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ID-relevant news from research arm, the Biologic Institute,

Similarity Happens:

Ann Gauger: I’ll bet you think that evolution has to do with explaining how we are all related by common descent. And I’ll bet you think that one of the chief pieces of evidence for common descent is homology, defined as similarity of form due to shared ancestry. This is pretty basic—Darwin’s theory is an argument from similarity.

However, biologists have known for some time that similarity is not always and everywhere the product of common descent. Organisms can display similarities of sequence, form, or life history that cannot be accounted for by their family tree. Homoplasy is the technical term assigned to such tree-jumping similarities, and ”convergent evolution” is the process by which they evolved. Conway Morris has written extensively on it. [1]

In the past, evolutionary biologists have dealt with homoplasy by ignoring it. Any trait identified as due to homoplasy was eliminated from their tree-drawing efforts. But now that we have access to DNA sequence data, we are finding more and more cases of homoplasy—similarity in sequence or structure that can’t possible be due to common descent—similarity that jumps across trees [2]. Phylogeneticists are urging caution, because the conflicting signals from different sequences can confuse tree-drawing algorithms [3].

It’s all the fault of those fundamentalists … oh, wait …

Applied Darwinism

Doug Axe: BIO-Complexity, an open-access peer reviewed science journal that focuses on the debate over design, enters its third volume with a paper [1] from the team at Baylor University led by Bob Marks (one of our affiliated scientists).

Like prior work from that team, the new paper by Winston Ewert, Bill Dembski and Bob Marks shows that computational implementations of the Darwinian mechanism only work in a very limited sense. In order to outperform random guessing, they have to be tailored to suit the specific problem of interest. In other words, for each problem to be tackled, someone who understands the best way to go about solving it has to construct a special version of a mutation-selection algorithm if that algorithm is going to be of any help.

That plainly contradicts the Darwinian idea that mutation and selection is a one-size-fits-all problem solver.

Wallace’s Conundrum:

Ann Gauger: The co-discoverer of the theory of evolution by natural selection, Alfred Russel Wallace, didn’t think human evolution could be explained solely in terms of Darwinian processes, at least as far as human cognition and behavior was concerned. And it cost him his scientific reputation.

Varki, Geschwind and Eichler [1] summarize it this way:

Wallace lost favour with the scientific community partly because he questioned whether natural selection alone could account for the evolution of human mind, writing: “I do not consider that all nature can be explained on the principles of which I am so ardent an advocate; and that I am now myself going to state objections, and to place limits, to the power of ‘natural selection’. How could ‘natural selection’, or survival of the fittest in the struggle for existence, at all favour the development of mental powers so entirely removed from the material necessities of savage men, and which even now, with our comparatively high civilization, are, in their farthest developments, in advance of the age, and appear to have relation rather to the future of the race than to its actual status?”

To even wonder is to be banished, unless you come up with some utterly fatuous account.

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20 Responses to ID-relevant news from research arm, the Biologic Institute,

  1. Convergent evolution must be invoked if discovery of like form and function is apparent.
    If the universe is from a creator with a program that is in effect then there would be like reply to like need.
    So biological relationship would be wrongly presumed.
    Things looking the same is a hint but not the final word on relationship.

    I do say marsupials are just placentals with pouches and looking identical to creatures elsewhere is the clue to this.
    Yet people looking like apes is only a special case because we are special and needed the best type of body for us. We had to fit in the program of nature.
    of coarse we have another source for this knowledge.

  2. Here’s something for the Biologic Institute to work on. Do a comparison of the genomes of bats and echo locating whales. Find the set of complex genes responsible for echolocation. If they are found to be identical or significantly identical, it would be proof of intelligent design. Why? Because whales and bats got separated into different branches of the tree of life eons before echolocation appeared in either species. Neither common descent, nor lateral gene transfer via viruses, nor convergence would be valid explanations. Only intelligent design in the form of code reuse would be the correct explanation.

  3. Here’s something for the Biologic Institute to work on. Do a comparison of the genomes of bats and echo locating whales.

    Well, they already work in a cave, and I hear they are putting in the whale tank …


  4. Here’s something for the Biologic Institute to work on. Do a comparison of the genomes of bats and echo locating whales. Find the set of complex genes responsible for echolocation. If they are found to be identical or significantly identical, it would be proof of intelligent design.

    Will this do?
    Liu et al (2010) Convergent sequence evolution between echolocating bats and dolphins. Current Biol 20:R53.

  5. OK, let’s try this again.

    In response to Mapou:

    Here’s something for the Biologic Institute to work on. Do a comparison of the genomes of bats and echo locating whales. Find the set of complex genes responsible for echolocation. If they are found to be identical or significantly identical, it would be proof of intelligent design.

    Will this article do? Liu et al. (2010) Convergent sequence evolution between echolocating bats and dolphins. Current Biol 20:R53.

    Apparently they sequenced the gene for a motor protein called Prestin that is expressed in the cochlea of the inner ear, and found amino acid sequence similarity between bats and dolphin in the carboxy-terminal region of the protein. The reason they attempted such a weird alignment in the first place was because they had previously found evidence of convergent evolution in this protein among unrelated bat species.

