Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations

Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering homologues as another example of natural kinds, comparing them with analogues as functionally defined kinds. Given that there are various types of natural kinds, I discuss the different theoretical purposes served by diverse kind concepts, suggesting that there is no clear-cut distinction between natural kinds and other kinds, such as functional kinds. Rather than attempting to offer a unique metaphysical account of 'natural' kind, a more fruitful approach consists in the epistemological study of how different natural kind concepts are employed in scientific reasoning.     

Levels of biological plausibility

Notions of mechanism, emergence, reduction and explanation are all tied to levels of analysis. I cover the relationship between lower and higher levels, suggest a level of mechanism approach for neuroscience in which the components of a mechanism can themselves be further decomposed and argue that scientists'' goals are best realized by focusing on pragmatic concerns rather than on metaphysical claims about what is ‘real''. Inexplicably, neuroscientists are enchanted by both reduction and emergence. A fascination with reduction is misplaced given that theory is neither sufficiently developed nor formal to allow it, whereas metaphysical claims of emergence bring physicalism into question. Moreover, neuroscience''s existence as a discipline is owed to higher-level concepts that prove useful in practice. Claims of biological plausibility are shown to be incoherent from a level of mechanism view and more generally are vacuous. Instead, the relevant findings to address should be specified so that model selection procedures can adjudicate between competing accounts. Model selection can help reduce theoretical confusions and direct empirical investigations. Although measures themselves, such as behaviour, blood-oxygen-level-dependent (BOLD) and single-unit recordings, are not levels of analysis, like levels, no measure is fundamental and understanding how measures relate can hasten scientific progress.This article is part of the theme issue ‘Key relationships between non-invasive functional neuroimaging and the underlying neuronal activity''.     

Would Industrial Ecology Exist without Sustainability in the Background?

Industrial ecology rests historically—even in a short lifetime of 15 years or so—on the metaphorical power of natural ecosystems. Its evolution parallels the rise of concerns over unsustainability, that is, the threats to our world's ability to support human life the emergence of sustainability as a normative goal on a global scale. This article examines the relationships between industrial ecology and sustainability and argues that, in its historical relationship to classical ecology models, the field lacks power to address the full range of goals of sustainability, however defined. The classical ecosystem analogy omits aspects of human social and cultural life central to sustainability. But by moving beyond this model to more recent ecosystem models based on complexity theory, the field can expand its purview to address sustainability more broadly and powerfully. Complexity models of living systems can also ground alternative normative models for sustainability as an emergent property rather than the output of a mechanistic economic model for society's workings.     

Falling giants and the rise of gene editing: ethics,private interests and the public good

This paper considers the tensions created in genomic research by public and private for-profit ideals. Our intent is to strengthen the public good at a time when doing science is strongly motivated by market possibilities and opportunities. Focusing on the emergence of gene editing, and in particular CRISPR, we consider how commercialisation encourages hype and hope—a sense that only promise and idealism can achieve progress. At this rate, genomic research reinforces structures that promote, above all else, private interests, but that may attenuate conditions for the public good of science. In the first part, we situate genomics using the aphorism that ‘on the shoulders of giants we see farther’; these giants are infrastructures and research cultures rather than individual ‘heroes’ of science. In this respect, private initiatives are not the only pivot for successful discovery, and indeed, fascination in those could impinge upon the fundamental role of public-supported discovery. To redress these circumstances, we define the extent to which progress presupposes research strategies that are for the public good. In the second part, we use a ‘falling giant’ narrative to illustrate the risks of over-indulging for-profit initiatives. We therefore offer a counterpoint to commercialised science, using three identifiable ‘giants’—scientists, publics and cultures—to illustrate how the public good contributes to genomic discovery.     

