Intelligent Design

“Turbulent times in the world of phylogeny”

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Oh, now you’re in for it, Laura — someone is going to put you on the Naughty Female Science Journalists list. Right next to Catherine Shaffer of Wired.

Readers will have to pop for a New Scientist subscription to see the whole of Laura Spinney’s piece about new puzzles in reconstructing the Tree of Life, from the June 13 issue, but here’s the bit of science crack they’re giving away to hook you:

IF YOU want to know how all living things are related, don’t bother looking in any textbook that’s more than a few years old. Chances are that the tree of life you find there will be wrong. Since they began delving into DNA, biologists have been finding that organisms with features that look alike are often not as closely related as they had thought. These are turbulent times in the world of phylogeny, yet there has been one rule that evolutionary biologists felt they could cling to: the amount of complexity in the living world has always been on the increase. Now even that is in doubt.

While nobody disagrees that there has been a general trend towards complexity – humans are indisputably more complicated than amoebas – recent findings suggest that some of our very early ancestors were far more sophisticated than we have given them credit for. If so, then much of that precocious complexity has been lost by subsequent generations as they evolved into new species. “The whole concept of a gradualist tree, with one thing branching off after another and the last to branch off, the vertebrates, being the most complex, is wrong,” says Detlev Arendt, an evolutionary and developmental biologist at the European Molecular Biology Laboratory in Heidelberg, Germany.

The idea of loss in evolution is not new. We know that snakes lost their legs, as did whales, and that our own ancestors lost body hair. However, the latest evidence suggests that the extent of loss might have been seriously underestimated. Some evolutionary biologists now suggest that loss – at every level, from genes and types of cells to whole anatomical features and life stages – is the key to understanding evolution and the relatedness of living things. Proponents of this idea argue that classical phylogeny has been built on rotten foundations, and tinkering with it will not put it right. Instead, they say, we need to rethink the process of evolution itself.

It is not hard to see how the mistake might have happened

21 Replies to ““Turbulent times in the world of phylogeny”

  1. 1

    Reason vs. faith. I hear it all the time from ID-opponents. And it makes me smile.

    They are hanging on by sheer force of will and a faith commitment.

  2. 2
    scordova says:

    However, the latest evidence suggests that the extent of loss might have been seriously underestimated. Some evolutionary biologists now suggest that loss – at every level, from genes and types of cells to whole anatomical features and life stages – is the key to understanding evolution and the relatedness of living things. Proponents of this idea argue that classical phylogeny has been built on rotten foundations, and tinkering with it will not put it right. Instead, they say, we need to rethink the process of evolution itself.

    And this paradigm change was forseen by world class Cornell geneticist and ID proponent, John Sanford in his book: Genetic Entropy

    Yet another triumph for an ID prediction!

  3. 3
    Jehu says:

    It is consistent with Sanford but not for those that see evolution as a telic process moving towards greater complexity.

  4. 4
    Jehu says:

    I think even more significant for phylogeny is the failure of organisms to resolve into a single phylogenetic tree at the molecular level. Rather they form multiple competing alternative trees.

  5. 5
    bFast says:

    Jehu, thanks for the post. It was most enlightening.

  6. 6
    Borne says:

    Don’t fear, the Darwinists will hang on to their faith for dear life until the last impossible moment.

    And then, they will say, “I don’t believe it. Prove it to me and I still won’t believe it.” (Doug Adams)

    …then slowly drift off into oblivion with the greatest scientific blunder and embarrassment of all history.

  7. 7
    Jehu says:

    bFast,

    Glad you liked it and I do think that it is a huge problem for common descent. Here is a key quote,

    “ Many recent studies have reported support for many alternative conflicting phylogenies … in all studies, a large fraction of characters—genes, PICs or RGCs—disagree with the optimal phylogeny, indicating the existence of serious conflict in the DNA record … the conflict among these and other studies … are representative of those encountered at a variety of time depths across the TOL. What is exceptional about these clades is that they have received the greatest data collection efforts and analysis. The persistent resolution of problems in the face of (a) increasing amounts and different kinds of data and (b) state-of-the-art analytical methodology suggest that other less–well analyzed, absolutely or relatively short stems in the TOL may pose similar challenges and be refractory to resolution with comparable datasets.”

