Wednesday, January 1, 2014

Gene Regulation Not Enough in Human Evolution

Getting Even More Circuitous

One of the favorite proof texts for evolution are the genome comparisons between species, in general, and the human-chimpanzee comparison in particular. As the Smithsonian explains:

No matter how the calculation is done, the big point still holds: humans, chimpanzees, and bonobos are more closely related to one another than either is to gorillas or any other primate. From the perspective of this powerful test of biological kinship, humans are not only related to the great apes – we are one. The DNA evidence leaves us with one of the greatest surprises in biology: the wall between human, on the one hand, and ape or animal, on the other, has been breached. The human evolutionary tree is embedded within the great apes.

The evolutionist’s appeal to this genomic evidence is problematic for several reasons. Of course a successful test of a prediction does not mean evolution is true. The claim above that the wall “has been breached” is silly and amounts to the fallacy of affirming the consequent. What is worse, this test has been a failure, not a success, for evolution. There are the identical or near-identical DNA sequences in distant species and the massive genome differences in highly similar species. Both these findings falsified predictions and were shocking to evolutionists.

Beyond these obvious problems which evolutionists, such as at the Smithsonian, ignore, there is the problem that the chimp-human DNA differences do not seem nearly enough to account for the differences between the species. Can a few DNA swaps here and there make a human from an ancient primate? It does not seem likely, so behind this triumphant claim of evolutionists lies a failure to even understand how such evolution could have occurred.

That raises an even more profound problem for evolution. For one idea evolutionists have for how humans may have evolved from an earlier primate is by gene expression. That is, perhaps an important mechanism in evolving humans was not so much modifying the genes, but modifying how much the genes are used, to create proteins.

But this involves a more complicated evolutionary pathway. Instead of DNA mutations that simply modifying genes which create proteins that do a few tasks in the cell, we need DNA mutations that modify how genes are regulated. Such regulation is part of an immense and incredibly complex network, particularly in humans, and it is not at all clear how chance mutations could modify and enhance it.

Recently this story has become even more difficult for evolution as a new study shows that the path from gene expression to protein expression is not as straightforward as was thought. Simply put, the two are not necessarily paired as increasing one, for example, does not necessarily increase the other. As the paper explains:

We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.

Those genes with significant expression differences between the human and chimp were thought to be important drivers of evolution. Did not the expression level difference between the species occur after they diverged from a common ancestor and was that not part of what created humans (even though we have no idea how)? Now evolutionists are not certain. As one evolutionist explained:

Some of these patterns of mRNA regulation have previously been thought of as evidence of natural selection for important genes in humans, but this can no longer be assumed.

Not only can that no longer be assumed, but the evolutionary mechanisms just became even more complicated. First evolutionists thought humans evolved by mutating genes which create proteins that do a few tasks in the cell. That didn’t work so they added DNA mutations that modify how genes are regulated. Now that is not working so they must add DNA mutations that modify how the expression product (the mRNA transcript) is regulated. So now the evolutionary pathway is even more complicated.

14 comments:

  1. A few notes on the extreme difficulty developmental Gene Regulatory Networks place on Darwinian presuppositions:
    http://www.uncommondescent.com/intelligent-design/gene-regulation-not-enough-in-human-evolution/#comment-485636

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  2. The number of a-plausible hypotheses required to imply the posited lineages (including the posited, undiscovered intermediates) in the posited time-frames was already in the millions. And yet all those a-plausible hypotheses don't imply any novel observations any more successfully than the positing of various numbers of separate ancestors. Thankfully we've spent MILLIONS upon MILLIONS of dollars for this impressive result!! And even greater benefits to the subsidizers of this research seem just ahead!!!!

    Happy New Year!! :)

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  3. Wow, what a torrent of posts. The readers are truly blessed. I hope your not using your Christmas holidays to create these posts.

    Merry Christmas, and a Happy New Year

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  4. CH: The evolutionist’s appeal to this genomic evidence is problematic for several reasons.

    Does CH present genuine criticism? Let’s look in detail.

    CH: Of course a successful test of a prediction does not mean evolution is true.

    Evolution might be false? But that’s a bad criticism because it’s equally applicable to any theory. As such, it can’t even be used in a critical way.

    CH: The claim above that the wall “has been breached” is silly and amounts to the fallacy of affirming the consequent.

