Ditto. The larger question is how does the linear sequence of DNA (primary sequence) ultimately drive the spatio-temporal development program that leads to mature differentiated cells working together at the organoid / organ / organism scale. How do cells know what to do in time and space as the organism grows? How is that logic encoded in the genome?
Eric Davidson did a bunch of pioneering work meticulously "debugging" this spatiotemporal genomic logic in the sea urchin. Pretty amazing. Eukaryotes like us have control elements directly upstream of our genes (trans-acting aka close acting) and also 100,000's of base pairs distant (cis-acting). The region of DNA directly preceding the beginning of an open reading frame at the start of a gene usually has a sequence of DNA motifs that bind proteins that can increase or decrease expression of the gene. Davidson and others showed that the transcription factor proteins that bind to these control motifs actually have additional other proteins that bind to them, in literally a layer on top, and that the sequences of proteins in this second layer recruit a tertiary layer of proteins that conditionally cause more or less gene expression, depending on their identities. You could say the secondary and tertiary layers are a form of "abstraction" in a literal sense, since they encode a hierarchy of logical operations.
Here's an open-access overview of Davidson's work which incidentally illuminates a lot of these concepts in more detail for a lay audience: "ERIC DAVIDSON: STEPS TO A GENE REGULATORY NETWORK FOR DEVELOPMENT" by Ellen Rothenberg, 2016; doi: 10.1016/j.ydbio.2016.01.020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828313/
to see the decoded logic in pseudocode and with a diagram, see "cis-Regulatory control circuits in development", Howard and Davidson, 2004, Developmental Biology, vol 271, https://doi.org/10.1016/j.ydbio.2004.03.031 (open access)
Eric Davidson did a bunch of pioneering work meticulously "debugging" this spatiotemporal genomic logic in the sea urchin. Pretty amazing. Eukaryotes like us have control elements directly upstream of our genes (trans-acting aka close acting) and also 100,000's of base pairs distant (cis-acting). The region of DNA directly preceding the beginning of an open reading frame at the start of a gene usually has a sequence of DNA motifs that bind proteins that can increase or decrease expression of the gene. Davidson and others showed that the transcription factor proteins that bind to these control motifs actually have additional other proteins that bind to them, in literally a layer on top, and that the sequences of proteins in this second layer recruit a tertiary layer of proteins that conditionally cause more or less gene expression, depending on their identities. You could say the secondary and tertiary layers are a form of "abstraction" in a literal sense, since they encode a hierarchy of logical operations.
Here's an open-access overview of Davidson's work which incidentally illuminates a lot of these concepts in more detail for a lay audience: "ERIC DAVIDSON: STEPS TO A GENE REGULATORY NETWORK FOR DEVELOPMENT" by Ellen Rothenberg, 2016; doi: 10.1016/j.ydbio.2016.01.020 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4828313/
to see the decoded logic in pseudocode and with a diagram, see "cis-Regulatory control circuits in development", Howard and Davidson, 2004, Developmental Biology, vol 271, https://doi.org/10.1016/j.ydbio.2004.03.031 (open access)