L3 - Biology-Ecology

The students will have to carry out a bibliographical analysis on a theme of their choice, validated by the persons in charge of the UE. Under the tutelage of a teacher-researcher, students will have to answer the problematic they are working on through an analysis of the available bibliography. They will have to assess the state of the art in the field they are working on, identify areas of uncertainty and controversy, and the open questions that remain to be resolved. They will have to carry out a true critical scientific analysis of the available bibliography, and not be satisfied with a report of the bibliography. They will have to follow the conventions of writing a scientific article, involving the citation of sources, the synthesis of information through illustration, the problematization and the synthesis of scientific results.

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This course is an extension of the Basic Evolution course and introduces the main concepts of evolutionary ecology in order to understand and formalize in a simple way the evolutionary and ecological mechanisms that shape biodiversity at different scales of integration.

This course is designed as a coherent whole where lectures, tutorials and practical work are complementary. The notions are approached by example and then formalized with mathematical models, which are confronted with experience and real data.

It will deal with population dynamics (intra- and interspecific competition), ecological niche and will detail the mechanisms of evolution and their genetic consequences at the population level: natural selection (including sexual selection), influence of reproduction regimes, genetic drift. The practical sessions will allow students to learn the mathematical formalization of notions seen in class and their simple computer modeling as well as the analysis of data sets. The practical exercises will allow the realization and the analysis in small groups of 2 experiments of 1 month each (with writing of a report and oral presentation) in order to develop the methodology and the scientific reasoning.

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The EU is organized into five major themes:

Theme 1: Gene mapping and recombination. Concepts of molecular biology related to gene expression, DNA repair and epigenetic processes.

Theme 2: Introduction to molecular evolution: Measuring the intensity of selection in genetic divergence. Molecular clock and variation in evolutionary rates created by the action of natural selection. Neutralist theory of evolution.

Theme 3: Introduction to genomics: composition and size of genomes. Importance of repeated elements. Notion of genetic linkage and local effect of selection. Influence of demography.

Theme 4: Molecular tools for biodiversity: Barcoding, eDNA, metabarcoding. Molecular taxonomy. Limitations of hybridization. Applications in conservation.

Theme 5: Extranuclear heredity. Symbiosis, parasitism and co-evolution (intra-cellular: e.g. Wolbachia). Notion of extended phenotype.

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Genesis, nature and fate of deposits in sedimentary basins.

Cycle of 15 courses / lectures / debate and TP/TD

Content of the integrated courses (sedimentary basins, alteration of continents),

(e.g. sediment transport, detrital and carbonate environments, factors affecting sedimentation: sequence stratigraphy, diagenesis)

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This course aims to provide students with an integrative approach to the morphology, anatomy and development of the vegetative and reproductive systems of spermatophytes, from an ecological, functional and evolutionary perspective. This approach is implemented by the students through a supervised project, centered on the study of a model plant, taking into account the inter-individual variability, the different stages of development, the stationary conditions and the biological type.

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The structure of this course is similar to that developed in S4. The objective is to provide students with knowledge on the biology, ecology and evolution of three taxonomic groups in question. Beyond the identification of species (which will be largely addressed), this course will deal with the evolution and systematics of the taxonomic group in question, fundamental ecology (evolutionary and functional ecology), applied ecology (conservation), physiology, legislation, as well as study and identification methods.

After a general introduction course, 2 axes of work will be proposed in parallel. One will focus on cryptogams (algae, lichens, mosses and fungi), the other on fauna (Chiroptera & Arthropoda).

Cryptogams

The objective of this component is to familiarize students with the extremely diverse organisms that are bryophytes, phaeophytes and fungi. The principle is 1) to approach these little known diversities through a naturalistic approach, 2) to place these observations in an evolutionary perspective (phylogenetic aspects), and 3) to link the observations to the role of these organisms in terrestrial and marine ecosystems.

Finally, the module will address aspects of daily life, economics or citizenship related to species (toxicology, food, medicine).

