shrink)

The evolutionary problem of the units of selection has elicited a good deal of conceptual work from philosophers. We review this work to determine where the issues now stand.

This paper analyzes the concept of biodiversity in conservation biology and assesses potential methods for its measurement.

A number of recent biologists have used multi-level selection theory to help explain the major transitions in evolution. I argue that in doing so, they have shifted from a ‘synchronic’ to a ‘diachronic’ formulation of the levels of selection question. The implications of this shift in perspective are explored, in relation to an ambiguity in the meaning of multi-level selection. Though the ambiguity is well-known, it has never before been discussed in the context of the major transitions.

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to this (...) controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (shrink)

David Hull's analysis of conceptual change in science, as presentedin his book, Science as a Process (1988), provides a useful framework for understanding one of the scientific controversies in which he actively and constructively intervened, the units of selectiondebates in evolutionary biology. What follows is a brief overview ofthose debates and some reflections on them.

The conflation of two fundamentally distinct issues has generated serious confusion in the philosophical and biological literature concerning the units of selection. The question of how a unit of selection of defined, theoretically, is rarely distinguished from the question of how to determine the empirical accuracy of claims--either specific or general--concerning which unit(s) is undergoing selection processes. In this paper, I begin by refining a definition of the unit of selection, first presented in the philosophical literature by William Wimsatt, which (...) is grounded in the structure of natural selection models. I then explore the implications of this structural definition for empirical evaluation of claims about units of selection. I consider criticisms of this view presented by Elliott Sober--criticisms taken by some (for example, Mayo and Gilinsky 1987) to provide definitive damage to the structuralist account. I shall show that Sober has misinterpreted the structuralist views; he knocks down a straw man in order to motivate his own causal account. Furthermore, I shall argue, Sober's causal account is dependent on the structuralist account that he rejects. I conclude by indicating how the refined structural definition can clarify which sorts of empirical evidence could be brought to bear on a controversial case involving units of selection. (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

John Dupré explores the ways in which we categorize animals, including humans, and comes to refreshingly radical conclusions. He opposes the idea that there is only one legitimate way of classifying things in the natural world, the 'scientific' way. The lesson we should learn from Darwin is to reject the idea that each organism has an essence that determines its necessary place in the unique hierarchy of things. Nature is not like that: it is not organized in a single system. (...) For instance, there is no universal principle by which organisms can be sorted into species. We are obliged to accept that different classificatory schemes are equally valid, and to take a pluralistic view of biology and the human sciences. These provocative and readable essays move on to discuss a set of contentious topics relating to human nature. To start with, Dupré argues that the concept of a universal human nature should be rejected. He questions the relevance of evolution to explanation of human behaviour, and casts doubt on the concept of normality in human behaviour. He shows that misunderstanding of biology and evolution has lead to widespread misconceptions about human sex and gender-in particular, about sexual behaviour and gender roles. The books concludes with a pair of essays about the differences between humans and animals, which may not be quite so clear-cut as we think. (shrink)

Whenever the state of a biological system is not determined solely by present conditions but depends on its past history, we can say that the system has memory. Bacteria and bacteriophage use a variety of memory mechanisms, some of which seem to convey adaptive value. A genetic type of heritable memory is the programmed inversion of specific DNA sequences, which causes switching between alternative patterns of gene expression. Heritable memory can also be based on epigenetic circuits, in which a system (...) with two possible steady states is locked in one or the other state by a positive feedback loop. Epigenetic states have been observed in a variety of cellular processes, and are maintained by diverse mechanisms. Some of these involve alternative DNA methylation patterns that are stably transmitted to daughter molecules and can affect DNA–protein interactions (e.g., gene transcription). Other mechanisms exploit autocatalytic loops whereby proteins establish the proper conditions for their continued synthesis. Template polymers other than nucleic acids (e.g., components of the cell wall) may also propagate epigenetic states. Non‐heritable memory is exemplified by parasitic organisms that bear a signature of their previous host, such as host‐controlled modification of phage DNA or porin hitchhiking in predatory bacteria. The heterogeneous nature of the examples known may be indicative of widespread occurrence of memory mechanisms in bacteria and phage. However, the actual extent, variety and potential selective value of prokaryotic memory devices remain open questions, still to be addressed experimentally. BioEssays 24:512–518, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Richard Lewontin's (1970) early work on the units of selection initiated the conceptual and theoretical investigations that have led to the hierarchical perspective on selection that has reached near consensus status today. This paper explores other aspects of his work, work on what he termed continuity and quasi-independence, that connect to contemporary explorations of modularity in development and evolution. I characterize such modules and argue that they are the true units of selection in that they are what evolution by natural (...) selection individuates, selects among, and transforms. (shrink)

