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“Is it your understanding that the defendant used an analogy which used the word design to describe a structure in biology, DNA."

Interesting idea to put yourself on trial, and you seem to have a handle on some of the biology and genetics involved in "the case". However, it seems you're starting off on the wrong foot and wind up barking up the wrong tree by relying on anything to do with design or structure -- which you apparently acknowledge by entering a "guilty" plea.

The whole point of the biological definitions is that they're based on the presence of transitory reproductive processes: no process, no sex. See my earlier points about clownfish and hundreds of other species which change sex over the course of their lives. Which are simply incompatible with any definitions based on structure or design.

But given your apparent "guilty" plea, I'm at a loss to interpret this later statement of yours:

AH: "... the witness is committing the same error I mentioned in my initial comments on the bipedal analogy, one cannot claim that something is designed and also not designed at the same time and in the same respect."

I assume your "witness" is that Cleveland Clinic source you're quoting though didn't more than skim them so can't say that they're saying both designed and not-designed. Somewhat irrelevant in either case -- more on which later -- but it does highlight a common misperception that genes and chromosomes are more or less like blueprints -- entirely different kettles of fish; see:

https://blogs.scientificamerican.com/observations/dna-is-not-a-blueprint/

But quite agree with you that something can't be A and not-A, at least simultaneously. Though I expect they may have different senses to the word in mind. But consider a definition from Google/Oxford that is roughly equivalent to those blueprints:

"design: a plan or drawing produced to show the look and function or workings of a building, garment, or other object before it is built or made"

Many people want to make the sex chromosomes, the karyotypes, into those plans and drawings that "build" the sexes. But a blueprint for a car is entirely different from the car itself. In addition to which, many different blueprints -- for millions of species -- all lead to the eventual existence of processes -- in the "as-built models" -- that produce large or small gametes:

https://en.wikipedia.org/wiki/Sex-determination_system

That's what makes the biological definitions for the sexes "universal".

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