According to a widely held view, scientific modelling consists in entertaining a set of model descriptions that specify a model. Rather than studying the phenomenon of interest directly, scientists investigate the phenomenon indirectly via a model in the hope of learning about some of the phenomenon’s features. I call this view the description-driven modelling (DDM) account. I argue that although an accurate description of much of scientific research, the DDM account is found wanting as regards the mechanistic modelling found in (...) many branches of biology. By analysing research practices in cancer immunology concerning the development of mechanistic models of the process of cancer metastasis, this paper presents and argues for a complementary account of scientific modelling, herein called the experimentation-driven modelling (EDM) account. In EDM, scientists investigate a set of experimental systems and then integrate the results obtained from experiments into a mechanistic model. While EDM shares some key features with DDM, the two are epistemically very different approaches to research. (shrink)

Ontologies of living things are increasingly grounded on the concepts and practices of current life science. Biological development is a process, undergone by living things, which begins with a single cell and (in an important class of cases) ends with formation of a multicellular organism. The process of development is thus prima facie central for ideas about biological individuality and organismality. However, recent accounts of these concepts do not engage developmental biology. This paper aims to fill the gap, proposing the (...) lineage view of stem cells as an ontological framework for conceptualizing organismal development. This account is grounded on experimental practices of stem cell research, with emphasis on new techniques for generating biological organization in vitro. On the lineage view, a stem cell is the starting point of a cell lineage with a specific organismal source, time-interval of existence, and ‘tree topology’ of branch-points linking the stem to developmental termini. The concept of ‘enkapsis’ accommodates the cell-organism relation within the lineage view; this hierarchical notion is further explicated by considering the methods and results of stem cell experiments. Results of this examination include a (partial) characterization of stem cells’ developmental versatility, and the context-dependence of developmental processes involving stem cells. (shrink)

Model organism databases are used extensively for knowledge retrieval and knowledge sharing among biologists. With the invention of genome sequencing and protein profiling technologies, large amount of molecular data provides practical insights into the molecular study of model organisms. The knowledge-intensive characteristic of model organism databases provides a reference point for the comparative study of other species. In this paper, I argue that algorithms could be used to facilitate cross-species research. I emphasize the epistemic significance of algorithms in the integration (...) of data for cross-species research. I examine (1) how algorithms guide data integration in model organism databases; and (2) the importance of algorithms for the use of model organism database in the cross-species research. I argue that an extrapolation from the stored data to other species is possible in virtue of the fact that algorithms can facilitate two modes of data integration—viz., inter-level and cross-species integration. Lastly, I examine the implication of the data integration role of an algorithm in light of mechanistic explanation. (shrink)

Biologists often study particular biological systems as models of a phenomenon of interest even if they already know that the phenomenon is produced by diverse mechanisms and hence none of those systems alone can sufficiently represent it. To understand this modeling practice, the present paper provides an account of how multiple model systems can be used to study a phenomenon that is produced by diverse mechanisms. Even if generalizability of results from a single model system is significantly limited, generalizations concerning (...) specific aspects of mechanisms often hold across certain ranges of biological systems, which enables multiple model systems to jointly represent such a phenomenon. Comparing mechanisms that operate in different biological systems as examples of the same phenomenon also facilitates characterization and investigation of individual mechanisms. I also compare my account with two existing accounts of the use of multiple model systems and argue that my account is distinct from and complementary to them. (shrink)

It is assumed that scientific models contain no superfluous model elements in scientific representation. A representational model is constructed with all the model elements serving the representational purpose. The received view has it that there are no redundant model elements which are non-representational. Contrary to this received view, I argue that there exist some non-representational model elements which are essential in scientific representation. I call them representation-supporting model elements in virtue of the fact that they play the role to support (...) the representational role of representational model elements. Representation-supporting model elements, which have a characteristic of dependability, are not to be eliminated in the process of modeling although they are playing second fiddle to representational model elements in scientific representation. (shrink)

