Darwinian Evolution and the Gaps

2021 Dec 5

The story of evolution as told by Darwin was an epic tale about natural capabilities. In the story, these natural mechanisms caused new, increasingly complex creatures to come into existence. Always in the narrative, slight changes accumulated and resulted in complex new descendent plants or animals.

However, this story is based on an extrapolation far beyond the things observed in science. It is a story with significant gaps. Only rather modest changes are observed in nature (like wolf ancestor to dogs). What the evidence actually shows is minor changes to animal features. Recently we have found that this is either due to losses of genetic information (broken genes) or due to repeatable changes in non-genetic control parameters (epigenetic controls). Neither of these are a mechanism for creation of new features or new body plans.


Scientists are trained to look for natural causes for all effects seen in the natural world. They are also infused with the idea that only naturalistic explanations are acceptable for science. This training is so intense that many scientists additionally believe that naturalistic explanations are (or will be) available for all observable effects, and that non-naturalistic explanations lack truth or value. note

This is severely unfortunate because there are things that we can see because of our science which cannot be explained by science. The book Return of the God Hypothesis documents three of these (the existence of the universe, fine tuning of the universe, the existence of life). Others include The (im)Probability of Life, the hard problem of consciousness and the existence of objective moral values (e.g. certain things are objectively morally wrong). These are things that solid reason and/or science indicates is beyond naturalism to explain.

It is unfortunate some also think that non-naturalistic explanations lack truth or value. They might say this in the positive form of: “Only scientific statements that are naturalistic are reliably truthful and have value.” However, by inspection, this statement can be seen to be a self-refuting idea (because this metaphysical statement cannot be proven scientifically). Therefore, the statement must be invalid, and not true.

Science literally is based on metaphysics that cannot be proved by science. (See Darwinian Metaphysics)

Unfortunately, scientific methods are not useful for testing metaphysical concepts. Unfortunately also, most scientists are not trained for thinking correctly about metaphysics. Their metaphysical conclusions then mistakenly exceed their credentials.

See also:

This naturalistic approach in science also existed in Darwin’s time. Some thinkers had started developing ideas of evolution before Darwin. Darwin’s original contribution was the argument that an evolutionary mechanism was naturalistically capable of producing all the variety in living things.

Until Darwin, the only viable explanation for variety in the biological realm was that God had created every different kind of plant or animal. This thinking was an irritant for those who wanted to expand naturalistic explanations as far as they could, and a problem for those who didn’t like the idea of a God.

Darwin very much wanted to produce an explanation for the biological world that relied only on naturalistic processes. Because of his theory then, he argued there was no need for a God. And so Darwinian evolution became a direct naturalistic substitute for God. If there is a naturalistic process that produces all of the biological features and variations that we see around us, what need is there of God to have produced it? note Therefore, Darwinian evolution has been the God of naturalistic biology.

Of course there is the completely unsolved problem of abiogenesis, the origin of life. Before evolution can become operational, it first requires life.

However, life from non-life is best seen as naturalistically impossible - not only on earth, but anywhere in this universe. (See The Probability of Life)

Nature is Limited

Science regularly observes changes in biology. Gene flow, mutations, and epigenetic controls make small-range changes to species all the time. This level of evolution is clear and certain. But, we consistently also observe that there are hard limits beyond which organisms can't be changed (or they will die).

Darwin, however, promoted something different than this which we consistently observe. He gave us a theory of transmutation between species. His evolution is not just the small scale changes over time that we see. Darwinian evolution is an account of all species coming from a universal common ancestor. It is biological change writ very large.

Darwin had no knowledge about genetics like we now have. He had no actual understanding of the mechanism he was basing his theory on. (Genetics was discovered 100 years later.) His original theory of change due to "variation" therefore has been modernized. (This is what is called neo-darwinian synthesis and more recently the extended evolutionary synthesis.) The problem in biological science, however, is that evidence does not give support for (the updated) Darwinian processes being able to create new body plans and features as the theory requires. This effect has not been observed either in evidence about the past (as in paleontology) or in experimental evidence in the present.

