Surface water sources in the oil producing Niger Delta region of Nigeria are highly susceptible to pollution by petroleum hydrocarbons and so it is important to understand the microbial diversity of such ecosystems. Water and sediment samples were collected between April-August, 2013 from Bodo creeks and taken to Environmental Microbiology laboratory of University of Portharcourt for analysis. A total of thirty aerobic heterotrophic bacterial strains isolated ranged from 3.0 - 7.0 × 104 cfu for surface water and 1.6 (...) - 5.6 × 104 cfu for sediment samples of Bodo creek using serial dilution and spread plate technique. Pure cultures of bacteria were obtained on the basis of their morphological characteristics and subjected to biochemical tests and further classified on the basis of 16S rRNA gene sequence analysis. The DNA was isolated from size fractionated samples and the diversity of bacteria in each fraction was studied using PCR amplification of partial 16S rRNA. The sequences were submitted to NCBIGen bank for identification and assigning of accession numbers. The isolated aerobic heterotrophic bacteria belong to the families of Enterobacteriaceae, Bacilliceae, Alcaligenaceae, Pseudomonadaceae, Flavobactericeae and Planococcaceae. (shrink)

Background: Food-borne outbreaks have been associated with sourcing unsafe food. Therefore, the first preventative strategy should be to source safe food. Even if the sourced food is safe, measures need to be put in place to ensure that it remains safe during the transfer, storage, preparation and serving activities that follow. An understanding of the ship food supply and transfer chain will help to illustrate the points at which the food can become contaminated en route to the point of consumption. (...) Objectives: The study was conducted in selected sea port in the core Niger Delta to assessed the microbiological quality of food served at different ship galley to crew and passengers and compared it to standard. Methods: Samples of food were taken from three (Port Harcourt Area one (PHSP), Warri (WSP) and Koko (KSP)) seaports within the South-South zone for laboratory analysis to uncover food spoilage microorganisms capable of causing disease outbreak among ship which could result to Transborder diseases. Eleven samples of different ready to eat food were collected from the locations, which included cooked rice; fried fish, irish potato porridge, vegetable soup, griki, pepper soup, fried irish potato, salad and bread were collected randomly. The samples were prepared and analyzed using standard procedures. Mean viable counts of aerobic and anaerobic bacteria were determined, ranging from (13×103cfu/g to 78×104 cfu/g) for ready to eat food. Results: Based on the finding KSP I, KSP J and KSP K food samples had the highest bacterial contamination on food while WSP F, WSP G and WSP H food samples had the least with the following isolates Salmonella spp, Nocardia spp, Shigella spp, Listeria spp, Bacillus cereus, Leuconostoc spp, Acinetobacter spp, Acetobacter spp, campylobacter spp, Clostridium spp and Vibrio spp which revealed that the isolates were susceptible to any of these antibiotics Septrin, Chloramphenicol, Gentamycin, Tarvid, Streptomycin, Reflacin, Augumetin, Ceporex, Nalidixic acid, Ampicillin, Ciproflox, Penicillin and Erythromycin. Conclusion: Thus, ships operators and regulatory body are expected to take all practicable measures to ensure that they do not receive unsafe or unsuitable food and maintain adequate food temperature at all time. (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)

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)

Microalgae in the wild often form consortia with other species promoting their own health and resource foraging opportunities. The recent application of microalgae cultivation and deployment in commercial photobioreactors (PBR) so far has focussed on single species of algae, resulting in multi-species consortia being largely unexplored. Reviewing the current status of PBR ecological habitat, this article argues in favor of further investigation into algal communication with conspecifics and interspecifics, including other strains of microalgae and bacteria. These mutualistic species form (...) the ‘phycosphere’: the micro-environment surrounding microalgal cells, potentiating the production of certain metabolites through biochemical interaction with cohabitating microorganisms. A better understanding of the phycosphere could lead to novel PBR configurations, capable of incorporating algal-microbial consortia, potentially proving more effective than single-species algal systems. (shrink)

From Bacteria To Bach and Back is an ambitious book that attempts to integrate a theory about the evolution of the human mind with another theory about the evolution of human culture. It is advertised as a defense of memes, but conceptualizes memes more liberally than has been done before. It is also advertised as a defense of the proposal that natural selection operates on culture, but conceptualizes natural selection as a process in which nearly all interesting parameters are (...) free to vary. This liberal conception of key concepts creates space for philosophical innovation, but occasionally makes the empirical content of the theory difficult to pin down. Nevertheless, the book is full of scientific insight, wit, and humor. It will undoubtedly become a cause of both controversy and inspiration for those interested in naturalistic theories of human culture. (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.

