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Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map.…
This paper explores the idea that information is an essential and distinctive feature of living systems. Unlike non-living systems, living systems actively acquire, process, and use information about their environments to respond to…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…
Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from…
Biological and robotic grasp and manipulation are undeniably similar at the level of mechanical task performance. However, their underlying fundamental biological vs. engineering mechanisms are, by definition, dramatically different and can…
After more than a century of concerted effort, physics still lacks basic principles of spontaneous self-organization. To appreciate why, we first state the problem, outline historical approaches, and survey the present state of the physics…
Galaxies, in particular disc galaxies, contain a number of structures and substructures with well defined morphological, photometric and kinematic properties. Considerable theoretical effort has been put into explaining their formation and…
This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to…
Vegetation patterns are abundant in arid and semiarid ecosystems, but how they form remains unclear. One of the most extended theories lies in the existence of scale-dependent feedbacks (SDF) in plant-to-plant and plant-water interactions.…
Self-organization of heterogeneous particle swarms is rich in its dynamics but hard to design in a traditional top-down manner, especially when many types of kinetically distinct particles are involved. In this chapter, we discuss how we…
Over the last decade, significant progress has been made in understanding complex biological systems, however there have been few attempts at incorporating this knowledge into nature inspired optimization algorithms. In this paper, we…
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The…
We discuss a simple model of co-evolution. In order to emphasise the effect of interaction between individuals the entire population is subjected to the same physical environment. Species are emergent structures and extinction, origination…
The third (or organismic) view of space states that space is neither lifeless nor neutral, but a living structure capable of being more living or less living, thus different fundamentally from the first two mechanistic views of space:…
It is proposed that self-organisation (SO) in non-equilibrium systems is governed by a general principle: it emerges when a minute subset of system configurations are exceptionally stable and long-lived to survive the noise generated by the…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological…