Calcineurin is a Ca2+/calmodulin‐activated protein phosphatase that is conserved in eukaryotes, from yeast to humans, and is the conserved target of the immunosuppressive drugs cyclosporin A (CsA) and FK506. Genetic studies in yeast and fungi established the molecular basis of calcineurin inhibition by the cyclophilin A–CsA and FKBP12–FK506 complexes. Calcineurin also functions in fungi to control a myriad of physiological processes including cell cycle progression, cation homeostasis, and morphogenesis. Recent investigations into the molecular mechanisms of pathogenesis in Candida (...) albicans and Cryptococcus neoformans, two fungi that cause life‐threatening infections in humans, have revealed an essential role for calcineurin in morphogenesis, virulence, and antifungal drug action. Novel non‐immunosuppressive analogs of the calcineurin inhibitors CsA and FK506 that retain antifungal activity have been identified and hold promise as candidate antifungal drugs. In addition, comparisons of calcineurin function in both fungi and humans may identify fungal‐specific components of calcineurin‐signaling pathways that could be targeted for therapy, as well as conserved elements of calcium signaling events. BioEssays 24:894–903, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

Fungi are sessile, highly sensitive organisms that actively compete for environmental resources both above and below the ground. They assess their surroundings, estimate how much energy they need for particular goals, and then realise 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 behaviour accordingly. These highly diverse competences show us that this is possible owing to sign-mediated communication (...) processes within fungal cells, between the same, related and different fungal species, and between fungi and non-fungal organisms. Intraorganismic communication involves sign-mediated interactions within cells and between cells. This is crucial in coordinating growth and development, shape and dynamics. Such communication must function both on the local level and between widely separated mycelium parts. This allows fungi to coordinate appropriate response behaviors in a differentiated manner to their current developmental status and physiological influences. (shrink)

Transposons are ubiquitous genetic elements discovered so far in all investigated prokaryotes and eukaryotes. In remarkable contrast to all other genes, transposable elements are able to move to new locations within their host genomes. Transposition of transposons into coding sequences and their initiation of chromosome rearrangements have tremendous impact on gene expression and genome evolution. While transposons have long been known in bacteria, plants, and animals, only in recent years has there been a significant increase in the number of transposable (...) elements discovered in filamentous fungi. Like those of other eukaryotes, each fungal transposable element is either of class I or of class II. While class I elements transpose by a RNA intermediate and employ reverse transcriptases, class II elements transpose directly at the DNA level. We present structural and functional features for such transposons that have been identified so far in filamentous fungi. Emphasis is given to specific advantages or unique features when fungal systems are used to study transposable elements, e.g., the evolutionary impact of transposons in coenocytic organisms and possible experimental approaches toward horizontal gene transfer. Finally, we focus on the potential of transposons for tagging and identifying fungal genes. BioEssays 20:652–659, 1998.© 1998 John Wiley & Sons Inc. (shrink)

Arbuscular mycorrhizal fungi are considered as a potential biotechnological tool for improving phytostabilization efficiency and plant tolerance to heavy metal-contaminated soils. However, the mechanisms through which AMF help to alleviate metal toxicity in plants are still poorly understood. A greenhouse experiment was conducted to evaluate the effects of two AMF species on the growth, Pb accumulation, photosynthesis and antioxidant enzyme activities of a leguminous tree at Pb addition levels of 0, 500, 1000 and 2000 mg kg-1 soil. AMF symbiosis (...) decreased Pb concentrations in the leaves and promoted the accumulation of biomass as well as photosynthetic pigment contents. Mycorrhizal plants had higher gas exchange capacity, non-photochemistry efficiency, and photochemistry efficiency compared with non-mycorrhizal plants. The enzymatic activities of superoxide dismutase, ascorbate peroxidases and glutathione peroxidase were enhanced, and hydrogen peroxide and malondialdehyde contents were reduced in mycorrhizal plants. These findings suggested that AMF symbiosis could protect plants by alleviating cellular oxidative damage in response to Pb stress. Furthermore, mycorrhizal dependency on plants increased with increasing Pb stress levels, indicating that AMF inoculation likely played a more important role in plant Pb tolerance in heavily contaminated soils. Overall, both F. mosseae and R. intraradices were able to maintain efficient symbiosis with R. pseudoacacia in Pb polluted soils. AMF symbiosis can improve photosynthesis and reactive oxygen species scavenging capabilities and decrease Pb concentrations in leaves to alleviate Pb toxicity in R. pseudoacacia. Our results suggest that the application of the two AMF species associated with R. pseudoacacia could be a promising strategy for enhancing the phytostabilization efficiency of Pb contaminated soils. (shrink)

Among mycologists, questions persist about what entities should be treated as the fundamental units of fungal populations. This article articulates a coherent view about populations of heterokaryotic fungi and the individuals that comprise them. Using Godfrey-Smith’s minimal concept of a Darwinian population, I argue that entities at two levels of the biological hierarchy satisfy the minimal concept in heterokaryotic fungi: mycelia and nuclei. I provide a preliminary answer to the question of how to understand the relation between these (...) two populations. This article contributes to discussions about the nature of biological individuality, organismality, and evolutionary transitions. (shrink)

