We observe all the "clues." And Russ2 has presented evidence here of it happening today, including bacteria which have evolved beneficial traits through mutations. So we can observe the evidence, form hypotheses based on it, and test those hypotheses. We would not make much scientific progress in any area of we narrowed our definition of truth to only that which can be directly observed in the moment.

We know enough about the evolution of organisms such as foraminifera that they can be used as index fossils. Geologists, for example, use these index fossils to help them find coal and oil deposits. If index fossils were not good predictors of where things are in the geological record, then how would they be able to do this? Does this not show that there is something more to their pattern of distribution than mere randomness?

And why, if God created all creatures that ever existed in the last 6000 years, do we not find trilobites mixed with dinosaurs and dinosaurs mixed with humans in the fossil record? Fossils are found in faunal succession across the world. This is either because they evolved over a long period of time, or because God for some reason wanted it to appear that they had. Unless you have a third explanation?