Metaphors for describing the introduction, impacts, and management of non-native species are numerous and often quite outspoken. Policy-makers have adopted increasingly disputed metaphorical terms from scientific discourse. We performed a critical analysis of the use of strong metaphors in reporting scientific findings to policy-makers. Our analysis shows that perceptions of harm, invasiveness or nativeness are dynamic and inevitably display multiple narratives in science, policy or management. Improving our awareness of multiple expert and stakeholder narratives that exist in the context of (...) non-native species management, as well as metaphorical alternatives, is critical. (shrink)

Some critics of invasion biology have argued the invasion of ecosystems by nonindigenous species can create more valuable ecosystems. They consider invaded communities as more valuable because they potentially produce more ecosystem services. To establish that the introduction of nonindigenous species creates more valuable ecosystems, they defend that value is provisioned by ecosystem services. These services are derived from ecosystem productivity, the production and cycling of resources. Ecosystem productivity is a result of biodiversity, which is understood as local species (...) richness. Invasive species increase local species richness and, therefore, increase the conservation value of local ecosystems. These views are disseminating to the public via a series of popular science books. Conservationists must respond to these views, and I outline a method of rejecting such arguments against controlling invasive species. Ecological systems are valuable for more than local productivity and biodiversity is not accurately described by a local species count. (shrink)

Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary (...) biologists. Because these sciences are typically interested in different temporal and spatial scales, we describe what is required to assess phenotypic plasticity at different levels. We explore the inevitable tradeoffs of experiments conducted at the genotype vs. species level, outline components of experimental design required to identify plasticity at different levels, and review some examples from the recent literature. Moreover, we suggest that a successful invader may benefit from plasticity as either (1) a Jack-of-all-trades, better able to maintain fitness in unfavourable environments; (2) a Master-of-some, better able to increase fitness in favourable environments; or (3) a Jack-and-master that combines some level of both abilities. This new framework can be applied when testing both ecological or evolutionary oriented hypotheses, and therefore promises to bridge the gap between the two perspectives. (shrink)

An analysis is presented of published methods that have been used by experimenters to justify the reliability of the theory of invasion of microorganisms into cultured cells. The results show that, to demonstrate this invasion, many experimenters used two or more methods that were based on independent technical and theoretical principles, and by doing so improved the reliability of the theory. Subsequently I compare this strategy of 'multiple derivability' with other strategies, discussed in the literature in relation to the mesosome, (...) a bacterial organelle that had been detected with the electron microsope, but which appeared later to be an artifact. I propose that different strategies have been applied in this problem, and multiple derivability may have been the decisive one. Finally I discuss the idea that multiple derivability may help to anchor theories in a larger network of theories. (shrink)

Natural selection [Darwin 1859] is perhaps the most important component of evolutionary theory, since it is the only known process that can bring about the adaptation of living organisms to their environments [Gould 2002]. And yet, its study is conceptually and methodologically complex, and much attention needs to be paid to a variety of phenomena that can limit the efficacy of selection [Antonovics 1976; Pigliucci and Kaplan 2000]. In this essay, I will use examples of recent work carried out in (...) my laboratory to illustrate basic research on natural selection as conducted using a variety of approaches, including field work, laboratory experiments, and molecular genetics. I also discuss the application of this array of tools to questions pertinent to conservation biology, and in particular to the all-important problem of what makes invasive species so good at creating the sort of problems they are infamous for [Lee 2002]. (shrink)

Allelopathy is an important biological phenomenon in exotic plant invasions. Studies about this phenomenon can help us to understand how plant interactions influence plant colony and ecosystem functioning. Both alligator weed (Alternanthera philoxeroides, Ap) and crofton weed (Eupatorium adenophorum, Ea) are important destructive exotic species in China. Their allelopathic effects on native plant species are well documented. However, whether alligator weed and crofton weed antagonize each other regarding plant growth? There is largely unknown currently. Here we report that the leaf (...) extract from crofton weed possesses the negative effect on the growth of alligator weed. The results showed that root growth of alligator weed could be seriously inhibited by aqueous extract from crofton weed, exhibited as no root or a few roots if only. Consistent with the inhibition of root growth, we observed changes of physiological and biochemical parameters in treated alligator weed. The chlorophyll content, the root activity and the acetolactate synthase (ALS) activity were significantly decreased; while the rate of superoxide anion (O2-), the malondialdehyde (MDA) content, the peroxidase (POD) activity, and the shikimic acid content were remarkably increased in the treated alligator weed plants. These physiological analyzes suggested that the main allelopathic effects of crofton weed were mainly through affecting the integrity of cell membrane and the activity of the key enzymes. Further, these data also imply that one exotic species has the potential value to be used in bio-control of the other exotic species. (shrink)