A widely cited roadblock to bridging ecological psychology and enactivism is that the former identifies with realism and the latter identifies with constructivism, which critics charge is subjectivist. A pragmatic reading, however, suggests non-mental forms of constructivism that simultaneously fit core tenets of enactivism and ecological realism. After advancing a pragmatic version of enactive constructivism that does not obviate realism, I reinforce the position with an empirical illustration: Physarum polycephalum (a slime mold), a communal unicellular organism that leaves slime trails (...) that form chemical barriers that it avoids in foraging explorations. Here, environmental building and sensorimotor engagement are part of the same process with P. polycephalum coordinating around self-created, affordance-bearing geographies, which nonetheless exist independently in ways described by ecological realists. For ecological psychologists, affordances are values, meaning values are external to the perceiver. I argue that agent-enacted values have the same status and thus do not obviate ecological realism or generate subjectivism. The constructivist-realist debate organizes around the emphasis that enactivists and ecological theorists respectively place on the inner constitution of organisms vs. the structure of environments. Building on alimentary themes introduced in the P. polycephalum example and also in Gibson’s work, I go on to consider how environment, brain, visceral systems, and even bacteria within them enter perceptual loops. This highlights almost unfathomable degrees of mutually modulating internal and external synchronization. It also shows instances in which internal conditions alter worldly configurations and invert values, in Gibson’s sense of the term, albeit without implying subjectivism. My aim is to cut across the somatic focus of enactive constructivism and the external environment-oriented emphasis of ecological realism and show that enactivism can enrich ecological accounts of value. (shrink)

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)

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)

Is shadowboxing an effective form of functional exercise? What physiological and morphological changes result from an exercise program based exclusively on shadowboxing for 3 weeks? To date, no empirical research has focused specifically on addressing these questions. Since mixed martial arts (MMA) is the fastest growing sport in the world, and since boxing and kickboxing fitness classes are among the most popular in gyms and fitness clubs worldwide, the lack of research on shadowboxing and martial arts-based fitness programs in the (...) extant literature is a shortcoming that the present article aims to address. This case study involved a previously sedentary individual engaging in an exercise program based exclusively on shadowboxing for 3 weeks. Body composition and heart rate data were collected before, throughout, and upon completion of the 3-week exercise program to determine the effectiveness of shadowboxing for functional fitness purposes. An original shadowboxing program prepared by an Everlast Master Instructor and NASM Certified Personal Trainer (NASM-CPT) and Performance Enhancement Specialist (NASM-PES) was used for this 3-week period. The original shadowboxing program with goals, techniques, and combinations to work on throughout the 3-week program is included in this article. This case study demonstrates that a 3-week exercise program based exclusively on shadowboxing can increase aerobic capacity, muscle mass, bone mass, basal metabolic rate, and daily calorie intake, and decrease resting heart rate, fat mass, body fat percentage, and visceral fat rating in a previously sedentary individual. The results of this research demonstrate that shadowboxing can be a safe and effective form of exercise leading to morphological and physiological improvements including fat loss and increased aerobic capacity. The results of this research also demonstrate that the Tanita BC-1500 is a reliable tool for individuals to evaluate their own fitness progress over time. (shrink)

In this essay, we aim to ground an alliance between Cynthia Willett’s theory of an ethics of eros and Hasana Sharp’s argument for a politics of renaturalization. Both approaches seek a vocabulary and practices for ethical life, which is not circumscribed by the requirement of rationality and is deeply attentive to relationships. The relations to which an ethics of eros and renaturalization must attend include social relations – the tender ministrations of mothers, lovers, and friends that sustain and nourish (and (...) sometimes threaten) each of us. Our lives, bodies, and minds, however, are also deeply involved with the nonhuman environment. Our existence depends on air, water, bacteria, shelter, and infinite other nonhuman beings. Our desires and needs include a habitable environment and even "biophilia." The increasing fragility of our ecosystems suggests that there is more need than ever for an ethics that goes not just beyond man – although that is certainly an ongoing project – but beyond the human. This essay is an attempt to ally our approaches in the feminist effort to produce a broad basis for ethics, allowing for a robust consideration of nonhuman nature. (shrink)

Antibiotic-resistant bacteria pose a serious threat to our health. Our ability to destroy deadly bacteria by using antibiotics have not only improved our lives by curing infections, it also allows us to undertake otherwise dangerous treatments from chemotherapies to invasive surgeries. The emergence of antibiotic resistance, I argue, is a consequence of various iterations of prisoner’s dilemmas. To wit, each participant (from patients to nations) has rational self-interest to pursue a course of action that is suboptimal for all (...) of us. The standard solutions to prisoner’s dilemma look to realign cost-benefit such that individuals’ interests match those of the collective. However, the lack of a global organization to enforce an effective carrot-and-stick system makes it unlikely that we can solve the antibiotic resistance problem this way. I argue that our best chance might be an attempt to teach altruism and convince individuals to act not out of their self-interests. (shrink)

