There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe‐derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential (...) of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno‐suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution‐driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments. (shrink)

The initial relationships between organisms leading to endosymbiosis and the first eukaryote are currently a topic of hot debate. Here, I present a theory that offers a gradual scenario in which the origins of phagocytosis and mitochondria are intertwined in such a way that the evolution of one would not be possible without the other. In this scenario, the premitochondrial bacterial symbiont became initially associated with a protophagocytic host on the basis of cooperation to kill prey with symbiont‐produced (...) toxins and reactive oxygen species (ROS). Subsequently, the cooperation was focused on the digestion stage, through the acidification of the protophagocytic cavities via exportation of protons produced by the aerobic respiration of the symbiont. The host gained an improved phagocytic capacity and the symbiont received organic compounds from prey. As the host gradually lost its membrane energetics to develop lysosomal digestion, respiration was centralized in the premitochondrial symbiont for energy production for the consortium. (shrink)

Coral bleaching has attracted considerable study, yet one central question remains unanswered: given that corals and their Symbiodinium symbionts have co‐evolved for millions of years, why does this clearly maladaptive process occur? Bleaching may result from evolutionary conflict between the host corals and their symbionts. Selection at the level of the individual symbiont favors using the products of photosynthesis for selfish replication, while selection at the higher level favors using these products for growth of the entire host/symbiont community. (...) To hold the selfish lower‐level units in check, mechanisms of conflict mediation must evolve. Fundamental features of photosynthesis have been co‐opted into conflict mediation so that symbionts that fail to export these products produce high levels of reactive oxygen species and undergo programmed cell death. These mechanisms function very well under most environmental conditions, but under conditions particularly detrimental to photosynthesis, it is these mechanisms of conflict mediation that trigger bleaching. (shrink)

Lynn Margulis’s writing about symbiosis has profoundly influenced contemporary evolutionary theory, as well as continental and analytic philosophy of science, the materialist turn, and new materialism. Nonetheless, her work, and all symbiosis or evolution, is founded on a paradox: symbiosis fictionalizes customary accounts of the origin and evolution of species, yet it is impossible to speak of symbiosis (cross-species association) unless species-boundaries have been posited in advance. Thus, a tension is legible throughout Margulis’s work between the drive to surpass the (...) limits of species-definitions as they have been traditionally understood, and a need to maintain them in order that there can be “symbiosis” at all. Margulis criticized neo-Darwinian accounts of evolution in part because she saw symbiogenesis as debunking the theory that life was defined by individualistic competition. More recently, Myra Hird has suggested that the gift, such as it has been theorized by certain anthropologists and philosophers, could adequately figure symbiosis and the ethical relations founded on it. I turn to Derrida’s writing on the gift to suggest that, if a gift worthy of the name chances to happen, it necessarily exceeds scientific, theoretical, and philosophical knowledge. (shrink)

Linear chromosomes shorten in every round of replication. In Drosophila, telomere‐specialized long interspersed retrotransposable elements (LINEs) belonging to the jockey clade offset this shortening by forming head‐to‐tail arrays at Drosophila telomere ends. As such, these telomeric LINEs have been considered adaptive symbionts of the genome, protecting it from premature decay, particularly as Drosophila lacks a conventional telomerase holoenzyme. However, as reviewed here, recent work reveals a high degree of variation and turnover in the telomere‐specialized LINE lineages across Drosophila. There appears (...) to be no absolute requirement for LINE activity to maintain telomeres in flies, hence the suggestion that the telomere‐specialized LINEs may instead be neutral or in conflict with the host, rather than adaptive. (shrink)