Wildlife

The objective is for the student to acquire/improve a body of knowledge on the biology of arthropods and chiropterans, which are taxonomic groups with a great deal of interest, both from the point of view of studies in fundamental ecology (ethology, evolutionary ecology, functional ecology), in applied ecology (conservation biology) and in environmental education / teaching. Beyond the identification of species, this line of work will deal with the evolution and systematics of these taxa, their physiology, their ecological and behavioral particularities, their roles in ecosystems. The teaching will integrate innovative pedagogical approaches, combining the use of traditional (visual recognition) and modern (acoustic identification by software) tools. Among the Arthropods, the groups particularly approached will be the Coleoptera, Lepidoptera, Odonata and Orthoptera which represent very diversified orders that will allow us to approach the notion of species which is central in biology. The identification of species will constitute a basis to study their biology, their ecology and to approach the notions of evolution and phylogeny.

Each group (Fauna - Cryptogams) will have at its disposal 12 hours of field trips (half of which will be common to both groups) to be carried out according to modalities to be defined (4 half-day trips, or 2 long one-day trips). The practical work could be set up on university sites (university campus - Labex CEMEB experimental field at the CEFE - Botanical Garden) suitable for the study of the various organisms.

Cross-cutting concept

The course is organized around a notion common to both groups of practical work which, through a reversed class, will allow to start from the observed species in order to identify central concepts in conservation biology. In S5, the notion of species (and associated entities such as subspecies, hybrids, etc.) will be widely approached, from a theoretical and practical point of view. This notion will allow to address 1. the foundations and limits of the different perspectives of the species (morphological, genetic, ecological), 2. the methodological problems related to the identification of taxa in the field and in the laboratory and 3. the problems that this generates from the point of view of species conservation. For this purpose, the students present at the end of the sequence a taxon, among those proposed in the EU, whose identification is complex.

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The aim of this course is to understand animal behavior in an integrative way, in the light of Tinbergen's four 'whys', from its ontogeny to its evolution: from its ontogeny, its neurobiological causes to its evolution and its biological functions. In addition to historical, conceptual and methodological contributions, the students will be accompanied in order to apprehend the diversity of the features involved as well as the diversity of the approaches and the associated scientific questionings.

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Ecotoxicology concerns the study of the effects of pollutants on living species and on the structure and functioning of ecosystems. This course aims to provide a better understanding of :

- the main types of organic and inorganic pollutants (historical or emerging), as well as their sources and the factors influencing their fate in the natural environment and in organisms

- the effects of pollutants on micro- and macro-organisms at different levels of biological integration (molecule, individual, communities),

- methods for assessing biological effects, environmental quality and ecotoxicological risk in the current European regulatory framework,

- bioremediation processes through several case studies.

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The objective of this course proposed in L3S5 is the acquisition of knowledge on the organization, development and functioning of different physiological systems in animals. More specifically, the functions of circulation, thermoregulation, hormonal regulation and nervous integration will be approached according to a comparative approach (examples drawn from different taxonomic groups) and in an evolutionary context. Questions related to the bioethical aspects of animal physiology experimentation will also be addressed.

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This teaching unit will aim to address the elements necessary to understand the way of life of the major groups of unicellular organisms at the basis of the functioning of ecosystems (viruses, bacteria, archaea, and unicellular eukaryotes ....). The courses allow us to approach the biological organization of each type of organism, the modalities of reproduction, the diversity, to lead to notions of ecology. We will approach the role of these microorganisms in the functioning and dynamics of ecosystems, by considering the interactions that these organisms maintain with other living beings (notion of "symbiosis" in all its variations).

The practical work will:

 - the implementation of techniques allowing bacterial enumeration (CFU), the identification of a particular strain from an environmental sample

 - highlighting the diversity of phytoplankton (unicellular algae) in aquatic environments (fresh water)

 - the identification of the specificity of interactions between bacteria and bacteriophages

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The major objective is to learn the basics of comparative anatomy of chordates, so as to be able to compare and classify them, before tracing the key stages of their evolutionary history. The teaching is integrative in the sense that it uses both present-day organisms and the fossil record, in order to document the evolutionary history of the clade in its entirety and in all its aspects. Anatomical, biomechanical, phylogenetic, and ecomorphological approaches will be addressed in lectures in order to illustrate the diversity and major characteristics of chordates. The practical sessions (and the practical sessions) will illustrate the evolution of the diversity of the integuments, the skeleton, the musculature, the digestive and respiratory systems over long time scales.

