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The End of Natural Selection

Playing off the title of Dr. Dembski’s new book, I’m going to cite three articles that are summarized at PhysOrg.com just this past week. I don’t have access to any of them, but let’s just take a look at what these summaries report. I think it’s quite interesting.

First, there is this article, DNA study sheds new light on horse evolution, that informs us that ancient species of zebras and horses are actually much more related to the modern day versions than previously thought. Here’s what they say:

The study used bones from caves to identify new horse species in Eurasia and South America, and reveal that the Cape zebra, an extinct giant species from South Africa, were simply large variants of the modern Plains zebra. The Cape zebra weighed up to 400 kilograms and stood up to 150 centimetres at the shoulder blades.

“The Plains zebra group once included the famous extinct quagga, so our results confirm that this group was highly variable in both coat colour and size.”

while concluding that:

“Overall, the new genetic results suggest that we have under-estimated how much a single species can vary over time and space, and mistakenly assumed more diversity among extinct species of megafauna,” Professor Cooper says.

This now means that the already tiny portion of “intermediate forms” that RM + NS produces in reduced in size. And perhaps greatly. This weakens what Darwin would call the “principle of divergence” and weakens the notion of gradualism that is implicit in his theory.

Next, there is this article: Introns: A mystery renewed.

Here we read:

“Remarkably, we have found many cases of parallel intron gains at essentially the same sites in independent genotypes,” Lynch said. “This strongly argues against the common assumption that when two species share introns at the same site, it is always due to inheritance from a common ancestor.”

which now calls into question prior notions of “proof” of common descent, and, I would think, requires a new look at how transposons operate.


Still further is this :

“Our molecular analyses have enabled us to reject a number of hypotheses for the mechanism of intron origins, while clearly indicating an entirely unexpected pathway — emergence as accidents arising during the repair of double-strand breaks,” Lynch said.

Over the years I have maintained that the “randomness” we supposedly see in species could easily be explained by a directed process utilizing random operators. My motivation for this is that from an engineering standpoint, if you design a creature that will have to adapt to changing envirnoments, then some method of adaptation needs to be built into the architecture. And now, here is evidence that supports the ID approach, and which, again–for the umpteenth time–is a “surprise” for Darwinists. As well, this exposes a weakness in the random mutation portion of RM + NS.

Now the seeming “coup de grace”: it is an article reviewed at PhysOrg with the heading Evolution may take giant leaps. Here is a summary of their experiment:

The new research, carried out by Mark Pagel and colleagues at the University of Reading, in England, studied 101 groups of plant and animal species and analyzed the lengths of branches in the evolutionary trees of thousands of species within these groups. The lengths of the branches are a measure of the time elapsed between two species branching off.

The researchers then compared four models of speciation to determine which best accounted for the rate of speciation actually found. The Red Queen hypothesis, of species arising as a result of an accumulation of small changes, fitted only eight percent of the evolutionary trees. A model in which species arise from single rare events fitted eighty percent of the trees.

Then, we read–which gives rise to this post’s heading:

The work suggests that natural selection may not be the cause of speciation, which Pagel said “really goes against the grain” for scientists who have a Darwinian view of evolution. The model that provided the best fit for the data is surprisingly incompatible with the idea that speciation is a result of many small small events, Pagel said.

Is it really so big a surprise that gradualism is unsustainable? We’ve been trying to tell them this for a long time now. As I say, the end is near: random is no longer random, but directed; and NS is not gradual. The more genomes are investigated, the more Darwinism will end up being part of the “dustheap of history.” Just think, this is just a week’s worth of experiments. What will next year bring?

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22 Responses to The End of Natural Selection

  1. This article pleases me greatly. I have oft (and long) contended that ‘natural selection’ is a meaningless phrase and I am delighted to see that it is finally being caught out.

  2. PAV, nice article.

    Isn’t this exactly the shift in thinking that James Shapiro has been talking about for years?