Việc các khu vực thiên nhiên bị xâm lăng bởi các giống loài thực vật, động vật lạ khá phổ biến. Ở Việt Nam đã từng có nạn ốc bươu vàng gây điêu đứng, tới nay vẫn còn nhiều di chứng. Chẳng hạn, ngay hiện giờ nếu quan sát các ruộng đồng, đầm nước... vẫn bắt gặp rất nhiều trứng và cả ốc bươu lớn bé, đã lai tạp qua thời gian. Chúng tàn phá ruộng đồng, cả lúa, rau, lẫn (...) cỏ do rất phàm ăn. Tuy vậy, để có kết luận về mức tàn phá của nạn xâm nhập sinh học, trên phương diện kinh tế, nghiên cứu của Turbelin et al. [1] có giá trị thông tin quan trọng. (shrink)

Traditional accounts of the role of learning in evolution have concentrated upon its capacity as a source of fitness to individuals. In this paper I use a case study from invasive species biology—the role of conditioned taste aversion in mitigating the impact of cane toads on the native species of Northern Australia—to highlight a role for learning beyond this—as a source of evolvability to populations. This has two benefits. First, it highlights an otherwise under-appreciated role for learning in (...) evolution that does not rely on social learning as an inheritance channel nor “special” evolutionary processes such as genetic accommodation (both of which many are skeptical about). Second, and more significantly, it makes clear important and interesting parallels between learning and exploratory behaviour in development. These parallels motivate the applicability of results from existing research into learning and learning evolution to our understanding of the evolution of evolvability more generally. (shrink)

In biomedical measurement, biomarkers are used to achieve reliable prediction of, and useful causal information about patient outcomes while minimizing complexity of measurement, resources, and invasiveness. A biomarker is an assayable metric that discloses the status of a biological process of interest, be it normative, pathophysiological, or in response to intervention. The greatest utility from biomarkers comes from their ability to help clinicians (and researchers) make and evaluate clinical decisions. In this paper we discuss a specific methodological use of clinical (...) biomarkers in pharmacological measurement: Some biomarkers, called ‘surrogate markers’, are used to substitute for a clinically meaningful endpoint corresponding to events and their penultimate risk factors. We confront the reliability of clinical biomarkers that are used to gather information about clinically meaningful endpoints. Our aim is to present a systematic methodology for assessing the reliability of multiple surrogate markers (and biomarkers in general). To do this we draw upon the robustness analysis literature in the philosophy of science and the empirical use of clinical biomarkers. After introducing robustness analysis we present two problems with biomarkers in relation to reliability. Next, we propose an intervention-based robustness methodology for organizing the reliability of biomarkers in general. We propose three relevant conditions for a robust methodology for biomarkers: (R1) Intervention-based demonstration of partial independence of modes: In biomarkers partial independence can be demonstrated through exogenous interventions that modify a process some number of “steps” removed from each of the markers. (R2) Comparison of diverging and converging results across biomarkers: By systematically comparing partially-independent biomarkers we can track under what conditions markers fail to converge in results, and under which conditions they successfully converge. (R3) Information within the context of theory: Through a systematic cross-comparison of the markers we can make causal conclusions as well as eliminate competing theories. We apply our robust methodology to currently developing Alzheimer’s research to show its usefulness for making causal conclusions. (shrink)

