I like that you provided such a well thought out debate, but there is a lot to be said about it, mainly what struck my interest was the above paragraph. As a programmer I would think the problem of DNA would be more apparent to you; that is to say, any given animal's genetic makeup is not only its working code, but a log of every other past version, comment or error log, if you haven't already, you should really research the field of evolutionary development, which explains how and why certain things are turned on and off in a genome."The incremental, gradual accumulation of genes is a myth. We can see that a creature that is so primitive as the sea-sponge can have just as complex genome as any other animal. If we compare genome sizes and the number of genes between different species we can't say that birds have more complex DNA than fish or that fish have more complex DNA than sponges. The evolutionary progression is apparent only on the surface, only in physical structures and it's not clearly evincible in genetic information. Genetic complexity is not related to structural complexity."
While this doesn't explain every strange gene in say, a sea sponge, it gives us a great grasp of why an amoeba's DNA could fit a platypus's within it several times over, because the amoeba is massively times older and has breed so quickly it has become a catalog of trillions of different versions of the same thing. The same goes for a bird, but in the bird's case it doesn't have a history of growing in tiny pools of water, it has a vastly more interesting history with parts obviously not seen in their physical structure today; like teeth, or genes to make them bigger than elephants. (hence why we think they descend from dinosaurs, genetically it is pretty obvious)
Now to address your discussion in a more general scope, I see some problems with it that I don't see much evidence of how to get around. Namely; one, if you believe that a stew of chemicals got trapped in a bubble and as more chemicals got in the bubble got to big and popped into two smaller ones, eventually creating life, then why would all of known life for infinity be in that one cell, and more importantly, how? (Arsenic dwelling pond organisms do not share their immunity to a known toxin with us nor anything else). Two; if genetics is predetermined how has life survived such devastating events, luck? Take for example any number of mass extinctions, how does life coupe with death if it can't change its predetermined path? Three; if change is predetermined, why does change occur with selection in a population; hybrids, food crops, domestic animals, Mendel's peas, etc.
And finally, if every animal and plant's DNA is coded into every cell; can you fish me out a Plesiosaur sex cell, I want to clone one and release it in a heavily populated, land locked lake just for the laughs. Or perhaps a futuristic virus cell's DNA from a few million years from now, I'd love to bring it into existence early on and reek mass destruction upon the earth with my super-future-virus, Bwhahaha!...
Anyways, nice thread.