Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George Ellis (eds.), Cambridge University Pres

The evolution of brain architectures for predictive coding and active inference

This article considers the evolution of brain architectures for predictive processing. We argue that brain mechanisms for predictive perception and action are not late evolutionary additions of advanced creatures like us. Rather, they emerged gradually from simpler predictive loops (e.g. autonomic and motor reflexes) that were a legacy from our earlier evolutionary ancestors-and were key to solving their fundamental problems of adaptive regulation. We characterize simpler-to-more-complex brains formally, in terms of generative models that include predictive loops of increasing hierarchical breadth and depth. These may start from a simple homeostatic motif and be elaborated during evolution in four main ways: these include the multimodal expansion of predictive control into an allostatic loop; its duplication to form multiple sensorimotor loops that expand an animal's behavioural repertoire; and the gradual endowment of generative models with hierarchical depth (to deal with aspects of the world that unfold at different spatial scales) and temporal depth (to select plans in a future-oriented manner). In turn, these elaborations underwrite the solution to biological regulation problems faced by increasingly sophisticated animals. Our proposal aligns neuroscientific theorising-about predictive processing-with evolutionary and comparative data on brain architectures in different animal species. This article is part of the theme issue 'Systems neuroscience through the lens of evolutionary theory'

Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions

Hierarchical network structure as the source of power-law frequency spectra (state-trait continua) in living and non-living systems: how physical traits and personalities emerge from first principles in biophysics

What causes organisms to have different body plans and personalities? We address this question by looking at universal principles that govern the morphology and behavior of living systems. Living systems display a small-world network structure in which many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a power-law cluster size distribution. Their dynamics show similar qualities: the timeseries of inner message passing and overt behavior contain high frequencies or 'states' that are nested within lower frequencies or 'traits'. Here, we argue that the nested modular (power-law) dynamics of living systems results from their nested modular (power-law) network structure: organisms 'vertically encode' the deep spatiotemporal structure of their environments, so that high frequencies (states) are produced by many small clusters at the base of a nested-modular hierarchy and lower frequencies (traits) are produced by fewer larger clusters at its top. These include physical as well as behavioral traits. Nested-modular structure causes higher frequencies to be embedded in lower frequencies, producing power-law dynamics. Such dynamics satisfy the need for efficient energy dissipation through networks of coupled oscillators, which also governs the dynamics of non-living systems (e.g. earthquake dynamics, stock market fluctuations). Thus, we provide a single explanation for power-law frequency spectra in both living and non-living systems. If hierarchical structure indeed produces hierarchical dynamics, the development (e.g. during maturation) and collapse (e.g. during disease) of hierarchical structure should leave specific traces in power-law frequency spectra that may serve as early warning signs to system failure. The applications of this idea range from embryology and personality psychology to sociology, evolutionary biology and clinical medicine

The morphofunctional approach to emotion modelling in robotics

In this conceptual paper, we discuss two areas of research in robotics, robotic models of emotion and morphofunctional machines, and we explore the scope for potential cross-fertilization between them. We shift the focus in robot models of emotion from information-theoretic aspects of appraisal to the interactive significance of bodily dispositions. Typical emotional phenomena such as arousal and action readiness can be interpreted as morphofunctional processes, and their functionality may be replicated in robotic systems with morphologies that can be modulated for real-time adaptation. We investigate the control requirements for such systems, and present a possible bio-inspired architecture, based on the division of control between neural and endocrine systems in humans and animals. We suggest that emotional epi- sodes can be understood as emergent from the coordination of action control and action-readiness, respectively. This stress on morphology complements existing research on the information-theoretic aspects of emotion

Evolving hierarchical visually guided neural network agents to investigate complex interactions.

A complex system is a system with a large number of interacting components without any mechanism for central control that displays self organisation. Understanding how these interactions affect the overall behaviour of a system is of great interest to science. Indeed, researchers use a wide variety of models to investigate complex systems. The problem with most models is that they disregard the hierarchical nature of complex systems: they ignore the fact that components of real world systems tend to be complex systems as well. This prevents researchers from investigating the interactions taking place between the lower and the higher levels of the model which may be crucial in order to gain a full understanding of the examined phenomena and of complex systems in general. Therefore, this thesis introduces Mosaic World, a multi-agent model for the purpose of investigating interactions (focusing on 'complex' multilevel interactions) within a hierarchical complex system, in addition to other computational and biological hypotheses. Mosaic World comprises a population of evolving neural network agents that inhabit a changing visual environment. By analysing the interactions that occur within Mosaic World, this thesis demonstrates the importance of incorporating hierarchical complexity into a model, and contributes to our understanding of hierarchical complex systems by showing how selective pressures cause differentiation across levels. Additionally, the study of multilevel interactions is used to probe several hypotheses and provides the following contributions among others: Analysis of agent evolvability as affected by the usage of different types of structural mutations in the evolutionary process. Demonstration that agents controlled by modular neural networks are fitter than agents that are controlled by non-modular neural networks the improvement in fitness occurs through specialisation of modules. Empirical support for a biological theory suggesting that colour vision evolved as a method of dealing with ambiguous stimuli