• Method used determines which evolution story is told

    Genetic sequence comparisons are often used to try to establish relationships in evolution. But as Robert Deyes, writing over at Access Research Network, shows, the molecular "clock" often conflicts with the "tree of life.":

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    Writing over a decade ago, UCLA biologists Laura Maley and Charles Marshall noted how genetic sequence comparisons carried out between different animal phyletic groups can lead to significantly different interpretations of evolutionary relationships depending on which species is chosen to represent each group (Ref 1). Such a finding should raise concern amongst protagonists of molecular systematics who today use sequence data to determine evolutionary relationships. Yale University's Gavin Naylor showed just how inaccurate such comparisons could be in the context of the vertebrate evolutionary tree (Ref 2). Mitochondrial DNA sequence analyses of 19 different taxa generated an astounding result- frogs and fish were clustered in the same clade as chickens even though "strong morphological and fossil evidence" did not show these as being in any way related by a common ancestor (Ref 2). The same mitochondrial DNA sequences placed echinoderms- which include starfish and sea urchins- in closer proximity to the vertebrates than amphioxus even though, being a chordate, we would expect amphioxus to be closer (Ref 2). That is, if we give the evolutionary tree any credibility.

    Given such anomalies, one should be cautious about stating what we really do know about the evolutionary relationships between different classes of vertebrates. Nevertheless molecular biologist Thomas Sakmar and his colleagues from the Rockefeller University seemingly threw caution to the wind several years later when they redesigned the rhodopsin molecule- a visual, light perceiving pigment that is ubiquitous throughout nature (Ref 3).
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    Also just up at The Post-Darwinist, Denyse O'Leary's news and culture blog on the intelligent design controversy:

    Analyst: Blogs now considered mainstream media

    Expelled DVD released today, to brisk sales, more hit reviews

    Great offer! Get Ben Stein's Expelled - plus new book and earlier ID films

    Columnist: Regulate the Internet? Shut down the broadcast regulator instead!

    Liberal fascism: What it is and why you should care

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    Submitted by oleary on Tue, 2008-10-21 14:40.

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    johnadavison | Thu, 2008-10-23 11:41

    This is an important thread. Michael Denton in his first book, "Evolution: A Theory in Crisis," pointed out the same thing. He at that time questioned evolution. Actually this sort of thing is to be expected if one accepts a "Prescribed Evolution." If all living creatures originally shared a common biochemical potential as I believe, we should not be surprised to see common molecular expressions from distantly related organisms. The "Unversal Genome" hypothesis predicts the same thing. The important thing is to realize that such revelations in no way detract form the reality of evolutionary change in the past. The simplest explanation is that there were a limited number of possible molecular configurations available for organisms when they first appeared. The same line of reasoning can be applied to the problem of mimicy in the Lepidoptera and elsewhere. There is absolutely no reason whatever to assume that everything we observe in nature is somehow adaptive any more than we should assume that creatures are "struggling for existence," another Darwinian fantasy.

    "Animals are not always struggling for existence. Most of the time they are sitting around doing nothing at all."
    anonymous only because I can't recall who said it.

    I love it so!

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Thu, 2008-10-23 23:59

    Nowadays Darwinists attempt to explain away "common molecular expressions from distantly related organisms" with Horizontal Gene Transfer. They seek to identify the traces of HGT by the pattern it would leave behind and not necessarily positive evidence that HGT can occur in higher animals and result in coherent/functional macroevolution. That is, HGT would leave a pattern of identical (or very nearly identical) complex traits that cannot be explained by common descent, nor by atavism. The "complex trait" is is now also sought at the level of DNA sequence. For example, if the same DNA sequence (of, say, one thousand nucleotides) can be found that cannot be explained by common descent, nor by atavism, then it would be taken as "evidence for" lateral DNA transfer.

    Walter Remine's book documents a case of this that was proposed, and later revoked, entirely based on pattern. The case of "leghemoglobin" is a hemoglobin-like protein found in the roots of some legumes (which are plants). The protein sequence (the sequence of amino-acids) is so much like the hemoglobin found in vertebrates that lateral DNA transfer was widely claimed to be the cause.

