Eric Davidson: Steps to a gene regulatory network for development

Self-Organization and Genomic Causality in Models of Morphogenesis

The debate about what causes the generation of form and structure in embryological development goes back to antiquity. Most recently, it has focused on the divergent views as to whether the generation of patterns and form in development is a largely self-organized process or is mainly determined by the genome, in particular, complex developmental gene regulatory processes. This paper presents and analyzes pertinent models of pattern formation and form generation in a developing organism in the past and the present, with a special emphasis on Alan Turing's 1952 reaction-diffusion model. I first draw attention to the fact that Turing's paper remained, at first, without a noticeable impact on the community of biologists because purely physical-chemical models were unable to explain embryological development and often also simple repetitive patterns. I then show that from the year 2000 and onwards, Turing's 1952 paper was increasingly cited also by biologists. The model was updated to include gene products and now seemed able to account for the generation of biological patterns, though discrepancies between models and biological reality remained. I then point out Eric Davidson's successful theory of early embryogenesis based on gene-regulatory network analysis and its mathematical modeling that not only was able to provide a mechanistic and causal explanation for gene regulatory events controlling developmental cell fate specification but, unlike reaction-diffusion models, also addressed the effects of evolution and organisms' longstanding developmental and species stability. The paper concludes with an outlook on further developments of the gene regulatory network model.

RNA out of the mist

RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.

The idea of constancy in development and evolution - Scientific and philosophical perspectives

The ability of developmental systems to produce constant phenotypes, even in a wide range of different environments, and the longstanding stability of species are among the most remarkable phenomena in biology. I argue that understanding the longstanding constancy and stability of species or the constant outcome of development in different environments are also prerequisites for explaining stable change (i.e., change that does not consist of random plasticity). Various approaches to account for stable changes in development are based on the causal role of genes and an organized genome, mathematical-physical-chemical models, or a combination of both. I argue that the constancy of developmental outcome and the longstanding stability of species are associated with organisms' structural and organizational hierarchies, particularly highly organized gene-regulatory networks and genetic causality, which are fundamental principles of life. Mathematical-physical-chemical models that marginalize these principles cannot convincingly account for the observed constancy in development and evolution. However, an integration of physical-chemical processes such as reaction-diffusion mechanisms and genome-based mechanisms of form generation has recently proved fruitful in explaining the development of some periodic structures. Constancy and change were also major topoi in ancient Greek philosophy, in which prominent philosophical schools such as the atomists attempted to bridge the antinomy between them by basing stable change on constant entities. I argue that the idea of change, that is, change without losing complexity or even increasing it, being based on modifications of the otherwise reliable transmission of genomes over long periods of time has a historical parallel in the writings of these ancient speculative thinkers, notwithstanding the fundamental differences between the two thought systems.

Essay the (unusual) heuristic value of Hox gene clusters; a matter of time?

Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.

Does phenotypic plasticity initiate developmental bias?

The generation of variation is paramount for the action of natural selection. Although biologists are now moving beyond the idea that random mutation provides the sole source of variation for adaptive evolution, we still assume that variation occurs randomly. In this review, we discuss an alternative view for how phenotypic plasticity, which has become well accepted as a source of phenotypic variation within evolutionary biology, can generate nonrandom variation. Although phenotypic plasticity is often defined as a property of a genotype, we argue that it needs to be considered more explicitly as a property of developmental systems involving more than the genotype. We provide examples of where plasticity could be initiating developmental bias, either through direct active responses to similar stimuli across populations or as the result of programmed variation within developmental systems. Such biased variation can echo past adaptations that reflect the evolutionary history of a lineage but can also serve to initiate evolution when environments change. Such adaptive programs can remain latent for millions of years and allow development to harbor an array of complex adaptations that can initiate new bouts of evolution. Specifically, we address how ideas such as the flexible stem hypothesis and cryptic genetic variation overlap, how modularity among traits can direct the outcomes of plasticity, and how the structure of developmental signaling pathways is limited to a few outcomes. We highlight key questions throughout and conclude by providing suggestions for future research that can address how plasticity initiates and harbors developmental bias.

From Gregor Mendel to Eric Davidson: Mathematical Models and Basic Principles in Biology

Mathematical models have been widespread in biology since its emergence as a modern experimental science in the 19th century. Focusing on models in developmental biology and heredity, this article (1) presents the properties and epistemological basis of pertinent mathematical models in biology from Mendel's model of heredity in the 19th century to Eric Davidson's model of developmental gene regulatory networks in the 21st; (2) shows that the models differ not only in their epistemologies but also in regard to explicitly or implicitly taking into account basic biological principles, in particular those of biological specificity (that became, in part, replaced by genetic information) and genetic causality. The article claims that models disregarding these principles did not impact the direction of biological research in a lasting way, although some of them, such as D'Arcy Thompson's models of biological form, were widely read and admired and others, such as Turing's models of development, stimulated research in other fields. Moreover, it suggests that successful models were not purely mathematical descriptions or simulations of biological phenomena but were based on inductive, as well as hypothetico-deductive, methodology. The recent availability of large amounts of sequencing data and new computational methodology tremendously facilitates system approaches and pattern recognition in many fields of research. Although these new technologies have given rise to claims that correlation is replacing experimentation and causal analysis, the article argues that the inductive and hypothetico-deductive experimental methodologies have remained fundamentally important as long as causal-mechanistic explanations of complex systems are pursued.

Mechanistic philosophies of development: Theodor Boveri and Eric H. Davidson

Theodor Boveri's (1862-1915) and Eric Davidson's (1937-2015) achievements represent thoroughly two quite distant time frames in the history of the mechanistic approaches to development, that Jane Maienschein (2014) has characterized respectively as the era of the "experimental embryo" and of the "computed embryo". Nonetheless, Davidson's special bond to Boveri is meant to emphasize the genealogical continuity of an embryological tradition of mechanistic philosophy that, differently from molecular biology, is committed to an explanation of the hereditary transmission of organization. Davidson's genealogical claim is reconsidered through a contextualized analysis of the function of machine-like models and of the role of experiment in the making of their respective mechanistic philosophies. This analysis may help to shed light on resilience and change in the understanding of a mechanistic approach to development.

V. AM, Solanke AU, Singh NK, Sharma TR, Gaikwad K. Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis

Owing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC-936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP- D-glucose 4-epimerase) and validated as targets for three novel miRNAs, that is Ct-miR3130, Ct-miR3135 and Ct-miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan-producing species.

Hierarchy, determinism, and specificity in theories of development and evolution

The concepts of hierarchical organization, genetic determinism and biological specificity (for example of species, biologically relevant macromolecules, or genes) have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information (specificity) and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled "reductionist". However, the concepts have been marginalized or rejected in some of the research that in the late 1960s began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that 'molecular reductionism' has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular 'reductionism', in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology.

Eric Davidson and deep time

Eric Davidson had a deep and abiding interest in the role developmental mechanisms played in generating evolutionary patterns documented in deep time, from the origin of the euechinoids to the processes responsible for the morphological architectures of major animal clades. Although not an evolutionary biologist, Davidson's interests long preceded the current excitement over comparative evolutionary developmental biology. Here I discuss three aspects at the intersection between his research and evolutionary patterns in deep time: First, understanding the mechanisms of body plan formation, particularly those associated with the early diversification of major metazoan clades. Second, a critique of early claims about ancestral metazoans based on the discoveries of highly conserved genes across bilaterian animals. Third, Davidson's own involvement in paleontology through a collaborative study of the fossil embryos from the Ediacaran Doushantuo Formation in south China.