Here you will find publications, presentations and other scientific products of the Possible Life project.
Martin Zach & Gregor P. Greslehner. 2023. Biology & Philosophy 38
In this paper we address the issue of how to think about immunity. Many immunological writings suggest a straightforward option: the view that the immune system is primarily a system of defense, which naturally invites the talk of strong immunity and strong immune response. Despite their undisputable positive role in immunology, such metaphors can also pose a risk of establishing a narrow perspective, omitting from consideration phenomena that do not neatly fit those powerful metaphors. Building on this analysis, we argue two things. First, we argue that the immune system is involved not only in defense. Second, by disentangling various possible meanings of ‘strength’ and ‘weakness’ in immunology, we also argue that such a construal of immunity generally contributes to the distortion of the overall picture of what the immune system is, what it does, and why it sometimes fails. Instead, we propose to understand the nature of the immune system in terms of contextuality, regulation, and trade-offs. We suggest that our approach provides lessons for a general understanding of the organizing principles of the immune system in health and disease. For all this to work, we discuss a wide range of immunological phenomena.
Natalia Carrillo and Tarja Knuuttila. 2022. Studies in History and Philosophy of Science
Idealization is commonly understood as distortion: representing things differently than how they actually are. In this paper, we outline an alternative artifactual approach that does not make misrepresentation central for the analysis of idealization. We examine the contrast between the Hodgkin-Huxley (1952a, b, c) and the Heimburg-Jackson (2005, 2006) models of the nerve impulse from the artifactual perspective, and argue that, since the two models draw upon different epistemic resources and research programs, it is often difficult to tell which features of a system the central assumptions involved are supposed to distort. Many idealizations are holistic in nature. They cannot be locally undone without dismantling the model, as they occupy a central position in the entire research program. Nor is their holistic character mainly related to the use of mathematical and statistical modeling techniques as portrayed by Rice (2018, 2019). We suggest that holistic idealizations are implicit theoretical and representational assumptions that can only be understood in relation to the conceptual and representational tools exploited in modeling and experimental practices. Such holistic idealizations play a pivotal role not just in individual models, but also in defining research programs.
Marvin Rost and Tarja Knuuttila. 2022. Educ. Sci. 2022, 12(4), 276
Models are at the core of scientific reasoning and science education. They are especially crucial in scientific and educational contexts where the primary objects of study are unobservables. While empirical science education researchers apply philosophical arguments in their discussions of models and modeling, we in turn look at exemplary empirical studies through the lense of philosophy of science. The studied cases tend to identify modeling with representation, while simultaneously approaching models as tools. We argue that such a dual approach is inconsistent, and suggest considering models as epistemic artifacts instead. The artifactual approach offers many epistemic benefits. The access to unobservable target systems becomes less mysterious when models are not approached as more or less accurate representations, but rather as tools constructed to answer theoretical and empirical questions. Such a question-oriented approach contributes to a more consistent theoretical understanding of modeling and interpretation of the results of empirical research.
Natalia Carrillo and Sergio Martínez. 2022. Perspectives on Science
In philosophy of science, abstraction tends to be subsumed under representation, often
being described as the omission of a target’s features when it is represented. This approach to
abstraction sidesteps cognitive aspects of abstraction processes. However, cognitive aspects of
abstraction are important in understanding the role of historically grounded epistemic criteria
supporting modeling in science. Drawing on recent work on the relation between metaphor and
abstraction, we introduce the concept of paths of abstraction, and use historical and contemporary
examples to point to their role in guiding the development of relevance criteria which support
modeling strategies in science.
Tarja Knuuttila and Andrea Loettgers. 2022. Philosophy of Science
Synthetic biology has a strong modal dimension that is part and parcel of its engineering agenda. In turning hypothetical biological designs into actual synthetic constructs, synthetic biologists reach towards potential biology instead of concentrating on naturally evolved organisms. We analyze synthetic biology’s goal of making biology easier to engineer through the combinatorial theory of possibility, which reduces possibility to (re)combinations of individuals and their attributes in the actual world. While the last decades of synthetic biology explorations have shown biology to be much more difficult to engineer than originally conceived, synthetic biology has not given up its combinatorial approach.
