This paper aims to offer a new argument in defence bacterial species pluralism. To do so, I shall first present the particular issues derived from the conflict between the non-theoretical understanding of species as units of classification and the theoretical comprehension of them as units of evolution. Secondly, I shall justify the necessity of the concept of species for the bacterial world, and show how medicine and endosymbiotic evolutionary theory make use of different concepts of (...) bacterial species due to their distinctive purposes. Finally, I shall show how my argument provides a new source of defence for bacterial pluralism. (shrink)

Microbial biofilm created huge burden in treatment of both community and hospital infections. A biofilm is complex communities of bacteria attached to a surface or interface enclosed in an exopolysaccharide matrix and protected from unfavorable conditions such as presence of antibiotics, host defense or oxidative stresses. Biofilms are often considered hot spot for horizontal gene transfer among same or different bacterial species. Furthermore, bacteria with increased hydrophobicity facilitate biofilm formation by reducing repulsion between the extracellular matrix and the (...) bacterium. There is a marked increase in the rate of persons nonresponsive to antibiotic therapy for infections of the Urinary Tract (UTIs), burns and upper respiratory tract due to biofilm formations. It is estimated that 90% of nosocomial infections are mediated by biofilm. The role of biofilm in infections has become so great that the treatment of such antibiotic resistance infections is proving difficult and costly to health care systems. The biofilm related infections varied from dental plaque, destruction of prosthetic valve to death of cystic fibrosis patients. This review aims to provide a summary of role of bacterial biofilm and its clinical implications for the patients. (shrink)

Bacteria do many things as organized populations. We have recently learned much about the molecular basis of intercellular communication among prokaryotes. Colonies display bacterial capacities for multicellular coordination which can be useful in nature where bacteria predominantly grow as films, chains, mats and colonies. E. coli colonies are organized into differentiated non-clonal populations and undergo complex morphogenesis. Multicellularity regulates many aspects of bacterial physiology, including DNA rearrangement systems. In some bacterial species, colony development involves swarming (active (...) migration of cell groups). Swarm colony development displays precise geometrical controls and periodic phenomena. Motile E. coli cells in semi-solid media form organized patterns due to chemotactic autoaggregation. On poor media, B. subtilis forms branched colonies using group motility and long-range chemical signalling. The significances of bacterial colony patterns thus reside in a deeper understanding of prokaryotic biology and evolution and in experimental systems for studying self-organization and morphogenesis. (shrink)

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed (...) multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. Previous article in issue. (shrink)

Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique (...) of phylogenetic bacterial species, arguing that phylogenetic bacterial classification requires a questionable metaphysical commitment to the existence of essential genes. I conclude by considering how microbiologists have dealt with these biological complexities by using more pragmatic and not exclusively evolutionary accounts of species. I argue that this pragmatism is not borne of laziness but rather of the substantial conceptual problems in classifying bacteria based on any evolutionary standard. (shrink)

This text answers the question, posed by the editor, on the philosophical and social issues resulting from the synthetic assembly of a modified bacterial genome that was introduced in an existing bacterial species (M.mycoides)and so it was claimed to represent the first ever kind of synthetic life produced by human manipulation.

Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...) species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

Eshel Ben-Jacob’s manuscript entitled ‘Bacterial wisdom, Gödel’s theorem and creative genomic webs’ summarizes decades of work demonstrating adaptive mutagenesis in bacterial genomes. Bacterial genomes, each an essential part of a Kantian whole that is a single bacterium, are thus not independent of the environment as sensed; and a single bacterium is therefore a semiotic entity. Ben-Jacob suggests this but errs in 1) assigning autonomy to the genome, and 2) analogizing through computation without making clear whether he is (...) doing so for illustrative purposes or making committed ontological propositions. We reinterpret adaptive mutagenesis and related phenomena in ways both metaphysically rigorous and revealing. We conclude that bacteria are much farther removed from the ‘self-organizing’ world of inanimate process than from the Peircian world of signs; and a critical reappraisal of existing knowledge can enhance our understanding of selfhood, semiosis, and the roots of subjective experience. (shrink)

This collection of original essays--by philosophers of biology, biologists, and cognitive scientists--provides a wide range of perspectives on species. Including contributions from David Hull, John Dupre, David Nanney, Kevin de Queiroz, and Kim Sterelny, amongst others, this book has become especially well-known for the three essays it contains on the homeostatic property cluster view of natural kinds, papers by Richard Boyd, Paul Griffiths, and Robert A. Wilson.

