Bordeaux, June 3 – June 7, 2024.
Location
“Pôle de Vie” on Campus Carreire, 146 Rue Léo Saignat, 33000 Bordeaux.
Program
| Monday, June 3rd | Tuesday, June 4th | Wednesday, June 5th | Thursday, June 6th | Friday, June 7th |
| 9.00 – 10.00 Lecture by course leader The impressive role of philosophy & theory in immunology Thomas Pradeu |
9.00 – 10.00 Lecture by course leader The neuroscience of addiction Serge Ahmed |
9.00 – 10.00 Lecture by course leader Evolution & ecology: Predictions and unexpectedness: when the gazelle eats the lions Marie Vasse |
9.00 – 10.15 Group session 7 Finalizing presentations |
|
| 10.00 – 11.00 Tutorial Applying philosophical tools in PinS Fridolin Gross |
10.00 – 11.00 Tutorial What PinS is not. Philosophy and Scientific relevance Maël Lemoine |
10.00 – 11.00 Tutorial Bringing scientists and philosophers together Bertrand Daignan-Fornier |
10.15 – 11.00 Presentation of group results Group 3 |
|
| 11.00 – 11.30 Coffee Break |
11.00 – 11.30 Coffee Break |
11.00 – 11:30 Coffee Break |
11.00 – 11.30 Coffee Break |
|
| 11.30 – 13.00 Group session 1 |
11.30 – 13.00 Group session 3 |
11:30 – 13:00 Group session 5 Exchange with course leader from different group |
11.30 – 13.00 Presentation of group results Groups 1 and 5 |
|
| 13.00 – 14.00 Participant arrival |
13.00 – 14.30 Lunch / Meet the speakers |
13.00 – 14.30 Lunch / Meet the speakers |
13.00 – 14.30 Lunch / Meet the speakers |
13.00 – 14.30 Lunch / Meet the speakers |
| 14.00 – 14:45 Welcome and participant self-introductions |
14.30 – 15.30 Lecture by course leader Lesions and Persons: Philosophy in Neuropsychology Carl Craver |
14:30 – 17:00 Group session 4 First draft |
14.30 – 15.30 Lecture by course leader Philosophy of evolution: Philosophy in Phylogenetics: Braided Rivers All the Way Down Matt Haber |
14.30 – 16.00 Presentation of group results Groups 2 and 4 |
| 14.45 – 15.45 Tutorial What is “philosophy in science”? Jonathan Sholl |
15.30 – 17.00 Group session 2 |
15.30 – 17.00 Group session 6 |
16.00 – 16.30 Closing session |
|
| 15.45 – 16.15 Coffee Break & Group Picture |
17.00 – 17.30 Coffee Break |
17.00 – 17.30 Coffee Break |
17.00 – 17.30 Coffee Break |
|
| 16.15 – 17.15 Lecture by course leader The immune system: current concepts and the need for theory change Søren Paludan |
17.30 – 19.00 Social activity |
17.30 – 19.00 Speed dating Rapid one-on-one discussions with course leaders (optional) |
17.30 – 18.30 General discussion on PinS Chair: Jan Pieter Konsman |
|
| 17.15 – 18.15 Group meet-up |
||||
| 19.30 Apéro Aux 4 coins du vin (all participants) |
19.30 Speakers’ dinner |
Group Projects
An important part of the Summer School is a group activity in which you will go through the steps of a philosophy in science project under the guidance of a scientist and a philosopher. To make sure that the group work is interesting and relevant, we have asked our guest speakers to propose topics in line with their research interests. Below you will find materials to help you prepare for the project. We have assigned you to one of the groups based on your application profile. Please check which group you have been assigned to and read the corresponding description.
The reading materials can be found here. The password has been sent to you by email.
