Studies In History And Philosophy Of Biological And Biomedical Sciences[JOURNAL]
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200 papers
Viruses as living processes.
Dupré J, Guttinger S
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26994935 · Publisher ↗
The view that life is composed of distinct entities with well-defined boundaries has been undermined in recent years by the realisation of the near omnipresence of symbiosis. What had seemed to be intrinsically stable en...
The view that life is composed of distinct entities with well-defined boundaries has been undermined in recent years by the realisation of the near omnipresence of symbiosis. What had seemed to be intrinsically stable entities have turned out to be systems stabilised only by the interactions between a complex set of underlying processes (Dupré, 2012). This has not only presented severe problems for our traditional understanding of biological individuality but has also led some to claim that we need to switch to a process ontology to be able adequately to understand biological systems. A large group of biological entities, however, has been excluded from these discussions, namely viruses. Viruses are usually portrayed as stable and distinct individuals that do not fit the more integrated and collaborative picture of nature implied by symbiosis. In this paper we will contest this view. We will first discuss recent findings in virology that show that viruses can be 'nice' and collaborate with their hosts, meaning that they form part of integrated biological systems and processes. We further offer various reasons why viruses should be seen as processes rather than things, or substances. Based on these two claims we will argue that, far from serving as a counterexample to it, viruses actually enable a deeper understanding of the fundamentally interconnected and collaborative nature of nature. We conclude with some reflections on the debate as to whether viruses should be seen as living, and argue that there are good reasons for an affirmative answer to this question.
What is a virus species? Radical pluralism in viral taxonomy.
Morgan GJ
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26994934 · Publisher ↗
Early attempts in the 1960s at constructing a classification scheme for viruses were phenetic and focused on structural properties of the virion. Over time, the International Committee on the Taxonomy of Viruses (ICTV) h...
Early attempts in the 1960s at constructing a classification scheme for viruses were phenetic and focused on structural properties of the virion. Over time, the International Committee on the Taxonomy of Viruses (ICTV) has refined its definition of a virus species to include an appeal to evolutionary history. The current ICTV definition defines a viral species in terms of monophyly. The existence of prolific horizontal genetic transfer (HGT) among various groups of viruses presents a challenge to this definition. I argue that the proper response to this mode of evolution is to allow for radical pluralism. Some viruses can be members of more than one species; others don't form species at all and should be classified using new reticulate categories.
It is what it eats: Chemically defined media and the history of surrounds.
Landecker H
Stud Hist Philos Biol Biomed Sci · 2016 Jun · PMID 26992285 · Publisher ↗
The cultivation of living organs, cells, animals, and embryos in the laboratory has been central to the production of biological knowledge. Over the twentieth century, the drive to variance control in the experimental se...
The cultivation of living organs, cells, animals, and embryos in the laboratory has been central to the production of biological knowledge. Over the twentieth century, the drive to variance control in the experimental setting led to systematic efforts to generate synthetic, chemically defined substitutes for complex natural foods, housing, and other substrates of life. This article takes up the history of chemically defined media with three aims in mind. First, to characterize patterns of decontextualization, tinkering, and negotiation between life and experimenter that occur across disparate histories of cultivation. Second, to highlight the paradoxical historicity of cultivated organisms generated to be freed from context, as they incorporate and embody the purified amino acids, vitamins, plastics, and other artificial supports developed in the name of experimental control. Third, to highlight the figure-ground reversal that occurs as these cells and organisms are reconsidered as accidentally good models of life in industrialized conditions of pollution and nutrient excess, due to the man-made nature of their surrounds. Methodologically, the history of surrounds is described as an epigenetic approach that focuses on the material relations between different objects and organisms previously considered quite separately, from explanted organs to bacteria to plant cells to rats to human embryos.
How we may think: Imaging and writing technologies across the history of the neurosciences.
Borck C
Stud Hist Philos Biol Biomed Sci · 2016 Jun · PMID 26992284 · Publisher ↗
In the neurosciences, two alternative regimes of visualization can be differentiated: anatomical preparations for morphological images and physiological studies for functional representations. Adapting a distinction prop...
