Protein Folds and the Failure of the Neo-Darwinian Mechanism

What does it take to build an animal? Not out of clay, crayons, or macaroni, but a real life, in the flesh, animal. Or, to try to make things a bit easier than starting from scratch, what would it take to turn one animal, with a unique body plan, into another unique animal, by this I mean how do we cross a morphological taxonomical gap of, let’s say, phylum (which is the highest level category distinction within the animal kingdom). Well, its simple really, primarily it would take information. Lot’s of information. But, it would also take time, lot’s of time, that is, if we are hoping in a purely naturalistic process to accomplish our organic constructive wishes.

And still, it would take something else, something that would need to happen at the base layers of organic life, it would require, at this high of a taxonomical level, a successful mutation of a protein fold. What is a protein fold you ask? By definition, “A protein fold is a distinctive, stable, complex, three dimensional structure that enables proteins to perform specific biological functions.”1 Got it? Good, but why are these folds so important to our discussion? Well, “Since proteins are crucial to almost all biological functions and structures, protein folds represent the smallest unit of structural innovation in living systems.”2 Hence, they are the building blocks of all organic life and all its immensely wonderful complexities, and thus, for organic life to have the bio-diversity that we observe today, there must have been significant successful change within these folds, assuming any type of common-decent model (which for the record, I do not think needs to be assumed), for the development of life, as evidenced in the fossil record, to have actually occurred.

As we consider this, the questions come quickly. How rare are these protein folds? Will a mutation always be successful? Will the animal survive a mutation significant enough to alter a body plan? If so, will the positive mutation be retained, or fixed, into the given population? The questions are legion, but perhaps we should start with the governing mechanisms. Excluding, for this post anyway, less popular, though trending, models of Evolutionary Extended Synthesis (think chemical self-organization) the dominant evolutionary model remains the Neo-Darwinian concept of natural selection acting upon random mutations.3 So, the succulent questions are obvious, do the mechanisms of Neo-Darwinian evolution have the capabilities to develop and retain these required protein folds? And, can they produce these developments, within the confines of their own mechanistic laws, in the required amount of time during the history of life on planet earth, roughly 3.8 billion years ago? (For any Christian readers who might start scratching their heads at that number, I’d refer you to my previous post as to why I have no theological reason to object to it: An Analogical Interpretation of Genesis 1, and look for my forthcoming post: “Genesis 1 is ‘Exalted Prose Narrative.’”4)

Before we address the time factor, we must remember that not any amino acid sequence (which generates the unique fold) will do. What we need, for our animal project, is a functional sequence. Working from peer-reviewed results published in the Journal of Molecular Biology by former Cambridge researcher and microbiologist Doulas Axe5, Stephen Meyer concludes, “For every DNA sequence that generates a short functional protein fold of just 150 amino acids in length, there are [1077] nonfunctional combinations—[1077] amino acid arrangements—that will not fold into a stable three-dimensional protein structure capable of performing a biological function.”6 Essentially, the nonfunctional options far outweigh the functional options (that number is one hundred thousand, trillion, trillion, trillion, trillion, trillion, trillion, a number far exceeding the number of atoms in our galaxy). Also, notice Meyer’s mention of a short fold, most folds are far greater than 150 amino acids, but, as with any scientific endeavor, we should be very generous with setting the most favorable upper bounds for those positions that we are critiquing.

Now, as we remember that we are working within the confines of Neo-Darwinism, we now need to consider how a new sequence, if it were randomly found, would be transferred to a given population. An organism may have a variety of mutations throughout their entire life (though, the majority of evolutionary biologists agree that significant morphological mutation must happen at the embryonic level), but there is only one time in which any functional mutation could be passed on, you guessed it, reproduction. So, how many times in the history of life, has life actually reproduced? The “extremely generous” estimate is roughly 1040 and that estimate consists vastly of bacteria like organisms. Considering our previous number of 1077 for the estimate of nonfunctional sequences, we start to realize a big statistical problem, a time and numbers problem. We have roughly 3.5 billion years of life on earth with only 1040 opportunities for the transmission of a functional protein fold, but a 1 in 1077 chance of randomly finding such a fold! Thus, the Neo-Darwinian probability of transmitting just one fold, or just one of the “smallest unit[s] of structural innovation in living systems,” is a staggering 1037! 7 As Meyer concludes, “It follows that it is overwhelmingly more likely than not that a random mutational search would have failed to produce even one new functional (information-rich) DNA sequence and protein in the entire history of life on Earth… And, of course, the building of new animals would require the creation of many new proteins, not just one.”8

It doesn’t stop there. If we consider just one biological event in the history of life we see how problematic our blind and random process really is. The Cambrian Explosion is an event that Darwin himself stated that he could “give no satisfactory answer” to explain it.9 It occurred between 540-515 million years ago, in which 20 of the 27 phyla suddenly emerge in just that 25 million year period; and which, from a geological perspective, is a blink of an eye.10 Regarding this event, Gunter Beckly, an acclaimed German paleontologist who has written over 70 peer-reviewed articles, and, I might add, who also converted to the Intelligent Design movement in 2015 from a previously antagonistic Darwinian perspective,11 says the following:

Several unexpected features of the Cambrian explosion from a Darwinian point of view are: (1) the sudden appearance of novel animal forms; (2) an absence of transitional intermediate fossils connecting the Cambrian animals to simpler Precambrian forms; (3) a startling array of completely novel animal forms with novel body plans; (4) a pattern in which radical differences in form in the fossil record arise before more minor, small-scale diversification and variations. This latter pattern turns on its head the Darwinian expectation of small incremental changes only gradually resulting in larger and larger differences in form.12

