L3 - Biology-Ecology

Students will be asked to carry out a bibliographical analysis on a topic of their choice, validated by the UE supervisors. Under the tutelage of a teacher-researcher, students will have to answer the problem they have set themselves by analyzing the available bibliography. They will have to assess the state of the art in the field they are working on, identifying areas of uncertainty and controversy, and open questions that remain to be resolved. They will have to carry out a genuine critical scientific analysis of the available bibliography, and not simply report on it. They will have to follow the conventions of scientific article writing, involving citation of sources, synthesis of information through illustration, problematization and synthesis of scientific results.

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This course is an extension of the "Fundamentals of 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, with lectures, tutorials and practical work complementing each other. Notions are approached by example, then formalized using mathematical models, which are compared with experience and real data.

It will deal with population dynamics (intra- and interspecific competition), ecological niches and will detail the mechanisms of evolution and their genetic consequences on a population scale: natural selection (including sexual selection), influence of reproductive regimes, genetic drift. The practical sessions will enable students to master the mathematical formalization of notions seen in class and their simple computer modeling, as well as the analysis of data sets. Practical work will enable students to carry out and analyze in small groups 2 experiments lasting 1 month each (with report writing and oral presentation), in order to develop methodology and scientific reasoning.

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The EU is organized into five main themes:

Theme 1: Gene mapping and recombination. Notions 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. Conservation applications.

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/debates and practical work/days

Content of integrated courses / practical / practical work, (sedimentary basins, alteration of continents,

sediment transport, detrital and carbonate environments, factors affecting sedimentation: sequence stratigraphy, diagenesis)

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The aim of this course is 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 students through a supervised project centered on the study of a model plant, taking into account inter-individual variability, different stages of development, site conditions and biological type.

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The structure of this course is similar to that developed in S4. The aim is to provide students with knowledge of the biology, ecology and evolution of the three taxonomic groups in question. In addition to species identification (which will be covered extensively), this course will cover the evolution and systematics of the taxonomic group in question, fundamental ecology (evolutionary and functional ecology), applied ecology (conservation), physiology, legislation and study and identification methods.

After a general introductory course, 2 parallel courses will be offered. One will focus on cryptogams (algae, lichens, mosses and fungi), the other on fauna (chiropterans & arthropods).

Cryptogams

The aim of this section 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.

Lastly, the module will cover aspects of daily life, economics and citizenship linked to species (toxicology, nutrition, medicine).

Fauna

The aim is for students to acquire/deepen a body of knowledge on the biology of arthropods and chiropterans, which are taxonomic groups of great interest, both from the point of view of studies in fundamental ecology (ethology, evolutionary ecology, functional ecology), applied ecology (conservation biology) and environmental education/teaching. In addition to species identification, this line of work will cover the evolution and systematics of these taxa, their physiology, ecological and behavioral characteristics, and their roles in ecosystems. Teaching will incorporate innovative pedagogical approaches, combining the use of traditional tools (visual recognition) and modern ones (acoustic identification using software). Among Arthropods, the groups to be particularly addressed will be Coleoptera, Lepidoptera, Odonata and Orthoptera, representing highly diversified orders that will best enable us to approach the notion of species, which is central in biology. Species identification will form the basis for studying their biology and ecology, and for tackling the notions of evolution and phylogeny.

Each group (Fauna - Cryptogams) will have at its disposal 12 hours of fieldwork (half of which will be common to both groups) to be carried out according to modalities to be defined (4 1/2-day outings, or 2 long one-day outings). Practical work can be carried out on university sites (university campus - Labex CEMEB experimental field at CEFE - Botanical Garden) that are suitable for studying different organisms.

Cross-cutting notion

The EU is organized around a notion common to both groups of practical work, which, through a reversed class, will enable us to use observed species as a starting point for identifying concepts central to conservation biology. In S5, the notion of species (and associated entities such as subspecies, hybrids, etc.) will be widely addressed, from both a theoretical and practical point of view. This notion will enable us to address 1. the foundations and limits of the various perspectives on species (morphological, genetic, ecological), 2. the methodological problems linked to the identification of taxa in the field and in the laboratory, and 3. the problems this generates from the point of view of species conservation. To this end, at the end of the sequence, students present a taxon, from among those proposed in the UE, whose identification proves to be complex.

