Peak Fallacy: Proteins Evolved Because They Evolved

In spite of common sense and the scientific evidence, evolutionists have once again shown that evolution is a miracle worker. A new paper by evolutionists in the world’s leading journal argues that proteins evolved after all, despite just about every shred of evidence mandating otherwise. And just how did evolution do it again? It turns out proteins evolved because they evolved. If only I had thought of that—I could be an evolutionist too.

Not even wrong

The new paper acknowledges that molecular reality “severely restricts” the mutational changes a protein can undergo. Indeed, “the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape” make all but about 2% of the possible mutational changes unacceptable.

But since we know evolution is a fact, then proteins too must have evolved. One is tempted to say the research is wrong, but that would be a compliment. For it isn’t even wrong—it is downright ridiculous.

The fact that it found its way into the world’s leading scientific journal is a testament to how badly evolution has infected science. In the paper (details below), the evolutionists conclude that similar proteins are evolving away from each other faster than distant proteins are evolving away from each other. Just like Hubble’s receding galaxies right? Wrong. Once again evolutionists make a flawed analogy with physics, but that’s another story.

With their circular findings in hand, the evolutionists leap to a series of equally circular conclusions: (i) Rest assured, proteins are still busy evolving though sequence space for evolution has not reached its limit, (ii) All that evidence against protein evolution must be misleading, (iii) Proteins must be evolvable by the magic of epistasis, and (iv) The results are yet more evidence for evolution.

And you thought epistasis was a problem for protein evolution. After all, it makes for a rugged fitness landscape in the protein sequence space, greatly complicating any evolutionary search. Silly you—the evolutionists have turned it into a virtue. Yes it may appear that proteins cannot tolerate much change, but what if that tolerance is ever-changing in just the right way due to epistatic effects? Then the tiny amounts of tolerable change could be, themselves, ever changing. And so evolution can magically find a maze-like path to another protein. Just when you thought you had seen peak fallacy, the evolutionary speculation reaches new heights.

A self-refuting theory

And as usual, what little legitimate science there is in the paper easily refutes the very idea the evolutionists purport to confirm. What the evolutionists get right is that if evolution were true then protein evolution would take a long, long time. What they don’t get around to thinking about is that this undermines their silly thought experiment, which begins 3.5 billion years ago with all manner of proteins already fully formed. That leaves only a few million years for their origin, which isn’t enough time to create them from a warm little pond.

The details

For those who like to waste time probing junk science, here is an explanation of the evolutionary folly in this paper. The evolutionists begin by assuming evolution happened. Not a good start if you want to prove evolution. But moving beyond the usual petitio principii, they next compare similar proteins and find what they think is a curious pattern.

Imagine, for example, three proteins with very similar sequences. These are illustrated below as Proteins 1, 2 and 3. Next, imagine a fourth protein that is a bit more different. If the first three proteins are siblings, the fourth is a cousin.

Now in the first three protein sequences, there are very few differences. One difference highlighted in the notional example below at the third position is the tyrosine amino acid (Y) in Protein 1. It is different from the lysine (K) in Proteins 2 and 3.

But note that Protein 1’s tyrosine is also different from Protein 4, which also has a lysine at the third residue position. When one of the first three proteins differs from the other two, it will likely differ from Protein 4 as well because Protein 4 is fairly similar.

Now consider a second example illustrated below. In this case, Protein 4 is more distantly related. It shares fewer sequence matches with the first three proteins. Because Protein 4 is more distant, differences among the first three proteins, by definition, are less likely to differ from the Protein 4 sequence.

Or in other words, there is a better chance that a difference in one of the first three proteins might actually match the corresponding Protein 4 amino acid. This is illustrated below, as Protein 1’s tyrosine now matches the tyrosine in Protein 4. That would be much more unlikely if Protein 4 was more similar, as in the first example above.

There is nothing clever or profound here. As Protein 4 becomes increasing distant from the first three proteins, it simply follows that differences among the first three might not differ from the fourth sequence.

This simplified explanation is not what the evolutionists did, but it gives a rough idea of the circuitous calculations the evolutionists used to try to confirm evolution. In the end, all they did was to prove a tautology. Below is their “key” result. The straight line illustrates the strong relationship between the distance between proteins and how the differences compare.

Only evolutionists could find this to be significant. As the graph not surprisingly shows, at short distances the differences in the protein sequences are more likely to show (as in the first example above). At greater distances, the differences are less likely to show (as in the second example above).

And given the degree of these differences, something must be slowing evolutionary progress. It must be epistatic effects which the evolutionists then enlist to contrive another one of evolution’s heroic just-so stories. In this case, the epistatic effects change as mutations accumulate so that mutations that once were not tolerable are now tolerable. And amazingly, these epistatic pathways just happen to lead to functional proteins that otherwise are so difficult to find in the protein sequence space.

If you don’t follow all this don’t worry. It is a silly, convoluted tautology that has no place in a scientific journal. Like a Rube Goldberg device that spits out A = A, the research is much ado about nothing.

And yet this is touted as new, novel evidence for protein evolution and common descent. As the evolutionists conclude:

Finally, our observation of receding protein sequences provides novel evidence of the common ancestry of life.

What an astonishing abuse of science. Yet here is how one professor responded to an earlier post of mine regarding protein evolution and this paper:

It's telling that he relies [especially in his point 4: Experiments show that proteins do not tolerate mutations very well] on his misunderstanding of a paper that he has cited repeatedly:

Sequence space and the ongoing expansion of the protein universe by Inna S. Povolotskaya & Fyodor A. Kondrashov, Nature 465, 922–926 (17 June 2010)

Would that I were the problem. Unfortunately evolutionary science—surely an oxymoron if there ever was one—is idiotic. To the uninitiated that may sound like hyperbole but it’s not. When something—like the idea that the universe and everything in it just happened to arise spontaneously—is idiotic, the best word to describe it is “idiotic.”

But when you point out the fallacies the evolutionists blame you. After all, evolution is a fact. Religion drives science and it matters.