Spatial waves and temporal oscillations in vertebrate limb development

Oscillatory phenomena in electrophysiological networks: The coupling between cell bioelectricity and transcription

Morphogenetic regulation during embryogenesis and regeneration rely on information transfer and coordination between different regions. Here, we explore theoretically the coupling between bioelectrical and transcriptional oscillations at the individual cell and multicellular levels. The simulations, based on a set of ion channels and intercellular gap junctions, show that bioelectrical and transcriptional waves can electrophysiologically couple distant regions of a model network in phase and antiphase oscillatory states that include synchronization phenomena. In this way, different multicellular regionalizations can be encoded by cell potentials that oscillate between depolarized and polarized states, thus allowing a spatio-temporal coding. Because the electric potential patterns characteristic of development and regeneration are correlated with the spatial distributions of signaling ions and molecules, bioelectricity can act as a template for slow biochemical signals following a hierarchy of experimental times. In particular, bioelectrical gradients that couple cell potentials to transcription rates give to each single cell a rough idea of its location in the multicellular ensemble, thus controlling local differentiation processes that switch on and off crucial parts of the genome.

Form, function, mind: What doesn't compute (and what might)

The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.

A Cellular Potts Model of the interplay of synchronization and aggregation

We investigate the behavior of systems of cells with intracellular molecular oscillators ("clocks") where cell-cell adhesion is mediated by differences in clock phase between neighbors. This is motivated by phenomena in developmental biology and in aggregative multicellularity of unicellular organisms. In such systems, aggregation co-occurs with clock synchronization. To account for the effects of spatially extended cells, we use the Cellular Potts Model (CPM), a lattice agent-based model. We find four distinct possible phases: global synchronization, local synchronization, incoherence, and anti-synchronization (checkerboard patterns). We characterize these phases via order parameters. In the case of global synchrony, the speed of synchronization depends on the adhesive effects of the clocks. Synchronization happens fastest when cells in opposite phases adhere the strongest ("opposites attract"). When cells of the same clock phase adhere the strongest ("like attracts like"), synchronization is slower. Surprisingly, the slowest synchronization happens in the diffusive mixing case, where cell-cell adhesion is independent of clock phase. We briefly discuss potential applications of the model, such as pattern formation in the auditory sensory epithelium.

Macroevolution, differentiation trees, and the growth of coding systems

An open process of evolution of multicellular organisms is based on the rearrangement and growth of the program of differentiation that underlies biological morphogenesis. The maintenance of the final (adult) stable non-equilibrium state (stasis) of a developmental system determines the direction of the evolutionary process. This state is achieved via the sequence of differentiation events representable as differentiation trees. A special type of morphogenetic code, acting as a metacode governing gene expression, may include electromechanical signals appearing as differentiation waves. The excessive energy due to the incorporation of mitochondria in eukaryotic cells resulted not only in more active metabolism but also in establishing the differentiation code for interconnecting cells and forming tissues, which fueled the evolutionary process. The "invention" of "continuing differentiation" distinguishes multicellular eukaryotes from other organisms. The Janus-faced control, involving both top-down control by differentiation waves and bottom-up control via the mechanical consequences of cell differentiations, underlies the process of morphogenesis and results in the achievement of functional stable final states. Duplications of branches of the differentiation tree may be the basis for continuing differentiation and macroevolution, analogous to gene duplication permitting divergence of genes. Metamorphoses, if they are proven to be fusions of disparate species, may be classified according to the topology of fusions of two differentiation trees. In the process of unfolding of morphogenetic structures, microevolution can be defined as changes of the differentiation tree that preserve topology of the tree, while macroevolution represents any change that alters the topology of the differentiation tree.