In biomedical measurement, biomarkers are used to achieve reliable prediction of, and useful causal information about patient outcomes while minimizing complexity of measurement, resources, and invasiveness. A biomarker is an assayable metric that discloses the status of a biological process of interest, be it normative, pathophysiological, or in response to intervention. The greatest utility from biomarkers comes from their ability to help clinicians (and researchers) make and evaluate clinical decisions. In this paper we discuss a specific methodological use of clinical (...) biomarkers in pharmacological measurement: Some biomarkers, called ‘surrogate markers’, are used to substitute for a clinically meaningful endpoint corresponding to events and their penultimate risk factors. We confront the reliability of clinical biomarkers that are used to gather information about clinically meaningful endpoints. Our aim is to present a systematic methodology for assessing the reliability of multiple surrogate markers (and biomarkers in general). To do this we draw upon the robustness analysis literature in the philosophy of science and the empirical use of clinical biomarkers. -/- After introducing robustness analysis we present two problems with biomarkers in relation to reliability. Next, we propose an intervention-based robustness methodology for organizing the reliability of biomarkers in general. We propose three relevant conditions for a robust methodology for biomarkers: (R1) Intervention-based demonstration of partial independence of modes: In biomarkers partial independence can be demonstrated through exogenous interventions that modify a process some number of “steps” removed from each of the markers. (R2) Comparison of diverging and converging results across biomarkers: By systematically comparing partially-independent biomarkers we can track under what conditions markers fail to converge in results, and under which conditions they successfully converge. (R3) Information within the context of theory: Through a systematic cross-comparison of the markers we can make causal conclusions as well as eliminate competing theories. We apply our robust methodology to currently developing Alzheimer’s research to show its usefulness for making causal conclusions. (shrink)

Methodology and theory in science are related to a philosophy in which the centric position of the first person, perception and cognition are made the exclusive focus for interpretation involving mirroring, symbolism, and need, criteria from which major first scientific works in Anthropology originated. A new orientation is found for some notions in physics and cosmology, especially those revolved around an ether as a substrate for the transmission of light that are used in explanation in Theory of Relativity, interpretation of (...) experiment. The interferometer and red shift, theory and experiment in biology, as well as aspects of Ancient Philosophies, and a modern age of extended means of communication are discussed and compared in critique with respect to a visual model, created mathematically, of an egg, that is used to demonstrate proposed physical and conceptual form. The Earth, civilization is argued to have a unaware two-timing complex in thinking social and behavioral aspects caused by the external invasion of spaces by unknown phenomenon dating back to the time of Eve and reflected from a philosophical incompleteness to a space structured with a like two-timed weave of conceptual and material form. (shrink)

Abstract: Lung cancer is the top reason of cancer-associated deaths globally. Surgery is the typical treatment for early-stage non-small cell lung cancer (NSCLC). Advancement in the knowledge of the biology of non-small cell lung cancer has shown molecular evidence used for systemic cancer therapy aiming metastatic disease, with a significant impact on patients’ overall survival (OS) and eminence of life. Though, a biopsy of overt metastases is an invasive technique restricted to assured positions and not effortlessly satisfactory in (...) the clinic. The examination of peripheral blood samples of cancer patients embodies a new basis of cancer-derived material, recognized as liquid biopsy, and its constituents (circulating tumour cells (CTCS), circulating free DNA (cfDNA), exosomes, and tumour-educated platelets (TEP)) may be gotten from nearly any body liquids. These constituents have shown to imitate features of the status of both the primary and metastatic diseases, aiding the clinicians to go towards a tailored medicine. In this paper, the reasons of lung cancer will be recognized and the risk elements that initiated the increase of infection, for instance Smoking, Disclosure to secondhand smoke, Disclosure to radon gas, Disclosure to asbestos and other compounds, Family past history of lung cancer, and decrease of the spread of disease and approaches of handling and prevention of lung cancer. (shrink)

In this paper, we apply the perspective of intra-organismal ecology by investigating a family of ecological models suitable to describe a gene therapy to a particular metabolic disorder, the adenosine deaminase deficiency (ADA-SCID). The gene therapy is modeled as the prospective ecological invasion of an organ (here, bone marrow) by genetically modified stem cells, which then operate niche construction in the cellular environment by releasing an enzyme they synthesize. We show that depending on the chosen order (a choice that cannot (...) be made on \textit{a priori} assumptions), different kinds of dynamics are expected, possibly leading to different therapeutic strategies. This drives us to discuss several features of the extension of ecology to intra-organismal ecology. (shrink)