One of the current problems in microbiology concerns the understanding of fitness in host-symbiont systems. A great deal of research and conceptual work has analysed how the host benefits from such associations; however, very little of this work has attempted to take the microbial perspective. Nevertheless, some scientists have argued that we should conduct more comparative studies of both microorganisms that interact with a host and their free-living counterparts in order to determine whether or not symbiosis is beneficial for (...) these microorganisms. In this paper, by means of analysing heritable symbiosis as a case study, I intend to provide a different perspective on this subject. Mainly, I argue that asking how the fitness of a given microorganism was changed during the evolution of heritable symbiosis may be theoretically unjustified at both the early and late stages of this process. The reason for this, I argue, is that, during the evolution of heritable symbiosis, the fitness of a microorganism becomes incommensurable with that of its free-living counterparts because their contexts become radically different; therefore, comparing their fitness makes little sense. My analysis is driven by the use of the ecological concept of fitness; accordingly, my conclusions are bound to this specific interpretation of fitness. (shrink)

Facultative bacterial endosymbionts can transfer horizontally among lineages of their arthropod hosts, providing the recipient with a suite of traits that can lead to rapid evolutionary response, as has been recently demonstrated. But how common is symbiont‐driven evolution? Evidence suggests that successful symbiont transfers are most likely within a species or among closely related species, although more distant transfers have occurred over evolutionary history. Symbiont‐driven evolution need not be a function of a recent horizontal transfer, however. Many (...) endosymbionts infect only a small proportion of a host population, but could quickly increase in frequency under favorable selection regimes. Some host species appear to accumulate a diversity of facultative endosymbionts, and it is among these species that symbiont‐driven evolution should be most prevalent. It remains to be determined how frequently symbionts enable rapid evolutionary response by their hosts, but substantial ecological effects are a likely consequence whenever it does occur. (shrink)

The coevolution of humans with their intestinal microflora has resulted in cooperative relationships that have shaped the biology and the genomes of these symbiotic partners. Bacteroides thetaiotaomicron is one such bacterial symbiont that is a dominant member of the intestinal microbiota of humans and other mammals. The recent report of the genome sequence of B. thetaiotaomicron1 is the first reported for an abundant Gram‐negative organism of the human colonic microbiota and, as such, provides the first glimpse on a genomic (...) scale of the genetic arsenal used by a Gram‐negative symbiont to dominate in this ecosystem. The genome has revealed large expansions of many paralogous groups of genes that encode products essential to the organism's ability to successfully compete in this environment. Most noteable is the organism's abundant machinery for utilizing a large variety of complex polysaccharides as a source of carbon and energy. The proteome also reveals the organism's extensive ability to adapt and regulate expression of its genes in response to the changing ecosystem. These factors, as well as others highlighted below, suggest an incredibly flexible and adaptable organism that is exquisitely equipped to dominate in its challenging and competitive niche. BioEssays 25:926–929, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

While examples of bacteria benefiting eukaryotes are increasingly documented, studies examining effects of eukaryote hosts on microbial fitness are rare. Beneficial bacteria are often called “mutualistic” even if mutual reciprocity of benefits has not been demonstrated and despite the plausibility of other explanations for these microbes' beneficial effects on host fitness. Furthermore, beneficial bacteria often occur in diverse communities, making mutualism both empirically and conceptually difficult to demonstrate. We suggest reserving the terms “mutualism” and “parasitism” for pairwise interactions where the (...) relationship is largely independent of other species and can be verified by measuring the fitness effect experienced by both partners. In hosts with diverse microbial communities, we propose re‐formulating some of the essential questions of symbiosis research – e.g. concerning specificity, transmission mode, and common evolutionary fates – as questions of community ecology and ecosystem function, allowing important biological interactions to be investigated without making assumptions about reciprocity. Understanding the fitness of host‐associated bacteria is a crucial component of investigations into the role of microbes in eukaryote evolution. (shrink)

Is it possible to explain and predict the development of living things? What is development? Articulate answers to these seemingly innocuous questions are far from straightforward. To date, no systematic, targeted effort has been made to construct a unifying theory of development. This novel work offers a unique exploration of the foundations of ontogeny by asking how the development of living things should be understood. It explores the key concepts of developmental biology, asks whether general principles of development can be (...) discovered, and examines the role of models and theories.The two editors have assembled a team of leading contributors who are representative of the scientific and philosophical community within which a diversity of thoughts are growing, and out of which a theory of development may eventually emerge. They analyse a wealth of approaches to concepts, models and theories of development, such as gene regulatory networks, accounts based on systems biology and on physics of soft matter, the different articulations of evolution and development, symbiont-induced development, as well as the widely discussed concepts of positional information and morphogenetic field, the idea of a. (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)

