Analogies to Motors

You misunderstood (though not your fault). Let me clarify. You said that since biological complexes (e.g. flagella) are - by definition - ‘motors’, this means it is not an analogy - rather it is ‘literal’ to say they are motors. However, I object to this by pointing out that putting things under the same category does not mean they are ‘literal’, nor does it negate the fact that they are analogies. This is what I meant to say when I said “no longer analogous”.

Let me reword my previous statement:

As I have already pointed out, providing clear explanations with references, at the crucial respects, these are fundamentally NOT alike whatsoever. You inadvertently admit this when you say the following:

In one sentence you say they are “so much alike” - yet - what does it mean when you must have a “broad enough” definition in order for the category to encompass biological complexes such that they meet *enough of the basic requirements"? To me, this just furthers my point that the machine analogy only gives attention to few similarities, which we happen to find significant as it makes the object much more familiar to us than they really are. This is a quirk of our heuristics. Whenever we find something we don’t understand, we frequently will compare it with things we do understand (or - at least - with things that seems more familiar to us).

I would say that this makes the machine analogy (at the very least) extremely poor and (very often) misleading, since such statements are counter to what they fundamentally are and how they work. Viewing the cell as a machine presents a cognitive hurdle to understanding the true nature of life. Even you yourself admit that it can be misleading. Indeed, it often is.

Anecdote.

Also, I would say that your understanding may be affected by the misleading machine analogies, at least to some degree, without realizing it. A clear sign of this is when you said that they are “so much alike”, even though they are not.