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This course is a natural continuation of the course " Quantification of Hazard " (HAV424B) presented in S4. It should provide the concepts for the construction of experimental protocols that answer biological questions and to associate appropriate models for the analysis of variability. A first part will be devoted to the construction of experimental protocols that answer a multitude of questions in the life sciences, i.e. by taking into account the inevitable dependence of statistical individuals, such as pairing, spatial or temporal structure of populations. This part will thus be the occasion to approach the notion of fluctuation, replication and pseudo-replication, which will be taken into account in the models built in the second part of the course. This second part will show the link between the experimental protocol and the modeling of the variability of a quantitative response variable, through the construction of models including several qualitative or quantitative variables. Particular attention will be paid to the conditions of application of these methods, to type I and type II errors, to the methods of estimating the parameters of the models constructed (including the likelihood) and to the interpretation of the estimated parameters. Each notion will be illustrated by the analysis of real biological data from several themes, thus helping students to discover not only modern and common biological questions but also the tools developed to answer them. Practical work in R will allow students to independently perform analyses on published biological cases.

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Through 5 main themes, we will link the principles of evolution and evolutionary ecology seen in the previous E.U. in a fundamental way and current societal applications.

These 5 main themes are: human evolution, biodiversity conservation, domestication of animal and plant species, evolutionary medicine, major crises and global disturbances

Two sessions on the comprehension and oral restitution of scientific articles are carried out in connection with the UE "Evolutionary ecology and its applications".

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For semester 6, students will have the choice between 2 types of student projects: (1) the implementation of a "Science Partners for the Classroom" (ASTEP) or (2) the setting up of a Data Acquisition and Processing (DAP) protocol. For the ASTEP project, the students will carry out a scientific dissemination project with kindergarten or primary school classes in the Hérault region (scientific themes defined by the partner schools). The students will then have to develop one or more experiments to be conducted with the classes, acquire data with the pupils and disseminate the scientific notions to the pupils concerned. For the ATD project, students will have to propose a data acquisition protocol to answer a scientific question of their choice. This protocol could be conducted in the field, in the classroom, or consist of a meta-analysis.

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The objective of the course is to provide an overview of the diversity of Angiosperms, approached through the prism of the most recent phylogenies proposed by theAngiosperm Phylogeny Group (APG). This phylogenetic framework will be supported throughout the course by the concrete observation of vegetative and floral characters of a selection of taxa spread over the whole phylogeny, in order to identify the synapomorphies of the main clades, the possible homoplasies, as well as the adaptations (floral biology, pollination, trophic interactions, etc.)

The students also learn about the diversity of Angiosperms from a floristic point of view, by creating a herbarium of species that are generally Mediterranean. They become familiar with the use of a flora and digital tools for identification (Pl@ntNet e-Flore of Tela Botanica, etc.).

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Through 5 main themes, we will link the principles of evolution and evolutionary ecology seen in the previous E.U. in a fundamental way and current societal applications.

These 5 main themes are: human evolution, biodiversity conservation, domestication of animal and plant species, evolutionary medicine, and major crises and global disturbances.

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The students of the general license of the University follow various introductory courses in ecology during their first two years of study. At the end of their third year, they are introduced to several fundamental concepts of adaptation of individuals to the environment and interactions between species (Concepts in Evolutionary Ecology HLBE503). In particular, they explore r/K evolutionary strategies, linking the adaptation of life cycles to disturbance regimes in natural environments. I propose to place the study of communities in continuity with these foundations, in order to illustrate the role of species' evolutionary strategies in community formation. This teaching will be based on a pedagogical sequence composed of lectures, tutorials and practical work carried out in the form of field projects.

The lectures will present the basics of community ecology in three blocks. The first will concern the definition of a community, and will approach the historical development of the discipline, through the perspectives of Gleason (1926) and Clements (1916). The second block will introduce the elements of description of communities, with the notions of diversities (alpha, beta, gamma) and their different indices. Finally, a third block will lead the students to think about the rules of assemblages in communities, through the role of evolutionary strategies r/K in successions, the notions of environmental filter and functional similarity limitation.