In view of the philosophical problems that vex the debate on situated affectivity, it can seem wise to focus on simple cases. Accordingly, theorists often single out scenarios in which an individual employs a device in order to enhance their emotional experience, or to achieve new kinds of experience altogether, such as playing an instrument, going to the movies or sporting a fancy handbag. I argue that this narrow focus on cases that fit a ‘user/resource model’ tends to channel attention (...) away from more complex and also more problematic instances of situated affectivity. Among these are scenarios in which a social domain draws individuals into certain modes of affective interaction, often by way of attunement and habituation to affective styles and interaction patterns that are normative in the domain in question. This can lead to a phenomenon that is not so much ‘mind extension’ than ‘mind invasion’: affectivity is dynamically framed and modulated from without, often contrary to the prior orientations of the individuals in question. As an example, I discuss affective patterns prevalent in today’s corporate workplace. I claim that workplace affect sometimes contributes to what is effectively a ‘hack’ of employees’ subjectivity. (shrink)

The most well-known goal of non-invasive prenatal testing (NIPT) is still to determine whether or not a fetus has trisomy 21. Since women often terminate the pregnancy upon a positive result, there is concern that the use of NIPT contributes to discrimination against persons with disabilities. If this concern is justified, it could have an impact on the wider social acceptability of existing testing practices and their potential further expansion. This paper demonstrates four different versions of the discrimination worry, (...) indicates how international policy papers have reacted to them, and identifies the ethically most relevant feature of the concern. (shrink)

This paper explores the ethical dimensions of lionfish removal and provides an argument supporting hunting lionfish for consumption. Lionfish are an invasive species found around the world. Their presence has fueled management strategies that predominantly rely on promoting human predation and consumption. We apply rights-based ethics, utilitarian ethics, and ecocentric environmental ethics to the question of whether hunting and eating lionfish is ethical. After applying these perspectives, we argue that, from a utilitarian perspective, lionfish should be culled. Rights-based ethics, (...) on the other hand, are not applicable in this case, while ecocentric environmental ethics would support lionfish removal. (shrink)

It is clear that invasive species do have their invasion boundaries, and the boundaries are constrained by the differences between their home and alien ecosystems. However, such constraints are weakened for some particular species due to their strong adaptability. From the information-processing perspective, species, as information-processing systems, are more likely to invade the habitats (infosphere) with features compatible with their systems. Low compatibility results in poor information exchange with the new infosphere, leading to the malfunction and eventual cessation of (...) the system. Suppose the system has a large range of compatibility (strong adaptability) to maintain its information exchange with the new infosphere. In that case, it can persist, adapt, and eventually become invasive to the new infosphere, completely different from the native one. (shrink)

It is common for conservationists to refer to non-native species that have undesirable impacts on humans as “invasive”. We argue that the classification of any species as “invasive” constitutes wrongful discrimination. Moreover, we argue that its being wrong to categorize a species as invasive is perfectly compatible with it being morally permissible to kill animals—assuming that conservationists “kill equally”. It simply is not compatible with the double standard that conservationists tend to employ in their decisions about who (...) lives and who dies. (shrink)

A biologically unavoidable sequence is an infinite gender sequence which occurs in every gendered, infinite genealogical network satisfying certain tame conditions. We show that every eventually periodic sequence is biologically unavoidable (this generalizes König's Lemma), and we exhibit some biologically avoidable sequences. Finally we give an application of unavoidable sequences to cellular automata.

Most current techniques to deal with invasive species are ineffective or have highly damaging side effects. To this end suppression-drives based on clustered regularly inter-spaced short palindromic repeats (CRISPR/Cas9) have been touted as a potential silver bullet for the problem, allowing for a highly focused, humane and cost-effective means of removing a target species from an environment. Suppression-drives come with serious risks, however, such that the precautionary principle seems to warrant us not deploying this technology. The focus of this (...) paper is on one such risk – the danger of a suppression-drive escaping containment and wiping out the target species globally. Here, I argue that in most cases this risk is significant enough to warrant not using a gene-drive. In some cases, however, we can bypass the precautionary principle by using an approach that hinges on what I term the ‘Worst-Case Clause’. This clause, in turn, provides us with a litmus test that can be fruitfully used to determine what species are viable targets for suppression-drives in the wild. Using this metric in concert with other considerations, I suggest that only three species are currently possible viable targets – the European rabbit, ship rat and Caribbean Tree Frog. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...) been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected and discussed, together with (...) the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Since Boorse [Philos Sci 44(4):542–573, 1977] published his paper “Health as a theoretical concept” one of the most lively debates within philosophy of medicine has been on the question of whether health and disease are in some sense ‘objective’ and ‘value-free’ or ‘subjective’ and ‘value-laden’. Due to the apparent ‘failure’ of pure naturalist, constructivist, or normativist accounts, much in the recent literature has appealed to more conciliatory approaches or so-called ‘hybrid accounts’ of health and disease. A recent paper by Matthewson (...) and Griffiths [J Med Philos 42(4):447–466, 2017], however, may bear the seeds for the revival of purely naturalist approach to health and disease. In this paper, I defend their idea of Biological Normativity against recent criticism by Schwartz [J Med Philos Forum Bioethics Philos Med 42(4):485–502, 2017] and hope to help it flower into a revival of naturalist approaches in the philosophy of medicine. (shrink)

