@Mercer
I am actually not sure where to start in dealing with your response. First you accuse me of bad faith in not having read and commented on your whole body of work. But I was given one paper and it was that paper I was commenting on. I was not making an extensive analysis of that paper either. Yes I know that you measured activity of the modified enzyme and that you demonstrated that it was fully functional. The point I was making was that you didn’t change the function. I was know in no way denigrating your work. Why would you think I was?
In our work we took one enzyme with a particular function that was related structurally to another enzyme with a different function and asked if we could convert the first enzyme to function like the second. That’s the change in function that we were seeking. A change in chemistries.
You don’t need to rehearse all the criticisms of that paper. I am well aware of them. But if you accuse me of not engaging what you wrote in later papers, then at least engage what we actually wrote. I can’t recognize our work in your comments. They seem irrelevant. And we seem to be talking past one another.
You are free to disagree with our work. The hostility is not derived from science, however. A scientific disagreement should not be hostile in its tone. This is something I ask of all those who want to discuss with me. Leave the hostility behind. Take me as operating in good faith. You can critique my science and point out where you think my methodology was wrong or what I should have included. But please critique what we actually did and pay attention to why we did it as described in the paper. Some of you have done this. And we can have a legitimate discussion of why something in the methods should’ve been included or why not. But to misread me or to misunderstand our purpose is unfortunate and counterproductive.
We were not trying to study proteins’ ability to interact with modified substrates if those proteins indeed still carried out the same chemical activity. We were not interested in studying enzymes that had activity toward multiple substrates and asking if they could be shifted to favor one of those substrates. We were asking how hard it is to shift a protein to a new function, a new chemical reaction it had not performed before. We were not trying to recreate history, to go back to the ancestral sequence and trace a pathway forward. We were asking how hard it would be to shift a protein to a new function. At least for our enzymes, the PLP-dependent transferases, you can’t do it with one or two mutations. This is not a surprise to just about every scientist I know. The point is that when you take into account the adaptive changes necessary for that transformation you end up requiring multiple genetic changes, more than just one base change is involved. You need increased expression because of weak activities , a gene duplicate to allow modification of one function while preserving the original. Then you need the base changes required for the new function. If the organism needs that new function, that specific function to solve a problem, and there is only one way to do it, then it must wait or around for all of those things to happen: a gene duplication, the mutations, the over expression. Then you would have a selectable new function. The argument isn’t that complex.
I understand that some of you despise me. If it were just a scientific problem, there would be no reason for such despising. The nearest I can come to understanding is that you think I have betrayed science. In reality I am trying to ask questions using science. You may disagree with my message, my results, or my conclusions. That is part of the scientific debate. Please read and understand what we were doing and critique that. Not some strawman or fantasy creation.
A few last point. First, I understand the view that the only way to get the two proteins we were working with was by retracing the ancestral path. The implication is that there is a very narrow set of solutions to the problem of getting these two functions from one original enzyme. And that should give pause. If evolution needs to be fine-tuned to that extent, where there are only a few paths to get to a final product, then how did we arrive at the thousands of different enzymes we have from some small set of original enzymes? Second, there are the people who say evolution does whatever it can, it chooses the next beneficial step whatever it is without respect to the needs of the organism. Is that the way to produce a functional metabolism? Third, @Mercer in no way did I intend to denigrate your work. You are reading into what I wrote something that isn’t there. Because I only discussed one paper and one part of that paper does not mean I think the rest of what you have done (which I didn’t know about because I didn’t go looking—I thought we were only dealing with the one), doesn’t mean I disrespect anything you have done. Far from it.