There is currently a great debate about whether the holobiont, i.e. a multicellular host and its residential microorganisms, constitutes a biological individual. We propose that resident microorganisms have a general and important role in the individuality of the host organism, not the holobiont. Drawing upon the Equilibrium Model of Immunity, we argue that microorganisms are scaffolds of immune capacities and processes that determine the constituency and persistence of the host organism. A scaffolding perspective accommodates the contingency and (...) heterogeneity of resident microorganisms while accounting for their necessity and unifying contributions to host individuality. In our symbiotic view of life, holobionts may not be organisms or units of selection, but macroorganisms cannot persist nor function as individuals without their scaffolding microorganisms. (shrink)

Microorganisms belong to the main regulators of insect populations under natural conditions. They perform this function in several ways. In the first place, bacterial metabolites exist which are as potent as chemical insecticides. In the second, entomopathogenic fungi and viruses spread deadly infections among insect populations. The use of advanced techniques in molecular biology, genetic engineering and biotechnology is increasingly expanding the potential of microorganisms as agents of insect pest control.

In this paper, we formulate and investigate a two-microorganism and single nutrient chemostat model with Monod-Haldane response function and random perturbation. First, for the corresponding deterministic system, we introduce the conditions of the stability of the equilibrium points. Then, using Lyapunov function and Itô’s formula, we investigate the existence and uniqueness of the global positive solution of the stochastic chemostat model. Furthermore, we explore and obtain the criterions of the extinction and the permanence for the stochastic model. Finally, numerical simulations (...) are carried out to illustrate our main results. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular (...) biocommunication between soil microorganisms. Th is includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

Environmental ethics has almost exclusively been focused on multicellular organisms. However, because microorganisms form the base of the world’s food chains, allowing for the existence of all higher organisms, the complexities of the moral considerability of microorganisms deserve attention. Despite the impossible task of protecting individual microorganisms—the paradigmatic example of the limitations to a Schweitzerian “reverence for life”—microorganisms can be considered to have intrinsic value on the basis of conation, along with their enormous instrumental value. This (...) intrinsic value even manifests itself at the individual level, although in this case the ethic can only be regulative (an ethical principle). Biocentrism is the most appropriate ethical framework for microorganisms, and the most useful normative framework for implementing the preservation and conservation of microorganisms. This ethic has implications for how we deal with disease-causing microorganisms. (shrink)

Communication is defined as an interaction between at least two living agents which share a repertoire of signs. These are combined according to syntactic, semantic and context-dependent, pragmatic rules in order to coordinate behavior. This volume deals with the important roles of soil bacteria in parasitic and symbiotic interactions with viruses, plants, animals and fungi. Starting with a general overview of the key levels of communication between bacteria, further reviews examine the various aspects of intracellular as well as intercellular biocommunication (...) between soil microorganisms. This includes the various levels of biocommunication between phages and bacteria, between soil algae and bacteria, and between bacteria, fungi and plants in the rhizosphere, the role of plasmids and transposons, horizontal gene transfer, quorum sensing and quorum quenching, bacterial-host cohabitation, phage-mediated genetic exchange and soil viral ecology. (shrink)

In the past few decades, increased awareness of environmental pollution has led to the exploitation of microbial metabolic potential in the construction of several genetically engineered microorganisms (GEMs) for bioremediation purposes. At the same time, environmental concerns and regulatory constraints have limited the in situ application of GEMs, the ultimate objective behind their development. In order to address the anticipated risks due to the uncontrolled survival/dispersal of GEMs or recombinant plasmids into the environment, some attempts have been made to (...) construct systems that would contain the released organisms. This article discusses the designing of safer genetically engineered organisms for environmental release with specific emphasis on the use of bacterial plasmid addiction systems to limit their survival thus minimizing the anticipated risk. We also conceptualize a novel strategy to construct “Suicidal Genetically Engineered Microorganisms (SGEMs)” by exploring/combining the knowledge of different plasmid addiction systems (such as antisense RNA‐regulated plasmid addiction, proteic plasmid addiction etc.) and inducible degradative operons of bacteria. BioEssays 27:563–573, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