Has science already answered the fundamental questions about the concepts of Life, Cosmos and Evolution? Has science not relegated these fundamental questions by following up on more immediate, “useful” and practical endeavors that ultimately ensure that the wheel of capitalism keeps spinning in its frantic search for material and economic progress? There is something terribly wrong with the current theory of evolution, understood as the Darwinian theory with its successive versions and extensions. The concept of natural selection, the cornerstone of (...) Darwinism, is logically inconsistent. This has been demonstrated in some of my latest academic publications. The entire conceptual framework of Darwinism is inadequate. Organisms do not compete with each other for the survival of the fittest. The fundamental relationship in Nature is not competition or confrontation, but interconnectivity, complementarity, and relational meaningfulness. A new theory of evolution is necessary to explain how it is possible that organisms as simple as bacteria, protozoa and diatoms could have generated organisms as complex as primates, and among them, the human being, a being capable of feeling and thinking, of suffering and enjoying, a being capable of having ideals and purposes. A theory that explains how it is possible that this being so complex, rich, and to some extent still unknown, has emerged from a single cell, an egg-cell, lacking all the capacities, riches and depths of human existence. Such a theory already exists. (shrink)

This book assembles recent research on memory and learning in plants. Organisms that share a capability to store information about experiences in the past have an actively generated background resource on which they can compare and evaluate coming experiences in order to react faster or even better. This is an essential tool for all adaptation purposes. Such memory/learning skills can be found from bacteria up to fungi, animals and plants, although until recently it had been mentioned only as capabilities (...) of higher animals. With the rise of epigenetics the context dependent marking of experiences on the genetic level is an essential perspective to understand memory and learning in organisms. -/- Plants are highly sensitive organisms that actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between ‘self’ and ‘non-self’. They process and evaluate information and then modify their behavior accordingly. -/- The book will guide scientists in further investigations on these skills of plant behavior and on how plants mediate signaling processes between themselves and the environment in memory and learning processes. (shrink)

This study emphasizes the importance of enhancing food safety and hygiene practices among sidewalk vendors to safeguard public health in Balayan Public Market. Employing a mixed-methods approach, with both quantitative and qualitative components, a diverse sample of 55 consumers, 5 sidewalk vendors, and 5 market administrators was selected using a combination of purposive and random sampling techniques under non-probability sampling. Microbial investigations were conducted during both the initial sampling and testing phase (A) and subsequent sampling and testing phase (B) on (...) popular street food items at Lipa Quality Control Inc., including chicken nuggets, chicken nugget sauce (sweet and vinegar), Isaw, Isaw sauce, Proben, Proben sauce, Calamares, Calamares Vinegar Sauce, Kwek- Kwek, and Kwek-Kwek sauce. The findings reveal that “Isaw and Chicken Nuggets Sauce (Sweet)” had a result of “Too Numerous To Count (TNTC),” indicating an extraordinarily high bacteria count. This underscores the imperative need to raise awareness and provide targeted guidance to sidewalk vendors regarding essential food handling, storage, and sanitation practices. Therefore, a sanitary action plan is developed to promote community engagement, educational initiatives, and regulatory support, enhancing food safety practices among sidewalk vendors and ensuring a safer and healthier food environment. (shrink)

According to F. Adams [this journal, vol. 68, 2018] cognition cannot be realized in plants or bacteria. In his view, plants and bacteria respond to the here-and-now in a hardwired, inflexible manner, and are therefore incapable of cognitive activity. This article takes issue with the pursuit of plant cognition from the perspective of an empirically informed philosophy of plant neurobiology. As we argue, empirical evidence shows, contra Adams, that plant behavior is in many ways analogous to animal behavior. (...) This renders plants suitable to be described as cognitive agents in a non-metaphorical way. Sections two to four review the arguments offered by Adams in light of scientific evidence on plant adaptive behavior, decision-making, anticipation, as well as learning and memory. Section five introduces the ‘phyto-nervous’ system of plants. To conclude, section six resituates the quest for plant cognition into a broader approach in cognitive science, as represented by enactive and ecological schools of thought. Overall, we aim to motivate the idea that plants may be considered genuine cognitive agents. Our hope is to help propel public awareness and discussion of plant intelligence once appropriately stripped of anthropocentric preconceptions of the sort that Adams' position appears to exemplify. (shrink)