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...) allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths’ arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats, I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...) species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

As free‐living organisms, alpha‐proteobacteria produce reactive oxygen species (ROS) that diffuse into the surroundings; once constrained inside the archaeal ancestor of eukaryotes, however, ROS production presented evolutionary pressures – especially because the alpha‐proteobacterial symbiont made more ROS, from a variety of substrates. I previously proposed that ratios of electrons coming from FADH2 and NADH (F/N ratios) correlate with ROS production levels during respiration, glucose breakdown having a much lower F/N ratio than longer fatty acid (FA) breakdown. Evidently, higher endogenous (...) ROS formation did not hinder eukaryotic evolution, so how were its disadvantages mitigated? I propose that the resulting selection pressures favoured the evolution of a variety of eukaryotic ‘innovations’: peroxisomes for FA breakdown, carnitine shuttles, the linkage of beta‐oxidation to antioxidant properties, uncoupling proteins (UCPs) and using mitochondrial uncoupling during beta‐oxidation to reduce ROS. Recently observed relationships between peroxisomes and mitochondria further support the model. (shrink)

Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, (...) vertical symbiont transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host. (shrink)

Holobionts are multicellular eukaryotes with multiple species of persistent symbionts. They are not individuals in the genetic sense— composed of and regulated by the same genome—but they are anatomical, physiological, developmental, immunological, and evolutionary units, evolved from a shared relationship between different species. We argue that many of the interactions between human and microbiota symbionts and the reproductive process of a new holobiont are best understood as instances of reciprocal scaffolding of developmental processes and mutual construction of developmental, ecological, and (...) evolutionary niches. Our examples show that mother, fetus, and different symbiotic microbial communities induce or constitute conditions for the development and reproduction of one another. These include the direct induction of maternal or fetus physiological changes, the restructuring of ecological relations between communities, and evolutionary selection against undesirable competitors. The mutual scaffolding and niche constructing processes start early—prior to amniotic rupture. We are evolutionarily, physiologically, and developmentally integrated holobiont systems, strung together through mutual reliance and mutual construction. Bringing the processes of niche construction and developmental scaffolding together to interpret holobiont birth conceptually scaffolds two new directions for research: in niche construction, identifying the evolutionary implications of organisms actively constructing multiple overlapping niches and scaffolds, and in Evolutionary Developmental Biology, characterizing evolutionary and ecological processes as developmental causes. (shrink)

Today’s bodies are akin to ‘walking sensor platforms’. Bodies either host, or are the subjects of, an array of sensing devices that act to convert bodily movements, actions and dynamics into circulative data. This article proposes the notions of ‘disembodied exhaust’ and ‘embodied exhaustion’ to conceptualise processes of bodily sensorisation and datafication. As the material body interfaces with networked sensor technologies and sensing infrastructures, it emits disembodied exhaust: gaseous flows of personal information that establish a representational data-proxy. It is this (...) networked actant that progressively structures how embodied subjects experience their daily lives. The significance of this symbiont medium in determining the outcome of interplays between networked individuals and audiences necessitates that it is carefully contrived. The article explores the nature and function of the data-proxy, and its impact on social relations. Drawing on examples that depict individuals engaging with their data-proxies, the article suggests that managing a virtual presence is analogous to a work relation, demanding diligence and investment. But it also shows how the data-proxy operates as a mode of affect that challenges conventional distinctions made between organic and inorganic bodies, agency and actancy, mortality and immortality, presence and absence. (shrink)

A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron‐rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution (...) are consistent with a general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification. (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)