The so-called ‘‘species problem’’ has plagued evolution- ary biology since before Darwin’s publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don’t seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical liter- atures on the (...) species problem, focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require—but cannot be settled by—empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein’s idea of ‘‘family resemblance’’ or cluster concepts, and to consider spe- cies as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among bio- logists and philosophers. The current proposal is con- ceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupre ́, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion pre- sented here is Templeton’s cohesion idea. (shrink)

For more than fifty years, taxonomists have proposed numerous alternative definitions of species while they searched for a unique, comprehensive, and persuasive definition. This monograph shows that these efforts have been unnecessary, and indeed have provably been a pursuit of a will o’ the wisp because they have failed to recognize the theoretical impossibility of what they seek to accomplish. A clear and rigorous understanding of the logic underlying species definition leads both to a recognition of the inescapable (...) ambiguity that affects the definition of species, and to a framework-relative approach to species definition that is logically compelling, i.e., cannot not be accepted without inconsistency. An appendix reflects upon the conclusions reached, applying them in an intellectually whimsical taxonomic thought experiment that conjectures the possibility of an emerging new human species. (shrink)

It has been widely argued that words are analogous to species such that words, like species, are natural kinds. In this paper, I consider the metaphysics of word-kinds. After arguing against an essentialist approach, I argue that word-kinds are homeostatic property clusters, in line with the dominant approach to other biological and psychological kinds.

Biofouling, the accumulation of microorganisms, is a major problem in paper mills processing paper and cardboard. This leads to the production of lower quality recycled products. Several studies have focused on the microbial content in the paper mill and the final products. Our aim was to determine the microbial biota in a bale of collected cardboard prior to entering the paper mill. Total genomic DNA was isolated and analyzed using two different methods for comparison purposes: 454 pyrosequencing and clone library. (...) A total of 3268 V6-V8 454 pyrosequencing reads and 322 cloned V6-V8 16S rRNA nucleotide sequences were obtained. Both methods showed the presence of three major bacterial genera: Bacillus, Solibacillus and Paenibacillus, all members of the spore-forming phylum Firmicutes. Pyrosequencing, however, revealed a richer and more diverse bacterial community than clone library. It showed the presence of additional minor Firmicute genera and of a small number of Proteobacteria. The sorting at the recycling plant, the storing, and the processing at the paper mill, the end uses, will all contribute to the bacterial microbiota present in a bale of collected cardboard as revealed here. (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)

In light of the phenomenon of multiple realizability, many philosophers wanted to preserve the mind-brain identity theory by resorting to a “narrow reductive strategy” whereby one (a) finds mental properties which are (b) sufficiently narrow to avoid the phenomenon of multiple realization, while being (c) explanatorily adequate to the demands of psychological theorizing. That is, one replaces the conception of a mental property as more general feature of cognitive systems with many less general properties, for example, replacing the conception of (...) pain as a general property across different species with a number of species-specific kinds of pain. Many critics focused on (c), arguing that species-specific properties are not explanatorily adequate because they do not capture what is common in pain across species. In this paper I focused on (b). I argued that if one carries the narrow reductive strategy out in such a way to avoid all multiple realizability that occurs within a species, for example, accommodating individual differences by postulating a more narrow pain-relative-to-an-individual-at-a-time, then the result is for all intents and purposes a claim about tokens and not types or properties at all (the position is now about individuals having properties at times, a structured token event). I also added an important point about explanation, viz., that properties-relative-to-individuals-at-times would not serve the explanatory goals of science by failing to generalize to other individuals. (shrink)

Book review of Richard A. Richards' The Species Problem: A Philosophical Analysis.

Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, (...) if at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

this requirement for adaptations. Emergent characters are always potential adaptations. Not all selection processes produce adaptations, however. The key issue, in delineating a selection process, is the relationship between a character and fitness. The emergent character approach is more restrictive than alternative schemas that delineate selection..