In the neurosciences, two alternative regimes of visualization can be differentiated: anatomical preparations for morphological images and physiological studies for functional representations. Adapting a distinction proposed by Peter Galison, this duality of visualization regimes is analyzed here as the contrast between an imaging and a writing approach: the imaging approach, focusing on mimetic representations, preserving material and spatial relations, and the writing approach as used in physiological studies, retaining functional relations. After a dominance of morphological images gathering iconic representations of brains and architectural brain theories, the advent of electroencephalography advanced writing approaches with their indexical signs. Addressing the brain allegedly at its mode of operation, electroencephalography was conceived as recording the brain's intrinsic language, extending the writing approach to include symbolic signs. The availability of functional neuroimaging signaled an opportunity to overcome the duality of imaging and writing, but revived initially a phrenological conflation of form and function, suppressing the writing approach in relation to imaging. More sophisticated visualization modes, however, converted this reductionism to the ontological productivity of social neuroscience and recuperated the theorizing from the writing approach. In light of the ongoing instrumental mediations between brains, data and theories, the question of how we may think, once proposed by Vannevar Bush as a prospect of enhanced human-machine interaction, has become the state of affairs in the entanglements of instruments and organic worlds.
Understanding viruses: Philosophical investigations.
Pradeu T, Kostyrka G, Dupré J
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26975220 · Publisher ↗
Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues (the definition of viruses, the individ...
Viruses have been virtually absent from philosophy of biology. In this editorial introduction, we explain why we think viruses are philosophically important. We focus on six issues (the definition of viruses, the individuality and diachronic identity of a virus, the possibility to classify viruses into species, the question of whether viruses are living, the question of whether viruses are organisms, and finally the biological roles of viruses in ecology and evolution), and we show how they relate to classic questions of philosophy of biology and even general philosophy.
Giant viruses: The difficult breaking of multiple epistemological barriers.
Claverie JM, Abergel C
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26972873 · Publisher ↗
The discovery of the first "giant virus", Mimivirus, in 2003 could solely have been that of an exceptional freak, a blind alley of evolution as occasionally encountered in biology, albeit without conceptual significance....
The discovery of the first "giant virus", Mimivirus, in 2003 could solely have been that of an exceptional freak, a blind alley of evolution as occasionally encountered in biology, albeit without conceptual significance. On the contrary, once broken this epistemological barrier, additional unrelated families of giant viruses such as the Pandoraviruses, the Pithoviruses and most recently Mollivirus, were quickly unraveled, suggesting that an entire chapter of microbiology had been ignored since Pasteur and Ivanovski. In this article, we examine to what extent the giant viruses challenge previous definitions of viruses, the diversity of forms they could take, and how they might have evolved from extinct ancestral cellular lineages. Inspired by the epistemology of Gaston Bachelard, we will also suggest the reasons for which giant viruses laid hidden in plain sight for more than a century. Finally, we propose a new definition for "viruses" that paradoxically emphasize the fact that they do not encode a single universally shared macromolecule or biochemical function.
Mutualistic viruses and the heteronomy of life.
Pradeu T
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26972872 · Full text
Though viruses have generally been characterized by their pathogenic and more generally harmful effects, many examples of mutualistic viruses exist. Here I explain how the idea of mutualistic viruses has been defended in...
Though viruses have generally been characterized by their pathogenic and more generally harmful effects, many examples of mutualistic viruses exist. Here I explain how the idea of mutualistic viruses has been defended in recent virology, and I explore four important conceptual and practical consequences of this idea. I ask to what extent this research modifies the way scientists might search for new viruses, our notion of how the host immune system interacts with microbes, the development of new therapeutic approaches, and, finally, the role played by the criterion of autonomy in our understanding of living things. Overall, I suggest that the recognition of mutualistic viruses plays a major role in a wider ongoing revision of our conception of viruses.
The ecological virus.
O'Malley MA
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26972871 · Publisher ↗
Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses - not usually considered to be organisms - would merely be part of the enviro...
Ecology is usually described as the study of organisms interacting with one another and their environments. From this view of ecology, viruses - not usually considered to be organisms - would merely be part of the environment. Since the late 1980s, however, a growing stream of micrographic, experimental, molecular, and model-based (theoretical) research has been investigating how and why viruses should be understood as ecological actors of the most important sort. Viruses, especially phage, have been revealed as participants in the planet's most crucial food webs, even though viruses technically consume nothing (they do not metabolize by themselves). Even more impressively, viruses have been identified as regulators of planetary biogeochemistry, in which they control cycles such as carbon, nitrogen and phosphorus - cycles on which all life depends. Although much biogeochemical research black-boxes the entities filling functional roles, it is useful to focus a little more closely to understand how viruses can be held responsible for the global processes of life. This paper will give a brief overview of the history of virus ecology and tease out the implications of large-scale ecological modelling with viruses. This analysis suggests that viruses should be conceptualized as ecological actors that are at least comparable and possibly equal to organismal actors. Ecological agency can therefore be distinguished from standard interpretations of biological agency.