    In other words, the more data they accumulate the more contradictory the phylogenetic tree gets. The sublte rhetoric at the end of the article indicates a quite “throwing in the towell” on ever getting a phylogenetic tree. BTW, notice that the article is co-written by Sean B. Carroll and was peer reviewed by Doolittle, among others.

  8. 8
    scordova says:

    In other words, the more data they accumulate the more contradictory the phylogenetic tree gets.

    That may be actually by design. The ID theory known as Biotic Message argues life is designed to resist a phylogenetic interpretation. Biotic Message, like Genetic Entropy are strong variants of ID theory.

    This is potentially another successful ID prediction! Congratulations John Sanford and Walter ReMine!

  9. 9
    magnan says:

    Jehu: “I think even more significant for phylogeny is the failure of organisms to resolve into a single phylogenetic tree at the molecular level. Rather they form multiple competing alternative trees.” … “….I do think that it is a huge problem for common descent.”

    The problem with denying common descent is the considerable bulk of circumstantial evidence in favor of it. This is why Behe is convinced of common descent. Of course circumstantial evidence isn’t proof. It is just that a new comprehensive theory has to both account for the new data and with the mass of apparent evidence that organisms have indeed developed by some process of descent with (major, apparently telic) modification at least at the class and family level of phylogeny.

    It seems to me a viable or at least arguable hypothesis would be where major injections of new genetic information occurred at these points, followed by a certain amount of diversification and evolutionary working out of the new designs. This latter process would not add new information, and ultimately would be self-limiting and degenerative along the lines of Sanford’s genetic entropy.

  10. 10
    bFast says:

    Jehu, “I do think that it is a huge problem for common descent.”

    I actually question whether this evidence seriously challenges common descent as I understand it. It certainly does challenge the MET.

    Consider, however, the working evolutionary model that we do have — that of the development of modern technology. We can, for instance, clearly see a trail of common descent and a series of relatively small inventions from the high-wheel bicycle to the modern multispeed bikes. However, when we do a materials analysis, we suddenly see things like titanium frames showing up, something that was first seen in aircraft and rockets. Intelligent causation will produce a near-tree that refuses to filter out as a clean tree, but renders as a bush. We are seeing exactly this kind of data in the tree of life.

    Now for the serious question — did the designer start from compnent materials a bunch of times, or did the designer tamper with the data of given individuals producing modified offspring. I have seen no evidence to suggest that the designer ever started from scratch. Rather, I see lots of evidence that active tweaking was involved. The bush does not prove that the designer used a method other than active tweaking. It certainly seriously challenges, however, the MET.

  11. 11
    Jehu says:

    bFast,

    Interesting points

    Intelligent causation will produce a near-tree that refuses to filter out as a clean tree, but renders as a bush. We are seeing exactly this kind of data in the tree of life.

    What we see is a nested heirarchy, which is not a phylogenetic tree but I guess could be considered a bush. I would agree that there is more “homology” in life than in human designed objects.

    However, I think the so-called homology we see is the result of a single designer. If there is common descent, I believe it is on the level of God taking a cell out of one organism and creating another organism, as He is described as doing in Genesis. In this respect, I think the common descent part is trivial relative to the creative input of God.

  12. 12
    Mats says:

    Sal,
    Are you by any chance ascribing to ID every single prediction done against Darwinism? It’s true that ID has a very large tent (it can even include theistic evolutionists) but I think credit is due to where it belongs.
    Walter ReMine identifies himself as a creationist consistently. Why not say that the Biotic Message has “creationist predictions confirmed by science” (like lack of phylogeny) ?