This chapter defends a pluralist understanding of species on which a normative species concept is viable and can support natural goodness evaluations. The central question here is thus: Since organisms are to be evaluated as members of their species, how does a proper understanding of species affect the feasibility of natural goodness evaluations? Philippa Foot has argued for a form of natural goodness evaluation in which living things are evaluated by how well fitted they are for (...) flourishing as members of their species, in ways characteristic of their species. She has further argued that assessments of moral goodness in humans are of the same evaluative form. However, natural goodness evaluations and, by extension, the natural goodness approach, do not garner justification in virtue of employing a scientifically privileged conception of species. The natural goodness approach is only justified given particular metaethical and normative commitments that are independent of naturalism, since the approach does not depend upon naturalism alone. (shrink)

Anne Conway rejects the view that creatures are essentially members of any natural kind more specific than the kind 'creature'. That is, she rejects essentialism about species membership. This chapter provides an analysis of one of Anne Conway's arguments against such essentialism, which (as I argue) is drawn from metaethical rather than metaphysical premises. In her view, if a creature's species or kind were inscribed in its essence, that essence would constitute a limit on the creature's potential to (...) participate in the divine good. It is this consideration that ultimately leads her to reject essentialism about species membership. The chapter concludes with an examination of some of the metaethical consequences of Conway's view as well as a lesson it can teach us about ideal adviser accounts of the good. (shrink)

Whitehead claims there is only one type of individual in the universe—the actual entity—but there are necessarily multiple tokens of this type. This turns out to be paradoxical. Nevertheless, a type of individuality that is necessarily plural because, for each token, relations to other tokens are constitutive is something familiar from ordinary language, everyday politics, and, not least, 19th century German social thought. Whitehead’s actual entity generalizes the notion of species-being we find in Fichte, Feuerbach, and Marx. The rationale (...) for the concept of species-being brings to light important social and political implications of Whitehead’s cosmology. (shrink)

This paper argues against the common, often implicit view that theories are some specific kind of thing. Instead, I argue for theory concept pluralism: There are multiple distinct theory concepts which we legitimately use in different domains and for different purposes, and we should not expect this to change. The argument goes by analogy with species concept pluralism, a familiar position in philosophy of biology. I conclude by considering some consequences for philosophy of science if theory concept pluralism is (...) correct. (shrink)

The name ‘pluralism’ frequently rears its head in political philosophy, but theorists often have different things in mind when using the term. Whereas ‘reasonable pluralism’ refers to the fact of moral diversity among citizens of a liberal democracy, ‘value pluralism’ is a metaethical view about the structure of moral practical reasoning. In this paper, I argue that value pluralism is part of the best explanation for reasonable pluralism. However, I also argue that embracing this explanation is compatible with political liberalism’s (...) commitment to avoiding controversial premises. According value pluralism an explanatory role does not entail according it a justificatory one. What’s more, explaining reasonable disagreement in terms of reasonable disagreement about value weights opens up space for direct appeal to substantive values within political liberalism. In particular, promoting a substantive political value when doing so does not conflict with other values is unproblematic. (shrink)

Kingfishers are a family, the Alcedinidae, of small to medium-sized, brightly colored birds in the order Coraciiformes. They have a cosmopolitan distribution, with most species found in the tropical regions of Africa, Asia, and Oceania, but also can be seen in Europe.

After introducing the new field of cultural evolution, we review a growing body of empirical evidence suggesting that culture shapes what people attend to, perceive and remember as well as how they think, feel and reason. Focusing on perception, spatial navigation, mentalizing, thinking styles, reasoning (epistemic norms) and language, we discuss not only important variation in these domains, but emphasize that most researchers (including philosophers) and research participants are psychologically peculiar within a global and historical context. This rising tide of (...) evidence recommends caution in relying on one’s intuitions or even in generalizing from reliable psychological findings to the species, Homo sapiens. Our evolutionary approach suggests that humans have evolved a suite of reliably developing cognitive abilities that adapt our minds, information-processing abilities and emotions ontogenetically to the diverse culturally-constructed worlds we confront. (shrink)

This afterword to Species and Beyond provides some reflections on species, with special attention to what I think the most significant developments have been in the thinking of biologists and philosophers working on species over the past 25 years, as well as some bad jokes.