The notion of a physiological individuals has been developed and applied in the philosophy of biology to understand symbiosis, an understanding of which is key to theorising about the major transition in evolution from multi-organismality to multi-cellularity. The paper begins by asking what such symbiotic individuals can help to reveal about a possible transition in the evolution of cognition. Such a transition marks the movement from cooperating individual biological cognizers to a functionally integrated cognizing unit. Somewhere along the way, did (...) such cognizing units simultaneously have cognizers as parts? Expanding upon the multiscale integration view of the Free Energy Principle, this paper develops an account of reciprocal integration, demonstrating how some coupled biological cognizing systems, when certain constraints are met, can result in a cognizing unit that is in ways greater than the sum of its cognizing parts. Symbiosis between V. Fischeri bacteria and the bobtail squid is used to provide an illustration this account. A novel manner of conceptualizing biological cognizers as gradient is then suggested. Lastly it is argued that the reason why the notion of ontologically nested cognizers may be unintuitive stems from the fact that our folk-psychology notion of what a cognizer is has been deeply influenced by our folk-biological manner of understanding biological individuals as units of reproduction. (shrink)

Abstract cantaloupe and honeydew melons are part of the muskmelon family, which originated in the Middle East. When picking either cantaloupe or honeydew melons to eat, you should choose a firm fruit that is heavy for its size, with no obvious signs of bruising. They can be stored at room temperature until you cut them, after which they should be kept in the refrigerator in an airtight container for up to five days. You should always wash and scrub the rind (...) of your melon before you cut it to remove any dirt or bacteria on the outside. In this paper, cantaloupe classification approach is presented with a dataset that contains approximately 1,312 of Cantaloupes and honeydews. Convolutional Neural Network (CNN) algorithms, a deep learning technique extensively applied to image recognition was used, for this task. The results found that CNN-driven classification applications when used in farming automation have the latent to enhance crop harvest and improve output and productivity when designed properly. The trained model achieved an accuracy of 99.74% on a held-out test set, demonstrating the feasibility of this approach. (shrink)

Biologists explain organisms’ behavior not only as having been programmed by genes and shaped by natural selection, but also as the result of an organism’s agency: the capacity to react to environmental changes in goal-driven ways. The use of such ‘agential explanations’ reopens old questions about how justified it is to ascribe agency to entities like bacteria or plants that obviously lack rationality and even a nervous system. Is organismic agency genuinely ‘real’ or is it just a useful fiction? (...) In this paper we focus on two questions: whether agential explanations are to be interpreted ontically, and whether they can be reduced to non-agential explanations (thereby dispensing with agency). The Kantian approach we identify interprets agential explanations non-ontically, yet holds agency to be indispensable. Attributing agency to organisms is not to be taken literally in the way we attribute physical properties such as mass or acceleration, but nor is it a mere heuristic or predictive tool. Rather, it is an inevitable consequence of our own rational capacity: as long as we are rational agents ourselves, we cannot avoid seeing agency in organisms. (shrink)

The concept of “life” certainly is of some use to distinguish birds and beavers from water and stones. This pragmatic usefulness has led to its construal as a categorical predicate that can sift out living entities from non-living ones depending on their possessing specific properties—reproduction, metabolism, evolvability etc. In this paper, we argue against this binary construal of life. Using text-mining methods across over 30,000 scientific articles, we defend instead a degrees-of-life view and show how these methods can contribute to (...) experimental philosophy of science and concept explication. We apply topic-modeling algorithms to identify which specific properties are attributed to a target set of entities (bacteria, archaea, viruses, prions, plasmids, phages and the molecule of adenine). Eight major clusters of properties were identified together with their relative relevance for each target entity (two that relate to metabolism and catalysis, one to genetics, one to evolvability, one to structure, and—rather unexpectedly—three that concern interactions with the environment broadly construed). While aligning with intuitions—for instance about viruses being less alive than bacteria—these quantitative results also reveal differential degrees of performance that have so far remained elusive or overlooked. Taken together, these analyses provide a conceptual “lifeness space” that makes it possible to move away from a categorical construal of life by empirically assessing the relative lifeness of more-or-less alive entities. (shrink)

One question of the bounds of cognition is that of which things have it. A scientifically relevant debate on this question must explain the persistent and selective use of psychological predicates to report findings throughout biology: for example, that neurons prefer, fruit flies and plants decide, and bacteria communicate linguistically. This paper argues that these claims should enjoy default literal interpretation. An epistemic consequence is that these findings can contribute directly to understanding the nature of psychological capacities.