The purpose of this paper is to discuss the biological plausibility of the pace of creation written in the genesis. A fascinating hypothesis is made on the central role of serotonin as a guide, as the director of the phenomena that enable the best use of light by the plant world, the growth, the regulation of mood in the complex molecular interactions that characterize the varying levels of consciousness. This hypothesis provides biological interpretations of the c.

Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb ‘need’ has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: their (...) objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of ‘normative’ are distinguished. On two of these, to describe a phenomenon or claim as ‘normative’ is to describe it as value-dependent. A description of a phenomenon or claim as ‘normative’ in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses. (shrink)

García-Barranquero et al explore the desirability of human ageing. They differentiate between chronological and biological views of ageing and contend that the positive aspects of ageing are solely linked to chronological ageing. Consequently, the authors embrace the potential for technological interventions in biological ageing. Contrary to their stance, I argue that there are sometimes desirable aspects associated with biological ageing. Therefore, proposals aiming to eliminate, mitigate or diminish biological ageing are not without problems.

methods that have shown promise for improving extreme risk analysis, particularly for assessing the risks of invasive pests and pathogens associated with international trade. We describe the legally inspired regulatory regime for banks, where these methods have been brought to bear on extreme ‘operational risks’. We argue that an ‘advocacy model’ similar to that used in the Basel II compliance regime for bank operational risks and to a lesser extent in biosecurity import risk analyses is ideal for permitting the (...) diversity of relevant evidence about invasive species to be presented and soundly evaluated. We recommend that the process be enhanced in ways that enable invasion ecology to make more explicit use of the methods found successful.. (shrink)

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...) organisms as essentially possessing some mechanisms that play this role. (shrink)

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data (...) processor to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality approaches to causal selection have received many criticisms, some of which miss their target. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria that uniquely singles out the gene as explanatorily significant in biology has led philosophers to overlook a prior problem. Before one can address whether Waters’s and Weber’s views successfully account for the explanatory significance of genes, one must ask whether either view satisfactorily meets (...) the necessary conditions for causal selection in the first place. An adequate defense of causal selection must meet two desiderata. First, there must be an explanatory property that sets some causes apart from others. Second, the property identified must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue that both fall short of meeting the second condition. I demonstrate this by showing how many of the biological technologies crucial to experimentation do not fit either view very well. I offer a more adequate proposal that accommodates non-actual and artificial causal variables. A consequence of my view is the following: When analyzing the causal selection practices of biologists, philosophers should consider the explanatory targets relevant to a research program – including ones whose explanans must appeal to biological technologies. I then explain how this proposal can inform the existing debate between Weber (2017) and Griffiths et al. (2015). (shrink)

The paper attempts to conciliate the important distinction between what-is, or exists, and what-is-not _thereby supporting Russell’s existential analysis_ with some Meinongian insights. For this purpose, it surveys the varied inhabitants of the realm of ‘non-being’ and tries to clarify their diverse statuses. The position that results makes it possible to rescue them back in surprising but non-threatening form, leaving our ontology safe from contradiction.