    So they took a flying leap and tried whales and dolphins. Only the dolphin worked; there the signal was strong enough to throw off the species tree alignment. Whether it’s significant enough to satisfy Mapou, I doubt, since the two proteins are not “significantly identical.”

    Or was this just a joke? If so, it’s not nice to laugh at Mother Nature. ;-)

  6. This is all extremely interesting!

    With respect to constraints and their influence on search efficiency, two things must be pointed out:

    1. research indicates that at least some available local search methods suffer from constraints rather than benefit (for reference see papers on contemporary local search SAT solvers).

    2. To judge if the problem is easy or hard to solve, one must establish its constrainedness. The intuition is: too many constraints render the problem overconstrained and easy; few or no constraints at all make the problem easily solvable. The really hard bit is the phase transition in between the two extremes. So to establish whether the problem is ‘easy’ or ‘hard’, one must know where it is in relation to the phase transition. Of course, easiness and hardness are relative. I suspect in practice for problems like this one in biology, some ‘easy’ ones may take a huge amount of time.

  7. Sorry for a misplaced comment. Comment #6 was about Steiner trees etc. on the biologic institute webpage.

  8. Here’s something for the Biologic Institute to work on. Do a comparison of the genomes of bats and echo locating whales. Find the set of complex genes responsible for echolocation. If they are found to be identical or significantly identical, it would be proof of intelligent design.

    No it wouldn’t; at least not in any sense more than ID is already proven. It might be one more line of evidence in the long list of evidence, but it would not be viewed as knock-down proof to anyone who is skeptical. Also, it wouldn’t be proof against evolution. Evolution does not have any specific details about what is and what isn’t possible. Anything goes. We have already seen this on numerous occasions. Finding something totally unexpected and against previous evolutionary thought will just be ascribed to “convergent evolution,” or some hypothetical ancestral relationship, or some horizontal transfer of information, or some new epicycle. We have to keep in mind that the evolutionary “explanation” for complex features is: stuff happens.

    The fact of design in life is already so well established by the evidence as to be obvious to anyone who is willing to engage in a moment’s reflection. ID stand or falls on the existence of complex specified information, of which there is already a plethora of examples. Finding one more isn’t going to convince anyone who is already inclined to rejecting the idea out of hand due to a priori philosophical commitments.

  9. … ‘philosophical’? or ‘religious’ commitments?

    The original meaning of ‘science’, adverting to knowledge, in a wiser age, it used to be said that theology was the Queen of the Sciences.

    Today, at some deep, primal level of their minds and hearts, the version of science of the ‘naturalists’ seems to have become the Queen of Theology.

    The slur on theology of Rober Heinlein, to the effect that it is ‘searching in a dark cellar at midnight for a black cat that isn’t there’, doesn’t begin to cover the wilful repudiation of knowledge by the ‘naturalist’, in favour of emotionally-satisfying, personal flights of fancy.

    It reminds me a bit of the contrast between Pontius Pilate on the Roman Governor’s Judgment seat, who at least expressed a glimmer of interest in the truth, however fleeting, and the avowal of a British civil-service mandarin, during the Spycatcher trial in Australia, that he had been ‘economical with the truth.’

  10. Eugene S,

    Did you ever succeed in posting your Steiner tree comment? To do so, you need to use our Facebook page at

    https://www.facebook.com/pages/Biologic-Institute/182588468516825,
    and then “like us”. This will allow you to comment.

    Or you can access our web page through tumbler, and add a comment there.
    http://www.tumblr.com/blog/bi010gic

  11. Eugene S,

    Did you ever succeed in posting your Steiner tree comment? To do so, you need to use our Facebook page at

    https://www.facebook.com/pages/Biologic-Institute/182588468516825,
    and then “like us”. This will allow you to comment.

    Or you can access our web page through tumblr, and add a comment there.
    http://www.tumblr.com/blog/bi010gic

  12. 12
    material.infantacy

    gauger, If I were to suggest an area of design research, it might be something like this.

    How might one go about transforming a T3SS into a flagellar motor (for instance) from a design point of view? How would an intelligent designer apply incremental changes to a system deployed in the wild, in order to transform one into the other, without reducing fitness? Or better even, but drastically more difficult, even for intelligence. How might a designer deploy a system that could bootstrap its own transformation from one state to another, after deployment in the wild?

    Explanations of how “evolution” might have done it are appearing more meaningless all the time, since they presuppose vast amounts of specified, complex functionality. If we know that the scale of the problem is huge from a design point of view, because we have some idea of what would be required (even if somewhat speculative) then it follows that random processes would have exponentially less efficacy to accomplish the same.

    It may not be possible to do something like this given our current understanding of biochemistry. However a design paradigm calls for a designer’s solutions, even if theoretical. If ID can build models that show what is required to incrementally transform systems (or even proteins) between extant states that are putatively related by “evolution” then perhaps ID would have the advantage of being able to reframe the debate.