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The aim of this teaching unit is to take an integrative approach to animal behavior, in the light of Tinbergen's four "whys", from ontogeny to evolution: from ontogeny and neurobiological causes to evolution and biological functions. In addition to historical, conceptual and methodological contributions, students will be coached to apprehend the diversity of traits involved, as well as the diversity of approaches and associated scientific questioning.

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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, community),

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

- bioremediation processes through several case studies.

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The aim of this L3S5 course is to acquire knowledge of the organization, development and functioning of various physiological systems in animals. More specifically, the functions of circulation, thermoregulation, hormone regulation and nerve integration will be approached from a comparative perspective (examples drawn from different taxonomic groups) and in an evolutionary context. Questions relating to the bioethical aspects of experimentation in animal physiology will also be addressed.

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This teaching unit will cover the elements needed to understand the way of life of the major groups of unicellular organisms at the basis of ecosystem functioning (viruses, bacteria, archaea and unicellular eukaryotes....). The course covers the biological organization of each type of organism, its modes of reproduction and diversity, leading to notions of ecology. We will look at the role of these microorganisms in the functioning and dynamics of ecosystems, considering the interactions that these organisms maintain with other living beings (the notion of "symbiosis" in all its variations).

Practical work will :

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

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

 - demonstrating the specificity of interactions between bacteria and bacteriophages

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The main 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 in their evolutionary history. Teaching is integrative in the sense that it draws on both present-day organisms and the fossil record, so as 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 to illustrate the diversity and major characteristics of chordates. Practical work (and practical sessions) will illustrate the evolution of the diversity of integuments, skeleton, musculature, digestive and respiratory systems over long time scales.

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This course is a natural continuation of the " Quantifying Hazards " course (HAV424B) presented in S4. It should provide the concepts for constructing experimental protocols that answer biological questions, and for associating appropriate models for analyzing variability. The first part will be devoted to the construction of experimental protocols that can answer a multitude of questions in the life sciences, i.e. taking into account the inevitable dependence of statistical individuals, such as pairing and the spatial or temporal structure of populations. This part of the course will also introduce 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. The second part of the course 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 methods for estimating the parameters of the models constructed (including likelihood) and to the interpretation of the estimated parameters. Each notion will be illustrated by the analysis of real biological data from a variety of themes, helping students to discover not only modern and current biological questions, but also the tools developed to answer them. Practical work in R will enable students to independently carry out analyses on published biological cases.

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

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

Two sessions on the comprehension and oral presentation of scientific articles are held in conjunction with the "Evolutionary ecology and its applications" UE.

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For semester 6, students will be able to choose between 2 types of student project: (1) setting up a "Partenaires Scientifiques pour la Classe" (ASTEP) scheme, or (2) setting up a Data Acquisition and Processing (ATD) protocol. For the ASTEP project, students will carry out a scientific outreach project with kindergarten or primary school classes in the Hérault region (scientific themes defined by the partner schools). The students will then develop one or more experiments to be carried out with the classes, acquire data with the pupils and disseminate the scientific concepts 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 carried out in the field, in the classroom or consist of a meta-analysis.

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

Students also learn about the diversity of Angiosperms from a floristic point of view, by creating a herbarium of generally Mediterranean species. They also learn how to use a flora and digital identification tools (Pl@ntNet e-Flore from Tela Botanica, etc.).

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

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

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Students in the University's general bachelor's program take a number of introductory ecology courses during their first two years of study. In L3, they are introduced to a number of fundamental concepts concerning the 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 include the study of communities in the continuity of these foundations, in order to illustrate the role of species' evolutionary strategies in community formation. The teaching will be based on a sequence of lectures, tutorials and practical work in the form of field projects.