These courses will be held in parallel with a sequence of tutorials that will be organized according to a "data production-analysis-interpretation" scheme. First, the use of seriousgames will allow the production of data based on simplified ecological mechanisms. For this purpose, several serious games allowing to simulate communities are currently under development. These data will be collected by the students, to prepare their analysis. This analysis will take place in the form of a workshop to allow students to familiarize themselves with the calculation of diversity indices. Finally, time will be given to a return to the bibliography in order to investigate if the patterns produced through the sequence have a biological reality, and if they have been observed in nature (independent work and report).

Once the TD sequence is over, students will start setting up in situ community ecology experiments through an introduction to field ecology in the form of independent projects. Within this TP, a workshop will test Grime's (1988) competitive (C), stress tolerant (S) and ruderal (R) strategies through the analysis of plant functional traits. Simple methods have recently been published that allow individuals(let alone communities) to be placed on Grime's triangle (Pierce et al., 2017). The sequence will begin with a field trip on campus: students will choose two contrasting environments (lawns, ruderal area, woods, old wall) on which they will conduct a floristic inventory. Following this, they will take several individuals of each species to the laboratory to measure different functional traits. Once the measurements have been made, they will be able to calculate the various indices related to the CSR strategy. The sequence will conclude with a report and an oral presentation. Other workshops are currently being developed.

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The UE will correspond to a situation to which the students will have to respond. The teaching team of the UE will represent the directions of engineering offices which are in charge of carrying out impact studies following a development project.

The students will play the role of experts from the study offices and will have to carry out analyses on the project area. They will have to provide a report of their impact study in which they will have identified the ecological stakes which they will have classified according to their importance. They will also have to present their studies orally.

The UE will be articulated around 6 sessions of TD of 2h at the beginning of the semester during which the following points will be approached:

TD1: Presentation of the EU, presentation of what an impact study is and what is expected from such a study (this part will be carried out by a professional whose job is to verify impact studies), presentation of the status of the studied areas: ZNIEFF, Natura 2000.

TD2 to 6: Presentation of analysis methods for different groups of organisms (plants, arthropods, herpetofauna, avifauna and chiroptera, soil fauna...).

For the remainder of the EU, students will be required to propose study protocols to estimate the potential impacts of the proposed project. The protocols set up will have to allow for the closest possible assessment of the impacts and the studies will have to budget their interventions. They will then have field sessions to set up their protocol, collect data and then analyze them. The pedagogical team will tutor the groups in order to guide them in their work. They will write a thesis based on a set of specifications provided by the educational team. This deliverable must be supported by field data and data from the bibliography. They will defend their file in front of the pedagogical team during an oral presentation.

Several study areas to carry out the work have been targeted in Montpellier: Triolet Campus, Mosson River, Parc de la Vallet, Montpellier Center, Parc Méric, Rives du Lez, Garrigues de la Lauze...

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This UE is a first approach of Conservation Sciences according to the points of view of the various actors:

- scientific approach: basic and practical approach to conservation and restoration of populations and communities

- societal approach: role of the scientist in the management of species and ecological environments, and interactions with other conservation actors (managers, local actors)

- ethical approach: reflection on the values of biodiversity (quantifiable, preferential, normative) and their applications according to different models, placed in a historical context (mainly ecosystem services and sustainable development)

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This introductory course will capitalize on the mathematical tools encountered throughout the bachelor's degree and particularly in the course of the Modeling of living organisms: theory (option of S4), in order to provide an overview of the different approaches and techniques for modeling living organisms. All the major families of mathematical models will be addressed: static (optimization problems, game theory) as well as dynamic (extensions of the systems seen in S4, introduction to stochastic processes). Examples of applications of these models will be diversified, covering many biological systems as well as different levels of organization (metabolic, epidemiological, meta-community models...). Particular attention will be paid to epistemological aspects (contributions of modeling to the construction of theories in life sciences) and practical aspects (identifiability, calibration, and parametric sensitivity on the one hand, numerical implementation/simulations on the other). Finally, it will be an opportunity for students to become familiar with the research themes involving modeling, developed in the Montpellier basin.

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This UE is structured according to a professional inventory approach during which students will be put in real situation to emphasize their naturalist skills. This one will consist of a field study, with mainly volume of field supervision through SPS for the project follow-up. In this, it is in line with the logic of the ex-CMI (Opus 4).