    Later, when we could sequence the underlying DNA itself, it was found that the DNA sequence was not so similar -- so the idea was revoked.

    That's an interesting tale from the history of science. The evidence for (macro-)evolution caused by Darwinian mechanisms is driven by pattern, not by sufficient experimental demonstrations.

    Today the compelling evidence against lateral DNA transfer is (you guessed it) pattern! Life's hierarchical patterns -- the phenograms and cladograms of multicellular life -- at the morphological level, embryological level, and even at the level of DNA sequence is compelling evidence against lateral DNA transfer. A Transposition pattern is substantially absent from multicellullar life.

    In other words, life's hierarchical patterns:

    1. ...are evidence against Transposition (e.g. lateral DNA transfer),
    2. ...are evidence against Atavism (also known as "genetic throwbacks),
    3. ....form the background data structure by which we identify homoplasy (i.e. "convergence), which is an abundant and profound evidence against non-foresighted evolution via Darwinian mechanisms, and
    4. ....unify all life as the work of one designer (or design team working together as one).

    BTW, There are studies that show a virus taking some DNA and inserting it into skin or organ cells of a creature such as ourselves, but this is not the same as inserting into the germ-line DNA in a fashion that enables the DNA to be carried on into the germ-line of surviving offspring. Does anyone know of ANY research that claims that HGT can account for macroevolution based upon evidence of this occurring and not just code comparisons?

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    johnadavison | Fri, 2008-10-24 00:07

    Patrick,

    Do you believe in evolution because there is nothing in your message that suggests that you do?

    I believe this requires a yes or no answer.

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Fri, 2008-10-24 04:04

    Define evolution. But I believe that macroevolution via intelligent mechanisms is possible, just not by Darwinian mechanisms.

    You're probably reacting to this comment: "which is an abundant and profound evidence against evolution". I should have finished that with "via Darwinian mechanisms".

    The main point was that I was skeptical of the unproven powers of HGT.

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    johnadavison | Fri, 2008-10-24 09:58

    I thought the Prescribed Evolutionary Hypothesis was an intelligence based mechanism. What do you think? Do you have something better to offer?

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Fri, 2008-10-24 16:07

    HGT = Horizontal Gene Transfer = Lateral DNA Transfer

    If intelligently controlled properly, HGT could be an additional mechanism for your Prescribed Evolutionary Hypothesis. Viruses could be a method for triggering Prescribed information in addition to internal triggers. But if that is indeed the case then entire system has suffered from entropy, deteriorating and becoming dangerous. Viruses could be called a system that has destabilized, gone wildly out of control, with the only remaining functionality focused on mere replication instead of a purpose. So, as you like to say, evolution (at least by this hypothetical mechanism) has ended.

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    johnadavison | Sat, 2008-10-25 10:39

    I don't buy horizontal gene transfer for a very simple reason. The great similarities between marsupial and placental wolves, saber-toothed cats and the many other analogous forms appeared in animals separated by millions of years temporally and thousands of miles spatially. The simplest explanation is that they were produced following the templates of pre-existing models which were present in those distantly related lineages. In other words these terminal archetypes were "prescribed" in those evolving genomes. They most certainly did not appear through some mysterious "convergent evolution" as the Darwinians would have us believe. For the same reason I reject Margulis' endosymbiosis hypothesis, especially since it cannot be demonstrated experimentally.

    In short -

    "Everything is determined... by forces over which we have no control."
    Albert Einstein

    That which IS determined most certainly WAS determined, probably millions of years ago. There has never been a role for chance in phylogeny or ontogeny.

    "Neither in the one nor in the other is there room for chance."
    Leo Berg, Nomogenesis, page 134

    The whole thing was planned from beginning to end and the end is any time now.

