Parsimony and the Fisher–Wright debate

In the past five years, there have been a series of papers in the journal Evolution debating the relative significance of two theories of evolution, a neo-Fisherian and a neo-Wrightian theory, where the neo-Fisherians make explicit appeal to parsimony. My aim in this paper is to determine how we can make sense of such an appeal. One interpretation of parsimony takes it that a theory that contains fewer entities or processes, (however we demarcate these) is more parsimonious. On the account that I defend here, parsimony is a ‘local’ virtue. Scientists’ appeals to parsimony are not necessarily an appeal to a theory’s simplicity in the sense of it’s positing fewer mechanisms. Rather, parsimony may be proxy for greater probability or likelihood. I argue that the neo-Fisherians appeal is best understood on this interpretation. And indeed, if we interpret parsimony as either prior probability or likelihood, then we can make better sense of Coyne et al. argument that Wright’s three phase process operates relatively infrequently.     

On evaluating the GM Nation? Public debate about the commercialisation of transgenic crops in Britain

Abstract

The public debate about GM crops that took place in Britain in 2002–03 was an unprecedented experiment for the UK in public engagement. The Government, which sponsored the exercise, made a pledge: to take into account lay perspectives, as well as the views of its expert advisers, when making a decision about the possible commercialisation of this controversial technology. As officially accredited but independent evaluators of the debate, we were given unique behind-the-scenes access to the organisation and execution of the debate process. In this paper we report on our findings, which reveal a debate process that, whilst innovative, suffered from a number of important flaws: in terms of both design and implementation. These shortcomings in part reflect constraints on time and budget, and the context of political pressure in which the debate took place. However, they also demonstrated a lack of design knowledge and availability of appropriate expertise: matters with an important bearing on future plans for such initiatives.     

The GM debate: science or scaremongering?

Many conversations on genetic modification over the past few years have begun with the words 'I'm not a scientist, but...' They usually go on to say they do not follow the scientific detail, but it doesn't seem right to tamper with genes. The media and pressure groups have fuelled the fire with emotive terms like 'Frankenstein food', 'genetic pollution' and 'mutant crops'. There are important lessons here, which are as much about people and society as they are about science.     

Resolving the limitation – regulation debate

Many recent ecological studies have demonstrated that animal populations are limited by their food. Examples are presented here to refute the view that natural populations are regulated by negative feedback mortality factors. Additionally, several incorrect statements in a recent publication are discussed, specifically (1) that there is no difference between the concepts of regulation and limitation; (2) that the debate is about what causes the time it takes a population to reach the carrying capacity of its habitat, not what sets that carrying capacity; (3) that the results of a laboratory experiment using a closed population with fixed amounts of food represents what happens in natural open populations with varying supplies of food; (4) that a thermostat analogy can be used, assuming that an “equilibrium” is controlling natural populations “from above” instead of the original steam analogy which says the varying input of a resource “from below” is the controlling factor.     

Paraphyletic group,PhyloCode and phylogenetic species—the current debate and a preliminary commentary

In this essay, three currently hotly debated issues in biological systematics, i.e., the paraphyletic group, the PhyloCode, and the phylogenetic species concept, have been briefly reviewed. (1) It is widely acknowledged that cladistics has made some positive contributions to the study of systematics. In particular, the employment of outgroup analysis for assessing character polarities, the application of synapomorphies to the inference of relationships between taxa, and the use of cladistic methods for reconstructing phylogeny, have all greatly facilitated the improvement of systematic approaches. A fatal flaw in cladistics is its refusal to accept paraphyletic groups. Frankly, we are adherents and practitioners of phyletics, and hence consider paraphyletic groups to be acceptable. For example, an AFLP analysis has shown that Zabelia (Caprifoliaceae) can be included in Abelia, but the members in Zabelia differ from those in Abelia not only in pollen morphology, but also in having persistent petioles dilated and connate at base, thus enclosing axillary buds, characters of adaptive significance obtained possibly when Zabelia members entered a new ecological niche, so we consider that they are better treated as two independent genera, though indeed such a treatment makes Abelia paraphyletic. (2) Some cladists pointed out that as the tool for communication and the system for information storage and retrieval, biological nomenclature is required to be unambiguous, unique and stable. They criticise the Linnaean rank-based system of nomenclature for failing to satisfy such requirements for the naming of clades and species. To address this problem, the PhyloCode is proposed in recent years, in which three definitions for clade naming are given, i.e., the node-based, the stem-based, and the apomorphy-based. We are of the opinion that since the Linnaean binominal system of botanical nomenclature has existed for nearly 250 years, the rejection of this system and the adoption of the PhyloCode would create a state of chaos in botanical nomenclature. This does not mean that there exist no merits in the proposals made by the PhyloCode supporters. We suggest that further studies should be conducted for its practical application. (3) It has been well known that there are many problems with the application of the biological species concept in plants, and thus at the present time the majority of plant systematists actually seldom use this concept in their practical work. The rapid development of cladistic approach has motivated the proposal of the phylogenetic species concept. This species concept is established based on three criteria, i.e., the autamorphy, the diagnosability and the basal exclusivity, hence the autamorphy species concept, the diagnosability species concept, and the genealogical concept are created respectively. Nevertheless, the morpho-geographical species concept is still predominantly adopted in plant systematics. When using this species concept, however, we should also take into account the data from other sources, particularly those from pollination biology, breeding system and molecular systematics.     

