SOPhiA 2018

Salzburgiense Concilium Omnibus Philosophis Analyticis

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Programme - Talk

Biological Individuality and other Issues in Contemporary Philosophy of Biology
(Affiliated Workshop, English)

The goal of this workshop is to provide a platform for international researchers and scholars in philosophy of biology, with particular emphasis on the issue of biological individuality. It is a major topic in philosophy of biology as well as biology itself.
Among the questions that will be addressed during the workshop are the following: What are the conditions for being a biological individual? What does being a biological individual imply? How can `biological individual' be best defined? How to account for microbiota and their interactions in relation to an organism and its biological individuality? How is biological individuality preserved through time?
This workshop brings together leading experts and young researchers from philosophy of biology and other areas of philosophy of science, thus promising to advance the philosophical and scientific debates surrounding the issues mentioned above.


10:00--10:15 Karim Baraghith & Gregor Greslehner: Introduction
10:15--11:00 Thomas Reydon: What does ''individuals thinking'' solve?
10:45--11:00 Coffee break
11:00--11:30 Özlem Yılmaz: 'Individual Plant' Why it matters?
Short break
11:30--12:00 Isabella Sarto-Jackson: Using Cognitive Biology to Tackle Individuality
12:00--14:00 Lunch break
14:00--14:30 Adrian Stencel & Agnieszka Proszewska: Some theoretical insights into the hologenome theory of evolution
14:30--14:45 Coffee break
14:45--15:15 Javier Suárez: A stability of traits model for the evolution of holobionts
15:15--15:30 Coffee break
15:30--16:00 Steve Elliot: An Account of Research Problems in Science


Steve Elliot (Arizona State University): An Account of Research Problems in Science
Heather Douglas (2014) has recently critiqued distinctions between pure and applied science as conceptually, historically, and practically ill-founded. She further argues that if we focus less on the explanatory functions of science, and more on other functions such as prediction and intervention, then we might develop a sense of progress in science that survives issues of major theory changes or paradigm shifts, especially if those functions are socially and ethically contextualized. How to do so remains an open project, and I here suggest one route by which to pursue it. I focus on the level of research projects, which scientists and philosophers widely conceptualize as addressing research problems, and which they judge as successful partly when those problems have been in fact addressed. How do scientists conceptualize and evaluate research problems? Traditional accounts of research problems focus only on problems to theories (Kuhn 1962, Laudan 1977, Nickles 1981). Given Douglas's critique of the pure/applied distinction, those accounts fail to capture the diverse range of problems pursued in science. I propose a new conceptual framework of problems that accounts both for theory-focused problems and for so-called practical problems, and I illustrate the account with a case from evolutionary biology. The account fits problem-solving practices within Douglas's critique, shows how projects are socially and ethically contextualized, and underwrites senses of success for individual projects and of progress across projects. I close by indicating how this account could infuence debates about biological individuality.

