So this gets a key claim that Marks makes, and I want to know if you agree with him:
It is not possible to calculate the Kolmogorov complexity of an object. However, it is possible to upper-bound the Kolmogorov complexity and thus lower-bound the algorithmic specified complexity. This means that something can be determined to be at least this specified, although the possibility that it is even more specified cannot be ruled out.
According to Marks, the consequences of using the wrong P is that ASC will be artificially low, and never artificially high. My ASC implementation is supposed to be a hard lower bound on CSI. Do you agree? If not, where did Marks go wrong?
After answering this question, I need you to choose either:
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If ASC (and my implementation) can never overestimate CSI, then we will keep my implementation and move to the next part.
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If you think we must carefully chose our implementation of ASC (the P) or we will overestimate CSI, that leaves you with two tasks: (1) explain were Marks when wrong and (2) give us the correct implementation by which we can compute ASC on biological sequences (DNA and/or protein sequences).
It seems a key point Marks is making is that even if we have the wrong compression algorithm, we are guaranteed to be under-estimating CSI with the ASC measure. I think you agree, as this appears to be your idea. If not, that would be really interesting. Curious which choice you will take…