Home » Intelligent Design » In other words, phylogenetic reconstruction is sheer fantasy …

In other words, phylogenetic reconstruction is sheer fantasy …

Here’s some research done 100 miles down the road from me. Note the sentence highlighted. The actual phylogenies here were experimentally known and yet standard evolutionary theory drew completely wrong conclusions. Oh, but it was a small population, small genomes, and intense selection pressure. Spare me.

“Exceptional Convergent Evolution in a Virus”
Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ.
Department of Zoology, Institute of Cellular and Molecular Biology, University of Texas, Austin 78712, USA. [email protected]

Replicate lineages of the bacteriophage phiX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

PMID: 9409816 [PubMed - indexed for MEDLINE]

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235 Responses to In other words, phylogenetic reconstruction is sheer fantasy …

  1. How well, I wonder, would the phylogenetic tree of mixed drinks generated using the PHYLIP package conform to the known history of the various drinks?

  2. 2

    It would be interesting to do a probabilistic analysis of this study. How much probabilistic resources did the phages have during the course of the experiment? Did they have enough to go through every possible substitution?

    If yes, then this type of study could be done with any conceivable selective pressure and the limits of evolutionary change available to the phages could be observed.

    If no, then the hypothesis could be made that the solutions found are not the only ones, since the phages found these particular solutions without enough probabilistic resources to get through the whole range. Since that would imply multiple solutions, it would be logical to further hypothesize that the solutions involve loss of information via different substitutions that degrade the integrity of whatever molecular structures are involved. That’s because it’s much easier to break something than build it, and there would be multiple ways to break whatever needed breaking, leading to a high probability for finding a solution and enabling the phages to find it without exhausting all possible substitutions.

  3. It would be interesting to do a probabilistic analysis of this study.

    For that matter, it would be interesting to do a probabilistic analsis of ALL Darwinism. Maybe it’s just to make them look humble {HA!} but scientists try to gloss their dogma in the language of probability. But that is the greatest weakness of Darwinism. If (and this is being generous!) we allow a probability of 0.9 for humans and chimps being ‘related’, how do we relate that to the probability of the Earth being, say, 14 billion years old or whatever this month’s figure is? Presumably the Order of Darwin will express THAT as a probability of (let’s be generous again) of 0.85. Does that not mean that the overall probability of Darwinism has moved down to (0.9 X 0.85) 0.765? And as we add in all the other assumptions (sorry, ‘probabilities’) do we not move further and further away from certainty? And they have the gall to call this FACT?

    It is MOST reassuring that this study of phylogenetics undermining Darwinism comes so soon after the Texas Government has reopened the way for teachers to show pupils the unencumbered facts of Man’s true place in the order of creation. As so often before, we look to America to take the lead in unmiring us from value-free degeneracy.

  4. Phylogenetic trees ultimately fail because the real pattern of life is a mosaic or a web, not a tree. So, the phylogenetic trees always end up containing inconclusive and contradictory data. The DNA that leads to one tree could just as easily be used to construct an entirely different tree. Therefore, in order to make the DNA fit the original assumption that a tree even exists in the first place a procrustean bed is fashioned for the data using the twin excuses of horizontal gene transfer and convergent evolution to cover up the contradictions. A third excuse, mutational hot spots can also be used to defend the tree. However, the mutational hot spot explanation must be handled with care because it is a double edge sword that effectively threatens the very assumptions upon which the tree was built in the first place.

  5. 5

    Oh, but it was a small population, small genomes, and intense selection pressure. Spare me.

    Don’t forget the “deep time” excuse (i.e. the experiment’s duration is short relative to evolutionary time)!

    Convergence, of course,is a common feature of design. It’s also precisely the opposite of “divergence”, which is supposed to be a hallmark of evolution.

    I note that one of the paper’s authors, David Hillis, was deeply involved in the recent textbook fiasco in Texas, taking the side of the evolutionists. Sometimes it seems these evolutionists ignore the import of their own papers. And aren’t us theists the ones who are supposed to be guilty of “compartmentalization”?

  6. I hope I see the ultimate rejection of neo-Darwinism in my life time. :) Stuff like this sorta thing is reassuring it’ll come sooner or later.

  7. Where is the logic police when you need them. Any theory which has at it’s heart the mechanism of random luck to explain the origin of specific structures is not a good theory at all.

  8. This just goes to show that evolutionary theory is not a good theory- not because it does not address the evidence but because it does not address “the main question” which it claims to explain about the evidence, which is usually “what caused or gave rise to X?” Chance (if it even exists) is not a good mechanism which apparently is what this study showed. Any theory that relies on randomness is by definition a theory which does not work. Randomness does not predict anyhting- or explain anything- it marks a hole within a theory- it is an excuse for data that the theory cannot reconcile. But in the case of this study we know the data is not junk – so therefore it must be the theory that is flawed.

  9. Where are the defenders of Darwinism when we need them?

  10. Dr Dembski,

    The authors showed that tools developed to look for bifurcating trees are bad at detecting star trees. On the whole, it seems to me that this research is cautionary about using models and tools outside of their intended areas of applicability.

    While you allow for three caveats (intense pressure, small population, small genome), the authors provide their own three. They agree with you on pressure. They disagree with you on population size, calling it “very large”. On the genome, they focus on the identical starting point, rather than the size.

    And yet, and yet something happened in those test tubes. The virus did adapt to changes in its environment, and it did do so by changes to the genome easily explicable by copying errors of the bacterial host machinery. The result was improved fitness by three orders of magnitude. RM+NS, ne? So I don’t think ‘modern evolutionary theory’ got it completely wrong. :)

    Perhaps I shouldn’t ask on a blog with this name, but do you have serious disagreements with the assumption of common descent in metazoa? I think we all agree tha the bottom of the tree of life is a web, a froth, a foam.

    Happy Easter to you!

  11. Random mutation, Natural Selection, probability, population genetics, Mendelian (sexual) genetics, none of these ever had anything to do with creative evolution. Every aspect of organic evolution, like every other aspect of the universe, was planned in advance, took place on a predetermined schedule and is, as nearly as we can determine, now finished with only extinction remaining. I know this will prove to be an unacceptable position here as elsewhere but it my conclusion based on all the available evidence.

    “La commedia e finita.”
    Pagliacci

    or soon will be!

    There now, In feel somewhat better.

    “Here I stand. I can do no otherwise.”
    Martin Luther

  12. I hope I see the ultimate rejection of neo-Darwinism in my life time. Stuff like this sorta thing is reassuring it’ll come sooner or later.

    You do realize this paper is over a decade old.

  13. Paper:

    One should read page 1505 of the paper, rather than simply the abstract.

    The authors conclude that convergence does not pose a problem for tree construction. Reconstruction methods accommodate for this. (And I would guess 12 yrs later the methods are even better). They used star convergence which is sensitive to convergence- you can use other methods. The phage has a abnormally high rate of convergence because of the experimental setup.

    In another study when a different phage was used (T7); with the result that parallel substitutions were 28x more rare. Consequently the phylogentic trees were accurately predicted.

    And so the paper continues past the abstract. So I would say that the phylogentic results were an artifact of the method. Furthermore these results are not common and do not occur with other tree methods and phages.

  14. 14

    This paper showed nicely that common selection can lead to extensive identity in DNA sequences. Thus, sequence comparison cannot always be used for inferring time of separation. This is exactly the point made by my MGD hypothesis. When we see a human and chimp identity of ~98%, we must first ask how much of that is due to common selection. The MGD says that there is a lot. The data are completely consistent with a pongid clade with human as the outgroup. Common selection for evolution of high intelligence could lead to more identity between human and chimp than between human and orangutan.

    MGD hypothesis here:
    http://precedings.nature.com/d.....ion/2/html

    A more recent paper on this topic here
    Genetics, Vol. 181, 225-234, January 2009, Copyright © 2009
    doi:10.1534/genetics.107.085225

    Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence
    Jonathan P. Bollback*,1 and John P. Huelsenbeck

    * Department of Biology, Evolutionary Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark and Department of Integrative Biology, University of California, Berkeley, California 94720

    1 Corresponding author: Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, King’s Bldgs., W. Mains Rd., Edinburgh, EH9 3JT, United Kingdom.
    E-mail: [email protected]
    Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions—if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives—which likely overlap more in the details of their adaptive solutions—will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.

  15. Here’s some research done 100 miles down the road from me

    and done 12 years from us as Bob O’H pointed out somewhere else. Here’s the reference:
    Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ: Exceptional convergent evolution in a virus. Genetics. 1997 Dec;147(4):1497-507.

    Bob further points to some incongruity of Dr. Dembski introduction

    but it was a small population

    and what the paper actually says:

    Three properties of the
    design may have led to the high rate of convergence, all of which are atypical of what is thought to apply to most
    organisms:
    [...]
    2. Strong, mass selection was operating on very large populations.

  16. Eintown,

    “I hope I see the ultimate rejection of neo-Darwinism in my life time. Stuff like this sorta thing is reassuring it’ll come sooner or later.”

    You do realize this paper is over a decade old.

    Neo-Darwinism will probably fall sooner or later regardless of this paper’s age. The paper may lose its importance, but neo-Darwinism seems to be dying either way. Of course though, believe what you will. I just hope I’m right in the end. ;)

  17. 17

    Darwinism died in 1871, 12 years after the publication of Darwin’s opus minimus, when St. George Mivart challenged the core of Darwin’s fantasy by asking the following question which I will paraphrase to make it understood by even the most dense of those who still support the most absurd proposal ever to reach the printed page.

    “How can natural selection have been involved in any way with the features of a structure which had not yet appeared?

    Mivart dedicated the whole of Chapter II to this perfect devastation of Darwin’s entire thesis –

    St. George Mivart, The Incompetency of “Natural Selection” to Account for the Incipient Stages of Useful Structures, “The Genesis of Species,” pages 35-75.

    Darwinism has died many times since Mivart, always to be resurrected each time by homozygous, congenitally atheist mystics who are not only stone deaf, like most pure white cats, to what Einstein called “the music of the spheres,” but also blind as the proverbial bat to the world which has always surrounded them.

    You can’t kill Darwinism any more than you can kill any other form of congenital bigotry. Darwinists are the perennial losers in the history of evolutionary thought. They are the handiwork of the second God I have postulated must once have existed, the malevolent one, who produced pathetic creatures like Paul Zachary Myers, Christopher Hitchens and Richard Dawkins. They really can’t help it. They were “born that way.”

    There is absolutely nothing that can be done either for them or with them except to do what I have been doing for some time, which is to laugh at them, just as Adam Sedgwick laughed when he read the the book his student, Charles Darwin had produced in 1859.

    “EVERYTHING is determined…by forces over which we have no control.”
    Albert Einstein, my emphasis.

    It is hard to believe isn’t it?

    I love it so!

  18. 18
    AmerikanInKananaskis

    Maybe it’s just me, but I thought that ID advocates were above this stuff.

    What, are we arguing for special creation now instead of pre-loading? I thought we accepted common descent but just disregarded methodological naturalism. (In fact, I believe there used to be a section on this website that said something exactly along those lines.)

    There are only four nucleotides to choose from in DNA so of course there’s going to be a lot of convergence. And of course it’s going to mess up a phylogeny. Look up “long-branch attraction”.

    This is basic stuff that anyone could sit down and figure out for themselves from first principles.

    Come on, if we’re going to make any inroads into science, we need a less juvenile approach to criticizing Darwinism than this.

  19. I hope I see the ultimate rejection of neo-Darwinism in my life time. Stuff like this sorta thing is reassuring it’ll come sooner or later.

    Domoman,

    I’m surprised that you find this study reassuring. As others have pointed out, it in no way invalidates phylogenetic reconstructions in general — it just shows the limitations of a certain methodology in certain circumstances.

    Genomics is lending tremendous support to modern evolutionary theory. For a nice overview, see Sean Carroll’s latest book, titled The Making of the Fittest.

  20. In #17 AmerikaninKananaskis wrote:

    “Come on, if we’re going to make any inroads into science, we need a less juvenile approach to criticizing Darwinism than this.”

    Unfortunately, there are some people who are incapable of making reasoned responses to arguments. Based on the evidence in this thread and many others like it in the past, this appears in most cases to be due to an obsession with calling people names, using purely ad hominem arguments, and resorting to megalomaniacal rants rather than logical arguments supported by evidence.

    As is apparent from their own words, such individuals are “in love” with fighting for its own sake, and forget that General Patton’s entire quote was “Compared to war all other forms of human endeavor shrink to insignificance. God help me, I do love it so”. This was also Mussolini’s feeling about war; that only in war did people rise to their full human potential. Is this the kind of attitude that makes for good science, or for that matter, for good people in a free and just society?

    As for how to deal with people who are apparently constitutionally incapable of carrying on a reasoned intellectual argument, the best thing to do under such circumstances is to do what you would do with schoolyard bullies: completely ignore them. Their comments should remain, however, as a public admonition to others on how not to make a persuasive intellectual argument.

  21. Reminds me of quantization error in communications. Quantization error is often and usefully modeled as a “noise” source. But this model is only valid for an ergodic ensemble of signals.

    Quantization error, the error between a signal and its quantized value, is deterministic. If you compare a particular signal to a quantized representation, its quantization error is deterministic, and for a periodic input harmonically related to the sampling period, the error and is periodic and very predictable.

    The noise model of quantization is useful, but it does not reflect reality.

    Point being, sometimes a model can be useful, but it doesn’t make it true.

    In this case, the fact that they did not get the result they expected for a small sample seems to suggest that the stochastic attributes they are ascribing the phenomenon, while potentially useful for explaining at a macroscopic level certain observations, is not a reflection of reality.

    This is a point that many evolanders don’t seem to understand: Models, even useful models, can be wrong.

    Another example is Tycho Brahe’s 16th century geocentric model of the solar system. This model was useful, and it was used to create navigational charts by others so that captains could sail the world’s seas. But the fact that the model was useful had no bearing on it as a reflection of reality.

  22. 22

    Another good example of that would be, if you believe the reports, acupuncture.

    Allen_MacNeill:

    The ability to admit error and change a viewpoint is the essential character of learning. Those who can admit no wrong imply they know everything, which makes them utter fools. You have proven to be of the former variety, and for that I respect you, regardless of your views on any issue.

  23. 23
    AmerikanInKananaskis

    How can natural selection have been involved in any way with the features of a structure which had not yet appeared?

    I beg of you, please. Don’t say this kind of thing. People who can’t make a coherent argument for ID should just take a backseat and let the real advocates like Michael Behe do their thing. (Although I don’t fully agree with his brand of ID, of all major proponents, his view is closest to mine, and he usually presents it in a decent manner.)

    Your “argument” isn’t even a strawman. It’s a pudding man. Please learn about what you’re criticizing.

  24. Allen MacNeill,

    Every one of the responses from me that were deleted on Scordova’s thread are now on display on my weblog, including your recommendation that I be banished from the discussion, something you had already seen to on your own weblog, just as your fellow Darwinians, P.Z. Myers, Wesley Elsberry and, indirectly, Richard Dawkins, did on theirs. There is no way to determine who the blog czars are at ARN and EvC who did the same thing.

    “A doctrine that is unable to maintain itself in clear light, but only in the dark, will of necessity lose its effect on mankind with uncalculable harm to human progress.”
    Albert Einstein

    I agree with you that everything that transpires should remain as living testimony to the character of the participants. I have seen to it on my weblog by copying there all my comments many of which Scordova deleted without explanation. I doubt very much if he deleted any of yours.

    The reason I do not ignore Darwinians like yourself is because you Darwinian have always ignored your many critics, some of the greatest biologists of the last 150 years, all of whom rejected the Darwinian fairy tale in its entirety.