A classic example of the arbitrary relation between the way a word sounds and its meaning is that microorganism is a very long word that refers to a very small entity, whereas whale is a very short word that refers to something very big. This example, originally presented in Hockett's list of language's design features, has been often cited over the years, not only by those discussing the arbitrary nature of language, but also by researchers of sound symbolism. While the (...) two groups disagreed regarding the role of arbitrariness and sound symbolism in language, they both agreed there is a nonsound symbolic relation between word length and entity size in this case. This paper shows that the length of the words whale and microorganism in fact reflects a sound symbolic pattern. An analysis of >600 languages from >100 language families shows that languages use longer words to denote the concept small than they do to denote the concept big. The paper thus shows how explicit judgments might differ from implicit cognitive association and the problem of relying on these in sound symbolism research. (shrink)

Collections are a group of multimeric proteins mostly consisting of 9–18 polypeptides organised into either ‘bundle‐of‐tulips’ or ‘X‐like’ overall structures. Each polypeptide contains a short N‐terminal segment followed by a collagen‐like sequence and then by a C‐terminal lectin domain. A collectin molecule is assembled from identical or very similar polypeptides by disulphide bonds at the N‐terminal segment, formation of triple helices in the collagen‐like region and clusters of three lectin domains at the peripheral ends of triple helices. These proteins can (...) bind to sugar residues on microorganisms via the peripheral lectin domains and subsequently interact, via the collagen‐like triple‐helices, with receptor(s) on phagocytes and/or the complement system to bring about the killing and clearance of the targets without the involvement of antibodies. The collectins can also bind to phagocyte receptor(s) to enhance phagocytosis mediated by other phagocytic receptors. Lack, or low levels, of collectin expression can lead to higher susceptibility to infections, especially during childhood when specific immunity has not fully developed. Therefore, the collectins play important roles in the enhancement of innate immunity. (shrink)

Over the last three decades, studies in microbiology have exposed a world of diverse and dynamic interactions. Through metagenomic sequencing, complex bacterial communities became visible and proved important for many biological phenomena. As a result of discovering the connection between microorganisms and organisms’ survival, the notion of the holobiont has become prominent and has been suggested as a biological individual. The view of the holobiont as an individual, commonly known as the Hologenome Theory, focuses on the interactions and relations (...) between the host and its symbionts in the host’s development and evolution. Today, the holobiont is at the heart of the debate on the nature of the biological individual, a debate which is connected to the same question about the nature of the individual organism. (shrink)

Over the last three decades, studies in microbiology have exposed a world of diverse and dynamic interactions. Through metagenomic sequencing, complex bacterial communities became visible and proved important for many biological phenomena. As a result of discovering the connection between microorganisms and organisms’ survival, the notion of the holobiont has become prominent and has been suggested as a biological individual. The view of the holobiont as an individual, commonly known as the Hologenome Theory, focuses on the interactions and relations (...) between the host and its symbionts in the host’s development and evolution. Today, the holobiont is at the heart of the debate on the nature of the biological individual, a debate which is connected to the same question about the nature of the individual organism. (shrink)

Thirty years ago, a number of human inborn errors in carbohydrate metabolism were explored with specific enzymatic tests on blood samples (hemolysates). Hereditary galactosemia was the first example. When the inoperative step in galactose metabolism was specified, the basis for the diet therapy used on the galactosemic infants, namely galactose‐free diet, could be shown to be securely founded.As far as galactose metabolism is concerned, the cells of the infant are faced with two problems: (i) the conversion of dietary lactose (galactosyl (...) glucose) to glucose and its catabolites involved in energy metabolism, and (ii) the conversion of dietary glucose or lactose to galactosyl units of glycolipids and glycoprotein cell structures.Subsequent studies on microorganisms revealed several types of hereditary defect in galactose metabolism. One type which permits the bacteria to develop a normal carbohydrate pattern in their cell walls includes an enzyme defect, like that described in the cells of the galactosemic infant. Two other types, with the inability to synthesize UDPGlc or UDPGal from glucose, do not permit the bacteria to build the fabric of the normal bacterial cell wall. This is the subject for discussion. (shrink)

Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral‐associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin‐repeat protein A and internalin B, which indirectly cause histone modifications in humans, (...) as well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral‐associated bacteria indicate that there are potential host epigenome‐modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs. Also see the video abstract here: https://youtu.be/CW9GbChjKM4. (shrink)