Thomas Reydon (Hannover): What does ''individuals thinking'' solve?
Philosophy of biology is seeing an increasing ''enthusiasm for individuality''. Not only has the concept of individuality (in biology as well as in other sciences) itself become a topic of investigation (e.g., Guay & Pradeu, 2016; Lidgard & Nyhart, 2017), but it is also increasingly argued that things that we hadn't seen as individuals actually are best thought of individuals. Perhaps the most famous case is Ghiselin's (1966; 1974) and Hull's (1976; 1977; 1978) suggestion that species are individuals and not kinds, a view that was presented as a ''radical solution to the species problem'' (Ghiselin, 1974). More recently, Rosenberg (2006) argued that genes (that is, gene types) are individuals, not kinds, and presented this view as a solution to the quest for a definition of the gene category. And Mariscal & Doolittle (2018) recently argued that life is an individual and not a kind of entities (i.e., the kind of living entities), presenting this as a radical solution to the search for a definition of life.
In all three cases, the strategy is the same: A term (`life', or `living being') or collection of terms (the various names of species, the various names of genes) are thought to be kind terms, and the problem is what makes entities into members of particular kinds. The problem turns out to be persistent, as no agreement is reached on the necessary and sufficient conditions for kind membership. Then, the suggestion is made that the reason for the persistent failure to solve the problem is that we had gotten the metaphysical category wrong: life, species, and genes are individuals, not kinds. This suggestion, then, is taken as a radical solution to the problem, because the search for conditions for kind membership has ended.
While such ``individuals thinking'' clearly solves the old problem (i.e., the search for conditions of kind membership), it raises new issues that are at least as hard to solve as the old problem ? or so I want to argue. In particular, these solutions replace questions about kind-member relations by parallel questions about individual-part relations, that are as hard to resolve as the original questions. For example, the claim that something is an individual by itself strongly underdetermines the relation between the individual and its parts (e.g., the individual called Drosophila melanogaster and the many fruit flies that allegedly are parts of this individual; the individual called `life' and the many living beings that are part of this individual). Thus, the question arises what, exactly, makes a fruit fly a part of its species or a gene token part of its gene type (lineage). What the cases mentioned above suggest, I will argue, is that at least in some cases in biology ``individuals thinking'' is not a feasible alternative for ``kinds thinking'' and we might need both perspectives to make sense of the metaphysics of the things under study.

-- Ghiselin, M.T. (1966): `On psychologism in the logic of taxonomic controversies', Systematic Zoology 15: 207--215.
-- Ghiselin, M.T. (1974): `A radical solution to the species problem', Systematic Zoology 23: 536--544.
-- Guay, A. & Pradeu T. (Eds) (2016): Individuals Across the Sciences, New York: Oxford University Press.
-- Hull, D.L. (1976): `Are species really individuals?', Systematic Zoology 25: 174--191.
-- Hull, D.L. (1977): `The ontological status of species as evolutionary units', in: Butts, R. & Hintikka, J. (Eds.): Foundational problems in the special sciences, Dordrecht: D. Reidel, pp. 91--102.
-- Hull, D.L. (1978): `A matter of individuality', Philosophy of Science 45: 335--360.
-- Lidgard, S. & Nyhart, L.K. (Eds) (2017): Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives, Chicago & London: University of Chicago Press.
-- Mariscal, C. & Doolittle, W.F. (2018): `Life and life only: A radical alternative to life definitionism', Synthese, online first.
-- Rosenberg, A. (2006): Darwinian Reductionism, Or, How to Stop Worrying and Love Molecular Biology, Chicago: University of Chicago Press.

Isabella Sarto-Jackson (Konrad Lorenz Institute for Evolution and Cognition Research (KLI), Klosterneuburg): Using Cognitive Biology to Tackle Individuality
The basic tenets of cognitive biology (Kovac 2000; 2015) hold that living systems strive to continue to exist and keep their onticity thereby continuously undergoing a process of knowledge acquisition (i.e., cognition). In order to persist, living systems must incessantly perform ontic work. This means, a system self-organizes, maintains stability, and remains distant from equilibrium by dissipating energy gradients and constructing kinetic barriers that prevent or retard destruction and dissipation. Onticity is accompanied by epistemic work, e.g., sensing, measuring, recording, and in some (more cognizant) cases, anticipating properties of the surroundings. Evolution of cognition can thus be seen as thermodynamic deepening, and the process of continuous increase of the distance from equilibrium reflects a measure of epistemic complexity. Epistemic complexity enfolds two processes: firstly, of the evolutionary past, and secondly, of the total set of potential actions to be performed in future.
According to cognitive biology, all levels of epistemic complexity in living systems -- from molecules, cells, tissues and organisms, to social institutions and culture -- represent embodied knowledge that has accumulated over evolutionary times and has been retained by natural selection. By contrast, nomic interactions of individual atoms and molecules, such as chemical reactions in the inanimate world, with no evolutionary history, are deterministic, timeless, and do not represent cognition.
Along this line of arguments, evolution of cognition is a unidirectional, cumulative process that voraciously dissipates all available energy gradients, uses them to increase its knowledge, and uses the knowledge to search for new gradients. Most importantly, data of the surroundings can be transformed into knowledge in a specific, subject-dependent way. This transformation process can be understood as information that is used by a system to reduce uncertainty (Kovac 2007). The acquired knowledge is embodied in the construction of individuals, suggesting that individuals can be described as ``copies'' of the same ontic and epistemic system. Therefore, biological individuality is assumed to be hierarchically nested, from molecular sensors up to organisms, communities, species, an individual at each level of hierarchy being a distinct cognitive subject engaged in ontic and epistemic work.
This idea of individuality converges with Krakauer et al. (2014) who have argued that biological individuality can be usefully understood in terms of informational individuality. Here, individuality is not formulated as binary, but continuous. Consequently, there may be multiple degrees of individuality at all levels of biological organization and some processes may possess greater individuality than others. Essential to individuality is the propagation of information forward in time and the concomitant reduction in uncertainty.
Following Krakauer et al., I will argue that information theoretic language can be used to quantify a system's degree of individuality. This approach relates individuals to statistical mechanics and thermodynamics without falling prey to physical reductionism (i.e., without explaining features of biological science through first principles of physics).