In his extensive and revolutionary work, the biologist and philosopher Jakob von Uexküll examined the animal kingdom, laying the first foundations for a wider reflection on non-human animal agency in ecosystems. However, the scientist did not include in his reflection on Umwelt plants and fungi, widely considered passive organisms in the 1900s. In this paper, we will try to find the contact points between the biologist’s theories and contemporary botanical discoveries, taking into account some of the findings on plant (...) agency, communication, and interaction even with fungi, crucial actors in the vegetal organization of the territory. The core of the work will be to demonstrate that plants could fit in an integrated and extended theory of Umwelt abandoning the “zoocentric” perspective that permeated the studies on botanical species. To achieve this aim, it will be necessary to first deconstruct the historical theorization of plants’ passivity, which has ancient roots and was enforced in some philosophical perspectives of the 20th century. Consequentially, with two focuses, the first one on communication and the second one on agency, the paper will highlight the possibilities and horizons that could be opened through a comparison between the theories of von Uexküll and nowadays botanical breakthroughs. (shrink)

This study aims at demonstrating the usefulness of the Pareto in- clusive criterion methodology for comparative analyses of fungi toxicity. The toxicity of fungi is usually measured using a scale of several ranks. In practice, the ranks of toxicity are routinely grouped into only four conventional classes of toxicity: from a class of no toxicity, low toxicity, and moderate toxicity, to a class of high toxicity. The illustrative material included the N = 61 fungi samples obtained from (...) three species: A. ochraceus, A. niger and A. flavus. In accordance with the Pareto approach, four partial criterions of the worst toxi- city were defined, a single criterion used for each conventional class of toxicity. Finally, the odds ratios (OR) were calculated separately for each partial cri- terion, and the significance of the hypotheses OR = 1 was estimated. It was stated that A. ochraceus fungi are distinctly more toxic than the two remaining ones with respect to the all considered four partial criterions, with significance equal to p = 0.04, p = 0.04, p = 0.007 and p = 0.005, respectively. Thus, the suggested method illustrated its utility in the case under study. (shrink)

Around the turn of the twentieth century, microbiologists in Western Europe and North America began to organize centralized collections of microbial cultures. Collectors published lists of the strains they cultured, offering to send duplicates to colleagues near and far. This essay explores the history of microbial culture collections through two cases: Johanna Westerdijk’s collection of phytopathogenic fungi in the Netherlands and Ernst Georg Pringsheim’s collection of single-celled algae at the German University in Prague. Historians of science have tended to (...) look at twentieth-century biological specimen collections as either repositories of communal research materials or storehouses of economically important biological variation. An examination of Westerdijk’s and Pringsheim’s collections illustrates how collectors, researchers, and patrons ascribed different kinds of value to collections featuring distinctive microbial life forms. This essay argues that characteristics of cultivated microorganisms, such as a fungus’s propensity to infect crops or an alga’s amenability to experimentation, shaped the trajectories of Westerdijk’s and Pringsheim’s collections as these collectors developed relationships with colleagues and patrons. Letters between Westerdijk and Pringsheim open a window onto divergences in their approaches to collecting cultures, while also shedding light on the aspirational internationality of the collections that resulted. (shrink)

This contribution to the Common Knowledge symposium “Fuzzy Studies” argues that the inclusion of space in form brings varying degrees of fuzziness and fluidity to all natural identities. Such inclusion is vital to evolutionary creativity, from subatomic to cosmic scales of natural energy flow. Examples abound throughout the natural world of indeterminate forms and processes unclassifiable under any of the discrete categories that are preferred and imposed by definitive theoretical models. Here, the much-neglected kingdom of the fungi is used (...) to illustrate the workings of a logic of fluid boundaries. (shrink)

Drawing upon ethnographic research on human living and producing with fungi, and Haraway’s theorization of sympoiesis and the model ecosystems of mycorrhizae developed in current mycological research, we offer a concept of _sympoietic growth_. Sympoiesis is a concept that suggests a way of thinking about growth as a more-than-human process and provides an alternative political imaginary both to current forms of economic growth and to the idea of “degrowth.” We explore human-fungi co-operation in forests, an urban park, and (...) a shopping mall, on a miso production farm, and in a Catholic parish to provide insights into the logic and relationships involved in sympoietic growth in the field of agriculture and food production. We argue that this form of food provision has a sustainable, (re)generative potential not only in ecological and social but also economic terms. In conclusion, we highlight three patterns of sympoietic growth: the absence of any urge to “take (back) control” over the multispecies dynamic on the part of the humans; a non-instrumental passion for more-than-human life; and a combination of intellectual and manual labor as a form of attachment to the more-than-human world. (shrink)

The species comprising the fungal endophyte genus “Epichloë ”are symbionts of cool season grasses. About half the species in this genus are strictly vertically transmitted, and evolutionary theory suggests that these species must be mutualists. Nevertheless, Faeth and Sullivan (e.g., 2003) have argued that such vertically transmitted endophytes are ’usually parasitic,’ and Müller and Krauss (2005) have argued that such vertically transmitted endophytes fall along a mutualism-parasitism continuum. These papers (and others) have caused confusion in the field. We used a (...) systematic review to show that close to half of the published papers in this field incorrectly categorize the interaction. Here, we develop the argument that advantages and disadvantages are not the same things as mutualism and parasitism and that experimental evidence must be interpreted in the context of theory. We argue that, “contra ”Faeth and Sullivan, it is highly unlikely that such strictly vertically transmitted endophytes can be parasites, and that, “contra ”Müller and Krauss, it is inappropriate to apply the continuum concept to strictly vertically transmitted endophytes. We develop a mathematical model to support and illustrate our arguments. We use the model to clarify that parasitism “requires ”some degree of horizontal transmission, and that while it is appropriate to use the continuum concept when referring to the genus as a whole, or to species that possess horizontal transmission, we argue that it is inappropriate to use the concept when referring to species that are strictly vertically transmitted. (shrink)