Biodiversity loss is happening at an unprecedented rate, and invasive species are one of the main contributors to the global biodiversity decline. Invasive species are alien (non-native) organisms that become overpopulated and cause environmental harm to the native environment. For example, a recent global meta-analysis shows that 30 invasive predator species have been linked to the extinction or endangerment of 738 vertebrate species, accounting for 58% of all bird, mammal, and reptile extinctions. For effective biology conservation, (...) some questions are worth answering: Do invasive species have any invasion limits? Or are they capable of invading habitats significantly different from their native environment due to their strong adaptability? (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)

In 1655 La Peyrère was the first to substantially argue for and popularize polygenism—the view that God created multiple original human mating pairs in separate acts of creation with numerous created before Adam. Positing or rejecting polygenism has been central to modern theorizing about human types and origins. Prominent recent interpreters have maintained that La Peyrère’s polygenism does not imply a hierarchy of human types. This paper reconstructs La Peyrère’s account and, in opposition to the dominant view, argues that his (...) polygenism produces a human species hierarchy. The Adamite species is superior to the Pre-Adamite species in virtue of its material composition, mode of creation, and form. The upshot is that La Peyrère’s theological system posits a proto-racialist conception of human types. (shrink)

According to Miranda Fricker, a hermeneutical injustice occurs when there is a deficit in our shared tools of social interpretation, such that marginalized social groups are at a disadvantage in making sense of their distinctive and important experiences. Critics have claimed that Fricker's account ignores or precludes a phenomenon I call hermeneutical dissent, where marginalized groups have produced their own interpretive tools for making sense of those experiences. I clarify the nature of hermeneutical injustice to make room for hermeneutical dissent, (...) clearing up the structure of the collective hermeneutical resource and the fundamental harm of hermeneutical injustice. I then provide a more nuanced account of the hermeneutical resources in play in instances of hermeneutical injustice, enabling six species of the injustice to be distinguished. Finally, I reflect on the corrective virtue of hermeneutical justice in light of hermeneutical dissent. (shrink)

Explains Aristotle's views on the possibility of continuous variation between biological species. While the Porphyrean/Linnean classification of species by a tree suggests species are distributed discretely, Aristotle admitted continuous variation between species among lower life forms.

Species is one of the most basic concepts for almost all branches of biology, and it is also one of the most controversial concepts. An important aspect of "the species problem" is the question of "what the ontological status of species is". Traditionally, the answer to the issue about "the ontological status of species" is biological essentialism. Biological essentialism claims that species is a "natural kind", which argues that all and only the members of a (...) species have a common essence. Each species is separated from all others by a sharp discontinuity. However, Darwin's evolutionary theory argues that species are gradual, and the boundaries between species are vague. This view conflicts with biological essentialism. With the continuous transmission of Darwin's theories, biological essentialism was gradually abandoned by philosophers and scientists. In recent years, some philosophers try to resurrect biological essentialism by using new biological resources. Their theories are known as New Biological Essentialism, which mainly includes three different approaches: The Barcode Theory of DNA, Relational Essentialism, and HPC Theory. However, there are so many defects in their theories that they don't provide a successful defense for biological essentialism. By analyzing these theories, I try to point out that the dilemma and failure of new biological essentialism dues to the conflict between its ontological presupposition and modern biological practice. The conflict leads to the tension between essentialism and biology. Further, I argue that the best way to eliminate the tension between biology and essentialism is to regard species as “heterogeneous kinds”. This new understanding of species abandons biological essentialism at the ontological level but retains the value of epistemology of regarding the species as “natural kinds”. (shrink)

Traditionally, species have been treated as classes. In fact they may be considered individuals. The logical term “individual” has been confused with a biological synonym for “organism.” If species are individuals, then: 1) their names are proper, 2) there cannot be instances of them, 3) they do not have defining properties, 4) their constituent organisms are parts, not members. “ Species " may be defined as the most extensive units in the natural economy such that reproductive competition (...) occurs among their parts. Species are to evolutionary theory as firms are to economic theory: this analogy resolves many issues, such as the problems of “reality” and the ontological status of nomenclatorial types. (shrink)