Biochemistry and molecular biology have been focusing on the structural, catalytic, and regulatory proper- ties of individual macromolecules from the perspective of clarifying the mechanisms of metabolism and gene expression. Complete genomes of ‘primitive’ living organisms seem to be substantially larger than necessary for metabolism and gene expression alone. This is in line with the findings of silent phenotypes for supposedly important genes, apparent redundancy of functions, and variegated networks of signal transduction and transcription factors. Here we propose that evolutionary (...) optimization has been much more intensive than to lead to the bare minima necessary for autonomous life. Much more complex organisms prevail. Much of this complexity arises in the nonlinear interactions between cellular macromolecules and in subtle differences between paralogs (isoenzymes). The complexity can only be understood when analyzed quantitatively, for which quantitative experimentation is needed in living systems that are as simple and manipulatable as possible, yet complex in the above sense. We illustrate this for the glutamine synthetase cascade in Escherichia coli. By reviewing recent molecular findings, we show that this cascade is much more complex than necessary for simple regulation of ammonia assimilation. Simulations suggest that the function of this complexity may lie in quasi-intelligent behavior, including conditioning and learning. (shrink)

Review of John Tyler Bonner: Randomness in Evolution. Princeton University Press, Princeton, 2013, 152 pp, £19.95 hbk, ISBN 978-0-691-15701-6.

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular (...) and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

Species are the basis of the taxonomic scheme. They are the lowest taxonomic category that are used as units for describing biodiversity and evolution. In this contribution we discuss the current species concept for prokaryotes. Such organisms are considered to represent the widest diversity among living organisms. Species is currently circumscribed as follows: A prokaryotic species is a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested (...) under highly standardized conditions. Although the number of described prokaryotic species is underrepresented in the living world, this phylo-phenetic or polythetic species concept currently in use is considered to be pragmatic, operational and universally applicable and successfully used for identification processes. (shrink)

The development of bacterial resistance to antibiotics is one of the best documented examples of contemporary biological evolution. Variability in the mechanisms of resistance depends on the diversity of genotypes in the huge bacterial populations, and also on the diversity of selective pressures that are produced along the antibiotic concentration gradients formed in the highly compartmentalized human body during therapy. These antibiotic gradients can be conceived as comprising selective compartments, each one of them defined as the concentration able to select (...) a particular genetic variant. In vitro experimental models confirm that some antibiotic resistant variants are selected only at certain selective concentrations of antibiotics. The correspondence between selective compartments and selectable variants could offer a way of describing more accurately the antibiotic selective landscapes and for taking measures to prevent the development of a major threat to the future of modern medicine. (shrink)

The development of bacterial resistance to antibiotics is one of the best documented examples of contemporary biological evolution. Variability in the mechanisms of resistance depends on the diversity of genotypes in the huge bacterial populations, and also on the diversity of selective pressures that are produced along the antibiotic concentration gradients formed in the highly compartmentalized human body during therapy. These antibiotic gradients can be conceived as comprising selective compartments, each one of them defined as the concentration able to select (...) a particular genetic variant. In vitro experimental models confirm that some antibiotic resistant variants are selected only at certain selective concentrations of antibiotics. The correspondence between selective compartments and selectable variants could offer a way of describing more accurately the antibiotic selective landscapes and for taking measures to prevent the development of a major threat to the future of modern medicine. (shrink)

Gradual degradation seems inevitable for non‐recombining sex chromosomes. This has been supported by the observation of degenerated non‐recombining sex chromosomes in a variety of species. The human Y chromosome has also degenerated significantly during its evolution, and theories have been advanced that the Y chromosome could disappear within the next ∼5 million years, if the degeneration rate it has experienced continues. However, recent studies suggest that this is unlikely. Conservative evolutionary forces such as strong purifying selection and intrachromosomal repair through (...) gene conversion balance the degeneration tendency of the Y chromosome and maintain its integrity after an initial period of faster degeneration. We discuss the evidence both for and against the extinction of the Y chromosome. We also discuss potential insights gained on the evolution of sex‐determining chromosomes by studying simpler sex‐determining chromosomal regions of unicellular and multicellular microorganisms. (shrink)

Philosophy of death particularly from an Indonesian perspective and quo vadis, microorganism culture in Indonesia.