Motile bacteria respond to environmental cues to move to more favorable locations. The components of the chemotaxis signal transduction systems that mediate these responses are highly conserved among prokaryotes including both eubacterial and archael species. The best‐studied system is that found in Escherichia coli. Attractant and repellant chemicals are sensed through their interactions with transmembrane chemoreceptor proteins that are localized in multimeric assemblies at one or both cell poles together with a histidine protein kinase, CheA, an SH3‐like adaptor protein, CheW, (...) and a phosphoprotein phosphatase, CheZ. These multimeric protein assemblies act to control the level of phosphorylation of a response regulator, CheY, which dictates flagellar motion. Bacterial chemotaxis is one of the most‐understood signal transduction systems, and many biochemical and structural details of this system have been elucidated. This is an exciting field of study because the depth of knowledge now allows the detailed molecular mechanisms of transmembrane signaling and signal processing to be investigated. BioEssays 28:9–22, 2006. © 2005 Wiley Periodicals, Inc. (shrink)

Historically, philosophers of biology have tended to sidestep the problem of development by focusing primarily on evolutionary biology and, more recently, on molecular biology and genetics. Quite often too, development has been misunderstood as simply, or even primarily, a matter of gene activation and regulation. Nowadays a growing number of philosophers of science are focusing their analyses on the complexities of development, and in Embryology, Epigenesis and Evolution Jason Scott Robert explores the nature of development against current trends in biological (...) theory and practice and looks at the interrelations between development and evolution, an area of resurgent biological interest. Clearly written, this book should be of interest to students and professionals in the philosophy of science and the philosophy of biology. (shrink)