Group 1: Causal bidirectionality in integrated systems involving the nervous system
Course leaders
Carl Craver, Jan Pieter Konsman
Group members
Héloïse Athéa, Doudja Boumaza, Éloi Demange, Sarah Diner, Rose Gatfield-Jeffries
Description
The scientific problem
The so-called gut–microbiota–brain axis has recently been put forward to describe “the network of connections involving multiple biological systems that allows bidirectional communication between gut bacteria and the brain …” (Morais et al. 2021, p. 242). In stress research, “[t]he connection between the brain and the gut microbiota is [considered as] bidirectional” with ‘psychological’ stress altering the composition of gut microbiota and gut microbiota influencing stress responses (Morais et al., 2021, p. 249; Misiak et al. 2021; Madison & Bailey 2024). The availability of techniques to characterize gut microbiota composition and tools to intervene on gut microbiota has favored explanations in terms of ‘upward’ causation, from the gut microbiota to brain function. This, in turn, has led to questions regarding neuroendocrine differences observed in mental disorders such as: “Can we shift the blame to gut microbiota?” (Misiak et al. 2021)
Questions regarding the relationship between stress and the microbiota-gut-brain axis can be seen as an illustration of the increasing awareness among life scientists that many of the biological systems they are studying seem to display bidirectional causality in the sense that some parts of these systems can cause effects in other parts (or in the whole system) as well as the latter being able to affect the former. Indeed, in neuroscience, brain structures are now often considered to be connected by reciprocal neuronal projections. Similarly, regarding the function of many of the peripheral organ systems that the brain can modulate, these organ systems can typically also influence brain function.
The objectives will be
- to formulate a scientific problem relative to causation and the gut microbiota brain axis,
- to mobilize philosophy of science ideas, for example regarding levels, interventions, and mechanisms, which are all notions used by (neuro)scientists, and
- to put forward considerations and to formulate criteria regarding the clarification and the possibility of disentangling causal influences in integrated systems.
In addition, participants are encouraged to think about forms (based on spatial or part-whole relationships) of down- and upward causation.
Some philosophical notions
The life sciences frequently appeal to interventions based on hypothetical what-if questions. In the determination of what is often called counterfactual dependency (by philosophers) between a putative cause (C) and effect (E), the invariance (stability) of the relationship under the intervention given some background conditions as well as the absence of the reverse counterfactual relationship, (Woodward & Hitchcock 2003). Some of these criteria have been further refined by appealing to the notions of specificity and proportionality of cause and effect (including time and space considerations), and hence the importance of the choice of levels of explanation (Woodward 2010).
Debates about levels have been legion in philosophy and have resulted in many distinctions and some proposals to eliminate levels. Since scientists in many different domains employ some notion of levels, getting rid of a broad class of uses of levels may have many unforeseen consequences. Instead, promoting the use of distinction of levels may be more fruitful, even though local elimination or reformulation of levels may still be called for. One distinction that may be useful is to view mechanistic levels as levels of organization (Craver, in press). Appealing to mechanisms is widespread in causal explanations in the life sciences. Considering a minimal definition, according to which “[a] mechanism for a phenomenon consists of entities (or parts) whose activities and interactions are organized so as to be responsible for the phenomenon” (Glennan & Illari 2018, p. 92), this is not surprising as this definition can be applied to many situations. However, in mechanisms, one can often distinguish constitutional (vertical) part-whole relationships and etiological (horizontal) relationships. Applying these distinctions has been proposed to help in framing questions regarding up- and downward causation (Craver & Bechtel 2007). Here the challenge will be to apply these different notions in an attempt to tease apart possible bidirectional causation along the so-called microbiota-gut-brain axis. Indeed, here we will explore debates about the relationship between the gut and the brain as an example of a multilevel and dense causal mechanism, with a multitude of interactions and relations that run across and between multiple levels of organization and link in causal relations things that are in fact quite distinct from one another. Our goal is to disentangle the conceptual issues from the empirical ones so that the experimental focus can be on establishing important relations (whatever their form) that can be used for the purposes of understanding and controlling the relationships between the gut and the brain.