Resident microorganisms, known as the microbiota, are essential for many physiological functions including protection against pathogens. Microbiota is indeed required for proper immune system development and function, and can also host-independently protect against infections. Thus, a co-constructed view of host protection involving both host and microbiota, named ’co-immunity,’ has been proposed, and the idea of an ’immunological holobiont’ has been suggested. Yet this view of co-immunity might be too limited, as experimental work has shown that the immune system is (...) involved in functions other than protection, essentially development and repair. Microbiota, through co-immunity, is thereby most likely involved in these functions, although strong evidence is currently lacking. Moreover, as our point of view is mainly host-centered, we may miss the implications of co-immunity at broader scales, including cellular and population levels. Intriguingly, co-immunity effects could be beneficial for one function and/or one level, while being detrimental for others. All these elements should be taken into consideration for microbiota manipulation, in order to avoid potentially harmful side effects. (shrink)

Microorganisms demonstrate conscious-like intelligent behaviour, and this form of consciousness may have emerged from a quantum mediated mechanism as observed in cytoskeletal structures like the microtubules present in nerve cells whichapparently have the architecture to quantum compute. This paper hypothesises the emergence of proto-consciousness in primitivecytoskeletal systems found in the microbial kingdoms of archaea, bacteria and eukarya. To explain this, we make use of the Subject–Object Model (SOM) of consciousness which evaluates the rise of the degree of consciousness to (...) conscious behaviourin these systems supporting the hypothesis of emergence and propagation of conscious behaviour during the pre-Cambrian partof Earth’s evolutionary history. Consciousness as proto-consciousness or sentience computed via primitive cytoskeletal structures substantiates as a driver for the intelligence observed in the microbial world during this period ranging from single-cellular to collective intelligence as a means to adapt and survive. The growth in complexity of intelligence, cytoskeletal system and adaptive behaviours are key to evolution, and thus supports the progression of the Lamarckian theory of evolution driven by quantum mediated proto-consciousness to consciousness as described in the SOM of consciousness. (shrink)

Microorganisms luxuriate in, plants push through, the humus, that is, the corpses of plants, insects, birds and mammals. Insects, fish, birds, and mammals nourish themselves with the flesh of plants on hand, and also with that of insects, fish, birds, and mammals. In the natural world, everything assimilates and is assimilated. Every animal, from amoebas to the blue whales, feels moments of fear, for they know they are vulnerable and mortal. As they eat what is at hand they sense (...) that what will eat them is already at hand. (shrink)

Microorganisms luxuriate in, plants push through, the humus, that is, the corpses of plants, insects, birds and mammals. Insects, fish, birds, and mammals nourish themselves with the flesh of plants on hand, and also with that of insects, fish, birds, and mammals. In the natural world, everything assimilates and is assimilated. Every animal, from amoebas to the blue whales, feels moments of fear, for they know they are vulnerable and mortal. As they eat what is at hand they sense (...) that what will eat them is already at hand. (shrink)

“When Species Meet is a breathtaking meditation on the intersection between humankind and dog, philosophy and science, and macro and micro cultures.” —Cameron Woo, Publisher of Bark magazine In 2006, about 69 million U.S. households had pets, giving homes to around 73.9 million dogs, 90.5 million cats, and 16.6 million birds, and spending over $38 billion dollars on companion animals. As never before in history, our pets are truly members of the family. But the notion of “companion species”—knotted from human (...) beings, animals and other organisms, landscapes, and technologies—includes much more than “companion animals.” In When Species Meet, Donna J. Haraway digs into this larger phenomenon to contemplate the interactions of humans with many kinds of critters, especially with those called domestic. At the heart of the book are her experiences in agility training with her dogs Cayenne and Roland, but Haraway’s vision here also encompasses wolves, chickens, cats, baboons, sheep, microorganisms, and whales wearing video cameras. From designer pets to lab animals to trained therapy dogs, she deftly explores philosophical, cultural, and biological aspects of animal-human encounters. In this deeply personal yet intellectually groundbreaking work, Haraway develops the idea of companion species, those who meet and break bread together but not without some indigestion. “A great deal is at stake in such meetings,” she writes, “and outcomes are not guaranteed. There is no assured happy or unhappy ending—socially, ecologically, or scientifically. There is only the chance for getting on together with some grace.” Ultimately, she finds that respect, curiosity, and knowledge spring from animal-human associations and work powerfully against ideas about human exceptionalism. One of the founders of the posthumanities, Donna J. Haraway is professor in the History of Consciousness Department at the University of California, Santa Cruz. Author of many books and widely read essays, including The Companion Species Manifesto: Dogs, People, and Significant Otherness and the now-classic essay “The Cyborg Manifesto,” she received the J. D. Bernal Prize in 2000, a lifetime achievement award from the Society for Social Studies in Science. (shrink)

