They are hardly fallacious. For example, in this article they made such fundamental errors in modeling evolution that no peer reviewer in any respectable journal would have recommended the paper for publication. They claimed that one species evolved from another existing species, which is wrong. Modern species share a common ancestor. If they wanted to truly model the evolution of the protein then they should have constructed a consensus sequence using a phylogeny of many related species, and then mutated that consensus sequence. They didn't. This is such a basic mistake that it could only pass peer review in an echo chamber.
The paper you reference there is mine. I am familiar with the most common objection to this paper, that we did not do ancestral reconstruction, a la Joe Thornton. There are two comments I can make in response to this criticism.
1. Our proteins are ancient, going back to the time of the first cellular metabolisms in bacteria_. They are only 33% identical. What is very similar are their folds. Reconstruction of an ancestral form is unlikely to work at such a distance. Thornton's first work was on steroid hormones that diverged about the time vertebrates first appeared, according to Thornton himself. The likelihood of success of any reconstruction for our proteins is poor.
2. More importantly, and this is the heart of the problem, ancestral reconstruction or retracing evolutionary history was not our goal. We wanted to determine whether it was possible to interconvert one related protein into another, starting with extant protein. Such interconversions must have happened in the beginning. The question we are asking is whether such interconversion between modern proteins is possible. Back when all these new proteins were first appearing, they managed to do it somehow.
Here is how we stated it in the paper:
A reasonable assumption, consistent with methods
used for reconstructing evolutionary histories, is that enzyme
pairs with high structural similarity should be most amenable
to functional conversion. Whether or not a particular conversion
> ever occurred as a paralogous innovation (or the direction
> in which it occurred if it did) **is not the point of interest here.**
Rather, the point is to identify the kind of functional innovation
> that ought to be among the most feasible within this
> superfamily and then to assess how feasible this innovation is.
Ancestral reconstruction and its success suggests that there are very few possible evolutionary paths between proteins A and B, in particular the one that was demonstrated to work in the lab. Even then, though, just one amino acid change could block the way forward, or the pathway may work only in one direction and not the other. That would seem to restrict protein evolution to a very narrowly defined set of pathways fine-tuned for the production of proteins we see now. How did that happen?
I know that everyone is always saying that there are many ways things could have happened (this is merely an expression of faith in the evolutionary process and a not demonstrated fact), that many paths forward are available. Ancestral reconstruction would seem to argue no, that there are in fact very few ways to transition from one enzyme activity to another, or one binding protein to another. That would argue for a high degree of fine-tuning for starting points, and a predictive design sophistication beyond mortal abilities.
For evolution to be true, though, in case you are not comfortable with the above, it must have been possible to get new proteins from old, by many pathways. It must be possible to convert closely related structures to each other's function; isn't that the assumption of gene duplication and recruitment, of cooption? Otherwise how could it happen? So what we demonstrated is that cooption, the reconfiguring on one protein to a new function, within the limits of a neo-Darwinian search, is beyond reach, at least in the case we tested. We actually did a follow-on paper where we expanded the search. You might want to take a look.
Besides what I have already said, this criticism you voiced was in its facts. You said "They claimed that one species evolved from another existing species, which is wrong. Modern species share a common ancestor." That is wrong. We did all our work in E coli, using E coli enzymes, and we weren't modifying species, we were modifying proteins. I invite you to go back and read the paper.
What I hear from you are repetitions of things that people said on anti-ID "echo chambers".
As to ENV as a whole, they have articles that are seriously misleading and outright lies.
As for the other criticisms, errors are possible. Please comment to the editor so we can correct them. Calling them lies is, however, immoderate in the extreme, and offensive. You accuse the writers of deliberate deceit, the attempt to deceive. It is this kind of attitude that keeps people like me away from BioLogos. Why fight against such bias? I thought I had made some progress, especially with you. It seems I was wrong.