    I realize that Shapiro “tows” the party line by describing his views under the guise of Natural Genetic Engineering…but still, it is clear that the mechanisms that have been taken for granted (er, enforced under the threat of professional dismemberment and of instant grant removal) are woefully incapable of producing the results seen in nature.

    A 21st Century View of Evolution (2005)

    Revisiting the Central Dogma (2009)

  3. Oh, lest anyone misunderstand.

    I am certainly not beyond being tribal. I still don’t forgive Shapiro for not backing Behe when he had the chance. :)

  4. We are near the end of the year of worship for one of the greatest frauds in history and probably the greatest fraud in science ever. That is Charles Darwin. With all the hoopla this year with special events, nothing of Darwin’s theory of evolution remains. Though they still bow from the waist to their idol in the evolutionary biology departments of the world. Worshiping false idols ring a bell!

    Darwin’s ideas were based on several concepts, all false.

    gradualism – yes gradualism works but it never develops anything of consequence. It is all trivial stuff evolutionary wise that results. – Strike One

    natural selection – yes natural selection works but it cannot develop anything new and at best all it can do is reshuffle the genes a little. As said before a side show in the game of life. – Strike Two.

    Malthusian competition, the concept that supposedly gave Darwin his big insight does not lead to anything new as we have millions of ecologies all around the world with organisms in each vying for existence and nothing happens. – Strike Three

    Now ordinarily this would be enough to retire any scientist from consideration but here we are dealing with the mighty Darwin.

    Species – there is no good definition of species and as we have gone over in recent discussions most of so called species are just different sub populations. And there is no evidence that the speciation process leads to anything except minor variants of the same population. Darwin’s title was about the origin of species, or the origin of something that hardly ever happened. It takes over 20 million years to get a slightly different bird species. Whoopee do. – Strike Four

    We are already giving Darwin some extra swings to see if he can hit anything but the final strike is

    Common Descent – there is no evidence that there was any naturalistic continuous descent with modification from prokaryotes to man. It was all a fiction in Darwin’s mind and still is in his worshippers. Even if one could work back naturally from today (we doubt that is possible) , there would be a dead end at the Cambrian. Strike Five

    So even with some extra strikes, the mighty Darwin doesn’t have any hits. He is 0 for 5 as he whiffs at everything thrown at him.

    Does any of this remind you of any science we see going on today? All full of hope and promise but it too may be a big Whiff.

  5. Will everyone reading this pass it along to pass along -
    insight and understanding of “science” might actually catch on and finally those holding the microphone could get booed off the stage.

  6. Upright BiPed:

    Thanks for the Shapiro link. I took a quick look and then printed it out. Will be reading it.

    Meanwhile, I note that Shapiro writes in the conclusion:

    “Significant evolutionary changes can result from altering
    the repetitive elements formatting genome system architecture, not just from altering protein and RNA coding sequences.”

    This made me think of something they wrote in the linked article on introns: they say that one of the introns studied was 500,000 nucleotides long.

  7. Interesting articles PaV, thanks. Do you have any ideas about how introns might be functional? I don’t know specifics but I’ve heard that sometimes the RNA transcript can get spliced differently to give rise to different proteins, meaning that introns are not always introns.

    Also, jerry your post reminds me of when I went to China to teach English. My kids asked me what I thought about Mao, who is their George Washington. I can’t remember what I said but you do have to be careful what you say about Mao over there. He is almost a god. Anyway, they told me that they thought Mao was a great leader who struggled for gender equality. Apparently that was the only thing he did worth talking about, since it was probably the only thing that can be positively spun.

  8. PaV:

    This now means that the already tiny portion of “intermediate forms” that RM + NS produces in reduced in size.

    Is that really a problem? IANAB, but it seems to me that greater than expected variation and geographic dispersion within species predicts a reduced number of intermediate species.

