The prior probabilities of phylogenetic trees

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different methods of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally.     

August Weismann on Germ-Plasm Variation

August Weismann is famous for having argued against the inheritance of acquired characters. However, an analysis of his work indicates that Weismann always held that changes in external conditions, acting during development, were the necessary causes of variation in the hereditary material. For much of his career he held that acquired germ-plasm variation was inherited. An irony, which is in tension with much of the standard twentieth-century history of biology, thus exists – Weismann was not a Weismannian. I distinguish three claims regarding the germ-plasm: (1) its continuity,(2) its morphological sequestration, and (3) its variational sequestration. With respect to changes in Weismann's views on the cause of variation, I divide his career into four stages. For each stage I analyze his beliefs on the relative importance of changes in external conditions and sexual reproduction as causes ofvariation in the hereditary material. Weismann believed, and Weismannism denies, that variation, heredity, and development were deeply intertwined processes. This article is part of a larger project comparing commitments regarding variation during the latter half of the nineteenth century. This revised version was published online in July 2006 with corrections to the Cover Date.     

The appeal to nature implicit in certain restrictions on public funding for assisted reproductive technology

Certain restrictions on public funding for assisted reproductive technology (ART) are articulated and defended by recourse to a distinction between medical infertility and social infertility. We propose that underlying the prioritization of medical infertility is a vision of medicine whose proper role is to restore but not to improve upon nature. We go on to mark moral responses that speak of investments many continue to make in nature as properly an object of reverence and gratitude and therein (sometimes) a source of moral guidance. We draw on the work of Ludwig Wittgenstein in arguing for the plausibility of an appeal to nature in opposition to the charge that it must contain a logical fallacy. We also invite consideration of the moral plausibility of some appeal to nature. Finally, we examine what follows in the case of ART. Should medicine respect as natural limits that should not be overcome: the need for a man and a woman in reproduction; menopause; and even declining fertility with age? We must first ask ourselves to what degree we should defer to nature in the conduct of medicine, at least in the particular if not the general case. This will involve also asking ourselves what we think is natural and in what instances and spirit might we defy nature. Divergent opinions and policies concerning who should receive ART treatment and public funding are more easily understood in view of the centrality, complexity and fundamental nature of these questions.     

Can the theory of evolution be falsified?

In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called the theory of common descent), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.     

Joel Faflak (ed.), Marking Time: Romanticism and Evolution

History and Philosophy of the Life Sciences - Prior to August Weismann’s 1889 germ-plasm theory, social reformers believed that humans could inherit the effects of a salubrious environment...     

On the nature of the species problem and the four meanings of 'species'

Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term 'species' as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem.     

August Weismann's theory of the germ-plasm and the problem of unconceived alternatives

I have argued elsewhere that scientific realism is most significantly challenged neither by traditional arguments from underdetermination of theories by the evidence, nor by the traditional pessimistic induction, but by a rather different historical pattern: our repeated failure to conceive of alternatives to extant scientific theories, even when those alternatives were both (1) well-confirmed by the evidence available at the time and (2) sufficiently scientifically serious as to be later embraced by actual scientific communities. Here I use August Weismann's defense of his influential germ-plasm theory of inheritance to support my claim that this pattern characterizes the history of theoretical scientific investigation generally. Weismann believed that the germ-plasm must become disintegrated into its constituent elements over the course of development, I argue, only because he failed to conceive of any possible alternative mechanism of ontogenetic differentiation. This and other features of the germ-plasm theory, I suggest, reflect a still more fundamental failure to imagine that the germ-plasm might be a productive rather than expendable resource for the cell. Weismann's case provides impressive support for the problem of unconceived alternatives while rendering its challenge to scientific realism deeper and sharper in a number of important ways.     