In fungi, cell fusion between genetically unlike individuals triggers a cell death reaction known as the incompatibility reaction. In Podospora anserina, the genes controlling this process belong to a gene family encoding STAND proteins with an N‐terminal cell death effector domain, a central NACHT domain and a C‐terminal WD‐repeat domain. These incompatibility genes are extremely polymorphic, subject to positive Darwinian selection and display a remarkable genetic plasticity allowing for constant diversification of the WD‐repeat domain responsible for recognition of non‐self. (...) Remarkably, the architecture of these proteins is related to pathogen‐recognition receptors ensuring innate immunity in plants and animals. Here, we hypothesize that these P. anserina incompatibility genes could be components of a yet‐unidentified innate immune system of fungi. As already proposed in the case of plant hybrid necrosis or graft rejection in mammals, incompatibility could be a by‐product of pathogen‐driven divergence in host defense genes. (shrink)

Most land plants associate with mycorrhizal fungi that can connect roots of neighboring plants in common mycelial networks (CMNs). Recent evidence shows that CMNs transfer warning signals of pathogen and aphid attack between plants. However, we do not know how defence‐related signaling via CMNs operates or how ubiquitous it is. Nor do we know what the ecological relevance and fitness consequences are, particularly from the perspective of the mycorrhizal fungus. Here, we focus on the potential fitness benefits for mycorrhizal (...) fungi and outline hypothetical scenarios in which signal transfer via CMNs is modulated in order to acquire the most benefit for the fungus (i.e. acquisition of carbon) for minimal cost. We speculate that the signal may be quantitative and may elicit plant defence responses on different levels depending on the distance the signal is transferred. Finally, we discuss the possibility of practical applications of this phenomenon for crop protection. (shrink)

Lichens are included in the classification system of fungi and have been used in medicine, pharmacy and industry from antiquity to present day in the treatment of various diseases. In this study, Peri Hyles Iatrikes of Dioscorides has been investigated and evaluated from lichenological point of view. It is found that, Dioscorides mentions about medical properties and uses of probable Parmelia species such as P. saxatilis (L.) Ach or P. sulcata Taylor.

A growing awareness of a subsurface fossil record of mostly hyphal fungi organisms stretching back through the Phanerozoic to ≈400 megaannum (Ma) and possibly earlier, provides an alternative view on hyphal development. Parallel with the emergence of hyphal fungi during Ordovician–Devonian times when plants colonized the land, which is the traditional notion of hyphal evolution, hyphae‐based fungi existed in the deep biosphere. New insights suggest that the fundamental functions of hyphae may have evolved in response to an (...) ancient subsurface endolithic life style and might have been in place before the colonization of land. To address the gaps in the current understanding of hyphal evolution a strategy based on research prospects involving investigations of uncharted geological material, new diagnostics, and comparisons to live species is proposed. (shrink)

This paper is an application of the principles of individuality found in Guay and Pradeu to illuminate biological individuality in mushrooms. I begin with the distinction between logico-cognitive individuals and ontological individuals, and then I argue for genidentity plus material continuity, as a minimum conception of ontological individuality in biology. Of the many materially-continuous genidenticals found in fungi, only those with functional roles in biological theory, either evolutionary or physiological, warrant consideration. Given numerous ways that theory picks out materially-continuous (...) genidenticals in fungi, I argue for a pluralistic account of mushroom individuality. (shrink)

The threshold from unicellularity to multicellularity has been crossed only in three major living domains in evolution with any lasting success. The hard problem was to create a multicellular self. Such a self is vulnerable to breakdown due to the unavoidable appearance of mutant anarchistic cells, and stringent semiotic scaffoldings had to emerge to prevent this. While a unicellular self may go on to live practically forever, the multicellular self most often must run through an individuation process ending in the (...) death of the individual. Due to basic differences in cells of plants, fungi and animals this individuation process poses very different challenges in the three kingdoms of plants, fungi and animals, and the solutions found to these differences are discussed. In the same time as multicellularity ushered life into the epoch of mortality it logically also led to the appearance of fertilization and thereby the need for a whole new set of elaborate semiotic scaffoldings. Multicellularity also opened the door to the formation symbiotic relations where cells with different genomes might collaborate or at least coexist inside the same body. All in all multicellularity led to an enormous diversification both of morphology space and the space of sensomotoric elaborations. New means for scaffolding of this expansion and diversification of possible life forms into functional patterns called for a corresponding growth in the space of semiotic tools and initiated a growth in semiotic freedom, that has continued to our days. (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)