On some theoretical grounds for an organism-centered biology: Property emergence, supervenience, and downward causation

In this paper, we investigate some theoretical grounds for bridging the gap between an organism-centered biology and the chemical basis of biological explanation, as expressed in the prevailing molecular perspective in biological research. First, we present a brief survey of the role of the organism concept in biological thought. We advance the claim that emergentism (with its fundamental tenets: ontological physicalism, qualitative novelty, property emergence, theory of levels, irreducibility of the emergents, and downward causation) can provide a metaphysical basis for a coherent sort of organicism. Downward causation (DC) is the key notion in emergentist philosophy, as shown by the tension between the aspects of dependence and nonreducibility in the concept of supervenience, preferred by many philosophers to emergence as a basis for nonreductive physicalism. As supervenience physicalism does not lead, arguably, to a stable nonreductive physicalist account, we maintain that a philosophical alternative worthy of investigation is that of a combination of supervenience and property emergence in the formulation of such a stance. Taking as a starting-point O’Connor’s definition of an emergent property, we discuss how a particular interpretation of downward causation (medium DC), inspired by Aristotelian causal modes, results in an explanation of property emergence compatible with both physicalism and non-reductionism. In this account of emergence, one may claim that biology, as a science of living organization, is and remains a science of the organism, even if completely explained by the laws of chemistry. We conclude the paper with a new definition of an emergent property.     

The maximum entropy formalism and the idiosyncratic theory of biodiversity

Why does the neutral theory, which is based on unrealistic assumptions, predict diversity patterns so accurately? Answering questions like this requires a radical change in the way we tackle them. The large number of degrees of freedom of ecosystems pose a fundamental obstacle to mechanistic modelling. However, there are tools of statistical physics, such as the maximum entropy formalism (MaxEnt), that allow transcending particular models to simultaneously work with immense families of models with different rules and parameters, sharing only well‐established features. We applied MaxEnt allowing species to be ecologically idiosyncratic, instead of constraining them to be equivalent as the neutral theory does. The answer we found is that neutral models are just a subset of the majority of plausible models that lead to the same patterns. Small variations in these patterns naturally lead to the main classical species abundance distributions, which are thus unified in a single framework.     

Key issues in achieving an integrative perspective on stress

An integrative perspective on molecular mechanisms of stress resistance requires understanding of these mechanisms not just in vitro or in the model organism in the research laboratory — but in the healthy or diseased human in society, in the cultivated plant or animal in agricultural production, and in populations and species in natural communities and ecosystems. Such understanding involves careful attention to the context in which the organism normally undergoes stress, and appreciation that biological phenomena occur at diverse levels of organization (from molecule to ecosystem). Surprisingly, three issues fundamental to achieving an integrative perspective are presently unresolved: (i) Is variation in lower-level traits (nucleotide sequences, genes, gene products) seldom, commonly, or always consequential for stress resistance? (ii) Does environmental stress reduce or enhance genetic variation, which is the raw material of evolution? (iii) Is the present distribution of organisms along natural gradients of stress largely the result of organisms living where they can, or is adaptive evolution generally sufficient to overcome stress? Effective collaboration among disciplinary specialists and meta-analysis may be helpful in resolving these issues.     

A Not-So-Gentle Refutation of the Defence of Homeopathy

In a recent paper, Levy, Gadd, Kerridge, and Komesaroff attempt to defend the ethicality of homeopathy by attacking the utilitarian ethical framework as a basis for medical ethics and by introducing a distinction between evidence-based medicine and modern science. This paper demonstrates that their argumentation is not only insufficient to achieve that goal but also incorrect. Utilitarianism is not required to show that homeopathic practice is unethical; indeed, any normative basis of medical ethics will make it unethical, as a defence of homeopathic practice requires the rejection of modern natural sciences, which are an integral part of medical ethics systems. This paper also points out that evidence-based medicine lies at the very core of modern science. Particular arguments made by Levy et al. within the principlist medical ethics normative system are also shown to be wrong.     

Simplification,Innateness, and the Absorption of Meaning from Context: How Novelty Arises from Gradual Network Evolution

How does new genetic information arise? Traditional thinking holds that mutation happens by accident and then spreads in the population by either natural selection or random genetic drift. There have been at least two fundamental conceptual problems with imagining an alternative. First, it seemed that the only alternative is a mutation that responds “smartly” to the immediate environment; but in complex multicellulars, it is hard to imagine how this could be implemented. Second, if there were mechanisms of mutation that “knew” what genetic changes would be favored in a given environment, this would have only begged the question of how they acquired that particular knowledge to begin with. This paper offers an alternative that avoids these problems. It holds that mutational mechanisms act on information that is in the genome, based on considerations of simplicity, parsimony, elegance, etc. (which are different than fitness considerations). This simplification process, under the performance pressure exerted by selection, not only leads to the improvement of adaptations but also creates elements that have the capacity to serve in new contexts they were not originally selected for. Novelty, then, arises at the system level from emergent interactions between such elements. Thus, mechanistically driven mutation neither requires Lamarckian transmission nor closes the door on novelty, because the changes it implements interact with one another globally in surprising and beneficial ways. Finally, I argue, for example, that genes used together are fused together; that simplification leads to complexity; and that evolution and learning are conceptually linked.     