Theory of the continuity of germ plasma according to the findings of modern biology

The main principles on the theory of germ plasma by A. Weismann are briefly presented; a number of his genetic-embryological hypotheses proved to be prophetic. Modern notions on the germ plasma are critically discussed, as well as the resulting from them the conception on continuity of totipotent cells (the source of germ cells) in the line of generations, that is historically connected with M. Nussbaum--A. Weismann's notions on continuity of the embryonic pathway. The term totipotency is sometimes used inaccurately; it means ability to formation of a whole organism. In Metazoa zygota and isolated blastomeres, at a regulative type of development, and groups of somatic cells or fragments of the organism, at an asexual reproduction and somatic embryogenesis, possess this ability. In ontogenesis totipotency is lost both by the somatic and by the germ cells because of their specialization and is recreated with the beginning of every ontogenesis when zygota is formed. The germ cells are always a product of the organism--unicellular or multicellular, and their specialization in all its manifestations is the result of integrative influences of the organism as a whole of them. Certain reasons are presented for supporting ideas on germ cells as one of the lines of cell differentiation. The main, if not the only contradiction in the problem concerning relation of the germ and somatic cells is, at the present time, the thesis on continuity of totipotent cells in the line of generations.     

Weismann Versus Morgan Revisited: Clashing Interpretations on Animal Regeneration

This paper has three principal aims: first, through a detailed analysis of the hypotheses and assumptions underlying Weismann’s and Morgan’s disagreement on the nature of animal regeneration, it seeks to readdress the imbalance in coverage of their discussion, providing, at the same time, a fascinating case-study for those interested in general issues related to controversies in science. Second, contrary to Morgan’s beliefs according to which Weismann employed a speculative and unempirical method of scientific investigation, the article shows that Weismann performed experiments, made observations and proposed ‘undogmatic’ theories open to refutation. Third, through the reconstruction of Weismann’s and Morgan’s disagreement, this study illustrates how biology, during the very late nineteenth and early twentieth centuries, was undergoing important changes. I argue that this controversy clearly and convincingly demonstrates how some important epistemic assumptions became increasingly problematic for some members of the younger generations of biologists. At the end of my discussion I will also argue that Weismann and Morgan both had strong well-grounded arguments supporting their conclusions; for this reason I suggest a few factors (“taken-for-granted” beliefs or assumptions) that could explain why their disagreement was doomed to remain unresolved. In particular, I will analyze their diverse explicative interests, their different theoretical concerns and their distinct use of the available evidence.     

Evolution, language and analogy in functional genomics.

Almost a century ago, Wittgenstein pointed out that theory in science is intricately connected to language. This connection is not a frequent topic in the genomics literature. But a case can be made that functional genomics is today hindered by the paradoxes that Wittgenstein identified. If this is true, until these paradoxes are recognized and addressed, functional genomics will continue to be limited in its ability to extrapolate information from genomic sequences.     

The search for a macroevolutionary theory in German paleontology

Summary Six schools of thought can be detected in the development of evolutionary theory in German paleontology between 1859 and World War II. Most paleontologists were hardly affected in their research by Darwin's Origin of Species. The traditionalists (School 1) accepted evolution within lower taxa (genera and families) but not for organisms in general. They also rejected Darwin's theory of selection. The early Darwinians (School 2) accepted Darwin's theory of transmutation and theory of selection as axioms and applied them fruitfully to the fossil record, thereby laying the foundation for the new research areas of phylogeny and paleo-biology. The enthusiasm of the early Darwinians faded when the fossil record and the problems of its interpretion became more widely known. The pluralists of the turn of the century (School 3) invented and adopted a wealth of hypothetical mechanisms in order to explain individual features of the fossil record. They failed, however, to provide one coherent theory. Dissatisfaction with this situation led to adoption of a dogmatic neo-Lamarckism (School 4), which was regarded as a coherent theory providing a fruitful research program. The rejection of the Lamarckian mechanism early in this century left paleontologists with only one kind of evolutionary mechanism: inner causes.Like many neo-Lamarckians several orthogeneticists (School 5) were highly interested in adaptation and did not see any contradiction between the inner causes of evolution and adaptation. The dominance of stratigraphical research programs in paleontology led in the 1930s and 1940s to a decrease in interest in adaptation. Stratigraphical records of taxa were accepted as meaningful in the context of evolutionary theory. Orthogenesis and the new concepts of saltation and cyclicism were amalgamated into one theory: typostrophism (School 6). This theory dominated German paleontology for decades after the war and only recently has the synthetic theory been seriously considered.Evolution was never very intensively discussed in German paleontology in the hundred years after Darwin's book. Most information used here comes from textbooks or from papers given on special occasions. It has been impossible to summarize how members of one school defended their views or discussed the ideas of competing schools.     