This paper criticizes Jerome Wakefield’s harmful dysfunction analysis of disorder by arguing that the conceptual linkage it establishes between the medical concepts of health and disorder and the prudential notions of well-being and harm makes the account inapplicable to nonsentient organisms, such as plants, fungi, and many invertebrate animals. Drawing on a previous formulation of this criticism by Christopher Boorse, and noting that Wakefield could avoid it if he adopted a partly biofunction-based account of interests like that often advocated (...) in the field of environmental ethics, I argue that integrating such an account of interests into the HDA would generate serious concerns. Specifically, it would make dysfunction sufficient for disorder and so reestablish between dysfunction and disorder precisely the kind of sufficiency relation that harm-requiring accounts of disorder strive to avoid; blur the line between the HDA’s dysfunction and harm components and, in so doing, deprive the HDA of its alleged main advantage over monistic dysfunction-based accounts of disorders like Boorse’s; and tie the HDA to an understanding of harm that is in itself problematic. I argue that these three concerns, and the dilemmas they generate, rob the HDA of much of its prima facie appeal, ultimately indicating that a satisfactory account of disorder should most likely eschew all references to prudential notions of well-being and harm. (shrink)

What general conclusions can be drawn about the reception of zymase, its relation to the larger shift from a protoplasm to an enzyme theory of life, and its status as a social phenomenon?The most striking and to me unexpected pattern is the close correlation between attitude toward zymase and professional background. The disbelief of the fermentation technologists, Will, Delbrück, Wehmer, and even Stavenhagen, was as sharp and unanimous as the enthusiasm of the immunologists and enzymologists, Duclaux, Roux, Fernback, and Bertrand, (...) and of Pfeffer, the experimental plant physiologist. Other skeptics—Voit, Kupffer, and Fischer—were conservatives in traditional fields. In all these cases it seems clear that professional commitments and outlook profoundly influenced the reception of zymase.In some cases there is a correlation with a specific earlier statement favoring the protoplasm theory or predicting a fermentation enzyme. Reynolds Green is a striking case of both. In 1893 he stated his belief that life processes in higher plants and fungi were identical, both being mediated by protoplasm.109 Thus he claimed that digestion was not carried out by enzymes, as in higher animals, but by the whole protoplasm, and so too fermentation in yeast: “All the metabolic processes must be carried out in the unicellular organism in the same mass of protoplasm.”110 But Green also insisted that there was no essential difference between “organized” and “unorganized ferments”; enzymes were simply more highly differentiated and specialized forms of primitive protoplasm. He spoke of “the alcoholic ferment” (that is, enzyme), and of intracellular enzymes—very advanced beliefs for 1893. Thus it is understandable why Green saw no reason to doubt his first negative results with yeast juice, and rushed into print. But it is also understandable that he persisted and soon became an outspoken advocate of Buchner's view; like Wroblewski and Pfeffer, he had already accepted the idea of an intracellular fermentation enzyme.The physiological chemists also fit the pattern in a special way. Physiological chemistry is generally regarded as the source of biochemistry; indeed, many early biochemists were trained in physiological chemistry, and imbibed there a progressive interest in enzymes and metabolism. It is not surprising, therefore, that on the whole Neumeister, Madfadyen, Wroblewski, and Loew accepted cell-free fermentation. But what is surprising, and significant, is the diversity of opinion in this group, from Abeles' living protoplasm to Wroblewski's organized array of active proteins. The feelings of the physiological chemists were mixed, and there was enough of the old protoplasm view in Macfadyen's and even Wroblewski's views to allow Buchner to see them as attacks on zymase. The ideas of physiological chemistry were also changing; the idea of protoplasm was already adjusting to the new interest in enzymes in the early 1890's. But in contrast to immunochemistry, the change in physiological chemistry was gradual, uneven, undramatic, and relatively invisible. For the new biochemistry, the tradition of physiological chemistry was the source of traditional conservatism as well as of new ideas of enzymes.In general, then, I claim that it was not experimental facts that determined attitudes toward zymase so much as previous commitments, experience, and expectations. Initially, at least, zymase was less a determinant of opinion than a touchstone of pre-existing opinion. Like a prism, it revealed the spectrum of existing attitudes toward vital phenomena.Also relevant here is the fact that the experimental evidence was entirely ambiguous; the interpretation of Buchner's experiments with antiseptics or dried yeast depended entirely on how far one was willing to stretch the scope of the terms “protoplasm” and “enzyme”. Likewise, how important one judged the instability of zymase to be, or the low level of in vitro activity, depended largely on one's point of view. There was no crucial experiment, no certain proof. Logically zymase could be regarded as protoplasm. A. Fischer did so in 1900;111 Macfadyen was still wavering in 1907;112 and Beijerinck was holding out as late as 1916.113 There were undoubtedly others. Besides the special case of Reynolds Green and the technologists, there are no recorded cases of conversion.But if there was no evidence to convert a dedicated protoplasmist, there was plenty to encourage a dedicated belief in the enzyme theory, and that, I believe, is precisely what happened. The arguments of Buchner et al in support of zymase had the greatest effect not on the protoplasmists but on those who were already predisposed toward the biochemical view. The zymase debate enabled the emerging group of biochemists to recognizethemselves as a group with a community of out-look and objectives; it brought the issue of protoplasm vs. enzyme into the open and gave it a specific and concrete issue on which to turn. The debate sharpened the biochemists' awareness that their point of view was becoming the new mainstream of biochemical thought.All this of course had an important secondary effect on those who opposed the new view, or who were not immediately concerned with it. After the zymase debate, it would have been almost impossible to ignore the new ideas; the dramatic and wide publicity the debate enjoyed would have made it difficult not to take sides. Buchner's successful defense of zymase itself became an important influence on opinion; the new movement had to be looked at with respect. But the primary effect of the debate, I assert, was on those who were already inclined to the new view. The outcome was not a mass conversion of individuals, nor the ejection of one idea by another. The sides probably did not change much; the real change was in the way each side regarded itself and its place in history. The zymase debate may perhaps best be regarded as a process of selection. Buchner's party became aware of itself as the new progressive point of view, while those holding the traditional view could no longer expound it publicly without appearing obstinate or old-fashioned. Thus the way was clear for the gradually wider establishment of the new ideas, especially among the new generation of biochemists. In this specific sense, the acceptance of zymase was a social phenomenon.This way of looking at the zymase debate also illuminates its coincidence with the emergence of biochemistry as a profession. The new professional trappings and organizations were the social manifestation of the new self-awareness gained from the zymase controversy. One of the most important effects on those disposed toward the new view was the awareness of an intellectual community and of the need to give that community social forms. The almost mythical importance of Buchner's “victory” over the old protoplasm theory that later became current is readily understandable. It was a useful ideology for a group anxious to assert the novelty of their approach, a novelty which they in fact felt quite keenly.But if the primary effect of the zymase controversy was on those predisposed to accept zymase, then obviously the success of zymase depended on the fact that change had already begun to occur. Indeed, one of the most striking, and again unexpected, results of this study is the extent to which the importance of enzymes was already recognized in the early 1890's. The new immunology clearly pointed the way. Macfadyen and Hans Buchner were looking for active proteins inside the cell in 1893. Reynolds Green, Wroblewski, and Pfeffer had all anticipated the discovery of a fermentation enzyme. Other discoveries in enzymology in the 1890's pointed the same way.114 Moreover, it is clear from this study that the old protoplams theory was adapting to the new discoveries concerning the importance of enzymes. The sidechains of the old protoplasm molecule were simply reinterpreted as enzymes, as in Wroblewski's theory, for example, or in Paul Ehrlich's extremely influential “sidechain theory” of antibody formation (1897). Despite the later views of Hopkins et al., the old protoplasm and the new enzyme theories were not irreconcilable; a continuity of development had already begun when zymase came so dramatically on the scene. Buchner himself observed that the difference between the two views had become largely verbal; in retrospect we might say, not verbal, but social and historical. The gap between the continuous change in ideas and the contemporary feeling of sharply discontnuous change is a measure of the elusive but real social and historical implications of the zymase debate, of the demise of an old establishment, and the emergence of a new.In retrospect, then, it is clear that a trend was already under way in various quarters when zymase appeared. But it was still a collection of isolated and dispersed events. The zymase controversy made the trend visible and gave it a dramatic unity. The debate influenced those who had already begun to change. It was so effective because things had begun to change and because it coincided with the direction of that trend. (shrink)