Recent discoveries in life sciences evidenced that changes in the composition of the microbiome and epigenetics represent two essential mechanisms at the basis of the biological evolution, since both allow a rapid change of the phenotype in response to both environmental and internal stimuli. Surprisingly, in the age of genomics we are discovering that each organism (and its evolution) cannot be explained by genes alone. The microbiome and the epigenetic machinery are frequently described as completely separate mechanisms, but actually symbionts (...) may act as epigenetic sources of heritable variation so that genomes, epigenomes and microbiomes are not independent traits, but a tripartite driver of the biological evolution of all organisms. (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)

This paper explores the connections between inheritance systems, evolvability and modularity. I argue that the transmission of symbiotic micro-organisms is an inheritance system, and one that is evolutionarily significant because symbionts generate biologically crucial aspects of their hosts’ organisation through modular developmental pathways. More specifically, I develop and defend five theses.

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)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

In their paper “How Causal are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers,” Lynch, Parke, and O’Malley successfully argue that certain causal attributions made to the microbiome have not satisfied Koch’s postulates nor the interventionist framework. However, their argument involves an implicit assumption that cases such as H. pylori are sufficiently similar to cases involving the microbiome, such that causal attributions to both should be evaluated according to the same causal framework. Our commentary targets this assumption. First, (...) we introduce the historical circumstances that led to the formulation of Koch’s postulates in order to differentiate the case of the microbiome from that of infectious bacteria. Then, we introduce the concept of the holobiont, the idea that hosts and their symbionts should be conceptualized as a metaphysical and biological unit. Finally, using the holobiont concept, we argue that Koch’s postulates and the interventionist framework are ill-equipped to handle the microbiome. We conclude by suggesting that a revision of what counts as microbiological causality within the holobiont is justified. (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)

The book integrates humans’ biological lives as animals with acculturation and interaction within diverse social worlds. Recent work in evolutionary biology, the social theory of practices, and cognition as embodied and enactive shows how aspects of human life often treated as social or cognitive are integrated “naturecultural” phenomena. Human evolution enables people’s varied biological development in practice-differentiated environments sustained by ongoing niche reconstruction. These naturecultural aspects of human life include language and other expressive repertoires; cultivated bodily skills; differentiated practical and (...) cultural domains and their associated settings and equipmental complexes; critical assessment of lives and practices; and power and resistance. This interdependent, practice-differentiated way of life explains how humans are accountable and responsive to diverse normative concerns. Our moral, social, practical, skillful, epistemic, conceptual, aesthetic, and other normative concerns are evolved, “two-dimensional” transformations of other animals’ one-dimensional biological success or failure in sustaining their lineages. These diverse normative concerns are not already-determinate norms, however. They indicate what is at issue and at stake in the ongoing development of various practices and their mutual interdependence, including how people express and reason about those issues discursively. Social power is thereby also a normative phenomenon, expressing how causal capacities and actions reconfigure the normative significance of other people’s situations. The book primarily addresses the biological significance of people’s situated involvement with one another. It nevertheless also highlights the social-ecological interdependence of people’s practice-differentiated ways of life with many non-human companion species, from microbial symbionts and pathogens to domesticated or commensal plants and animals. (shrink)

The most enigmatic feature of polytene chromosomes is their banding pattern, the genetic organization of which has been a very attractive puzzle for many years. Recent genome‐wide protein mapping efforts have produced a wealth of data for the chromosome proteins of Drosophila cells. Based on their specific protein composition, the chromosomes comprise two types of bands, as well as interbands. These differ in terms of time of replication and specific types of proteins. The interbands are characterized by their association with (...) “active” chromatin proteins, nucleosome remodeling, and origin recognition complexes, and so they have three functions: acting as binding sites for RNA pol II, initiation of replication and nucleosome remodeling of short fragments of DNA. The borders and organization of the same band and interband regions are largely identical, irrespective of the cell type studied. This demonstrates that the banding pattern is a universal principle of the organization of interphase polytene and non‐polytene chromosomes.Editor's suggested further reading in BioEssaysCaught in the act: Rapid, symbiont‐driven evolution AbstractFunction and evolution of sex determination mechanisms, genes and pathways in insects Abstract. (shrink)