    I repeat my conviction that there is not a word in the Origin of Species that ever had anything to do with either true speciation or the appearance of any other taxanomic category. Nor is there anything of significance in the voluminous writings of Gould, Mayr, Provine, Fisher, Wright, Haldane etc, etc. either. They were all armchair theoreticians who collectively and singly contributed nothing of real significance to the solution of the great mystery of phylogeny.

    Real scientists not only theorize: they TEST their hypotheses and when they are found to be without foundation they reject them instantly and never revive them. This the Darwinians have steadfastly failed to do. They still refuse to test Darwin’s finches for one reason only. They are terrified at the prospect that they are a single species which is virtually certain to be the result anyway as we have learned from the field observations by the Grants.

    Darwinians, of which you are a typical example, still insist on stubbornly pursuing a phantom which never existed, a phylogeny which was driven by chance even as everything we have discovered and continue to discover from both the experimental laboratory and the fossil record pleads for a planned and guided evolutionary sequence which, in my opinion, has reached its terminal phase.

    In short, Darwinians ARE NOT SCIENTISTS. They are, nearly without exception, Deists or Humanists or Unitarians, which as far as I am concerned are forms of atheism. I am not sure where the Quakers fit in this picture but I am of the opinion that they rarely mention God. At the head of Church Steet here in Burlington stands the Unitarian Church erected in 1809. I have been in that “church” and there is not a single religious symbol to be found there or in its “hymnal.”

    I am in agreement with Robert Broom that there was a Plan, a word he had the temerity to capitalize, much to the horror of the Darwinian zealots who pretended he had never existed. I further believe the Plan has been realized with the present biota which represents the final products of a guided orthogenesis the terminal product of which was ourselves along with those of our fellow creatures which have not yet become extinct, never to be replaced. In short -

    “A past evolution is undeniable, a present evolution undemonstrable.”

    I do not expect others to agree with my assessment, but I do expect that I will not be expelled here for presenting it as I have from so many other forums with which the internet is so inordinately blessed. It is out of my hands in any event because -

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

    We are all victims in a determined universe. Some of us have been luckier than others. Each of us is convinced that he is one of the lucky ones. I do not believe that is possible.

  25. JAD

    Real scientists not only theorize: they TEST their hypotheses and when they are found to be without foundation they reject them instantly and never revive them.

    Maybe I’ve missed it but have Semi-Meiosis and Prescribed Evolution ever been tested?
    IIRC, semi-meiosis has been discussed at UD by DaveScot but he didn’t provide links to any tests. Actually, he concluded that Jesus may have had a 1n genome.

  26. 26

    sparc, whoever that is and we probably will never know. Why else would he insist on using an alias? A person who must hide his identity should not be taken seriously and will not be by this investigator. Nevertheless, I will attempt to answer his question.

    Before I begin, it was decent of DaveScot to finally, after deleting them in a fit of pique, leave my papers available here at Uncommon Descent, although all comments are now closed which is fine with me. That does not mean they should not be read!

    A guided evolution follows as the only conceivable alternative to an evolution driven by chance. Darwinism has repeatedly been proven to be without foundation. In the Law this is known as the exhaustion of all remedies and it is a perfectly valid criterion when applied to experimental and descriptive science. In Physics it led to the rejection of the Ether, in Chemistry the Phlogiston.

    It is true that, as far as I know, my Semi-meiotic Hypothesis (SMH) has not been tested with suitable material. Suitable material would be female frogs (or other animals or plants) known to be heterozygous for one or more chromosme inversions or other chromosome rearrangements. It is to be predicted that the diploid gynogenetically produced offspring of such females would be females one half of which would be like the wild type mother, the other half a new female species. This new female species could then hybridize with males of the original species and establish a new bisexual species through ordinary Mendelian means.

    This theoretical reconstruction is given credibility since it is now apparent through the work of Eric Trinkhaus that Homo sapiens and Neanderthal hybridized. Thus the Semi-meiotic hypothesis remains valid until tested and found to be without foundation. I was unable to obtain suitable material to test my hypothesis and was in fact “expelled” from my laboratory, rendering such a test quite impossible further to pursue. Until it is tested expermentally, the SMH will, like every other untested hypothesis, remain perfectly valid.

    Let me add that the most tested and failed hypothesis in all of science is the Darwinian fairy tale. All tests (when actually applied) have revealed nothing more than intraspecific varieties none of which are incipient species in any event.

    Darwinians, not being scientists, choose not to test their “hypothesis” because they are terrified of what such tests will probably disclose. Darwin’s finches are the perfect example. The canary is a finch and has been in domestication for centuries. Why haven’t Darwin’s finches been domesticated and tested? I will tell you why. Don’t expect Darwinians to test their devout beliefs when there is an excellent chance a test will prove to be intellectual suicide!

    They have also failed to follow through on the fact that the Galapagos marine and terrestrial iguanas are also known, like the finches, to spontaneously hybridize. My God the marine and terrestrial igauanas are still assumed to be in separate genera, a most unlikely reality considering they hybridize.

    It is hard to believe isn’t it?

    Not at all. It is par for the Darwinian golf course, eighteen black holes from which the truth can never escape!

    Furthermore, I have provided both indirect and direct evidence for a “prescribed” evolution in both my 2000 and 2005 published papers, both of which are available on the side bar here under my name. If you had read these papers you would know that and would not be asking that question. Furthermore, the idea of a planned evolution can be traced all the way back to William Bateson as I have explained both here and elsewhere.

    It is absurd to think that Jesus was a haploid.

    “You can lead a man to the literature but you cannot make him read it.”
    John A Davison

    Or even if he does read it, you cannot make him comprehend.

    I hope this helps but my experience here as elsewhere leads me to doubt that it will. That suits me just fine!

  27. Dr Davison,

    Previously you were asked about your species concept, and you replied that if two animals could be mated, even artificially in the lab, and produce fertile offspring, then they were the same species. This was a question in respect to Darwins finches.
    How does that apply to the frogs and human/Neanderthal matings you are discussing here? It seems to me that in both cases, your species concept would say that there is no new species of frog, and humans and Neanderthals were the same species.

  28. 28

    Nakahima

    Evolution did not take place gradually as the Darwinians still maintain. It took place by several series of discrete steps with each organism discretely different from ist predecessor. That does not mean that there would be tcomplete sterility between adjacent members of each guided series.

    Here is an example of what I mean. The chinmpanzee karyoptype differs from ours by about twelve chromosome rearrangements. I speculate that that indicates that there were twelve discrete species, now all extinct that have existed since the chimp and the human had a common ancestor. Neanderthal is uquestionably a separate species from Homo sapiens. That does not mean it could not produce a fertile hybrid with Homo sapiens. Indeed it seems it did! If evolution took place stepwise as I have proposed, one chromosome rearrangement at a time, the reconstruction I have offered is perfectly reasonable. One thing is certain. Single chromosome rearrangements or even a few simultaneous ones are not going to produce total sterility. When there are several as between the horse and the donkey, one can be fairly certain that the hybrid, though viable, will be sterile due to the improbability that it can produce balanced gametes during meiosis.

    I hope this serves to explain my proposed explanation for a stepwise yet nonDarwinian speciation. Everything we know from the karyotypes of Primates indicates that the whole Order may have diversified strictly through the reorganization of a common ancestral structural genome.

    However, when it comes to the origin of the different Orders of animals or plants such an explanation is undoubtedly inadequate. Actually what we see in the fossil record resembles the Biblical origin of “kinds” and for all I know may indicate special creation at the taxonomic level of Order differences.

    The fossil record is crawling with unexplained gaps that still escape explanation. Until they are explained we must give possible credence to the Biblical account. That doesn’t trouble me in the least nor should it for any objective student of the great mystery of phylogeny. Of course Darwinians can never even consider such a scenario as they believe that it is intrinsic in the nature of nonliving matter to spontaneously organize itself into living, evolving creatures, something I regard as absurd. If that were possible, it would have been demonstrated in the laboratory long ago.

    So you see why I must remain a Creationist until it is proven that is no longer necessary. Under the circumstances I do not regard that as an untenable position.

    I hope this helps.

  29. 29

    Let me say also that there is no compelling reason to assume a single ancestor either and plenty of reasons not to. Leo Berg, the greatest Russian biologist of his day and, in my opinion the greatest evolutionary biologist of all time, had this to say about what the real unbiased evidence indicated.

    “Organisms have developed from TENS OF THOUSANDS of primary forms, i.e, polyphyletically.”
    Nomogenesis, page 406, my emphasis.

    His conclusion is in perfect accord with what the fossil record really has disclosed and there is absolutetly nothing in it that can be refuted based on our present knowledge. A monophyletic evolution is no more established than a monotheistic God. They are both based on pure ideological assumption without a shred of ascertainable fact to justify them. Those who choose to believe in either will never be scientists. Real scientists believe what has been proven to be true. Neither monophyleticism nor monotheism qualify and it is very possible that they never will.

    My own persona peference is for two Gods one benevolent, the other malevolent. How else can we account for pathetic creatures like Paul Zachary Myers, Christopher Hitchens and Richard Dawkins on the one hand and great scientists like Leo Berg, Robert Broom, William Bateson, Richard B. Goldschmidt, Otto Schindewolf and Pierre Grasse on the other hand? The answer is we can’t!

  30. 30
    AmerikanInKananaskis

    John A. Davison:

    I get the impression that you do not know what you’re talking about, and that you mask this fact with obfuscationism and tl;dr.

    Paraphrasing you, I would like to know why your own quote does not apply to yourself:
    Davison, not being a scientist, chooses not to test his “hypothesis” because he is terrified of what such tests will probably disclose.
    -
    If you have not already, I suggest you read Darwin’s Black Box to learn how a scientist should present the case for ID.

  31. Mr MacNeil,

    I fear that you have jumped to a conclusion @20. To me, it appears that Mr AmerikaninKansasKis’ @18 comment on juvenile approach was aimed at the opening post, not at the comment of Dr. Davison which immediately preceded it.

    I have no more love of preacherly grandstanding descending into frothy-mouthed invective than you do. I only ask you as a person with respect for science and respect for your own personal principles not to participate in derailing yet another thread.

  32. Dr Davison,

    Thank you @28 for your explanation, but I then do not see how domesticating and breeding Darwin’s finches will prove they are a single species. It seems that fertile hybrids of closely related species prove nothing.

    I apologize to other participants if it seems I am hijacking the thread by pursuing these questions.

  33. 33

    John “Credentials” Davison:

    “A monophyletic evolution is no more established than a monotheistic God. They are both based on pure ideological assumption without a shred of ascertainable fact to justify them. Those who choose to believe in either will never be scientists.”

    What?

  34. mauka in #19 said:
    “Genomics is lending tremendous support to modern evolutionary theory. For a nice overview, see Sean Carroll’s latest book, titled The Making of the Fittest.”

    If it is, Jerry Coyne would not employ cheating to explain in his latest book “Why evolution is true”.

    The modern evolution theory consists of two opposite sub-theories, NeoDarwinism/natural selection and the neutral theory. NeoDarwinism or natural selection is largely irrelevant to molecular evolution, or, more precisely, contradicted by molecular data. As a result, a theory based on the negation of NeoDarwinism or natural selection, the neutral theory, is used to explain molecular evolution, in particular the molecular clock. And the neutral theory is however widely acknowledged to be an incomplete explanation and has countless contradictions of its own.

    But the only theory Coyne ever talks about in his book is NeoDarwinism or natural selection. There are very few sentences that mention molecular evolution. And these in fact mislead the readers into believing that NeoDarwinism is supported rather than contradicted by facts of molecular evolution. Here is what Coyne wrote: “Evolution theory predicts, and data support, the notion that as species diverge from their common ancestors, their DNA sequence change in roughly a straight-line fashion with time.”
    Does Coyne really expect the lay readers to know that the ‘evolution theory’ here means the neutral theory, when it is never mentioned in the book and must negate the key idea of Darwin? If the lay readers, after reading this, then believe incorrectly that NeoDarwinism predicts the major facts of molecular evolution, is it the readers’ fault or the author’?

    If cheating/misrepresentation was employed to explain why evolution is true, it really means it is false. We are here more precise in our definition than the cheater: evolution here just means the Darwinian theory.

    The neutral theory is in great contradiction to NeoDarwinism:
    1. It makes a fool of natural selection.
    2. It was never predicted by NeoDarwinism.
    3. It was called Non-Darwinian evolution by two of the founders of the neutral theory, King and Jukes in 1969.
    4. It was ‘unthinkable’ to neodarwinists. Quote: “The constant rate of evolution was unthinkable for classical evolutionists, who had studied the evolution of morphological characters (Simpson, Mayr).” from Nei and Sudhir Kumar, 2000, Molecular evolution and phylogenetics, page 188
    To a reader of Coyne’s book, evolution theory is neodarwinism/natural selection and vice versa. That theory is contradicted by molecular data. Coyne has certainly succeeded in misleading them to believe the exact opposite. That is shame to science.
    Essentially no laymen, not even most biologists who are not evo specialists, ever heard of the neutral theory. And yet, half of all data on evolution are interpreted by this theory (the other half morphology and fossils). Neodarwinims is contradicted by half of all data on evolution and yet Coyne’s book says that it has no factual contradictions.

  35. 35
    AmerikanInKananaskis

    shuangtheman, you are a perfect example of why ID advocates need to be educated about evolution before they open their mouths.

    Neutral theory and neo-Darwinism are perfectly compatible.

    One says that most DNA changes are selectively neutral. The other says that changes that are NOT selectively neutral will be seized upon by natural selection.

    What’s not to get?

    Seriously. I came to this site after reading some thought-provoking work by Dembski and others, and because the racist/genocidal/eugenic implications of Darwinism were so obvious that I thought I should align myself against them. I really didn’t know that most of the minor-league ID advocates know so little about what they criticize.

  36. 36
    AmerikanInKananaskis

    Nakashima, yes you are right. My original comment @18 was directed at Dr. Dembski, not at Dr. Davidson.

    Unfortunately, I skipped over Allen’s comment (because I don’t particularly care what he has to say) and didn’t catch his error. Thanks for pointing it out.

  37. AmerikanInKananaskis

    I am certainly familiar with that kind of rationalization.

    My point however is:

    Jerry Coyne should not cheat and mislead. He should not spin data that falsify neodarwinism into something of the opposite. If you are honest, ask him to retract the book.

    Second, if human and yeast differ by 60% in a gene, the neutral theory says that all these differences are neutral to yeast as well as to human. This means that natural selection/neodarwinism has nothing to do with the genetic changes that is associated with the evolution to human from simple organisms. Try teach this message of the neutral theory to the lay public.

    There is a reason for Coyne et al to avoid the neutral theory. it simply cannot be taught together with neodarwinism without making a joke of the latter.

    Plus, the neutral theory is false. Essentially, the molecular data has yet to be correctly interpreted by any existing theory. The new MGD hypothesis is the first theory that interprets all the data, molecular or not, without a single contradiction.
    http://precedings.nature.com/d.....ion/2/html

  38. Nakashima:

    “it did do so by changes to the genome easily explicable by copying errors of the bacterial host machinery. The result was improved fitness by three orders of magnitude. RM+NS, ne? So I don’t think ‘modern evolutionary theory’ got it completely wrong.”

    I have not read the paper, but usually the designation of something as a “copying error” has turned out to be vastly wrong throughout biology. I’m sure there are some cases of copying errors, but what really seems to be in play is what Caporale calls an “implicit genome” – that is, the genome has not only its present value, but an implicit set of options available to it – paths for it to navigate to. These are not copying errors, but rather guiding structures to tell the cell the optimum places to make changes, and even in many cases they way in which the changes should happen.

    The simplest and easiest to understand of these are SSRs – short repetitive sequences that mainly mutate by adding and removing copy numbers, not by changing the individual base pairs. These often adjust regulation of larger regions of gene expression. It would be difficult to classify such mutations as “copying errors” when it seems to be acting like a tuning knob with the purpose of manipulation.

