Que signifie « se ressembler » en biologie?

La biologie travaille sur des particuliers. De par son historicité, chaque entité biologique est unique. Nous devons pourtant les regrouper pour parvenir à en parler de manière générale. Nos classifications sont destinées à communiquer nos concepts, et ce faisant elles reflètent une intention. Comme nous sommes en science, nous préférons les procédures de regroupement (agglomératives) aux procédures de division, lesquelles finissent toujours par isoler les particuliers. En systématique, science des classifications, la géométrie de nos concepts est celle d’une hiérarchie par emboîtement, du plus général au plus particulier, plutôt qu’une hiérarchie par empilement (comme dans le cas de la scala naturae), parce que les premières pratiquent l’inclusion tandis que les secondes pratiquent l’inclusion et l’exclusion. Les êtres biologiques sont traversés par une foule de ressemblances différentes, et la ressemblance globale, à vouloir les saisir toutes, n’en saisit rigoureusement aucune. Elle ne se distingue pas de la différence globale. Or, nous voulons travailler sur les partages, pas sur les différences, lesquelles finissent par isoler les entités. Ces partages, ce sont des attributs communs ou des propriétés partagées : c’est la ressemblance vue en mosaïque (qui donnera lieu à un mosaïcisme phylogénétique). Mais quel type de ressemblance est pris en compte ? La ressemblance topologique est prioritaire (principe des connections), vient ensuite la ressemblance de forme et celle du processus de genèse (ou de mise en place : ontogénèse). La ressemblance de fonction est trop trompeuse pour être prise en compte. Mais trompeuse au regard de quel but ? Nous classons pour parler des origines de ce qui existe. La classification moderne des êtres vivants reflète leur généalogie passée, ou du moins ce que nous pouvons en reconstruire indirectement (la phylogénie). Et pour cela, la ressemblance topologique est la plus efficace.Biology works on particular subjects. Because of its historicity, each biological entity is unique. Yet we need to bring them together to be able to talk about them in a general way. Our classifications are to communicate our concepts, and thus they reflect an intention. As we are in science, we prefer grouping (aka agglomerative) procedures to division procedures, which always end up isolating individuals. In systematics, the science of classifications, the geometry of our concepts is that of a hierarchy by nesting, from the most general to the most particular, rather than a stacking hierarchy (as in the case of scala naturae), because nesting is an inclusive practice while scaling is both inclusive and exclusive. Biological entities are crisscrossed by a host of different resemblances, and the overall resemblance, in trying to capture them all, does not capture any of them. It is indistinguishable from global difference. Yet we want to work on shared traits, not on differences, which wind up isolating entities. These shared traits are common attributes or shared properties. This is resemblance seen as a mosaic (which will lead to a phylogenetic mosaicism). Among the various types of resemblance, which is the one we choose? Topological resemblance, defined by the principle of connection, is the priority. Then come resemblance in forms and resemblance in developing processes (ontogeny). Functional resemblance is too misleading for consideration, with regards to our goals, since we classify in order to reflect common origins of entities. Modern classification of living things reflects their past genealogy, at least what we can reconstruct from it (phylogeny) based on our best inferences. For that purpose, topological resemblance is the most efficient

Did glacial advances during the Pleistocene influence differently the demographic histories of benthic and pelagic Antarctic shelf fishes? – Inferences from intraspecific mitochondrial and nuclear DNA sequence diversity