    Notice: I am not saying that the Biotic Message is not an ID prediction. I am saying that, you could at least be more specific and point out that Walter ReMine’s position is that the Biotic Message is a creationist theory (more specific than ID).

    Secondly, don’t forget to mention the other things the Biotic Message says:
    1) life was designed for survival
    2) Life was designed to resist all naturalistic interpretation
    3) Life was designed to point to ONE Designer
    This last point clearly distinguishes ID from Walter’s book. ID makes no claims about the Designer, while the Biotic Message is very specific on that.

    Thirdly, the Biotic Message is totally against evolution (goo-to-you evolution), while ID is not against evolution per se, but only against unguided evolutionism.

    But anyway, I have no problem with the Biotic Message being used as an ID prediction/theory, as long people are careful enough to point out that Walter’s theory is a creationist theory primarly. It just so happens that that theory, obviously, is in agreement with ID.

    God bless
    (PS: You’l probably reply and say that ReMine is not an young earth creationist. Yes, that is obvious by his book)

  13. 13
    Mung says:

    And this paradigm change was forseen by world class Cornell geneticist and ID proponent, John Sanford in his book: Genetic Entropy

    Genetic Entropy is about accumulation, not loss.

  14. 14
    Mung says:

    The ID theory known as Biotic Message argues life is designed to resist a phylogenetic interpretation.

    The Biotic Message argues that life is designed to resist a evolutionary explanations. Even young earth creationists accept phylogenetics and phylogenetic trees, they just deny that ALL life is related by descent from a common ancestor.

  15. 15
    bFast says:

    Jehu, “I believe it is on the level of God taking a cell out of one organism and creating another organism, as He is described as doing in Genesis.” I presume you are referring to God making Eve from a rib of Adam. However, the Bible speaks of making Adam from dust. As such the obvious interpretation is that God made Adam from component parts, not from the bacteria etc that happened to be floating around in that earth.

    The evidence I have seen suggests that the designer modified a great ape (CA w/ chimp) to make a pre-human, and modified the pre-human to make man.

  16. 16
    scordova says:

    Genetic Entropy is about accumulation, not loss.

    Accumulation of errors (genetic entropy) implies loss of function, thus depending on what concept one is tallying, genetic entropy is about loss as well.

  17. 17
    scordova says:

    Mats asked:

    Why not say that the Biotic Message has “creationist predictions confirmed by science” (like lack of phylogeny) ?

    That is a good question.

    Because I don’t want ICR, AiG, or other similar organizations to be hinted at getting credit when Biotic Message-type research was funded by the Discovery Institute. See: Part of the Discovery Institute’s secret research program uncovered.

    I don’t recall that ReMine even appealed to even one verse from the Bible in his argument! That is different from what most people perceive as creationist ideas, namely, arguing special creation from Genesis. ReMine did no such thing, and that is more consistent with the manner ID arguments are made.

    Sandford argued in a manner similarly. I don’t recall Sanford saying we’re supposed to believe were are specially created because the Word of God says so. Thus I put him more in the category of ID.

    You are correct that these are theories of special creation, but I don’t liken the manner of argument to that of what most people nowadays perceive as creationism, namely, “the Bible said it, therefore I believe it”.

    I would submit, using defending the Christian faith and it’s claims with “the Bible said it, therefore I believe it” is probably inconsistent with 1 Pet 3:15. Where one is commanded to give reasons and an able defense of the faith, not mere restatements of what one believes.

    I know I seem a bit harsh on some of my fellow YECs, they’ve left a bad taste in my mouth, from Dr. Dino, to Ted Haggard, to John Mackay, etc. See Good creationist vs. bad creationist.

    I don’t like the climate where every mistake or offering the words “I’m undecided” is treated like one is willfully in league with Lucifer or some sort of moral compromiser. I did not want ReMine or Sanford’s work associated with that culture. The link I provided to CMI shows exactly where that sort of culture ends up. Very little is done in the way of science relative to the investment in preaching and moralizing….