The article discusses two bioart projects that bring the symbolically core human substances of blood, sweat and tears into technologically mediated relationships with plants and fungi to explore human kinship with other species: Tarah Rhoda’s BS&T (short for ‘blood, sweat and tears’) and OurGlass, and Saša Spačal’s MycoMythologies: Patterning. The article analyses the art projects through the lens of the molecular gaze and different perspectives on kinning, bringing anthropological conceptualizations of kinship together with Haraway’s pathways to connect with other (...) species. How can bioart use technologies to explore interspecies kinship through a molecular gaze? And may such artworks contribute to the toning down of human exceptionality in the face of a precarious future? We find that artworks providing a molecular gaze on interspecies biological processes may risk a decontextualized approach to complex relational processes but may also create new visions of filiation even with biological organisms imagined to be genetically distant from humans, thus spurring awareness of the fragile interrelationships among species. (shrink)

A central goal of philosophy of perception is to uncover the nature of sensory capacities. Ideally, we would like an account that specifies what conditions need to be met in order for an organism to count as having the capacity to sense or perceive its environment. And on the assumption that sensory states are the kinds of things that can be accurate or inaccurate, a further goal of philosophy of perception is to identify the accuracy conditions for sensory states. In (...) this paper I recommend a novel approach to these core issues, one that draws heavily on game-theoretic treatments of signaling in nature. A benefit of the approach is that it helps us to understand why biologists attribute sensory powers to such a diverse range of organisms, including plants, fungi, and algae. (shrink)

We hypothesize that aspects of animal multicellularity originated before the divergence of metazoans from fungi and social amoebae. Polarized epithelial tissues are a defining feature of metazoans and contribute to the diversity of animal body plans. The recent finding of a polarized epithelium in the non‐metazoan social amoeba Dictyostelium discoideum demonstrates that epithelial tissue is not a unique feature of metazoans, and challenges the traditional paradigm that multicellularity evolved independently in social amoebae and metazoans. An alternative view, presented here, (...) is that the common ancestor of social amoebae, fungi, and animals spent a portion of its life cycle in a multicellular state and possessed molecular machinery necessary for forming an epithelial tissue. Some descendants of this ancestor retained multicellularity, while others reverted to unicellularity. This hypothesis makes testable predictions regarding tissue organization in close relatives of metazoans and provides a novel conceptual framework for studies of early animal evolution.Editor's suggested further reading in BioEssays Searching for Eve: Basal metazoans and the evolution of multicellular complexity Abstract. (shrink)