Scientific proposal based on mobilization of philosophical notions
The last challenge will be to formulate a proposal for (neuro)scientists based on these philosophical notions that would allow these scientists to tease apart causal influences in systems in which bidirectional (up- and downward) causation seems possible. This stage may, on the one hand, be expected to be relatively straightforward, but may, on the other hand, also be complicated by that fact scientists are already familiar with some notions of intervention, level and mechanisms.
Preparation
Essential readings
Background readings
Group 2: Is the chronic brain disease model of addiction challenged by the possibility of spontaneous remission?
Course leaders
Serge Ahmed, Maël Lemoine, Jonathan Sholl
Group members
Garance Castino, Jeremy Guttman, Yingying Han, Stephen Rowe
Description
If addiction is explained by a permanent change in major functional circuits of the brain, the possibility of spontaneous remission from addiction (e.g., following single life events) sounds implausible. Yet, since such remissions are documented, they seem to question the chronic brain disease model of addiction. Is it really the case? What would remain of that model, if spontaneous remission was taken seriously?
Preparation
Participants should read, in the following order:
Group 3: Early immune defenses: How and Why?
Course leaders
Hannah Kaminski, Søren Riis Paludan, Thomas Pradeu
Group members
Carla Feliciano, Coral González Martínez, Jacob Hamel-Mottiez, Kristina Humphreys
Description
Why is this question important and timely in today’s immunology?
Early host defense barriers eliminate many viruses before infections are established, and clear others so they remain subclinical or cause only mild disease. As such the first immunological reactions to invading pathogens are of utmost importance but remain incompletely understood. Immunology is a field that has historically been shaped by broad concepts, including the pattern recognition theory that currently dominates innate immunology, and which proposes that pattern recognition receptors should be considered as “the first line of defense” against pathogens (Medzhitov and Janeway 2002). However, the responses evoked by pattern recognition receptors potently induces inflammation, and although we are frequently exposed to viruses, we do not often have fever. Moreover, some organs and cell types are highly sensitive to inflammation, and are unlikely to mount inflammatory response as the immediate response to viruses. Therefore, it can be argued that there is currently no unifying and broadly accepted theory for the biological principles that govern the first line of host defense. This is needed to explain clinically important phenomena such as: (i) Subclinical elimination of infections, (ii) Transmission of infections, (iii) Zoonotic “hosting” of viral reservoirs, (iv) Antiviral defense by inflammation-sensitive organs/cells. It is hence important to build a theory that can explain the first line of defense against infections.
Assignment
Laying the foundations of a rigorous and useful conceptual and theoretical account of early immune defenses.
Guiding Question
How can we collectively build a novel conceptual and theoretical framework to shed light on early immune defenses, and how can philosophical tools be useful for achieving this goal?
More specific guiding questions
- Why are the current accounts of early immune defenses unsatisfactory?
- What goals should an alternative account of early immune defenses achieve?
- Which immunological phenomena should be included in a novel conceptual and theoretical account of early immune defenses? For example, should this account include only responses to viruses, or responses to other microbes as well? Should it include other situations, such as cancer and autoimmunity? Should we include the early immune responses to the microbiome and to viruses that belong to the virome (e.g., TTV)? Can we figure out whether early immune response are involved in virus latency?
- Are early immune responses that do not come with inflammation the product of a specific form of homeostasis? If so, which one?
- Why and how did anti-inflammatory early immune responses evolve? Both excessive inflammation and insufficient inflammation can be extremely costly in terms of fitness, so how was a balance reached with regard to such fundamental trade-offs?
- Epistemologically, when exactly must a novel theoretical framework emerge in a given scientific domain? What are the most central components of a satisfactory theory? How can philosophers of science help in building a novel scientific theory?
Preparation
Essential
Additional
If you have no background in immunology, please read pages 3-13 of Pradeu’s Philosophy of Immunology, which give a very basic introduction:
Group 4: The Emergence of Individuals in Microbiology
Course leaders
Matt Haber, Marie Vasse
Group members
Aurore Aymerie dit Eymeric, Yasmin Bar-Tzlil, Jonah Branding, Ge Fang, Cassandra Zie Yang
Description
Background/Sample Case
Knowing that groups of bacteria virtually inhabit and are key components of all types of ecosystems have fostered vast empirical and theoretical research. The very object of such research, however, may be elusive: are we investigating the behavior, ecology and/or evolution of single cells? Of populations? Of communities? And which of those can function as individuals?