In this commentary on Daniel Dennett's 'From Bacteria to Bach and Back', I make some suggestions to strengthen the meme concept, in particular the hypothesis of cultural parasitism. This is a notion that has both caused excitement among enthusiasts and raised the hackles of critics. Is the “meme” meme itself an annoying piece of malware, which has infected and corrupted the mind of an otherwise serious philosopher? Or is it an indispensable theoretical tool, as Dennett believes, which deserves to be (...) spread far and wide? (shrink)

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is (...) to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

This selective review explores biologically inspired learning as a model for intelligent robot control and sensing technology on the basis of specific examples. Hebbian synaptic learning is discussed as a functionally relevant model for machine learning and intelligence, as explained on the basis of examples from the highly plastic biological neural networks of invertebrates and vertebrates. Its potential for adaptive learning and control without supervision, the generation of functional complexity, and control architectures based on self-organization is brought forward. Learning without (...) prior knowledge based on excitatory and inhibitory neural mechanisms accounts for the process through which survival-relevant or task-relevant representations are either reinforced or suppressed. The basic mechanisms of unsupervised biological learning drive synaptic plasticity and adaptation for behavioral success in living brains with different levels of complexity. The insights collected here point toward the Hebbian model as a choice solution for “intelligent” robotics and sensor systems. Keywords: Hebbian learning; synaptic plasticity; neural networks; self-organization; brain; reinforcement; sensory processing; robot control . (shrink)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue that this (...) analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

Deep learning, a transformative force in computational biology, has reshaped biological data analysis and interpretation terrain. This review delves into the multifaceted role of deep knowledge in this field, exploring its historical roots, inherent advantages, and persistent challenges. It investigates explicitly its application in two pivotal domains: DNA sequence classification, where it has been used to identify disease-causing mutations, and protein structure prediction from sequence data, where it has enabled the accurate determination of protein tertiary structures. Moreover, it offers (...) a glimpse into the future trajectory of this dynamic field, sparking intrigue and excitement about the potential of deep learning. Deep learning, a powerful tool in computational biology, can be traced back to the inception of 'threshold logic,' a fusion of algorithmic principles and mathematical frameworks devised to mimic cognitive processes. This seminal breakthrough, which introduced the concept of a threshold function that could be used to model complex decision-making processes, paved the way for deep learning to decipher intricate patterns embedded within vast biological datasets. Deep learning presents many benefits, including precise disease diagnosis, novel drug discovery, and personalized medicine facilitation. Its prowess lies in handling vast, intricate datasets while enhancing generalization capabilities, a testament to its evolution and development that we can appreciate. (shrink)

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of Standard (...) Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Is it possible to know anything about life we have not yet encountered? We know of only one example of life: our own. Given this, many scientists are inclined to doubt that any principles of Earth’s biology will generalize to other worlds in which life might exist. Let’s call this the “N = 1 problem.” By comparison, we expect the principles of geometry, mechanics, and chemistry would generalize. Interestingly, each of these has predictable consequences when applied to biology. (...) The surface-to-volume property of geometry, for example, limits the size of unassisted cells in a given medium. This effect is real, precise, universal, and predictive. Furthermore, there are basic problems all life must solve if it is to persist, such as resistance to radiation, faithful inheritance, and energy regulation. If these universal problems have a limited set of possible solutions, some common outcomes must consistently emerge. In this chapter, I discuss the N = 1 problem, its implications, and my response (Mariscal 2014). I hold that our current knowledge of biology can justify believing certain generalizations as holding for life anywhere. Life on Earth may be our only example of life, but this is only a reason to be cautious in our approach to life in the universe, not a reason to give up altogether. In my account, a candidate biological generalization is assessed by the assumptions it makes. A claim is accepted only if its justification includes principles of evolution, but no contingent facts of life on Earth. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the (...) basis of distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

Not the publicly asserted reasons (humanitarianism and self-defense) but cooptation of oil reserves was the objective behind the US invasion of Iraq in 2003. This underlying motive utterly fails to satisfy just war jus ad bellum conditions. This prioritization of petroleum is well documented and is consistent with decades old US policy towards the Middle East, especially as codified by Anthony Cordesman in 1998 and US DoD's Strategic Assessment 1999 and then adopted by Bush II. This fraudulent use of military (...) force raises a question as to how motives for war can be accurately identified prior to falsely justified belligerence. Some positive signs are noted herein as to political philosophers' better use of Rawls's reflective equilibrium. (shrink)