Museums might seem to be the enemy of metabolism: mausoleums that preserve collections and their knowledge-producing potential, out of time. We argue that museums are in fact intensely metabolic: in their attempts to manipulate the life course and temporalities of objects they proliferate metabolic processes, limits, and potentials. We suggest that looking at the museum in this way can help articulate pressing practical as well as theoretical issues: storage rooms are “constipated,” as traditional practices of disposal cannot keep pace with (...) rapidly growing collections from an over-productive present. The paper consists of three main sections. First, we follow imaginations of the museum as preserver, contrasting these with more recent descriptions of the museum as metabolism, and highlighting the intimate relationship between the two. We describe the material and metaphorical ways in which objects and their meanings are transformed within a “museum metabolism,” and suggest that cultivating such transformations might help to imagine new approaches to problems of proliferation and disposal. This leads us to The Living Room, a workshop and installation at Medical Museion in Copenhagen, where we encourage fringe objects destined for disposal to metabolize, entangled with living heritage eaters such as fungi and worms. Following Ian Bogost, this is a piece of “metabolic carpentry”; a thinking machine that explores ontology by practicing it. In the third main section, we reflect on this approach, and on how materially producing metabolic paradoxes might open new avenues for thinking about their concrete consequences, within an ethos of hospitality. We conclude by arguing for the creative potential of metabolism to link objects, organisms, and environments, emphasizing exchanges between transformation and stability at co-constituting interfaces. (shrink)

All species continuously evolve to adapt to changing environments. The genetic variation that fosters such adaptation is caused by a plethora of mechanisms, including meiotic recombination that generates novel allelic combinations in the progeny of two parental lineages. However, a considerable number of eukaryotic species, including many fungi, do not have an apparent sexual cycle and are consequently thought to be limited in their evolutionary potential. As such organisms are expected to have reduced capability to eliminate deleterious mutations, they (...) are often considered as evolutionary dead ends. However, inspired by recent reports we argue that such organisms can be as persistent as organisms with conventional sexual cycles through the use of other mechanisms, such as genomic rearrangements, to foster adaptation. (shrink)

Overview The evolution of multicellularity raises questions regarding genomic and developmental commonalities and discordances, selective advantages and disadvantages, physical determinants of development, and the origins of morphological novelties. It also represents a change in the definition of individuality, because a new organism emerges from interactions among single cells. This volume considers these and other questions, with contributions that explore the origins and consequences of the evolution of multicellularity, addressing a range of topics, organisms, and experimental protocols. Each section focuses on (...) selected topics or particular lineages that present a significant insight or challenge. The contributors consider the fossil record of the paleontological circumstances in which animal multicellularity evolved; cooptation, recurrent patterns, modularity, and plausible pathways for multicellular evolution in plants; theoretical approaches to the amoebozoa and fungi (cellular slime molds having long provided a robust model system for exploring the evolution of multicellularity), plants, and animals; genomic toolkits of metazoan multicellularity; and philosophical aspects of the meaning of individuality in light of multicellular evolution. Contributors Maja Adamska, Argyris Arnellos, Juan A. Arias, Eugenio Azpeitia, Mariana Benítez, Adriano Bonforti, John Tyler Bonner, Peter L. Conlin, A. Keith Dunker, Salva Duran-Nebreda, Ana E. Escalante, Valeria Hernández-Hernández, Kunihiko Kaneko, Andrew H. Knoll, Stephan G. König, Daniel J. G. Lahr, Ottoline Leyser, Alan C. Love, Raul Montañez, Emilio Mora van Cauwelaert, Alvaro Moreno, Vidyanand Nanjundiah, Aurora M. Nedelcu, Stuart A. Newman, Karl J. Niklas, William C. Ratcliff, Iñaki Ruiz-Trillo, Ricard Solé . (shrink)

Human microbiome research has revealed that legions of bacteria, viruses, and fungi live on our skin and within the cavities of our bodies. New knowledge from these recent studies shows that humans are superorganisms and that the microbiome is indispensible to our lives and our health. This volume explores some of the science on the human microbiome and considers the ethical, legal, and social concerns that are raised by this research.

The most interesting biological molecules are long polymers. In analogy with human alphabetic languages, they can be called texts and analysed, as to the primary structure, as sequences of letters or of words . It is considered that the study of words, in a linguistic approach, may contribute positively to the understanding of molecular interactions . The molecular and human languages and dialects are contrasted. The molecular one is peculiarly distinct from the human, for instance, by its use of a (...) tridimensional morphology, temporal dynamics, absence of spacings and punctuation, and overlapping messages. A mathematical method is presented, for discovering words in texts. The word AAA was studied in the evolution of the 5S ribosomal RNA. It was shown that this word is more frequent in less complex organisms and less frequent in the more complex ones, in the fungi, plants, and vertebrates lineages. In the two latter ones, the degree of genie variability was also reduced. To the contrary, a moderate degree of usage of this word persisted in the whole invertebrates lineage, where a high degree of genie variability was maintained. In mitochondria, plastids and mycoplasmas, the frequency of the word AAA was increased, consistently with their need for interactions with a wider range of variation. These behaviors indicate that the monotonous AAA word allows for ambiguity in interactions. With the evolution of organic complexity and of greater molecular specificity, ambiguous words were progressively avoided.As moléculas biológicas mais interessantes são longos polímeros. Em analogia com a linguagem humana alfabética, estes podem ser chamados de textos, e analisados, quanto à estrutura primária, como sequência de letras ou de palavras . Considera-se que o estudo das palavras, em abordagem de tipo lingüístico, possa contribuir para o entendimento das interações moleculares. As linguagens e dialetos, moleculares e humanos, são contrastados. A linguagem molecular se distingue peculiarmente da humana, por exemplo, por utilizar forma tridimensional, dinâmica temporal, ausência de espaçamento e pontuação, e sobreposição de significados. Apresenta-se um método matemático para descoberta, de palavras em textos. A palavra AAA foi estudada na evolução do RNA ribossômico 5S. Observou-se que esta palavra é mais freqüente em organismos menos complexos e menos freqüente nos mais complexos, das linhagens de fungos, plantas e vertebrados. Nas duas últimas, reduziu-se também o grau de variabilidade gênica. Pelo contrário, grau moderado de freqüência da palavra persistiu em toda a linhagem dos invertebrados, com manutenção paralela de alto nível de variabilidade gênica. Nas mitocôndrias, plastídeos e micoplasmas, a freqüência da palavra AAA foi aumentada, de acordo com sua necessidade de interações com maior amplitude de variação. Esses comportamentos indicam que a palavra monótona AAA permite ambigüidade de interações. Com a evolução da complexidade orgânica e da maior especificidade molecular, as palavras ambíguas foram progressivamente evitadas. (shrink)