    As I said, I’m sure some copying errors do occur, and occasionally they may bring benefit, but most of the evidence so far, in the places which have had the most study, seem to indicate that there are systems in place guiding the mutation of DNA to a large extent. The places where “copying error” is thrown about is usually either in cases where the mechanism has not been fully researched, or when it is a metaphysical presupposition that all changes must be, by definition, “copying errors”.

  39. Sorry about the confusion in the numbering of comments. Because my comments are always held for moderation, they do not appear for several hours (sometimes more than a day), and during that period of time the numbers of the comments changes.

    To avoid this problem from now on, I will not include a reference to the comment number, but will simply paste the comment to which I am referring.

  40. AmerikaninKananaskis wrote:

    “I came to this site after reading some thought-provoking work by Dembski and others, and because the racist/genocidal/eugenic implications of Darwinism were so obvious that I thought I should align myself against them.”

    As has been amply demonstrated in previous threads at this website, virtually all philosophical and religious traditions can be distorted by people pursuing racist, genocidal, and eugenic programs. There is no evidence from evolutionary biology that directly supports such programs, and considerable evidence acquired since 1945 that can be used to oppose them. For more on this subject, please read Stephen Jay Gould’s book, The Mismeasure of Man.

  41. 41
    AmerikanInKananaskis

    Second, if human and yeast differ by 60% in a gene, the neutral theory says that all these differences are neutral to yeast as well as to human.

    No. You’re wrong. That’s not what it says at all. That’s beyond incorrect.

    There is a reason for Coyne et al to avoid the neutral theory. it simply cannot be taught together with neodarwinism without making a joke of the latter.

    Say wha? All textbooks on evolutionary theory contain extensive treatments of both, including how they interact.

    Please, before you make these claims, learn what you’re talking about. Things like this are an embarassment to people who actually want to see ID promoted.

  42. Textbooks and primary journal articles are an entirely different matter from popular books to lay public. Can you pick a Joe on the street who knows who Kimura is? Not one in a million. yet thanks to books by Coyne et al, nearly all know who Darwin is. But it is Kimura’s theory not Darwin’s that is relevant to the modern study of evolution in the past 46 years.

    Again, answer the question: can you honestly say that Coyne did the right thing in his book by misrepresenting contradicting facts as supporting evidence for neodarwinism? if you do not want to address this question, you have no business in the matter of truth.

  43. AmerikanInKananaskis

    shuangtheman says: “Second, if human and yeast differ by 60% in a gene, the neutral theory says that all these differences are neutral to yeast as well as to human.”

    AmerikanInKananaskis says: “No. You’re wrong. That’s not what it says at all. That’s beyond incorrect.”

    here is what Kimura says on this:
    “The neutral theory claims that the great majority of evolutionary changes at the molecular (DNA) level are caused not by Darwinian selection but by random fixation of selectively neutral or nearly neutral mutants.”
    Kimura, M. (1986). “DNA and the Neutral Theory”. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 312 (1154): 343–354. doi:10.1098/rstb.1986.0012.

    Rephrase this using our example:
    The neutral theory claims that the great majority of evolutionary changes at the molecular (DNA) level, i.e., the 60% difference between yeast and human, are caused not by Darwinian selection but by random fixation of selectively neutral or nearly neutral mutants.

    I dont think you know anything substantial about the neutral theory.

  44. AmerikanInKananaskis

    It is clear that you are a fake ID follower. if you are not, you should jump on any opportunity to discredit Darwin followers. Coyne’s book is the latest and best opportunity to do so. Now, do you dare to do it or not by simply say in your next post here that Coyne cheated in his book?

  45. JAD, if you really want to know who I am you may have a look here.

    Back to your “hypothesis”:

    Suitable material would be female frogs (or other animals or plants) known to be heterozygous for one or more chromosme inversions or other chromosome rearrangements. It is to be predicted that the diploid gynogenetically produced offspring of such females would be females one half of which would be like the wild type mother, the other half a new female species. This new female species could then hybridize with males of the original species and establish a new bisexual species through ordinary Mendelian means.

    I.e., you would consider children of individuals with balanced trisomies as new species, would you? E.g., female Down patients with (45, xx, t(14,21q)) or (45, xx, t(21q,21q)).
    Still, some of their offspring would be normal due to inheritance of normal copies of chromosome 21. Thus; if you were right a single woman would have children of two different species.

  46. #33 tragic mishap

    John “Credentials” Davison:

    “A monophyletic evolution is no more established than a monotheistic God. They are both based on pure ideological assumption without a shred of ascertainable fact to justify them. Those who choose to believe in either will never be scientists.”

    What?

    I’ll also ask: Huh?

    John, if you mean we will never scientifically validate a monotheistic belief over polytheistic, well, maybe. there may be arguments against that, but it would at least appear to be reasonably logical. Refer to Denise’s last post, her five arguments for why religious faith is not “belief without evidence”:

    2. Some doctrines are based on logic. For example, why are there not Two Gods? Well, what happens when the irresistible force meets the immovable object? The point is, it can’t happen. So there are not Two Gods. Or Many.

    The problem with your post is the assumption that if you believe in a monotheistic God, you “will never be a scientist”. What does one have to do with the other? And why is your belief in two Gods (if you were being serious) immune from the same illogical, arbitrary statement? Perhaps because it was illogical and abritrary to begin with, lending itself no obligation to any rational, fair application?

    Personally, I think the traditional Christian view makes more sense than any other (one of many reasons I am Christian), which is one God, and a powerful force, Satan, who is still hopelessly powerless compared to the one true God (hence the necessity yet fullness of santification through Christ’s sacrifice). Combine that with other factors, like those listed in Denyse’s post:

    1. Evidence (at least of god(s)) – finely tuned universe, complex, specified biological structures, consciousness, altruism

    4. Testimony – I have much greater reason to belief dozens of people who risked/sacrificed their lives reporting events that where witnessed (and not denied) by hundreds or thousands of people rather than one guy, hungry for power, alone in a cave, who had “prophetic revelations” which directly conflict with previous revelations.

    5. Experience – Everything that’s happened in my life has pointed to the validity and truth of the Bible

    While my belief is still not based (entirely) on scientificly validated evidence, that doesn’t mean I can’t be a scientist (i.e. “engage in a systematic activity to aquire knowledge”, in its broadest terms). And I would argue that my belief is more logically validated than your own (or what little of it you just disclosed, if that is truly your belief), but that would probably enter into the realm of philosophy.

  47. Mr JohnnyB,

    Since the paper is about reproduction of viruses in a bacterial host, I think it is directed at the issue of mutation by copying error, not the more general kinds of genomic variation that can happen in cells.

    One thought I had from reading the paper was that they didn’t sequence the E. coli host at the end of the runs to see if it had evolved also.

  48. Mr Shuangtheman,

    I’m sure Coyne’s book is fascinating, but it is not part of the primary scientific literature. If ID cannot critique, and eventually contribute to, the primary scientific literature, it doesn’t matter what you feel about popularizations. This thread was started to discuss a paper in the primary literature. Can we please continue discussing it?

  49. 49

    Nakashima in #32

    If two forms produce fertile hybrids they are BY DEFINITION the same species. It was Theodosius Dobzhansky, a Darwinian by the way, who gave us this unambiguous, eminently testable definiton of what a species really is. It is sound as a dollar, it is testable and its results are not to be ignored. That is why the Darwinians choose not to use it.

    Here is an example to illustrate the point. Some Darwinians claim that dog varieties represent “evolution in action.” Among these are Richard Dawkins, and at one time William Provine although I am unsure as to his present postion.

    They have cynically ignored a well documented instance which involved a spontaneous union between a male St. Bernard and a female Dachshund. The Dachshund delivered a single pup which proved to be fertile herself, thereby proving beyond any doubt that the Dachshund and the St. Bernard were the same species. The pup was named “rollmops” because her body rubbed on the ground. She had inherited her short legs from her mother but a very large body from her father. During her pregnancy her body dragged on the ground to such an extent that it had to be protected by towels. The case is fully documented in “Inheritance in Dogs” by Ojvind Winge, the distinguished Danish geneticist, page 44. Using Dobzhansky’s physiological definition we now know that the wolf, the coyote and the varieties of dogs are actually a single species. That any Darwinian should neglect these facts is a disgrace. So you see the varieties of dogs are no more different species than are the members of Darwin’s precious finches.

    Just because some taxonomist somewhere in the distant past has decided that two forms are separate species means absolutely nothing. In the absence of the physiological criterion, no such conclusion is ever valid.

    I am willing to bet that a cross between a Chihuahua and a Great Dane would result in fertile pups in either direction. It would undoubtely require artificial insemination. If the bitch is the Great Dane I predict she will have a very large litter, possibly a world record. If the bitch is the chihuahua and the sire is the Great Dane (the son of a bitch), she will have a single pup for the same reason that the Dachshund bitch had a single pup when she was inseminated by the St. Bernard. This isnan example of what is known as embryonic regulation.

    I have been trying to find someone who is willing to offer their pets up for this very important experiment, but so far no one pays any attention to me as is typical of many of my proposals, includimg some I have made right here at Uncommon Descent! That neither surprises me nor troubles me as I have supreme confidence in my science and that of the sources on which mine is so firmly based.

    You must understand that Darwinians are not scientists. If they were they would have performed these experiments years ago. For all I know they may have and, unhappy with the results, they ignored them. I wouldn’t put anything past a Darwinian. They are so committed against the notion of a planned and guided evolution that they have abandoned science entirely to expend all their energies to the denigration of those of us who do believe in a planned and guided evolution. The classic examples of this “congenital syndrome” are provided by the dynamic duo of P.Z. Myers and Richard Dawkins, neither of whom ever did an evolutionary experiment in their lives and probably never will. They have gone so far as to give up science entirely to dedicate the rest of their miserably unhappy lives to the conversion of every living human being to “universal atheism” by denigrating any person or institution that was so out of touch with reality as to believe that there was a purpose in the world that we all see around us. As is well known, they are now peddling Tshirts, coffee mugs and bumper stickers, all emblazoned with the big red A for ATHEISM.

    It is hard to believe isn’t it?

    Not at all. There it is for all to see.

    I can’t wait to enjoy the vituperation this will evoke.

  50. I can’t wait to enjoy the vituperation this will evoke.

    It was a pretty sensible post to me, JAD.

  51. 51

    Nakashima: This thread was started to discuss a paper in the primary literature. Can we please continue discussing it?

    My impression of ID people is that they know very little about molecular evolution. In fact no one does. The theoretical foundation for the interpretation of molecular evolution is largely incorrect. This paper is a good example.

    If ID really wants to contribute to the scientific literature, it needs to come up with scientific explanations of factual data that scientists collect daily. The best opportunity is to come up with a theory to explain the molecular clock and other molecular data accumulated in the past 46 years. These data remains unexplained by any of the existing theories, neodarwinism, neutral theory, ID, etc.

  52. Nakashima

    “Since the paper is about reproduction of viruses in a bacterial host, I think it is directed at the issue of mutation by copying error, not the more general kinds of genomic variation that can happen in cells.”

    This is only true if you assume that viruses are not part of a designed system. There is no reason why virus DNA does not make use of the mutational system of the host in the same way that it makes use of its copying system.

  53. Allen McNeill said:

    rants rather than logical arguments supported by evidence…

    That is a very sorry statement coming from a die-hard Darwinian fundamentalist that has never seen through the smoke and mirrors of virtually all Darwinian explanations. It gets worse…

    As for how to deal with people who are apparently constitutionally incapable of carrying on a reasoned intellectual argument,…

    Even atheist astrophysicist Fred Hoyle saw through the Darwinian tree of imagination passing off as reasoned intellectual argument. Maybe ask yourself why he said Darwinists were mentally ill?
    Gets even worse…

    the best thing to do under such circumstances is to do what you would do with schoolyard bullies

    Bullies!? That’s like the devil calling Mother Theresa a rotten sinner.

    But then you Darwinists know a whole lot about academic bullying eh? You’re the great experts at it these days. Darwinists have such a wonderful track record – of witch hunting, discriminating and persecuting – that it pales compared to what scientists did to Galileo by using the highest power of their day against him!

    Darwinists have revealed themselves as pathologically paranoid of any dissent and thus exhibit fascist behavior towards all dissidents!

    Get real Allen. This kind of talk from any Darwinist makes them look lost in the woods without a compass or even knowledge of the existence of north and south poles.

  54. 54

    shuangtheman in #48

    I have proposed with the Prescribed Evolutionarty Hypothesis (PEH) that all of organic evolution has resulted from the controlled release from inhibition of an enormous stockpile of preformed specific information. Furthermore I have presented both direct and indirect evidence favoring this proposal. This hypothesis is based on the realities that we know with certainty occur during the development of every creature as it develops from the egg (ontogeny). Do you not agree that all the necessary information for the adult is already contained in the egg even before it begins to develop?

    All I have done with the PEH is to assume that was also true with our original ancestor, millions of years ago. This notion is not original with me as it was proposed by William Bateson and Leo Berg long ago. To understand the reasons I have reached this perspective I recommend that you read my
    “An evolutionary manifesto: a new hypothesis for organic change.” You will find it under John A. Davison on the side bar along with other of my evolutionary papers.

    Of course if you have already rejected my hypotheis there is no point in responding to my suggestion. Let me say however that the PEH is in full accord with the Universal Genome Hypothesis (UGH). Both are based on the same body of facts, facts that show that the information thought to be of recent origin may often be found in very simple primitive organisms. I have summarize some of this evidence recently discovered evidence in my 2005 paper “A Prescribed Evolutioary Hypothesis” also available on the side bar.

    Most important, in order to liberate ourselves from the Darwinian model we must first discard it in its entirety as it is completely without foundation. It has always been that way.

    We are currently engaged in a very real war for our very souls. Are we accidents as the Darwinians insist or are we the ultimate products of a planned phylogeny? I favor the latter position because it is required by the present state of our knowledge.

    I agree with Leo Berg as he commented on both ontogeny and phylogeny -

    “Neither in the one nor in the other is there room for chance.”
    Nomgenesis, page 134.

    Ontogeny remains the best model for phylogeny and I rely on it heavily.

    There is no middle ground between Darwinian atheism and a purposeful goal directed evolution. Each can take his pick as I have taken mine.

    “Everything is determined…by forces over which we have no control.” Albert Einstein, a summary in complete accord with the Prescribed Evolutionary Hypothesis.

    I hope this helps.

  55. 55

    Pardon my typos. I am a lousy proof reader.

  56. 56

    John,

    I am familiar with all your papers. You may right, in the sense that most religions may be, that there is a God. But saying God has role in evolution is not a theory that can direct daily research. Neither is saying that there is designer for this and that.

    What one needs is a theory that explains and predicts facts that scientists collect everyday. If yeast A shares 40% identity in a gene with yeast B as well as with human, which is called the genetic equidistance result first found in 1963 by Margoliash, we need a theory to explain this.

    neodarwinism would predict that yeast A and B should be much more closer than A is to human. This has been proven to be sheer nonsense. Thus, came the molecular clock and the neutral theory, which says yeast B and human have the same mutation rate or clock rate. This is also sheer nonsense as one can easily prove that yeast and human have vastly different mutation rates and generation times.

    So the genetic equidistance result, also called molecular equidistance by Mike Denton in his 1986 book, remains a puzzle. Can the PEH or ID theory explain it? I dont think so. For ID to make inroads to science, start with an explanation to this result that can be tested?

  57. 57

    Borne,

    Far, far, far be it for me to offer any aide to Allen MacNeil…but… I am fairly certain he was reacting to the constant beating he has taken from Davison over the past few days.

    Wheather that beating was by chance or neccesity, is not my call. Davison will have to speak for himself (which no one can imagine not happening).

    Beyond that, your observations are on the money.

    …carry on.