Developmental biology is a theory of interpretation. Developmental signals are interpreted differently depending on the previous history of the responding cell. Thus, there is a context for the reception of a signal. While this conclusion is obvious during metamorphosis, when a single hormone instructs some cells to proliferate, some cells to differentiate, and other cells to die, it is commonplace during normal development. Paracrine factors such as BMP4 can induce apoptosis, proliferation, or differentiation depending upon the history of the responding (...) cells. In addition, organisms have evolved to alter their development in response to differences in temperature, diet, the presence of predators, or the presence of competitors. This allows them to develop the phenotype, within the limits imposed by the genotype, best suited for the immediate habitat of the organism. Most developing organisms have also evolved to expect developmental signals from symbionts, and these organisms develop abnormally if the symbiont signals are not present. Thus Hoffmeyer’s “vertical semiotic system” of genetic communication and “horizontal semiotic system” of ecological communication are integrated during development. (shrink)

Robustness is a fundamental property of biological systems, observed ubiquitously across species and at different levels of organization from gene regulation to ecosystem. The theory of biological robustness argues that robustness fosters evolv-ability and that together they entail various tradeoffs as well as characteristic architectures and mechanisms. We argue that classes of biological systems have evolved to enhance their robustness by extending their system boundary through a series of symbioses with foreign biological entities . A series of major biological innovations (...) has been achieved by events consistent with this framework: horizontal gene transfer, serial endosymbiosis, oocytes-mediated vertical infection, and host-symbiont mutualism for bacterial flora. Self-extending symbiosis contributes to robustness because symbiotic foreign biological entities can enhance the adaptative capacity of the system against environmental perturbations as well as contribute novel functions. In addition, evolutionary history indicates that the degree of symbiosis achieved has substantially changed from tight integration into the genome to loose integration as bacterial flora . The most dramatic example can be seen in the symbiosis of host immune system and bacterial flora in which substantial function of host defense depends on the proper maintenance of bacterial flora and its adaptive capability. Biological systems following this type of evolutionary path might have attained high levels of functionality, robustness, and evolvability. Thus, robustness, evolution, and self-extending symbiosis may form essential system principles for biology. (shrink)

The consideration of ‘mutual benefits’ and partner cooperation have long been the accepted standpoint from which to draw inference about the onset, maintenance and breakdown of the coral‐algae endosymbiosis. In this paper, I review recent research into the climate‐induced breakdown of this important symbiosis (namely ‘coral bleaching’) that challenges the validity of this long‐standing belief. Indeed, I introduce a more parsimonious explanation, in which the coral host exerts a ‘controlled parasitism’ over its algal symbionts that is akin to an enforced (...) domestication arrangement. Far from being pathogenic, a range of well‐established cellular processes are reviewed that support the role of the coral host as an active ‘farmer’ of the energy‐rich photoassimilates from its captive symbionts. Importantly, this new paradigm reposes the deleterious bleaching response in terms of an envelope of environmental conditions in which the exploitative and captive measures of the coral host are severely restricted. The ramification of this new paradigm for developing management strategies that may assist the evolution of bleaching resistance in corals is discussed. (shrink)

In order to explain several discrepancies between the gene-recombination phenomena in phages and in higher organisms, we assume that theT 2 phage, after entering the bacterium, divides in three parts corresponding to the three “chromosomes' whichHershey andRotman have traced in this phage. The three parts are supposed to be able to divide further by rupture or by the action of other “chromosome fragments”. Each fragment is supposed able to reproduce inside the bacterium as a more or less independent unit and (...) before lysis of the bacterium the various parts are assumed to reunite in complete sets of genes each forming a new phage.After discussing the experimental facts supporting these assumptions, we show that the assumptions are in perfect agreement with the theory of the symbiosis of genes, a theory which seems necessary in order to explain the ability of the “chromosome-fragments” to reunite into complete phages.Also the problems arising with respect to the sexual reproduction in bacteria is discussed under the point of view of the symbiosis theory. The assumption is made that the hereditary material is transduced from bacterium to bacterium by ultramicroscopic virus-like particles “genophores”. In several lysogenic bacteria the genophores are supposed still able to act as parasites instead of symbiontes towards some other sensitive bacteria. The experimental facts supporting this assumption are analyzed, and new experimental tests suggested. (shrink)

A renaissance of virus research is taking centre stage in biology. Empirical data from the last decade indicate the important roles of viruses, both in the evolution of all life and as symbionts of host organisms. There is increasing evidence that all cellular life is colonized by exogenous and/or endogenous viruses in a non-lytic but persistent lifestyle. Viruses and viral parts form the most numerous genetic matter on this planet.

