You cannot make an organism simply with the nuclear DNA, it requires the structures of the cell, and the correct environment to develop in order to successfully grow into an adult. DNA on it's own is a relatively inert, uninteresting chemical - it requires a complex set of other chemicals and structures to perform it's array of functions. However (with the important exception of Mitochondria) all the information required to produce these cellular structures and the correct growing environment, etc. is itself in the DNA, it's just enacted by the parent, not the offspring.
One important point to remember when talking about DNA is that while the analogy of an "instruction set" is widely used as a simple way to understand DNA for a non technical audience it is only an analogy and one shouldn't get too wedded to it when trying to understand how DNA actually functions.
How exactly any of this is supposed to pose any kind of a problem for evolution I have no idea?
Do you really think that's a response, Elhardt? You didn't respond to a single one of the points that have been raised so far, you didn't even respond to the points I made in the post you replied to.
According to him, if the developmental plan is not fully specified by the DNA, then mutations to DNA are not enough to produce a new type of animal (or species)
This is either a) bollocks, or b) sophistry, depending on how you interpret it. It's bollocks for the reasons we've already pointed out several times (i.e. although an egg is not specified by the DNA of the offspring it is specified by the DNA of the mother).
Or it's sophistry because it's trivial true. DNA is not a "plan", it's a chemical; it operates through the action of other chemicals to produce new chemicals. These chemicals interact with each other and the environment in ways that DNA does not specify. The laws of physics do that. True enough but utterly meaningless for the question at hand.
And even if it wasn't a) bollocks, or b) sophistry, it still doesn't follow! It doesn't make any sense to claim that because DNA doesn't 100% describe an organism it can't mutate and evolve - that's like claiming that because the ingredients in a cake don't 100% control how it comes out, you can't make different cakes by changing the ingredients.
Here's something that I've wanted to know because it's related. Where exactly is the "3D geometry data" that defines for example, the shape of your skull, located? If cells need to differentiate themselves into structures like that, where is that specified? Sounds like membrane patterns and microtubule arrays according to Wells. But if those only come about under DNA control, then it's back to the DNA. But DNA doesn't hold "shape data" does it?
Nothing like learning a bit of biology before you decide you're qualified to criticise it, is there? Or, to quote Ben Goldacre, "it's a bit more complicated than that".
DNA codes for proteins, and which proteins are expressed at which times and under which circumstances. Three dimensional shape is produced by chemical gradients which affect gene expression, and which themselves are formed by the differential timing of gene expression. So, no shape data, but everything that is needed to produce shape.