The metaphor that viruses are living is alive and well, but it is no more than a metaphor.
van Regenmortel MH
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26970895 · Publisher ↗
Virologists often use anthropomorphic metaphors to vividly describe the properties of viruses and this has led some virologists to claim that viruses are living microorganisms. The discovery of giant viruses that are lar...
Virologists often use anthropomorphic metaphors to vividly describe the properties of viruses and this has led some virologists to claim that viruses are living microorganisms. The discovery of giant viruses that are larger and have a more complex genome than small bacteria has fostered the interpretation that viral factories, which are the compartments in virus-infected cells where the virus is being replicated, are able to transform themselves into a new type of living viral organism called a virocell. However, because of the widespread occurrence of horizontal gene transfer, endosymbiosis and hybridization in the evolution of viral genomes, it has not been possible to include metaphorical virocells in the so-called Tree of Life which itself is a metaphor. In the case of viruses that cause human diseases, the infection process is usually presented metaphorically as a war between host and virus and it is assumed that a virus such as the human immunodeficiency virus (HIV) is able to develop new strategies and mechanisms for escaping protective host immune responses. However, the ability of the virus to defeat the immune system is solely due to stochastic mutations arising from the error-prone activity of the viral enzyme reverse transcriptase. The following two types of metaphors will be distinguished: an intentionality metaphor commonly used for attributing goals and intentions to organisms and the living virus metaphor that considers viruses to be actually living organisms.
Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question.
Koonin EV, Starokadomskyy P
Stud Hist Philos Biol Biomed Sci · 2016 Oct · PMID 26965225 · Full text
The question whether or not "viruses are alive" has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the stat...
The question whether or not "viruses are alive" has caused considerable debate over many years. Yet, the question is effectively without substance because the answer depends entirely on the definition of life or the state of "being alive" that is bound to be arbitrary. In contrast, the status of viruses among biological entities is readily defined within the replicator paradigm. All biological replicators form a continuum along the selfishness-cooperativity axis, from the completely selfish to fully cooperative forms. Within this range, typical, lytic viruses represent the selfish extreme whereas temperate viruses and various mobile elements occupy positions closer to the middle of the range. Selfish replicators not only belong to the biological realm but are intrinsic to any evolving system of replicators. No such system can evolve without the emergence of parasites, and moreover, parasites drive the evolution of biological complexity at multiple levels. The history of life is a story of parasite-host coevolution that includes both the incessant arms race and various forms of cooperation. All organisms are communities of interacting, coevolving replicators of different classes. A complete theory of replicator coevolution remains to be developed, but it appears likely that not only the differentiation between selfish and cooperative replicators but the emergence of the entire range of replication strategies, from selfish to cooperative, is intrinsic to biological evolution.
Trackable life: Data, sequence, and organism in movement ecology.
Benson ES
Stud Hist Philos Biol Biomed Sci · 2016 Jun · PMID 26948240 · Publisher ↗
Over the past decade an increasing number of ecologists have begun to frame their work as a contribution to the emerging research field of movement ecology. This field's primary object of research is the movement track,...
Over the past decade an increasing number of ecologists have begun to frame their work as a contribution to the emerging research field of movement ecology. This field's primary object of research is the movement track, which is usually operationalized as a series of discrete "steps and stops" that represent a portion of an animal's "lifetime track." Its practitioners understand their field as dependent on recent technical advances in tracking organisms and analyzing their movements. By making movement their primary object of research, rather than simply an expression of deeper biological phenomena, movement ecologists are able to generalize across the movement patterns of a wide variety of species and to draw on statistical techniques developed to model the movements of non-living things. Although it can trace its roots back to a long tradition of statistical models of movement, the field relies heavily on metaphors from genomics; in particular, movement tracks have been seen as similar to DNA sequences. Though this has helped movement ecology consolidate around a shared understanding of movement, the field may need to broaden its understanding of movement beyond the sequence if it is to realize its potential to address urgent concerns such as biodiversity loss.
Natural selection and mechanistic regularity.
DesAutels L
Stud Hist Philos Biol Biomed Sci · 2016 Jun · PMID 26921876 · Publisher ↗
In this article, I address the question of whether natural selection operates regularly enough to qualify as a mechanism of the sort characterized by Machamer, Darden, and Craver (2000). Contrary to an influential critiq...