Carrillo, Natalia & Tarja Knuuttila. 2021. in Alejandro Cassini and Juan Redmond (eds.) Models and Idealizations in Science: Fictional and Artifactual Approaches. Springer.
There are two traditions of thinking about idealization offering almost opposite views on their functioning and epistemic status. While one tradition views idealizations as epistemic deficiencies, the other one highlights the epistemic benefits of idealization. Both of these, however, identify idealization with misrepresentation. In this article, we instead approach idealization from the artifactual perspective (Knuuttila 2005, 2011, 2017), comparing it to the distortion-to-reality accounts of idealization, and exemplifying it through the case of the Hodgkin and Huxley model of nerve impulse. From the artifactual perspective, the epistemic benefits and deficiencies introduced by idealization frequently come in a package due to the way idealization draws together different resources in model construction. Accordingly, idealization tends to be holistic in that it is not often easily attributable to just some specific parts of the model (even though it might seem so at first glance). Instead, the idealizing process tightly embeds theoretical concepts and formal tools into the construction of a model.
Knuuttila, Tarja & Andrea Loettgers. 2021. Perspectives on Science 9(4).
This paper examines two parallel discussions of scientific modeling which have invoked experimentation in addressing the role of models in scientific inquiry. One side discusses the experimental character of models, whereas the other focuses on their exploratory uses. Although both relate modeling to experimentation, they do so differently. The former has considered the similarities and differences between models and experiments, addressing, in particular, the epistemic value of materiality. By contrast, the focus on exploratory modeling has highlighted the various kinds of exploratory functions of models in the early stages of inquiry. These two perspectives on modeling are discussed through a case study in the field of synthetic biology. The research practice in question explores biological control by making use of an ensemble of different epistemic means: mathematical models and simulations, synthetic genetic circuits and intracellular measuring devices, and finally electronic circuits. We argue that the study of exploratory modeling should trace the ways different epistemic means, in different materialities, are being combined over time. Finally, the epistemic status of such novel investigative objects as synthetic genetic circuits is evaluated, with the conclusion that they can function as both experiments and models.
Knuuttila, Tarja. 2021. European Journal for Philosophy of Science.
The epistemic value of models has traditionally been approached from a representational perspective. This paper argues that the artifactual approach evades the problem of accounting for representation and better accommodates the modal dimension of modeling. From an artifactual perspective, models are viewed as erotetic vehicles constrained by their construction and available representational tools. The modal dimension of modeling is approached through two case studies. The first portrays mathematical modeling in economics, while the other discusses the modeling practice of synthetic biology, which exploits and combines models in various modes and media. Neither model intends to represent any actual target system. Rather, they are constructed to study possible mechanisms through the construction of a model system with built-in dependencies.
Pättiniemi, Ilkka, Rami Koskinen & Ilmari Hirvonen. 2021. Acta Philosophica Fennica.
We review some of the major accounts in the current epistemology of modality and identify some shared issues that plague all of them. In order to provide insight into the nature of modal statements in science, philosophy, and beyond, a satisfactory epistemology of modality would need to be suitably applicable to practical and theoretical contexts by limited beings. However, many epistemologies of modality seem to work only when we have access to the kind of knowledge that is at least currently beyond our reach. Or, in the extreme case, it is argued that even if we knew all the relevant information about the respective domain – or even the entire state of the world – there would still remain a special class of modal truths that would be left unaccounted for. Neither picture bodes well for practical applicability, nor for the philosophical justification of these epistemologies. This is especially the case as we hold that one of the main motivations for modal inquiry typically arises in cases of imperfect information and limited cognitive resources. We close by providing a partial remedy to the situation by suggesting an overall framework of relative modality (RM) that can be used to both unify some existing modal epistemologies and, at the same time, make them more metaphysically modest.
Ijäs, Tero & Rami Koskinen. 2021. European Journal for Philosophy of Science 11:39.