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

These courses will run in parallel with a "data production-analysis-interpretation" sequence of tutorials. Initially,serious games will be used to generate data based on simplified ecological mechanisms. To this end, several serious games for simulating communities are currently under development. These data will be collected by the students in preparation for their analysis. This will take the form of a computer-based workshop to familiarize students with diversity index calculations. Finally, time will be set aside to go back to the bibliography to find out whether the patterns produced by the sequence have a biological reality, and whether they have been observed in nature (independent work and report).

Once they have completed the TD sequence, students will start setting up in situ community ecology experiments through an introduction to field ecology, in the form of autonomous projects. This includes a workshop to 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 make it possible to place individuals(a fortiori communities) 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 zone, woods, old wall) on which they will carry out a floristic inventory. Following this, they will take several individuals of each species back to the laboratory to measure various functional traits. Once the measurements have been made, they will be able to calculate the various indices linked to the CSR strategy. The sequence will conclude with a report and an oral presentation. Other workshops are currently under development.

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The UE will consist of a case study to which the students will have to respond. The teaching staff of the UE will represent the management of design offices responsible for carrying out impact studies following a development project.

The students will play the role of experts from the consultancy firms, and will have to carry out analyses of the project area. They will have to provide a report on their impact study, in which they will have identified the ecological issues and ranked them according to their importance. They will also have to give an oral presentation of their study.

The UE will be structured around 6 2-hour TD sessions at the beginning of the semester, during which the following points will be covered:

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

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

For the remainder of the EU, students will be asked to propose study protocols for estimating the potential impacts of the planned project. The protocols set up will have to enable impacts to be assessed as closely as possible, and the studies will have to budget their interventions. They will then be given time in the field to set up their protocol, collect data and analyze it. The teaching team will tutor the groups to guide them in their work. They will write a dissertation based on specifications provided by the teaching team. This deliverable must be supported by field data and bibliographical data. They will defend their work in front of the teaching team during an oral presentation.

Several study areas were 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: fundamental and practical approach to the conservation and restoration of populations and communities

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

- ethical approach: reflection on biodiversity values (quantifiable, preferential, normative) and their application 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 "Modeling the living world: theory" course (S4 option), to provide an overview of the different approaches and techniques for modeling the living world. All the major families of mathematical models will be covered: both static (optimization problems, game theory) and dynamic (extensions of the systems seen in S4, introduction to stochastic processes). Examples of applications of these models will be diversified, covering a wide range of biological systems as well as different levels of organization (metabolic, epidemiological, meta-community models, etc.). 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, digital implementation/simulations on the other). Last but not least, it will provide an opportunity for students to familiarize themselves with research themes involving modeling, developed in the Montpellier area.

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This UE is structured around a professional inventory approach, during which students will be put in real-life situations to showcase their naturalist skills. It will consist of a field study, mainly involving field supervision by SPS for project follow-up. In this respect, it is in line with the logic of the former 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 vary from year to year, and will be chosen by the teaching team according to opportunities for collaboration with organizations interested in the proposed approach. The organizations approached are :

- Conservatoire des Espaces Naturels de Languedoc Roussillon

- Zoo du Lunaret, manager of the Lez reserve

- Montpellier metropolis

The feedback will consist of a common deliverable for the whole class, including a hierarchy of conservation issues. The organizations managing the areas studied 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. Taken together, these notions provide the keys to infer the stratigraphic context and past environments in which extinct organisms lived.

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Introduce students to an integrated approach to plants by studying the morpho-anatomical characteristics of stems and roots. They will discover the spatio-temporal coordinated construction of root and stem architectures through adaptations of Mediterranean and tropical species. Reproductive structures and the diversity of biological types will also be taken into account. This course is designed to prepare students for a Master's degree in BioGET, and is based on the natural environment and local and regional infrastructures (Serre Amazonienne, Villa Thuret, Jardin Château La Pérouse).

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This course provides an introduction to the ecology of continental freshwater and marine ecosystems, as well as to the interface 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, emphasizing both their similarities and their differences, and the abiotic and biotic factors that govern the organization of the communities of organisms that inhabit them.

