Figure 3 shows that, regardless of their similarity, ancient proteins are still diverging from each other and therefore have not yet reached the limit of their sequence divergence. … Our data reveal an ongoing expansion of the protein universe, such that most extant protein sequences are still diverging from each other and from the ancestral LUCA sequence, and have not yet reached the structural and functional limits in sequence space.
But in fact their results show no such thing. Indeed, that would be quite amazing given that science clearly shows protein evolution to be unlikely. It would be the reversal of a wealth of evidence. What they do show is the results of a circuitous analysis and comparison of many different proteins. It would require substantial scientific investigation to come to any firm conclusions about just what those comparisons portend.
What is obvious is that the evolutionists, in typical fashion, have presented a bizarre and heroic conclusion that is without scientific basis. There is nothing in the data about “ancient proteins” that are “still diverging” from an “ancestral LUCA.” Once again, the results are force fitted into the evolutionary narrative, over against scientific evidence and without warrant.
Evolutionists drink their own bathwater
In spite of its scientific problems, this paper is being cited by other evolutionists as an authoritative finding and confirmation of protein evolution. For example, one evolutionist, referring to this paper wrote “The protein universe is currently still expanding …”
In another instance, evolutionists wrote that their research “is entirely in accord with a recent insightful analysis of protein evolution that invoked extensive epistasis to account for the retarded divergence seen in ancient proteins.”
Call it garbage-in, garbage-out, or blowback, or drinking their own bathwater, this is how evolutionary claims propagate. It begins with religious and metaphysical claims for evolution. From there science is enlisted to service the religion. Empirical evidence is twisted and force-fit as necessary, and then cited uncritically as though it is legitimate science.
The duty of a scientist
All of this is a serious breach of scientific duty. For scientists must practice their profession with integrity and, above all, interpret and explain the evidence accurately to the rest of society. Unfortunately evolutionists not only promote a religious theory, they also misrepresent the many scientific failures of the theory. In fact, incredibly, they maintain there are no scientific problems with theory. All of the science, they insist, confirms their bizarre idea, with only the details left to be figured out.
Even this paper on protein evolution is staunchly defended as yet another scientific confirmation of evolution. One professor commented that the paper has a sound basis and that my review of the paper was due to my “profound misunderstanding of the article.” Regarding my point, that for two distant proteins, an amino acid is not likely to change the distance between them, the professor wrote:
It is well known that a single random walker moves away from the point of origin, on average: the distance squared is proportional to the number of steps taken. The same is true for two random walkers: the square of the distance between them grows, on average, no matter what the initial distance was.
This is true for random walkers in Euclidean space, and is typically taught in introductory material. This is probably what the professor was thinking of. But of course protein sequence space is non Euclidean. Amino acids are categorical and unordered. The professor continued:
Cornelius seems to think that closely related proteins should diverge fast and more distant relatives less so.
I think that because it is rather obvious, as I pointed out with some simple examples.
What Cornelius forgets is that we are dealing not with two proteins but with many. Suppose that the proteins have been mutating for a long time and have uniformly filled the configuration space. (For simplicity, think that there is one protein in every configuration.) … This factor, missing from Cornelius's analysis, makes the observed numbers of proteins mutating to and away from a reference equal.
Here the professor raises a meaningless distinction. First, while problems with one or two or three dimensions are common, protein sequence spaces are in the hundreds of dimensions. It would be impossible to have enough different species to have a protein in every configuration. For instance, for a 200 amino acid protein there are 10^260 different possible sequences (a one with 260 zeros after it).
But beyond that, the professor thinks that the effect of a substitution on the distance between two protein sequences is independent of the distance. Specifically, he thinks the substitution has an equal chance of moving toward or away from a reference sequence. But he gets his math all wrong trying to arrive at this impossible conclusion. Let’s have a look at his example.
Consider the five residue reference sequence: NLKIG. There are a total of 5*19 or 95 sequences that have only one amino acid different from the reference. So these 95 sequences completely fill the sequence space at this given distance from our five residue reference sequence.
Now for each of these neighboring sequences, consider a single amino acid substitution. There are 19 such substitutions possible per residue. So the number of possible substitutions, in each of the 95 sequences, is also 5*19 or 95.
Now of these 95 substitutions, exactly one of them changes the neighboring sequence toward the reference sequence. 18 of them change the neighboring sequence into a different neighboring sequence. And 4*19 or 76 move the neighboring sequence away from the reference sequence.
You can repeat these computations for the other 94 neighboring sequences, but of course the answers are the same. It makes no difference whether you look at one neighboring sequence or all 95 of them. The probability of a substitutions moving toward the reference sequence is 1/95 whereas the probability of a substitutions moving away the reference sequence is 76/95.
The professor continues with an analogy about people randomly walking about an island:
At any given moment, a friend's step can be toward or away from you with equal probabilities
That is false. In two dimensions it is close to equal, but with more dimensions the disparity increases. Nonetheless the professor concludes:
In equilibrium, the outward and inward fluxes are the same at any radius. This is a key idea behind the work of Povolotskaya and Kondrashov. Cornelius completely missed it.
Again this is false. It doesn’t matter how long sequences have been changing, or how full the sequence space is. The paper provides results which no doubt mean something, but a confirmation of evolution they are not.
How can evolutionists so consistently misinterpret science so badly? There is no mystery here. Evolutionists must have their theory so they will do whatever is necessary to force-fit the science to support it. Religion drives science and it matters.
We are now entering the irrational stage of the discussion. When evolutionists are confronted with their logical fallacies, metaphysical mandates or misrepresentations of science, the discussion inevitably does not end well.
In this case, the professor now says that his concerns have dealt with the academic problem of infinitesimal steps in his random walk. That’s strange, I thought he was discussing an example of people walking around on an island. That is a real-world problem with finite, not infinitesimal, step sizes.
This is important because the problem at hand, amino acid substitutions in proteins, also deals with finite step sizes (not to mention categorical and unordered variables). So now the professor can claim victory for an irrelevant problem.