Okay, I'm going to try to answer what I can but we really need to use the same terms soon. I'm willing to follow the concensus but as it is I think alot of cunfusion is arizing from terminology.

1. I was imagining that activation sites are 8 to 11 bits long. If we have 50 reactions, 8 bits means that roughly 1 of every 5 random bit patterns does soemthing, which is still really high in my opinion. 11 bits means 1 out of 40 actually does something, which is closer to the right direction.

Remeber that that's 1 out of 40 for any single 11 bit pattern. Most enzymes (that long string of bits with ultiple activation sites) are probably like 50+ bits long. In 50 bits you're bound to find some 11 bit long activation pattern. I don't have time for a statistical test to find better numbers, but we can play around with it.

2. Almost right. Multiple sites don't mean that they are more efficient, just that there are more possible routes for any single substance to go through.

Say you have a 20%, 30% and 90%. The efficiency of htat enzyme (or complex if you prefer) is the average, or 47%. If something messes up the 20%, it will actually increaes the efficiency. If something copies the 90% to another part of the enzyme, then it will increase the efficiency. You get the idea.

4. A pattern has no start or stop. It's just a pattern. 101101 is an activation site, say. Then whenever you can find 101101 in a bit pattern, that's an activation site. If you have 101101101 as your pattern, you actually have two overlapping activation sites.