AssemblingLife Kick-Off Workshop

The AssemblingLife project, in collaboration with the Centre for Philosophy and the Sciences (CPS), organizes a kick-off workshop on the 10th and 11th of June, 2024, at the University of Oslo. The primary objective is to get the AssemblingLife project off to a good start by delving into the understanding and explanation of life and living processes with an emphasis on self-assembly and self-organisation.

Everyone is welcome! (but registration for lunch is now closed) 

Program

Monday, 10th of June (GSH, Undervsiningsrom 2)

Tuesday, 11th of June (GSH, Grupperom 7)

Abstracts

Presentation of the AssemblingLife Project

Gry Oftedal (University of Oslo)

I will present the background and the plans for the project and sketch som paths that will be relevant to take in our research the next five years, focusing on self-assembly and self-organization processes.

Self assembly in the living cell

Harald Stenmark (Centre for Cancer Cell Reprogramming, University of Oslo and Institute for Cancer Research, Oslo University Hospital)  

Self-assembly, the spontaneous assembly of smaller components into larger structures, played a major role in the origin of life, and it is essential for all cells in our body. Examples include the assembly of cellular membranes that enclose the cells and its organelles, the cytoskeleton that controls cell motility and cell division, and the ribosomes that translate mRNA molecules into proteins. Whereas many cellular processes require the catalytic activities of specialized proteins called enzymes, self-assembly is driven by the physical principle of energy minimization. In this lecture I will highlight a few self-assembly processes within the living cell, and discuss their importance.

Biophysical modelling of self-organisation of cells and membrane bound proteins

Andreas Carlson (Department of Mathematics, University of Oslo)

Biological phenomena that spans decades in length scales with self-organisation of patterns. Examples of these forms span the patterning of proteins on membranes, the collective motion of cells, and the clusters of mussels, to name but a few examples. 

In this talk I will discuss how we use mathematical and computational modelling to describe self-organisation of membrane bound proteins and cells in biological phenomena based on biophysical principles. First, I will illustrate how basic mechanical principles 

 and mathematical modelling have given ways to describe describe self-organisation phenomena. Finally, I will give some examples of how we approach the modelling of some specific biological phenomena.

How new ideas about self-assembly in biology may change our way of explaining living organization 

Alvaro Moreno (University of the Basque Country)

In this talk I will defend a view of biological organization that, instead of opposing SO and SA, considers them to be complementary and intertwined processes. Although living organisms are complex organizations that actively – and autonomously – maintain their identity by dissipating energy under FFE conditions, they do so by building complex local structures, which spatially and kinetically control many physical and chemical processes. Many of these constraints are self- assembled macromolecular structures whose assembled functional state is achieved “for free.” In turn, the functional structures of SA are maintained and modulated in the context of the dissipative organization that they contribute to creating. Only at the nanoscale, assembly processes and catalytically harnessed reactions (along with a host of nanomechanical processes) could easily create causal loops, not only between chemical reactions, but also between components and structures that act as boundary conditions in the processes that generate them.

Recent research on what has been called “dissipative self-assembly” (DSA) goes even further in this way to look at the roles of SA and far-from-equilibrium self-organization in cellular functioning. DSA are, in fact, complex SA structures that, within the cellular (or MC) organization, change their metastable structure through controlled energetical inputs. In turn, these changes control many other metabolic (or developmental) processes, thus showing the deep organizational entanglement between dissipative self-maintaining dynamic processes and SA material constraints in biological systems.

This new view raises many philosophical questions and challenges on the way mechanistic and organismic approaches have been used to explain how living organisms work, and prompts us to reconsider some fundamental issues of biological theory, such as how the complex organization of living organisms are maintained far from equilibrium, what is the explanatory role of (macromolecular) “machines” in the cell, and how to understand the relation between “materiality” and “organization” in the constitution of living systems.

What is self-assembly? Towards a non-exclusive definition.