Eight groups of 5 students will work on the inventory of a specific taxon within the framework of a clearly identified scientific problem. The study area will be different from one year to the next, and will be chosen by the teaching team according to opportunities for collaboration with organizations interested in the proposed approach. The organizations approached are :

- the Conservatoire des Espaces Naturels de Languedoc Roussillon

- the Zoo du Lunaret, manager of the Lez reserve

- the metropolis of Montpellier

The feedback will consist of a common deliverable for the whole class, including a hierarchy of conservation issues. The management organizations of the studied areas will be invited to the presentations.

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The aim of this course is to acquire, reinforce and synthesize notions and knowledge in evolutionary paleontology, sedimentology and paleoecology, and apply them to the fossil world. Together, these notions provide the keys to infer the stratigraphic context and the past environments in which extinct organisms lived.

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Introduce students to an integrated approach of the plant by studying the morpho-anatomical characteristics of stems and roots. To make them discover the spatio-temporal coordinated construction of root and stem architectures through adaptations of Mediterranean and tropical species. Reproductive structures as well as the diversity of biological types will also be taken into account. This course is positioned as a preparation for the continuation in Master BE BioGET course and relies on the natural environment and local and regional infrastructures (Amazonian Greenhouse, Villa Thuret, Jardin Château La Pérouse).

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This course represents an introduction to the ecology of continental freshwater and marine ecosystems, as well as to the interface environments between these two compartments, i.e. mangroves, estuaries and deltas. They will be approached both from the point of view of their structure and from the point of view of their functioning by insisting on both their common points and their differences, and on the abiotic and biotic factors which govern the organization of the communities of organisms which populate them.

They should provide an overview of these ecosystems or hydrosystems and their functioning at various scales.

The first part of the course is entirely dedicated to theoretical teachings, the second part includes introductory sessions to the field trips, the field trips themselves and the practical sessions in which the data collected in the field are analyzed and shared.

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Molecular tools are an integral part of studies to describe and characterize biodiversity. The course will present various molecular approaches (barcoding, metabarcoding and environmental DNA, etc.) to describe, characterize and quantify this diversity at intra- or interspecific, population or ecosystem levels, and (2) to present their fields of application at different scales of time and space. The course will include practical aspects aimed at learning about, implementing, analyzing and reporting on these techniques. Group work in interaction with researchers and teacher-researchers will be privileged.

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One of the goals of this course is to synthesize notions and knowledge acquired in animal biology (anatomy, systematics) and ecology to describe and understand the morphology and evolution of vertebrate morphologies. In addition to dealing with present-day groups, this course will focus on extinct fossil groups, especially their contribution to the understanding of the different eco-morphological adaptations (e.g. acquisition or return to aquatic life, acquisition of flight) that have marked the evolutionary history of clades.

This course also aims to provide theoretical and practical bases in phylogeny (cladistics) to trace the evolution of a clade (distance, parsimony and likelihood methods), both on molecular and phenotypic characters (present and fossil).

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Adaptations to the "parasitic" way of life are studied on all parasitic organisms (viruses, bacteria, eukaryotes) by including different scales of analysis "from molecules to populations".

Thus, the coevolution between hosts and parasites will be considered from the point of view of host-parasite molecular and cellular dialogues (immunity-escape - exploitation of host resources...) but also from the point of view of morpho-anatomical structures involved in adaptation to the infra-host site or in survival in the external environment, and finally from the point of view of behavioral adaptations for the encounter with the host (favoring).

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ORPAL is an ecology course in APP (1/3 field and 2/3 laboratory work). Based on concepts and methods of Ecology, this course aims at discovering historical ecology (study of the interactions between Man and his environment over variable chronological periods) and the main applications in paleoecology, from the definition of the problem, sampling in the field, data acquisition to the interpretation and writing of a scientific article (see https://biologie-e cologie.com/exemples-travaux/). This course is an interesting theoretical and experimental prerequisite for the ACCES, CEPAGE, PALEONTOLOGY, ECOSYSTEMS or BIOGET courses.