    Start with a species characterized by wide variation dispersed over wide geographic distances, as described in these findings. A subpopulation becomes a founder population for a new species. In some instances such subpopulations will be composed primarily of “outlier” variants that are quite morphologically different from the modal form for that species.

    The later observed degree of divergence between these now distinct species would reflect in large measure that original within-species variation, and not, therefore, require the postulation of numerous species of “intermediate form.”

    What do you think?

    Upright Biped:

    One “toes the line.”

  9. Voice Coil [8]:

    Is that really a problem? IANAB, but it seems to me that greater than expected variation and geographic dispersion within species predicts a reduced number of intermediate species.

    The reduction that I’m referring to is that of total number of species. This means that, yes, there are fewer number of intermediate species since those that were considered separte species having separte lineages will not be clustered along a single lineage.

    But this isn’t the picture Darwin gives us. We should find gobs of extinct intermediate forms, and we don’t. Now, species that were previously considered ‘intermediate’ will now be seen as kinds of varieties of a single genomic line, and this adds to the problem of having any proof at all of gradualism. Darwin thought of varieties as species in the making. This discovery tells us that what we thought were species in their own right should now be thought of as varieties. This is not good news for NS and Darwinism no matter how you slice it.

  10. PaV:

    The reduction that I’m referring to is that of total number of species.

    The finding concerned a reduction in the number of recent equid species. The researchers speculate regarding the implications of that finding for other incompletely understood radiations, such as in genus Homo.

    Now, species that were previously considered ‘intermediate’ will now be seen as kinds of varieties of a single genomic line…

    In the instance of some recent equid species.

    This discovery tells us that what we thought were species in their own right should now be thought of as varieties.

    In the instance of some recent equid species.

    Declaring this true for species generally isn’t remotely warranted by this single interesting finding.

  11. It gets worse. I just looked at the abstract of the phylogeny study in Nature. Here’s part of that abstract:

    We find that the hypotheses that speciation follows the accumulation of many small events that act either multiplicatively or additively found support in 8% and none of the trees, respectively. A further 8% of trees hinted that the probability of speciation changes according to the amount of divergence from the ancestral species, and 6% suggested speciation rates vary among taxa. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation. This model predicts a constant rate of speciation, and provides a new interpretation of the Red Queen: the metaphor of species losing a race against a deteriorating environment is replaced by a view linking speciation to rare stochastic events that cause reproductive isolation. Attempts to understand species-radiations or why some groups have more or fewer species should look to the size of the catalogue of potential causes of speciation shared by a group of closely related organisms rather than to how those causes combine.

    This from the magazine of record when it comes to Darwin’s theory.

  12. Voice Coil [9],

    First, the horse lineage is touted as one of the ‘best documented’ cases of evidence for “intermediate forms”. So, that this has to do with horses is really significant, no matter you much you want to downplay it.

    Second, why on earth would you—supposedly a scientific thinker—make the presumption that what is true of the horse and zebra lineage is not true of others? What would your reasons be for justifying that this finding cannot be generalized? (Other than it’s an “inconvenient truth”?)

  13. By comparison, 78% of the trees fit the simplest model in which new species emerge from single events, each rare but individually sufficient to cause speciation.

    Man this looks like the hopeful monster theory.

  14. PaV:

    why on earth would you—supposedly a scientific thinker—make the presumption that what is true of the horse and zebra lineage is not true of others? What would your reasons be for justifying that this finding cannot be generalized? (Other than it’s an “inconvenient truth”?)

    I said nothing about presuming that what is true of equids is not true of other clades, or cannot be generalized. I said that declaring that this finding is true for species generally isn’t remotely warranted on the basis a single study. Much more work needs to be done to determine how generalizable these findings are.

    Therefore what IS warranted is further empirical work of this kind in other clades.

  15. Voice Coil,

    Fair enough.