Some methodological issues in macroecology

Recent years have seen the emergence of "macroecology" as a distinct research program in biology. It is concerned with geographical scale patterns in assemblage structure and, as such, of necessity relies heavily on approaches that are nonexperimental and that depend on the availability of reliable information for large numbers of species. This gives rise to a particular set of analytical issues that need to be addressed when conducting studies of macroecological patterns. In this article, we draw attention to nine such issues that we consider to be of particular importance. Our aim is to aid the development of what we believe to be an important subject area by identifying some of the more common problems that may confound studies, as well as some of their solutions.     

Teleosemantics re-examined: content,explanation and norms

This essay reviews a collection of thirteen critical essays on the work of Ruth Millikan. The collection covers a broad range of her work, focusing in particular on her account of simple intentionality, her theory of concepts and her metaphysical views. I highlight and briefly discuss three issues that crop up repeatedly though the collection: (1) Millikan’s externalism (and in particular, her emphasis on how intentional states are used, rather than how they are produced); (2) the nature of intentional explanation; and (3) the normativity of meaning.     

Developmental Models for Estimating Ecological Responses to Environmental Variability: Structural,Parametric, and Experimental Issues

Developmental models that account for the metabolic effect of temperature variability on poikilotherms, such as degree-day models, have been widely used to study organism emergence, range and development, particularly in agricultural and vector-borne disease contexts. Though simple and easy to use, structural and parametric issues can influence the outputs of such models, often substantially. Because the underlying assumptions and limitations of these models have rarely been considered, this paper reviews the structural, parametric, and experimental issues that arise when using degree-day models, including the implications of particular structural or parametric choices, as well as assumptions that underlie commonly used models. Linear and non-linear developmental functions are compared, as are common methods used to incorporate temperature thresholds and calculate daily degree-days. Substantial differences in predicted emergence time arose when using linear versus non-linear developmental functions to model the emergence time in a model organism. The optimal method for calculating degree-days depends upon where key temperature threshold parameters fall relative to the daily minimum and maximum temperatures, as well as the shape of the daily temperature curve. No method is shown to be universally superior, though one commonly used method, the daily average method, consistently provides accurate results. The sensitivity of model projections to these methodological issues highlights the need to make structural and parametric selections based on a careful consideration of the specific biological response of the organism under study, and the specific temperature conditions of the geographic regions of interest. When degree-day model limitations are considered and model assumptions met, the models can be a powerful tool for studying temperature-dependent development.     

Applications of genetic programming in cancer research

The theory of Darwinian evolution is the fundamental keystones of modern biology. Late in the last century, computer scientists began adapting its principles, in particular natural selection, to complex computational challenges, leading to the emergence of evolutionary algorithms. The conceptual model of selective pressure and recombination in evolutionary algorithms allow scientists to efficiently search high dimensional space for solutions to complex problems. In the last decade, genetic programming has been developed and extensively applied for analysis of molecular data to classify cancer subtypes and characterize the mechanisms of cancer pathogenesis and development. This article reviews current successes using genetic programming and discusses its potential impact in cancer research and treatment in the near future.     

Poverty and inequality: challenges for the IAB: IAB presidential address

This paper focuses on poverty and inequality in the world today. First, it points out how this topic is a main concern for the IAB. Second, it proposes 'new' theoretical tools in order to analyze global justice and our obligations towards the needy. I present John Rawls's denial that the egalitarian principle can be applied to the global sphere, his proposed weak duty of assistance, and his consideration of endemic poverty as essentially homegrown. In opposition, I focus on Thomas Pogge as representative of a cosmopolitan view who also holds a critical position towards the international systems which allow and cause poverty. I endorse the general normative proposal that defends every human being as an ultimate unit of moral concern, as well as the strategy of moving away from the charity model of bilateral aid to the realm of rights and duties. These ideas should redesign and broaden the normative and practical roles of institutions, and should also help provide a new approach on bioethical issues such as drug patenting or the imbalance in global research and neglected diseases.     