They should provide an overview of these ecosystems or hydrosystems and how they function at different scales.

The first part of the course is devoted entirely to theory, while the second includes introductory sessions for field trips, the field trips themselves and practical sessions for analyzing and pooling the data collected in the field.

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Molecular tools are an integral part of studies aimed at describing and characterizing biodiversity. The aim of the course is to present various molecular approaches (barcoding, metabarcoding and environmental DNA, etc.) for (1) describing, characterizing and quantifying this diversity at intra- or interspecific, population or ecosystem levels, and (2) presenting their fields of application at different scales of time and space. The course will include practical aspects aimed at familiarizing students with these techniques, implementing them, analyzing the resulting data and reporting on them. Priority will be given to group work in interaction with researchers and teacher-researchers.

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One of the aims 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 present-day groups, this course will focus on extinct fossil groups, in particular their contribution to understanding the various 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 a theoretical and practical grounding in phylogeny (cladistics) for tracing the evolution of a clade (distance, parsimony and likelihood methods), both for molecular and phenotypic traits (present-day and fossil).

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Adaptations to the "parasitic" lifestyle are studied on all parasitic organisms (viruses, bacteria, eukaryotes), 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-escapement-exploitation of host resources, etc.), but also from the point of view of morpho-anatomical structures involved in adaptation to the sub-host site or in survival in the external environment, and finally from the point of view of behavioral adaptations for encountering the host (promotion).

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ORPAL is an APP ecology course (1/3 fieldwork and 2/3 laboratory work). Based on Ecology concepts and methods, this course aims to introduce students to historical ecology (the study of interactions between man and his environment over variable chronological periods) and its main applications in paleoecology, from problem definition, field sampling and data acquisition to interpretation and the 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 differences

- atmospheric structure, 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 above a cultivated plot to estimate evapotranspiration

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

- climate measurement methods, bioclimate indices ;

- Practical work on computer: climatic data, modern archives (century), oscillations and trends;

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

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

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

- past and future climate change, and their impact on biodiversity.

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At the end of this course, students will have acquired the basic knowledge needed to prepare and 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-raising workshops for the general public.

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Universities are often perceived as inaccessible places for large sections of society. As part of the UniverlaCité program, which aims to bring the university to life in disadvantaged neighborhoods, the students will be setting up scientific workshops for schoolchildren in disadvantaged areas. 

The EU will offer students the opportunity to :

1- share their own experiences and enhance the value of the knowledge they have acquired at the University, with a view to responding as effectively as possible to the needs of society.

2- Reveal and develop scientific communication skills through the design and production of teaching aids adapted to the target audience.

The course will take the form of tutorials and project follow-up (SPS) on pre-defined themes. The socio-cultural situation of sensitive urban areas will be addressed in the first class. This first TD will also serve to lay the foundations for the UE, present the UniverlaCité system in detail and give a broad overview of scientific mediation.

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

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

• degradation of natural environments, leading to loss of quality of natural resources (various forms of pollution) and loss of biodiversity
• climate change
• the artificialization of living environments
• new therapeutic approaches
• the globalization of trade
• standardized lifestyles

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In today's society, science is at the heart of many ethical, economic and societal issues. The aim of this course is to get students to 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 more aware of how to use scientific arguments in society, and to develop their critical faculties. In other words, it's an open-minded UE, enabling students to take a broader view while maintaining a scientific approach, in other words, "taking their heads off the handlebars".

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

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

- 2CM= 3h on the role of scientists in society (historical approach and discussion of 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, ... Starting with a press article, students work in groups to produce a presentation (to be included in the assessment), the aim of which is to provide a historical context, present opposing points of view with arguments (ethical and scientific arguments), and then lead a debate. Each debate session (3h) will have a theme, and researchers or ECs will be invited to take part in the jury and propose a summary at the end.

Working in groups for the duration of the course, students will produce a bibliographical synthesis on a topic of their choice, with a well-constructed argument, illustrated with carefully chosen examples, placing the subject in the context of the history of science and bioethical considerations. The idea is not just to give 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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