M.J. -
Thank you for the compliment. And believe me, if you can get computers you can get this. People tend to overcomplicate this... :)
Nylonase is just an enzyme plain and simple, and it has been coached to being expressed in other bacterium simply by placing them in an environment where they had nothing else around but nylon. The bacteria either had the mutation to consume nylon or they didnt, and thus they survived and reproduced or they didnt. And it was not that that mutation was just laying around there waiting for us to make nylon.
Here is an example, we could come up with a new cloth/material called xyz in eighty years. This could be a material, like nylon, that does not exist in nature, and we will be introducing something completely knew to the environment, thus changing it, just like we did with nylon. Now right now, there could be bacterium that have the genes to consume xyz because they just happen to. These bacteria will see no survival advantage through this, and if they are still alive, they will probably see no dissadvantage. What will happen? These traits will get reabsorbed into the population and will spread about as effectively as other useless traits. Then more bacteria will appear with this same mutation, and others, and they will dissapear back into the population because no advantage was offered and the trait is still useless. But, when we change the environment by producing xyz eighty years from now, like we did with nylon, then that trait is no longer useless. Then when bacteria are confined to an environment with just xyz as a potential food source you can see the emergence of a new strain. See what I mean? So is nylonase close to other existing enzymes? Yes. But that is not the point. It was suddenly that the environment changed to where that enzyme was suddenly useful. These same bacteria have mutated and either died as a result, or discarded and moved on, from other such mutations that would have allowed them to consume materials we have not yet introduced into the environment. Now on to your actual question...
I dont mean this in a condescending way at all, so please dont take it that way, but you gave me the courtesy of a direct reply, so I will do the same for you. The issue you seem to be having is that you want to create a line in the sand between Micro and Macro evolution. But your own definitions of micro and macro evolution are a contradiction against reality, and you seem to be attempting to compartmentalize terms into boxes they were never meant to be confined into. While not uncommon, this stems from a misunderstanding of how genes are expressed.
You ask me if nylonase would be close enough to other enzymes to allow for a micro-evolution solution to the problem, and I assume by that that you mean it according to your personal definition of microevolution, which is "Micro evolution is the natural optimization of the parameters of EXISTING genetic functions...otherwise known as natural selection." The answer to your question is "no", but your definition is also not correct. For starters, this particular strain of flavobacterium could not have digested nylon without the introduction of this new thymine nucleotide.
This is about as bare bones as one can do it, and not accurate for more then illustrative purposes, but I think that this will help it make sense. Nucleotides are grouped up in threes and then expressed. So lets say I have genetic sequence (this is very simplistic): AGT TCT AGC TTG GCA and on. Now lets introduce a Thymine nucleotide in codon three...what happens? That same sequence becomes AGT TCT ATG CTT GGC A...
It isnt hard to see why most mutations of this type, known as a frame shift, have negative outcomes for the organism. But on the rare occasion they are not immediately fatal, and in rarer cases they lend a survival advantage, based on the environment at that time. Make sense?
Now back to your definition(s), which for simplicities sake I will restate here:
Micro evolution is the natural optimization of the parameters of EXISTING genetic functions...otherwise known as natural selection.
Macro evolution would be the spontaneous generation of entirely new functions.
Natural Selection occurs when the environment lends an advantage or a disadvantage to your survivability as an individual, thus allowing you to live long enough to spread your traits through the population. Your "existing" genetic makeup will help you live, or be the reason that you die sooner. You received most of your "existing" traits from your parents, and a few of them from mutations. If you are healthy in our present environment, then most likely any mutations you have were not expressed, or have no direct survival advantages or disadvantages. If the ozone layer dissapears tomorrow and everyone gets skin cancer but you, then those mutations at that time give you a survival advantage and your children will probably enjoy the same benefits (assuming you are not the only person to survive). This mutation may or may not be the result of new genetic information, but regardless your survivability would be the result of natural selection.
Your attempt to confine natural selection into the box of micro evolution is not appropriate, and I would speculate that it comes from your own stance which is one where you dont want your particular definition of "macro" evolution to exist, as in the "spontaneous generation of new functions". It is from here that your understanding of what evolution actually is seems to derail.
It is not that we are looking for the spontaneous generation of new functions, as most functions will never be expressed since the environment usually doesnt allow for it, and usually kills you for acquiring the trait. But it is the slow accumulation of changes over time, like what we all see everywhere, that leads to what we define as speciation.
Did I answer your question? If not, please let me know how I didnt and I will make another attempt...