The key assumption behind evolutionary epistemology is that animals are active learners or ‘knowers’. In the present study, I updated the concept of natural learning, developed by Henry Plotkin and John Odling-Smee, by expanding it from the animal-only territory to the biosphere-as-a-whole territory. In the new interpretation of natural learning the concept of biological information, guided by Peter Corning’s concept of “control information”, becomes the ‘glue’ holding the organism–environment interactions together. The control information guides biological systems, from bacteria to (...) ecosystems, in the process of natural learning executed by the universal algorithm. This algorithm, summarized by the acronym IGPT (information-gain-process-translate) incorporates natural cognitive methods including sensing/perception, memory, communication, and decision-making. Finally, the biosphere becomes the distributed network of communicative interactions between biological systems termed the interactome. The concept of interactome is based on Gregory Bateson’s natural epistemology known as the “ecology of mind”. Mimicking Bateson’s approach, the interactome may also be designated “physiology of mind”—the principle behind regulating the biosphere homeostasis. (shrink)

The goal of this paper is to establish a hierarchical level of deception which does not apply only to humans and non-human animals, but also to the rest of the living world, including plants. We will follow the hierarchical categorization of deception, set forth by Mitchell (1986), in which the first level of deception starts with mimicry, while the last level of deception includes learning and intentionality, usually attributed to primates. We will show how such a hierarchy can be attributed (...) to bacteria, plants, and fungi, see that self-deception is not inherent only to humans, and then connect the evolutionary roots of deception with the philosophical notion of intentionality. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “ biodiversity ”: the issues of defining the units of biodiversity (...) and of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity. (shrink)

Any attempt to develop biosemiotics either towards a new biological ground theory or towards a metaphysics of living nature necessitates some kind of naturalization of its semiotic concepts. Instead of standard physicalistic naturalism, a certain kind of semiotic naturalism is pursued here. The naturalized concepts are defined as referring only to the objects of our external experience. When the semiotic concepts are applied to natural phenomena in biosemiotics, there is a risk of falling into anthropomorphic errors if the semiotic concepts (...) remain mentalistic. It is suggested that there really is an anthropomorphic error or “hidden prototype fallacy” arising from Peirce’s prototype for semiosis: the research process of an experimental scientist. The fallacy lies in the concept of the object of representation — it is questionable whether there are any objects of representation for bacteria and whether the DNA-signs have any objects. The conclusion is that Peircean semiotic concepts are naturalizable but only if they are based on some more primitive concept of representation. The causal origins of representations are not relevant, only their anticipative consequences (i.e. meaning). (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants (...) during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (shrink)

Niche construction is a concept that captures a wide array of biological phenomena, from the environmental effects of metabolism to the creation of complex structures such as termite mounds and beaver dams. A central point in niche construction theory is that organisms do not just passively undergo developmental, ecological, or evolutionary processes, but are also active participants in them Evolution: From molecules to men, Cambridge University Press, Cambridge, 1983; Laland KN, Odling-Smee J, Feldman MW, In: KN Laland and T Uller (...) Evolutionary causation: Biological and philosophical reflections, MIT Press, Cambridge, MA, 2019). In this paper, we distinguish between two fundamentally different ways in which organisms are active participants: as agents and as contributors. Roughly, organisms act as agents when niche constructing effects are a result of a goal-directed behavior over which the organisms have some degree of control. Organisms act as contributors when the niche constructing effects do not arise from a goal to perform the constructive activity. As illustrative examples we discuss plants altering leaf-morphology to optimize light exposure as reported by Sultan and bacteria creating novel niches through excreting energy-rich metabolites. The difference between agential and contributional niche construction is important for understanding the different ways organisms can actively participate in development, ecology, and evolution. Additionally, this distinction can increase our understanding of how the capacity of agency is distributed across the tree of life and how agency influences developmental and evolutionary processes. (shrink)

Recent work in the philosophy of biology argues that we must rethink the biological individual beyond the boundary of the species, given that a key part of our essential functioning is carried out by the bacteria in our intestines in a way that challenges any strictly genetic account of what is involved for the biological human. The gut is a kind of ambiguous other within our understanding of ourselves, particularly when we also consider the status of gastro-intestinal disorders. Hegel (...) offers us theoretical tools to describe and understand our relationship to our gut. His description of our selves as continually mediated through otherness is strikingly compatible with the kind of structure contemporary biology presents us with. His accounts of digestion and habit, contextualized by his logic, help point toward an understanding of selfhood as porous and yet still capable of being sufficiently unified for us to make sense of ourselves, one which allows us to acknowledge otherness within us while still having enough unity for agency. (shrink)

