In my field, animal developmental biology, and in what could be regarded as its “deep time derivative,” the evolutionary biology of the animal body plan, there exist two kinds of experimentally supported causal explanation. These can be described as “rooted” and “unrooted.” Rooted causal explanation provides logical links to and from the genomic regulatory code, extending right into the genomic sequences that control regulatory gene expression. The genomic regulatory code ultimately determines the developmental process in a direct way, since subsequent (...) developmental events all depend directly and specifically on what regulatory genes are being expressed and where in the developing organism they are being expressed.. (shrink)

In the maximal form of indirect development found in many taxa of marine invertebrates, embryonic cell lineages of fixed fate and limited division capacity give rise to the larval structures. The adult arises from set‐aside cells in the larva that are held out from the early embryonic specification processes, and that retain extensive proliferative capacity. We review the locations and fates of set‐aside cells in two protostomes, a lophophorate and a deuterostome. The distinct adult body plans of many phyla develop (...) from homologous set‐aside cells within homologous larvae. We argue that the stocks from which these phyla arose utilized these respective larvae, and the diversity of their adult body plans reflects diverse pattern formation processes executed in their set‐aside cell populations. Chordates and arthropods develop directly, but share adult characters with indirectly developing phyla. Thus the deuterostome and protostome stocks that were ancestral to chordates and arthropods, respectively, also utilized maximal indirect development. (shrink)

Developmental processes in complex animals are directed by a hardwired genomic regulatory code, the ultimate function of which is to set up a progression of transcriptional regulatory states in space and time. The code specifies the gene regulatory networks (GRNs) that underlie all major developmental events. Models of GRNs are required for analysis, for experimental manipulation and, most fundamentally, for comprehension of how GRNs work. To model GRNs requires knowledge of both their overall structure, which depends upon linkage amongst regulatory (...) genes, and the modular building blocks of which GRNs are heirarchically constructed. The building blocks consist of basic transcriptional control processes executed by one or a few functionally linked genes. We show how the functions of several such building blocks can be considered in mathematical terms, and discuss resolution of GRNs by both “top down” and “bottom up” approaches. BioEssays 24:1118–1129, 2002. © 2002 Wiley‐Periodicals, Inc. (shrink)

In 2012, we published a computational automaton, based on the most comprehensive gene regulatory network (GRN) model yet available (Peter, Faure, and Davidson 2012). This model had been synthesized over the previous years from extensive experimental studies on specification mechanisms in the endomesodermal territories of the sea urchin embryo. The GRN model explicitly indicated the dynamically changing interactions occurring at the cis-regulatory control sequences of almost 50 genes, mostly encoding transcription factors (the proteins that specifically recognize cis-regulatory DNA sequence and (...) cause expression or inactivity of the genes these sequences control). The GRN model encompasses all regulatory genes .. (shrink)

The successes of molecular developmental biology over the last ten years have been particularly impressive in those directions favored by its major paradigms. New technologies have both guided and been guided by the progress of the field. I review briefly some of the major insights into embryonic development that have derived from research in four specific areas: early embryogenesis of various forms; “pattern formation”; evolutionary conservation of regulatory elements; and spatial mechanisms of gene regulation. There remain many major problem areas, (...) some of which may require new orientations to solve. (shrink)