Self-organization in biology and development

Scaffold-Free Strategies in Dental Pulp/Dentine Tissue Engineering: Current Status and Implications for Regenerative Biological Processes

Conventionally, root canal treatment is performed when the dental pulp is severely damaged or lost due to dental trauma or bacterial endodontic infections. This treatment involves removing the compromised or infected pulp tissue, disinfecting the root canal system, and sealing it with inert, non-degradable materials. However, contemporary endodontic treatment has shifted from merely obturating the root canal system with inert materials to guiding endodontic tissue regeneration through biological approaches. The ultimate goal of regenerative endodontics is to restore dental pulp tissue with structural organization and functional characteristics akin to the native pulp, leveraging advancements in tissue engineering and biomaterial sciences. Dental pulp tissue engineering commonly employs scaffold-based strategies, utilizing biomaterials as initial platforms for cell and growth factor delivery, which subsequently act as scaffolds for cell proliferation, differentiation and maturation. However, cells possess an intrinsic capacity for self-organization into spheroids and can generate their own extracellular matrix, eliminating the need for external scaffolds. This self-assembling property presents a promising alternative for scaffold-free dental pulp engineering, addressing limitations associated with biomaterial-based approaches. This review provides a comprehensive overview of cell-based, self-assembling and scaffold-free approaches in dental pulp tissue engineering, highlighting their potential advantages and challenges in advancing regenerative endodontics.

On Effect of Chloroform on Electrical Activity of Proteinoids

Proteinoids, or thermal proteins, produce hollow microspheres in aqueous solutions. Ensembles of the microspheres produce endogenous spikes of electrical activity, similar to that of neurons. To make the first step toward the evaluation of the mechanisms of such electrical behaviour, we decided to expose proteinoids to chloroform. We found that while chloroform does not inhibit the electrical oscillations of proteinoids, it causes substantial changes in the patterns of electrical activity. Namely, incremental chloroform exposure strongly affects proteinoid microsphere electrical activity across multiple metrics. As chloroform levels rise, the spike potential drops from 0.9 mV under control conditions to 0.1 mV at 25 mg/mL. This progressive spike potential decrease suggests chloroform suppresses proteinoid electrical activity. The time between spikes, the interspike period, follows a similar pattern. Minimal chloroform exposure does not change the average interspike period, while higher exposures do. It drops from 23.2 min under control experiments to 3.8 min at 25 mg/mL chloroform, indicating increased frequency of the electrical activity. These findings might lead to a deeper understanding of the electrical activity of proteinoids and their potential application in the domain of bioelectronics.

The generation of the flower by self-organisation

The essence of the Turing-Child theory (Schiffmann, 1991, 2017) is the direct and spontaneous conversion of chemical energy into simultaneous differentiation and morphogenesis, and all localised biological work and localised entropy-reducing processes. This is done via the identification of the Turing instability with cAMP and ATP being the Turing morphogens that mutually fulfil the five Turing inequalities. A flower model like the ABC model is derived from experiments with mutations. But what actually generates the model in real development? That is, how do genes of class A come to be expressed in the sepal and petal whorls, genes of class B in the petal and stamen whorls, and genes of class C in the stamen and carpel whorls. We suggest that the generation of the ABC model occurs via sequential compartmentalisation by Turing-Child eigenfunction patterns similar to the one occurring in Drosophila (Schiffmann, 2012). We also suggest a similar mechanism for the generation of the dorso-lateral-ventral polarity and bilateral symmetry. A mechanism for the generation of the regular location of the floral organs is also suggested. The symmetry and regularity of flowers, which are the source of their attraction and beauty, stem from the symmetry and regularity of the Turing-Child eigenfunctions. The central problem in developmental biology is the endless regress. This endless regress is halted by the Turing-Child pre-patterns and this is illustrated on a central example in flower generation. Both the shape and the chemistry - the steady-state rate of ATP synthesis and hydrolysis - of the Turing-Child pre-patterns are exactly what is required. Art and science meet in flower formation.

