Different kinds of gaps

A common objection to a god-of-the gaps argument is of course that if we invoke a god to explain what we currently can’t explain, we run the risk of a shrinking or even disappearing god as scientific knowledge advances (e.g. the ‘BioLogos article Are gaps in scientific knowledge evidence for God?’). However, gaps in our scientific knowledge are not the same as gaps in scientific explanation; and it seems to me that in biology some explanatory gaps get larger as we discover more.

For example, by the 1950s-60s we knew the amino acid sequence of several proteins and realised that given the number of possible amino acid sequences for a protein of typical length, the probability of finding the right amino acid sequence (if it’s specific) is prohibitively low (e.g. Wistar Symposium, 1966).

By the 1970s it was known that proteins fold into a specific 3D conformation (or a few) that is determined by and dependent on their amino acid sequence, and is essential for their function. This has some significant implications for an evolutionary origin of proteins:

  1. Because a typical polypeptide must have a minimum length of about 70 amino acids in order to fold, it means that proteins (especially enzymes) could not have started out as short polypeptides (even though this is still widely believed and often present in textbooks).

  2. Because for folding to work the amino acids in the middle of the protein need to fit together closely (like a 3D jigsaw) while still connected by the polypeptide backbone, it explains why at least major parts of the amino acid sequence must be fairly specific.

  3. As we started to learn about how enzymes function we realised that they have active sites composed of specific amino acids which must in the right places in the linear sequence so that they are positioned correctly in relation to each other in the folded protein, which also constrains a protein’s amino acid sequence.

During this time we also began to learn about the structure of genes and how they work. At the very least, for a functioning protein, not only must there be a sequence of DNA that codes for a useful protein, but it must be downstream of a control sequence which will e.g. bind the enzyme that transcribes the DNA into RNA. So, from an evolutionary perspective, not only must a potentially-useful protein-coding sequence arise, but a viable control region must also arise at more-or-less the same time and place, which clearly compounds the odds against it occurring. And we have learned that most genes are much more complex than this basic arrangement e.g. with multiple regulatory sequences, in various positions in relation to the protein-coding sequence.

We have also learned that most proteins (whether structural or enzymes) do not function in isolation but necessarily in conjunction with others, often as components of a protein complex e.g. ATP synthase which has at least 9 types of protein components, some in multiple copies. For every situation where multiple proteins are essential for a function (and the component proteins have no independent function) for each and every component protein, the protein-coding sequence (and control sequences, although these can be shared) must arise independently and yet arise or come together at the same time and place. Unfortunately, this compounded improbability facing an evolutionary origin of proteins is rarely acknowledged.

Some may wonder whether natural selection could help. But the straightforward answer is ‘no’, because natural selection operates on differential fitness, but most of a protein’s sequence needs to be right before it has any function / fitness. (Dawkins’ METHINKSITISLIKEAWEASEL may illustrate the principle of cumulative selection, but it does not illustrate natural selection. Specifically, it is totally inapplicable to the evolution of proteins (although I think he intended it to be) because getting small parts of an amino acid sequence correct (a few letters in his sequence) will not give you a protein with any function.)

In summary, since recognising the prima facie improbability of proteins in the 1960s and that it is a challenge to an evolutionary origin, the more we have learned about proteins, genes etc., rather than explaining how they might have evolved despite this improbability, it has exposed an even greater challenge. That is, although gaps in our knowledge have decreased, this explanatory gap has increased.

How might future scientific discoveries overcome the challenges to an evolutionary explanation for the origin of proteins? There are 2 possibilities where further research might conceivably produce knowledge that might overcome the prima facie case against an evolutionary origin of proteins:

  1. We know that some variation in amino acid sequence is permissible. What if (we found that) the number of possible variations is so high that it constitutes a significant proportion of the total possible sequences (for a given length of amino acids) such that there is a realistic chance that a random search will find one that works? This seems unlikely given the constraints on a protein’s amino acid sequence, but …

  2. What if we found some basis that could guide an evolutionary search through sequence space so that a search does not need to be random? It seems hard to envisage how this could work without at least something akin to fitness on which natural selection could operate, but …

It seems to me that both of these are not only speculative, but from what we do know there is a prima facie against them. And if so, then what is the basis for thinking that proteins have arisen in an evolutionary way?

Although I introduced this post in the context of god-of-the-gaps, my primary interest in raising this issue is not to promote an argument for God but to reopen what I think is a fundamental flaw in the theory of evolution, and to question the presumption that explanatory gaps will always be closed, or even narrowed, by scientific discoveries. Sorry it’s so long an introduction, but hopefully it’ll prompt a useful discussion.

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If God however doesnt exist ,whats the answer to evil? Are we to believe that we have evolved for solely purpose is to harm and survive?Survive for what?What purpose? What for?

