Yes. The previous design hypothesis I discussed was front-loading, which is indirect design. However, the two hypotheses I have discussed are not necessarily incompatible. Let me explain.
If you designed the bacterial flagellum into the initial cells, there's no need to front-load it into existence. Thus, under this view, the bacterial flagellum was engineered, but there's still plenty of room for front-loading. I'm trying to focus on a molecular machine that could have been in the first life forms because then you could have both direct engineering and front-loading.
But doesn't this rather deprive your ideas of any predictive power? You can take any two things that look like homologues. You can see if the observations still fit your idea if they were actually analogues created In The Beginning. If the observations let you down, then no problem, you can just say: "oh, well then, they really are homologues; I said that that wasn't incompatible with my latest idea". Heads you win, tails you don't lose.
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I hope to get round to the main substance of your OP ... soonish.
Edited by Dr Adequate, : No reason given.
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