<p>Abstract</p> <p>Background</p> <p>Circum-Antarctic waters harbour a rare example of a marine species flock – the Notothenioid fish, most species of which are restricted to the continental shelf. It remains an open question as to how they survived Pleistocene climatic fluctuations characterised by repeated advances of continental glaciers as far as the shelf break that probably resulted in a loss of habitat for benthic organisms. Pelagic ecosystems, on the other hand, might have flourished during glacial maxima due to the northward expansion of Antarctic polar waters. In order to better understand the role of ecological traits in Quaternary climatic fluctuations, we performed demographic analyses of populations of four fish species from the tribe Trematominae, including both fully benthic and pelagic species using the mitochondrial cytochrome b gene and an intron from the nuclear S7 gene.</p> <p>Results</p> <p>Nuclear and cytoplasmic markers showed differences in the rate and time of population expansions as well as the likely population structure. Neutrality tests suggest that such discordance comes from different coalescence dynamics of each marker, rather than from selective pressure. Demographic analyses based on intraspecific DNA diversity suggest a recent population expansion in both benthic species, dated by the cyt b locus to the last glacial cycle, whereas the population structure of pelagic feeders either did not deviate from a constant-size model or indicated that the onset of the major population expansion of these species by far predated those of the benthic species. Similar patterns were apparent even when comparing previously published data on other Southern Ocean organisms, but we observed considerable heterogeneity within both groups with regard to the onset of major demographic events and rates.</p> <p>Conclusion</p> <p>Our data suggest benthic and pelagic species reacted differently to the Pleistocene ice-sheet expansions that probably significantly reduced the suitable habitat for benthic species. However, the asynchronous timing of major demographic events observed in different species within both "ecological guilds", imply that the species examined here may have different population and evolutionary histories, and that more species should be analysed in order to more precisely assess the role of life history in the response of organisms to climatic changes.</p

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Why do we not teach that the earth is flat?

Scientific explanations of the Origins (of Earth, life, species, Man …) are contested nowadays even within schools. A school curriculum is a strong political act. In the French context, as far back as 1792, republicans have put knowledge at the heart of the development of French citizenship. In state schools, we teach knowledge, not religious beliefs or opinions. This implies, however, that one must be able to tell the difference. We propose a typology using two criteria. First, is the claim upheld individually or collectively? And second, does the legitimacy of the claim come from an authority figure or from a rational justification? We emphasise the collective nature and the autonomy of the process by which scientific knowledge is validated, as the direct by-products of experimental reproducibility. These characteristics have as a consequence that science is implicitly secular on an international scale. The reproducibility of experiments relies on four fundamental cognitive expectations which are described here: initial scepticism of the facts, principle of realism, rationality and methodological materialism. Failure to fulfil these expectations discredits any claim creationism may make to qualify as scientific

Face aux créationnismes, comment apprendre aux élèves à distinguer croyances, savoirs et opinions ?

Lecointre Guillaume. Face aux créationnismes, comment apprendre aux élèves à distinguer croyances, savoirs et opinions ?. In: Raison présente, n°188, 4e trimestre 2013. Croyance et connaissance. pp. 35-42

L'innovation dans l'évolution

In Systematics the use of the word «innovation » can be confusing. Among mammals, the opposed thumb is an innovation that characterizes primates. However, today's opposed thumbs cannot be innovations because their presence among primate species date back to 70 m.y.a. This apparent contradiction comes from the confusion between innovation as an event and innovation as a character state. In Systematics and in evolutionary Biology, an event is an innovation not according to the rarity of what appears, but according to the retrospective consideration of what it led to.L'usage du mot «innovation » en systématique peut conduire à des paradoxes... Au sein des mammifères, le pouce opposable est une innovation qui caractérise les primates. Pourtant, les pouces opposables d'aujourd'hui ne sont nullement une innovation puisque leur présence date de 70 millions d'années. Cette contradiction apparente vient d'une confusion entre l'innovation-événement et l'innovation-état. En systématique et en biologie évolutive, un événement est «innovation » non pas en vertu du caractère unique de ce qui apparaît, mais par la considération rétrospective de ce à quoi il a conduit.Lecointre Guillaume. L'innovation dans l'évolution. In: Les Cahiers du Musée des Confluences. Revue thématique Sciences et Sociétés du Musée des Confluences, tome 7, 2011. Innovation. pp. 87-94