Meaning has traditionally been regarded as a problem for philosophers and psychologists. Advances in cognitive science since the early 1960s, however, broadened discussions of meaning, or more technically, the semantics of perceptions, representations, and/or actions, into biology and computer science. Here, we review the notion of “meaning” as it applies to living systems, and argue that the question of how living systems create meaning unifies the biological and cognitive sciences across both organizational and temporal scales.

The role of Brachyury and other T-box genes in the differentiation of mesoderm and endoderm of vertebrates is well established. Recently, homologues of Brachyury have been isolated from an increasing number of diverse organisms ranging from Cnidaria to vertebrates and insects. Comparative expression and function analysis allows the origin of the mesoderm and the evolution of the developmental role of Brachyury gene family in metazoans to be traced. The data suggest that an ancestral function of Brachyury was to designate a (...) blastoporal region that had distinct properties in induction and axis elongation. A subset of blastoporal cells expressing Brachyury and other genes that convey specific mesodermal functions may have segregated as a distinct cell population from this region in the course of mesoderm evolution. BioEssays 23:788–794, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

In one of the first genetic screens aimed at identifying induced developmental mutants, Nadine Dobrovolskaïa-Zavadskaïa, working at the Pasteur Laboratory in the 1920s, isolated and characterized a mutation affecting Brachyury, a gene that regulates tail and axial development in the mouse. Dobrovolskaïa-Zavadskaïa's analysis of Brachyury and other mutations affecting tail development were among the earliest attempts to link gene action with a tissue-specific developmental process in a vertebrate. Her analyses of genes that interacted with Brachyury led to the discovery of (...) the t-haplotype chromosome of mouse. After 70 years, Brachyury and the multiple genes with which it interacts continue to occupy a prominent focus in developmental biology research. A goal of this review is to identify the contributions that Dobrovolskaïa-Zavadskaïa made to our current thinking about Brachyury and how she helped to shape the dawn of the field of developmental genetics. BioEssays 23:365–371, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and (...) selection become, for example, bidirectional information flows between scales, while the notions of “cooperation” and “competition” become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale‐free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system. (shrink)

We present a metapopulation dynamic model for the diffusively-coupled rock-paper-scissors game with mutation in scale-free hierarchical networks. We investigate how the RPS game changes by mutation in scale-free networks. Only the mutation from rock to scissors occurs with rate μ. In the network, a node represents a patch where the RPS game is performed. RPS individuals migrate among nodes by diffusion. The dynamics are represented by the reaction-diffusion equations with the recursion formula. We study where and how species coexist or (...) go extinct in the scale-free network. We numerically obtained the solutions for the metapopulation dynamics and derived the transition points. The results show that, with increasing mutation rate μ, the extinction of P species occurs and then the extinction of R species occurs, and finally only S species survives. Thus, the first and second dynamical phase transitions occur in the scale-free hierarchical network. We also show that the scaling law holds for the population dynamics which suggests that the transition points approach zero in the limit of infinite size. (shrink)