We know that the information was not front-loaded because we know - for a fact, as proven by "co-speciating" species - that these informational changes are the result of environment and mutation, not pre-programmed changes happening over time.
Its only your darwinistic belief.
Remember when I disproved that back in More Evidence of Evolution - Geomyidae and Geomydoecus?
You have chosen an exaple that somehow fits into darwinistic schema. There are many examples when the relationship is so complicated that it cannot prove co-speciation.
One of them is phylogeny of human tapeworms. Listen to what absurd conclusion this "phylogeny" led: The closest relatives of human tapeworms did not colonize either cows or pigs. Instead, they lived inside East African herbivores such as antelopes, with the lions and hyenas that kill them as their final hosts. So the darwinian conclusion (or better another weird darwinian fancy) is this one: human ancestors followed lions and ate the remains after them.
So the parasite switch to humans and afterwards to pigs. So human were scavengers by parasite phylogeny conclusion. Believe it if you like.
If I understand what you're referring to, you read wrong. The Human Genome Project results from Venter's Celera company came from whole-genome shotgun sequencing of nuclear DNA, not RNA.
Venter started with EST (Expressed Sequence Tag) which he obtained analyzing cDNA. As you know cDNA served only to store genes carried by RNA. They wanted to avoid to sequence junk DNA (Brenner for instance believed that junk DNA make 97% of DNA) so they focused their research on RNA where genes are present.