This paper analyzes the notion of possibility in biology and demonstrates how synthetic biology can provide understanding on the modal dimension of biological systems. Among modal concepts, biological possibility has received surprisingly little explicit treatment in the philosophy of science. The aim of this paper is to argue for the importance of the notion of biological possibility by showing how it provides both a philosophically and biologically fruitful category, as well as introducing a new practically grounded way for its assessment. More precisely, we argue that synthetic biology can provide tools to scientifically anchor reasoning about biological possibilities. Two prominent strategies for this are identified and analyzed: the design of functionally new-to-nature systems and the redesign of naturally occurring systems and their parts. These approaches allow synthetic biologists to explore systems that are not normally evolutionarily accessible and draw modal inferences that extend in scope beyond their token realizations. Subsequently, these results in synthetic biology can also be relevant for discussions on evolutionary contingency, providing new methods and insight to the study of various sources of unactualized possibilities in biology.
Hirvonen, Ilmari, Rami Koskinen & Ilkka Pättiniemi. 2021. Synthese.
Recent epistemology of modality has seen a growing trend towards metaphysics-first approaches. Contrastingly, this paper offers a more philosophically modest account of justifying modal claims, focusing on the practices of scientific modal inferences. Two ways of making such inferences are identified and analyzed: actualist-manipulationist modality (AM) and relative modality (RM). In AM, what is observed to be or not to be the case in actuality or under manipulations, allows us to make modal inferences. AM-based inferences are fallible, but the same holds for practically all empirical inquiry. In RM, modal inferences are evaluated relative to what is kept fixed in a system, like a theory or a model. RM-based inferences are more certain but framework-dependent. While elements from both AM and RM can be found in some existing accounts of modality, it is worth highlighting them in their own right and isolating their features for closer scrutiny. This helps to establish their relevant epistemologies that are free from some strong philosophical assumptions often attached to them in the literature. We close by showing how combining these two routes amounts to a view that accounts for a rich variety of modal inferences in science.
Kriegleder, Moritz. 2021. Constructivist Foundations 16(3).
I reflect on the notion of lived space and affective resonance as discussed in the target article in the light of the theory of active inference. Interpreting perceptual presence as a form of enactive inference could link the findings presented in the article to a richer theoretical framework that allows for quantitative modelling and neurophenomenological extensions of the present study design. Implementing mutual constraints from complementary neurological or behavioral data could validate or adapt the categories derived in the article.
Greslehner, Gregor P. 2021. Archives of Virology 166.
I will offer a conceptual analysis of different notions of structure and function of viral immunogens and of different structure-function relationships. My focus will then be on the mechanisms by which the desired immune response is induced and why strategies based on three-dimensional molecular antigen structures and their rational design are limited in their ability to induce the desired immunogenicity. I will look at the mechanisms of action of adjuvants (thus the wordplay with Janeway’s “immunologist’s dirty little secret”). Strategies involving adjuvants and other (more successful) vaccination strategies rely on taking into account activities and functions (“what is going on”), and not just the structures involved (“who is there”), in binding in a “lock and key” fashion. Functional patterns as well as other organizational and temporal patterns, I will argue, are crucial for inducing the desired immune response and immunogenicity. The 3D structural approach by itself has its benefits – and its limits, which I want to highlight by this philosophical analysis, pointing out the importance of structure-function relationships. Different functional aspects such as antigenicity, immunogenicity, and immunity need to be kept separate and cannot be reduced to three-dimensional structures of vaccines. Taking into account different notions of structure and function and their relationships might thus advance our understanding of the immune system and rational HIV vaccine design, to which end philosophy can provide useful tools.
Koskinen, Rami. 2020. ChemBioChem 21: 2591
Besides having potential medical and biosafety applications, as well as challenging the foundations of biological engineering, xenobiology can also shed light on the epistemological and metaphysical questions that puzzle philosophers of science. This paper reviews this philosophical aspect of xenobiology, focusing on the possible multiple realizability of life. According to this hypothesis, what ultimately matters in understanding life is its function, not its particular building blocks. This is because there should, in theory, be many different ways to build the same function. The possibility of multiple realizability was originally raised in the context of AI’s hypothesized capacity to realize mental functions. As we still do not have any incontrovertible examples of digital minds, not to mention alien life of foreign biochemistry, the best way to test this philosophical idea is to examine the recent results and practices of synthetic biology and xenobiology.