Pavlov's conceptualization of unconditional reflexes, or instincts, within the framework of the theory of higher nervous activity

According to I. P. Pavlov's theory of higher nervous activity, the establishment and dissolution of conditional reflexes enhances the higher organism's adaptation to the external environment. Pavlov asserted that, ontogenetically, conditional reflexes are based upon innate, unconditional reflexes (UR) or instincts. Pavlov did not distinguish between URs and instincts, but he preferred the former term. Phylogenetically the URs emerged out of well-established conditional reflexes during the development of higher organisms. An outgrowth of the experimental conditioning procedure, developed during the second decade of this century, was the observation and delineation of new URs. While studying human nervous and psychiatric disorders in the 1930s, Pavlov elucidated other URs. Pavlov identified 13 major URs, but he failed to formulate an exhaustive classification scheme of URs.     

Sex, Death, and Evolution in Proto- and Metazoa, 1876–1913

In the period 1875–1920, a debate about the generality and applicability of evolutionary theory to all organisms was motivated by work on unicellular ciliates like Paramecium because of their peculiar nuclear dualism and life cycles. The French cytologist Emile Maupas and the German zoologist August Weismann argued in the 1880s about the evolutionary origins and functions of sex (which in the ciliates is not linked to reproduction), and death (which appeared to be the inevitable fate of lineages denied sexual conjugation), an argument rooted in the question of whether the ciliates and their processes where homologous to other cellular organisms. In the beginning of the twentieth century, this question of homology came to be less important as the ciliates were used by the British protozoologist Clifford Dobell and the American zoologist Herbert Spencer Jennings to study evolutionary processes in general rather than problems of development and cytology. For them, homology mattered less than analogy. This story illustrates two partially distinct problems in evolutionary biology: first, the question of whether all living things have common features and origins; and second, whether their history and current nature can be described by identical mechanisms. Where Maupas (contra Weismann) made the ciliates qualitatively the same as all other organisms in order to create a cohesive evolutionary theory for biology, Jennings and Dobell made them qualitatively different in order to achieve the same end. This revised version was published online in July 2006 with corrections to the Cover Date.     

Meiosis in perspective.

Our understanding of meiosis springs from two suggestions made by Weismann in 1887. One was that meiosis would be found to compensate for fertilization in the life cycles of both sexes and all organisms. The other was that the development of sexual reproduction in evolution depended on the value of meiosis in exposing the results of genetic recombination to natural selection. In confirming these propositions we were bound to discover that the properties of meiosis appear both as the causes and the consequences of evolution: it is the hinge on which turns the evolution of breeding method, reproductive habit, life cycle and hereditary structure, that is the genetic system, in all sexually reproducing species of organism. We have had three main fields of attack on our problem. First, there was the natural variation of meiosis including that of two-track hereditary within the species: here, animals took the lead. Secondly, there was the experimental field - both with genetic controls such as polyploidy and the sterilizing mutations of mitosis as well as meiosis, and with physical and chemical controls: here, the higher plants and micro-organisms have given us our great opportunities. Thirdly, we have the widening field where physicochemical knowledge and genetic control converge and collaborate. In all this work we have to be aware that meiosis works with chromosomes which always have the two functions of accomplishing evolution and of implementing its results in heredity. In consequence, the adaptation of meiosis is perpetually imperfect.     

The 1999 Crafoord Prize lectures. Neo-Lamarckian experimentalism in America: origins and consequences

The 1890s and the first decades of the twentieth century saw a vigorous debate about the mechanisms of evolutionary change. On one side, August Weismann defended the selectionist hypothesis; on the other, Herbert Spencer defended neo-Lamarckian theory. Supporters of Spencer, notably the American paleontologist and evolutionary theorist Henry Fairfield Osborn, recognized that the questions raised by Weismann and Spencer could only be settled experimentally. They called for the application of experimental methods, and the establishment of a new institution for the purpose of confirming the inheritance of acquired characters. To a great extent, the experimental program championed by Osborn and others was implemented and, although it failed to reveal soft inheritance and was soon eclipsed by Mendelian and chromosomal genetics, it did make significant and lasting contributions to evolutionary biology. Thus the importance of methodological and institutional innovation and theoretical pluralism to the progress of science is illustrated and underscored.     