The policy chicken and the science egg. Has applied ecology failed the transgenic crops debate?

Ecology has a long history of research relevant to and impacting on real-world issues. Nonetheless problems of communication remain between policy-makers and scientists because they tend to work at different levels of generality (policy deals with broad issues, science prefers specific questions), and complexity (policy-makers want simple answers, ecologists tend to offer multi-factorial solutions) and to different timescales (policy-makers want answers tomorrow, ecologists always seem to want more time). These differences are not unique to the debate about the cultivation of transgenic crops. Research on gene flow is used to illustrate how science and policy are intimately bound together in a value-laden, iterative and messy process unlike that characterised by the ‘encounter problem—do science—make policy’ model. It also demonstrates how the gap between science and policy is often characterised by value-laden language. Scientists involved in ERA for transgenic crops may find their engagement with policy- and decision-makers clouded by misunderstanding about what one should expect from the other. Not the least of these, that science can define harm, is explored in a discussion of the UK Farm Scale Evaluations of herbicide-tolerant GM crops. The varied responses to these extensive trials highlight the problems of linking specific scientific experiments with broad policy objectives. The problems of applied ecology in the transgenic crops debate are not unique but may differ from other areas of environmental policy in the intense politicisation of the debate, the emphasis on assessment of risk and the particularly broad policy objectives.     

Heterogeneous assemblages of bioethics and science: the “pre-embryo” debate in America

This paper explores the “pre-embryo” debate in America to analyze the relationship between scientific uncertainty and moral decision-making. This paper explores how an ethical debate among bioethicists around the term “pre-embryo” has been transformed into a scientific “fact” debate between developmental biology and embryology. This transformation is driven by the scientism of ethical reasoning that stresses scientific claims to increase the credibility of ethical claims. This paper concludes that the “pre-embryo” debate is not an ethical controversy over a unified science but rather credibility struggles between two heterogeneous assemblages of science and bioethics.     

Of lice and men: The return of the ’comparative parasitology‘ debate

The question of whether or not parasite phylogeny provides information about host relationships (‘comparative parasitology’) reached a peak in 1957 in a vigorous debate between Gunther Timmermann and Ernst Mayr. Timmermann argued that parasites were associated with their hosts by descent and that this produced congruent host and parasite phylogenies. In contrast, Mayr argued that parasites were often associated by colonization and that this led to incongruence between host and parasite phylogenies. To test these differing views. Adrian Paterson, Russell Gray and Graham Wallis derived a procellaniform phylogeny. This tree is here compared with Timmermann's tree based on the relationships of feather lice. Timmermann's tree is more similar to the seabird phylogeny than would be expected by chance. Thus, support is found for the ‘comparative parasitology’ approach.     

Will GM animals follow the GM plant fate?

Despite being both Genetically Modified Organisms (GMOs), GM plants and GM animals share few similarities outside the laboratory premises. Whilst GM plants were soon embraced by industry and became a commercial success, only recently have GM animals reached the market. However, an area where GM animals are likely to follow the GM plant path is on their potential to cause social unrest. One of the major flaws of the 90s GMO crisis was the underestimation of the influence that different players can have in the adoption of new biotechnological applications. In this article we describe the unique evolution of GM animals in two of the most important fields: the pharmaceutical and the breeding sectors. For our analysis, we have subdivided the production chain into three governance domains: Science, Market and Public. We describe the influence and interaction of each of these domains as a vehicle for predicting the future adoptability of GM animals and to highlight conflicting areas.     