Knuuttila, Tarja & Rami Koskinen. 2020. Synthese.
The recent discussion of fictional models has focused on imagination, implicitly considering fictions as something inconcrete. We present two cases from synthetic biology that can be viewed as concrete fictions. Both minimal cells and alternative genetic systems are modal in nature: they, as well as their abstract cousins, can be used to study unactualized possibilia. We approach these synthetic constructs through Vaihinger’s notion of a semi-fiction and Goodman’s notion of semifactuality. Our study highlights the relative existence of such concrete fictions. Before their realizations, neither minimal cells nor alternative genetic systems were any well-defined objects, and the subsequent experimental work has given more content to these originally schematic imaginings. However, it is as of yet unclear whether individual members of these heterogeneous groups of somewhat functional synthetic constructs will eventually turn out to be fully realizable, remain only partially realizable, or prove to be outright impossible.
Knuuttila, Tarja & Andrea Loettgers. 2020. In Sune Holm and Maria Serban (eds.) Living Machines? Philosophical Perspectives on the Engineering Approach in Biology. Routledge.
One striking feature of the contemporary modeling practice is its interdisciplinarity: the same function forms and equations, and mathematical and computational methods are being transferred across disciplinary boundaries. Within philosophy of science this interdisciplinary dimension of modeling has been addressed by both analogy and template-based approaches that have proceeded separately from each other. We argue that a more fully-blown account of model transfer needs both perspectives. We examine analogical reasoning and template application through a detailed case study on the transfer of the Ising model from physics into neuroscience. Our account combines the analogy and template-based approaches through the notion of a model template that highlights the conceptual side of model transfer.
Knuuttila, Tarja. 2020. In Wenceslao J. Gonzalez (ed.) Language and Scientific Research. Palgrave Macmillan.
This paper discusses modeling from the artifactual perspective. The artifactual approach conceives models as erotetic devices. They are purpose-built systems of dependencies that are constrained in view of answering a pending scientific question, motivated by theoretical or empirical considerations. In treating models as artifacts, the artifactual approach is able to address the various languages of sciences that are overlooked by the traditional accounts that concentrate on the relationship of representation in an abstract and general manner. In contrast, the artifactual approach focuses on epistemic affordances of different kinds of external representational and other tools employed in model construction. In doing so, the artifactual account gives a unified treatment of different model types as it circumvents the tendency of the fictional and other representational approaches to separate model systems from their “model descriptions.”
Knuuttila, Tarja & Mary S. Morgan. 2019. Philosophy of Science 86: 641-661.
De-idealization as a topic in its own right has attracted remarkably little philosophical interest despite the extensive literature on idealization. One reason for this is the often implicit assumption that idealization and de-idealization are, potentially at least, reversible processes. We question this assumption by analyzing the challenges of de-idealization within a menu of four broad categories: de-idealizing as recomposing, de-idealizing as reformulating, de-idealizing as concretizing, and de-idealizing as situating. On closer inspection, models turn out much more inflexible than the reversal thesis would have us believe, and de-idealization emerges as a creative part of modeling.
Noichl, Maximilian. 2019. Synthese.
This paper presents an approach of unsupervised learning of clusters from a citation database, and applies it to a large corpus of articles in philosophy to give an account of the structure of the discipline. Following a list of journals from the PhilPapersarchive, 68,152 records were downloaded from the Reuters Web of Science-Database. Their citation data was processed using dimensionality reduction and clustering. The resulting clusters were identified, and the results are graphically represented. They suggest that the division of analytic and Continental philosophy in the considered timespan is overstated; that analytical, in contrast to Continental philosophy does not form a coherent group in recent philosophy; and that metaphors about the disciplinary structure should focus on the coherence and interconnectedness of a multitude of smaller and larger subfields.
Knuuttila, Tarja & Vivette García-Deister. 2019. Studies in History and Philosophy of Science 77: 101-111.