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not (...) be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. ‘Grey nomenclatures’ are defined as those that employ names that are either intentionally or accidentally non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, ‘grey names’ also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community’s nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content. (shrink)

In The Mushroom at the End of the World: On the Possibility of Life in Capitalist Ruins, Anna Lowenhaupt Tsing explains how bare land is formed. Capitalism produces ‘ruins’ by stripping living beings of the capacity to form their own ecological relations, a necessary condition for the reproduction of life. Contemporary capitalism alienates living beings from ecological relations, i.e. capitalism generates “the ability to stand alone, as if the entanglements of living did not matter. Through alienation, people and things become (...) mobile assets; they can be removed from their lifeworlds in distance-defying transport to be exchanged with other assets from other life worlds, elsewhere” (Tsing 2021, 5). Cutting the threads of the web of life through capitalist alienation, however, produces bare land as a side effect, infertile waste deprived of the means to reproduce itself without capitalist support. Alienation is the deracination of living beings from their lifeworld, transforming them into passive cogs for capitalist accumulation. However, Tsing upholds matsutake mushrooms, rare fungi popular among Japa- nese foodies, as exemplars of the resilience of ecological relations. Even amidst ruins, matsutakes successfully form beneficial relations with other living beings, like pine trees, other fungi and human beings. The insistent capacity to regenerate ecological relations is the ineluctable means of reproduction for the matsutake mushroom. Even at the end of the world, the matsutake persists by perpetually co-producing new lifeworlds for itself and fellow living beings (see also Haraway 2016). I claim that Tsing’s approach to capitalist alienation is descriptively convinc- ing but lacks the affective force for ecological class consciousness. Tsing surveys the web of life from the perspective of living beings quite distant from humankind, articulating a theoretical diagnosis rather than a political exhortation. On an affective level, it is challenging to generate ecological class consciousness among the (presumably) human readers of my chapter if they are presented with only the biographies of mushrooms growing far beyond my home. As Chantal Mouffe (2018, 72) argues, the construction of an emphatically political identity requires an appeal to the affects, like hope, indignation or compassion. Latour and Schultz also stress that ecological politics currently suffers from an affective misalignment, with people failing to identify with the fate of their increasingly inhospitable environments (2022, 47). Why would European humans care about these unknown fungi? The reproduction of our CO2-intensive livelihoods largely depends on the emission of bare land elsewhere, so in the short run, we stand to benefit more from putting our heads in the sand. I employ Chakrabarty’s (2021) suggestion of grounding post-humanist politics first in strategic anthropocentrism to subsequently push for a post-humanist expansion of our human understanding. One must first feel personally interpellated by the crisis of the global means of reproduction before one can grasp the need for an ecological class politics beyond human confines. I turn to John Steinbeck’s 1939 novel The Grapes of Wrath as a kindred spirit with more mobilising potential. Steinbeck tells the story of a family of impoverished farmers from Oklahoma, the Joads, travelling to California in pursuit of a better life, yet only encountering more poverty, exploitation and anti-immigrant racism. Steinbeck describes in detail the environmental and social devastation, but he focuses on the commodified labour power of migrant farmers rather than commodified mushrooms. Steinbeck’s main characters are also uprooted from their entangled histories in the land and community of rural Oklahoma, but they present a more familiar face of the ecological class deprived of the means of reproduction. Steinbeck’s outcry against alienation-as-deracination is clear, but the shift in perspective facilitates the empathetic outrage required for building ecological class consciousness. Steinbeck’s strategic anthropocentrism helps human readers understand why alienation-as-deracination is a concern. (shrink)