Holism and reductionism are usually seen as opposite and mutually exclusive approaches to nature. Recently, some have come to see them as complementary rather than mutually exclusive. In this book I have argued that, even stronger, they should be seen as mutually dependent and co-operating research programmes. I have discussed holism and reductionism in biology in general and in ecology in particular. After an introductory chapter I have provided an overview of holistic and reductionistic positions in biology, and of the (...) reduction problems to which they relate. I have argued that it is extremely important to distinguish between ontological, epistemological and methodological aspects of these problems. The overview has shown that there are actually several approaches to reduction problems in biology, which can be characterized as more or less radically or moderately holistic or reductionistic. It has shown also that there are three major ’contradistinctions’ between holism and reductionism in biology, to wit the doctrine of emergence versus the reduction thesis; functional explanations versus causal explanations; and phenomenology versus mechanicism. In later chapters I have shown that these ’contradistinctions’ are not really contradistinctions at all. In the next chapters I have discussed the terms ’reduce’ and ’reduction’ in science. In chapter 3 I have discussed the reduction of laws and theories. I have shown that there are many different types of reduction depending on the auxiliary hypotheses that are being used in addition to the reducing theory: approximation-, aggregation, correlation and/or identification-hypotheses. The distinctions between these types has later, in chapter 5, proved to be of great importance in defining the concept of ’emergence’. The major conclusion of chapter 3 was that reduction is an epistemological issue, pertaining to logical relations between statements or systems of statements. It should not be confused, therefore, with ’ontological reduction’, certainly not in one of its ordinary senses, such as diminishing, devaluating or the like. Scientific reductions are, with the exception of instrumentalistic reductions, kinds of explanation, and, moreover, non-eliminative kinds of explanation. This means that a reduced law or theory is not eliminated by the reducing theory but rather consolidated or even reinforced. The ontology of the reduced law or theory is thereby also being consolidated. In chapter 4 I have argued that the same holds for reductions of concepts. Concept reductions are supposed to be accomplished by means of so-called ontological identity relations, which are in turn supposed to connect terms in the law or theory to be reduced, which do not occur in the reducing theory, with theoretical terms of the reducing theory. Because they are called ontological identity relations, several philosophers have thought that concept reductions imply some form of ontological reduction. And because they often occur in the context of micro-reductions, some have even thought that concept reductions are themselves micro-reductions. As a result, the idea has arisen that ontological identity relations are connections between macro-concepts and micro-concepts. However, concept reductions by means of ontological identity relations cannot be micro-reductions, because micro-reduction is, by definition, reduction with an aggregation step. Moreover, ontological identity relations are relations between different representations of and the same type of thing or attribute. That is, they express different epistemological sides of the same ontological coin. Therefore, concept reductions cannot be considered ontological reductions either, certainly not in the ordinary sense of diminishing, devaluating or the like. Thus, concept reduction is, like law or theory reduction, an epistemological issue: it pertains to relations between, in this case, different concepts or representations of one and the same type of thing or attribute. ’Ontological reduction’, then, may, in the context of scientific reductions, actually be considered a contradiction of terms. In chapter 5 I have linked this conclusion to the emergence thesis and to the alleged contradistinction between this thesis and the reduction thesis. I have shown that the doctrine of emergence actually consists of two separate claims, namely an ontological thesis stating that a whole has emergent properties which the component parts do not possess, neither separately nor in other partial combinations; and an epistemological thesis stating that emergent properties of wholes are ’in principle’ irreducible. I have argued that the first claim may be regarded as a valid, universal thesis about relations between properties of wholes and properties of parts, but that the second claim is untenable. I have discussed many emergent properties of wholes, biological as well as physico-chemical, that have proved to be explainable in terms of micro-theories about the component parts and auxiliary hypotheses. Once again, however, it is important to realize that reduction is an epistemological issue, whereas emergence, in the sense of thesis, is an ontological one. It is not ’wholes’ or ’emergent properties of wholes’ that are being reduced but statements about them. Reduction is a kind of explanation, not of explaining-away. Thus, it leaves the ontology of whatever is reduced fully intact. I have developed a new definition of the term ’emergence’ which expresses emergence in terms of the auxiliary hypotheses that may be used in reductions, in particular aggregation-, correlation- and identification-hypotheses. This has even lead to two very remarkable conclusions. First, emergence may be considered the opposite of ontological identity. And second, if there were no emergence, there wouldn’t be any reductions either. to reduce.) In this respect, therefore, there is absolutely no contradistinction between holism and reductionism. On these grounds I have introduced my thesis that holism and reductionism should rather be seen as mutually dependent, and hence co-operating, research programmes than as conflicting views of nature or of relations between sciences. Holistic programmes play an important role in science as guide programmes for reductionistic programmes by discovering or developing macro-laws or -theories about phenomena at the level of wholes, which they themselves, however, cannot explain. For these explanations they depend on the fruits of reductionistic programmes. If the latter succeed in providing the explanations they act as supply programmes for the holistic guide programmes. Reductionistic programmes depend in turn on holistic programmes for providing the macro-laws or -theories that call for these explanations. In chapter 6 I have discussed an example of this mutual dependency in the form of the reduction of the Bohr-effect in animal physiology. I have shown that this law has been reduced to the theory of allostery, applied to hemoglobin molecules in red blood cells, and that this application of the theory of allostery has been reduced to the theory of chemical bonding. I have also shown that at least six research programmes were involved in these reductions, and that the relations between these programmes can be characterized very well in terms of the model of holistic guide programmes and reductionistic supply programmes. The only, but highly significant, qualification appearing from example was that the terms ’holistic’ and ’reductionistic’ are extremely relative and should always be related to a certain given level of organization. In chapter 7 I have resolved the remaining contradistinction between holism and reductionism in biology, viz. the need for functional explanations and the demand that explanations be causal. I have shown that