  58. 58
    AmerikanInKananaskis

    Oh, how I love being called a “fake ID follower.” Hilarious. I guess promoting self-criticism and intellectual honesty in the promotion of ID is something to be avoided.

    You know, if I were a conspiracy theorist, I could say the same about you. Just watch:

    “No one who makes arguments as obviously hollow and meaningless as you could possibly be on our side. You’re intentionally setting up strawmen for the Darwinists to knock down.”

    You see how easy that is?

    Grow up, Huang. I’m done with you.

  59. 59
    AmerikanInKananaskis

    And so I can’t be said to have ignored your question, I will answer it.

    “Yes”, Coyne cheated in his book. It vastly over-simplifies numerous things, and he claims consilience where there is none. (For example, as I recall, at some point he says something like all genes point to the proper species tree. This is simply untrue, but it’s actually easily explained in terms of lineage sorting, etc.) All in all, it’s not a particularly good book because it forgoes ACCURACY for EASE OF EXPLANATION (aka propaganda).

    Nevertheless, this doesn’t change the fact that you are simply WRONG about your claims of neutral theory. And apparently unable to admit it.

    I have made my own view of ID clear here already. Biological limitations were ‘pre-loaded’ in order to guide evolution and increase biodiversity. I fully trust in the power of natural selection and random mutation otherwise.

    NOW I’m done with you.

  60. 60

    AmerikanInKananaskis
    “Nevertheless, this doesn’t change the fact that you are simply WRONG about your claims of neutral theory.”

    My view and challenge to neutral theory actually got published in peer reviewed journals. Here are two:
    The Genetic Equidistance Result of Molecular Evolution is Independent of Mutation Rates
    http://www.omicsonline.com/Arc.....1.092.html

    Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are
    http://www.pubmedcentral.nih.g.....id=2649772

    What do you have to show for your understanding, shall we misunderstanding, of the neutral theory?

    But I am glad that you passed the honesty test about cheating by Coyne. All Darwin followers failed that test when I challenged them. Okay, you are a true IDer. But you do need to learn more about Darwinism in order not to grant it too much credit. Start with calling natural selection random. I am astonished that ID people has yet to refute this stupid claim and even grant this to be true. For example, Jonathan Wells granted this when he debated Massiomo Pigliuchi, http://video.google.com/videop.....ent=safari

    For my refutation of this lie, see here,
    http://thegoldengnomon.blogspo.....hance.html

  61. Dr Davison,

    On this thread, you’ve made the following statements:

    This theoretical reconstruction is given credibility since it is now apparent through the work of Eric Trinkhaus that Homo sapiens and Neanderthal hybridized.

    Neanderthal is uquestionably a separate species from Homo sapiens.

    If two forms produce fertile hybrids they are BY DEFINITION the same species.

    I don’t think that all three can be true.

  62. 62

    shuantheman

    I have no idea how anyone can hope to understand a preplanned, prescheduled phylogeny. It is not necessary to understand how this is possible. It is only necessary to prove that it is so. I believe that proof is already at hand. The same can be said for how many Gods there are or were. There is no doubt in my mind that the forces we now call Gods must have once existed. Actually, my suggestion on there being two, one benevolent, the other malevolent is already part of the Judeo-Christian ethic. Isn’t Satan (Lucifer) a fallen angel? Satan is my second God and his handiwork is evident in those that refuse to postulate any Gods at all now or in the past. They are known as atheists and Richard Dawkins, Christpher Hitchens and P.Z. Meyers are the results of Satan’s influence. I regard those three in particular as truly evil. They are deliberately trying to undermine everything that made Western civilization great. Can you imagine a scientist plastering his atheist pontifications on the sides of London busses? You don’t have to imagine it as it is a reality. And how about Myers calling the President of the United States “asshole-in-chief” and calling the Holy Father “bennie.” That is just the surface of the hideous invective that is Myers’ constant daily fodder for his adoring fellow gutter-mouthed Darwinian atheist flock. Incidentally, Pharyngula is a member of MacNeill’s blogroll. Others include Panda’s Thumb and richarddawkins.net. I list those blogs and many others on my sidebar under the caption “Darwinian Sorcery.” I have been banished from them all and I am proud of it.

    I am nominally a Roman Catholic who has to struggle between faith and science as many other scientists have before me. The simple truth is that nobody knows a damn thing about God or Gods. All I do know is that there had to be one or more in the past to produce the world we now see around us.

    For Catholic and nonCatholic alike I recommend “How the Catholic Church built Western Civilization” by Thomas E. Woods Jr.

    The word evolution derives from the Latin verb “evolvo” meaning to unfold as the pages of a book. All I am saying is that some thing or some things wrote the book.

  63. 63

    Nakashima in #58.

    If you follow your reasoning to its logical conclusion all the products of evolution are a single species. My insistence that Neanderthal was a separate species of the genus Homo is based on the same morphological characters that led others to conclude the same. Today we no longer have the intermediate forms to examine and test.

    I have offered a perfectly reasonable reconstruction which you seem mostly interested in discrediting. Thanks and keep up the productive work.

  64. JAD,

    Catholics believe in one God, the Father Almighty, maker of heaven and earth and of all things visible and invisible.

    Satan is no god. His fall was because he sought to be like God.

  65. Dr Davison,

    OK, so we are dropping statement 3, the species definition based on fertile hybrids. I agree with that choice. Though now I don’t see why you’ve insisted on the domestication of Darwin’s finches.

  66. Mr Nakashima,

    I’m trying to eliminate some confusion on my part.

    I’m curious what your definition of species is and/or examples. To me it has always seemed a fuzzy definition even with college courses, or maybe I’m confusing the debates past and discussions now with old course material.

    Dr Davison stated,

    “If two forms produce fertile hybrids they are BY DEFINITION the same species. It was Theodosius Dobzhansky, a Darwinian by the way, who gave us this unambiguous, eminently testable definiton of what a species really is. It is sound as a dollar, it is testable and its results are not to be ignored. That is why the Darwinians choose not to use it.”

    Do you agree with the initial statement in bold? It appears you do not. If not, why not? I was going to say more, but in an attempt of getting clear definitions and understanding where you stand, I’ll stop here.

    I appreciate the new posters here at UD. And hope you continue.

  67. Dr Huang,

    “My impression of ID people is that they know very little about molecular evolution. In fact no one does.”

    This is a refreshing attitude. This blog has both scientist and lay people. And “ID people” might include anyone from Dembski, Meyers, or John Sanford, Cornell geneticist, author of Genetic Entropy to lay people like me :), a college educated software analyst, but with little knowledge of molecular evolution theory except undergrad courses and what I’ve read recently. I’m rusty to say the least on current issues. As to who post here day to day, some are highly qualified. At the very least its open dialogue I enjoy that is not found at other blogs where doctrine is enforced above realistic questioning of failed theory to date. In fact the ridicule escalates to levels of hatred it seems at other blogs.

    “The theoretical foundation for the interpretation of molecular evolution is largely incorrect.”

    Would you tell that to the Darwinist? And maybe you can elaborate what “is largely incorrect?” Include your data on molecular clocks if you like?

    I look forward to reading your paper(s). The abstract I read on molecular clocks is intriguing. Hope you continue to post here.

    “If ID really wants to contribute to the scientific literature, it needs to come up with scientific explanations of factual data that scientists collect daily.”

    They are working on it. Please see Biologic Institute

    “The best opportunity is to come up with a theory to explain the molecular clock and other molecular data accumulated in the past 46 years.”

    It is interesting that Francis Crick considered DNA Code to be generated by intelligence, possibly seeded. The question is, are there optimal design codes and laws of design? If so, what then do we know today of our own design constraints for optimum performances and do they exist in nature?

    Linguistically, why must scientist use engineering metaphors to desribe pieces of the puzzel in organic life? For example, like ATP – “smallest motor in the world?” Is this trivial, or a language forced upon researchers? Why must a motor be described in RPM between human made inboard motors for example and flagellum? There is no other way of comparison but in engineering terms of force, velocity and motion. A nano structure far surpassing anything our best engineers have made to date.

    I’m also curious why you consider the molecular clock one of the best opportunities? And what do you see as other opportunities in the molecular data?

    “These data remains unexplained by any of the existing theories, neodarwinism, neutral theory, ID, etc.”

    Agreed. But ID has only formed within the last 10yrs or so, and only seriously got off the ground in research efforts the last year or so. Darwinism has 150yr head start. Plus at least 70yr dominance in research funding.

    Today, if anyone dare mention Design as an alternative, your career can be ruined if you do not have tenure. The Darwinist still own the financial structure. They still have the keys to appointed chairs and funding.

    They are backed by the Media. Media can care less or does little to expose the hypocrisy at major US universities.

  68. 68

    Nakashima in #65

    I don’t insist on the domestication of Darwin’s finches at all. I already KNOW they are all the same species. That has been established by the Grants based on field observations of spontaneous crosses. I was only pointing out that the Darwinians are afraid to test their silly hypothesis. THEY ARE NOT SCIENTISTS because scientists TEST their hypotheses.

    You and others as well don’t seem to understand that there is ABSOLUTELY NOTHING in neoDarwinism that ever had anything whatsoever to do with an ascending evolution which is no longer in progress, ABSOLUTELY NOTHING. It is a flaming joke, an hallucination, a fantasy which has no substance and should have been discarded the same day that Darwin published his silly little book. As a matter of fact it WAS discarded by Adam Sedgwick, Darwin’s geology professor the same day he read it. It has since been discarded countless times by real honest-to-God scientists. It has survived only in the minds of congenital atheists like Ernst Mayr, Stephen J. Gould, Paul Zachary Myers, Richard Dawkins and Uncommon Descent’s own house Darwinian, Allen MacNeill.

    The Darwinian atheist based hoax will continue to survive as long as such poor souls breathe. Darwinism, like liberalism in general, has been shown to have a strong congenital component. So has whether or not one believes in a Creator. Darwinism is a deficiency disease for which there is no present cure. It is perfectly resistant to any form of reasoned arguement. It is impervious to experiment, every one of which has shown it to be without foundation. In short, it is a “disaster,” a blight upon the face of experimental and descriptive science, and a perennial embarrassment to all those institutions which still permit its faculties to perpetuate it. Evolution should be taught as an undeniable reality for which the mechanism by which it took place (past tense) is still not known. Then it might be appropriate to ask the studnet whether or not he thinks it took place by chance.

    I offer Otto Schindewolf’s summary of the evolutionary sequence with which I am in complete agreement -

    “This leads to the conclusion that the main features of the evolutionary trend were laid out RIGHT FROM THE START with the abrupt, discontinuous production of the type, and with evolutionary potential being restricted RIGHT FROM THE START to certain paths.”
    Basic Questions in Paleontology, page 360, my emphasis in caps.

    In other words a “Prescribed” evolution.

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

  69. 69

    This is for Tribune 7 whoever that is and I’m sure I will never know.

    Yes sir! Whatever you say sir! I will never make that mistake again sir! Plesae forgive me sir!

  70. Dr Davison,

    So spontaneous fertile crosses establish Darwin’s finches as a single species. I have to assume humans and Neanderthals are a single species also, by that logic. Is that correct?

  71. Mr DATCG,

    You are very kind to ask me my opinions.

    I prefer the definition of ‘an interbreeding population in nature’, which I think is from Mayr. However, I realize that this definition breaks down in places. Ring species, for example. Also for asexual life and single celled life that exchange DNA easily via conjugation.

    It’s a fuzzy category. If a virus gets embedded in the human genome, are we the same species? Obviously not. If scientists remove huge swaths of non-coding DNA from a mouse, did it stop being a mouse? No. So whether it is approached from genetic, cladistic, or operational perspectives, it remains fuzzy. I accept that. The world has no responsibility to fit our categories.

  72. 72

    Nakashima #70.

    I proposed a viable mechanism for true speciation through the semi-meiotic production of a new species in a single step. I then presented a reasonable means by which that new female could breed with a male of the original wild type and through ordinary Mendelian means a new species could be established. This can offer a rational explanation for the fact that Homo sapiens/Neanderthal hybridization apparently did occur.

    In fact I can say with some certainty that any new soecies must have coexisted for at least a short period of time with its immediate ancestor. You see I do not believe in special creation. That does not mean that it did not occur.

    I don’t believe you even understand the cytological mechanics of this process. You also don’t understand that sterility is a matter of degree.

    You are hell bent on one goal only which is to denigrate my semi-meiotic hypothesis whatever it takes.

    Well I am sorry Nakashima, but you have failed miserably. Now if you think you have succeeded, I recommend that you publish a paper expoaing my SMH as a failed hypothesis, something no one has yet done. They won’t either until it has been subjected to the testimony of experimental science.

    Now if you want to dispense with an untested hypothesis, that is your business but I am pretty sure you won’t find a decent journal that will publish your paper. You sure aren’t going to destroy my hypothesis with mere words. Science doesn’t work that way. I thought everybody knew that by now.

    Speaking of partial sterility, why hasn’t someone tried to see if a human/chimp hybrid could be produced? While it might very well be viable, I can be absolutely certain that it would be sterile for the same reason that a mule is.

    Josef Goebbels, Hitler’s Minister of Propaganda once said -

    “It has not yet been demonstrated that non-Aryans cannot hybridize with apes.”

    Apparently the Germans had tried and failed.

    Have a nice day!

  73. Dr Davison,

    Thank you for your wishes of a nice day. It is spring, and nice days are coming more and more frequently!

    I have no wish to destroy your semi-mieotic hypothesis. I am merely trying to understand how your various statements fit together. I fully accept the matter of degree in sterility, but I have trouble seeing how it is reconciled with a rigid species concept.

  74. Nakashima-san

    Here is the link to JAD’s PDF on his SMH

    It is interesting and more sensible than NDE.

  75. Nakashima-san

    Just about all of us here accept evolution to some degree.

    If you accept say, that lions and house cats have a common ancestor, you are going to have to come up with an explanation as to how they came to be different species.

    This does not mean that the word “species” should be loosely defined or meaningless, but for evolution, even as to this degree, to be true, the definition would have to break down at some point.

  76. DATCG

    When I say no one understands molecular evolution, I mean no one, Darwin followers or ID followers. No one can make a single informative statement in this field that has not countless contradictions. The most commonly taught information on molecular evolution is this statement from the NAS booklet on evolution: “If two species have a relatively recent common ancestor, their DNA sequences will be more similar than the DNA sequences for two species that share a distant common ancestor.” But this statement is not completely true and has countless contradictions. See here my rebuttal of this statement and the response from the esteemed Darwin follower Francisco Ayala. http://www.amazon.com/review/R8WB8ZQSOUVGC

    The only meaningful statement in molecular evolution that has no contradictions is ‘the inverse relationship between genetic diversity and epigenetic complexity.’ The equivalent of this in more general terms is ‘the more the order/complexity of the organism relative to others, the less the disorder/randomness of the organism relative to others.’ This message is what the MGD hypothesis is all about. To increase complexity, one must reduced randomness and disorder. For example, human and bacteria. Human can tolerate very few randomness in terms of random mutations, comparing to bacteria. In evolution, there is gradual decrease in mutation rates associated with increase in genome size or organismal complexity. See here. http://blogs.sciencemag.org/or.....d-clu.html

    Now reducing mutation/variation is slow bleeding to death to the Darwinian process. How can such process by itself leads to its own death? It would make sense only if an opposite force is pushing for order increase and disorder decrease.

    The key new question for ID to ponder is what is causing the decrease in mutation rates and mutations/randomness in general during the evolution process from simple to complex or from high disorder to high order. Mutation/variation in DNA is good in the Darwinian process, but is bad for the process of creating complexity and must be suppressed. And it is suppressed, which is supported by all factual observations as explained by my MGD paper.

    “I’m also curious why you consider the molecular clock one of the best opportunities? And what do you see as other opportunities in the molecular data?”

