And as we know, there are some serious limitations on what we can do with the brain.
Yes, but imagine not only that we have complete access to the brain's source code, but that the brain is digitally implemented and any component can be changed at whim. What could we achieve? At the very least, some very helpful things, if not superintelligence:
We already have examples of drugs and diseases that boost cognitive performance. Personally, I've been hyperthyroid before. The cognitive boost at the peak was very pronounced. This can't be sustained in wetware (at the moment) for various reasons. None of those reasons, as far as I've seen, would matter in silicon. Sustainable hyperthyroidism via alterations to my 'source code' alone would make me 5 times more productive.
Once a mechanism of action is understood, it's likely it can be increased, at least a little. For instance, nootropes (such as piracetam, huperzine a, modafinil) work via chemical pathways. It seems reasonable to expect that bypassing the chemical aspect and directly tweaking the code should provide better results. If nothing else the quality and quantity of the dose can be regularized and optimized much more efficiently. This isn't even mentioning all the drugs that can't cross the blood-brain barrier but which could be directly 'injected' into individual neurons in a simulation, which is a tiny subset of all the 'drugs' that could be tried from directly changing the way the neuron works. Many nootropes, too, either diminish in effect over time (for chemical reasons) or tax the body in unsupportable ways, as with hyperthyroidism: neither of these would pose a problem for a silicon brain, which could be permanently pumped up on a whole cocktail of crazy drugs and mood modifiers without worrying about the damage being done to the endocrine system or any other fragile wetware.
In short, an uploaded human with access to its source code and an understanding of neurology and biochemistry, while probably falling short of superintelligence, would have a hell of an advantage over meatspace humans, even without hardware acceleration.
As promised, here is the "Q" part of the Less Wrong Video Q&A with Eliezer Yudkowsky.
The Rules
1) One question per comment (to allow voting to carry more information about people's preferences).
2) Try to be as clear and concise as possible. If your question can't be condensed to a few paragraphs, you should probably ask in a separate post. Make sure you have an actual question somewhere in there (you can bold it to make it easier to scan).
3) Eliezer hasn't been subpoenaed. He will simply ignore the questions he doesn't want to answer, even if they somehow received 3^^^3 votes.
4) If you reference certain things that are online in your question, provide a link.
5) This thread will be open to questions and votes for at least 7 days. After that, it is up to Eliezer to decide when the best time to film his answers will be. [Update: Today, November 18, marks the 7th day since this thread was posted. If you haven't already done so, now would be a good time to review the questions and vote for your favorites.]
Suggestions
Don't limit yourself to things that have been mentioned on OB/LW. I expect that this will be the majority of questions, but you shouldn't feel limited to these topics. I've always found that a wide variety of topics makes a Q&A more interesting. If you're uncertain, ask anyway and let the voting sort out the wheat from the chaff.
It's okay to attempt humor (but good luck, it's a tough crowd).
If a discussion breaks out about a question (f.ex. to ask for clarifications) and the original poster decides to modify the question, the top level comment should be updated with the modified question (make it easy to find your question, don't have the latest version buried in a long thread).
Update: Eliezer's video answers to 30 questions from this thread can be found here.