I am not advocating the position mind you...
Yes, I realize that. I'm mostly just thinking aloud.
we can tell when something is designed by humans i.e. clovis artifacts, Mt. Rushmore etc...
Right, because as humans ourselves we're exposed to the idea of humans making things. And that's how we find out if a thing had been designed, in the past - comparing it to things that are being designed right now.
On the other hand, there's no aspect to a clovis point that you could use to infer the existence of humans if you didn't already know that humans exist. There's no magic design essence that is imparted to those things that are designed, so the answer to your question:
what would indicate it in a natural system.
would be, in my opinion, "nothing at all." There's no part of an object that can tell you it was designed unless you're looking at a part specifically designed for the purpose of telling you it was designed. (The "maker's mark" idea.)
Life is nothing like anything we've ever seen designed. Ergo it seems reasonable to me to assume that it was not designed.