When parasites have different interests in regard to how their host should behave this can result in a conflict over host manipulation, i.e. parasite induced changes in host behaviour that enhance parasite fitness. Such a conflict can result in the alteration, or even complete suppression, of one parasite's host manipulation. Many parasites, and probably also symbionts and commensals, have the ability to manipulate the behaviour of their host. Non‐manipulating parasites should also have an interest in host behaviour. Given the frequency (...) of multiple parasite infections in nature, potential conflicts of interest over host behaviour and manipulation may be common. This review summarizes the evidence on how parasites can alter other parasite's host manipulation. Host manipulation can have important ecological and medical consequences. I speculate on how a conflict over host manipulation could alter these consequences and potentially offer a new avenue of research to ameliorate harmful consequences of host manipulation. (shrink)

After a short review of the historical development of the problem of cytoplasmic inheritance, the principles for the proof of cytoplasmic inheritance were discussed. At present the proof can be based on the maternal transmission of plasmagenes, on the missing of mendelian segregation and on the possibility of a segregation during ontogenetic development. In the following the most important possibilities for errors and their refutation onEpilobium were discussed: elimination of genotypes , abnormal cytology , maternal aftereffects , predetermination , nuclear (...) produced plasmagenes and transmission of parasites or symbionts as virus . At the end the principles for the distinction between different cytoplasmic constituents were discussed. (shrink)

The intracellular symbiosis of leafhoppers is the first system in which the morphological description is extended to understand the principles of symbiosis on a molecular level. Host, symbionts and environment exist in mutual dependence with respect to pH, osmotic pressure, inorganic and organic substances. Symbionts function primarily as mediators between host and environment. They became integrated in the course of evolution, enabling the host to adapt to changing nutritional and other environmental conditions. Comparison with other symbiontic systems shows that this (...) seems to be a general principle.According to the endosymbiontic theory of eukaryotic cells, this is true also for mitochondria, chloroplasts, and possibly other cellular organelles. Thus, the intracellular organelles and the endosymbionts appear to represent functions of the same principle on a different level of integration. This can be interpreted as support for the endosymbiontic theory of eukaryotic cell. (shrink)

Memes are not best understood as semantic information stored in brains, but rather, as whatever is imitated or copied in culture. Whereas other theories treat culture as an adaptation, for memetics it is a parasite turned symbiont that evolves for its own sake. Memetics is essential for understanding today's information explosion and the future evolution of culture. (Published Online November 9 2006).

Insight into animal biology and development provided by classical genetic analysis of the model organism Drosophila melanogaster was an incentive to develop advanced genetic tools for this insect. But genetic systems for the over one million other known insect species are largely undeveloped. With increasing information about insect genomes resulting from next generation sequencing, RNA interference is now the method of choice for reverse genetics, although it is constrained by the means of delivery of interfering RNA. A recent advance to (...) ensure sustained delivery with minimal experimental intervention or trauma to the insect is to exploit commensal bacteria for symbiont‐mediated RNA interference. This technology not only offers an efficient means for RNA interference in insects in laboratory conditions, but also has potential for use in the control of human disease vectors, agricultural pests and pathogens of beneficial insects. (shrink)