-- Kovac, Ladislav (2000) Fundamental Principles of Cognitive Biology. Evolution and Cognition 6, 51-?69
-- Kovac, Ladislav (2007) Information and Knowledge in Biology. Plant Signaling & Behavior 2, 65--73
-- Kovac, Ladislav (2015) Closing Human Evolution: Life in the Ultimate Age. Springer, Dordrecht
-- -Krakauer, David, Bertschinger, Nils, Olbrich, Eckehard, Ay, Nihat and Flack, Jessica C. (2014) The Information Theory of Individuality. ArXiv

Adrian Stencel & Agnieszka Proszewska (Jagiellonian University, Poland): Some theoretical insights into the hologenome theory of evolution
Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts as a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated.
In this talk, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. As a background for the discussion we chose the debate about the units of selection as presented by Godfrey-Smith, which is, as we believe, the most detailed elaboration of this sort. Then, we argue that holobionts do not fullfil requirements distiguished by Godfrey-Smith and, thus, should not be generally considered units of selection. Secondly, we present the idea that, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. This can be achieved by analysing the idea idea of holobiont based on the concept of organismality, developed by Queller and Strasmann.

Javier Suárez (Logos Universidad de Barcelona, Spain & Egenis: The Centre for the Study of Life Sciences, University of Exeter (UK)): A stability of traits model for the evolution of holobionts
Holobionts are biological entities that consist of a multicellular eukaryotic host plus its symbiotic microbiome. Holobionts are omnipresent in the living world and they are supposed to bear traits, resulting from the dynamic interactions between the host and its symbionts. Defenders of the holobiont view have recently developed the ''hologenome concept of evolution,'' according to which holobionts are units of selection in evolution (Rosenberg & Zilber-Rosenberg 2013, 2015; Theis et al. 2016; Roughgarden et al. 2017). This claim has been recently criticized by many, who argue that holobionts cannot be considered units of selection because the entities that compose a holobiont are not faithfully transmitted intergenerationally as a unit and, therefore, their influence in the holobiont is not evolutionarily constant. As inheritance is taken as a necessary condition for a biological entity to be a unit of selection, critics argue, the fact that inheritance is intergenerationally disrupted undermines the conceptual possibility of holobionts being units of selection (Moran & Sloan 2015; Douglas & Werren 2016).
In this talk, I contest this argument by distinguishing between the notions of stability of species and stability of traits. Stability of species demands that the different species that integrate a holobiont are faithfully transmitted every generation for the holobiont to be a unit of selection. Stability of traits, however, is based on the concept of group selection and it only requires the existence of a statistical correlation among the traits that are identified across generations of holobionts for holobionts to be units of selection: whether (or whether not) the species that are responsible for the appearance of the traits reoccur every generation is conceptually irrelevant for holobionts to be units of selection. I defend that the arguments that have been offered against the role of holobionts as units of selection assume the idea of stability of species, which I argue to be conceptually mistaken for representing the concept of units of selection. I further argue that the idea of stability of traits is more suitable for capturing the role of holobionts as units of selection, as it identifies the minimal properties that must be discovered for any entity to evolve by natural selection. Finally, I conclude presenting the relationship between the two notions and speculating about how the notion of stability of traits would affect the conceptualization of the units of selection.

