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Wild-type T7 is a superb organism for discovering the primary components of a biological system [Studier, 1972]. However, is the original T7 isolate also best suited for understanding how all parts of the phage are organized to encode a functioning whole?
Physical Model to further understand biology
We are interested in questions of how the genetic components of an organism are organized on the genome to carryout functions such as development even in the face of significant environmental variations. However, to rigorously answer these questions, we need to first understand how changes in genome organization lead to changes in the timing and level of gene expression. However our efforts to create empirical computational models based on observations of the primary genetic elements and mechanisms governing gene expression have fallen short of providing system-level predictive capacity. It is unclear whether the differences between our measurements and models are due to our inability to parameterize and simulate the complex biophysical processes involved, or our understanding of the biophysical processes is just incorrect or incomplete. Moving forward, instead of further studying wild-type T7, we can try encoding our understanding of the biophysical processes onto a new genome. We will try to only encode those functions which we understand, while actively removing those that we don't. Differences between the behavior of the engineered and wild-type phage will highlight gaps in our understanding, and will lead to follow-on science.
New Model Organism
On the other hand, our interest in T7 is somewhat arbitrary. If we can construct a better model organism that will let us study hypotheses of how the organization of genetic components make up a biophysical system, it may not be necessary to relate that back to the wild type.
T7.1 -- Our initial attempt to rebuild the T7 genome.
T7.2 -- A more ambitious effort that revisits some of our initial ideas that were tabled in T7.1.