Protein disorder and autoinhibition: The role of multivalency and effective concentration

Current Opinion in Structural Biology, Journal Year: 2023, Volume and Issue: 83, P. 102705 - 102705

Published: Sept. 29, 2023

Language: Английский

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Using Multilevel Temporal Factorisation to Analyse Structure and Dynamics for Higher-Order Adaptive and Evolutionary Processes

Lecture notes in computer science, Journal Year: 2024, Volume and Issue: unknown, P. 378 - 392

Published: Jan. 1, 2024

Language: Английский

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Organisms Need Mechanisms; Mechanisms Need Organisms

History, philosophy and theory of the life sciences, Journal Year: 2023, Volume and Issue: unknown, P. 85 - 108

Published: Dec. 12, 2023

Abstract According to new mechanists, mechanisms explain how specific biological phenomena are produced. New mechanists have had little say about relate the organism in which they reside. A key feature of organisms, emphasized by autonomy tradition, is that organisms maintain themselves. To do this, rely on mechanisms. But must be controlled so produce for responsible when and manner needed organism. account controlled, we characterize as sets constraints flow free energy. Some flexible can acted other mechanisms, control utilize information procured from its environment alter appropriate circumstances. We further show living organized heterarchically—control carried out primarily local controllers integrate acquire well procure The result not a hierarchy but an integrated network has been crafted over course evolution.

Language: Английский

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Mechanisms of skillful interaction: sensorimotor enactivism & mechanistic explanation

Philosophical Psychology, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 29

Published: Feb. 14, 2024

The mechanistic model depicts scientific explanations as involving the discovery of multi-level, organized components that constitute a target phenomenon. Meanwhile, sensorimotor enactivism purports to offer scientifically informed account perceptual experience skill-laden interactive relationship, constitutively both perceiver and world, rather than an agent-bound representation world. Insofar identifies empirically tractable phenomenon – skillful agent-world interaction explanation establishes subpersonal this phenomenon, two approaches allow for fruitful division labor in investigating experience. On closer inspection, however, challenges arise. First, "representation challenge" arises because promising attempts set out implementational details our with world implicate cognitive representations, creating tension enactivism's nonrepresentational commitments. Second, "reconstitution when not only uncovers some established but plays role "reconstituting" This means that, through mechanisms, may be reconceived such its constituents are wholly organism-bound. We explore compatibility mechanism examine possible solutions. result is clearer understanding tensions opportunities learning between frameworks.

Language: Английский

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Six strategies for framing theoretical research questions

Authorea (Authorea), Journal Year: 2024, Volume and Issue: unknown

Published: April 17, 2024

Theory is a small but critical component of the biological research process, and complements observational experimental approaches. However, early career biologists receive little training on how to frame theoretical question and, thus, evaluate when theory has successfully answered question. Here we develop guide with six verbal framings for models in biology. These correspond different roles one might play as theorist: "Advocate", "Explainer", "Instigator", "Mediator", "Semantician", "Tinkerer". are drawn from combinations two starting points (pattern or mechanism) three foci (novelty, robustness, conflict). We illustrate each these examples specific questions, by drawing recent papers fields ecology evolutionary show same topic can be approached slightly perspectives, using framings. clarifying model's framing debunk common misconceptions theory: that simplifying assumptions bad, more detail always better, anything you want, modelling requires substantial math knowledge. Finally, provide roadmap researchers use identify serve blueprint their own projects.Keywords:mathematical biology, methodology, narratives, pedagogy, scientific writing, ecologyTake theorist personality quiz here: https://z.umn.edu/theorypersonality Introduction biology (and science broadly) conducted, serves many purposes, including explore logical consistency ideas, simplest model predict observed phenomena, demonstrate complexity situation, suggest ways looking at empirical data, generate novel hypotheses, possible ranges behaviour system [1,2]. take range forms verbal, conceptual, computational, mathematical. Broadly, scaffolding [3] helps us make sense observations experiments. Yet, primarily approaches up portion overall literature; only 18% most theory-heavy journals within presented findings [4,5]. Perhaps due this representation, scientists design interpret (particularly mathematical theory) [6], especially compared amount they Lack could result an absence conversation among about best practices designing interpreting theory. clearly not case; example, people have debated do long been field. Levins' seminal paper [7] argued key aims realism, precision, generality. Since no accomplish all simultaneously, need sets prioritise so find true understanding point(s) where results intersect [7]. May [8] cautioned against having uneven balance models; extensive some aspects while keeping others vague convey false much realism includes. In contrast Levins May, called prioritising type over others. For Holling [9] field had enough what he 'strategic' (that sacrifice precision focus generality), needed 'tactical' models. Evans et al. [10] similarly embracing complex means achieving generality through generating testable predictions. The opposite argument also made: Marquet [11] development 'efficient' theories fewer parameters precise. addition, written arguing value whole, parallels between studies conducted both [1] [12]. conversations translated into guidance newcomers conduct communicate This lack creates barrier new research. response, there number 'how-to' guides aimed breaking down researchers. broad audiences include suggestions like stating context assumptions, reducing irrelevant complexities (adjusting target audience), clear standardised notation, analogies narratives facilitate links existing information [13,14]. another how-to guide, Edwards Auger-Méthé [15] advice choosing notation. There read ecology. Shoemaker [13] readers spend extra time engaging math, equations components working them peers, connecting general class models, reconstructing exploring parameter space get better handle them. Other frameworks lab work, empirically-based calculations, test either predictions [16,17]. Overall, who reading broadly before start project, completed project want it clearly. contrast, less middle stage process: choose – gap. Even never pose questions themselves will (e.g., work). Thus, benefit framed order help successful. Here, fill gap providing Theoretical often starts out model, reasoning set expected occur. Verbal arguments far, relying intuition leads astray [18]. It turning (or narrative-based) computational) form clarity extend [19]. argue converse true: improve usefulness computational model. Below, present research, describing 'personality type' role mutually exclusive; idea multiple roles. thinking used address Framing (also proof-of-concept [12]) fundamentally link outcomes. Another way view linking 'patterns' (outcomes interest) 'mechanisms' (processes those outcomes) (Figure 1). When researcher developing typically mechanism(s) pattern(s) expect. core part process concretely specifics patterns mechanisms determining conditions under which linked. propose writing grant proposals manuscripts), pattern mechanism point then connect other. understand cause (i.e., causes). Alternatively, considering consequences). addition points, goal pitched focus: novelty, conflict. Taken together, lead theory, (Table

Language: Английский

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Six personas to adopt when framing theoretical research questions in biology

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2024, Volume and Issue: 291(2031)

Published: Sept. 1, 2024

Theory is a critical component of the biological research process, and complements observational experimental approaches. However, most biologists receive little training on how to frame theoretical question and, thus, evaluate when theory has successfully answered question. Here, we develop guide with six verbal framings for models in biology. These correspond different personas one might adopt as theorist: ‘Advocate’, ‘Explainer’, ‘Instigator’, ‘Mediator’, ‘Semantician' ‘Tinkerer’. are drawn from combinations two starting points (pattern or mechanism) three foci (novelty, robustness conflict). We illustrate each these examples specific questions, by drawing recent papers fields ecology evolutionary show same topic can be approached slightly perspectives, using framings. clarifying model’s framing debunk common misconceptions theory: that simplifying assumptions bad, more detail always better, anything you want modelling requires substantial maths knowledge. Finally, provide roadmap researchers new use identify serve blueprint their own projects.

Language: Английский

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New Mechanism

History, philosophy and theory of the life sciences, Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 12, 2023

This Open Access book addresses the epistemological and ontological significance as well scope of new mechanism

Language: Английский

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