The argument from incredulity has not held up well. Nature is infinitely more clever, creative, and patient than (if I may say) you, or I. Anything that can reproduce is foundation for a next stage. Each individual in each generation may sport an innovation, which if reproduced joins the rest. Five million years is a very long time, too long really for human apprehension. (How many times could a pharmacist fill your prescription, in that time?) Whales' niche favors increasing size, although, that filled, other niches were discovered by porpoises.
You are aware that all species that existed 500 million years ago are extinct, leaving only their descendants? That would include our common ancestor, leaving squids, and us, and fruit flies. (Some coeval species left fossils, though probably not that one.) But the gene that places our eyes, inserted into a fruit fly chromosome at a place dictating growth of a body part, grows an eye there. A fruit fly eye, of course.
It is interesting that your dogma is gradualism, and you explain gradualism through gradualism.
Then you appeal to the God of time, but many great paleothologists and mathematician have demonstrated that it is not enough !
Please note that I am not a fixist creationnist, apparition (evolution ?) of species happened in history, but what is the engine of evolution ?
Where the new information to build new orders, reigns, branches, proteins, functions, organs, orders, species, came from ?
Chance applied to a code can by no way create new functions. It is easy to understand as any programmer will tell you. There is no computer science domain, neither developpers who use chance to create or improve a computer program.
Nevertheless, a computer can run more generations than nature had for many new species to appear.
If positive mutation happen, it is a build-in system, it cannot be pure chance (a lot of maths on the subject)
If it is a build-in system, it is one more mystery to explain how chance can create codes, coders, decoders, engines, pumps, pipes, organs, species, self-replicating systems, and also self-improving systems.
You argue that software is impossible, but here we are using it. Where did the ideas that went into the software come from? Were they all divinely inspired, or were they logical next steps upon what came before?
Careful: claiming software you wrote is divinely inspired will not go over well at code review, particularly if you insist it doesn't need to pass tests.
I argue random mutations applied to software does not create any new fonctions, it breaks eveverything.
Also that any usable software was designed by a mind.
Where comes this mind from is another question.
Which random mutated software are you using ?
You will acknowledge, I hope, that biological systems are much more forgiving of random mutations than software is. We don't need intelligent choice when Nature just tries everything, and keeps what works. Not efficient or quick, but Nature doesn't mind. Nature acknowledges no deadlines. Or goals.
So, a series of not-excessively-harmful monkey-patches accumulate under stringent testing to significant improvement. We don't need to guess about that: it has been demonstrated by laboratory experiment, which you may read all about if you care to. Or don't, and continue parroting Behe's sterile talking points long after they have been thoroughly discredited.
You are aware that all species that existed 500 million years ago are extinct, leaving only their descendants? That would include our common ancestor, leaving squids, and us, and fruit flies. (Some coeval species left fossils, though probably not that one.) But the gene that places our eyes, inserted into a fruit fly chromosome at a place dictating growth of a body part, grows an eye there. A fruit fly eye, of course.