  16. PaV:

    It is unclear to me whether your interpretation of the Orlando study (“This now means that the already tiny portion of “intermediate forms” that RM + NS produces in reduced in size”) is intended to support doubt of Darwin’s central insight: that organisms are related by common descent. Certainly that is the context within which the topic most often arises. If so, you must ignore the Pagel study.

    The Pagel study, with its analysis of “the lengths of branches in the evolutionary trees of thousands of species within these groups” was conducted within the framework of common decent, which incorporates the claim that each pair of species has a LCA. Their methods are intelligible only within that framework. If you reject common descent, then you must ignore the Pagel study entirely rather than interpret its results as challgening to Darwinism.

    Conversely, if you accept Pagel’s results, then you perforce accept the reality of common descent, and accept that all pairs of species have LCAs, regardless of the relative paucity of “intermediate forms.” Therefore you must accept that Orlando’s results have no bearing upon the reality of common descent.

    The issues of gradualism and pan-adaptionism have otherwise been debated for decades within the context of evolutionary theory (see Gould’s The Structure of Evolutionary Theory for a good “summary.”)

  17. PaV: Now the seeming “coup de grace”: it is an article reviewed at PhysOrg with the heading Evolution may take giant leaps.

    It’s not “giant leaps” as normally construed. It’s speciation. In many cases, it takes an expert to identify the differences between closely related species. Anyone familar with how flowering plants or beetles speciate will be very comfortable with this finding. Small changes in sex organs can lead to reproductive isolation.

    As Voice Coil points out above, it supports and is supported by Common Descent.

  18. tragic mishap [7]

    I believe introns actually produce RNA transcripts and are implicated in gene regulation. But the extremely large ones, especially the repeating ones, are very hard to understand. It’s possible that the long repeats play some structural/protective role. But this is pure speculation.

    Zachriel [17]

    No. It’s “giant leaps” as in “giant leaps”. You’re confusing adaptive radiations with singular events that produce new lineages. They’re just not the same.

  19. From the shocking title onward, Fodor and Piattelli-Palmarini have set the cat among Darwin’s pigeons. In arguing why the operation of natural selection says nothing about the causal mechanisms underlying the evolution of coextensive traits in an organism, they take us to the conceptual fault line at the heart of Darwin’s theory. My prediction is that Fodor and Piattelli-Palmarini’s book will raise hackles galore wherever the theory of natural selection is all too glibly misused, not only in studies of the ontogeny and phylogeny of biology, but also in those great overlapping disciplines of philosophy, psychology, linguistics, and behavior—in short, human nature. This book will set the agenda for years to come. It cannot be ignored if the study of evolution is to be honest with itself.” —Gabriel Dover, Professor of Evolutionary Genetics, Universities of Leicester and Cambridge, and author of Dear Mr. Darwin: Letters on the Evolution of Life and Human Nature

    http://www.amazon.com/What-Dar.....038;sr=1-5

  20. Zachriel: It’s not “giant leaps” as normally construed. It’s speciation. In many cases, it takes an expert to identify the differences between closely related species.

    PaV: It’s “giant leaps” as in “giant leaps”.

    I assume that’s meant to clarify.

    The study concerns speciation, not large changes in adaptive structures. My comment had nothing to do with adaptive radiations.

  21. I believe introns actually produce RNA transcripts and are implicated in gene regulation

    Introns are part of the primary RNA transcript. They also may play a role in nonsense-mediated-decay (NMD), which is a mechanism by which certain aberrant mRNA’s are eliminated before being translated into protein. Mike Lynch thinks the early proliferation of introns may have been a coevolutionary byproduct of the development of an efficient NMD mechanism. See Lynch’s book, The Origins of Genomoic Architecture, pp 265-270.

  22. No. It’s “giant leaps” as in “giant leaps”.

    It is worth noting that the phrase “giant leaps” appears to have originated with the Physorg editors. It isn’t present in the abstract, nor does the abstract describe anything resembling “giant leaps.” (I don’t have access to the article itself, however).

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