Archaea are microorganisms that are distinct from bacteria and eukaryotes. They are prevalent in extreme environments, and yet found in most ecosystems. They are a natural component of the microbiota of most, if not all, humans and other animals. Despite their ubiquity and close association with humans, animals and plants, no pathogenic archaea have been identified. Because no archaeal pathogens have yet been identified, there is a general assumption that archaeal pathogens do not exist. This review examines whether this (...) is a good assumption by investigating the potential for archaea to be or become pathogens. This is achieved by addressing: the diversity of archaea versus known pathogens, opportunities for archaea to demonstrate pathogenicity and be detected as pathogens, reports linking archaea with disease, and immune responses to archaea. In addition, molecular and genomic data are examined for the presence of systems utilised in pathogenesis. The view of this report is that, although archaea can presently be described as non‐pathogenic, they have the potential to be (discovered as) pathogens. The present optimistic view that there are no archaeal pathogens is tainted by a severe lack of relevant knowledge, which may have important consequences in the future. BioEssays 25:1119–1128, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

A mark of the cognitive should allow us to specify theoretical principles for demarcating cognitive from non-cognitive causes of behaviour in organisms. Specific criteria are required to settle the question of when in the evolution of life cognition first emerged. An answer to this question should however avoid two pitfalls. It should avoid overintellectualising the minds of other organisms, ascribing to them cognitive capacities for which they have no need given the lives they lead within the niches they inhabit. But (...) equally it should do justice to the remarkable flexibility and adaptiveness that can be observed in the behaviour of microorganisms that do not have a nervous system. We should resist seeking non-cognitive explanations of behaviour simply because an organism fails to exhibit human-like feats of thinking, reasoning and problem-solving. We will show how Karl Friston’s Free-Energy Principle (FEP) can serve as the basis for a mark of the cognitive that avoids the twin pitfalls of overintellectualising or underestimating the cognitive achievements of evolutionarily primitive organisms. The FEP purports to describe principles of organisation that any organism must instantiate if it is to remain well-adapted to its environment. Living systems from plants and microorganisms all the way up to humans act in ways that tend in the long run to minimise free energy. If the FEP provides a mark of the cognitive, as we will argue it does, it mandates that cognition should indeed be ascribed to plants, microorganisms and other organisms that lack a nervous system. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Beginning in the 1940s, mass production of antibiotics involved the industrial-scale growth of microorganisms to harvest their metabolic products. Unfortunately, the use of antibiotics selects for resistance at answering scale. The turn to the study of antibiotic resistance in microbiology and medicine is examined, focusing on the realization that individual therapies targeted at single pathogens in individual bodies are environmental events affecting bacterial evolution far beyond bodies. In turning to biological manifestations of antibiotic use, sciences fathom material outcomes of (...) their own previous concepts. Archival work with stored soil and clinical samples produces a record described here as ‘the biology of history’: the physical registration of human history in bacterial life. This account thus foregrounds the importance of understanding both the materiality of history and the historicity of matter in theories and concepts of life today. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (shrink)

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a (...) problem with this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation–conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology. (shrink)

Besides its use in basic research, the DNA:RNA hybridization technique has helped the development of genetic engineering: it is instrumental in the isolation of specific genes that can be inserted into foreign cells, thus modifying their genetic information. Plants, animals, and microorganisms can now be altered to yield improved crops, pest-resistant plants, and a cheaper source of important proteins or drugs. The social relevance of genetic engineering received official sanction in 1980 when the U.S. Supreme Court ruled that genetically (...) modified organisms can be patented. In this article I have tried to describe the discovery of the DNA:RNA hybridization technique as the successful outcome of years of intelligent and patient research in many laboratories, of inductive and deductive processes in the minds of many biologists. The synthesis that led to the final result and to the early development of the technique was made possible by the coming together of two brilliant scientists, Sol Spiegelman and Benjamin Hall. (shrink)