The non-equilibrium basis of Turing Instability and localised biological work

Turing's theory for biological pattern formation is based on the instability of the homogeneous state, which occurs if certain key criteria are met. The problem of how chemical energy is converted to localised biological work requires one to understand not only the basis of localised power generation, but also the age-old puzzle of how organisms decrease their entropy; these problems can only be solved by the identification of the Turing Instability. At the heart of this is how natural selection, not chemistry, has fashioned the large non-equilibrium overall affinity (ΔG is a large negative quantity) for the oxidation of the fuel molecules. Natural selection has also resulted in the homeostasis at non-equilibrium values of the hydrolysis of molecules like ATP, GTP, which are the energy links between the overall oxidation of the fuel and biological work. The conditions for such homeostasis are central requirements for the Turing Instability and are the essence of being alive. The Turing-Child (TC) patterns are the spontaneous primary spatial cause not only of localised biological work in multicellular systems (especially those in patterning and development) but also of intracellular patterns including the mitotic spindle and the contractile ring. The Turing picture comprises the nonuniform distribution of the concentrations of the Turing morphogens, cAMP and ATP, and the Child picture is the resulting nonuniform distribution of the metabolic rate and of power. The TC pattern is shaped as the dominant eigenfunction in the combination of eigenfunctions which provides the spatial pattern of the Turing morphogens. The TC patterns and the bifurcation parameter manifest quantisation and symmetry as in music and in applications of quantum mechanics. The notion of correlation diagrams is also introduced.

Molecular bioelectricity: how endogenous voltage potentials control cell behavior and instruct pattern regulation in vivo

In addition to biochemical gradients and transcriptional networks, cell behavior is regulated by endogenous bioelectrical cues originating in the activity of ion channels and pumps, operating in a wide variety of cell types. Instructive signals mediated by changes in resting potential control proliferation, differentiation, cell shape, and apoptosis of stem, progenitor, and somatic cells. Of importance, however, cells are regulated not only by their own V_mem but also by the V_mem of their neighbors, forming networks via electrical synapses known as gap junctions. Spatiotemporal changes in V_mem distribution among nonneural somatic tissues regulate pattern formation and serve as signals that trigger limb regeneration, induce eye formation, set polarity of whole-body anatomical axes, and orchestrate craniofacial patterning. New tools for tracking and functionally altering V_mem gradients in vivo have identified novel roles for bioelectrical signaling and revealed the molecular pathways by which V_mem changes are transduced into cascades of downstream gene expression. Because channels and gap junctions are gated posttranslationally, bioelectrical networks have their own characteristic dynamics that do not reduce to molecular profiling of channel expression (although they couple functionally to transcriptional networks). The recent data provide an exciting opportunity to crack the bioelectric code, and learn to program cellular activity at the level of organs, not only cell types. The understanding of how patterning information is encoded in bioelectrical networks, which may require concepts from computational neuroscience, will have transformative implications for embryogenesis, regeneration, cancer, and synthetic bioengineering.

Endogenous bioelectrical networks store non-genetic patterning information during development and regeneration

Pattern formation, as occurs during embryogenesis or regeneration, is the crucial link between genotype and the functions upon which selection operates. Even cancer and aging can be seen as challenges to the continuous physiological processes that orchestrate individual cell activities toward the anatomical needs of an organism. Thus, the origin and maintenance of complex biological shape is a fundamental question for cell, developmental, and evolutionary biology, as well as for biomedicine. It has long been recognized that slow bioelectrical gradients can control cell behaviors and morphogenesis. Here, I review recent molecular data that implicate endogenous spatio-temporal patterns of resting potentials among non-excitable cells as instructive cues in embryogenesis, regeneration, and cancer. Functional data have implicated gradients of resting potential in processes such as limb regeneration, eye induction, craniofacial patterning, and head-tail polarity, as well as in metastatic transformation and tumorigenesis. The genome is tightly linked to bioelectric signaling, via ion channel proteins that shape the gradients, downstream genes whose transcription is regulated by voltage, and transduction machinery that converts changes in bioelectric state to second-messenger cascades. However, the data clearly indicate that bioelectric signaling is an autonomous layer of control not reducible to a biochemical or genetic account of cell state. The real-time dynamics of bioelectric communication among cells are not fully captured by transcriptomic or proteomic analyses, and the necessary-and-sufficient triggers for specific changes in growth and form can be physiological states, while the underlying gene loci are free to diverge. The next steps in this exciting new field include the development of novel conceptual tools for understanding the anatomical semantics encoded in non-neural bioelectrical networks, and of improved biophysical tools for reading and writing electrical state information into somatic tissues. Cracking the bioelectric code will have transformative implications for developmental biology, regenerative medicine, and synthetic bioengineering.