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- weather/climate difference

- structure of the atmosphere, radiation balance, greenhouse effect, wind circulation, depressions/anticyclones, tropical cyclones, tornadoes

- general ocean circulation (Munk, main currents, Conveyor Belt)

- geographical distribution and definition of climates

- current climate change

- global water cycle, hydrological balance, water balance, energy balance over a cultivated plot to estimate evapotranspiration

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Understand the weather and know how to use the climato for an ecologist / naturalist.

- climate measurement methods, bioclimate indices;

- Computer workstation: climatic data, modern archives (century), oscillations and trends;

- weather reminders, dominant parameters: from the major biomes to the topoclimate ;

- average climate vs. extreme events, their role and impacts on biodiversity ;

- Group work (restitution): regional themes, shared oral presentation;

- past and future climate changes, their impacts on biodiversity.

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At the end of this course, students will have acquired the basic knowledge required to prepare and correctly carry out a scientific communication operation adapted to a target audience, both orally and in writing. They will also be able to design educational material and awareness workshops for the general public.

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Universities are often perceived as inaccessible places for a large part of society. As part of the UniverlaCité program, which aims to bring the university to life in priority neighborhoods, the students will develop scientific workshops intended for a school audience in REP. 

The EU will offer students the opportunity to:

1- share their own experiences and enhance the value of their knowledge acquired at the University in order to respond as best as possible to the needs of the societal context.

2- to reveal and develop skills in terms of scientific communication through the elaboration and realization of pedagogical materials adapted to the concerned public.

The UE will take place in the form of TD and project follow-up (SPS) on previously defined themes. The socio-cultural situation of sensitive urban areas will be addressed during the first TD. This first TD will also serve to lay the foundations of the UE, to present in details the UniverlaCité device and to make a broad presentation of the scientific mediation.

The following tutorials will serve as sessions during which the students, divided into groups, will have to propose activities to be set up. The constraints that will be given to them by the teaching staff will be: the target public, the theme (which will be defined by the teaching staff and which will be renewed each year) and the need to propose activities 'outside the classroom'.

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The major human and animal health issues related to global change, i.e. :

• the degradation of natural environments, leading to the loss of quality of natural resources (various pollutions) and the loss of biodiversity
• climate change
• the artificialization of living environments
• new therapeutic methods
• the globalization of trade
• the standardization of lifestyles

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The sciences in today's society are at the heart of many ethical, economic and societal issues. The aim of this course is to make students reflect on their knowledge and practices through a historical approach to the construction of knowledge and through reflections on the bioethical aspects of science, the place of researchers in society and the relationship between science and society. The aim is to make students aware of the use of scientific arguments in society and to debate in order to confront supported points of view in a contradictory manner, and to develop their critical sense. It is therefore an opening course, allowing students to take a broader view while maintaining a scientific approach, in other words, to "lift their heads from the handlebars".

- 7CM = 10.5h for History of Science, pan-historical and pan-geographical approach

- 4 CM = 6h to present the concepts of bioethics and the critical approach that will be necessary for the debates (methodology of the controversy, complexity, issues, arguments of authority)

- 2CM= 3h on the role of scientists in society (historical approach and discussion on possible pitfalls)

- 2TD= 3h on cognitive biases, notions of epistemology, language traps, and notion of proof, major types of erroneous reasoning

- 4 sessions of 2TD= 4x3h= 12h of debates on themes at the heart of scientific and societal controversies: GMOs, Vaccination, Pharmacogenetics and genetic testing, Endocrine disruptors, Feeding the planet, Demographic challenge, Climate change, Transhumanism, Cloning and assisted reproduction, Animal experimentation, Neuroscience and marketing, Biological warfare, Nanotechnologies, ... We start with a press article and the students in groups produce a presentation (participate in the evaluation) whose goal is to propose a historical context, present the antagonistic points of view argued (ethical and scientific arguments), and then lead a debate. Each debate session (3h) will have a theme, researchers or EC will be invited to participate in the jury and propose a synthesis at the end.

In groups and for the duration of the course, students will produce a bibliographical synthesis on a theme of their choice, with a well-constructed argument, illustrated with carefully chosen examples, placing the subject in a history of science dimension with bioethical considerations. The idea is not to just make the history of a subject, but on the contrary to insist on the links with the progression of scientific knowledge and the ethical questions raised.

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