It has become increasingly clear that there is a vast array of microorganisms on and in the human body, known collectively as the human microbiome. Our microbiomes are extraordinarily complex, and this complexity has been linked to human health and well-being. Given the complexity and importance of our microbiomes, we struggle with how to think about them. There is a long list of competing metaphors that we use to refer to our microbiomes, including as an “organ” containing our “second (...) genome,” as a “symbiont” in the human “holobiont,” and as an ecological “community” in the human “ecosystem,” among others. Each of these makes different assumptions about the fundamental biology of the human-microbe system, with important implications for how we choose to study microbiomes, and the therapies we envision for correcting microbiome-linked disorders. We believe that it is time to move beyond metaphors, and we propose a scientifically pluralist approach that focuses on characterizing fundamental biological properties of microbiomes such as heritability, transmission mode, rates of dispersal rates, and strength of local selection. Such an approach will allow us to break out of the confines of narrow conceptual frameworks, and to guide the exploration of our complexity as chimeric beings. (shrink)

This paper develops a general approach to how society should compensate for losses that individuals incur due to public health interventions aimed at controlling the spread of infectious diseases. The paper falls in three parts. The first part provides an initial introduction to the issues and briefly outlines five different kinds of public health interventions that will be used as test cases. They are all directed at individuals and aimed at controlling the spread of infectious diseases (1) isolation, (2) quarantine, (...) (3) recommended voluntary social distancing, (4) changes in health care provision for asymptomatic carriers of multi-resistant microorganisms, and (5) vaccination. The interventions will be briefly described including the various risks, burdens and harms individuals who are subject to these interventions may incur. The second part briefly surveys current compensation mechanisms as far as any exist and argue that even where they exist they are clearly insufficient and do not provide adequate compensation. The third part will then develop a general framework for compensation for losses incurred due to public health interventions in the infectious disease context. This is the major analytical and constructive part of the paper. It first analyses pragmatic and ethical arguments supporting the existence of an obligation on the part of the state to compensate for such losses, and then considers whether this obligation can be defeated by (1) resource considerations, or (2) issues relating to personal responsibility. (shrink)

In the late nineteenth century, French naturalists were global leaders in microbial research. Louis Pasteur advanced sterilization techniques and demonstrated that dust particles in the air could contaminate a putrefiable liquid. Pasteur’s discoveries prompted a new research program for the naturalists of the Talisman and Travailleur expeditions: to recover uncontaminated water and mud samples from the deep sea. French naturalists Adrien Certes and Paul Regnard both independently conducted experiments to address the question of whether microorganisms inhabited the oceans and (...) whether organic material in the deep sea was subject to decomposition. The experiments of Certes and Regnard have largely been omitted from histories of microbiology and marine science. However, an examination of their work is crucial for understanding the context in which marine microbiology first developed. At the end of the nineteenth century, marine microbiology emerged from the disciplinary melding of terrestrial microbial ecology, experimental physiology, and the then-nascent field of deep-sea biology. (shrink)

