I have addressed this paper many, many, many times. Why do you ignore it?
In that paper, they mutated a beta-lactamase gene. How did they determine that the protein had no function? They tested it against ONE substrate. Just one. There are literally billions of possible substrates, yet they only looked at a single substrate.
How can you claim that a protein has no function when you only test it against one substrate?
And I have relied to it. The test was to do with proteins being able to make functional folds by manipulating single molecules at a time to see if they could handle the changes. It didn't matter whether there was one substrate. One would be better so that they could focus the tests and results. It was about the steps to make a change in a protein from its existing function into a new functional protein shape that was not previously there. They found it would take at least 6 mutations to make a simple functional change in the protein and that this was well beyond what evolution through mutations could do. Here is another test he did along similar lines.
The Case Against a Darwinian Origin of Protein Folds
Douglas D. Axe
Abstract
Four decades ago, several scientists suggested that the impossibility of any evolutionary process sampling anything but a miniscule fraction of the possible protein sequences posed a problem for the evolution of new proteins. This potential problem-the
sampling problem-was largely ignored, in part because those who raised it had to rely on guesswork to fill some key gaps in their understanding of proteins. The huge advances since that time call for a careful reassessment of the issue they raised. Focusing specifically on the origin of new protein folds, I argue here that the sampling problem remains.
The difficulty stems from the fact that new protein functions, when analyzed at the level of new beneficial phenotypes, typically require multiple new protein folds, which in turn require long stretches of new protein sequence. Two conceivable ways for this not to pose an insurmountable barrier to Darwinian searches exist. One is that protein function might generally be largely indifferent to protein sequence. The other is that relatively simple manipulations of existing genes, such as shuffling of genetic modules, might be able to produce the necessary new folds. I argue that these ideas now stand at odds both with known principles of protein structure and with direct experimental evidence. If this is correct, the sampling problem is here to stay, and we should be looking well outside the Darwinian framework for an adequate explanation of fold origins.
https://www.researchgate.net/public...e_Against_a_Darwinian_Origin_of_Protein_Folds
This paper supports what I have been saying about protein folds needing to be within very narrow parameters to be functional for life. That there is a massive space of possible folds that can be created and that darwinian evolution that works on a blind process of random mutations will either not be able to find these few proteins in the time that even the earth has been in existence or that it will be forever dealing with sick and malfunctioning examples which should then show evidence for this in life for which we dont see. Life is pretty well precisely made and functional even way back in the early history of existence.
The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law.
However, in the case of one class of very important organic forms-the basic protein folds-advances in protein chemistry since the early 1970s have revealed that they represent a finite set of natural forms, determined by a number of generative constructional rules, like those which govern the formation of atoms or crystals, in which functional adaptations are clearly secondary modifications of primary "givens of physics." The folds are evidently determined by natural law, not natural selection, and are "lawful forms" in the Platonic and pre-Darwinian sense of the word, which are bound to occur everywhere in the universe where the same 20 amino acids are used for their construction. We argue that this is a major discovery which has many important implications regarding the origin of proteins, the origin of life and the fundamental nature of organic form.
http://www.ncbi.nlm.nih.gov/pubmed/12419661