Re: The Intelligent Designers - who were they?
(Please try to keep in mind that the "Intelligent Design" people are determined to prove that they are being scientific, and not just looking for an excuse to jump straight to theological conclusions of magic that they already had in mind)
Ok, I think I can play the game.
In order to avoid magic, we need to posit an extraterrestrial race with very advanced and subtle biotech knowledge.
Any changes which were made to the biology of this planet would have to be so subtle that they are barely detectable (since we haven't detected any).
For example, to force mammals to branch into a primate so that you could eventually get a human, would require not only a small but well focused change to the genetics (and a means to make sure the genes became commonplace in the population), but also the ability to predict the interaction of the new species with a changing environment over millions of years. Then of course, the genome would have to be repeatedly tweaked to keeping it going along the track you wanted, otherwise the natural pressures of selection and variation would make the result wander.
First problem: How to insert a new gene. This is an easy one, steal an animal, extract a gene and insert the new gene with alien super technology. You do this in the sex cells, and then reproduce a new critter.
Second problem: Get the critter into the population and make sure it reproduces and doesn't get killed by a big nasty predator, or a virus. But, maybe if you do it with a while bunch of critters and watch them closely, you can make it work. You can zap nasty predators with a needle laser from orbit or something.
Big problem: Anticipating the environment and interactions of other natural develpments. But maybe if they've been doing this long enough, the quirks of evolution and natural environments are predictable enough to get your change into the population.
So now the aliens have a population of new critters just slightly different enough from their predecessors that the genetic changes aren't glaringly obvious. The aliens are zapping predators from orbit and giving their critters cold medicine to make sure they live long enough to reproduce.
Next problem: All the changes have to be subtle, so you've got to repeat this process almost constantly to build up enough variation in the population to replicate all the differing sub-species we find in the fossil record and in existing populations.
Ok, that won't work. Let's try this...
Extra Terrestrials use specially designed viruses to alter genetic material in terrestrial organisms.
They periodically seed the planet with viruses designed for a given species which will induce a genetic change over time. They crank out the virus, freeze it into ice pellets and drop the pellets anywhere they like.
Each change still has to be very subtle so that it goes undetected in the history of life on Earth (because we detect no abberations currently), however, lots of little changes can be made over and over again just by modifying your gene-cracking virus.
The big problem here is that in order to target a large change a million years down the line, you have to have an extremely detailed understanding of genetics and of how the new species will tend to evolve, because even though you're tweaking the process, the basic elements of natural selection and variation are still present, and they are always in play. The preassure to maintain a given growth track would be a never ending battle.
How's that? ET's with super genetic knowledge who use repeated exposure to engineered viruses to continually nudge raw evolution onto a desired track. In order to prove the theory, we would need to find evidence of engineered viruses which insert genetic code, and we would need to differentiate those viruses from natural viral behavior which insert non-engineered genes.