Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BackgroundFor a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields.ResultsWe compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift).ConclusionsApart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01378396
http://hal.upmc.fr/hal-01378396
http://hal.upmc.fr/hal-01378396/document
http://hal.upmc.fr/hal-01378396/file/unity.pdf
DOI : 10.1186/s13062-016-0145-2

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper investigates the narrative challenges and opportunities that contemporary virology offers to popular science and to fiction. The study of viruses reveals extremely complex relations, playing out over different physical and temporal scales. Viruses constitute a heterogeneous population whose interactions with living organisms occur on multiple levels, and whose numbers are vastly superior to human and even bacterial populations on earth. The resulting challenges for narration can be grouped into three main formal questions. The first is the problem of scale, since the numbers and sizes of virus and host populations are vastly different, as are the temporalities over which they transform and survive. The second is the complexity of actants, since viruses are involved in relations where destruction and mutual benefit can overlap, and genetic transformations are played out over many generations. The third is the choice of images through which to convey their behaviours: many existing metaphors in microbiology, such as “chimeras”, “parasites” or “kill-the-winner dynamics”, carry the narrative potential of a mythological and/or theatrical imagination.These questions will first be examined as challenges encountered in the narration of biology for vulgarization purposes, and effects on narrative forms will be outlined: shifts in focalization in order to create multiscalar perspectives; unstable actantial models as expressions of complex relations; and the use or resistance to narrative structures implied by several key metaphors in virological discourse. These formal characteristics will then be presented through two case studies drawn from contemporary fiction. In his “scientific fable” Conflits Intérieurs (2015), microbiologist Eric Bapteste creates a multiscalar narrative by using humans and viruses as both protagonists and narrators in a battle of ideas. In the graphic novel aâma (2011-2014), Frederik Peeters explores the ambiguous potential, both symbiotic and threatening, of a meta-organism uniting humans with microscopic agents. Both these novels play with scale, metaphor and actants so as to question the fundaments of human identity. They posit the act of narration as a defining human attribute, and consequently use the narrative voice as an arena in which we observe the weakening of the notion of the subject by microbiology.
“Narrative, Cognition & Science” Symposium
Erlangen, Germany

hal-01434744
https://hal.archives-ouvertes.fr/hal-01434744

Éditeur(s) : HAL CCSD Botanical Society of America
Résumé :  
Tree buckling risk (actual height/critical buckling height) is an important biomechanical trait of plant growth strategies, and one that contributes to species coexistence. To estimate the diversity of this trait among wide samples, a method that minimizes damage to the plants is necessary. On the basis of the rarely used, complete version of Greenhill's model (1881, Proceedings of the Cambridge Philosophical Society 4(2): 65-73), we precisely measured all the necessary parameters on a sample of 236 saplings of 16 species. Then, using sensitivity (variance) analysis, regressions between successive models for risk factors and species ranks and the use of these models on samples of self- and nonself-supporting saplings, we tested different degrees of simplification up to the most simple and widely used formula that assumes that the tree is a cylindrical homogeneous pole. The size factor had the greatest effect on buckling risk, followed by the form factor and the modulus of elasticity of the wood. Therefore, estimates of buckling risk must consider not only the wood properties but especially the form factor. Finally, we proposed a simple but accurate method of assessing tree buckling risk that is applicable to a wide range of samples and that requires mostly nondestructive measurements.
ISSN: 0002-9122

hal-01032059
https://hal.archives-ouvertes.fr/hal-01032059

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely ``processually equivalent'' entities, ``processually versatile'' entities, and ``stabilized'' entities.
ISSN: 0169-3867

hal-01544796
https://hal.archives-ouvertes.fr/hal-01544796
DOI : 10.1007/s10539-012-9350-2

Éditeur(s) : HAL CCSD HUMANA PRESS INC
Résumé : International audience
Ever since Darwin, the familiar genealogical pattern known as the Tree of Life (TOL) has been prominent in evolutionary thinking and has dominated not only systematics, but also the analysis of the units of evolution. However, recent findings indicate that the evolution of DNA, especially in prokaryotes and such DNA vehicles as viruses and plasmids, does not follow a unique tree-like pattern. Because evolutionary patterns track a greater range of processes than those captured in genealogies, genealogical patterns are in fact only a subset of a broader set of evolutionary patterns. This fact suggests that evolutionists who focus exclusively on genealogical patterns are blocked from providing a significant range of genuine evolutionary explanations. Consequently, we highlight challenges to tree-based approaches, and point the way toward more appropriate methods to study evolution (although we do not present them in technical detail). We argue that there is significant benefit in adopting wider range of models, evolutionary representations, and evolutionary explanations, based on an analysis of the full range of evolutionary processes. We introduce an ecosystem orientation into evolutionary thinking that highlights the importance of ``type 1 coalitions'' (functionally related units with genetic exchanges, aka ``friends with genetic benefits''), ``type 2 coalitions'' (functionally related units without genetic exchanges), ``communal interactions,'' and ``emergent evolutionary properties.'' On this basis, we seek to promote the study of (especially prokaryotic) evolution with dynamic evolutionary networks, which are less constrained than the TOL, and to provide new ways to analyze an expanded range of evolutionary units (genetic modules, recombined genes, plasmids, phages and prokaryotic genomes, pangenomes, microbial communities) and evolutionary processes. Finally, we discuss some of the conceptual and practical questions raised by such network-based representation.
EVOLUTIONARY GENOMICS: STATISTICAL AND COMPUTATIONAL METHODS, VOL 2

ISBN : 978-1-61779-584-8
hal-01544801
https://hal.archives-ouvertes.fr/hal-01544801
DOI : 10.1007/978-1-61779-585-5_4