Religion persists, even within enlightened secular society, because it has adaptive functions. In particular, Ralph Wendell Burhoe's theory holds that religion is the repository of cultural wisdom that most encourages mutual altruism among nonkin, long-term social survival, and human progress. This article suggests a variant of Burhoe's rationalized naturalistic view. Cognitive theism is a proposal that secularists sometimes take religion on its own terms by suspending disbelief about God. If we consider particular human capacities and limitations in memory, perception, personality, (...) and motivation, the regulated “mind expansion” of cognitive theism may help us to evaluate, coordinate, and invigorate things in a modern environment. In this environment, communicative and travel technologies have led to a high loading of consciousness with a historically unusual diverse range of experiences and responsibilities, a high rate of cultural change relative to biological evolution, and a tendency to factionalize. Burhoe's extension of the concept of symbiosis to the coevolution of culture and genes is modified here in recognition of individual differences and of individuals' potential for choosing strategies, recombining in groups, and learning. In human biocultural symbiont pools, cultural phenomena can evolve while changing partners in a dance with genetic substrates, a dance that broadly supports these substrates. In the context of diversity and incessant change in a large predominantly secular community, Judeo-Christian monotheism can have a valuable advisory unifying function. (shrink)

Our food and farming system is not socially, economically or ecologically sustainable. Many of the ills are a result of market competition driving specialization and linear production models, externalizing costs for environmental, social and cultural degradation. Some propose that market mechanisms should be used to correct this; improved consumer choice, internalization of costs and compensation to farmers for public goods. What we eat is determined by the path taken by our ancestors, by commercialization and fierce competition, fossil fuels and demographic (...) development. Based on those, governments and the food industry are the choice architects who determine what we eat; consumer choice plays a marginal role. Using market mechanisms to internalize cost and compensate farmers for public goods has been proposed for decades but little progress has been made. There are also many practical, ethical and theoretical objections to such a system. The market is not a good master for a sustainable food system. Instead we need to find new ways of managing the food system based on food as a right and farming as a management system of the planet Earth. The solutions should be based on relocalization of food production and de-commodification of food and our symbionts, the plants and animals we eat. (shrink)

I formulate in relational terms the ubiquitous biological interaction of symbiosis. I explicate the topology of the different modes of relational interactions of (M, R)-networks, the entailment diagrams that model the host and the symbiont. These modes all have biological realizations as various categories of symbiotic relationships, ranging from mutualism to parasitism to infection.

In this paper I challenge the notion that a healthy and resilient coral is (in all cases) a fast‐growing coral, and by inference, that a reef characterised by a fast trajectory toward high coral cover is necessarily a healthy and resilient reef. Instead, I explain how emerging evidence links fast skeletal extension rates with elevated coral‐algae (symbiotic) respiration rates, most‐often mediated by nutrient‐enlarged symbiont populations and/or rising sea temperatures. Elevated respiration rates can act to reduce the autotrophic capacity (photosynthesis:respiration (...) ratio) of the symbiosis. This restricts the capacity of the coral host to build and maintain sufficient energy reserves (e.g. lipids) needed to sustain essential homeostatic functions, including sexual reproduction and biophysical stress resistance. Moreover, it explains the somewhat paradoxical scenario, whereby at the ecological instant before the reef‐building capacity of the symbiosis is lost, a reef can look visually at its best and be accreting CaCO3 at its maximum. (shrink)

–Whether celebratory or critical, STS research on science-industry relations has focused on the blurring of boundaries and hybridization of codes and practices. However, the vocabulary of boundary and hybrid tends to reify science and industry as separate in the attempt to map their relation. Drawing on interviews with the head of a research center in plant biology, this article argues that biology and biotech are symbionts. In order to be viable and productive, symbiosis needs to be carefully managed and given (...) room for divergence within mutual dependence. This process does not take place as the negotiation of a preexisting science-industry boundary. Rather, viability is obtained through a strategy of circumventing the science-industry food chain and sequestering biotech components within the research center. Symbiosis allows academic scientists to do biology while at the same time demonstrating entrepreneurial spirit. (shrink)