In this article, I address the question of whether natural selection operates regularly enough to qualify as a mechanism of the sort characterized by Machamer, Darden, and Craver (2000). Contrary to an influential critique by Skipper and Millstein (2005), I argue that natural selection can be seen to be regular enough to qualify as an MDC mechanism just fine-as long as we pay careful attention to some important distinctions regarding mechanistic regularity and abstraction. Specifically, I suggest that when we distinguish between process vs. product regularity, mechanism-internal vs. mechanism-external sources of irregularity, and abstract vs. concrete regularity, we can see that natural selection is only irregular in senses that are unthreatening to its status as an MDC mechanism.
Data graphs and mechanistic explanation.
Burnston DC
Stud Hist Philos Biol Biomed Sci · 2016 Jun · PMID 26871740 · Publisher ↗
It is a widespread assumption in philosophy of science that representations of data are not explanatory-that they are mere stepping stones towards an explanation, such as a representation of a mechanism. I draw on instan...
It is a widespread assumption in philosophy of science that representations of data are not explanatory-that they are mere stepping stones towards an explanation, such as a representation of a mechanism. I draw on instances of representational and explanatory practice from mammalian chronobiology to suggest that this assumption is unsustainable. In many instances, biologists employ representations of data in explanatory ways that are not reducible to constraints on or evidence for representations of mechanisms. Data graphs are used to represent relationships between quantities across conditions, and often these representations are necessary for explaining particular aspects of the phenomena under study. The benefit of the analysis is two-fold. First, it provides a more accurate account of explanatory practice in broadly mechanistic investigation in biology. Second, it suggests that there is not an explanatorily "fundamental" type of representation in biology. Rather, the practice of explanation consists in the construction of different types of representations and their employment for distinct explanatory purposes.
Contingency, convergence and hyper-astronomical numbers in biological evolution.
Louis AA
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26868415 · Publisher ↗
Counterfactual questions such as "what would happen if you re-run the tape of life?" turn on the nature of the landscape of biological possibilities. Since the number of potential sequences that store genetic information...
Counterfactual questions such as "what would happen if you re-run the tape of life?" turn on the nature of the landscape of biological possibilities. Since the number of potential sequences that store genetic information grows exponentially with length, genetic possibility spaces can be so unimaginably vast that commentators frequently reach of hyper-astronomical metaphors that compare their size to that of the universe. Re-run the tape of life and the likelihood of encountering the same sequences in such hyper-astronomically large spaces is infinitesimally small, suggesting that evolutionary outcomes are highly contingent. On the other hand, the wide-spread occurrence of evolutionary convergence implies that similar phenotypes can be found again with relative ease. How can this be? Part of the solution to this conundrum must lie in the manner that genotypes map to phenotypes. By studying simple genotype-phenotype maps, where the counterfactual space of all possible phenotypes can be enumerated, it is shown that strong bias in the arrival of variation may explain why certain phenotypes are (repeatedly) observed in nature, while others never appear. This biased variation provides a non-selective cause for certain types of convergence. It illustrates how the role of randomness and contingency may differ significantly between genetic and phenotype spaces.
What are narratives good for?
Beatty J
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26806602 · Publisher ↗
Narratives may be easy to come by, but not everything is worth narrating. What merits a narrative? Here, I follow the lead of narratologists and literary theorists, and focus on one particular proposal concerning the ele...
Narratives may be easy to come by, but not everything is worth narrating. What merits a narrative? Here, I follow the lead of narratologists and literary theorists, and focus on one particular proposal concerning the elements of a story that make it narrative-worthy. These elements correspond to features of the natural world addressed by the historical sciences, where narratives figure so prominently. What matters is contingency. Narratives are especially good for representing contingency and accounting for contingent outcomes. This will be squared with a common view that narratives leave no room for chance. On the contrary, I will argue, tracing one path through a maze of alternative possibilities, and alluding to those possibilities along the way, is what a narrative does particularly well.
What was historical about natural history? Contingency and explanation in the science of living things.
Harrison P
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26795077 · Publisher ↗
There is a long-standing distinction in Western thought between scientific and historical modes of explanation. According to Aristotle's influential account of scientific knowledge there cannot be an explanatory science...