Skeletons, noise and population growth: the end of an old debate?

Population dynamics models remain largely deterministic, although the presence of random fluctuations in nature is well recognized. This deterministic approach is based on the implicit assumption that systems can be separated into a deterministic part that captures the essential features of the system and a random part that can be neglected. But is it possible, in general, to understand population dynamics without the explicit consideration of random fluctuations? Here, we suggest perhaps not, and argue that the dynamics of many systems are a result of interactions between the deterministic nonlinear skeleton and noise.     

Animal morality: What is the debate about?

Empirical studies of the social lives of non-human primates, cetaceans, and other social animals have prompted scientists and philosophers to debate the question of whether morality and moral cognition exists in non-human animals. Some researchers have argued that morality does exist in several animal species, others that these species may possess various evolutionary building blocks or precursors to morality, but not quite the genuine article, while some have argued that nothing remotely resembling morality can be found in any non-human species. However, these different positions on animal morality generally appear to be motivated more by different conceptions of how the term “morality” is to be defined than by empirical disagreements about animal social behaviour and psychology. After delving deeper into the goals and methodologies of various of the protagonists, I argue that, despite appearances, there are actually two importantly distinct debates over animal morality going on, corresponding to two quite different ways of thinking about what it is to define “morality”, “moral cognition”, and associated notions. Several apparent skirmishes in the literature are thus cases of researchers simply talking past each other. I then focus on what I take to be the core debate over animal morality, which is concerned with understanding the nature and phylogenetic distribution of morality conceived as a psychological natural kind. I argue that this debate is in fact largely terminological and non-substantive. Finally, I reflect on how this core debate might best be re-framed.     

Challenges for transgene detection in landraces and wild relatives: learning from 15 years of debate over GM maize in Mexico

Maize is one of the world’s five staple cereals and its traditional varieties constitute a global resource critical to future agricultural development. Fifteen years ago, claims that transgenes had spread into traditional landrace maize in Mexico started an international discussion on the scale and significance of transgene flow from genetically modified (GM) crops to centres of crop origin and genetic diversity. The initial discovery of transgenes in landrace maize sparked an intense environmental dispute in which the culture and traditions of indigenous people were seen as threatened by the unchecked spread of biotechnological inventions from multinational corporations. This dispute was reflected in a political and legal battle over the regulatory status of GM crops in Mexico, which continues today as approvals of GM maize for cultivation remain subject to contestation in the courts. These legal, political and environmental disputes have been fanned by the existence of a significant scientific controversy over the methods for GM detection. The use of various approaches and a lack of harmonized methods specific for monitoring and detection of transgenes in landraces has generated both positive and negative results for GM contamination in Mexico over the years. In this paper, we review the peer-reviewed literature on transgene detection in Mexican maize and highlight the challenges associated with transgene detection in landraces. In doing so, we identify the key methodological aspects under dispute and pinpoint the research bottlenecks and needs for building the capacity to effectively monitor transgene escape from GM crops to wild relatives or landraces.     

Secular oscillations in the stratigraphic record—an acute debate

Work on secular oscillations of the ocean-atmosphere system has reached a particularly interesting stage, characterized by competing models that alternately invoke endogenic and celestial drivers. The most widely accepted concept is the icehouse-greenhouse cycle with an approximate length of 300 Ma. The concept holds that in the past 600 Ma the Earth has oscillated between a glacial mode and one of rather warm, equable climate; correlative changes in mineralogy of marine carbonates and evaporites as well as abundance of igneous intrusions point to an endogenic cause, most probably variations in the rates of plate motion and mantle convection that modulate sea level and the level of atmospheric CO₂ and thus climate. However, the 300-Ma icehouse-greenhouse cycle leaves important data unexplained. The history of glaciations as well as certain climate indicators, such as sea-surface temperatures derived from oxygen isotopes, indicate oscillations with wave lengths of 130–150 Ma. Such oscillations have been observed in the reconstructed cosmic-ray flux of the past 1000 Ma; they may modulate climate via low-level cloud cover. The debate about long-term climate oscillations poses several distinct questions for sedimentary geologists.