The role of self-organization in developmental evolution

In developmental and evolutionary biology, particular emphasis has been given to the relationship between transcription factors and the cognate cis-regulatory elements of their target genes. These constitute the gene regulatory networks that control expression and are assumed to causally determine the formation of structures and body plans. Comparative analysis has, however, established a broad sequence homology among species that nonetheless display quite different anatomies. Transgenic experiments have also confirmed that many developmentally important elements are, in fact, functionally interchangeable. Although dependent upon the appropriate degree of gene expression, the actual construction of specific structures appears not directly linked to the functions of gene products alone. Instead, the self-formation of complex patterns, due in large part to epigenetic and non-genetic determinants, remains a persisting theme in the study of ontogeny and regenerative medicine. Recent evidence indeed points to the existence of a self-organizing process, operating through a set of intrinsic rules and forces, which imposes coordination and a holistic order upon cells and tissue. This has been repeatedly demonstrated in experiments on regeneration as well as in the autonomous formation of structures in vitro. The process cannot be wholly attributed to the functional outcome of protein-protein interactions or to concentration gradients of diffusible chemicals. This phenomenon is examined here along with some of the methodological and theoretical approaches that are now used in understanding the causal basis for self-organization in development and its evolution.

Morphogenetic fields in embryogenesis, regeneration, and cancer: non-local control of complex patterning

Establishment of shape during embryonic development, and the maintenance of shape against injury or tumorigenesis, requires constant coordination of cell behaviors toward the patterning needs of the host organism. Molecular cell biology and genetics have made great strides in understanding the mechanisms that regulate cell function. However, generalized rational control of shape is still largely beyond our current capabilities. Significant instructive signals function at long range to provide positional information and other cues to regulate organism-wide systems properties like anatomical polarity and size control. Is complex morphogenesis best understood as the emergent property of local cell interactions, or as the outcome of a computational process that is guided by a physically encoded map or template of the final goal state? Here I review recent data and molecular mechanisms relevant to morphogenetic fields: large-scale systems of physical properties that have been proposed to store patterning information during embryogenesis, regenerative repair, and cancer suppression that ultimately controls anatomy. Placing special emphasis on the role of endogenous bioelectric signals as an important component of the morphogenetic field, I speculate on novel approaches for the computational modeling and control of these fields with applications to synthetic biology, regenerative medicine, and evolutionary developmental biology.

Turing-Child field underlies spatial periodicity in Drosophila and planarians

The regular spatial periodicity manifested in Drosophila gene expression has been considered as a test case for the involvement of a Turing system in biology. It was expected--if such involvement exists--to find a spatially periodic protein distribution where the proteins are Turing morphogens. The failure to find such a periodic distribution of Turing proteins, and the experimental findings of the involvement of different combinations of regulatory proteins and different binding sites for the different stripes of a periodic gene expression, has resulted in the dismissal of the involvement of a Turing system in Drosophila periodicity and segmentation. But if one is willing to allow a Turing system in the level of post-translational modification of proteins instead of in the protein level, one can explain the regular spatial periodicity of gene expression. The source of the spatial periodicity of gene expression does not lie in the regulatory proteins, but in the spatially periodic post-translational modification of these broadly distributed upstream regulatory proteins. The post-translational modification provides the missing spatial information for the regular pattern of 14 stripes. We report that such a field with segmental spatial periodicity that can affect downstream proteins and modify them post-translationally and periodically has been observed. This is the Turing-Child (TC) field. We explain the recent observation in Drosophila of phosphorylated transcription factor distributed with segmental periodicity, the disappearance of the spatially periodic gene expression when the regulatory protein loses its normal ability to be phosphorylated, and the spatially periodic segmental groove formation. Just as the reduction of Turing wavelength causes the appearance of 14 stripes in Drosophila so it causes the appearance of bipolar 2-headed Planaria.

Self-organization in and on biological spheres

Three biological settings involving self-organization performed by the Turing-Child field inside a sphere and on its surface are considered. In the first setting the interior of a sphere made up of cells communicating via gap junctions is considered. It is suggested that the Turing-Child self-organization is the cause of radial polarization, the first differentiation of an early mammalian embryo. In the second setting, the Turing example of gastrulation of a hollow cellular sphere is considered. It is shown that Child's experimental patterns are predicted and explained by the Turing-Child theory. The third setting is the interior of a biological cell, and it is suggested that it is the self-organization of the Turing-Child field that causes the formation of the mitotic spindle.