What is W. V. O. Quine’s relationship to classical pragmatism? Although he resists the comparison to William James in particular, commentators have seen an affinity between his “web of belief” model of theory confirmation and James’s claim that our beliefs form a “stock” that faces new experience as a corporate body. I argue that the similarity is only superficial. James thinks our web of beliefs should be responsive not just to perceptual but also to emotional experiences in some cases; Quine (...) denies this. I motivate James’s controversial view by appealing to an episode in the history of medicine when a researcher self-experimented by swallowing a vial of bacteria that at the time had not been studied in much detail. The researcher’s commitment to his own as-yet untested hypothesis was based in part on emotional considerations. Finally, I argue that Quine’s insistence that emotions can never be relevant to adjusting our web of belief reflects a tacit holdover of one of logical positivism’s crucially anti-pragmatist commitments—that philosophy of science should focus exclusively on the context of justification, not the context of discovery. James’s emphasis on discovery as a (perhaps the) crucial locus for epistemological inquiry is characteristic of pragmatism in general. Since Quinean epistemology is always an epistemology of justification, he is not happily viewed as a member of the pragmatist tradition. (shrink)

In experimental settings, scientists often “make” new things, in which case the aim is to intervene in order to produce experimental objects and processes—characterized as ‘effects’. In this discussion, I illuminate an important performative function in measurement and experimentation in general: intervention-based experimental production (IEP). I argue that even though the goal of IEP is the production of new effects, it can be informative for causal details in scientific representations. Specifically, IEP can be informative about causal relations in: regularities under (...) study; ‘intervention systems’, which are measurement/experimental systems; and new technological systems. (shrink)

Context: At present, we lack a common understanding of both the process of cognition in living organisms and the construction of knowledge in embodied, embedded cognizing agents in general, including future artifactual cognitive agents under development, such as cognitive robots and softbots. Purpose: This paper aims to show how the info-computational approach (IC) can reinforce constructivist ideas about the nature of cognition and knowledge and, conversely, how constructivist insights (such as that the process of cognition is the process of life) (...) can inspire new models of computing. Method: The info-computational constructive framework is presented for the modeling of cognitive processes in cognizing agents. Parallels are drawn with other constructivist approaches to cognition and knowledge generation. We describe how cognition as a process of life itself functions based on info-computation and how the process of knowledge generation proceeds through interactions with the environment and among agents. Results: Cognition and knowledge generation in a cognizing agent is understood as interaction with the world (potential information), which by processes of natural computation becomes actual information. That actual information after integration becomes knowledge for the agent. Heinz von Foerster is identified as a precursor of natural computing, in particular bio computing. Implications: IC provides a framework for unified study of cognition in living organisms (from the simplest ones, such as bacteria, to the most complex ones) as well as in artifactual cognitive systems. Constructivist content: It supports the constructivist view that knowledge is actively constructed by cognizing agents and shared in a process of social cognition. IC argues that this process can be modeled as info-computation. (shrink)

Tyler Burge (2010) provided a scathing critique of all programs for naturalizing concepts of representation, especially teleological naturalizing programs. He tended to demonstrate that “representational content” is a concept that cannot be reduced to more fundamental biological or physical ideas. According to him, since the 1970s, the concept of representational content has been firmly established in cognitive psychology as a mature science and utilized inadequate explanations. Since Dretske’s program is Burge’s primary objective, this paper concentrates on Dretske’s perspective. Following Burge’s (...) criticisms, I concur that Dretske’s naturalizing program trivializes the complex concept of representational content in cognitive science by applying it to bacteria, protozoa, etc. There is a superior explanation, namely Burge’s alternative idea of “registering information.” I do not believe, however, that this spells the end of naturalization programs. There is no reason to deny that at least some biological functions entail representational capacities with perceptual constancy, if not all. Cases of genuine perception, representing the accurate distal causes of proximal stimuli under various conditions, contribute to fitness. It is not by accident that representational content plays a role in cases of genuine perception. Consequently, I will argue that accuracy and biological fitness cannot be separated. (shrink)

This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...) heat shock—the heat shock response system—in Escherichia coli bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. (shrink)

Although quantum mechanics can accurately predict the probability distribution of outcomes in an ensemble of identical systems, it cannot predict the result of an individual system. All the local and global hidden variable theories attempting to explain individual behavior have been proved invalid by experiments (violation of Bell’s inequality) and theory. As an alternative, Schrodinger and others have hypothesized existence of free will in every particle which causes randomness in individual results. However, these free will theories have failed to quantitatively (...) explain the quantum mechanical results. In this paper, we take the clue from quantum biology to get the explanation of quantum mechanical distribution. Recently it was reported that mutations (which are quantum processes) in DNA of E. coli bacteria instead of being random were biased in a direction such that the chance of survival of the bacteria is increased. Extrapolating it, we assume that all the particles including inanimate fundamental particles have a will and that is biased to satisfy the collective goals of the ensemble. Using this postulate, we mathematically derive the correct spin probability distribution without using quantum mechanical formalism (operators and Born’s rule) and exactly reproduce the quantum mechanical spin correlation in entangled pairs. Using our concept, we also mathematically derive the form of quantum mechanical wave function of free particle which is conventionally a postulate of quantum mechanics. Thus, we prove that the origin of quantum mechanical results lies in the will (or consciousness) of the objects biased by the collective goal of ensemble or universe. This biasing by the group on individuals can be called as “coherence” which directly represents the extent of life present in the ensemble. So, we can say that life originates out of establishment of coherence in a group of inanimate particles. (shrink)