Here we propose to explore the concept of (transition to) individuality in bacterial groups. While selection and co-option have been traditionally presented as causes of collective-level reproduction, Black et al (2020) examine how ecological conditions may shape the emergence of the cell collectives. They propose a model in which ecological cycles of cell growth, dispersal, and colonization on discrete resource patches lead to two fundamentally different evolutionary outcomes depending on the dispersal regime. Only in the slow regime cells evolve restrained growth rate (and even cell differentiation and division of labor). This work is an example of an alternative narrative to understand the evolution of collectivity.
Assignment
Consider the guiding questions below as applied to the case described above. How are the empirical and conceptual questions intrinsically bound to one another?
Guiding Questions:
- When should we regard groups of bacteria as individuals?
- More precisely, what sorts of behaviors do bacteria display that generate a collective identity as a new biological individual?
This is not merely an empirical question, but a conceptual one as well. Namely, what sort of criteria ought we employ to determine when groups of bacteria may be regarded as a biological individual?
More specific guiding questions:
- Is there a single set of criteria that we ought to employ in the case of microbes, or are there multiple different criteria we might employ? If the latter, does that mean we are employing different notions of biological individuality, or are we capturing different facets of a complex notion?
- If there are different criteria of individuality we might employ, how do we determine which criteria are the correct ones to use for the research problem at hand?
- Are the criteria we ought to use to assess microbial individuality distinctive from other levels of biological organization, or are we discovering general criteria that applies generally across biology.
- How do the criteria of individuality that we employ direct empirical research questions? For example, how do competing criteria change the way we think about a biological individual’s boundaries, identity, or composition? What, if anything, is at stake in these competing claims (e.g., do we end up with competing ‘counts’ of the number of individuals)?
- Do biological individuals come in degrees? What sort of persistence criteria do we expect of individuals, e.g., may biological individuals persist only ephemerally, may they exist intermittently with gaps, or must they persist without interruption over a relevantly meaningful amount of time?
Preparation
Essential readings
Additional readings
Group 5: Division of labor across the tree of life
Course leaders
Bertrand Daignan-Fornier, Fridolin Gross
Group members
Claudio Davini, Claudia Gadaleta, Jokūbas Janušauskas, Tianqin Ren, Sebastian Sander Oest
Description
Division of labor is of central importance in biology and an idea that is increasingly used in relation to a variety of phenomena in different taxa, from microbes (e.g. West & Cooper 2016) to social insect colonies to the evolution of modularity in plants and animals (e.g. Rueffler et al. 2012) and the evolution of human societies (e.g. Nakahashi & Feldman 2014). On closer inspection, however, this concept appears to be used in very different ways in different biological contexts. This raises the crucial question of whether division of labor in biology is a unified concept at all and whether similar reasoning and modeling can be used in the different contexts in which it is applied. Are there different forms of division of labor and should we reconsider and redefine it based on the different forms it takes in the tree of life? Are there common underlying features of the division of labor in different biological contexts? Do the molecular mechanisms involved in the division of labor tell us more than just how it happens?
More specifically, we propose in this project
- to gain an overview of the different explanations and models of division of labor and the different molecular mechanisms proposed at the level of microorganisms or multicellular organisms
- to systematically investigate the similarities and differences within and between these levels and to ask whether these differences are in degree or in kind
- to propose a meaningful classification of the cellular division of labor across the tree of life on this basis.
Preparation
In preparation we would like all of you to read the following paper:
In addition, each member of the group should pick one among the following papers and prepare a small summary of the main ideas. Please note that some of them can be a little technical. So it would be good if you coordinate among yourselves who chooses which paper, depending on your respective interests and background.