I don't see how genetics allowing for instinctual/"inherent" knowledge requires a creator.

Once upon a time there was a bug that had a little sticky bit on it's butt, it had a billion descendants when one of them randomly had a gene that affected it's behavior such that it, I don't know, rested on high surfaces using the sticky bit and was safer from predators or something, and then had slightly more kids than the rest. And one of those kids randomly had a gene that gave it more sticky stuff, and one of it's kids used it a little more effectively, and so on and so forth. And that probably takes somewhere from tens of thousands to a few million years.

That's not meant to be literal, but that's the story in my head, and it doesn't feel like a huge leap to get to complex behaviors like webs.

That's the story. Genetic lottery propagates and amplifies (life-)winning traits forward, but who knows.

Name an example of an advantage spontaneously manifesting outside of directed breeding by humans.

I really don't follow. Define programming in your context? Is it distinct from encoding physical structures like wings? Is it meaningful to separate physical structures and structures invoking physical behavior?

A column of rock erodes, and a piece falls. The piece did not learn to fall. It just _did_, subject to the rules that governed the process of its creation (different meaning) and its environment.

Specifically birds know how to fly or swim without being taught. Having raised birds that haven't seen or known another bird they just "do". They don't practice. It's like they are just waiting. Same with the language. They can understand like kind. When introduced to their own kind they aren't afraid but reunited.