Im fine with God of the gaps.For me amognst this messed up world that has no meaning whatsoever and that 99% of people look for personal gain and dont care about others ,the only logical solution in my mind is God.

I might be “programmed” to think this way by evolution but ive gone trough the stage of atheism and i couldnt handle it.

Abiogenesis isn’t part of evolutionary theory. And while I hear that strides are being made toward plausible explanaitons of the beginnings of life, it also remains true right now that it is still more of a frontier with many more unknowns in it. Biological evolution, on the other hand, is much more established by now. Not that it doesn’t have plenty of unknowns still ripe for exploration and further discovery too - but the presence of mysteries yet to be solved doesn’t change the fact that no other explanation of how former life gave rise to the present diversity of life - no other explanation comes even close to explaining all of the data that evolutionary theory makes sense of.


And no unnatural explanation explains anything about existence down the chain of being.

Those are two entirely separate issues. We will never be able to close the explanatory gaps in any area. But that doesn’t relate to any alleged flaw in the theory of evolution. Such as?

I am not sure that you’ve established what you sought to demonstrate. Namely,

It seems like your main argument is that in this one case, explanatory gaps appear to have gotten larger with more scientific inquiry - therefore it makes sense to consider alternative explanations for gaps in the explanation of natural phenomena. Would you say that in certain cases, it makes more sense to be open to supernatural explanations but in other cases, it makes less sense to be open to supernatural explanations? After all, the general rule seems to work the other way around, where explanatory gaps are closed or narrowed by scientific mechanisms - like with the evolution of bacterial flagellum for example or with the stability of the solar system.


Thanks Mervin.

Abiogenesis isn’t part of evolutionary theory.

Whilst the challenges facing an evolutionary origin of proteins are certainly a major obstacle to the origin of life, they are also applicable to the emergence/origin of ‘higher’ life forms. To give just a couple of examples:

  1. Compared with prokaryotes, eukaryotes have considerable extra biochemical machinery for processing genetic information.
    The nuclear pore is an excellent example of a multi-component protein structure. In yeast there are about 30 different protein components, each in multiple copies, see https://www.ncbi.nlm.nive .gov/pmc/articles/PMC2169373/ . (In humans there are 34 different proteins, with a total of 456, see https://www.science.org/doi/10.1126/science.aaf1015)
    And, of course. nuclear pores are not just holes, but they play a key role in effecting and controlling the transport of macromolecules into/out of the nucleus: in effect they are enzymes as well as structural proteins.

  2. The emergence of organisms with hard parts (esp in the Cambrian) required new enzymes to synthesise these – e.g. to synthesise organic matrices such as chitin or collagen, and/or to implement a range of biomineralization. And of course, for some, the hard part is partly / mainly composed of proteins, such as sclerotein, spongin or keratin.

  3. The structural protein alpha-keratin occurs only in vertebrates. And beta-keratin, which is fundamentally different from alpha-keratin, in terms of its structure and the structure of its genes, occurs only in reptiles and birds (which of course arose at a much later stage).

As well as straightforward examples such as these, I must mention the genetic and molecular basis of embryonic development. In the 19th century, biologists thought of biological tissues as more-or-less plastic, in the sense of how they formed embryonically and how they could vary from generation to generation. That’s why Darwin thought that the variation which he observed, e.g. due to breeding, could be extrapolated more-or-less without limit, given enough generations. But we now know that organisms develop through the precisely orchestrated action of genes, involving a complex interplay of transcription factors etc. And observed variation is due to mixing/segregating existing genetic material in different ways. So any new structure would require a new array of interdependent genes.

One of the evolutionary myths, recognising that many proteins are similar across a wide range of organisms, is that evolution has proceeded not through acquiring new genes, but ‘only’ through reorganising the expression of existing ones – as if this were an easy thing to do. But the more we find out about how embryonic development is implemented, the more we see that it just isn’t realistic to think that constructive changes could occur through opportunistic mutations.

To give just one example of what I’m referring to: As well as the novel structural proteins required for an eye, a key feature for a transparent lens is that the organelles (including the nucleus) in the cells of the lens fibres must be removed so that they don’t scatter the light passing through. Whatever the processes are that implement this (I think we don’t know yet), even if it uses common cellular constituents such as the cytoskeleton, it must require some serious coordinated rewiring of the genetic mechanisms that control it (including of course, to ensure that they are implemented in the lens-fibre cells, but not others).

These are the sorts of examples why I think it is misplaced to put faith in future scientific research that it will resolve the challenges facing an evolutionary origin of biological systems. It seems to me that the more we discover, the higher is Dawkins’ Mount Improbable, and the stronger is the case that it cannot be scaled by a series of small steps that have a realistic chance of occurring. (Dawkins just assumes that steps can be as small as he likes, not recognising that genes set a lower limit – but that’s another story.)

