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> One issue I see is that you want to have a debate in your terms where the questions make sense if you already have the beliefs you have. Rosen it proposing a perspective that is different.
> <snip>
> These are not the questions that Rosen answers. He is concerned with science and examining the assumptions of physics to find ways to broaden its application to biology. His main goal was to understand what life is. That lead to fundamental work on problems in modern science. But he is first and foremost a scientist not a philosopher.
> The first step, as I see it, is to understand the current limitations of the modern scientific paradigm. Before worrying about whether Rosen provides a "better" alternative. Even if he only shows the problems it is of huge value. But he does much more.

I've only spent four or five hours digging into Rosen's work and that of his students, and I have to say that I found nothing that would encourage me to go further. I originally trained as a theoretical physicist, and then retrained as a biologist (as in, pass as a complete native in both fields, not physicist who dabbled in biology). Rosen's stuff on "modeling relations" is hardly new. The (M,R)-systems don't seem at all revolutionary. When the contradiction is distilled (Louie and Kercel's 'Topology and Life Redux') it appears to be a simple failure to understand that physical systems evolve in time. There is some kind of obsession with Aristotelian classification of causes mapping to cycles, but the proper response when a classification like that breaks down is to stop using it. I can't find any use of his work to illuminate any area of biology (as Everett's interpretation did for quantum mechanics) or to trigger any scientific advance (as the Bohm-de Broglie interpretation did for quantum mechanics in Bell's theorem), so at this point I would need fairly strong evidence to not write him off as a crank.

The complaint about the Church-Turing thesis and ambiguity all seems off base. Of course a part of an interacting system isn't a program. It's a coprogram, operating on codata (see Atkey and McBride, 'Productive Coprogramming with Guarded Recursion').

>> What actually goes wrong if I try to simulate life? Every high-level contradiction means that some detail doesn't work the way it's expected.
> That is again framed in your paradigm.

You keep using this word. I do not think it means what you think it means. Paradigm shifts as Kuhn described come about because a great accumulation of observations that cannot be adequately modeled in the previous framework.

Coming back to your presentation, I have some serious qualms. First, let's dispose of "engineering" since everyone besides engineers busy doing it seems to have some idealized idea of what it is. My father, a civil engineer, always told me it was doing a particular kind of work in a way that you would be able to stand up in court and defend it.

"Modern science assumes reductionism" is one of those things that I have heard for decades and no one has ever made good on the statement. Either it means we model in terms of only some of the properties of the system and ignore others in which case the only good answer is: of course, and the map (the model) is not the territory; or it means that modern science models only in terms of describing a thing as composed of a more fundamental set of things and so forth, in which case, yes, small parts of modern physics, chemistry, biology, etc. are devoted to trying to link the models of their field to the models of another field, but most aren't, so it's just wrong.

Then there's stuff about design, which is simply not well posed enough to say anything about. It's being contrasted to some fictional ideal of engineering, and saying "a roc is larger than a unicorn" is not a particularly useful statement. And in places it is clearly contradictory, such as slide 6 where you say "Defies explanation" and "Can be modeled with category theory." It's one or the other. And usually good design does not defy explanation. If you ask a the designer, they can probably tell you exactly how they ended up with what they have and why. I can certainly do so for the novel and short stories I wrote, the sonatas and art songs I have written, the furniture I have built, and the software I have produced.

I would suggest that if you haven't managed to pick out something you can explain clearly from Rosen yet, it may not be worth your time. There are rabbit holes that are utterly beguiling. Developing physics from information theory is another of them. The lesson is that the dawning feeling that you often feel just before a jump in understanding need not always presage such a jump. It may just be a will-o-the-wisp leading you into a swamp.