Saturday, November 21, 2009

De Novo Genes: What We Know and Don’t Know

I once debated an evolutionist who listed a dozen or so major areas of evidence he said proved evolution. The problem was each of the areas of evidence was problematic for evolution. True, one could find within those areas, as he did, supportive evidences. But the story was not so simple. In fact the areas of scientific evidence, when carefully examined from a theory-neutral perspective, reveal all kinds of problems for evolution. Is evolution false? Is it true? The answer is there are no easy answers. There certainly are substantial scientific problems with Darwin’s idea—that much we do know. If evolution is true then there is much we have to learn about science. But the scientific evidence can tell us something else, and with far more certainty. It tells us that we should not turn to evolutionists for a serious evaluation of the scientific evidence.

It is both shocking and disappointing how grossly evolutionists misrepresent science. This becomes painfully obvious when they, as with the evolutionist I debated, claim problematic areas of evidence as powerful proofs. Consider, for example, the findings of de novo genes.

One of the facts of biology that evolutionists claim as powerful supporting evidence is the many similarities in genes between the different species. There are many such similar genes, and they certainly do fall in the list of supporting evidence. But if such genomic similarities are powerful evidence for evolution, then what about the genomic differences?

There are, in fact, substantial genomic differences even between otherwise allied species. And it stands to reason that these evolutionary surprises would fall in the list of contradictory evidence, right?

Wrong. With evolutionists, all evidences support evolution, one way or another. Evolutionist Arthur Hunt, for instance claims that the findings of de novo genes refutes the notion that evolution alone can’t do the job “in no uncertain terms.” The idea that proteins can’t arise from scratch, explains Hunt, “is an illusion.

And just how did evolution perform this feat? According to Hunt and the evolutionists, at some point in evolutionary history a segment of DNA recruited the machinery needed to begin coding for a protein. Fortunately that DNA segment contained the proper message so the resulting peptide was indeed a functioning protein. And of course subsequent mutations may have enhanced or modified the newly minted molecular machine.

There you have it. No details regarding how likely (or should I say unlikely) a non coding segment of DNA just happens to code for a functioning protein. No details on how often this would have to occur in order to evolution to get lucky.

Now don’t get me wrong—I’m not saying this evolutionary interpretation is impossible. I wasn’t there and, frankly, I don’t know enough to calculate the probabilities. (I don’t think any else does either which would explain why evolutionists haven’t provided them).

We do have some relevant experimental data. A functioning protein arising from a random DNA sequence of about 400 base pairs is extremely unlikely. Even shorter sequences need millions upon millions of tries to get anything even slightly functional.

But of course mere function isn’t good enough in the evolutionary world. Becoming fixed in the population requires useful function, or luck, or some combination of the two. And then there is the recruitment of the machinery to make the sequence code for a protein. How many times would that have to occur, and what are the probabilities?

Impossible? Certainly not, but we’re a long way from certainty. Unfortunately, certainty is precisely what Hunt and the evolutionists have. We can argue about what the scientific evidence implies, but it does not give us certainty about questions of origin. We are simply nowhere close to the evolutionist’s claim that their theory is a fact just as much as is gravity.

The claims of evolutionists are both shocking and disappointing. We scientists have the serious responsibility of public trust. Others depend on us for a fair and honest assessment of what the scientific evidence reveals—and what it doesn’t reveal. We do them, and science, an injustice by providing anything less.


  1. "A functioning protein arising from a random DNA sequence of about 400 base pairs is extremely unlikely"

    How do you define "functioning"? From an evolutionary perspective, aren't "functioning" preteins the ones whose corresponding genes remain active after many generations due to the lack of destructive consequences upon interaction with the environment? If so, it seems to me that this probability cannot be accurately computed without taking the environment into account.

  2. Cornelius, I have discussed details - pathways going from non-descript non-coding DNA to protein, estimates of probability, and the like - on my blog. I cannot cut and paste the links here, so I would encourage you to go to "The "Art" of ID Critcism" category there and persue the many essays that deal with these issues.

  3. Dr. Hunter,

    As I layman, what I have come to know about evolution has come from books and articles and blogs such as yours that are intended for the layman.

    It seems that at the core of most of what I have read is the mantra of "radom variation and natural selection." I have not come across any serious discussion of what an evolutionary event, such as the evolution of the eye, would actually entail.

    The description of the evolution of the eye is a classic example of what I would consider a superficial treatment of the problem. We are treated to a series of eyes of varying complexity, beginning with the eye spot and ending with the mammalian eye, and we are supposed to be convinced that the eye can evolve.

    But the eye is part of complex system of interrelated parts -- blood vessels, muscles, nerves, and skeletal structures -- whose design and manufacturing must be coordinated in space and time for everything to work.

    Has anyone ever attempted what might be called an engineering analysis of the visual system -- or any other organic system for that matter -- and described all the parts and all the steps that are required to bring about the existence of that system?