This paper presents and defends an account of the coincidence of biological organisms with mereological sums of their material components. That is, an organism and the sum of its material components are distinct material objects existing in the same place at the same time. Instead of relying on historical or modal differences to show how such coincident entities are distinct, this paper argues that there is a class of physiological properties of biological organisms that their coincident mereological sums do not (...) have. The account answers some of the most pressing objections to coincidence, for example the so-called grounding problem , that material coincidence seems to require that coinciding objects have modal differences that do not supervene on any other properties. (shrink)

In this essay, we discuss Simona Ginsburg and Eva Jablonka’s The Evolution of the Sensitive Soul from an interdisciplinary perspective. Constituting perhaps the longest treatise on the evolution of consciousness, Ginsburg and Jablonka unite their expertise in neuroscience and biology to develop a beautifully Darwinian account of the dawning of subjective experience. Though it would be impossible to cover all its content in a short book review, here we provide a critical evaluation of their two key ideas—the role of (...) Unlimited Associative Learning in the evolution of, and detection of, consciousness and a metaphysical claim about consciousness as a mode of being—in a manner that will hopefully overcome some of the initial resistance of potential readers to tackle a book of this length. (shrink)

This fourth preprint in the Systemic Continuum Paradigm (PSC) series extends autopoiesis—traditionally confined to living organisms—across non-biological substrates such as advanced neural networks, robotics, and augmented intelligence. Building on the prior three preprints, we argue that self-maintenance and operational closure can arise whenever synergy surpasses a critical threshold, irrespective of substrate. Key contributions include: 1. Revisiting Autopoiesis Beyond Biology: Grounding Maturana & Varela’s concept of self-production in the PSC framework to show how informational “metabolism” can maintain system identity without (...) purely biochemical loops. 2. Thresholds of Synergy: Explaining how internal systemic balance (ISB) triggers emergent closure (ESB) when certain Systemic Thresholds (ST) are crossed—even in AI or hybrid bio-tech systems. 3. Metrics and Empirical Pathways: Introducing and refining ICS, CNS, MDO, and SDI for non-biological autopoiesis, paving a route for experimental validation and bridging the gap between metaphorical descriptions and operational measures. 4. Filogenetic Analogies: Drawing on the unpredictability of terrestrial evolution to illustrate how synergy-driven leaps in artificial systems could mirror major evolutionary transitions, with humans acting as catalysts rather than detached creators. 5. Addressing the Metabolic Critique: Differentiating informational reconfiguration from strict biological reproduction, while defending the view that both processes can yield genuine self-maintenance under PSC criteria. By dissolving strict boundaries between “natural” and “artificial” autopoiesis, this preprint contributes to a revolutionary dialogue in systems theory—one that redefines “life,” “intelligence,” and “agency” as emergent phenomena shaped by synergy thresholds rather than substrate constraints. (shrink)

This paper contains my attempt to pastiche the Lacanian philosopher and social theorist Renata Salecl. The pastiche focuses on the effects of coronavirus on liberal societies, the invasion of Ukraine, and offers a definition which I think is of interest to analytic philosophy.

The paper examines the relationship between the biological and the social in morals. Its conclusion is that the biological is one among other sources of moarls. The social developed as another, much more dynamic source. An important role is played by free will or the moral freedom, especially on the individual morals level. It is the consequences, and especially social consequences, that in the author's viewpoint to the actual state of social and individual morals.

“Impermanent Biological Phenomena” July 2021, Buddhism and Culture (a Korean-language Buddhist magazine sponsored by the Foundation for the Promotion of Korean Buddhism), Korea.

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet (...) it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

A minimal essentialism (‘intrinsic biological essentialism’) about natural kinds is required to explain the projectability of human science terms. Human classifications that yield robust and ampliative projectable inferences refer to biological kinds. I articulate this argument with reference to an intrinsic essentialist account of HPC kinds. This account implies that human sciences (e.g., medicine, psychiatry) that aim to formulate predictive kind categories should classify biological kinds. Issues concerning psychiatric classification and pluralism are examined.

I develop an account of the role that biology plays in the Timaeus’ view of nous and other aspects of cognitive life. I begin by outlining the biology of human cognition. I then argue that these biological views shine an important light on different aspects of the soul. I then argue that the human body is particularly friendly to nous, paying special attention to the heart and the liver. I next consider the ways that the body fails to (...) protect our nous. I conclude by comparing human nous with the cognition of non-humans. (shrink)