1. Not enough time. New genes are found in species which allow only for a few million years for protein evolution.
2. Too important. These new genes are not functionally less important, as they should be if they recently evolved.
3. Wrong patterns. Protein sequences provide plenty of violations of evolution’s expected pattern, and the violations are not merely evolutionary “noise.”
4. Inflexible. Experiments show that proteins do not tolerate mutations very well. They rapidly lose their function with only a few mutations, so the evidence indicates that to evolve to a protein you need to start very close to it.
5. Not searchable. The protein design space is astronomically large and experiments show it provides no guidance as to where the fully functioning proteins are in the space. Like looking for a needle in a haystack, the hay provides no guidance.
I have discussed this issues here, here, here, here and here. Now if you already believe evolution is true and you don’t mind ignoring the obvious scientific evidence and you don’t restrict yourself to plausible explanations then, yes, you can explain all of the many issues with protein evolution using a variety of non scientific, just-so stories.
But for those who respect science, the evidence we currently have is clear. In fact, unlike most of the evolution narrative which appeals to a great many contingencies over a great many years in the past, protein evolution is more amenable to scientific experimentation. The just-so stories give way to the raw data of experiments which, not surprisingly, clearly show protein evolution to be unlikely.
Of course evolutionists attempt to spin the results of these experiments to favor their theory. They ignore monumental assumptions and use calculations that unrealistically favor evolution. But even then—even giving evolution every advantage—protein evolution is nonetheless unlikely.
For instance, in one case evolutionists concluded that the number of evolutionary experiments required to evolve their protein (actually it was to evolve only part of a protein and only part of its function) is 10^70 (a one with 70 zeros following it). Yet elsewhere evolutionists computed that the maximum number of evolutionary experiments possible is only 10^43. Even here, giving the evolutionists every advantage, evolution falls short by 27 orders of magnitude.
The theory, even by the evolutionist’s own reckoning, is unworkable. Evolution fails by a degree that is incomparable in science. Scientific theories often go wrong, but not by 27 orders of magnitude. And that is conservative.
How conservative? In order to educate readers about the science, as opposed to the evolution mythology, I wanted to explain not only the 27 orders of magnitude shortfall, but also why even that estimate is grossly under valued.
So I explained the several evolutionary assumptions involved. For instance, the evolutionists computed that a maximum of 10^43 evolutionary experiments are possible by assuming a time span of 4 billion years. But that is unrealistic.
Even evolutionists agree that evolutionary innovations, including proteins, arise rapidly, on the order of some tens of millions of years, or in some cases even in just a few million years. So their time span was two to three orders of magnitude too long.
In response to this, one professor made this comment:
The "evolutionist" authors to whom Dr Hunter refers (Dryden, Thomson and White, 2008), assumed a time-frame for the biological activities of bacteria on earth of four billion (4*10^9) years (a commonly accepted value).
An order of magnitude is a factor of 10, so Dr Hunter proposes that a more realistic value for the duration of existence of bacteria on earth is 100- to 1,000-fold less than 4*10^9 years, or between 4*10^7 and 4*10^6 years. That's between 40 million and 4 million years! (Faithful readers may recall Dr Hunter's previous essay on a Cambrian fossil that was dated to ~515 million years ago!)
What was he thinking?
Again, it is unrealistic to use the entire time span of bacteria on earth. Proteins must have evolved much faster than that. Indeed, the bacteria themselves are full of proteins. So giving the bacteria a four billion year time frame leaves much less time to evolve their proteins.
In another example, the evolutionists computed the maximum of 10^43 evolutionary experiments are possible by assuming a protein size of 50 amino acids. I pointed out that this is extremely small as very few proteins are this short. Indeed, the vast majority of protein domains are far longer than 50 residues. Single domain proteins, and domains in multiple-domain proteins are typically in the hundreds of residues.
In response to this, the professor made this comment:
On the contrary:
"The size of individual domains also varies widely (Fig. 6C), from 36 residues in E-selectin (lesl) (Graves et al., 1994), a two-domain protein, to 692 residues in lipoxygenase-1 (2sbl, chain B) (Boyington et al, 1993), also a two-domain protein. However, very large domains are the exception. The distribution peaks at around 100 residues per domain and 80.3% of the domains are comprised of less than 200 residues. Very similar distributions have been observed in smaller non-redundant data sets. Siddiqui and Barton (1995), using DOMAK to assign domains for a data set of 230 protein chains, found that 90% of domains comprised less that 200residues. Holm and Sander (1994) using PUU on a dataset of 330 protein chains, also observed a domain size distribution that peaked at 100 residues."
Domain assignment for protein structures using a consensus approach: Characterization and analysis
Of 787 proteins studied, 370 (47%) had domains smaller than 100 residues (Fig 6C).
Here the professor simply reinforces my point. As the graph below shows, the protein domain sizes range from about 50 to about 700 and the majority (approximately two-thirds) are longer than 100 residues. The evolutionists used the extremely short value of 50 to try to improve their chances, but that is unrealistic.
The 27 orders of magnitude estimate, as miraculous as it is, is a ridiculously low-ball figure. The problem is so complicated we don’t have a good understanding of what the right number is, but a conservative estimate is 10^100 (100 orders of magnitude). For a typical protein of 250 amino acids, its gene has about 10^450 different possible sequences and the protein has about 10^325 different possible sequences. Thus this 10^100 estimate is an incredibly tiny fraction of the theoretical total.
What the right figure is no one knows, but the evidence we do have is clear. Protein evolution is profoundly unlikely. So why don’t evolutionists simply acknowledge this conclusion? Why don’t evolutionists go by the science? The answer, of course, is that this never was about the science in the first place. Religion drives science, and it matters.