Finally (again!) -

no other explanation comes even close to explaining all of the data that evolutionary theory makes sense of

I’m sure you know that no amount of evidence consistent with a theory can prove it’s true. But inconsistent evidence can disprove it. If, as I think, there is a fundamental flaw in the theory of evolution because it can’t account for the origin of proteins, genes etc., this flaw cannot be ignored even if evolution is the right explanation for some observations, such as natural selection, adaptation, speciation.

And your flawless alternative is what?

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Hi Klax,

And no unnatural explanation explains anything about existence down the chain of being

I’m not sure what you’re asking here?

Those are two entirely separate issues. We will never be able to close the explanatory gaps in any area. But that doesn’t relate to any alleged flaw in the theory of evolution. Such as?

I agree they’re separate. However, I think there’s a difference between never being able to close explanatory gaps in an area, and the sort of explanatory gap that I think exits re evolution.

In the first, we may never be able to get to the bottom of some physical phenomena. E.g. it was once thought that atoms were indivisible; then we learned about protons, neutrons and electrons, and thought these were fundamental particles; now we know about fermions and bosons, and I think the current ‘standard model’ considers these to be elementary particles (or are the corresponding wave functions more fundamental?); but perhaps in due course we will find these aren’t fundamental. But presumably there isn’t an infinite regress, and something really is fundamental.

But it seems to me that the explanatory gap for the evolutionary origin of genes etc. is different. Standard evolutionary theory claims to explain how the first life (to avoid argument(!) I’ll accept it doesn’t include the origin of life) has developed into the diversity of life, and has done so through the normal operation of natural processes. But it seems to me that from what we know of how the relevant natural processes operate, the origin of useful genes is so unlikely that it isn’t credible that evolution could keep striking it lucky. Recognising this, some evolutionists think / hope that one day we’ll find a property or process that can realistically guide to workable solutions. This is what I alluded to in my first post; and maybe it’s what you have in mind?

And your flawless alternative is what?

Falsifiability is lauded as a key feature of a scientific theory. In theory(!), if we are going to take falsifiability seriously, if we find reliable evidence that clearly falsifies a theory then we should accept the theory as falsified. So I don’t need to come up with an alternative. However, you’re in good company, because Thomas Kuhn observed:

No process yet disclosed by the historical study of scientific development at all resembles the methodological stereotype of falsification by direct comparison with nature. The decision to reject one paradigm is always simultaneously the decision to accept another, and the judgement leading to that decision involves the comparison of both paradigms with nature and with each other (Structure of Scientific Revolutions, Ch 8).

And the trouble is, of course, that many see the only alternative as supernatural, such as Jerry Coyne in Why evolution is true. He starts his section on ‘Can selection build complexity’ by commenting:

But first we must ask: what’s the alternative theory? We know of no other natural process that can build a complex adaptation.

Which implies he knows it’s very unlikely; but he rejects the alternative because he doesn’t like it, not because it couldn’t work.

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There is no need to take falsifiability seriously when it comes to rationality. We have all the evidence we’ll ever need to know with p=1 certainty that abiogenesis occurs wherever it rains long enough. I.e. on many quadrillions of worlds throughout our insignificant, infinitesimal, typical, mediocre universe of infinite for sempiternity. Just as there is 0.00…0…% doubt that life evolves minds, that the accelerating decrease in frequency of light is correlated with the accelerating expansion of spacetime, that something like eleven dimensional branes in bulk intersecting creates universes. There is no warrant for not being rational because the hard empirical science is forever out. That’s a cop out. A turning of the head to the blind spot as big as the elephant in the room. As usual that started with the Greeks.

While I’m sure you genuinely believe this, I’m not sure it matters to you all that much.

For example, take one of your “impossible” scenarios - what if we do close the explanatory gap someday? Probably you would still think evolution is wrong and then just move the goalpost to another explanatory gap. Perhaps you would do this because you have some prior belief that evolution is wrong - at least that’s what I usually see from people who argue evolution like you are in this thread. I don’t know what your motivations are here, but for the majority of people I meet who reject evolution, they know that it is wrong because of some faith commitment.

I am kind of tired of the dancing around real issues that I sometimes see. I’m not sure if you are doing that here, but it almost seems like it. For example, you say:

That’s the idea that many people who reject evolution have - all they need to do is prove that it can’t explain something, either presently or ever, and then leave it “open-ended” as to what a better explanation would be. There is a very big nudge, nudge, wink, wink going on when people do this. They pretend that they are honest in their questioning, but what is motivating them is not to understand things or come up with a better natural explanation; instead - their “curiosity” and “honest questioning” comes from religious commitments that already need to reject evolution.