    The molecular clock is a tautological interpretation of the most remarkable result in molecular evolution, the genetic equidistance result. It is wrong but is the foundation for the field of molecular evolution. To replace the clock is to restore truth and sanity to the field. The MGD hypothesis is my attempt to do so.

  77. shuangman:

    In response to your post [76], I suggest you try and find some of the writings of the 19th century engineer Ferguson Jenkin ( there is no ‘s’ at the end!). He develops an argument that goes along the line that as the more complex something becomes, the fewer the possibilities there are for newer forms. He uses the example of a crystal to make his point. It’s been four years since I read it, and I can’t even remember where I ran into it. But try online.

    Dr. Davison: This is a link [ http://www.physorg.com/news127667797.html ] to a PhysOrg article that came out almost a year ago to the day. It involves a lizard species transplanted from one Adriatic island to another. After the transplant, in LESS than 35 years time, it develope cecal valves in its stomach to handle the increased amount of plant life in its diet. It strikes me as Lamarkian—because of the rapidity—more so than a chromosomal change (I suspect if you took this new ‘form’, it would easily procreate and multiply with the lizards from the original island), but I would be interested in your take on it.

  78. 78

    Tribune 7

    Thanks for calling attention to my papers, something I have been recommending for some time. In it one can find an explicit explanation of semi-meiotic cytology complete with a diagram and two examples of its occurrence in contemporary organisms. The same explanation and diagram can be found in my unpublished “An Evolutionary Manifesto” also available on the side board here and elsewhere. The Manifesto, some 50 pages in length, summarizes my evolutionary perspective circa 2000. Since then my views have changed some with an emphasis on my conviction that evolution is no longer in progress.

    Of course none of this is acceptable to the Darwinians which is fine with me!

    Thanks again.

  79. 79

    Pav in #77

    That is an interesting example. What is critical is back crossing the transplanted forms to the parental forms on the original island and to do these crosses reciprocally to look for possible maternal effects. It is not unusual for transplanted animals to undergo great initial increases in number and variability. Witness the population explosions that characterized the introduction of the English Sparrow when it was introduced into North America and the rabbits when introduced into Australia. If this is truly Lamarckian it should be reflected genetically and if it is, it will very signifcant. I will remain skeptical until such demonstration materializes. Once again, the proof is in the genetic experiments.

    Darwin’s finches also show profound morphological changes related to diet which are clearly not Lamarckian because they are freely reversible. Many organisms have hidden phenotypic lability which selection can act upon. Any reversible effect is neither Lamarckian nor Darwinian because evolution has never been a reversible phenomenon.

  80. 80

    Pav

    Chromosome restructurings are instananeous and so were all creative evolutionary events. Gradualism is just one more defect in the Darwinian model. I do not believe that any organism ever gradually transformed into another one, and I know of not a single example of its occurrence.

  81. I have no idea how complex cecal valves are, so I am not going to that argument against the Darwinian mechanism being responsible for these results. But if this incredibly quick change happened in a Darwinian fashion, that means at least one lizard developed cecal valves, giving it a selection advantage, leading to the trait spreading throughout the population. Forget the wildly short time scale, how much of an advantage it really is, etc…if just 10 lizards without cecal valves was able to come up with a cecal-valve-weilding lizard within 36 years (presumably early in the period, to allow the proliferation of the trait, assuming a Darwinian mechanism), wouldn’t the same genetic mutation be present in some lizards in a population of hundreds or thousands on their home island? If it really was an “accident” that the feature arose on the new island, wouldn’t the same “accident” happen at the same rate on the home island, even if they aren’t advantageous? I’m not saying that the home island should also be loaded with lizards with cecal valves, just that SOME lizards should have cecal valves just due to genetic mutations (if, presumably, that’s how it arose on the new island).

    If there aren’t any cecal valves on the home island, this is a clear case of some type of front-loaded evolution: biological structures responding to environmental changes, not environmental changes selecting random biological structure change.

  82. Chromosome restructurings are instantaneous and so were all creative evolutionary events. Gradualism is just one more defect in the Darwinian model.

    The minimum mutation that can occur when DNA is replicated is a change in a single nucleotide. Such a tiny can nonetheless result in a large effect in the phenotype, for example as occurs with the mutation that results in achondroplasia.

    Would Dr. Davison consider this a saltational event? If so, all mutations are instantaneous saltations. Or are we playing semantic games here?

  83. Such a tiny change>/b> can…

  84. Blimey!

    Such a tiny change can…

  85. Alan Fox:

    Such a tiny can nonetheless result in a large effect in the phenotype, for example as occurs with the mutation that results in achondroplasia.

    But that doesn’t even lead to a new species.

    You not only need to account for new species but new body plans and body parts.

  86. You not only need to account for new species but new body plans and body parts.

    What are body plans and body parts made of, Joe? I think they are made of cells. I think you are falling into the same semantio trap as the good Professor and DaveScot, from whom you borrowed the line.

  87. 87

    I see Alan Fox is still following me around whereever I go as the self appointed one man goon squad for Wesley Elsberry, P.Z. Myers and Richard Dawkins.

    As always he contributes nothing to any discussion, issuing only sarcastic mindless drivel. I have no intention of honoring him by responding to him. I long ago lost all respect for him and his cronies from Pharyngula, richardawkins.net, Panda’s Thumb and especially After the Bar Closes, Wesley Elsberry’s “inner sanctum.” I recommend that others ignore him as well.

    Fox has a special affection for me. He suffers from a severe case of geriatrophilia. In other word he likes old guys a lot, at least this one!

    It is hard to believe isn’t it?

    Not at all. It has been going on for at least three years.

  88. Alan Fox:

    What are body plans and body parts made of, Joe?

    The question isn’t what are they made out of, the question is what makes them?

    What is it Alan, that controls cellular differentiation thus making all the uniquely specialized cells- which happen to have the same DNA?

    Geez Alan why don’t you just address the point instead of flailing away while back-peddling?

    “Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes in Weismann’s “unambiguous bearers of information” or to view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a very small fraction of all known genes, such as developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene.”
    Michael John Denton page 172 of Uncommon Dissent

    And as I said in another thread you can’t even account for the evolution of the eye/ vision system via selected mutations.

    So it appears it is you who have fallen for something and you don’t have any idea what it is.

  89. Mr Tribune7,

    Yes, it is interesting that the event of speciation is the real test of our definitions of species.

  90. 90

    Is anyone in the materialist’s camp planning a response to uoflcard’s analysis?

  91. 91

    Well…in any case uoflocard, I hope you get a response on the Adriatic Lizards. You can search UD and see the original discussion when the paper first appeared.

    I had it saved…the general web response was typical:

    “they developed an entirely new biological feature that didn’t exist in their ancestral population, which ID has claimed is not possible. If the genetics confirm it, it will be definitive proof of macroevolution, and ID will once again have to revise their “theory” to include yet another concept of evolutionary biology that has been proven”

    Strawmen, by means of misrepresentation. And, seemingly unable to comprehend that the event basically eliminates RV+NS as the mechanism.

  92. Fox has a special affection for me. He suffers from a severe case of geriatrophilia. In other word he likes old guys a lot, at least this one!

    It is hard to believe isn’t it?

    You should know this from your main follower VMartin.

  93. 93

    It is very possible that there is nothing left in the genome indicating a program by which evolution took place (past tense). It is my opinion that, like ontogeny, phylogeny involved (past tense) the LOSS of potential with geological time rather than a GAIN.

    Is the adult organism capable of any further differentiation? No, is my answer. Once again ontogeny presents the model for phylogeny. This is one of the reasons I am now convinced that creative evolution is no longer in progress.

    The development of the individual proceeds from a totipotent egg to the adult by a series of steps each of which further limit possible changes. In other words ontogeny proceeds largely, if not enturely, by inhibition. So apparently did phylogeny.

    This notion is not original with me.

    William Bateson anticipated this view of phylogeny nearly a century ago. He regarded phylogeny as -

    “an unpacking of an original complex which contained within itself the whole range of diversity which living things present.”
    Quoted by Leo Berg, Nomogenesis, page 359.

    The source of Bateson’s statement is -

    Bateson, W., Nature 93: 635-642, 1914.

    Leo Berg agreed with Bateson’s view of the evolutionary process -

    “Evolution is in a great measure an unfolding of pre-existing rudiments.”
    Nomogenesis, page 406.

    So it is no wonder that the Darwinians have ignored both the “Father of Modern Genetics” and the greatest Russian biologist of his generation.

    It is hard to believe isn’t it?

    Not at all. It is par on the eighteen hole golf course of Darwinian mysticism, the most ridiculous proposal in the history of science.

    I love it so!

  94. John A Davison,

    Is it possible that the genetic sequence does not do anything except carry out the orders of a program that resides somewhere in/ on the cell?

    This program would be similar to a computer program in that a computer program is not the disk but resides on the disk.

    Joe Gallien

  95. Let me add something to my question, which I thought of last night. I said if ZERO cecal valves were found on the home island, it would be a bad sign for NDET, which still holds. But even if some were found, if they are less numerous than you would statistically suspect based on the rate in which they appeared on the new island, it would still be a bad sign for NDET. The cecal valves that formed on the original island could have been triggered in a few specimens, but not triggered as frequently as on the new island.

    This is not as clear cut as there being zero cecal valves on the original island, because some questions might be unanswerable, especially the question of how many lizards (on either island) inherited cecal valves rather than developed tham (whether Darwinian, Lamarackian, whatever).

  96. Replace “suspect” in the first paragraph with “expect” … sorry for not proofreading.

    But even if some were found, if they are less numerous than you would statistically expect based on the rate in which they appeared on the new island, it would still be a bad sign for NDET.

  97. There is no such thing as a “rate of appearance” of any real evolutionary change. I don’t know how many times I have to repeat this, but EVERY evolutionary event from speciation to the appearnce of every other taxonomic category was an instantaneous event exactly as the fossil record very clearly shows. Only Darwinians insist on gradualism because they refuse to acknowledge what the fossil record demonstrates very clearly.

    Incidentally, this is not a matter for “debate.” “Debates” never resolved anything either in science or in any other aspect of human endeavor.

    Pardon my impatience on this very important matter, so resume debating if you must. I have little more to add here.

  98. “We might as well stop looking for the missing links as they never existed….The first bird hatched from a reptilian egg.”
    Otto Schindewolf

  99. Joe writes:

    And as I said in another thread you can’t even account for the evolution of the eye/vision system via selected mutations.

    If you mean me personally, Joe. No, I doubt I could give an account of the possible hierarchy of development of the mammalian eye. One problem is that eyes don’t generally fossilize, so most of the evidence of possible pathways is in extant organisms. There are many accounts of how this might have happened. If you are genuinely interested in finding out more, why not start with this Wikipedia article. It gives plenty of links to other sources.

    BTW, how does Intelligent Design theory account for the appearance of eyes? Does it suggest why vertebrate eyes and cephalopod eyes are similar but differ in important ways, for instance?

  100. …I did a tiny bit of research (one google search, clicked the 2nd link, as the 1st had already been posted on this thread). It wasn’t until after I read the article that I noticed it was from an ID blog. But in it, I found this quote from the authors of the study (not the authors of the ID blog) (emphasis added):

    “These valves are similar in overall appearance and structure to those found in herbivorous lacertid, agamid, and iguanid lizards and are not found in other populations of P. sicula (the lizard in question) or in P. melisellensis.”

    Here is the final paragraph from the blog. It also doubts the possibility of a Darwinian mechanism, but in a different way (not enough time to develop the mechanism, even if an incremental, beneficial pathway is imagined). It seems to come to a similar conclusion, though, that the possibility for cecal valves were pre-programmed in the lizards, awaiting activation:

    The cecal valve finding is, however, dramatic. This is the finding that drew the comment that the animals “are evolving in ways that would normally take millions of years to play out”. There can be no rationale for a Darwinian mechanism here – involving incremental assembly of the cecal valve. There is no time for this, even if a gradualist route could be found. No, the relevant genetic information must be present in the ancestors and epigenetic factors can be inferred to have activated the relevant mechanisms to make the structure. This research is revealing that organisms have a capacity for variability that goes significantly beyond their current phenotype. This implication has not escaped the attention of creationist biologists, who find this research a vindication of their view that animal radiations are rapid and the expression of innate variability embedded in the genome. It would be an interesting and educational activity for students to evaluate this theoretical model alongside others – although we can already be confident that Darwinism would not fare well in the exercise.

    Here’s the link: Rapid morphological change in lizards

  101. 101

    cha-ging

  102. So John,

    You claim that all necessary information for all organisms was preloaded at the moment or moments of initial creation my one or more gods, I believe? This then unfolds in saltationary leaps at (appropriate) moments.

    In your hypothesis, what keeps organisms in lockstep with their niches? In the modern theory of evolution this is taken care of by adaptation by the environment. Are the saltations controlled by supernatural forces?

  103. how does Intelligent Design theory account for the appearance of eyes?

    It doesn’t. It simply says the data indicates eyes to be designed :-)

    Does it suggest why vertebrate eyes and cephalopod eyes are similar but differ in important ways, for instance?

    Nope. Nor does it suggest why camera lenses are similar but different in important ways to cephalopod eyes.

    Alan, ID is not anti-evolution. Nor is it anti Six-Day Creationism.

    It’s just a rabbit test for design.

  104. In your hypothesis, what keeps organisms in lockstep with their niches? In the modern theory of evolution this is taken care of by adaptation by the environment. Are the saltations controlled by supernatural forces?

    OTOH, how does NDE account for the saltations evident in the fossil record?

    According to NDE how many mutations to the genome would be required to turn LUCA into an elephant? Is reasonable to think this could occur using any observed rate of mutation?

  105. And as I said in another thread you can’t even account for the evolution of the eye/vision system via selected mutations.

    If you mean me personally, Joe. No, I doubt I could give an account of the possible hierarchy of development of the mammalian eye.

    No one can Alan.

    No one even knows if an eye/ vision system can “evolve” from a population that never had one.

    There are many accounts of how this might have happened.

    Nothing within the realm of science though.

    BTW I have read just about everything there is on the subject.

    That is why I can say what I do in full confidence.

    BTW, how does Intelligent Design theory account for the appearance of eyes?

    Observers need a means of observing.

    And seeing that the universe was designed for scientific discovery, well there you have it.

  106. Alan Fox,

    The only evidence for the evolution of the vision system is that we have observed varying degrees of complexity in living organisms, from simple light sensitive spots on unicellular organisms to the vision system of more complex metazoans, and we “know” that the first population(s) of living organisms didn’t have either. Therefore the vision system “evolved”.

    Isn’t evolutionary “science” great!

  107. [Intelligent design] simply says the data indicates eyes to be designed.

    Where, When? How? What data?

  108. OTOH, how does NDE account for the saltations evident in the fossil record?

    I don’t think evidence shows “saltations” (not in the Goldsmchidt sense, certainly. So the necessity for an explanation does not arise.

  109. Alan Fox:

    Where, When? How? What data?

    Where, when and how are irrelevant questions and expose an ignorance of ID.

    These questions can only be answered by studying the design in question.

    And the data is in all scientific papers.

  110. According to NDE how many mutations to the genome would be required to turn LUCA into an elephant? Is reasonable to think this could occur using any observed rate of mutation?

    I don’t know, and I suspect nobody else does. But Toe is the only explanation that fits with the evidence. Do you think elephants were on the ark with Noah?

  111. Alan, ID is not anti-evolution. Nor is it anti Six-Day Creationism.

    It’s just a rabbit test for design.

    Do you mean evolution occured as the evidence shows, but that natural selection was assisted by input from an unknown source, at unknown moments, or is there more to it? What’s a rabbit test?

  112. 112

    Alan,

    What’s a rabbit test?

    The rabbit test of ID shows whether the world has been impregnated by a designer.