  • Evidence from the past: --> note
  • Darwin knew very well that the fossil record of his day did not support his theory.
    • Evolution requires gradual change, but the fossil evidence is of discontinuity everywhere.
    • Darwin wrote that he hoped additional fossil evidence would fill in these gaps, but that has not happened.
    • We know that the fossils we have at present are an accurate documentation of the species because our fossil samples have followed the standard "collectors" curve. New samples reinforcingly confirm the patterns already seen. So, the data indicates reliable completeness, and the discontinuity problem has become increasingly certain.
  • Darwin strenuously argued that evolution only and continuously happens by slow gradual changes. (This is appropriate since sudden changes are lethal.) However:
    • Eldredge and Gould invented the punctuated equilibrium sub-theory of evolution to account for the consistent sudden appearance of new species without apparent precursors.
    • They also stressed that "stasis is data" about the lack of change after species appearance. (This means that evolution is not continuous, and therefore is not Darwinian, and so it is without Darwin's plausible mechanism.)
    • This article discusses that they instead suggested allopatric speciation (having to do with isolated populations) to answer the lack of evidence, and for how change could happen quickly. This idea of speciation however is grounded in a lack of evidence; there is no actual evidence that this was the evolutionary mechanism.
  • A phylogenetic graph is for showing the relatedness of types of organisms. It is usually made as a branching tree from ancestors (tree of life), and the leaf nodes have fossils. (Fossil evidence only exists at the tips of the tree.) Note that the branch nodes reliably have no fossils.
    • This is because evidence for the organisms at the branch points does not exist.
    • Darwinian evolution, however, predicts the opposite: there should be fossils of the shared ancestors.

Watch Gunter Bechly Explains What The Fossil Evidence Really Says

  • This video by a paleontologist is very interesting, understandable, authoritative and highly recommended.
  • Fossil evidence actually creates problems for Darwinian evolution.
  • Evidence in the present: --> note

I looked for documentation of a evolutionary change that brought some new organism into existence - like a carrot, or a deer. There apparently is no evidence of something like that, although there are cases of species differentiation.

This page promoting evolutionary speciation lists examples of speciation and attributes them to gene flow. Only one case (Chlorella vulgaris, listed as ambiguous) resulted in a classification differentiation higher than species (that is, a non-trivial change). Another page promoting beneficial mutations listed examples, but didn't say any of them resulted in speciation. And another credible pro-evolution site (no longer available) said explicitly (without attribution) there had been no observation of species transmutation.

That does not mean that the evidence doesn't exist - it is possible something on the order of the examples these sites give might yet turn up. However, all these species transmutation examples were quite modest. By that, I mean that their differentiators were modest - nothing like (for instance) the distance between a rat and a bat.

I discuss the results of some long-term evolution experiments. They have not shown any evolutionary transmutation of species even though the generation counts have been quite high. Transmutation should have been evolutionarily very reasonable.

Absence of evidence is never evidence of absence of course (that Darwinian evolution is absent). On the other hand, when the evidence does not support the Darwinian theory of evolution of species, then the theory is questionable.

As some have said, evolution can account for the survival of the fittest, but not the arrival of the fittest.

Explanatory Power

Theories are simplified models of the real world. They are useful for their explanatory power about things we have observed and for prediction of things we will observe.

Therefore a theory should have mechanisms and structure that consistently match to observations. For instance, gravitation theory explains how and why a falling apple, the moon and a galaxy spiral arm move. It explains the way they moved last year and how they will move tomorrow. (One rule matches to what we observe from the small to the vast. And the calculations consistently match to past movements and future movements.)

So a good theory should be able to reliably predict what will happen. It should be able to supply descriptions of its functional mechanisms and when they operate. And we expect evidence to support the theory by accurate correspondence between the two in some detail.

However, evolution has a problem of predicting what will happen and when because it actually has many mechanisms to account for special cases. note It is not certain which mechanism will be in effect until observations afterward; then the mechanism can be identified. (See Except When It Doesn't) This is not a good scientific theory; this is ad hoc story telling.

