Interesting question. Does anyone know the answer?:
Rediscovering Intelligent Design Posted, by Kieran Healy: Here is a likely poorly-specified question for biologists... The premise is unlikely (something that kills people—all people—but leaves the rest of the world standing) but intriguing. ...
I wondered, what if, long, long after our disappearance, some other species arose on earth at least as intelligent as us and eventually started doing evolutionary and molecular biology. Let’s say they have a working theory of evolution much like our own. Now say for the sake of argument that a bunch of transgenic organisms produced by humans have survived and prospered in the interim. So our future biologists find things like a bacteria that produces insulin, or a plant that secretes insecticide, or rice that is high in beta carotene, or more exotic stuff as needed.
I’m wondering, would such organisms even present themselves as empirical anomalies? (That is, how much would you have to know about genomes and evolution for them to seem odd?) And if they did seem odd, how would they be explained? That is, would the evidence of their intelligent design by a previous, now-extinct species be clear? ... Would some Arthropod-staffed functional-equivalent of the Discovery Institute point its claw at some of these organisms, saying they were anomalies that could only be explained by the intervention of a divine intelligence? Would Charles Crustacean find a story that could account for their evolution by natural selection? I’m particularly interested in whether the artificial provenance of transgenic organisms would be clear on internal evidence alone. I don’t know anything about this stuff, so probably the answer is “Yes” for reasons obvious to experts. But if it weren’t …
Here's the uninformed answer of an economist. I don't think they could tell because if the organism had anomalous traits, they would be genetically selected out over time and thus would not even be observable in the future. Making insulin is a waste of energy if it provides no benefit to the organism.
If they weren't anomalous and provided some sort of competitive advantage, then it would appear to be an evolved trait. The key is that the organism's genetic structure would not be static over time, but instead would evolve in response to its environment. If such evolution wipes out all traces of anything that looks (and is) anomalous in the environment the organism lives, then there will be no way to detect prior design. A counter argument is that there may be dependence on initial conditions, i.e. even though the organism evolves over time, the paths it can follow are set by its initial genetic structure and hence anomalies can still be identified later (traces of insulin making are still evident). Which means all I've done is re-ask the question - are initial conditions detectable later - not answer it.
Okay, I've thrashed around enough. Anyone know the real answer?