  113. “natural selection was assisted by input from an unknown source,”

    This indicates that you do not understand the debate. Natural selection is a minor factor in the evolution debate and possibly the most over blown concept in the history of science. The debate is over how variation was created. Best expressed by Hugo DeVries assessment in 1904, that the survival of the fittest does not explain the arrival of the fittest”

  114. John Davison – I understand your frustration and disgust dealing with the huge number of irrational Liars For Darwin that inhabit both the Internet and academia. However please realize that your posts (both here and elsewhere) are some of the most enlightening I’ve read and are much appreciated by me. I’m sure many here feel the same.

    I don’t blame Allen MacNeill, P.Z. Myers, etc. for avoiding you like the plague. Your 50+ years of studying biology combined with your ruthless attitude towards their atheistic religion must send shivers down their spines.

  115. 115

    You folks don’t need me here. You have Alan Fox to converse with. Furthermore, there is no room for “debate” in science and there never will be. There is only discovery.

    Enjoy the “debate.” If anything important surfaces, which doesn’t seem very likely, let me know.

    jadavison.wordpress.com

  116. 116

    “Davison is the Darwinians’ worst nightmare.”
    Terry Trainor

  117. According to NDE how many mutations to the genome would be required to turn LUCA into an elephant? Is reasonable to think this could occur using any observed rate of mutation? . . .I don’t know, and I suspect nobody else does.

    It’s a question with an objective answer that can be approached methodologically, Why would someone not have an answer, even a tentative one?

    But Toe is the only explanation that fits with the evidence.

    Expect for the part about the indications of saltations, and inability to address whether the mutation rate fits the theory.

    Do you mean evolution occured . .

    I mean ID does not address evolution, pro or con — unless one is defining evolution in such a way that it arbitrarily precludes consideration of design, which would make it dogma and not science.

    What’s a rabbit test?

    An old test for pregnancy. It would only give a yes or no. Other relevant questions — who’s the father, boy or girl — would not be addressed. Despite the limitation, the rabbit test was obviously not useless.

    ID simply says the data indicates eyes to be designed . . . Where, When? How? What data?

    The eye is a device that performs a specific function and has enough complexity to preclude it from coming about by chance. Now you can attempt to address the probability problem — and the concerns Darwin himself had with the eye — via a stepwise evolution from photosensitive skin, but even that would still not account for the complexity of the DNA coding for the production of proteins for the eye and its interactions with the nervous system.

  118. This indicates that you do not understand the debate.

    Absolutely, Jerry§ Please enlighten me. Does ID have a hypothesis or theory that explains the current diversity of life?

    Natural selection is a minor factor in the evolution debate and possibly the most over blown concept in the history of science.

    I disagree. I think it is the central issue.

    The debate is over how variation was created.

    If you mean there is no serious alternative explanation to natural selection, we can agree here.

    Best expressed by Hugo DeVries assessment in 1904, that the survival of the fittest does not explain the arrival of the fittest”

    Well, if you mean, how did life get started on Earth, the toE does not attempt to tackle that issue. I am a pessimist with Hubert Yockey and Robert Shapiro on the OOL issue. Unless we fiond evidence from extraplanetary sources, OOL will remain a speculative subject.

  119. It’s a question with an objective answer that can be approached methodologically, Why would someone not have an answer, even a tentative one?

    For the same reason that I can’t tell you how many grains of sand are on my local beach. It is unanswerable. Or rather, the answer is not tractable to human observation.

  120. …but even that would still not account for the complexity of the DNA coding for the production of proteins for the eye and its interactions with the nervous system.

    This is “The Holy Grail” of biochemistry, to predict nucleotide sequences that would produce proteins of specific function. Again, i am a bit of a pessimist in how long it will be before we start to make progress in this field.

  121. For the same reason that I can’t tell you how many grains of sand are on my local beach. It is unanswerable.

    That question is very much answerable, at least with regard to a reasonable estimate. Determine the parameters of your beach — length, width, depth of sand — count the grains in a sample and extrapolate.

  122. This is “The Holy Grail” of biochemistry, to predict nucleotide sequences that would produce proteins of specific function. Again, i am a bit of a pessimist in how long it will be before we start to make progress in this field.

    Well, ID is science which means it can be falsified but what you suggest would not be the falsification. The falsification would be showing how the sequences directing the functional and specific production of proteins came about without design.

  123. 123

    It is unanswerable. Or rather, the answer is not tractable to human observation.

    So, will you be joining materialists everywhere calling for an end to the current default assumption that life began by chance and necessity?

    As I have asked before, what will you be calling your movement?

  124. Upright BiPed says:

    So, will you be joining materialists everywhere calling for an end to the current default assumption that life began by chance and necessity?

    Why should life be necessary?

    The current default assumption is that natural phenomena have natural causes. Perhaps this is because of the complete lack of evidence for the “non-natural”.

    An I.D. research program aimed at demonstrating positive evidence for the existence of the non-natural would be a good step towards changing this default assumption, don’t you think?

  125. 125

    iconofld “The current default assumption is that natural phenomena have natural causes”

    This is insufficient as a statement of the paradigm, and is a strawman stuffed with red herrings as well, if you don’t mind me mixing metaphors.

    1) The current paradigm does not ONLY say that “natural” effects have “natural” causes – it says that agency must be removed as a causal explanation despite any evidence of any kind to the contrary. This is an edict born of ideology – and is not connected to science, knowledge, falsifiablility, rationale, reason, or the evidence itself.

    2) ID does not posit anything whasoever beyond the empirically observable evidence that may be shared between all people – regardless of what they may, or may not, think is the cause of those empirically observable effects.

    Iconofld “An I.D. research program aimed at demonstrating positive evidence for the existence of the non-natural would be a good step towards changing this default assumption, don’t you think?”

    No, it wold be the end of ID as a scientific effort. But, thanks for asking.

  126. Concerning the very rapid appearance of the cecal valves in certain isolated populations of lizards. This special adaptation is apparently already present in other lineages of lizards. Isn’t it most reasonable that these animals shared the same ancestry, in which the cecal valve design was developed once. Then the lizards went through repeated cycles of adaptation and readaptation in varied habitats in which the initially developed cecal valve design was expressed if needed, repressed if not needed, but retained for future use. Thus the rapid cecal valve development in the isolated population was just expression of a recessive characteristic retained in the genome because it was very useful in some environments. Not evidence either for or against ID.

  127. Upright BiPed

    The current paradigm does not ONLY say that “natural” effects have “natural” causes – it says that agency must be removed as a causal explanation despite any evidence of any kind to the contrary. This is an edict born of ideology – and is not connected to science, knowledge, falsifiablility, rationale, reason, or the evidence itself.

    I would have thought that “agency” is readily accepted, but perhaps we’re thinking of different uses of the word.

    But there’s a reason for being suspicious of suggestions of intelligent agency by unknown agents. This is because our species has a long record of seeing volition where it isn’t. Anything from the evil spirits that cause disease to the gods who control the weather, etc.

    I.D. is very human in this respect, but if someone sees design in a complex little pathogen, it’s hardly surprising if the scientific establishment is suspicious, and thoughts of the dark ages of the evil spirits come to mind.

    I haven’t personally seen any evidence for design in biology, but others do, so it seems to be subjective rather than scientific. I read an interesting article a while ago about children preferring explanations like “it rains to make the flowers grow” over “it rains because of evaporation.” Somehow, I.D. reminds me of this.

    I see no reason why bacterial flagella shouldn’t be produced naturally by evolution, and I see no reason why there shouldn’t be complex chemical formations in a complex universe.

  128. Alan Fox:

    But Toe is the only explanation that fits with the evidence.

    But there isn’t any genetic evidence that demonstrates that the changes required are even possible via changes to the genomes.

  129. iconofid:

    I haven’t personally seen any evidence for design in biology, but others do, so it seems to be subjective rather than scientific.

    Perhaps you should try taking a look.

    Just what part of transcription, with its proof-reading, error-correction, editing, and translation into another type of molecule that will then do some work, strikes you as being cobbled together via unguided processes?

    BTW our hitory is also full of times in which the design inference has withheld scrutiny.

    But you have identified the way to refute ID- just start supporting YOUR position!

    Imagine that- if you could just demonstrate that there isn’t any need for a designer then the design inference would fade away just like those cases you were thinking of.

  130. Alan Fox:

    This is “The Holy Grail” of biochemistry, to predict nucleotide sequences that would produce proteins of specific function.

    ID could lead the way- That is because the information that determines the function is NOT in the sequence itself.

    And progress will be slow because of a lack of resources.

  131. 131

    iconofld,

    I haven’t tons of time, so allow me to be brief. :-)

    From your post you simply sound like you’ve accepted the party line and justified to yourself that no further discovery of the underlying issues is required. I say that this is fairly normal, but others might call you a cow.

    I would have thought that “agency” is readily accepted, but perhaps we’re thinking of different uses of the word.

    This comment is a bit of head-in-sand, or is simply misinformed (again fairly common).

    “We say that these events are accidental, due to chance. And since they constitute the only possible source of modifications in the genetic text, itself the sole repository of the organism’s hereditary structures, it necessarily follows that chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution” -Monod

    “We take the side of science in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, and in spite of the tolerance of the scientific community for unsubstantiated just-so-stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counterintuitive, no matter how mystifying to the uninitiated.” -Lewontin

    These quotes are so old and weathered – and insisted upon with every fibre of science. It’s odd indeed to have someone actually suggest that agency is even considered at all.

    But there’s a reason for being suspicious of suggestions of intelligent agency by unknown agents. This is because our species has a long record of seeing volition where it isn’t. Anything from the evil spirits that cause disease to the gods who control the weather, etc.

    Firstly, ID is the study of the artifacts of agency, not the agent. Why? Because there is nothing in those artifacts that allows that study. IOW, its evidence based, and nothing else.

    Secondly, the corrective measure to the historical context you raise is to stop seeing agency where agency is not empirically inferred. It’s been a couple hundred years and several million thinkers since that became clear. Mission accomplished. On the other hand, the irrational corrective measure is to hide ourselves from the evidence and simply say that we must not see agency even under the strongest possible inference to it, and (at the same time) the complete lack of inference to either chance or necessity. Now how smart are we?

    I.D. is very human in this respect, but if someone sees design in a complex little pathogen, it’s hardly surprising if the scientific establishment is suspicious, and thoughts of the dark ages of the evil spirits come to mind.

    Someone? Do you mean like a plumber or a priest? What if the someone is Dean Kenyon who wrote The Book on chemical evolution (and stayed with it until he could no longer justify that nucleic information is the output of physio-dynamic forces such as those found in Newtonian Mechanics, Einstein’s Relativity, Maxwell’s Electromagnetic Field, or Quantum Mechanics)? Or Mike Behe, or Michael Denton or David Abel, or Mike Gene?

    And “suspicious”? The scientific establishment is not suspicious; they are systematically guarding their ideology from a rational evidenced-based scientific attack by highly-trained men and women who know of what they speak. There may be a subtle difference there that is not so subtle, if you don’t say it so fast. Dark Ages? Please be realistic.

    I haven’t personally seen any evidence for design in biology

    http://www.tbiomed.com/content.....2-2-29.pdf

    http://mdpi.com/1422-0067/10/1/247/pdf

    I read an interesting article a while ago about children preferring explanations like “it rains to make the flowers grow” over “it rains because of evaporation.” Somehow, I.D. reminds me of this.

    Why not just find an ID proponent and spit in their face? Don’t wince at this; is comparing David Abel’s scientific argument childish any more respectful?

    I see no reason why bacterial flagella shouldn’t be produced naturally by evolution, and I see no reason why there shouldn’t be complex chemical formations in a complex universe.

    Really? Then perhaps Dean Kenyon should study under you. After all, judging by the standards you’ve set forth, he’s immediately comparable to a child wishing to see what he wishes to see.

    - – - – - – - – - –

    Please consider reading some of the actual scientific argument being made. You might find it less easily or carelessly dismissed.

  132. Secondly, the corrective measure to the historical context you raise is to stop seeing agency where agency is not empirically inferred. It’s been a couple hundred years and several million thinkers since that became clear. Mission accomplished. On the other hand, the irrational corrective measure is to hide ourselves from the evidence and simply say that we must not see agency even under the strongest possible inference to it, and (at the same time) the complete lack of inference to either chance or necessity. Now how smart are we?

    Wow. You do have a way with words, UB!

  133. That question is very much answerable, at least with regard to a reasonable estimate. Determine the parameters of your beach — length, width, depth of sand — count the grains in a sample and extrapolate.

    Exactly!

    But you seem to demand an impossible level of detail for the evolution of Elephant (modern African,) from LUCA, or will an estimate suffice?

  134. So, will you be joining materialists everywhere calling for an end to the current default assumption that life began by chance and necessity?

    No, because I don’t know how life got started on Earth, and I think OOL is an untractable problem without extraterrestrial evidence, such as evidence of life on Mars, and should that exist or have existed, whether or not it shows similarity to life on Earth. (As I have said before!)

    As I have asked before, what will you be calling your movement?

    Thus no need for any campaigns.

  135. 135

    ShawnBoy in #114.

    I forgot to thank you for your kind words.

  136. Joseph:

    “Perhaps you should try taking a look.”

    I have.

    “Just what part of transcription, with its proof-reading, error-correction, editing, and translation into another type of molecule that will then do some work, strikes you as being cobbled together via unguided processes?”

    You mean intelligently guided, presumably, not guided by environmental pressure and constraints. My answer is: all of it.

    As I said in the post you’re replying to, I see no reason why there shouldn’t be complex chemical formations in a complex universe.

    If a chemical self-replicator replicates with variation for billions of generations, then advantageous increases in complexity would be favoured, and evolvability itself would be selected for in an ever changing environment. The result would be complex cells.

    You might be surprised by the results, but I’m not.

  137. Upright Biped:

    “From your post you simply sound like you’ve accepted the party line and justified to yourself that no further discovery of the underlying issues is required. I say that this is fairly normal, but others might call you a cow.”

    Wrongly read, then. Loads of discovery of the underlying issues is required, IMO.

    As to your list of I.D. supporters with scientific qualifications, and your claim that I’m being disrespectful, that’s not entirely true. I think I’ve actually read at least one article/paper at some time by every name you mentioned, and in the case of one (Michael Behe) an entire book (Darwin’s Black Box – about eight years ago).

    But are you mentioning names with good qualifications as an argument from authority? And are you being respectful of the ~ 99% of scientists who are not “I.D.ers” and whom you see as ideologically driven, and perhaps as “cows”?

    Perhaps they should study under you?

    I’ll try to explain with an example from outside I.D. I assume that you’re not a young earth creationist. If you look at the YEC’s list of supporters with scientific qualifications, you can find PhDs in a variety of fields. There are geologists who firmly believe that the earth is less than ten thousand years old.

    Given the enormous number of scientists in the world, how much respect should I have for this handful, and would I be right in suggesting that they’re driven by something other than scientific method and curiosity?

    “Secondly, the corrective measure to the historical context you raise is to stop seeing agency where agency is not empirically inferred.”

    Certainly. And what I meant by agency being accepted was when we see it in ourselves and other animals.

    Where we seem to differ is that I would not infer it on the basis of complexity, information and function, all things difficult to quantify and define. I don’t infer design by making analogies to things we ourselves design, and I don’t think it constructive to stick designers in the gaps in our knowledge (or to call them “null hypotheses”).

  138. “Just what part of transcription, with its proof-reading, error-correction, editing, and translation into another type of molecule that will then do some work, strikes you as being cobbled together via unguided processes?”

    You mean intelligently guided, presumably, not guided by environmental pressure and constraints.

    No I mean UNGUIDED processes.

    THAT is what is being debated, unguided vs guided processes.

    And there isn’t any data which woulkd demonstrate unguided processes can do such a thing.