At the end of the day, there are a LOT of successes of evolutionary theory, but those are casually swept under the rug and not even talked about. I know I certainly was never presented with evidence for evolution. All I was ever told or read about were things scientists can’t explain (either perceived or actual), with the implication that a better explanation is God supernaturally created things. Which if He did, He must have done it in such a way that it looks like evolution occurred, maybe with Him inserting in a cool gene or nucleotide sequence from time to time.


There are different kinds of gaps. With that I agree. But you have not described any. Gaps in scientific knowledge and gaps in scientific explanation are the same thing. Yes some gaps get larger as we discover more. Science does not always proceed incrementally. Sometimes we discover new things that transform how we understand everything and thus provide the explanations which were lacking.

So what are the different gaps – ones to which the the “god of the gaps” objection does not apply?

  1. There are gaps due to the very nature and process of scientific inquiry.
  2. There are gaps which science itself discovers and require us to accept.

An example of the first one is that the method of science requires our hypotheses to be about things which can be tested. Thus hypotheses about things which are not even falsifiable like the existence of God can never be a valid scientific hypothesis. An example of the second is the discovery of quantum physics which has forced us to accept that there are events where the outcome can never be explained or calculated from within the accepted premises of the scientific worldview. This discovery resulted in considerable consternation, confusion, and even outrage by dedicated scientists who had devoted themselves the belief that science could find the cause of all events. Einstein proposed that there were hidden variables determining the results of these events but it has been proven that no such hidden variable exist.

Both these are different types of gaps which the “god of the gaps” objection does not apply to, and they provide considerable material for the religious to look for their own explanations outside of the methods of scientific inquiry. There is no a-priori reason to insist that all truth claim be capable of objective testing and more reason to think that this is rare. And the establish fact that all events are not determined by pre-existing states in the scientific worldview is good justification for the idea there is more to reality than what science describes.

Hi Matthew

I’ll answer the first part of your comment quickly (I’ll respond to your other and previous comments in due course), because it’s straightforward - you’re wrong. As I’ve written elsewhere (not on BioLogos), I’ve been a Christian since childhood, and pursued science at school, and accepted evolution; you could say I was a theistic evolutionist, although I didn’t know the term then. It was studying science at university, especially biochemistry, that prompted me to question evolution (even though it was of course the given behind all of the biological subjects). If I thought evolution were sound as a scientific theory I would happily revert to being a theistic evolutionist. You can see from my posts in Why do we think of the Bible as the Word of God? that I have a low (using the word theologically) view of the Bible; I certainly don’t think we should try to read it scientifically. And I wish creationists would reconsider their position, because I think their anti-scientific comments give cause for the sort of sentiments you express here, and make it harder for scientific arguments against evolution to be heard.

Prey do . . . .

When reading the article about the flagellum mentioned here, I only see a large gap. Not a closed or narrowed gap. You can’t close close a gap just by saying that it is closed.

Rationality is continuous. There are no gaps.

Is that rational?

You tell me. Tell me where the gap in rationality is. Tell me where unreason, magic, fantasy should apply.

Okay. I am glad that you clarified a little more of where you are coming from. I’ll certainly have to take you at your word as you know your own thoughts best. You’ll have to forgive me though as that’s what they all say- and by they all say I mean many Christians who reject theory of evolution. Most Christians who reject evolution do say the same thing that they are taking an honest look at the data and are making an honest inquiry- very different from the dishonest evolutionists.

I did forget about another possibility earlier when I wrote:

Another common thing that people do is this:

Essentially any possible scientific explanation is dismissed pretty much by default as never good enough. You may be familiar with how young earth creationists call attempts at scientific explanations for perceived problems or gaps as “rescuing devices.” I could go through various scientific literature and potentially answers some more of your specific gap questions but I think I would be wasting my time. I would imagine that you will have preposterously high standards of evidence and end up rejecting anything I could ever present.

I guess my last question would be what do you think actually happened in the past then? How do you yourself explain the origin of species or various evolutionary novelties? There are a lot of successes of evolutionary theory and it has been as successful scientific framework to make a lot of new discoveries. It would probably be a good idea to start here instead of on the fringes of areas where there isn’t a strong scientific consensus.


Hi Leyton, first let me say I am not a scientist, but I do appreciate good scientific dialogue. Something about the way you are addressing the question, leads me to think about a philosophical question with the gap between an observable change and what caused it. It might be caused by another occurrence that is possible to observe, and to which the same question applies. Or in a manner of speaking it was caused by nothing. Or it was caused by something which does not occur. Like an unmoved mover.

The thing that I find fascinating is the way in which an unmoved mover would be unobservable by nature. Such that it would presumably be impossible to empirically determine what causes certain things.