The description of how individual models in families of models are related to each other is crucial for the general philosophical understanding of model-based scientific practice. We focus on the Capital Asset Pricing Models (CAPM) family, a cornerstone in financial economics, to provide a descriptive analysis of model relations within a family. We introduce the concepts of theoretical and empirical complementarity to characterise model relations. Our complementarity analysis of model relations has two types of payoff. Specifically regarding the CAPM, our (...) analysis reveals why this model family, which has been empirically contested, has yet remained popular and important: the different models that have been added over time have made new empirically and theoretically complementary contributions to the model family. More generally, our analysis reveals the dynamic character of model-based scientific practice. Characterising relations between models as theoretically and/or empirically complementary yields three hitherto underappreciated lessons: (i) actual modelling purposes are not always primarily epistemic, (ii) a model's individual import is relative, not absolute, and (iii) there is an important interplay between theory and data models. Faithfully characterising scientific modelling in this way facilitates subsequent analysis of models' epistemic import. (shrink)

ion is one of the important processes in scientific modeling. It has always been implied that abstraction is an agent-centric activity that involves the cognitive processes of scientists in model building. I contend that there is an autonomous aspect of abstraction in many modeling activities. I argue that the autonomous process of abstraction is continuous with the agent-centric abstraction but capable of evolving independently from the modeler’s abstraction activity.

Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model that is capable of generating new material models. I contend that generative mechanisms of a generative material model are not to be conflated with biological mechanisms: the former (...) is a mechanism manipulated and altered by the modeler while the latter is a naturally occurring mechanism. I examine the ways in which idealization may contribute to the generative mechanism in generating new model organisms. I articulate that the component parts and activities in a generative mechanism are to a large extent shaped by idealization in generative material modeling. Although biological mechanisms do have a role to play in the generation of model organisms, I propose that we shall view the generative mechanism as a hybrid of biological mechanisms and modeling activities. I shall argue that the notion of generative mechanisms as hybrid mechanisms is different from the extant conceptions of mechanisms in various aspects. (shrink)

Generative models have been proposed as a new type of non-representational scientific models recently. A generative model is characterized with the capacity of producing new models on the basis of the existing one. The current accounts do not explain sufficiently the mechanism of the generative capacity of a generative model. I attempt to accomplish this task in this paper. I outline two antecedent accounts of generative models. I point out that both types of generative models function to generate new homogenous (...) models in the sense that the latter is a straightforward derivative of the former, both of which share many similar features. Unfortunately, both accounts are implicit about the generative capacity of generative models. Using a case study, I articulate that a two-staged process of abstraction and idealization in modeling may contribute to the generative capacity of a scientific model. I also demonstrate that this two-staged process may go beyond the capacity of generating new homogenous models to generating new heterogeneous models. (shrink)

Advances in research on human cerebral organoids (HCOs) call for a critical review of current research policies. A challenge for the evaluation of necessary research regulations lies in the severe uncertainty about future trajectories the currently very rudimentary stages of neural cell cultures might take as the technology progresses. To gain insights into organotypic cultures, ethicists, legal scholars, and neuroscientists rely on resemblances to the human brain. They refer to similarities in structural or functional terms that have been established in (...) scientific practice to validate organotypic cultures as models for brain research. In ethical discourse, however, such similarities are also used to justify assumptions about the potential risk to cause harm to HCOs. Ethicists assume that as the technology advances, organotypic cultures will increasingly resemble the human brain, raising more complex ethical issues. I argue that such reasoning is not justified given the heterogeneity of HCOs that have been modified to enable scientists to pursue their research goals. I then discuss the implications this line of thought has for advocates of the precautionary principle, focussing on those suggestions which propose adopting research regulations to the presence of bodily warning signs deemed worthy of protection. In doing so, I illustrate that the prevalent assumptions on similarity in ethical discourse ultimately risk disproportionately restricting research. I conclude that given the severe uncertainty about the technology’s future development, ethical discourse might benefit from narrowing the time frame for anticipation. (shrink)