In the light of contemporary allelopathic research, the intuitively based statements of the early botanists stand up surprisingly well. The walnut tree is now understood to affect the growth of neighboring plants via juglone leached from the leaves, roots, and fruits.118 The replant or soil sickness problem of peach orchards has been related to the toxigenic breakdown of amygdalin, a constituent of peach roots.119 The declining yield of many crop species grown under continuous monoculture has been linked to the accumulation (...) of allelopathic substances in the soil, especially through the mediation of microorganisms.120 Numerous plants cited by de Candolle as being injurious, such as Erigeron,121 thistle (Cirsium),122 flax (Linum),123 and various crucifers (such as Brassica nigra),124 have been found to posses marked allelopathic activity. Over fifty years before the discovery of rhizobia, de Candolle considered the excretory material of legumes to be beneficial to cereals.125Modern reviews of allelopathy commonly credit de Candolle with an insight that was not equaled by the technology of his era.126 In fairness to his detractors, his toxin theory of plant interactions was largely the by-product of an outdated and misconstrued notion of plant nutrition. His critics and most earlier botanists had similarly erred in seeking a single factor responsible for plant growth, much as had the alchemists sought the legendary philosopher's stone. Taking all this into account and considering the forceful personality of Liebig, one can readily appreciate how, 130 years ago, Liebig's theories preempted and stifled those of de Candolle.Today, with modern techniques of plant physiology and soil biochemistry, allelopathy has been shown to be a real but subtle factor in the dynamics of natural and agricultural plant communities. It is unfortunate that the single-mindedness characteristic of previous centuries still persists. The dichotomy between allelopathy and competition is exacerbated by the inherited bias toward the nutritional model of plant interaction fostered by Liebig, and is accentuated in the fact that in modern nutritional studies it is still basically unnecessary to consider plant-plant chemical interactions and their concomitant effects, whereas in allelopathic investigations the converse is regarded as axiomatic.In summary, de Candolle should not be seen as “a prophet crying in the wilderness,” as Fisher would have it.127 The bases of de Candolle's concept of allelopathy were the dubious experiments of Macaire and his own obsolete theory of plant nutrition. Despite this, modern experimental work indicates that allelopathy is important in many plant interactions. De Candolle seems to have been right, at least in part—but for the wrong reasons. (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)

Holobionts are symbiotic assemblages composed by a macrobe host plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, (...) the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl’s account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host’s microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective. (shrink)

It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term “holobiont” was introduced as a name for the biological unit made up by a host and all of (...) its associated microorganisms, and much of this new debate about biological individuality has focused on whether holobionts are integrated individuals or communities. In this paper, I show how parts of the holobiont can span both characterizations. I argue that most holobionts share more affinities with communities than they do with organisms, and that, except for maybe in rare cases, holobionts do not meet the criteria for being organisms, evolutionary individuals, or units of selection. (shrink)

Frederick Griffith was an English bacteriologist at the Pathological Laboratory of the Ministry of Health in London who believed that progress in the epidemiology and control of infectious diseases would come only with more precise knowledge of the identity of the causative microorganisms. Over the years, Griffith developed and expanded a serological technique for identifying pathogenic microorganisms, which allowed the tracing of the sources of infectious disease outbreaks: slide agglutination. Yet Griffith is not remembered for his contributions to (...) the biology and epidemiology of infectious diseases so much as for discovering the phenomenon known as ‘transformation’. Griffith’s discovery, for many, was a pure case of serendipity whose biological relevance had also largely escaped him. In this paper, I argue that the key to understanding the significance of bacterial transformation – and the scientific legacy of Fred Griffith – rests not only on it initiating a cascade of events leading to molecular genetics but also on its implications for epidemiology based on the biology of host–parasite interactions. Looking at Griffith’s entire career, instead of focusing only on the transformation study, we can better appreciate the place of the latter within Griffith’s overall contributions. Presented in this way, Griffith’s experiment on bacterial transformation also ceases to appear as an anomaly, which in turn leads us to rethink some of the most prevalent historical conceptions about his work. (shrink)

Starting from research on biotechnology and its applications to living organisms, this paper presents the key features of modern-day synthetic biology, as well as its main ethical implications. The analysis of the paradox of the concept of robustness in the creation of microorganisms through synthetic biology leads us to address the topic of vulnerability, applied to man, but also to all other living beings. The concept of “enhanced human being” will strengthen the link between complexity and vulnerability as inherent (...) features of living beings. Reflecting upon the importance of considering vulnerability applied to man’s three-fold dimensions - physical, psycho-social and spiritual - and their interaction with their environment, we will define a type of anthropology which may constitute the basis of the study on the ethical implications of synthetic biology. This will lead to present the purpose of an ethical limit to the temptation of « allmightiness », which the concept of enhanced human being could entail, and vulnerability as a defining feature of all living beings. (shrink)

We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call “epistemic misalignment.” An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epistemic misalignments, due (...) to the different temporal scales that 16S rRNA provides information about and the temporal scales that are required to know about the functionality of some microorganisms. We show how some of these exist in contemporary microbiome science and urge microbiome scientists to take some measures to avoid them, as they may question the credibility of the field as a whole. (shrink)