The concept of ecosystem services is a way of visualizing the instrumental value that nature has for human beings. Most ecosystem services can be performed by more than one species. This fact is sometimes used as an argument against the preservation of species. However, even though substitutability does detract from the instrumental value of a species, it also adds option value to it. The option value cannot make a substitutable species as instrumentally valuable as a non-substitutable (...) species, but in many cases, it can add enough value to make the species more valuable than the projects that threaten its existence. (shrink)

Over 1.5 million living animal species have been described—of which around 1 million are insects—but it has been estimated there are over 7 million animal species in total. Animals range in length from 8.5 micrometres to 33.6 metres. In this paper an Artificial Neural Network (ANN) model, was developed and tested to predict animal species. There are a number of features that influence the classification of animal species. Such as the existence of hair/ feather, if the (...) animal gives birth or spawns, it is airborne, aquatic, predator, toothed, backboned, venomous, has –fins, has-tail, cat-sized, and domestic. A model based on the Multilayer Perceptron Topology was proposed and trained, using data set what was collected from UCI Machine Learning Repository. Evaluation of the proposed model shows that the ANN model is able to correctly predict the animal category with 100% accuracy. (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)

Abstract: In this study, we explore the possibility of classifying the plant species. We collected the plant species from Kaggle website. This dataset encompasses 544 samples, encompassing 136 distinct plant species. Recent advancements in machine learning, particularly Artificial Neural Networks (ANNs), offer promise in enhancing plant Species classification accuracy and efficiency. This research explores plant Species classification, harnessing neural networks' power. Utilizing a rich dataset from Kaggle, containing 544 entries, we develop and evaluate a neural (...) network model. Our neural network, featuring a single hidden layer, achieves remarkable results—a staggering 100% accuracy and a minute average error rate of 0.002. Beyond performance metrics, we delve into the intricacies of plant Species classification through feature importance analysis. The most influential features— Vegsout, durflow, semiros, pdias, begflow, wind, leafy, autopoll and insects— uncover the physiological traits underpinning accurate rice classification. This research contributes to advancing rice classification methods and highlights the potential of ANNs in optimizing agricultural practices, ensuring plant safety, and bolstering global trade. (shrink)

This paper explains the metaphysical implications of the view that species are individuals (SAI). I first clarify SAI in light of the separate distinctions between individuals and classes, particulars and universals, and abstract and concrete things. I then show why the standard arguments given in defense of SAI are not compelling. Nonetheless, the ontological status of species is linked to the traditional "species problem," in that certain species concepts do entail that species are individuals. I (...) develop the idea that species names are rigid designators and show how this provides additional motivation for SAI. (shrink)

The nature of “the self” has been one of the central problems in philosophy and more recently in neuroscience. This raises various questions: Can we attribute a self to animals? Do animals and humans share certain aspects of their core selves, yielding a trans-species concept of self? What are the neural processes that underlie a possible trans-species concept of self? What are the developmental aspects and do they result in various levels of self-representation? Drawing on recent literature from (...) both human and animal research, we suggest a trans-species concept of self that is based upon what has been called a “core-self” which can be described by self-related processing as a specific mode of interaction between organism and environment. When we refer to specific neural networks, we will here refer to the underlying system as the “core-SELF.” The core-SELF provides primordial neural coordinates that represent organisms as living creatures—at the lowest level this elaborates interoceptive states along with raw emotional feelings while higher medial cortical levels facilitate affective-cognitive integration . Developmentally, SRP allows stimuli from the environment to be related and linked to organismic needs, signaled and processed within core-self structures within subcorical-cortical midline structures that provide the foundation for epigenetic emergence of ecologically framed, higher idiographic forms of selfhood across different individuals within a species. These functions ultimately operate as a coordinated network. We postulate that core SRP operates automatically, is deeply affective, and is developmentally and epigenetically connected to sensory-motor and higher cognitive abilities. This core-self is mediated by SCMS, embedded in visceral and instinctual representations of the body that are well integrated with basic attentional, emotional and motivational functions that are apparently shared between humans, non-human mammals, and perhaps in a proto-SELF form, other vertebrates. Such a trans-species concept of organismic coherence is thoroughly biological and affective at the lowest levels of a complex neural network, and culturally and ecologically molded at higher levels of neural processing. It allows organisms to selectively adapt to and integrate with physical and social environments. Such a psychobiologically universal, but environmentally diversified, concept may promote novel trans-species studies of the core-self across mammalian species. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance (...) purposes. (shrink)

Can Wittgenstein's famous family resemblance concept be applied to resolve the problem of defining species in biology?