Although the interdisciplinary nature of contemporary biological sciences has been addressed by philosophers, historians, and sociologists of science, the different ways in which engineering concepts and methods have been applied in biology have been somewhat neglected. We examine – using the mechanistic philosophy of science as an analytic springboard – the transfer of network methods from engineering to biology through the cases of two biology laboratories operating at the California Institute of Technology. The two laboratories study gene regulatory networks, but in remarkably different ways. The research strategy of the Davidson Lab fits squarely into the traditional mechanist philosophy in its aim to decompose and reconstruct, in detail, gene regulatory networks of a chosen model organism. In contrast, the Elowitz Lab constructs minimal models that do not attempt to represent any particular naturally evolved genetic circuits. Instead, it studies the principles of gene regulation through a template-based approach that is applicable to any kinds of networks, whether biological or not. We call for the mechanists to consider whether the latter approach can be accommodated by the mechanistic approach, and what kinds of modifications it would imply for the mechanistic paradigm of explanation, if it were to address modelling more generally.
Koskinen, Rami. 2019. Philosophy of Science 86: 1123-1133.
Critics of multiple realizability have recently argued that we should concentrate solely on actual here-and-now realizations that are found in nature. The possibility of alternative, but unactualized, realizations is regarded as uninteresting because it is taken to be a question of pure logic or an unverifiable scenario of science fiction. However, in the biological context only a contingent set of realizations is actualized. Drawing on recent work on the theory of neutral biological spaces, the paper shows that we can have ways of assessing the modal dimension of multiple realizability that do not have to rely on mere conceivability.
Koskinen, Rami. 2019. European Journal for Philosophy of Science 9:15.
Recently, several critics of the multiple realizability thesis (MRT) have argued that philosophers have tended to accept the thesis on too weak grounds. On the one hand, the analytic challenge has problematized how philosophers have treated the multiple realization relation itself, claiming that assessment of the sameness of function and the relevant difference of realizers has been uncritical. On the other hand, it is argued that the purported evidence of the thesis is often left empirically unverified. This paper provides a novel strategy to answer these worries by introducing a role for multiple realizability in the context of biological engineering. In the field of synthetic biology, bioengineers redesign the evolutionary realizations of biological functions, even constructing artificial chemical surrogates in the laboratory. I show how in the rational design approach to biological engineering, multiple realizability can function as a design heuristic in which the sameness of function and difference of realizers can be controlled. Although practically motivated, this engineering approach has also a theoretical, exploratory component that can be used to study the empirical limitations of multiple realizability. Successful realization of the engineering designs would amount to a concrete demonstration of multiple realizability, taking evidence for MRT beyond what is readily found in nature.
Knuuttila, Tarja & Andrea Loettgers. 2018. In Bas van Fraassen, and Isabelle Peschard (eds.) The Experimental Side of Modeling. University of Minnesota Press, 118-147.
Abstract of the collected volume: Offering a radically new conception of the role of data in the scientific modeling process, this cutting-edge volume offers a multifaceted view on experiments as designed and shaped in interaction with the modeling process. Highlighting the mediating role of models and the model-dependence (as well as theory-dependence) of data measurement, it proposes a normative and conceptual innovation in scientific modeling.
Koskinen, Rami. 2017. European Journal for Philosophy of Science 7(3): 493–506.
Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is argued that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems.
Knuuttila, Tarja & Andrea Loettgers. 2017. Biology & Philosophy 32: 1185-1203.
The attempt to define life has gained new momentum in the wake of novel fields such as synthetic biology, astrobiology, and artificial life. In a series of articles, Cleland, Chyba, and Machery claim that definitions of life seek to provide necessary and sufficient conditions for applying the concept of life—something that such definitions cannot, and should not do. We argue that this criticism is largely unwarranted. Cleland, Chyba, and Machery approach definitions of life as classifying devices, thereby neglecting their other epistemic roles. We identify within the discussions of the nature and origin of life three other types of definitions: theoretical, transdisciplinary, and diagnostic definitions. The primary aim of these definitions is not to distinguish life from non-life, although they can also be used for classificatory purposes. We focus on the definitions of life within the budding field of astrobiology, paying particular attention to transdisciplinary definitions and diagnostic definitions in the search for biosignatures from other planets.