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    I think it would help the conversation to differentiate between Darwinian Common Descent and Common Descent compatible with ID hypotheses (which is fine with a historical picture of "bushes" and not a consistent Darwinian Tree Of Life). For example, you wouldn’t expect to find the same information being used for the same function in divergent lines from a Darwinian viewpoint if they’re geographically isolated or if the divergence supposedly took place a very large amount of time before.

    Instead of resolving a tree we’re getting bushes since we cannot find the gradual informational links that would be expected of Darwinian Common Descent. Using the theme of “islands of functional information”, these bushes could also be called “archipelagos of functional information” which must be bridged by informational leaps. Designed mechanisms could bridge (or traverse) these informational leap, thus producing Designed Common Descent.

    Another thing that ID proponents predicted is homologous information where none would be expected if Darwinian mechanisms were responsible for macro-evolution. Like the platypus, for example, whose genome is a patchwork of mammal, reptile, and bird.

    Chromosomal sex determination in the platypus was also discovered to be a combination of mammal and bird systems. Yet Darwinists like Talk Origins say:

    “birds are thought to have evolved from dinosaurs in the Jurassic about 150 million years ago, and that mammals are thought to have evolved from a reptile-like group of animals called the therapsids in the Triassic about 220 million years ago. No competent evolutionist has ever claimed that platypuses are a link between birds and mammals.”

    In the past I’ve mused what might happen if the genomes for animals not considered to be related were compared. My predication would be that we’d find evidence for front-loading, other scenarios, and information re-use in general. I personally want to see a comparison of North American flying squirrels and Australian sugar gliders. If it's same or similar information Darwinists may attempt to claim HGT, but that hypothesis seems to defy belief considering the geographical distances involved.

    Often the the convergent evolution storytelling card is played…you’d think Darwinist would have run out of cards in that deck by now. Universal common descent from a single LUCA may be true itself but the historical narratives we have now may not be true themselves. Some ideas like land mammals to whales may have never existed (or persisted to this day) if the bearded buddha had never posited his bear story. If front-loading and universal common descent are both true then why couldn’t the whale have evolved entirely in the ocean and received the mammal-like features from internal prescribed information?

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    johnadavison | Sat, 2008-10-25 21:20

    I have no intention of "helping the conversation." I have stated my position here, elsewhere and in several published papers. What is there to discuss? Since when has "discussion" ever had anything to do with the search for the truth? When did "debate" ever resolve anything? It was you IDists that insisted on a "debate." That was a fatal error and is the primary reason Darwinian mysticism still prevails. Debates are for high school and college debating teams, lawyers and politicians. There is no place for debate in science and never has been. Got that? Write that down.

    I am getting tired of all this crap. It is an exercise in futility. Visit my blog and learn some real science.

    jadavison.wordpress.com

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Sat, 2008-10-25 22:38

    Where did you get the idea I was arguing or "debating". I was just discussing recent trends in Darwinian thought, adding my thoughts onto your earlier comment. And if you think that discussing this topics is pointless then why are you even bothering to post?

    Also, the only reason I made the distinction between the forms of Common Descent is because most Darwinists assert that if Common Descent is true then macroevolution via Darwinian mechanisms is true; which is false.

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    johnadavison | Sat, 2008-10-25 23:47

    There is very little evidence for common descent and it has nothing to do with the Darwinian fairy tale. I am through wasting my time on this thread as my position has always been clear.

    I'll post again when someone introduces a thread worthy of my attention.

    Since you seem to be in charge here, if you don't like what I have to say, ban me. I couldn't care less. I have better things to do than engage in semantic nonsense with you or anyone else for that matter, here or elsewhere.

    jadavison.wordpress.com

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Sun, 2008-10-26 20:00

    I won't ban you, I'm just puzzled why you seem upset with me based upon my comments.