Alfred Kühn (1885-1968) and developmental evolution

Alfred Kühn (1885-1968) was known as one of the most comprehensive zoologists of his time. His research program in developmental physiological genetics was one of the first successful attempts to integrate the experimental study of development and heredity. It led him to discover the first known reaction chain from gene to phenotype. Kühn also foresaw many elements of modern evolutionary developmental biology and as a student of Weismann and mentor to many developmental geneticists of the late 20th century directly connects Weismann with molecular developmental genetics.     

On the inappropriate use of the naturalistic fallacy in evolutionary psychology

The naturalistic fallacy is mentionedfrequently by evolutionary psychologists as anerroneous way of thinking about the ethicalimplications of evolved behaviors. However,evolutionary psychologists are themselvesconfused about the naturalistic fallacy and useit inappropriately to forestall legitimateethical discussion. We briefly review what thenaturalistic fallacy is and why it is misusedby evolutionary psychologists. Then we attemptto show how the ethical implications of evolvedbehaviors can be discussed constructivelywithout impeding evolutionary psychologicalresearch. A key is to show how ethicalbehaviors, in addition to unethical behaviors,can evolve by natural selection.     

Evolutionary arguments against moral realism: Why the empirical details matter (and which ones do)

The aim of this article is to identify the strongest evolutionary debunking argument (EDA) against moral realism and to assess on which empirical assumptions it relies. In the recent metaethical literature, several authors have de-emphasized the evolutionary component of EDAs against moral realism: presumably, the success or failure of these arguments is largely orthogonal to empirical issues. I argue that this claim is mistaken. First, I point out that Sharon Street’s and Michael Ruse’s EDAs both involve substantive claims about the evolution of our moral judgments. Next, I argue that combining their respective evolutionary claims can help debunkers to make the best empirical case against moral realism. Some realists have argued that the very attempt to explain the contents of our endorsed moral judgments in evolutionary terms is misguided, and have sought to escape EDAs by denying their evolutionary premise. But realists who pursue this reply can still be challenged on empirical grounds: debunkers may argue that the best, scientifically informed historical explanations of our moral endorsements do not involve an appeal to mind-independent truths. I conclude, therefore, that the empirical considerations relevant for the strongest empirically driven argument against moral realism go beyond the strictly evolutionary realm; debunkers are best advised to draw upon other sources of genealogical knowledge as well.     

Parental investment theory: The role of past investment

The role of past investment in parental-care behaviour has often been controversial. Some researchers have argued that organisms basing present investment on past investment are committing the 'Concorde fallacy'. Others have incorporated life history theory to suggest that investing according to past investment is one component of investing according to expected future reproductive success: a parent can use past investment as well as other information, such as brood size, to make its optimal parental-investment decisions. Although parental-investment research is still in its infancy, the incorporation of life history theory suggests that the Concorde fallacy is a misleading concept.     

Brief communication: Effect of size biases in the coefficient of variation on assessing intraspecific variability in the prosimian skeleton

Lack of independence of data points or the pooling fallacy has been suggested as a potential problem in the study of handedness in nonhuman primates, particularly as it relates to whether hand use responses should be recorded as individual events or bouts of activity. Here, I argue that there is no evidence that the concept of statistical independence of data points or the pooling fallacy is a problem in the evaluation of population‐level handedness in previous studies in nonhuman primates. I further argue these statistical concepts have been misapplied to the characterization of individual hand preferences. Finally, I argue that recording hand use responses as bouts rather than events has no significant effect on reports of hand use in nonhuman primates and, in fact, may unintentionally bias hand use toward the null hypothesis. Several suggestions for improvement in the measurement and statistical determination of individual handedness are offered in the article. Am J Phys Anthropol 151:151–157, 2013. © 2013 Wiley Periodicals, Inc.