Symmetry breaking and convergent extension in early chordate development

The initiation of axis, polarity, cell differentiation, and gastrulation in the very early chordate development is due to the breaking of radial symmetry. It is believed that this occurs by an external signal. We suggest instead spontaneous symmetry breaking through the agency of the Turing-Child field. Increased size or decreased diffusivity, both brought about by mitotic activity, cause the spontaneous loss of stability of the homogeneous state and the evolution of the metabolic pattern during development. The polar metabolic pattern is the cause of polar gene expression, polar morphogenesis (gastrulation), and polar mitotic activity. The Turing-Child theory explains not only the spontaneous formation of the invagination in gastrulation but also the coherent cell movement observed in convergence and extension during gastrulation and neurulation. The theory is demonstrated with respect to experimental observations on the early development of fish, amphibian, and the chick. The theory can explain a multitude of experimental details. For example, it explains the splayed polar progression of reduction in the fish blastoderm. Reduction starts on that side of the blastoderm margin, which will initiate invagination several hours later. It progresses toward the blastoderm center and somewhat laterally from this future "dorsal lip". This is precisely as predicted by a Turing-Child system in a circle. And for a fish like zebrafish with a blastoderm that is slightly oval, reduction is observed to progress along the long axis of the ellipse, which is what Turing-Child theory predicts. In general the shape and the chemical nature of the experimental patterns are the same as predicted by the Turing couple (cAMP, ATP). Embryological polarity and convergent extension are based on polar eigenfunction and saddle-shaped eigenfunction, respectively.

Induction and the Turing-Child field in development

The central problem in biological development is the understanding of epigenesis. The dominant theory of development in the last 80 years that also purports to explain epigenesis is induction theory. It suggests that development is driven by sequential inductions where each "induction" (in one sense of the word induction) is effected by the action of an inducing part of the embryo on a responding part of the embryo. The theory stems from Spemann and Mangold (W.Roux' Arch.f.Entw.d.Organis.u.mikrosk.Anat.100 (1924) 599) who transplanted a tissue from the dorsal blastopore lip of Triturus into the ventral ectoderm of another gastrula and thus initiated and "induced" (in another sense of the word induction) gastrulation and embryogenesis in the ventral side of the host that became a double embryo (siamese twins). We explain this induction, i.e. the formation of the double embryo, according to the Child theory and the Turing-Gierer-Meinhardt theory when it is also assumed that cAMP and ATP are the Turing activator and inhibitor, respectively. Spemann and Mangold (W.Roux' Arch.f.Entw.d.Organis.u.mikrosk.Anat.100 (1924) 599) also suggested that the ingressing mesoderm induces the overlying ectoderm to form the neural plate and neural tube. This 'neural induction', the 'primary embryonic induction', became the cornerstone of induction theory, i.e. of the sequential induction concept referred to above. But we argue that the metabolic gradients that precede and accompany neurulation, as obtained by Child, also for Triturus, arise through a Turing self-organization if it is assumed that cAMP and ATP are the Turing morphogens, and these gradients are the cause and primary event of neurulation. Thus there is no need to invoke the 'neural induction'. It is argued that fundamental events such as gastrulation and also organ formation are caused by the Turing-Child field and not by sequential induction. Similar principles, such as bud formation caused by a radial metabolic pattern that transforms to a longitudinal pattern, govern the formation, for example, of the mouth and the gut. The formation and localization of bottle cells is explained according to the Child-Turing field and modern biochemistry. The chemical metabolic pre-pattern precedes, and causes, morphogenesis and differentiation as envisaged by Turing. The Spemann and Mangold (W.Roux' Arch.f.Entw.d.Organis.u.mikrosk.Anat.100 (1924) 599) transplantation experiment when performed on a sea urchin duplicates not only the phenotype but also the metabolic (reduction) pattern. These experimental results, by Horstadius, predicted by Child, follow from the Turing-Gierer-Meinhardt theory if it is assumed that cAMP and ATP are the Turing morphogens. If the transplantation is performed not onto the whole sea urchin but onto only a part of it, that manifests only a part of the metabolic pattern, then from the part a phenotypic whole underlain by a normal and a whole metabolic pattern can be rescued. These experimental results of Horstadius follow from Turing theory if cAMP and ATP are the Turing morphogens. Understanding how to transform a part into a whole can be valuable in regenerative medicine. Unspecific induction of a secondary amphibian embryo is similar to the induction of posterior structures at the anterior pole of an insect, and the "double abdomen" (and Kalthoff's experimental results) of the midge Smittia resulting from UV irradiation of the anterior pole, can be explained by Meinhardt theory of unspecific induction if ATP is the Turing morphogen. When not working on regeneration, Child investigated intact living organisms and his observation method was not disruptive to normal development, whereas workers in induction theory work with pieces and in general disrupt normal development. We conclude that the Turing-Child field causes all development and explains epigenesis. Sequential induction does not explain epigenesis and does not exist in normal development. But induction in the sense of a transplantation leading to double embryo or rescuing a whole phenotype from a part is of interest.