Sebastian Sander Oest (University of Oslo)

Self-assembly describes a highly diverse class of phenomena and has consequently been defined in a multitude of ways. According to Halley and Winkler (2008), these definitions are often mutually inconsistent and conflate self-assembly with self-organization. To amend this situation, they propose their own definitions distinguishing the two phenomena in terms of thermodynamic dissipation. In this talk I will argue that this approach is mistaken and that self-assembly should not exclude self-organization. To argue this point, I attend to features involved in the historical development of the self-assembly concept and motivating its use in contemporary research. Taking an operational stance on scientific definitions, a definition centering on reversibility does a better job at integrating these features and thus better facilitates inquiry into self-assembly phenomena.

Emergence in a world of process

John Dupre (University of Exeter)

Long ago I wrote about reductionism, and why it didn’t work. If the properties or dispositions to behave, are not reducible, that is fully explainable by appeal to properties of its constituent parts, they are emergent. Then, I supposed that this was just a brute fact, not susceptible to or requiring any further explanation. More recently I have come to believe that the world is composed entirely of processes. Where there are what seem to be persistent things these should be understood as stable or better, stabilised, processes. Such apparent things, in fact, emerge from the surrounding web of process. In this talk, I shall explain why this emerging also implies the more traditional sense of “emergent” sketched above.

Middle-Out Approaches in Modeling and Making Multiscale Materials

Julia Bursten (University of Kentucky)

In materials science and increasingly in philosophy of science, multiscale approaches to modeling and understanding materials are overtaking bottom-up and even some top-down approaches. A multiscale approach to materials modeling begins with the acknowledgment that material properties and behaviors are the result of characteristic structures and processes appearing at multiple length, time, and energy scales. Rather than seeking to identify which characteristic structures are “fundamental” or “correct” or “real,” multiscale approaches emphasize connecting information, concepts, models, and measures from studies of a material at different scales to develop reliable predictions and coherent explanations of material properties and behaviors. In many instances of materials modeling, the middle or meso scale plays a crucial role in shaping material behavior. For instance, the size and distribution of grains in metal alloys is a mesoscale structural feature of alloys that impacts macroscopic material behavior more directly than the sheer microstructural composition of the alloy. In my remarks, I will build on an in-progress collaboration with the philosopher Robert Batterman to explore middle-out approaches to modeling active materials, a class of materials that exhibit some form of self-assembly in their material properties of interest. I will suggest that middle-out approaches are preferable to bottom-up or top-down approaches in the modeling of active materials, and that they may serve as a useful guide for the work of the AssemblingLife project.

Functions in self-assembled entities: the case of proteins’ functions 

Francesca Bellazzi (University of Birmingham/University of Oslo)

Functions are easily attributed to living things, such as traits of organisms. However, functional attribution is less clear when it regards complex macromolecules, such as proteins. This is made even more complex because proteins have a function that depends on how their folding. For instance, haemoglobin has the function of carrying oxygen around the body. However, what does it mean that haemoglobin - a complex macro molecule - has a function?

This paper explores functional attribution to proteins and argues that proteins' biochemical functions correspond to a specific subset of chemical and geometrical structural properties contributing to specific evolved biological processes. This account enriches the one proposed in Bellazzi 2022, by adding the consideration of geometrical physical properties to chemical ones for protein function. Moreover, it explores also evolutionary and environmental considerations. Specifically, I will consider whether some features of proteins' shape can be taken as a trait, and then a form of evolutionary biological functions can be attributed to proteins. The structure of the argument will be the following. The paper will first consider what is the problem of protein function using moonlighting proteins as a case study. Then, it will discuss the account of biochemical functions proposed by Bellazzi 2022 and why it is not enough to account for proteins' functions. It will argue that the proposal needs to be expanded by considering physical-geometrical properties. It will then conclude by considering whether such properties can provide grounds for ascribing evolutionary biological functions to proteins too.

Disentangling self-organization and gene regulation

James DiFrisco (The Francis Crick Institute)         

Abstract: This talk will examine the relationship between self-organization in tissues and gene regulatory networks in cells during morphogenesis. I contest the view that these are alternative or competing explanatory factors, arguing that they must necessarily work together in morphogenesis. I suggest that self-organization critically contributes to the nonlinearity of the genotype-phenotype map, for example by conferring robustness to morphogenesis through mechanochemical feedback, and that the nonlinearity of the genotype-phenotype influences evolvability.

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