This paper seeks to propose a direction of research based upon the transformation of Merleau-Ponty's thinking with respect to animal life over the course of his writings. In his earlier works, Merleau-Ponty takes up the position that “life” does not mean the same thing when applied to an animal and a human being because of the manner in which the “human dialectic” alters the human being's relation to life. In his later works, particularly in his lectures on nature, this position (...) softens so that the relationship between animals and humans becomes non-hierarchical, but remains essentially the same: there may be no “rupture” between humans and animals, but they are still essentially distinct insofar as all non-humans can be grouped into a single class of “animality.” I attempt to show that Merleau-Ponty fails to follow through with his most radical insights with respect to the relationships between living beings by preserving this distinction and suggest some ways in which we might today confront this problem through the works of Merleau-Ponty in a way that he did not. The proposal, then, is to take seriously “dialectical” biology and develop a Merleau-Pontian conception of species based upon the interrelations of living beings and their environments rather than focusing solely on organisms as discrete units. The conclusion then considers what the consequences of this understanding might be for our understanding of Merleau-Ponty's ontology in general. (shrink)

The species problem is often described as the abundance of conflicting definitions of _species_, such as the biological species concept and phylogenetic species concepts. But biologists understand the notion of species in a non-definitional as well as a definitional way. In this article I argue that when they understand _species_ without a definition in their mind, their understanding is often mediated by the notion of _good species_, or prototypical species, as the idea of ``prototype'' is (...) explicated in cognitive psychology. This distinction helps us make sense of several puzzling phenomena regarding biologists' dealing with species, such as the fact that in everyday research biologists often behave as if the species problem is solved, while they should be fully aware that it is not. I also briefly discuss implications of this finding, including that some extant attempts to answer what the nature of species is have an inadequate assumption about how the notion of species is represented in biologists' minds. (shrink)

The Nilgiri sholakili is an endangered and endemic bird species found in the Nilgiris at altitudinal ranges of over 1000m, mainly north of the Palghat gap. Also known as the Nilgiri shortwing or Nilgiri blue robin, it is a song bird found in the shola forest lower canopy and forest floor, a threatened habitat. The two subspecies of shortwing distributed in western ghats are the Sholicola major (Jerdon 1841) and the Sholicola albiventris (Blanford 1868) also known as the white-bellied (...) shortwing. The white-bellied shortwing is found mainly around the Palni hills and south of the Palghat gap. The Nilgiri sholakili is a small dark slaty blue bird, with a buff white upper belly and tan/ rufous towards the flanks. For a bird its size, its song is longwinded, composed of high warbling notes and buzzy whistles. (shrink)

Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures, in terms of the topological properties of the system, or in (...) terms of equilibrium. The role of mathematics in bowtie structured systems and in topologically constrained systems has recently been examined in different papers. However, the specific role that mathematical properties play in equilibrium explanations requires further examination, as different authors defend different interpretations, some of them closer to the new-mechanistic approach than to the structural model advocated by Huneman. In this paper, we cover this gap by investigating the explanatory role that mathematics play in Blaser and Kirschner’s nested equilibrium model of the stability of persistent long-term human-microbe associations. We argue that their model is explanatory because: i) it provides a mathematical structure in the form of a set of differential equations that together satisfy an ESS; ii) that the nested nature of the ESSs makes the explanation of host-microbe persistent associations robust to any perturbation; iii) that this is so because the properties of the ESS directly mirror the properties of the biological system in a non-causal way. The combination of these three theses make equilibrium explanations look more similar to structural explanations than to causal-mechanistic explanation. (shrink)