The human microbiome is the bacteria, viruses, and fungi that cover our skin, line our intestines, and flourish in our body cavities. Work on the human microbiome is new, but it is quickly becoming a leading area of biomedical research. What scientists are learning about humans and our microbiomes could change medical practice by introducing new treatment modalities. This new knowledge redefines us as superorganisms comprised of the human body and the collection of microbes that inhabit it and reveals (...) how much we are a part of our environment. The understanding that microbes are not only beneficial but sometimes necessary for survival recasts our interaction with microbes from adversarial to neighborly. This volume explores some of the science that makes human microbiome research possible. It then considers ethical, legal, and social concerns raised by microbiome research. Chapters explore issues related to personal identity, property rights, and privacy. The authors reflect on how human microbiome research challenges reigning views on public health and research ethics. They also address the need for thoughtful policies and procedures to guide the use of the biobanked human samples required for advancing this new domain of research. In the course of these explorations, they introduce examples from the history of biomedical science and recent legal cases that shed light on the issues and inform the policy recommendations they offer at the end of each topic's discussion.This volume is the product of an NIH Human Microbiome Project grant. It represents three years of conversations focused on consensus formation by the twenty-seven members of the interdisciplinary Microbiome Working Group. (shrink)

Ethylene (C2H4) is a gaseous plant hormone produced by higher and lower (green) plants and, when grown on appropriate substrates, also by fungi, yeasts and bacteria. Ethylene is involved in many developmental processes in plants and is biologically active in trace amounts (10 – 100 nl/I of air) that may be present in the outside air due to industrial air pollution(1). Fruit ripening and flower senescence especially, in a variety of commercially important crops, are dramatically stimulated by ethylene. Following (...) characterization of the genes coding for the key enzymes in ethylene biosynthesis, i.e. ACC synthase and ACC oxidase, it has become clear that their expression is regulated in a complex manner involving developmental, hormonal and tissue‐specific factors. This was recently very elegantly demonstrated for the expression of ACC oxidase genes in developing petunia flowers by Tang et al.(2). The spatial and temporal expression patterns, especially in the reproductive organs, suggest a hitherto unknown role for ethylene in reproductive processes such as the self‐incompatible response and the secretion of cellular exudate by the stigma and nectary. (shrink)

In all domains of life, transmembrane proteins from the ATP‐binding cassette (ABC) transporter family drive the translocation of diverse substances across lipid bilayers. In pathogenic fungi, the ABC transporters of the pleiotropic drug resistance (PDR) subfamily confer antibiotic resistance and so are of interest as therapeutic targets. They also drive the quest for understanding how ABC transporters can generally accommodate such a wide range of substrates. The Pdr5 transporter from baker's yeast is representative of the PDR group and, ever (...) since its discovery more than 30 years ago, has been the subject of extensive functional analyses. A new perspective of these studies has been recently provided in the framework of the first electron cryo‐microscopy structures of Pdr5, as well as emergent applications of machine learning in the field. Taken together, the old and the new developments have been used to propose a mechanism for the transport process in PDR proteins. This mechanism involves a “flippase” step that moves the substrates from one leaflet of the bilayer to the other, as a central element of cellular efflux. (shrink)

The Western world is experiencing a resurgence of interest in the therapeutic potential of psychedelics, most of which are derived from plants or fungi with a history of Indigenous ceremonial use. Recent research has revealed that psychedelic compounds have the potential to address treatment‐resistant depression and anxiety, as well as post‐traumatic stress disorder and addictions. These findings have contributed to the decriminalization of psychedelics in some jurisdictions and their legalization in others. Despite psychedelics’ opaque legal status, numerous companies and (...) individuals are profiting from speculative investments with few, if any, benefits accruing to Indigenous Peoples. In this paper, we suggest that the aptly named “psychedelic renaissance,” like the European Renaissance, is made possible by colonial extractivism. We further suggest that Indigenous philosophical traditions offer alternative approaches to reorient the “psychedelic renaissance” towards a more equitable future for Indigenous Peoples, psychedelic medicines, and all our relations. (shrink)

While seeking novel food sources to feed the increasing population of the globe, several alternatives have been discussed, including algae, fungi or in vitro meat. The increasingly propagated usage of farmed insects for human nutrition raises issues regarding food safety, consumer information and animal protection. In line with law, insects like any other animals must not be reared or manipulated in a way that inflicts unnecessary pain, distress or harm on them. Currently, there is a great need for research (...) in the area of insect welfare, especially regarding species-specific needs, health, farming systems and humane methods of killing. Recent results from neurophysiological, neuroanatomical and behavioral sciences prompt caution when denying consciousness and therefore the likelihood of presence of pain and suffering or something closely related to it to insects. From an animal protection point of view, these issues should be satisfyingly solved before propagating and establishing intensive husbandry systems for insects as a new type of mini-livestock factory farming. (shrink)

Spatial and diagrammatic reasoning is a significant part not only of logical abilities, but also of logical studies. The authors of this paper consider some novel trends in studying this type of reasoning. They show that there are the following two main trends in spatial logic: (i) logical studies of the distribution of various objects in space (logic of geometry, logic of colors, etc.); (ii) logical studies of the space algorithms applied by nature itself (logic of swarms, logic of (...) class='Hi'>fungi colonies, etc.). (shrink)

In the last few years, the idea of human being has been enlarged from the individual closeness to morphogenetic openness. Concurrently with discovers and researches into invisible worlds that live with human beings – microbes, fungi, bacteria, etc. – a debate has opened up that agrees with recent positions in the field of ontology. The human being is capable of poietic openness and is defined by relations. Anyway, an absence of a rigorous conceptualisation of the individualising process remains latent (...) to the discourse. A classic principle of individualisation is probably incomplete. This paper brings into dialogue individualisation with singularisation through the manifestation process of expression in accordance with recent theoretical enactments of hybridisation processes. (shrink)