Abstract: In this article we analyse the issue of what accounts for developmental potential, i.e., the possible phenotypes a developing organism can manifest during ontogeny. We shall argue in favour of two theses. First, although the developing organism is the unit of development, the complete causal basis for its potential to develop does neither lie entirely in itself as a whole nor in any specific part of itself (such as its genome). Thus, the extra-organismal environment must be counted as one of the three necessary, partial and complementary causal bases for development potential. Secondly, we shall defend a constructivist view of the developmental process. If the genome, the developing organism and the extra-organismal environment are to be counted as proper elements of the causal basis for an organism's developmental potential, the latter is not a given. Rather, it is the result of an interaction-based construction, a process sometimes generating genuine developmental novelty. We will thus argue for an interactionist multi-causal basis view of developmental potential construction. We contend that our view provides a biologically tenable and metaphysically coherent account of developmental dynamics.

Abstract: Abstract The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given the set of elements, the reactions between them (chemical or otherwise), and with various elements catalysing certain reactions, a Reflexively Autocatalytic F-generated (RAF) set is a subset R $$'$$ ′ of reactions that is self-generating from a given food set, and with each reaction in R $$'$$ ′ being catalysed from within R $$'$$ ′ . RAF theory has been applied to various phenomena in theoretical biology, and a key feature of the approach is that it is possible to efficiently identify and classify RAFs within large systems. This is possible because RAFs can be described as the (nonempty) subsets of the reactions that are the fixed points of an (efficiently computable) interior map that operates on subsets of reactions. Although the main generic results concerning RAFs can be derived using just this property, we show that for systems with at least 12 reactions there are generic results concerning RAFs that cannot be proven using the interior operator property alone.

Abstract: Long since, people tried to solve the mystery of the way that led to the appearance and propagation of living entities. However, no harmonious understanding of this mystery existed, because neither the scientifically grounded source minerals nor the ambient conditions were proposed and because it was groundlessly taken that the process of living matter origination is endothermal. The Life Origination Hydrate Theory (LOH-Theory) first suggests the chemical way capable of leading from the specified abundant natural minerals to origination of multitudes of multitudes of simplest living entities and gives an original explanation for the phenomena of chirality and racemization delay. The LOH-Theory covers the period up to origination of the genetic code. The LOH-Theory is grounded on the following three discoveries based on the available information and on the results of our experimental works performed using original instrumentation and computer simulations. (1) There is the only one triad of natural minerals applicable for exothermal thermodynamically possible chemical syntheses of simplest living-matter components. (2) N-base, ribose, and phosphdiester radicals and nucleic acids as whole are size-compatible with structural gas-hydrate cavities. (3) The gas-hydrate structure arises around amido-groups in cooled undisturbed systems consisting of water and highly-concentrated functional polymers with amido-groups.The natural conditions and historic periods favorable for simplest living matter origination are revealed. The LOH-Theory is supported by results of observations, biophysical and biochemical experiments, and wide application of original three-dimensional and two-dimensional computer simulations of biochemical structures within gas-hydrate matrix. The instrumentation and procedures for experimental verification of the LOH-Theory are suggested. If future experiments are successful, they, possibly, could be the first step on the way to industrial synthesis of food from minerals, i.e., to execution of the work that is performed by plants.

Abstract: Transitive inference (TI) refers to social cognition that facilitates the discernment of unknown relationships between individuals using known relationships. It is extensively reported that TI evolves in animals living in a large group because TI could assess relative rank without deducing all dyadic relationships, which averts costly fights. The relationships in a large group become so complex that social cognition may not be developed adequately to handle such complexity. If members apply TI to all possible members in the group, TI requires extremely highly developed cognitive abilities especially in a large group. Instead of developing cognitive abilities significantly, animals may apply simplified TI we call reference TI in this study as heuristic approaches. The reference TI allows members to recognize and remember social interactions only among a set of reference members rather than all potential members. Our study assumes that information processes in the reference TI comprises (1) the number of reference members based on which individuals infer transitively, (2) the number of reference members shared by the same strategists, and (3) memory capacity. We examined how information processes evolve in a large group using evolutionary simulations in the hawk-dove game. Information processes with almost any numbers of reference members could evolve in a large group as long as the numbers of shared reference member are high because information from the others' experiences is shared. TI dominates immediate inference, which assesses relative rank on direct interactions, because TI could establish social hierarchy more rapidly applying information from others' experiences.

Abstract: Abstract The Modern Synthesis has received criticism for its purported gene-centrism. That criticism relies on a concept of the gene as a unit of instructional information. In this paper I discuss information concepts and endorse one, developed from Floridi, that sees information as a functional relationship between data and context. I use this concept to inspect developmental criticisms of the Modern Synthesis and argue that the instructional gene arose as an idealization practice when evolutionary biologists made comment on development. However, a closer inspection of key claims shows that at least some associated with the Modern Synthesis were in fact adopting the data led definition I favour and made clear arguments for the role of developmental processes beyond genetic input. There was no instructional gene.

Abstract: This paper focuses on physiological integration in multicellular systems, a notion often associated with biological individuality, but which has not received enough attention and needs a thorough theoretical treatment. Broadly speaking, physiological integration consists in how different components come together into a cohesive unit in which they are dependent on one another for their existence and activity. This paper argues that physiological integration can be understood by considering how the components of a biological multicellular system are controlled and coordinated in such a way that their activities can contribute to the maintenance of the system. The main implication of this perspective is that different ways of controlling their parts may give rise to multicellular organizations with different degrees of integration. After defining control, this paper analyses how control is realized in two examples of multicellular systems located at different ends of the spectrum of multicellularity: biofilms and animals. It focuses on differences in control ranges, and it argues that a high degree of integration implies control exerted at both medium and long ranges, and that insofar as biofilms lack long-range control (relative to their size) they can be considered as less integrated than other multicellular systems. It then discusses the implication of this account for the debate on physiological individuality and the idea that degrees of physiological integration imply degrees of individuality.