There is a long-standing distinction in Western thought between scientific and historical modes of explanation. According to Aristotle's influential account of scientific knowledge there cannot be an explanatory science of what is contingent and accidental, such things being the purview of a descriptive history. This distinction between scientia and historia continued to inform assumptions about scientific explanation into the nineteenth century and is particularly significant when considering the emergence of biology and its displacement of the more traditional discipline of natural history. One of the consequences of this nineteenth-century transition was that while modern evolutionary theory retained significant, if often implicit, historical components, these were often overlooked as evolutionary biology sought to accommodate itself to a model of scientific explanation that involved appeals to laws of nature. These scientific aspirations of evolutionary biology sometimes sit uncomfortably with its historical dimension. This tension lies beneath recent philosophical critiques of evolutionary theory and its modes of explanation. Such critiques, however, overlook the fact that there are legitimate modes of historical explanation that do not require recourse to laws of nature. But responding to these criticisms calls for a more explicit recognition of the affinities between evolutionary biology and history.
Counterfactuals and history: Contingency and convergence in histories of science and life.
Hesketh I
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26791094 · Publisher ↗
This article examines a series of recent histories of science that have attempted to consider how science may have developed in slightly altered historical realities. These works have, moreover, been influenced by debate...
This article examines a series of recent histories of science that have attempted to consider how science may have developed in slightly altered historical realities. These works have, moreover, been influenced by debates in evolutionary science about the opposing forces of contingency and convergence in regard to Stephen Jay Gould's notion of "replaying life's tape." The article argues that while the historians under analysis seem to embrace contingency in order to present their counterfactual narratives, for the sake of historical plausibility they are forced to accept a fairly weak role for contingency in shaping the development of science. It is therefore argued that Simon Conway Morris's theory of evolutionary convergence comes closer to describing the restrained counterfactual worlds imagined by these historians of science than does contingency.
"Replaying Life's Tape": Simulations, metaphors, and historicity in Stephen Jay Gould's view of life.
Sepkoski D
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26790344 · Publisher ↗
In a famous thought experiment, Stephen Jay Gould asked whether, if one could somehow rewind the history of life back to its initial starting point, the same results would obtain when the "tape" was run forward again. Th...
In a famous thought experiment, Stephen Jay Gould asked whether, if one could somehow rewind the history of life back to its initial starting point, the same results would obtain when the "tape" was run forward again. This hypothetical experiment is generally understood as a metaphor supporting Gould's philosophy of evolutionary contingency, which he developed and promoted from the late 1980s until his death in 2002. However, there was a very literal, non-metaphorical inspiration for Gould's thought experiment: since the early 1970s, Gould, along with a group of other paleontologists, was actively engaged in attempts to model and reconstruct the history of life using computer simulations and database analysis. These simulation projects not only demonstrate the impact that computers had on data analysis in paleontology, but also shed light on the close relationship between models and empirical data in data-oriented science. In a sense, I will argue, the models developed by paleontologists through simulation and quantitative analysis of the empirical fossil record in the 1970s and beyond were literal attempts to "replay life's tape" by reconstructing the history of life as data.
A case study in evolutionary contingency.
Blount ZD
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26787098 · Publisher ↗
Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history o...
Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit(+)), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit(+) trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.
It all adds up …. Or does it? Numbers, mathematics and purpose.
Conway Morris S
Stud Hist Philos Biol Biomed Sci · 2016 Aug · PMID 26783082 · Publisher ↗
No chimpanzee knows what a square root is, let alone a complex number. Yet not only our closest ape cousins but even some invertebrates, possess a capacity for numerosity, that is the ability to assess relative numerical...
No chimpanzee knows what a square root is, let alone a complex number. Yet not only our closest ape cousins but even some invertebrates, possess a capacity for numerosity, that is the ability to assess relative numerical magnitudes and distances. That numerosity should confer adaptive advantages, such as social species that choose shoal size, is obvious. Moreover, it is widely assumed that numerosity and mathematics are seamlessly linked, as would be consistent with Darwinian notions of descent and modification. Animal numerosity, however, involves sensory processes (usually vision, but other modalities such as olfaction can be as effective) that follow psychophysical principles, notable the Weber-Fechner law. In contrast, mathematics may require sensory mediation but is an abstract process. The supposed connection between these processes is described as supramodality but the mechanisms that allow humans, but not animals, to engage in even simple mathematics are opaque. Here, I argue that any resolution will depend on proper explanations for not only mathematics, but language and by implication consciousness. In this light, concepts of purpose are not intellectual mirages but legitimate descriptions of the worlds in which we are embedded. These are both visible (and tangible) and invisible (and although intangible, equally real).
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