"That is an incredibly ignorant and naive statement."
There is context there that is important.
Old Regular was insiting that entropy prevents evolution. Yet the version of entropy he is pushing would also prevent life itself. The point was that entropy is no more a threat to evolution than it is to life itself. If entropy does not prevent life, then it does not prevent evolution.
Now if you wish to make a case that it does, please do so. We have gone down that path before. If you do not, then please recognize the context of the statement. It was in reference to whether entropy prevents evolution. It was not addressing any other objections.
"There is no way known or seen for a cell to make a de novo protein."
But there is. One way is duplication and mutation. The mutation can take many different forms. Here is one example.
"Adaptive evolution after gene duplication," Hughes AL, Trends Genetics, 2002 Sep.18(9):433-4.
A gene was duplicated and one of the copies mutated to give rise to a new function.
In a variation on this theme, two genes that have been duplicated can be combined into a new gene. Here is an example of that.
"Selective sweep of a newly evolved sperm-specific gene in Drosophila," Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL, Nature. 1998 Dec 10;396(6711):572-5.
Another way to produce new proteins exists without even having to mutate the genes. It is called alternative splicing. Genes consists of exon and intron sections. During the process of converting the DNA to protein, the introns are removed and the exons spliced together. Yet organisms can change this splicing such that while the original protein is still made, a new protein is also made by various changes to the process. Maybe an intron is not removed. Maybe an extra exon is removed. There are even more complicated examples. In each case, a new protein is formed from the same raw genetic material without changing the protein that works. When you add point mutations and the copying around of transposable elements, this becomes an even better way to make new proteins.
Another way to get new proteins is to get them from other species. An example. A retrovirus can insert its genetic material into its host. Sometimes this happens in a germ line cell and the virus DNA gets passed on. It happens often enough that a sizable percentage of our DNA are retroviral inserts. These genes can also be subject to mutation and might be made into something useful. Here is an example of that happening.
"Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis," Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM, Nature 2000 Feb 17;403(6771):785-9.
"If a cell could make a new type of protein for itself, the cell 'innards' would not know what to do with it and would dissemble it rather quickly to use the amino acids to form proteins it did know what to do with."
Except that we have observed new proteins being made and the organisms seem to know what to do with them. The new proteins are not that different from the old usually.
"And then there is the matter of mutations. ALL mutations EXCEPT the hot spot back and forth mutations (which only go back and forth and do not march onward into the unknown!) result in loss -- sometimes of useful information, sometimes of chemical behavior, sometimes correct protein folding. But always there is a loss."
See above for examples that do not involve loss.
"Same with nylon eating bacteria and antibiotic resistant bacteria. Each case is attributed to a loss, in the latter case, of protein folding."
What?
Let's look specifically at the evolution of resistance to the antibiotic vancomycin.
Vancomycin works by attacking the D-alanyl-D-alanine in the cell wall of the bacterium. There are two genes, VanR and VanS, whose job is to make proteins to detect the presence of vancomycin. When detected, a cascade of other enzymes are created to protect the cell. VanH starts by converting precursor materials into D-lactate. VanA then joins the D-lactate with D-alanyl to make D-alanyl-D-lactate, instead of D-alanyl-D-alanine which is usually used in the cell wall. VanX hydrolyzes the D-alanyl-D-alanine that is still being made before it can be used in the cell wall.
This is the usual process, but there are variations. Some bacteria have VanB instead of VanA to make D-alanyl-D-lactate. Some bacteria replace the D-alanyl instead and make D-serine-D-alanine component instead of D-alanyl-D-lactate.
Once the resistance evolved, it was spread through plasmids.
And before you say that this was just a latent feature that became activated in response to the antibiotic please tell us just why you think that bacteria would be carrying around a gene such as VanX that hydrolyzes its own cell wall.