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    johnadavison | Sun, 2008-10-26 23:50

    Well thanks for admitting who is in charge as if I didn't already know. You elitist "authors" are all alike, petty little autocrats, each running his private little empire while contributing nothing of substance himself. Did Dembski turn this pathetic little blog over to you or was it O'Leary? What have any of you ever contributed to our understanding of the twin mysteries of ontogeny and phylogeny? Not a damn thing and you never will. You are all too busy kicking the dead horse of Darwinian mysticism. You "IDists" have become your own worst enemies by reducing the search for the truth to a mindless debate. There is not a shred of truth in the Darwinian fairy tale yet you dignify the atheist swine by trying to reason with them. Wake up, grow up, put up or shut up.

    Why do I waste my time?

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Mon, 2008-10-27 05:24

    I've never been shy about stating that I'm an admin here. Bill owns the site and server but Denyse has been given control. BTW, on this site ALL users have the ability to write blog posts, not just admins.

    Nor have I ever claimed that I'm an evolutionary biologist or some such thing. I have ideas for research but no resources or avenues in which to pursue them. I'm "merely" an engineer whose hobby is biology. Partially because I feel that this "hobby" will eventually come to encompass my field. My interest in ID came about through my interest in nanotechnology. I look forward to the day when I'll write code in a high level language (Cb?) which is then translated into an organism that creates a product--perhaps a house.

    "You are all too busy kicking the dead horse of Darwinian mysticism."

    Actually, I'd agree on that point. Why bother with the old dead ideas? Newer ideas such as the “evolving holistic synthesis” (MacNeill's term) "might" be interesting, which I doubt, but honestly I'd rather see a focus on developing ID-compatible hypotheses and research. But other than urging people to do as such there's not much I personally can do other than provide IT support...at least for the time being.

    In any case, John, I've been more than polite considering the insults you continue to throw against me. If you see any faults within the ID community feel free to point them out but please restrain yourself from outright hostility.

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    johnadavison | Mon, 2008-10-27 13:28

    Don't confuse objectivity with hostility. The simple truth is that I have been banished from Uncommon Descent on three different occasions because I happened to differ ever so slightly from the positions held by its elitist "authors" like yourself.

    For a change of pace, try this little gem on for size. I'll bet you will agree with it.

    http://jadavison.wordpress.com/2008/01/06/predictions/#comment-987

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    Patrick | Mon, 2008-10-27 13:56

    "petty little autocrats"

    "pathetic little blog"

    "Not a damn thing"

    "mindless debate"

    "atheist swine"

    "Wake up, grow up, put up or shut up."

    That's what I'm talking about. Antagonizing people usually does not help your case--whatever the subject may be--whether they be supporters, opponents, or observers.

    "The simple truth is that I have been banished from Uncommon Descent on three different occasions because I happened to differ ever so slightly from the positions held by its elitist "authors" like yourself."

    I'm aware of the animosity between you and David Springer. As far as I'm aware he does not even visit here. There's no reason to take out your hatred for David on everyone else.

    On the political topic I don't have much to say. I'm not a big fan of either candidate, but I'd agree that Obama is the worse of the two if only 1/10 of what is said about him is true.

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    johnadavison | Wed, 2008-10-29 02:39

    The symbiotic relationship between Dembski and Springer is obvious. That is why Springer keeps using the "Imperial We." It was Dembski who was the first to ban me with Springer to repeat it twice more. Springer now owns Uncommon Descent and if you don't realize it yet you are not a very astute observer. He even brags about his eternal tenure there. Springer does not believe a thing that O'leary and Dembski hold sacred. He has recently and proudly displayed himself as a closet materialist (Darwinian). Springer is a parasite who has successfully invaded and now dominates Uncommon Descent with his insatiable ego and his devious machinations. He makes Machiavelli look like Mother Theresa. He has destroyed Uncommon Descent as a voice for the Christian ethic. In his own words -

    "I love being right" and "The Lord giveth and the Lord taketh away."

    It is hard to believe isn't it?

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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    johnadavison | Thu, 2008-10-30 07:47

    http://www.iscid.org/boards/ubb-get_topic-f-6-t-000370-p-98.html

    My most recent message.

    "A past evolution is undeniable, a present evolution undemonstrable."
    John A. Davison

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