Özlem Yılmaz (KLI (Konrad Lorenz Institute for Evolution and Cognition Research), Klosterneuburg): 'Individual Plant' Why it matters?
Plant Science involves many areas of biology. First, I will talk a bit on Phenomics and Genomics in Plant Science and why Plant Phenomics has been getting more and more attention recently. Then I will argue: it is very clear that plant scientists are dealing with ?processes not things? (Dupré 2012) and thinking life as processes is a very good way for our understanding of plant life. I will give example cases from Plant Physiology area and I will emphasize: `individual plant' is very important in these experiments.
Phenome of an individual plant is a process that is constituted from many complex interacting processes: evolutionary, developmental, ecological, physiological, molecular. Although scientists are usually concerned about a phenotypic trait through one area of biology, they consider other processes too in their experiment designs. For example: C3 and C4 plants have different leaf anatomies than each other; along with those anatomies, they also have some different physiological activities in photosynthesis. Both the leaf anatomies and the physiological activities are some kinds of stabilized processes that have been obtained and have been actively sustained through many kinds of interacting processes. C4 plants have evolved as having a carbon-concentrating mechanism. C4 and C3 plants have also different kinds of interactions with their environments than each other. When we observe, or measure a phenotypic trait, related to photosynthetic activity, of a plant, we are aware that: the fact if it is a C3 or C4 plant affects that trait. There are many other factors that we should consider: species, sub-species, cultivar etc. of the plant (about its genome; so, affecting its phenome), at which stage of development it is in, what kind of environment it is living in, what kind of environments it has lived in (affecting its phenome and epigenome), what kind of environments its parents -- recent ancestors -- lived it (about its epigenome; so, affecting its phenome). Another very important factor is plant microbiota, which is in interaction (directly or indirectly) with all the processes of the individual plant (we may even say they are part of the individual plant). For example, there are many species of bacteria that is living in and around the roots of plants. They may affect plants in many ways, for example: they usually make it easy for plants to acquire nutrients from the soil (e.g. some of these bacteria, like Rhizobium, do nitrogen fixation) and they affect adaptation and acclimation to the stress conditions.

--Dupré J. (2012) Processes of Life. Oxford University Press
--Dupré J. (2018) The Metaphysics of Evolution Article in Interface focus: a theme supplement of Journal of the Royal Society interface · January 2018
--Taiz L Zeiger E. (2010) Plant Physiology. Fifth Edition. Sinauer Associates, Inc.

Organisation: Karim Baraghith (Düsseldorf) & Gregor Greslehner (Salzburg).

Chair: Karim Baraghith & Gregor Greslehner
Time: 10:00-16:00, 15 September 2018 (Saturday)
Location: SR 1.006

Steve Elliot 
(Arizona State University, USA)

Thomas Reydon 
(University of Hanover, Germany)

Isabella Sarto-Jackson 
(KLI, Austria)

Adrian Stencel 
(Jagiellonian University, Poland)

Agnieszka Proszewska 
(Jagiellonian University, Poland)

Javier Suárez 
(Logos Universidad de Barcelona & Egenis: The Centre for the Study of life Sciences, Spain & UK)

Özlem Yılmaz 
(KLI, Austria)

Testability and Meaning deco