The future‐like‐ours argument,animalism, and mereological universalism

Which metaphysical theories are involved—whether presupposed or implied—in Marquis’ future‐like‐ours (FLO) argument against abortion? Vogelstein has recently argued that the supporter of the FLO argument faces a problematic dilemma; in particular, Marquis, the main supporter of the argument, seems to have to either (a) abandon diachronic universalism (DU) or (b) acquiesce and declare that contraception is morally wrong. I argue that the premises of Marquis’ argument can be reasonably combined with a form of unrestricted composition and that the FLO argument is better viewed as including animalism, i.e., the thesis that we are animals.     

The response of the tidepool sculpin, Oligocottus maculosus, to hypoxia in laboratory, mesocosm and field environments

Animals living in the intertidal zone experience regular, predictable fluctuations in physical parameters including temperature, oxygen and salinity and rely on behavioural, physiological and biochemical mechanisms to cope with environmental variation. In the present study, behavioural strategies induced by aquatic hypoxia (e.g. emergence) were performed at similar oxygen tensions across laboratory, mesocosm and field environments; the number of individuals performing these behaviours at any one time was similar in mesocosms and the field. The use of aquatic surface respiration (ASR) was more plastic than emergence behaviour, occurring at a lower oxygen tension in juveniles than adults and being influenced by the addition of alarm substance. Oxygen uptake was lower in air than in water in adults but, in contrast, oxygen uptake was not influenced by the respiratory medium in juveniles. In the laboratory, 72 h of forced emergence did not affect whole body concentrations of lactate but when ASR and emergence were prevented within mesocosm environments there was a significant elevation of lactate. The present study highlights the benefits of transcending traditional laboratory/field boundaries allowing the responses of laboratory-held animals to environmental fluctuation to be integrated with how these animals perform in their natural environment.     

Just How Emergent is the Emergence of Semiosis?

Studying the origin of semiosis is a task obscured by terminological and metaphysical issues which create an ambiguous set of definitions for biosemiotics when referring to the concept of emergence. The question is, how emergent can semiosis be? And what are the conditions for semiosis to be an emergent of a certain type? This paper will attempt to briefly deal with the general terminology of emergence from a philosophical point of view and will discuss the characterization of semiosis as an emergent phenomenon based on the distinctions made by Bedau, Kim and Chalmers. Accordingly, we will consider the possibility of strong and weak emergence in an attempt to bring some clarity to what it means for something in biosemiotics to be an emergent and how the philosophical concepts play out when applied to biosemiotic research. In inquiring into the metaphysical status of semiosis, we change our semiotic theories to correspond to the assumptions contained in the elementary objects of our theories. This being the case, the way semiosis–the constitutive element that it is for semiotics–is taken to be with regards to its possible ontology, will conduct to different research objects for the long-term investigation of its origins and necessary conditions.     

Making sense of ocean biota: How evolution and biodiversity of land organisms differ from that of the plankton

The oceans cover 70% of the planet's surface, and their planktonic inhabitants generate about half the global primary production, thereby playing a key role in modulating planetary climate via the carbon cycle. The ocean biota have been under scientific scrutiny for well over a century, and yet our understanding of the processes driving natural selection in the pelagic environment - the open water inhabited by drifting plankton and free-swimming nekton - is still quite vague. Because of the fundamental differences in the physical environment, pelagic ecosystems function differently from the familiar terrestrial ecosystems of which we are a part. Natural selection creates biodiversity but understanding how this quality control of randommutations operates in the oceans - which traits are selected for under what circumstances and by which environmental factors, whether bottom-up or top-down - is currently a major challenge. Rapid advances in genomics are providing information, particularly in the prokaryotic realm, pertaining not only to the biodiversity inventory but also functional groups. This essay is dedicated to the poorly understood tribes of planktonic protists (unicellular eukaryotes) that feed the ocean's animals and continue to run the elemental cycles of our planet. It is an attempt at developing a conceptually coherent framework to understand the course of evolution by natural selection in the plankton and contrast it with the better-known terrestrial realm. I argue that organism interactions, in particular co-evolution between predators and prey (the arms race), play a central role in driving evolution in the pelagic realm. Understanding the evolutionary forces shaping ocean biota is a prerequisite for harnessing plankton for human purposes and also for protecting the oceanic ecosystems currently under severe stress from anthropogenic pressures.