functional explanations are perfectly legitimate explanations which in a sense can be reconstrued as causal explanations. I have argued that functional explanations are indispensable components of more comprehensive, causal-evolutionary explanations, because the latter appeal to the adaptive value, and hence the function, of the property to be explained. In that sense functions can be regarded as adaptations, and functional explanations can be regarded as a sort of ’short-hand’ for evolutionary explanations. Finally, I have shown that in the context of functional explanations, too, co-operation of holistic and reductionistic research programmes occurs. In part 2 I have applied my thesis to ecology. I have shown that in ecology too, holismreductionism disputes notwithstanding, co-operation of holistic and reductionistic research programmes occurs, or, in so far as this appears to be not the case, that it should be strived after. In chapter 8 I have given an overview of reduction problems in ecology and of the various approaches to these problems. I have noticed that in ecology, too, there are several, radical, moderate and anti-reductionistic research strategies, with respect to the levels of both ecosystems, communities and populations. I have also noticed, however, that concrete solutions to reduction problems in ecology are frustrated by what is called the intellectual immaturity or the anomalous status of ecology. This refers to the almost complete lack of general laws and theories in ecology, at least at the higher levels of communities and ecosystems. Of a number of possible causes I have lifted out two, which lend themselves to philosophical analysis and clarification. The first one is the ambiguity of a major part of the ecological vocabulary. This was the subject of chapters 9 and 10. The second is the inhibitory effect which holism-reductionism disputes have on the growth of knowledge. This was the subject of chapter 13. In chapter 9 I have discussed the concept of an community. It appeared that the term ’community’ is used for several different entities at various levels of organization. This ambiguity alone seems to be sufficient for the lack of ’general’ laws and theories about ’communities’. My purpose in chapter 9 was to try and contribute to a solution of this problem. In doing so I have argued, first, that it seems wise to use the term ’community’ only for groups of species belonging to a single taxonomic or phylogenetic group, and to use the term ’biocoenosis’ for the higher level of organization, defined as the biotic component of an ecosystem. Next I have argued that, although species within communities may of course interact with each other, interaction is itself not a necessary or sufficient condition for community membership. Finally, I have hit upon what is known as the most notorious problem in community ecology, to wit the boundary problem, as well as the problem of heterogeneity. I have found that the cause of these problems lies in the fact that communities are almost invariably being seen as groups of populations occurring together in space and time, whereas the empirical fact is rather that populations of different species mostly do not occur together in the same space, and, moreover, that the species composition of communities changes continuously. This has lead to the suggestion that a community had better be defined as the group of individuals of two or more species occurring in the area of intersection of populations of these species. It is only in such intersection areas that one can really talk of the co-occurrence of species. I have shown the empirical adequacy of this definition by discussing various salt marsh plant communities on the Dutch island of Schiermonnikoog. In chapter 10 I have clarified two other important, yet highly controversial, concepts in ecology, to wit habitat and niche. It appeared that there are at least four different habitat concepts in ecology, and as many niche concepts, the additional complication being that two of these habitat concepts correspond to two of these niche concepts, whence the distinction between habitat and niche is blurred. In addition, different habitat concepts appeared to correspond to different environment concepts and also to different biotope concepts. My purpose in chapter 10 was to disentangle all these concepts from one another and to supply each of them with a suitable term. I have done so by keeping a close eye on commonly accepted notions about habitat differentiation and niche differentiation, two ’principles’ allowing one to explain the coexistence or non-coexistence of species in communities. The results can be found in boxes 5 and 7 in chapter 10. In chapter 11 I was finally able to substantiate my claim that in ecology, too, co-operation of holistic and reductionistic research programmes occurs. I have discussed the reduction of the classical competition model of Lotka and Volterra to modern niche theory. The Lotka/Volterra model is a phenomenological model: it describes the possible effects of competition between two species. Modern niche theory, on the other hand, is a mechanistic theory, in which both the objects of competition and a mechanism are being specified. I have shown that the reduction was established with the help of a relatively simple identification hypothesis and two relatively simple aggregation hypotheses, making it yet another example of heterogeneous microreduction in biology. In the reduction, the Lotka/Volterra model acted as a holistic guide programme and modern niche theory acted as a reductionistic supply programme. In chapter 12 I have discussed another example of co-operation in the form of the approximative reduction of MacArthur and Wilson’s equilibrium theory of island biogeography. I have argued that this can be seen as a holistic model, which has been of great unifying and especially heuristic value, but which in time has been found to be a bit too simple and in some respects had to be corrected. Therefore, it can also be seen as an idealization in the sense of the model of idealization and concretization, which subsequent research programmes have concretized. Because these concretizations have a reductive character, we can see in this structure of idealization and concretization yet another example of the co-operation of holistic and reductionistic research programmes in ecology. A philosophically interesting side-conclusion was that the model of idealization and concretization thus appears to apply also to relations between research programmes, and not only to programme-internal developments. In chapter 13 I have discussed an example of the inhibitory effect that holism-reductionism disputes may have on the growth of knowledge. The example concerns a controversy in island biogeography over the role of interspecific competition in structuring communities. This controversy has lasted for about ten years, appeares to have died out rather than to have been resolved, and has produced nothing new in the field of explanations of community structure. I have shown that the major factors underlying the controversy were differing, in casu holistic and reductionistic, views of communities. Though this presented a problem for my thesis, I have argued that, ultimately, the controversy can be resolved, and in a sense has been resolved, in a way that corroborates my thesis. In the epilogue, finally, I have mentioned some remaining problems concerning the adequacy of the present reduction model in dealing with reduction in ecology. These problems pertain to the question of specificty of ecological laws and theories, the likelihood that reductions in ecology generally occur on the basis of several reducing micro-theories, and the possible relationship between the former two points. (shrink)