  4. Cornelius said: " wasn’t there and, frankly, I don’t know enough to calculate the probabilities. (I don’t think any else does either which would explain why evolutionists haven’t provided them)."

    I'm not sure this is true. There seems to be quite a burgeoning field of study that is trying to do this very thing. Here's one book (of many) on the topic:

  5. Cornelius said: "...I don’t know enough to calculate the probabilities."


    "We do have some relevant experimental data. A functioning protein arising from a random DNA sequence of about 400 base pairs is extremely unlikely."

    Don't these two statements contradict each other? On the one hand you admit you don't understand how to calculate the probabilities...yet only a couple of sentences later it doesn't stop you saying that such an event is "extremely unlikely". Based on what? Your own incredulity or some actual data?

  6. Dr. Hunter,

    Echoing Doublee's general point, I am also a layman who has learned much about Evolution Theory and Intelligent Design Theory through non-technical discussions. After having read many different sources I find one discussion sorely lacking, namely, how the machinery for manipulating functioning proteins arose.

    Almost all discussions begin with some statement about coding or non-coding regions of DNA, then jump to some assertion about how a non-coding region of DNA was fortuitously mutated to something functioning. But missing from the discussion is any consideration of the origin of the cellular machinery that processes the DNA during transcription, or the cellular machinery that processes mRNA at the ribosome, or the cellular machinery that processes a protein chain by bending it into a useful molecular shape.

    The situation appears to me to be similar to arguing about a certain activity at an assembly station while ignoring the assembly line and the manufacturing plant in which the entire process is housed. Discussing the intricacies of joining part A to part B misses the point when the mechanism producing the join (the assembly station on an assembly line within a manufacturing plant) is left wholly out of the picture.

    What, for instance, produced the ribosome upon which the mRNA is translated? Does DNA code for a ribosome? If so, how is it that DNA coded for a ribosome when there was no ribosome upon which to decode the code building a ribosome? How did the code (DNA) arise without the simultaneous appearance of the decoder (ribosome, etc.)?

    Darwin and those of his era looked at the cell as a blob of protoplasm, little more than a bag of milky water. In their ignorance of the incredible machinery within the cell it was easy to imagine that "things just happened" to produce life. Evolution appeared reasonable. Modern scientists are repeating the same error, only today they ignore the machine while pontificating on a nut or bolt.

  7. Excellent article Dr. Hunter. Only evolutionists could claim genetic similarity AND genetic differences are BOTH 'evidence' for their 'theory.' How many false predictions must occur before evolutionists admit there's a problem with their 'theory'???

  8. Nice article.

    Regardless of the evidence it supports the theory of evolution. Reminds me of global warming.

  9. David Medici said: "Modern scientists are repeating the same error, only today they ignore the machine while pontificating on a nut or bolt."

    I find this comment odd. Perhaps I misunderstand this, but if David is referring to a lack of research around the origins of DNA, or research related to RNA or ribosomes, he should do some Googling. Even as a layman I can see this is a very active field of research. Here's one such link referring to the type of research being conducted:

    I hardly think scientists are ignoring "the machine" - quite the contrary in fact.

  10. CWest:

    Riffing on Davids' analogy:

    The point is that debate tends to focus on whether one bolt in a living machine could have gotten there by chance, and misses the point that the living machine is comprised of numberless bolts, securing numberless bulkheads, containing numberless mechanisms, all comprising an incredibly intricate machine... which manufactures bolts.

    You may argue that the bolt could have fallen from space and punched its own perfectly-sized hole, and that the heat of re-entry fused it into place. That makes a kind of sense. You can visualize this story, illustrate it in all the little childrens' textbooks, and animate it for all the popular science programs.

    However, that argument is not remotely credible when you consider the incredible interrelatedness of all the components. How did the bolts, the bulkheads, and the mechanisms all arise simultaneously, so that they could all begin their coordinated activity of bolt manufacture?

    This is how it is with naturalistic Neo-Darwinism. Any single element could -- conceivably -- have found its place by accident -- perhaps. Taken together, however, it is all too unlikely, unless you load the deck by excluding all other alternatives.

  11. In a designed world I would expect de novo genes to arise, even by chance.

    This is why ORIGINS is so important.

    If design is not required for the ORIGIN of functional proteins and living organisms, then design certainly is not required for any subsequent de novo proteins.

    But anyways Dr Spetner's "Not By Chance" puts this is a good perspective.

    Thta being that only point mutations can be considered "random". For example gene duplications followed by an product-altering change could very well be an example of a "built-in response to environmental cues".

    And things like T-URF 13 could be a malfunction in coding caused by the stress of artificial selection.

  12. Joe:

    Could you elaborate on the following statement?

    In a designed world I would expect de novo genes to arise, even by chance.

    I just want to make sure I understand you properly.