    Bear in mind, the vast majority of great YEC thinkers were OECs or very sincere TE’s who truly had a heart for God. Perhaps we should rather seek them out rather than drive them away.

    But, now I digress. I hope that answers your question somewhat. Even in terms of money and endorsements, ReMine and Sanford’s work received substantial support from the ID side, not the “Biblical” creationists.

    God bless you too.

  18. 18
    bFast says:

    Scordova, you have well expressed my experience with the YEC community when you said, “I don’t like the climate where every mistake or offering the words “I’m undecided” is treated like one is willfully in league with Lucifer or some sort of moral compromiser.” I know that Dembski has been given a lot of heat for accepting YECers into the fold. I would hope that ID is able to accept those who can present an evidence-based case, but can point the “the Bible says so” types in another direction. I believe the Bible, and teach it in Bible class. However, it is toutology, unacceptable logic, to use Biblical declaration as validation of the Bible’s accuracy.

  19. 19
    christopheratlee says:

    bFast, you wrote that the evidence points to God taking an ape, re-engineering that ape into a proto-human and then finally reworked a new species (genetically engineered?)man?

    I would appreciate it if you would flesh this out a bit. I find this idea
    to be fascinating.

    Also, what is your denominational affiliation if I may ask.

  20. 20
    Mats says:

    Salvador,

    Because I don’t want ICR, AiG, or other similar organizations to be hinted at getting credit when Biotic Message-type research was funded by the Discovery Institute. See: Part of the Discovery Institute’s secret research program uncovered

    Several problems with thie above words:

    1. The fact that *you* don’t want ICR or AiG to get the credit for the Biotic Message (TBM) doesn’t change the fact that the author intended his thesis to be a creationist theory, NOT an ID theory (even though it is in agreement with ID, since ID is more abstract than the Message Theory). You can’t change the authors intent only bkz you don’t like this or that organization. That’s not logical.

    2. The link you gave is NOT about the Biotic Message, but about what Walter is doing in terms of his research TODAY, The BM was written in 1993, if I am not mistaken. I don’t understand how you can conflate one of the problems Walter raised in his book in 1993 (Haldane’s Dilemma), with his present day research. I mean, the fact that ReMine is working TODAY in an ID related field, doesn’t mean that his 1993 book was primarly an ID book.

    I don’t recall that ReMine even appealed to even one verse from the Bible in his argument!

    He doesn’t have too, in order for his book to be a creationist book. I am sure you are aware that you can make a case for creationism without refering to the Holy Bible, right? Duane Gish used to do that.

    Secondly, there are Muslim creationists too, and they do NOT refer to the Bible. Would you dismiss them as creationists just bkz they do not quote the Judeo-Christian Holy Book?
    Ilogical.
    ReMine’s book is a thesis laying out a specific creationist theory, meaningly,
    a) Life was designed for survival
    b) Life was designed to look UNLIKE evolution
    c) Life was designed by ONE Designer.

    This last point is at odds with ID since ID makes no claims about the Designer. I think you missed that.
    Oh, and don’t forget that the Biotic Message is a theory that attacks evolution , something that ID does not. ID can be in harmony with evolution and common descent, whereas Message Theory cannot.
    So, no, the Biotic Message is not an ID theory but a creationist theory.

    If by creationist, people automatically assume “ICR” or “AiG”, then it’s their problem, not Walter’s.

    God bless

  21. 21
    scordova says:

    Mats,

    This is an important discussion, but in deference to Paul Nelson, I’d like further discussion of Biotic Message to continue elsewhere as that is not really central to the topic. Yes, I was the one who mentioned first, and I accept the responsibility. I’d like to make amends by opening further discussion elsewhere:

    You and others are invited to continue the discussion at YoungCosmos: Is Biotic Message a Creationist or ID theory? And other questions…

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