For the classic watchmaker analogy to apply to organisms, living things had better be analogous to artifacts such as watches which are literally finished products. That’s not to say a creature must come with a make and model number stamped into it, but the creature’s body must appear to function according to an apparent purpose or design. Otherwise, the appeal to artifacts we intelligently design wouldn’t make for a strong analogy with organisms, and the design argument for God would be weak at best.

When you talk about the lack of gradual evolution in the fossil record, I believe you’re talking about phyla, not species. Most of the major animal phyla seem to arise spontaneously in the Cambrian Explosion. But there’s plenty of fossil evidence of gradual change between species within a much more general body type.

What Paley says is, “Every indication of contrivance, every manifestation of design, which existed in the watch, exists in the works of nature; with the difference, on the side of nature, of being greater or more, and that in a degree which exceeds all computation.”

Is there supposed to be some crucial difference between the universe as a whole and “the works of nature”? The universe is just the set of all existing natural things which Paley compares to watches. And it’s funny that Paley should speak of the “works of nature,” since that expression implies that nature is doing the work, which is evidently the case, as my article points out.