Metaseiulus occidentalis is a representative of an important family of mites (Arthropoda: Chelicerata: Acari: Phytoseiidae) that are effective predators of pest mites in agricultural crops around the world. Like many arthropods, this mite contains multiple genomes, including the genomes of several microbial symbionts as well as its own mitochondrial and nuclear genomes. The mitochondrial genome is “mitey” large at 25 kb, due to duplication and triplication of genes. By contrast, the nuclear genome is “mitey” small at 88 Mb. This mite (...) has a parahaploid genetic system, tolerates inbreeding, and has a haploid chromosome number of 3. This predator was genetically improved for use in agriculture by developing strains that lacked the ability to overwinter in diapause or were resistant to multiple pesticides, and can be genetically modified using recombinant DNA methods. Sequencing the nuclear genome would provide useful insights that could enhance genetic improvement programs that would result in improved pest management, could provide genes needed to resolve the evolutionary relationships of this family, and could serve as a model for understanding the evolution and genetics of chelicerate arthropod predators. (shrink)

Resistance to the drugs used in the treatment of many infectious diseases is increasing, while microbial infections are being found to be responsible for more life‐threatening diseases than previously thought. Despite a large investment in the invention and application of high‐throughput screening techniques involving miniaturization and automation, and a diverse array of strategies for designing and constructing various chemical libraries, relatively few new drugs have resulted. Natural products, however, have been a major source of drugs for centuries. Since some of (...) them are produced by organisms as a result of selection in favour of improved defense against competing deleterious microorganisms, in principle they would be less likely to incur resistance. Furthermore, the production of those defensive secondary metabolites is inducible because their original function is a response to environmental challenges. Moreover, symbioses, co‐habitation associations between two or more different species of organisms, are universal in nature, and the production of secondary metabolites by symbiotic microbes may be an important adaptation allowing microbes to affect their hosts. Therefore, co‐culture strategies, using combinations of plant cell–pathogenic microbes, plant cell–endophytes (or symbionts), and symbiont–pathogenic microbes, based on the principles of chemical defense and the known mechanisms of organism interactions, may be an efficient general approach in the search for new anti‐microbial drugs. BioEssays 26:808–813, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

A correspondence allows application of Landau and Lifshitz’ formulation of Le Chatelier’s principle from statistical physics to a simple 2-D model of biological symbiosis. The insight: symbionts stabilize the occupation of narrow peaks on fitness landscape.

Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, we (...) discuss the host’s microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host–microbiome (collectively termed a “holobiont”) interactions in a given behavior, may underpin a potentially important cognitive bias – which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking – that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited. (shrink)

Some neurotropic enteroviruses hijack Trojan horse/raft commensal gut bacteria to render devastating biomimicking cryptic attacks on human/animal hosts. Such virus-microbe interactions manipulate hosts’ gut-brain axes with accompanying infection-cycle-optimizing central nervous system disturbances, including severe neurodevelopmental, neuromotor, and neuropsychiatric conditions. Co-opted bacteria thus indirectly influence host health, development, behavior, and mind as possible “fair-weather-friend” symbionts, switching from commensal to context-dependent pathogen-like strategies benefiting gut-bacteria fitness.

Este artigo investiga as diferentes concepções de “Sujeito” de acordo com o corpus teórico do filósofo Paul B. Preciado. As categorias analisadas são: os processos subjetivos e técnicos de sujeição social e servidão maquínica na era farmacopornográfica; o sujeito Playboy e petrosexorracial; a Multidão, seus múltiplos devires e as micropolíticas de resistência à opressão; a metamorfose dos sujeitos em agentes revolucionários e os simbiontes políticos, postulados por Preciado em seu mais recente livro publicado, Dysphoria mundi. Como Preciado articula todas estas (...) concepções, considerando ainda as linhas de fuga da submissão, isto é, o horizonte filosófico de resistência onto-epístemo-política, metamorfose e até a possível superação da dominação capitalística? Os procedimentos metodológicos foram baseados na pesquisa bibliográfica (livros, artigos e crônicas), de modo a evidenciar o contraste, as semelhanças, diferenças e interstícios entre a teoria de Preciado e as suas principais referências. Os resultados obtidos indicam uma linearidade consistente entre-categorias, os desafios em materializar as teorias revolucionárias na realidade cotidiana, bem como estratégias práticas que contribuem para a organização ontopolítica proposta por Preciado. (shrink)