    I realize this may be pie in the sky thinking, but I’m attempting to think in a less reflexive way to the outlandish claims of Darwinian evo, and focus on what we know: systems configured for a specific purpose require design input, and transforming one system into a another, especially in an incremental and automated way, is monumentally difficult. Just how difficult something like this would be from a design paradigm is perhaps a useful tool in understanding why Darwinian mechanisms are just not capable of doing so, in any but the most hopeful and vague of imaginings.

  13. material.infantacy,
    You are assuming that incremental change to new function is within reach.

    We have already demonstrated that for proteins, conversion to new chemistry may be beyond reach of incremental transitions. That is in my paper with Doug Axe in BIO-Complexity last year.

    On the flagellum, there is good reason to think that the TTSS is derived from the flagellum, not the other way around. It is always easier to change a pattern by deleting elements than building new ones. We will continue to test the limits of gene duplication and divergence, which the current way evolutionary biologists suggest flagellar evolution happened.

    The problem is the origin of new traits, or innovations. We can find examples where traits are lost, or suddenly appear, but no examples where traits appear gradually. Take the evolution of the wing. I know there are debates in the literature over how or from what structure insects evolved wings. The truth is wings are either there or they are not.

    An example from ants: there are winged and wingless species. The winged species have the genetic cascade that specifies wing-building. The wingless castes have the same cascade but with one or a few regulatory elements missing, hence no wings. No hint of a partial wing or partial pathway toward having wings.

    What I am saying is that the incremental approach is an evolutionary hold-over. New is new, even if some of the parts have been retooled for a new function.

  14. 14
    material.infantacy

    guager, thanks for the reply. I’ll take a moment here to clarify my thoughts. Please don’t feel obligated to respond, but please feel free. The T3SS to Flagellar motor was perhaps a bad example. I’m aware that there is evidence that the pathway is reversed, but as you suggested, it’s not as impressive a feat to knock features out as it is to design and build them.

    Of course we have two options to consider when evaluating the rise of life and novelty of features. Either it happens by necessity and has a purely materialistic cause, or the intervention of a designing intelligence is required.

    Reasonably I choose the latter. However then there are at least three possible scenarios: 1) species were created according to kind, and observed changes in species over time is the result of preprogrammed capacity for intra-species variation, along with the loss of genetic information; 2) some form of universal common descent with front loading is the case, and the information required to bootstrap one species from another was preloaded into the genome, and likely also in one or more other yet undiscovered areas; 3) some form of universal common descent is the case, and the designer saw fit to intervene at discrete points in time, in order to affect changes by the input novel information. There are other scenarios one could imagine, but that essentially covers the basis I believe.

    If #2 or #3 are the case, then some transition method or another must be possible. Any process that begins with a single-celled organism which branches multiple times, to end with a large diverse population of living creatures, has some incremental path or another. Certainly these are not increments which are amenable to neo-Darwinian processes, but they are increments just the same, in the case of #2 and #3. I agree that for many cases it’s just not possible to affect any transition from one state to another. In these cases, we can infer that either the system was added discretely at a point in history, or the program for its construction and the timing of its appearance (or the trigger response thereof) was already present. (If life is designed to evolve in that way, there may be sequences still awaiting activation.)

    The evidence must exist to determine how a designer plans the construction of an ecosystem’s radically diverse populations, as we can determine how designers construct other complex systems; and I can’t seem rule out that whatever process was used to unfold diversity, if such is indeed the case, it’s amenable to discovery. But maybe it’s not as interesting or as informative an avenue as I imagine.

    Thanks again, and I’ll go find the paper you mentioned. (If I am off base here, please feel free to straighten me out!)

    Best,
    m.i.

  15. 15
    material.infantacy

    Forgive me: gauger not guager. Apologies!

  16. M.I.,
    Let me return to the subject of this post, which was ID relevant news content from our Biologic blogs. The first blog quoted above is called “Similarity happens!”, and can be found in full either at our website, or at ENV.

    Why is this relevant? All your proposals assume common descent. Until recently I also accepted common descent as the explanation for the patterns of similarity we see in life. Then I ran across a pattern that in my mind *couldn’t* be explained by common descent. I began to investigate other cases of tree-jumping similarity.

    The blog is an introduction to the problem. I have posted a few other examples on our Facebook page.

    What is the one thing intelligent designers can do that evolution can’t? ID can inject new pattern de novo, or borrow pattern from elsewhere and retool it. So maybe we need to look for discontinuities and incongruencies where new pattern has been injected. Look for tree-jumping or uniqueness or innovation. Break the mold!

  17. 17
    material.infantacy

    gauger, my #1 was essentially direct special creation (no UCD in that one) which is the scenario I favor. I definitely don’t accept UCD by default!

    I did read the article you mentioned, but I’ll read it again with our conversation in mind.

    Thanks for the exchange!

  18. 18
    material.infantacy

    This looks like a typo in the Similarity Happens article:

    “it is not confined to just bacteria where horizontal gene transfer if common”

  19. Thanks for the correction!

  20. Ann,

    Many Thanks for the suggestion. The Steiner tree paper is a really good one I think.

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