Evolutionary mechanisms include

  • Mutation
    • gene mutations
      • DNA replication
      • spontaneous lesions
      • point mutations
      • frame shifts
      • transposible genetic elements
    • chromosome mutations
      • duplications
      • deletions
      • inversions
    • genome mutations
      • aneuploidy
      • euploidy
  • Recombination
  • Non-random mating (sexual selection)
  • Gene flow
    • horizontal gene transfer
  • Genetic drift
    • Founder effect
    • Population bottleneck
  • Endosymbiosis
  • Natural selection
    • directional selection
    • stablizing selection
    • disruptive selection

The Requirement

What evolution must be able to explain is the gain in specified complex information in species across time. Biological systems run on information control systems that are stored in codes. All new species require new codes. (This new information gives them new body plans and new functions.) These codes are vast, highly structured, highly compressed, highly efficient and highly integrated. Everything that math and science tells us about information systems says that this kind of content cannot be produced by random processes.

Mutation and natural selection are the fundamental basis of neo-Darwinian evolution. Natural selection turns out to be just a weak sorting effect from survivability. Mutation is randomness in action. The two of these together could not be an effective tool for change. And yet on the theory of evolution, they were able to craft the superlatives of biology. This is not plausible.

The suggested evolutionary mechanism is like saying that a really good novel can be composed by repeatedly adding words to a manuscript at random and then re-submitting it to an editor for approval. The imaginary great book is made by just doing this again and again over years and years and years.

However, an actual great book only comes into existence by careful work by a skillful writer that intelligently makes it a coherent whole.

It is only since the turn of the last century that we have developed the capability to sequence large sections of DNA. Therefore it is only very recently that we have been able study how genetics actually changes. What has been found was not what was conventionally expected.

Mutations are changes in DNA sequences, so until very recently we had no actual evidence either for or against the function of Darwinian evolution. The problem is that these new studies have shown us that evolutionary change is consistently due to losses of genetic information. The evidence now shows that what we consistently see in biological evolution is the throwing away of features to enable survival in the moment. note This is best called de-evolution and it does not match to a theory that claims to show how information is gained.

How can this be?

  • Imagine that you are on a pleasure boat and you have gotten into a big storm. You would throw anything heavy overboard (deck chairs, food, radio, etc) to keep from sinking and dying.
  • Imagine you are crossing a big desert in your car, but there are no fuel stations there. Your car could go farther if it was lighter. If you ran out of fuel, you would die. So you might remove and discard the doors, extra seats, etc to survive the trip.

Like this, broken genes enable improved survival for an organism in the moment. It may look like a positive development until you actually look at the details of what has happened.

Now that we have gained the ability to observe DNA, we are seeing that the vast majority of cases that bring any (reproductive) benefit do so by means of loss of function. Damage and loss of information happens nearly 100% of the time. (See Darwin Devolves, Behe, 2019) The cases where gain of function is due to gain of information is on the order of fractions of a percent; this is as good as pure zero because the cumulative trend between the two is what matters, and cumulatively it is damage, not gain.

The Gaps

Natural evolutionary mechanisms are promoted in the story of life and variation. However, there are two kinds of gaps in this context. Gaps that a god explains away, and gaps in scientific theories.

Evolution seemed to be able to do much for a long time. What we thought we were able to observe became extrapolated into larger things. A grand story was told of evolution's capabilities and of species expansion. There were gaps, but the theory became god-like and was used to fill in all the gaps. note

God-like language is consistently even used to describe the actions of evolution. See A Question of Purpose.

See also Two Kinds of Explanations

Like other god-of-the-gaps theories however, the places where Darwinian evolution legitimately continues to explain well in correspondence to evidence are becoming smaller and smaller. Newest evidence is showing that the naturalistic Darwinian god is no god at all because the mechanisms of the theory turn out not to be what actually happens. And on the other side, the explanatory gaps of the theory of evolution have increased because of on-going work in science.

However, believers in the Darwinian god are resistant to the evidence of their god failing because they are metaphysically committed. They hold that all is well in the world of their theory. However, the foundations their god sits have eroded and the god of evolution is near toppling.