    Yet we have direct evidence of intelligent agencies doing that type of thing.

    As I said in the post you’re replying to, I see no reason why there shouldn’t be complex chemical formations in a complex universe.

    OK but I am talking about how those chemicals and their formation came to be.

    Ya see inside of a living cell we have amino acids in very close proximity to one another.

    Yet they do NOT spontaneously form a chain.

    The same goes for nucleotides.

    IOW there isn’t anything with nature, operating freely that demonstrates that specified complexity required for living organisms can arise via unguided processes.

    Science has demonstrated that only life begets life.

    If a chemical self-replicator replicates with variation for billions of generations, then advantageous increases in complexity would be favoured, and evolvability itself would be selected for in an ever changing environment.

    Where did those replicators come from?

    And how did they incorporate the transcription and translation processes required by living organisms?

    Ya see YOU don’t have anything in the way of science to answer those questions.

    Cells are far more than replicators.

    IOW it is obvious that you haven’t taken a look- either that or you just don’t understand what you were seeing.

  139. Alan Fox:

    But you seem to demand an impossible level of detail for the evolution of Elephant (modern African,) from LUCA, or will an estimate suffice?

    There isn’t any scientific data from genetics or biology that would demonstrate such a transformation is even possible.

    No one on this planet knows what makes an elephant and elephant.

    Therefor no one can say whether or not a non-elephant can “evolve” into an elephant.

  140. Alan,

    The point of the OoL is that if living organisms did NOT arise from non-living matter via unguided processes then there wouldn’t be any reason to infer the subsequent evolution was due solely to unguided processes.

    Also if it is shown that living organisms can arise from non-living matter via unguided processes, ID would fall.

  141. But you seem to demand an impossible level of detail for the evolution of Elephant (modern African,) from LUCA, or will an estimate suffice?

    An estimate guided by a testable methodology would be fine, and if we should compare such an estimate with observed rates of genetic mutation we should be able to determine the reasonableness of the NDE model.

  142. Well, ID is science which means it can be falsified…

    Only if the hypothesis being tested makes measurable predictions.

    … but what you suggest would not be the falsification. The falsification would be showing how the sequences directing the functional and specific production of proteins came about without design.

    Unless “Intelligent Design” is a physical process that manifests itself in some way that is detectable, it is invisible to Science, thus impossible to confirm or falsify its existence.

  143. Unless “Intelligent Design” is a physical process that manifests itself in some way that is detectable,

    That’s all it is. Phenomena have characteristics. Among the characteristics that a phenomenon could have is design.

    ID says that design has innate traits — this shouldn’t be controversial — and states what those traits are.

    If the traits ID claims are found not to be innate to design then ID is falsified.

  144. That’s all it is. Phenomena have characteristics. Among the characteristics that a phenomenon could have is design.

    This raises another issue that I can never get a satisfactory answer to. What is “design”? And, for that matter, what is “intelligence”? Part of the problem (for me at least) for ID theory is the reluctance to define terms consistently or even at all.

    ID says that design has innate traits — this shouldn’t be controversial — and states what those traits are.

    OK. So I must have missed that. Those traits are…?

    If the traits ID claims are found not to be innate to design then ID is falsified.

    Those traits are…?

  145. What is “design”?

    Before I give you a definition do you agree that it is something that exists?

  146. 146

    To conserve cyberspace -

    http://www.iscid.org/ubbcgi/ul.....108#001620

    my comment April 15, 2009, 8:40 AM

  147. JohnADavison[79]:

    (Sorry for not getting back to you sooner)Your comment about the sparrows clarifies pretty much what I had in mind. What I meant by “Lamarckian” was that the environment is responsible for such traits, and that these traits are subsequently inheritable, probably first having appeared through some kind of epigentic effect inter-generationally. And, I would expect that the traits would be reversible–all of which we see in your example of the English sparrows.

    I’m probably using the term “Lamarkian” too loosely. But, of course, it’s obvious that gradualism can in no way explain what we see in the case of this Adriatic lizard. There’s no way the information needed to ‘construct’ a cecal valve could have evolved in so short a period of time. But, of course, the death of ‘gradualism’ will have no effect at all on Darwinism, which explicitly (per Darwin INSISTS on gradualism), since, well, we’re dealing with ‘true believers’.

    Thanks for the response.

  148. Re: Cecal valves in Italian Wall lizards:

    (Sorry, long post. We really need a message-board-style format, as does just about every blog with more than a handful of comments on each post.)

    #126 magan:

    Concerning the very rapid appearance of the cecal valves in certain isolated populations of lizards. This special adaptation is apparently already present in other lineages of lizards. Isn’t it most reasonable that these animals shared the same ancestry, in which the cecal valve design was developed once. Then the lizards went through repeated cycles of adaptation and readaptation in varied habitats in which the initially developed cecal valve design was expressed if needed, repressed if not needed, but retained for future use. Thus the rapid cecal valve development in the isolated population was just expression of a recessive characteristic retained in the genome because it was very useful in some environments. Not evidence either for or against ID.

    I highlighted the most questionable text in bold in your post. Is it reasonable? Yes, there is some defensible logic behind the statement, therefore it is reasonable. Is it most reasonable? I don’t see any evidence for this being the case.

    It is only present in about 1% of all other lizard populations. From the evidence we have, assuming it is just a repressed, previously evolved trait, it is repressed for a vast majority of the time. Why would a trait that is selectively neutral for 99% of lizards not be degraded by unchecked genetic mutation and variation?

    Secondly, if it is a repressed trait, “repressed if not needed”, why did hatchlings exhibit the trait? I’m not an expert in gene regulation, so maybe regulated gene expression is hereditary? I didn’t think so, but could be wrong. Here is a quote from:

    Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource
    PNAS March 25, 2008 vol. 105 no. 12 4792-4795

    Although the presence of cecal valves and large heads in hatchlings and juveniles suggests a genetic basis for these differences, further studies investigating the potential role of phenotypic plasticity and/or maternal effects in the divergence between populations are needed.

    Let me rephrase this in my words, just for the sake of allowing others to critique my understanding of it. I just want to be sure I’m reading it correctly, since I’m not a biologist or geneticist:

    Although the presence of cecal valves and large heads in hatchlings and juveniles suggests that new genetic code was developed, we need to further study the potential role of regulated gene expression of previously existing genes to see if they can account for the differences.

    There is strong evidence against a neo-Darwinian development of the trait in these lizards once they stepped on the island. It was interesting going back and reading the post of this news on PZ Myer’s blog, Pharyngula. In the initial post, PZ said (emphasis added):

    The cecal valves are an evolutionary novelty, a brand new feature not present in the ancestral population and newly evolved in these lizards. That’s important. This is more than a simple quantitative change, but is actually an observed qualitative change in a population, the appearance of a new morphological structure.

    Evolution created something new, and it did it quickly (about 30 generations), and the appearance was documented. It’s still just a lizard, but we expected nothing else — and it’s now a lizard with novel adaptations for herbivory.

    He was too busy laughing at people who believe ZERO evolution happened to realize that it is incredibly unrealistic for this to be a novel creation from a naturalist viewpoint. After a couple hundred mud-slinging comments cursing and laughing at “creobots” and “IDiots”, the few that were left were pointing out that it didn’t make a whole lot of sense, and that the only realistic option for the naturalist camp would be to believe it is simply a repressed, previously evolved (when the safety and unobservability of deep time is available):

    Comment #334, joshTheGoods:

    Before I comment, I’d like to point out that I’m a naturalist that believes whole heartedly in the near fact of evolution and common descent. …

    …if I were a betting man my money would be on the idea that this is not the evolution of a new morphological trait. Please correct me if I’m wrong; is the statement: “a brand new feature not present in the ancestral population and newly evolved” possibly a mistake?

    As an aside: I also included his initial sentence, which I have found to be standard anywhere a naturalist questions something that the majority of naturalists have assumed to be true. It is fear of peers and leaders, which speaks volumes as to why so many don’t question the dogma of those in power. Why did he feel the need to sware allegiance to Darwinism? It doesn’t just happen on mud-slinging blogs like Pharyngula and Panda’s Thumb, but in peer-reviewed articles and in renowned science publications. Here’s a link to another Pharyngula post demonstrating this:

    New Scientist says Darwin was wrong

    The article basically says typical biological understanding is laughably simple and naiive from what really exists:

    If anyone now thinks that biology is sorted, they are going to be proved wrong too. The more that genomics, bioinformatics and many other newer disciplines reveal about life, the more obvious it becomes that our present understanding is not up to the job. We now gaze on a biological world of mind-boggling complexity that exposes the shortcomings of familiar, tidy concepts such as species, gene and organism.

    But at the end of the article, the swear to allegiance is there, as expected, and without any evidence supporting it:

    As we celebrate the 200th anniversary of Darwin’s birth, we await a third revolution that will see biology changed and strengthened. None of this should give succour to creationists, whose blinkered universe is doubtless already buzzing with the news that “New Scientist has announced Darwin was wrong”. Expect to find excerpts ripped out of context and presented as evidence that biologists are deserting the theory of evolution en masse. They are not.

    Basically, even though we’ve been wrong all along, we will continue to be right … err, something like that. Anyway, whatever happens, anyone believing there is a purpose is WRONG.

  149. Alan Fox:

    Only if the hypothesis being tested makes measurable predictions.

    Which leaves the theory of evolution out.

    Unless “Intelligent Design” is a physical process that manifests itself in some way that is detectable, it is invisible to Science, thus impossible to confirm or falsify its existence.

    The design is in the physical world and is open to empirical testing.

    Now to refute the design inference for any given thing all one has to do is demonstrate that it is reducible such that agency involvement is not warranted.

    As for “intelligence” well that is only to differentiate between apparent design on one side and optimal design on the other.

    It basically refrs to agency involvement.

    You can read all about it in “Nature, Design and Science” by Del Ratzsch.

    Ya se Alan ID does have defined terms- unlike your position which just states “it evolved” without even knowing if it could.

    So ID can be tested against those terms.

    And as with ALL scientific theories if disconfirming data is provided it either has to adjust or be abandoned.

    So read the book Alan and actually become educated of that which you are debating.

  150. 145

    tribune7

    04/16/2009

    8:42 am

    What is “design”?

    Before I give you a definition do you agree that it is something that exists?

    Why so coy? The word “design” exists as a noun and a verb. People design and build things. Designs are produced by entities such as people. But just having a word does not give something existence. How can I agree something exists before you tell me what that something is?

  151. Joseph @149

    Only if the hypothesis being tested makes measurable predictions.

    Which leaves the theory of evolution out.

    You have been corrected on your use of this not only erroneous but ridiculously easily refuted claim repeatedly, most recently in this thread (link not working for some reason):
    http://www.uncommondescent.com.....ent-312261

    Continuing to repeat this utterly basely claim merely shows your lack of knowledge of modern evolutionary theory and the practice of science. Normally, that would simply be good reason to ignore you as contributing no value to the discussion. Unfortunately, your behavior actively undermines the goals of those of us who would like ID to eventually be taken seriously as a scientific theory.

    Dr. Behe’s work is, in my opinion, more likely than that of Dr. Dembski to take the current ID hypothesis and make it a predictive, falsifiable, scientific theory. We’re not there yet. When we are, our credibility is going to be minimal because of ID “supporters” who make unfounded assertions like yours. It is all too easy for ID opponents to say “ID supporters don’t understand evolutionary theory.” or “ID supporters are just Liars for Jesus.”

    If you really want to see ID succeed, stop giving them that ammunition.

    JJ

  152. Joe:

    From page 3:

    A design is a deliberately intended or produced pattern.

    And:

    A pattern is an abstract structure which correlates in special ways to mind, or is mind correlative.

    Is everyone happy with these definitions? Can you point me to any passage of particular relevance in the book, Joe?

  153. PS: the quotes in #151 are from “Nature, Design and Science” by Delvin Lee Ratzsch

  154. 154

    Iconofld,

    So allow me to understand you more clearly.

    You say that you’ve read all this ID literature, but still, your initial assessment is that ID should look to study the “non-natural.”

    Does your suggestion sound coherent to the research you’ve read? What part of DBB brought you to this conclusion? What part of David Abel’s work suggests this? Why would you suggest that Abel abandon his research of the observable artifacts within nucleic sequencing in order to …do what?

    I use the word “coherent” in asking these questions, and I use it for a reason. (MerrWeb. “coherent” : marked by an orderly, logical, and aesthetically consistent relation of parts). So again I ask, given your claimed reading of the literature, what makes you suggest what you do?

    Also in your response, you imply that I tried to use Behe, Denton, Abel, etc as an argument from authority. I find this suggestion laughable. You’ve already made it clear that you think ID proponents are comparable to children looking up at the clouds; so exactly how much authority could I be appealing to? Are you now asking me to be incoherent as well?

    You also asks “are you being respectful of the ~ 99% of scientists who are not “I.D.ers” and whom you see as ideologically driven”.

    I can only respond to this by asking if it is acceptable (indeed proper) that I take them at their own words? If Lewontin says that science will only consider materialistic causes (to the stated and distinct exception of agency) despite “the patent absurdity” of the conclusions, and despite a “tolerance” for producing “unsubstantiated just-so-stories” as the result of a “prior commitment” to ignore agency – may I then deduced that science does indeed intend to ignore agency?

    And further, if it is then made perfectly clear that it is not the “methods and institution of science” that brings this condition about, but is rather a “forced” condition brought about by the idea(ological) belief that “materialism is an absolute” – may I then conclude that the condition is ideological in nature?

    So now to your question – Do I respect the conclusions of scientists who create patently absurd just-so-stories in order to ignore the evidence of agency (only) because they have a prior commitment to an ideological position on what that evidence can and cannot say? No, I don’t. I rather would ask what is their responsibility to the public that they are committed to serve? Does that responsibility contain any standards regarding honesty or integrity? If so, what exactly are those standards?

    In the previous paragraph I added the word “only” in parentheses. “…ONLY because they have a prior commitment…” Are you really suggesting that these scientist are afraid that someone might see a boogieman in a pathogen – the Dark Ages – as you seem to want to imply? Truly, you cannot be serious.

    So….

    In the face of the substantial and compelling scientific evidence for volitional agency in the sequencing of nucleic acids (also including tremendous collateral evidence from other areas of biology, as well as paleontology and the fossil record) you dutifully inject boogiemen beliefs from the Dark Ages as relief from what is implied by the evidence at hand today.

    And then you turn around and suggest these things cannot be trusted because those in the discussion are “driven by something other than scientific method and curiosity?”

    Do you have any idea how disconnected (incoherent) your reasoning appears? Really.

    - – - – - – -

    Sorry iconofld, I cannot take you seriously.

    Can you even give any sort of conceptual narrative whereby chance can coordinate function within the nucleic sequence from disparate results scattered along the nucleic chain?

    Can you offer the material explanation for how the ribosome comes to “know” the convention within the genetic code, or even what the stop codon means?

    Can you suggest a plausible narrative for RV+NS to cause the integrated information necessary for functioning cecal vales to suddenly appear in the genome of the Adriatic lizards in less that 30 generations?

  155. Hello Upright Biped:

    I notice you used the phrase “evidence of agency” a couple of times.

    Would you have an example?

    Is agency what produces a design or a deliberately intended or produced pattern, i. e. an abstract structure which correlates in special ways to mind, or is mind correlative?

  156. Joseph says:

    No I mean UNGUIDED processes.

    THAT is what is being debated, unguided vs guided processes.

    The reason I suggested that you meant intelligent guidance is because the word “guided” does not automatically imply sentience. As in:

    “She was guided by the light of the moon” or “the rolling hills guided the river on its winding course” or “the organisms’ evolutionary path was guided by the constraints of their environment”.

    And there isn’t any data which woulkd demonstrate unguided processes can do such a thing.