This important collection focuses on the nature and importance of biodiversity. The concept is clarified and its intrinsic and instrumental value are discussed. Even though the term biodiversity was invented in the 1980s to promote the cause of species conservation, discussions on biological diversity go back to Plato. There are many controversies surrounding biodiversity and a few of them are examined here: What is worthy of protection or restoration and what is the acceptable level of costs? Is it permissible to (...) kill sentient animals to promote native populations? Can species be reintroduced if they have disappeared a long time ago? How should the responsibilities for biodiversity be shared? This book will be of interest to philosophers of science and biologists, but also to anyone interested in conservation and the environment. (shrink)

: Despite its amazing morphological diversity, life as we know it on Earth today is remarkably similar in its basic molecular architecture and biochemistry. The assumption that all life on Earth today shares these molecular and biochemical features is part of the paradigm of modern biology. This paper examines the possibility that this assumption is false, more specifically, that the contemporary Earth contains as yet unrecognized alternative forms of microbial life. The possibility that more than one form of life arose (...) on Earth is consistent with our current understanding of conditions on the early Earth and the biochemical and molecular possibilities for life. Arguments that microbial descendents of an alternative origin of life could not co-exist with familiar life are belied by what we know of the complexity and diversity of microbial communities. Furthermore, the tools that are currently used to explore the microbial world – microscopy (with the aid of techniques such as DAPI staining and fluorescence in situ hybridization), cultivation and PCR amplification of rRNA genes – could not detect such organisms if they existed. Thus, the fact that we have not discovered any alternative life forms cannot be taken as evidence that they do not exist. (shrink)

Biodiversity studies comprise the systematic examination of the full array of different kinds of organisms together with the technology by which the diversity can be maintained and used for the benefit of humanity. Current basic research at the species level focuses on the process of species formation, the standing levels of species numbers in various higher taxonomic categories, and the phenomena of hyperdiversity and extinction proneness. The major practical concern is the massive extinction rate now caused by human activity, which (...) threatens losses in the esthetic quality of the world, in economic opportunity, and in vital ecosystem services. (shrink)

Genesis: The Evolution of Biology presents a history of the past two centuries of biology, suitable for use in courses, but of interest more broadly to evolutionary biologists, geneticists, and biomedical scientists, as well as general readers interested in the history of science. The book covers the early evolutionary biologists-Lamarck, Cuvier, Darwin and Wallace through Mayr and the neodarwinian synthesis, in much the same way as other histories of evolution have done, bringing in also the social implications, the struggles with (...) our religious understanding, and the interweaving of genetics into evolutionary theory. What is novel about Sapp's account is a real integration of the cytological tradition, from Schwann, Boveri, and the other early cell biologists and embryologists, and the coverage of symbiosis, microbial evolutionary phylogenies, and the new understanding of the diversification of life coming from comparative analyses of complete microbial genomes. The book is a history of theories about evolution, genes and organisms from Lamarck and Darwin to the present day. This is the first book on the general history of evolutionary biology to include the history of research and theories about symbiosis in evolution, and first to include research on microbial evolution which were excluded from the classical neo-Darwinian synthesis. Bacterial evolution, and symbiosis in evolution are also excluded from virtually every book on the history of biology. (shrink)