    Does it? Do you have a better explanation for this same DNA evidence? Here’s a hint: “Some designer just must have wanted the evidence to look that way” explains nothing. What about an explanation for the knowledge present in those genes?

    CH: There are the identical or near-identical DNA sequences in distant species and the massive genome differences in highly similar species. Both these findings falsified predictions and were shocking to evolutionists.

    Successful tests of predictions do not mean a theory is true, but absolutely any prediction found to be false indicates the underlying explanation is false? Really? If I predicted a car was used to travel across the US but found it was a mini-van instead, does that mean a theory that a four wheeled, gasoline powered vehicle was found false? Again, if we start out with the idea that theories are conjectured explanations about how the world works, we expect them to be incomplete and contain errors to some degree.

    Specifically, you’re conflating being surprised that a specific prediction was found in error with the epistemological idea that finding theories incomplete and containing errors is surprising. IOW, It’s only epistemologically surprising when you hold a specific theory of the growth of human knowledge. As such, you’re argument is parochial.

    Why don’t you start out by explain how that knowledge was created, then point out how the underlying theory behind evolution does not fit that explanation. Please be specific.

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    1. Scott: Do you have a better explanation for this same DNA evidence? Here’s a hint: “Some designer just must have wanted the evidence to look that way” explains nothing.

      J: Unless design is an inherently meaningless word, you're just dead wrong. It explains why it "looks like it does."

      Scott: Why don’t you start out by explain how that knowledge was created, then point out how the underlying theory behind evolution does not fit that explanation. Please be specific.

      J: Instead, why don't you define "knowledge" using conventional language. Please be specific.

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    2. “Some designer just must have wanted the evidence to look that way” explains nothing.

      You'll have to stop using this "evolution-of-the-gaps" fallacy. "Some designer wanted it that way" is a perfectly valid explanation for cars, and countering that cars aren't biological is only valid until we manage to purposefully make biological things.

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    3. Marcel,
      Some designer wanted it that way" is a perfectly valid explanation for cars

      We generally know why cars are designed and how they are manufactured, can the same be said for the " designer" of biological things? If so how?

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    4. Velik

      When I took time to study biology of the cell (up to a point-biology is boring for me) , I was surprised how great are similarities between cell processes and our human size automated process systems. Basic operating mode of the cell is homeostasis which is achieved by even more basic process of energy control which in turn is accomplished by clever arrangements of molecular components. We have two choices: either God or aliens did it.

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    5. So, as I said, this is only valid until we CAN say something about the designer of biological things. Evolution-of-the-gaps.

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    6. Eugen,
      was surprised how great are similarities between cell processes and our human size automated process systems.

      I get that, that is not exactly my question. On what basis does one assume life is a/ the goal of the intelligent designer without any knowledge of the designer? Life could just be a side effect just as easily, especially if life turns out to be plentiful. The designer could be designing on the cosmic scales.

      We know the car is the goal, from experience ,how do we know life is goal of the designer ?

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    7. Good questions you have are out of my "department". I don't know answers about goals or purposes etc... Life is fantastically organized chemical process carried out by nano machines. This much we can figure out.

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  5. Hume's Problem of Induction notwithstanding, I feel confident we can look forward to another Happy New Year of research published by evolutionary biologists, some of which will provide the ammunition for Dr Hunter's continuing battle against the iniquitous theory within whose framework those investigations are conducted. I suspect little if anything other than the familiar army of strawmen and epistemological nitpickings will be forthcoming from the proponents of Intelligent Design, although it would be nice as always to be proved wrong.

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    1. What was Hume's problem of induction, Ian? How did it not depend on assuming what he was criticizing? How can one find a problem with induction when it is inductive criteria that we use to distinguish between actual and merely apparent memories?

      Science is nothing that can be demarcated if it is not inductive. You naive falsificationists don't get it. You think all hypotheses can be tested. Test these without assuming what you need to demonstrate:

      1) Some apparent memories are actual memories.

      2) Some apparent sense perceptions aren't illusions.

      There's no getting around foundationalism. And there's no explanation of the truthfulness of foundational beliefs other than benevolent/competent design.

      Ian: it would be nice as always to be proved wrong.

      J: You won't be proved wrong. But you can just go away if you have free-will. But if you do have free-will, then you can't deny it as a logically possible mode of explanation that we should apply inductive criteria to.

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  6. Evos can't account for genetic regulatory networks

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