Thanks,
@adreno.
This is a complex topic, and I probably can't do justice to it. Its something I would like to see answered empirically, as all the theory does not necessarily give us a good picture. I may be able to say more in a couple of days when I get my new computer, this one has major limitations on how I use the net.
Increasing ATP production will lead to increased ROS. I am not sure that if energy is not used it will make much of a difference, due to the dynamics. Ramping up NAD etc may help energy production. On the other hand with more energy around the body may have more capacity to make more antioxidants. So provided there are no other major deficiencies, such as methylation problems or mineral deficiencies, then the body should (theoretically) cope. There are lots of potential caveats here though.
The problem with simple pathway analysis is that there are complex dynamics and feedback loops, and these can change everything.
The loss of electrons is indeed why we get reactive oxygen species though. See for example:
http://jp.physoc.org/content/552/2/335.full
It should not matter if there is more ATP around. Its the rate of activity in the electron transport chain that matters. However that rate of activity relates directly to energy expenditure. So its how much we do, and put demand on the electron transport chain, that matters most.
There are other sources of oxidative and nitrosative stress predicted in ME though, including failed NO synthesis leading to peroxynitrite. This ties in to B12 metabolism. Other sources include immunological activity.
Increasing NAD (and CoQ10) might indeed improve energy capacity. Its how much of that we use that determines the ROS, not how much ATP is hanging around, from what I see. As we improve our metabolic rate is likely to increase, which will automatically increase our ROS. However a faster metabolic rate will boost our capacity to make and recycle antioxidants.
So its fair to say that during improvement its a good idea to take it easy, but I agree we are likely to want to do more ... I have a huge list of things I want to do. CoQ10, lipoic, C, E and dealing with methylation will help; a lot. So will peroxynitrite scavengers.
On SOD, there are lots of people with low SOD. Progeria is a genetic SOD disorder. There is medical interest in creating SOD enhancing drugs, but I have not been following this research. Funny enough I had a chance to work on a PhD in this area when I was doing my biochem, but I had to decline as at about that point I realized my health was crashing again.
A big caveat to all this though is that we still do not really know what is wrong with the mitochondria in us. There is some evidence that one or more mitochondrial transporter proteins is not working right, largely from Myhill's research. If this is the case then the usual dynamics we are counting on may not fully apply. As usual, my mantra, we need more research.
However, as a caveat to the caveat, what counts is this - does it work? I use my lemon rules as a heuristic simply because reality often trumps theory. Its why science requires testing. For a patient this comes down to trying a protocol to see if it tastes like a lemon or not. Sometimes, even with all the theory, there is no other way available to us to be sure if something works or not.