This is true too, but it is important to distinguish between falsehoods and lies. Most likely, this is just what this biology professor thinks, without knowledge it is false.
What follows is not a full engagement with @bjmiller’s post, but some of the key errors that are worth pointing out for the benefit of those following along.
Not really. It is correct, and not mistaken. We know for a fact that functions can appear in “disordered” proteins, and that these functions can become more efficient as the functional fold is stabilized. This entirely undermines Axe’s argument. The fact that some proteins (most in mammal’s?) never need to be fully stabilized for their function severely undermine’s Axes entire argument. He is working of an antiquated view (i.e. decade old, so maybe not antiquity) protein function. He would have to turn back the clock of our understanding to be correct.
Incidentally, it’s about when he left science that disordered proteins were beginning to be understood. We’ve just grown in our understanding since his last paper was published.
If he is unaware of this research (and there are several different approaches) he is certainly not an expert in protein evolution. There are several approaches, and literally hundreds if not thousands of papers here. No bluff here, he should contact me and we’ll talk about it.
On this I would totally agree!
For example, this is the exact error that Doug Axe’s argument falls into. He is arguing in a circular way. His argument essentially assumes that extant proteins are the only way to achieve what we see, so therefore they must be rare because extant proteins are only a small space of sequence space. That ends up being the fundamental error of his approach. Quite ironically, Doug Axe’s argument is just the type of circular reasoning that needs to be avoided.
However, the reason I raised the issue of co-evolution is to show just one reason why Axe’s inference to inaccessibly rare function by studying mutational tolerance of extant proteins is invalid. He grossly misinterpreted his data, ignoring some of the fundamental principles of protein structure.
Just false. There are several mechanisms we know of that can build up complex functions from simple functions. This also deviates substantially from Axe’s argument in the first place. Ignorance of evolutionary science is not an argument against it. One can dispute it, but ignorance is not a rebuttal.
That is a nice just-so-story with great anthropomorphic flare. We could tell the same story about Abzymes too. Literally no meaningful difference at all. Describing how a enzyme works in anthropomorphic terms does not somehow remove the fact that we can find enzymes in a forward approach. And of course, we could tell beautiful anthropomorphic stories about them too. That is why this sort of rhetoric is not convincing.
This is another fairly interesting equivocation worthy of discussion.
Notice what is assumed here? The argument implies that new complex enzymes are required for most (or all?) major adaptations. That, it turns to be false, and to be clear, that claim is only implied, not clearly stated. One of the great surprises of biology, however, is that this is not generally true.
Let’s take one of the most stunning strings of major adaptation in history, the evolution of humans from common ancestors with apes. Our intuition might tell us this would require evolving a large number of new and complex proteins. Our intuitions would be wrong (sorry Axe). As far as I can tell, there is no evidence than any new enzymes were needed at all. It turns out:
- To a first approximation, humans and the great apes have the same proteins, just turned on and off (expressed and spliced) in different patterns.
- To a second approximation, some of these proteins have tweaks that subtly alter their function.
- To a third approximation, a small number (<100?) of peptides (not enzymes as far as we know!) might possibly have arisen with subtle functions very hard to pin down. It is entirely possible all these de novo proteins are spurious and none of them are important.
So as surprising as this is, we there is no evidence (I can find) that any new enzymes were required for humans to evolve over the last 6 million years. There are no complex enzymes that we have that a great ape does not. Take that in. It is a really stunning fact. New enzymes are not required for the most important evolutionary development to us, the rise of humans.
If the evolution of humans is not a major adaptation, nothing else really is. What we find is that for large organisms (like mammals), most major adaptation takes place by just rearranging things. To make an analogy, you can make a lot of things with lego pieces (see lego sculptures). You do not usually need a totally new types of pieces for major adaptive change. The Lego analogy is a weak analogy, yes. However, in this one sense, it is true. It just does not take a lot of new types of pieces to make new things. We just need to arrange them differently. That is one of the grand surprises of comparative genomics.
With this fact in mind, at best Doug Axes argument, at absolute best, it is an argument against the origin of life and against bacterial evolution. It may be an argument against God-free evolution in cases where enzymes are important for major adaptations in mammals (where?). However, it is not argument against the God-free evolution of humans from a common ancestor with the great Apes. Remember, he does not engage any of the evidence for the common descent of man. So even if he is correct (and he is not), this reduces to an origin of life argument.
Of course, I am not arguing for God-free evolution. I understand evolution as God’s providentially governed way of creating us. If we allow for God’s providential work, this would not even be a good argument against the origin of life.