When we consider the extreme odds of the Neo-Darwinian mechanism achieving just one functional protein fold in 3.5 billion years, are we really to believe that it could accomplish the creation of the required amount of novel and functional information of this magnitude in just 25 million years? Shall we truly believe that a mindless process is so adept at generating highly complex insightful and interpretive coding systems in such a radical fashion? If random mutation is grossly inadequate to produce the necessary and informed material, and natural selection itself just “shows up only after the hard work of invention has been done,”13 is it not that, in the word’s of Atheist philosopher Thomas Nagel, “the materialist Neo-Darwinian conception of nature is almost certainly false”?14

At what point does this amount of observable information not point to a most probable cause of an actual informer? When will we recognize that natural selection primarily governs information loss and decay, rather than producing what is beyond not only its own function, but also beyond the wildest reaches of its counterpart of random mutation? At what point can we set aside methodological naturalism and objectively consider the implications that, “Insight is so unique among causes—categorically different from every physical cause—that no other cause should do the work of insight”?15 Indeed, as we look at the stunning complexities that modern science allows us to observe, shall we not wonder, “Where does the programming—the algorithmic control—that ‘preprogrammed adaptive capacity’ of living organisms come from?” We know of only one source of such programming. Our uniform and repeated experience affirms that the only source for information-rich programs is intelligent agency. Or, as the information theorist Henry Quastler put it, “the creation of new information is habitually associated with conscious and rational activity.”16

Not too long ago, I asked my Sunday School class of first through fourth graders, “Can something come from nothing?” Despite their lack of philosophical training, they unanimously declared, “No!” This is intuitive logic built into the fabric of human thought. When we look at the requirements for information, when we look at the only observable causes of truly novel insight, when we dwell upon the staggering appearance of complete and unique body forms throughout the fossil record, are we really dealing with something less intuitive as to what must be the cause?17 Perhaps the reasons run at a deeper level, as former Atheist turned Christian C.S. Lewis wrote years ago in reference to Darwinian evolution, “That, then, is the first proof that popular Evolution is a Myth. In making it Imagination runs ahead of scientific evidence. The prosthetic soul of the big world’ was already pregnant with the Myth: if science has not met the imaginative need, Science would not have been so popular. But probably every age, within certain limits, gets the science it desires.”18


  1. J.P. Moreland, Stephen C. Meyer, Christopher Shaw, Ann K. Gauger, and Wayne Grudem, Theistic Evolution: A Scientific, Philosophical, and Theological Critique (Crossway, Wheaton, IL, 2017), Ch. 2 “Neo-Darwinism and the Origin of Biological Form and Information” by Stephen C. Meyer, 111-118
  2. Ibid.
  3. We must remember that those who believe in strictly materialistic processes of evolution will not describe this as a purely random process. The mutations that are derived are randomly generated, yet natural selection is a non-random mechanism that governs the effects and development of the evolutionary process. Furthermore, other means of selection are sometimes considered, such as “sexual selection,” whereby animals themselves show signs of preference when it comes to a mate. See: Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, (New York, NY: HarperOne, 2013), 5-6, 451
  4. I can say with Reformed theologian Gavin Ortlund, as I’ve come to accept the deep time of our universe, my awe of God has only increased, “If you see in the size of the universe a little flavor of God’s infinity, I believe you see in the age of the universe a little hint of his eternity.” Gavin Ortlund, “What I Learned from Church History about Science and Faith,” Youtube, Reasons to Believe, April 20, 2017, ; 49:30-42
  5. Douglas D. Axe, “Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors,” Journal of Molecular Biology, Vol. 301:585-595 (2000); Douglas D. Axe, “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds,” Journal of Molecular Biology, Vol. 341:1295–1315 (2004).
  6. Theistic Evolution, 111-118
  7. Meyer, Darwin’s Doubt, 202-03
  8. Theistic Evolution, 111-118
  9. Charles Darwin, On the Origin of Species by Means of Natural Selection, facsimile of the first ed. (London: John Murray, 1859; repr., Cambridge, MA: Harvard University Press, 1964), 396-97
  10. Theistic Evolution, Ch. 10 “The Fossil Record and Universal Common Ancestry” by Gunter Bechly and Stephen C. Meyer, 342; It should also be noted that the number of phyla are disputed, and even the classification in general, yet none of that calls into question the explosive appearance of unique body plans. Furthermore, the numbers I’ve used are on the conservative side. See: Meyer, Darwin’s Doubt, 31-34, 452
  12. Theistic Evolution, 343
  13. Theistic Evolution, Ch. 1 “Three Good Reasons for People of Faith to Reject Darwin’s Explanation of Life” by Douglas D. Axe, 99
  14. This comes from the sub-title of Thomas Nagel’s book Mind and Cosmos,,aps,367&sr=8-1
  15. Theistic Evolution, Ch. 1 “Three Good Reasons for People of Faith to Reject Darwin’s Explanation of Life” by Douglas D. Axe, 97
  16. Theistic Evolution, Ch. 8 “Theistic Evolution and the Extended Evolutionary Synthesis: Does It Work?” by Stephen C. Meyer, Ann K. Gauger, and Paul A. Nelson, 283
  17. For an entry level introduction to this material and idea, see: Douglas Axe, Undeniable: How Biology Confirms Our Intuition that Life is Designed, (New York, NY: HarperOne, 2016)
  18. C.S. Lewis, Christian Reflections, (Grand Rapids, MI: Eerdmans, 2014),105


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