The hygiene hypothesis offers an explanation for the correlation, well-established in the industrialized nations of North and West, between increased hygiene and sanitation, and increased rates of asthma and allergies. Recent studies have added to the scope of the hypothesis, showing a link between decreased exposure to certain bacteria and parasitic worms, and increased rates of depression and intestinal auto- immune disorders, respectively. What remains less often discussed in the research on these links is that women have higher rates (...) than men of asthma and allergies, as well as many auto-immune disorders, and also depression. The current paper introduces a feminist understanding of gender socialization to the epidemiological and immunological picture. That standards of cleanliness are generally higher for girls than boys, especially under the age of five when children are more likely to be under close adult supervision, is a robust phenomenon in industrialized nations, and some research points to a cross- cultural pattern. I conclude that, insofar as the hygiene hypothesis successfully identifies standards of hygiene and sanitation as mediators of immune health, then attention to the relevant patterns of gender socialization is important. The review also makes clear that adding a feminist analysis of gender socialization to the hygiene hypothesis helps explain variation in morbidity rates not addressed by other sources and responds to a number of outstanding puzzles in current research. Alternative explanations for the sex differences in the relevant morbidity rates are also discussed (e.g., the effects of estrogens). Finally, new sources of evidence for the hygiene hypothesis are suggested in the form of cross-cultural and other natural experiments. (shrink)

Organisms actively compete for environmental resources. They assess their surroundings, estimate how much energy they need for particular goals, and then realize the optimum variant. They take measures to control certain environmental resources. They perceive themselves and can distinguish between “self” and “non-self.” Current empirical data on all domains of life indicate that unicellular organisms such as bacteria, archaea, giant viruses, and protozoa as well as multicellular organisms such as animals, fungi, and plants coordinate and organize their essential life (...) functions through signaling processes. Signaling allows for real life coordination and organization and is a communicative action in which speciesspecific behavioral patterns and sign repertoires are used. Cells, tissues, organs, and organisms that communicate share several key levels that are essential to all life forms and which serve as a uniform tool for investigating biocommunication. (shrink)

Stove's article, 'So you think you are a Darwinian?'[ 1] was essentially an advertisement for his book, Darwinian Fairytales.[ 2] The central argument of the book is that Darwin's theory, in both Darwin's and recent sociobiological versions, asserts many things about the human and other species that are known to be false, but protects itself from refutation by its logical complexity. A great number of ad hoc devices, he claims, are used to protect the theory. If co operation is observed (...) where the theory predicts competition, then competition is referred to the time of the cavemen, or is reinterpreted as competition between some hidden entities like genes or abstract entities like populations. In a characteristic sally, Stove writes of the sociobiologists' oscillation on the meaning of kin altruism: Any discussion of altruism with an inclusive fitness theorist is, in fact, exactly like dealing with a pair of balloons connected by a tube, one balloon being the belief that kin altruism is an illusion, the other being the belief that kin altruism is caused by shared genes. If a critic puts pressure on the illusion balloon - perhaps by ridiculing the selfish theory of human nature - air is forced into the causal balloon. There is then an increased production of earnest causal explanations of why we love our children, why hymenopteran workers look after their sisters, etc., etc. Then, if the critic puts pressure on the causal balloon - perhaps about the weakness of sibling altruism compared with parental, or the absence of sibling altruism in bacteria - then the illusion balloon is forced to expand. There will now be an increased production of cynical scurrilities about parents manipulating their babies for their own advantage, and vice versa, and in general, about the Hobbesian bad times that are had by all. In this way critical pressure, applied to the theory of inclusive fitness at one point, can always be easily absorbed at another point, and the theory as a whole is never endangered.[ 3] Now, it is uncontroversial to assert that Darwinism is a logically complex theory, and that its relation to empirical evidence is distant and multi faceted. One does not directly observe chance genetic variations leading to the development of new species, or even continuous variations in the fossil record, but must rely on subtle arguments to the best explanation, scaling up from varieties to species, and so on.. (shrink)

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use (...) risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential. (shrink)

Following Mary Douglas' conviction that "dirt is never an isolated event", the present study aims at a systematic analysis of bodily projections of good and poor health (bacteria, diseases, im/purity etc.) into philological taxonomies of Republican China. Embedded in a global Renaissance discourse, modern Chinese representations of un/healthy language and un/healthy literature provided a system according to which the whole body of the national cultural heritage could be reexamined quickly and effectively.

