When a protein is deployed out of its usual context, it may be co-opted for a different function.
... or it
might mean "duplicated and adjusted protein" :
A fourth noteworthy possibility is that brand new parts are created. This typically comes from gene duplication, which is well known in biology. At first the duplicate genes make the same protein, but these genes may evolve to make slightly different proteins that depend on each other.
So these for "possibilities" here are like the various "possibilities" for the solution of an equation; depending upon the exact equation, we might have zero, one, or many soultions,
and an intelligent discussion needs to treat each of them as a possibility.
The case analysis resummarized:
We can summarize these four possibilities this way:
* Previously using more parts than necessary for the function.
* The parts themselves evolve.
* Deployment of parts (gene regulation) evolves.
* New parts are created (gene duplication) and may then evolve.
Now, let's treat these possibilities one-by-one:
The first of these only comes up if we are looking for IC.
well, more accurately, one and then the last group of three:
The others are the major forms of molecular evolution observed by biologists, phrased in terms of parts.
We've actually seen these type of events, and we know what they can do. In fact, they have been observed to do several different things:
We've seen the gradual emergence of new protein functions:
They can lead to new protein functions, sometimes slowly
We've seen abrupt emergence of new protein functions:
and sometimes, especially when parts are redeployed, abruptly.
We've seen new proteins created :
Gene duplication and changes in protein deployment may introduce a new protein 'part' into a system.
and we've seen proteins coevolve to chane the "new" proteins :
Then the parts may coevolve to do something better, but in a codependent manner so that all are required, without further change in the number of parts.
In other words, for a
hypothetical IC system to come into existence, we can look more closely at the definition of IC, and figure out that there are four different meanings we can attach to "IC," with four corresponding types of genetic events. We have also independently seen each of these four kinds of events, so we know that these described events are possible. Any argument that it is impossible for a hypothetical IC system to evolve is therefore deeply flawed.
But now, let's look at some specific examples of systems that have been considered IC. When we talk about a non-IC system, we should be able to make much clearer statements about how they
did arise, because we're not longer discussing the abstract and hypothetical. And so, on to nature:
But what happens in nature?
The rest of the article discusses seven specific examples of systems proposed as IC. Quoting from one example:
All three enzymes are required, so we have IC. How could this IC system have evolved? First of all, bacteria of this type could already metabolize some milder chlorophenols which occur naturally ("could" here is meant in the sense of capacity, not hypothesis -- DrK.) in small amounts. In fact the first and third enzymes were used for this. As a result the cell is triggered to produce them in the presence of chlorophenols The second enzyme (called PcpC) is the most interesting one; the cell produces it in sufficient quantity to be effective all the time instead of just when it is needed in its normal metabolic role. Thanks to this unusual situation PcpC is available when it is needed to help eat PCP.
The inefficient regulation of PcpC is evidently the key to the whole process. So far as biologists can tell, a recent mutation that changed the deployment of this enzyme is what made PCP degradation possible for this bacterium.
Notice the tone -- we're no longer discussing hypothetical situations, but one we understand, and the hedges -- aside from the omnipresent "as far as biologists can tell," which also applies to statements like "humans have two sexes" and "lions eat meat" -- have disappeared.
Basically, you (like your fellow creationists) are taking hedge words out of their proper context and presenting them as though they represented genuine confusion. For further examples, see any recent creationist discussion on the evolution of the eye. There's a wonderful quote from Darwin himself that creationists seem only to read half of.... (it's on the SkepticWiki, if you like.)
I will keep reading this thread if you guys keep it going. 