Libbie Henrietta Hyman (1888-1969): From developmental mechanics to the evolution of animal body plans

Libbie Hyman is the most influential comparative invertebrate zoologist of the 20th century in the English-speaking world. During the first part of her career Hyman conducted experimental research on the metabolic and developmental physiology of a host of invertebrates and vertebrate embryos. One important aim of these studies was to elucidate the hidden processes of morphogenesis. Some of the papers from this early phase of Hyman's career already contain the seeds for her subsequent occupation with comparative embryology and morphology to address questions about animal body plan evolution and metazoan phylogeny. Hyman's views on invertebrate evolution and phylogeny have become widely incorporated into textbooks, and until very recently Hyman's ideas have been equated with 'traditional' or 'classical' views on animal evolution. Hyman's enduring fame and significance for modern evo-devo is primarily based upon her magisterial six-volume series The Invertebrates, which is the most encompassing single-author synthesis of invertebrate structure and development of the 20th century. In The Invertebrates Hyman addressed numerous questions about the evolution of animal body plans and metazoan phylogeny that are nowadays core items on the research agenda of evo-devo. In addition, Hyman had a lasting influence on teaching with the publication of her widely used laboratory manuals for elementary zoology, and especially comparative vertebrate anatomy.

Segmentation and zooid formation in animals with a posterior growing region: the case for metabolic gradients and Turing waves

The discovery of periodic propagation of anteriorly moving pulses/stripes of gene expression in the presomitic mesoderm (PSM) of vertebrates has given new life to the clock and wavefront model, and other models of morphogenesis based on a molecular oscillator where the time periodicity is translated into spatial periodicity. Instead we suggest that segmentation, somitogenesis and metamerism in vertebrates and in invertebrates with a posterior growing region are based on a Turing-Child metabolic gradient that is progressively shifted posteriorly with the PSM as elongation, segmentation and somitogenesis proceed. This gradient corresponds to anteriorly propagating metabolic front in the PSM that drives the anteriorly propagating mRNA synthesis and which, together with mRNA degradation, explains stripe formation and spatial periodicity.The process of segmentation has been compared to zooid formation. We show that for annelids the metabolic profile behaves as a Turing field in the sense that an increase in the length of the system or a decrease of the Turing wavelength results in an additional peak in the posterior growing region as predicted by Turing theory. In particular, it is shown that the metabolic gradient that drives the segmentation is based on a Turing system.

Polarity and form regulation in development and reconstitution

In the literature, it is often assumed, for example with respect to Hydra, that several Turing systems coexist and it is also assumed that maintaining the polar profile, even when the system increases in size, is important for the polarity of the final phenotype. It is shown here that in reality there is only one Turing system, Child's system. To obtain a complete polar individual or organ, whether in reconstitution or development, it is essential that the complete succession of metabolic patterns occurs. Child's concepts of physiological dominance, subordination and isolation are interpreted in the light of Turing theory and in particular the Turing wavelength. It is emphasised, particularly by pointing to Child's metabolic patterns in coelenterates, both in development and in reconstitution, that it is the elongation that drives the succession polar metabolic pattern-->bipolar metabolic pattern, and this corresponds to the prediction of Turing theory supporting the thesis that Child's metabolic pattern is a Turing pattern. It is shown that if we assume that ATP is the Turing inhibitor then the many results of Child about the reduction of the scale of organisation with the decrease in the intensity of the energy metabolism correspond to the reduction of the Turing wavelength. The interplay between the Turing wavelength and the length of the form explains the conditions of reconstitution under which partial forms, wholes and form regulation are obtained. It is suggested that higher metabolism is responsible for both larger size and larger Turing wavelength thus securing form regulation. The results could be of importance in modern 'regenerative biology'. Heteromorphosis, i.e. animals with two heads (or two tails), one at each end, is explained by a bipolar Turing-Child metabolic pattern replacing a polar metabolic pattern. This can be brought about by chemical or by genetic means and indeed the prediction for Drosophila that the transition, wild type-->Bicaudal D, occurs because a polar Turing pattern is replaced by bipolar Turing pattern is confirmed, again if we accept that Child's metabolic pattern is the underlying Turing pattern. Child's experiments on Drosophila, including the requirement of critical length for metabolic polarity, are explained by Turing theory. Phenocopies and phenotypes are explained by the Turing-Child theory. It is shown that both Child's results about metabolic patterns and modern results for Hydra about gap junctions, 'endogeneous inhibitor' and gene expression, are correlated and explained by (cAMP, ATP) Turing theory. It is argued that the double-gradient hypothesis is incorrect in its original formulation and that it is Child's conception of succeeding metabolic patterns that is the correct one and that it corresponds to the prediction of the Turing theory.