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)

Life can be defined as combining two entities that rest on completely different physico-chemical properties and on a particular way of handling information. The cell, first, is a « machine », that combines elements which are quite similar (although in a fairly fuzzy way) to those involved in a man-made factory. The machine combines two processes. First, it requires explicit compartmentalisation, including scaffolding structures similar to that of the châssis of engineered machines. In addition, cells define clearly an inside, the (...) cytoplasm, and an outside. The cell envelope is more or less complicated in bacteria, and it is much more complicated in organisms made of cells with a nucleus (eukaryotes). Second, the machine also requires dynamic chemical processes, collectively named metabolism, that can be split into intermediary metabolism, managing chemical transformations and transport of small building blocks and management of energy (often with a rotating nanomachine, ATP synthase), and the macromolecule synthesis, salvage and turnover machinery which uses a variety of nanomachines, the ribosome being the most prominent one. The second entity which needs to be associated to life is the genetic program, in the form of the genome, composed of one or several chromosomes made of DNA. This is the entity which associates most clearly to information. -/- Natural selection uses information in a particular way: it is a process that uses energy to prevent degradation of any functional entity. This process keeps building up novel information within organisms. (shrink)

Commensal and pathogenic organisms employ camouflage and mimicry to mediate mutualistic interactions and predator escape. However, the immune mechanisms accounting for the establishment and maintenance of symbiotic bacterial populations are poorly understood. A promising hypothesis suggests that molecular mimicry, a condition in which different organisms share common antigens, is a mechanism of establishing tolerance between commensals and their hosts. On this view, certain bacteria may mimic the structural features of some of their host’s T-cell receptors (TCRs), namely those that (...) survive thymic selection due to their lack of complementarity to self-antigens. With such “holoimmunity” the mimicking micro-organisms avoid immune recognition as the copied TCRs become mirror images of an extended super-organismal self, consisting of symbiotic and host antigens. Accordingly, analysis of genomic and metagenomic data suggests a tripartite mimicry between TCRs, self-antigens, and commensal antigens that would serve as the basis for immune tolerance between these populations. And conversely, in an autoimmune scenario, both symbiotic microbes and the mimicked host tissue would be targeted for immune destruction. (shrink)

_ Source: _Page Count 20 This paper proposes a new deflationary reading of the metaphor of the “primitive sense of selfhood” in perception and proprioception, usually understood as an “experiential self-reference” that takes place before reflection and any use of concepts. As such, the paper is also a new defense of the old orthodox view that self-consciousness is a highly complex mental phenomenon that requires equally complex concepts. The author’s defense is a clear case of inference to the best explanation. (...) He argues that postulating an “experiential _self-reference_” to explain the “primitive sense of selfhood” is as explanatory overkill as attributing perceptions to bacteria to explain the remarkably sophisticated ways in which they adapt, attune, and respond to their environments. This is what the author calls trivialization of self-consciousness. The metaphor of the “primitive sense of selfhood” in perception and proprioception is far less extravagantly explained by what, based on Recanati, the author calls self-involvement without self-consciousness: there is no “experiential self-reference” because there is no _self-reference_ in the first place. Rather than being articulated as a constituent of the contents of her/his perceptions or proprioception, the self/subject is the key element of the circumstance of evaluation of these selfless contents. (shrink)

This paper aims to justify the concept of natural intelligence in the biosemiotic context. I will argue that the process of life is (i) a cognitive/semiotic process and (ii) that organisms, from bacteria to animals, are cognitive or semiotic agents. To justify these arguments, the neural-type intelligence represented by the form of reasoning known as anthropic reasoning will be compared and contrasted with types of intelligence explicated by four disciplines of biology – relational biology, evolutionary epistemology, biosemiotics and the (...) systems view of life – not biased towards neural intelligence. The comparison will be achieved by asking questions related to the process of observation and the notion of true observers. To answer the questions I will rely on a range of established concepts including SETI (search for extraterrestrial intelligence), Fermi’s paradox, bacterial cognition, versions of the panspermia theory, as well as some newly introduced concepts including biocivilisations, cognitive/semiotic universes, and the cognitive/semiotic multiverse. The key point emerging from the answers is that the process of cognition/semiosis – the essence of natural intelligence – is a biological universal. (shrink)

A retrospective of the debates on the origin of life: the virus or the cell? The virus needs a cell for replication, instead the cell is higher on the evolutionary scale of life. Viruses appear to have played a role in events such as the origin of cell life and the evolution of mammals. Even the simplest bacteria is far too complex to have appeared spontaneously at the beginning of evolution. Subsequently, evolution has been able to produce increasingly complex (...) systems. The first true cell may have already been a product of evolution, resulting from a primordial community. DOI: 10.13140/RG.2.2.32719.92328. (shrink)