Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Precis of neuroconstructivism: how the brain constructs cognition

Neuroconstructivism: How the Brain Constructs Cognition proposes a unifying framework for the study of cognitive development that brings together (1) constructivism (which views development as the progressive elaboration of increasingly complex structures), (2) cognitive neuroscience (which aims to understand the neural mechanisms underlying behavior), and (3) computational modeling (which proposes formal and explicit specifications of information processing). The guiding principle of our approach is context dependence, within and (in contrast to Marr [1982]) between levels of organization. We propose that three mechanisms guide the emergence of representations: competition, cooperation, and chronotopy; which themselves allow for two central processes: proactivity and progressive specialization. We suggest that the main outcome of development is partial representations, distributed across distinct functional circuits. This framework is derived by examining development at the level of single neurons, brain systems, and whole organisms. We use the terms encellment, embrainment, and embodiment to describe the higher-level contextual influences that act at each of these levels of organization. To illustrate these mechanisms in operation we provide case studies in early visual perception, infant habituation, phonological development, and object representations in infancy. Three further case studies are concerned with interactions between levels of explanation: social development, atypical development and within that, developmental dyslexia. We conclude that cognitive development arises from a dynamic, contextual change in embodied neural structures leading to partial representations across multiple brain regions and timescales, in response to proactively specified physical and social environment

Designing the interface between research, learning and teaching.

Abstract: This paper’s central argument is that teaching and research need to be reshaped so that they connect in a productive way. This will require actions at a whole range of levels, from the individual teacher to the national system and include the international communities of design scholars. To do this, we need to start at the level of the individual teacher and course team. This paper cites some examples of strategies that focus on what students do as learners and how teachers teach and design courses to enhance research-led teaching. The paper commences with an examination of the departmental context of (art and) design education. This is followed by an exploration of what is understood by research-led teaching and a further discussion of the dimensions of research-led teaching. It questions whether these dimensions are evident, and if so to what degree in design departments, programmes and courses. The discussion examines the features of research-led departments and asks if a department is not research-led in its approach to teaching, why it should consider changing strategies

Interpersonal Neural Entrainment during Early Social Interaction

Currently, we understand much about how children’s brains attend to and learn from information presented while they are alone, viewing a screen – but less about how interpersonal social influences are substantiated in the brain. Here, we consider research that examines how social behaviors affect not one, but both partners in a dyad. We review studies that measured interpersonal neural entrainment during early social interaction, considering two ways of measuring entrainment: concurrent entrainment (e.g., ‘when A is high, B is high’ – also known as synchrony) and sequential entrainment (‘changes in A forward-predict changes in B’). We discuss possible causes of interpersonal neural entrainment, and consider whether it is merely an epiphenomenon, or whether it plays an independent, mechanistic role in early attention and learning