Biological development is often described as a dynamic, emergent process. This is evident across a variety of phenomena, from the temporal organization of cell types in the embryo to compounding trends that affect large-scale differentiation. To better understand this, we propose combining quantitative investigations of biological development with theory-building techniques. This provides an alternative to the gene-centric view of development: namely, the view that developmental genes and their expression determine the complexity of the developmental phenotype. Using the model system Caenorhabditis elegans, we examine time-dependent properties of the embryonic phenotype and utilize the unique life-history properties to demonstrate how these emergent properties can be linked together by data analysis and theory-building. We also focus on embryogenetic differentiation processes, and how terminally-differentiated cells contribute to structure and function of the adult phenotype. Examining embryogenetic dynamics from 200 to 400 min post-fertilization provides basic quantitative information on developmental tempo and process. To summarize, theory construction techniques are summarized and proposed as a way to rigorously interpret our data. Our proposed approach to a formal data representation that can provide critical links across life-history, anatomy and function.
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Terminally-differentiated cell nomenclature identities and annotations by developmental birth time (min). (XLSX 121 kb)
Table of number of cells born at a specific developmental birth time sampling point (min) for five distinct somatic cell types. (XLSX 8 kb)
Table of somatic cell types by family, class, and developmental birth time (min). (XLSX 24 kb)
Table of cell families by number of family members and average developmental birth time (min). (XLSX 12 kb)
Pairwise alignments (per pairs of birth time sampling points) and calculation of alignment scores for CAST analysis. (XLSX 152 kb)
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Alicea, B., Gordon, R. & Portegys, T.E. Data-Theoretical Synthesis of the Early Developmental Process. Neuroinform (2021). https://doi.org/10.1007/s12021-020-09508-1
- Developmental biology
- Computational biology
- Data science
- Theoretical models
- Caenorhabditis elegans