    Let’s see. Do chemical reactions rearrange chemicals into new formations? Is life made of chemicals? Does chemical evolution happen? (remembering that the observable micro-evolution is all chemical, but after the point when we’ve defined chemical arrangements as life).

    So, I propose “chemical reactions” as the catalyst for OOL, and chemical evolution to explain the first thing that we might call life.

    “Yet we have direct evidence of intelligent agencies doing that type of thing.”

    The intelligent agencies that you observe are dependent on the cellular complexity that you’re trying to explain, and are themselves far more complex than the individual cells.

    If I.D. is to attempt to explain “FSCI”, it cannot evoke higher levels of “FSCI” to do that. You don’t explain something by claiming that it’s a prerequisite for itself.

    OK but I am talking about how those chemicals and their formation came to be.

    Ya see inside of a living cell we have amino acids in very close proximity to one another.

    Yet they do NOT spontaneously form a chain.

    The same goes for nucleotides.

    IOW there isn’t anything with nature, operating freely that demonstrates that specified complexity required for living organisms can arise via unguided processes.

    Aren’t you assuming that life isn’t natural in order to prove it? And aren’t you backing up Michael Shermer’s point on a recent thread that I.D.ers make “God of the gaps” arguments?

    Science has demonstrated that only life begets life.

    Not so. Cosmology tells as that the universe could not have always supported life, therefore eternal life is impossible, therefore there must have been a first life form or forms that did not come from other life. Hasn’t anyone in the I.D. movement figured that out yet?

    IOW it is obvious that you haven’t taken a look- either that or you just don’t understand what you were seeing.

    I understand when I’m seeing “intelligent designer of the gaps” arguments. These go:

    In the 19th, scientists had no idea how the sun could burn for hundreds of millions of years, let alone billions, so, the intelligent designer must be responsible.

    In the 20th century, the I.D.er gives up the task, but still does things like abiogenesis.

    What we do not know at any point in time does not equal “intelligent designer”, Joseph. The scientific attitude is to try and find out.

    OOL research is going on, but unlike sticking invisible beings in gaps, it takes hard work!

    I repeat my suggestion further up the thread that a search for positive evidence of the existence of the non-natural would be a natural course for I.D.

    The constant complaints about “materialism” on this site would be more convincing if we had the first scrap of evidence for the non-natural, don’t you think?

  157. Alan,

    There is much more to the book than just that one page.

  158. iconofid:

    The constant complaints about “materialism” on this site would be more convincing if we had the first scrap of evidence for the non-natural, don’t you think?

    Gee, according to science nature had a begining. That would mean even in YOUR scenario something non-natural is required.

    Is life made of chemicals?

    There isn’t anything that would demonstrate that life is reducible to chemical reactions.

    So, I propose “chemical reactions” as the catalyst for OOL, and chemical evolution to explain the first thing that we might call life.

    Good for you. However it is meaningless without any scientific data.

    Cosmology tells as that the universe could not have always supported life, therefore eternal life is impossible, therefore there must have been a first life form or forms that did not come from other life.

    Living organisms- life could be a separate entity and most likely is.

    IOW living organisms are the result of a combination of matter, energy, information and life.

    If I.D. is to attempt to explain “FSCI”, it cannot evoke higher levels of “FSCI” to do that.

    Not if it takes FCSI to get FCSI.

    THAT is the whole point.

    And again all YOU have to do is demonstrate that FCSI can arise without agency involvement.

    What part of that don’t you understand?

  159. Evidence of agency can be found in irreducible complexity and complex specified information.

    Now to refute that inference all one has to do is demonstrate that nature, operating freely, can account for it.

  160. There is much more to the book than just that one page.

    Sure, Joe. I am just hoping you can point me to the passages, or just an example, that you found particularly relevant to the concept of design, pattern or agency. Just a page number will be enough.

    Thanks in advance.

  161. Anyone able to define what FCSI is?

  162. #155 iconofid:

    The intelligent agencies that you observe are dependent on the cellular complexity that you’re trying to explain, and are themselves far more complex than the individual cells.

    If I.D. is to attempt to explain “FSCI”, it cannot evoke higher levels of “FSCI” to do that. You don’t explain something by claiming that it’s a prerequisite for itself.

    Maybe I’m misunderstanding the argument you are having, but this sounds like the strawman philosophy of Dawkin’s proof for why the existence of God is very unlikely. It is a materialist’s interpretation of what God is, which basically amounts to a super human, an amazingly complex organism with incredible power and knowledge. But this view represents a tiny fraction of the beliefs of all theistic people on Earth. As a Chrisitian, here are just a couple reasons why I believe God is a non-physical being, a spirit (both are quotes from Jesus):

    John 4:24: “God is spirit, and his worshipers must worship in spirit and in truth.”

    Luke 24:39: “See My hands and My feet, that it is I Myself; touch Me and see, for a spirit does not have flesh and bones as you see that I have”

    Or are we talking about something else, like scientists conducting OOL experiments being the “intelligent agencies”?

  163. Evidence of agency can be found in irreducible complexity and complex specified information.

    Now to refute that inference all one has to do is demonstrate that nature, operating freely, can account for it.

    Are you serious? All we have to do to refute irreducible complexity and CSI, which you have so far not defined and which rationalists suggest is an empty set, is to demonstrate they occur naturally?

    I think I’ll pass on that one. :)

  164. Before I give you a definition do you agree that (design) is something that exists? . . . Why so coy?

    Nothing coy, just trying be keep the discussion clear: For instance:

    The word “design” exists as a noun and a verb. People design and build things . . .But just having a word does not give something existence. How can I agree something exists before you tell me what that something is?

    You seem to be saying design exists and you describe it then you say you can’t agree that it exists until I tell you what it is despite it being something you apparently know.

    So to get to the point, we agree that design exists, right?

  165. 165

    Hello Alan,

    ID has offered several examples of agency, I would be truly surprised if you were not aware of them.

    For instance: The pattern in the sequencing of nuceoltides in DNA is an artifact of agency.

    They cannot have come to be the way they are by any rational narrative of chance, nor are they in any way the product of physio-dynamic necessity.

    An alternative explanation would be agency IF the pattern did indeed fit that explanation.

    You can decide for yourself.

    http://www.pubmedcentral.nih.g.....obtype=pdf

    http://mdpi.com/1422-0067/10/1/247/pdf

  166. Upright Biped says:

    Sorry iconofld, I cannot take you seriously.

    Never mind, and thanks for your lengthy reply, anyway.

    I’ll try to explain briefly, then you and others can tell me where I’m wrong.

    When you refer to “agency” with “volition” I’m taking it to mean that some kind of intelligent designer or designers are (or have been) involved in the life system we’re part of. To me, intelligence is a highly complex phenomenon. So, when someone like Michael Behe looks at the complex features of life on the molecular level, and implies that they require design, I’m taking it as if the “agent” must be exempt from the arguments made, because I don’t think you guys are suggesting a designer who is simpler than a bacterial flagellum.

    So, that’s why I suggest research aimed at finding scientific evidence for the non-natural, because, to me, all I.D. arguments imply its existence.

    As for biologists not yet knowing how many things work, see my “intelligent designer of the gaps” point above.

  167. 167

    Icon

    “So, I propose “chemical reactions” as the catalyst for OOL”

    Really….you need to spend a day with Dean Kenyon.

  168. 168

    Icon

    “I’ll try to explain briefly, then you and others can tell me where I’m wrong.”

    This is where you are wrong: ID cannot study the designer, however, that does not erase the observable artifacts of agency.

    I would have enjoyed it if you ACTUALLY addresses the evidence instead of flanking with The Designer mumbo, but, whatever.

    Not to worry though, we’ve seen this evasion before.

    Cheers….

  169. #159 Joseph:

    Emphasis added

    Evidence of agency can be found in irreducible complexity and complex specified information.

    Now to refute that inference all one has to do is demonstrate that nature, operating freely, can account for it.

    I disagree with the use of the word “can” in that statement. Because even demonstrating a possible pathway would refute that argument for intelligent agency, regardless of whether it actually happened that way. It is POSSIBLE that all of the chemicals for the first organism were all in the same place at the same time, and just happened to assemble at the precise moment (no, I know that is not what is believed to have happened by naturalists, but at least it is a KNOWN possible route). It is also POSSIBLE that in one early organism, all of the necessary proteins for the flagellum suddenly came about due to an incredibly lucky series of mutations. Basically, saltation is theoretically POSSIBLE, which means saltation is enough to falsify the proposition.

    The question really is DID it happen that way, or at least is it statistically probable that it happened in that way? This is what is lacking from the vast majority of just-so, imaginative evolutionary tales.

    I’ll use the examples of the Italian Wall lizards and they’re very peculiar development of cecal valves in a very shorrt period of time. If this had happened a million years ago. Let’s imagine five couples of lizards were on the original island, happily hunting insects on a giant piece of driftwood on the beach, when suddenly the wood was swept to sea, and after a few days/weeks (short enough to ensure the lizard’s survival…perhaps the driftwood is filled with tasty bugs to get them through the journey) ended up on the 2nd island, which is full of lush vegetation. The same thing happens…within a couple decades, the new lizard species has dominated the island, and they have larger heads, stronger bites and cecal valves in their digestive tracts. Let’s say a good number of lizards from both islands were somehow preserved (including their digestive tracs) for humans of the 19th-21st centuries to discover. What would be stated as the “fact” of what happend? That one specimen of the transplanted species developed cecal valves (or it developed slowly over many generations; I don’t know how complex they are), it created an advantage, however slight, and over many generations, perhaps hundreds or thousands, the trait spread through the rest of the population. Even though that’s NOT how it happened, that is how it would be understood as “fact” in scientific literature.

    This interpretation is lacking probability and statistics to back itself up. This dawned on me when I first watched Richard Dawkins’ demonstration of the possible evolutionary steps of the eye and the wing. For example, one of the first steps he mentions for the eye is a slight depression in a photosensitive patch of cells, which would give an advantage due to protection from scratches, etc. He then glosses to the next step, but wait — what good does that really do? It would only help with glancing blows, as almost any kind of direct blow would reach the cells. What percentage of these ancient creatures are failing to reproduce (early death, sexual selection, etc.) due to glancing blows to their photosensitive patches?

    Another “possible” evolutionary ladder for wings I saw (on TV, not Dawkins) was flightless creatures who developed feathers, and had an advantage because they could help propel themselves up inclines (like semi-fallen trees) to escape from predators. They further and further approached flight because the more lift they could provide, the steeper the incline they could scale, the more predators they could escape. It all seems reasonable, except for actual statistics of how many of these crude birds were scaling semi-fallen trees to escape predators, and how much of a deference it really made whether they could scale a tree at a 60-degree angle and a 70-degree angle. Basically, the most important science component was left out while the imagined story became fact.

  170. #163 Alan Fox:

    Evidence of agency can be found in irreducible complexity and complex specified information.

    Now to refute that inference all one has to do is demonstrate that nature, operating freely, can account for it.

    Are you serious? All we have to do to refute irreducible complexity and CSI, which you have so far not defined and which rationalists suggest is an empty set, is to demonstrate they occur naturally?

    No, I don’t think he’s saying to demonstrate that they occur naturally, as in that they occur in nature, but that they originated naturally. Specifically, that it is probable that the information originated naturally. Maybe I don’t understand your perplexion…

  171. Upright Biped:

    This is where you are wrong: ID cannot study the designer, however, that does not erase the observable artifacts of agency.

    But I can study the designer, and it appears that he’s exempt from your own arguments, so at least we know something about him. It appears that naturalists have to explain their mechanisms in detail, what they are and how they work, but I.D. is exempt. How convenient.

    I would have enjoyed it if you ACTUALLY addresses the evidence instead of flanking with The Designer mumbo, but, whatever.

    I’ve explained that I do not see complexity as evidence of design, and that I do not regard incomplete biological knowledge as evidence of a designer of the gaps. There is no evidence.

    Not to worry though, we’ve seen this evasion before.

    I can’t evade an invisible unknowable mechanism of biology. It evades us.

    Cheers….

    Cheers to you too, and may your mechanism of the gaps go with you.

  172. 172

    Icon,

    “But I can study the designer, and it appears that he’s exempt from your own arguments, so at least we know something about him.”

    Really, you can. I am interested in knowing how. Please tell us how you can study the designer. Also, please tell us what arguments he is exempt from. The arguments I have made are based on the patterns observed in DNA, please tell us what in Abel’s analysis are applicable to the designer so that we may then know how he is immune to them. Please be specific.

    It appears that naturalists have to explain their mechanisms in detail, what they are and how they work, but I.D. is exempt. How convenient.

    Really? Earlier I asked for any conceptual narrative (not even the finer details) you could give whereby:

    1)chance can coordinate function within the nucleic sequence from disparate results scattered along the nucleic chain?

    2)material explanation can account for how the ribosome comes to “know” the convention within the genetic code, or even what the stop codon means?

    3)a plausible explanation is made for RV+NS to cause the integrated information necessary for functioning cecal vales to suddenly appear in the genome of the Adriatic lizards in less that 30 generations?

    Yet, these questions you simply passed on. One might think that since these questions are at the very heart of the childish design argument, and further, that “naturalists have to explain (these) mechanisms in detail” then a explanation would be just a brief google away. Is that the case, or is it not the case?

    I’ve explained that I do not see complexity as evidence of design, and that I do not regard incomplete biological knowledge as evidence of a designer of the gaps. There is no evidence.

    Yes Icon, you have made yourself abundantly clear. You have used words like complexity, information, and intelligence is a recognizable manner – rather like swatting flys away from your picnic sandwich.

    Perhaps if you had demonstrated (even momentarily) the kind of personal sovereignty required to challenge your own position, then your swatting would have seemed more credible.

    But not to worry, you can start at any time. Please point to any paragraph in the peer-reviewed research I posted that you take issue with. Given your position and the depth of belief you give it, there should be more than a sufficient supply of arguments and counter evidence.

  173. Upright Biped:

    Yet, these questions you simply passed on. One might think that since these questions are at the very heart of the childish design argument, and further, that “naturalists have to explain (these) mechanisms in detail” then a explanation would be just a brief google away. Is that the case, or is it not the case?

    What you’re asking is for detailed descriptions of things that are current areas of research. The natural explanations must be given in the year 2008, because biological research, presumably, should be complete in that year.

    If not given, the intelligent designer of the gaps has “evidence”.

    The same with the paper you refer to. Lots of talk about gaps in current knowledge, then, for “null hypotheses”, read “natural explanations not yet available, so god is in the gaps.”

    None of this is positive evidence for intelligent design.

    As I pointed out to Joseph, what we don’t know at any particular time does not = intelligent design.

    Now, be positive, and devise an experiment which will demonstrate your mechanism in action, the mysterious designer designing.

    This can be done for mutation, selection and drift, as you know.

  174. “Now, be positive, and devise an experiment which will demonstrate your mechanism in action, the mysterious designer designing.”

    Why do we need to resort to an “experiment to determine mechanism of action” as prove? Isn’t coming to understand nature through observation doing science? Certainly it must. We can discuss differences as well as the connection between things.

    A young man can stand on the street corner and say “I am just a mammal”. Ask him “what is a mammal” he might say a type of animal. And then we pat him on the back and think he really knows science. He knows nothing and is clueless. Those who teach the theory of evolution are terrorist that strike at the freedom of the mind.

  175. 175

    Pav #147

    Thanks.

    I have no intention of participating on any thread which cultivates Alan Fox and attempts to reason with him. It is quite impossible. If you would like to further discuss this matter you are welcome to do it on my weblog. I have littrle more to offer here.

  176. 176

    Icon,

    It is clear that instead of addressing the evidence you would like to flank with the “god of the gaps’ charge. The reasons for this are just as obvious. So let’s go there for a moment shall we?

    The infamous gaps argument (stall) states that we know nothing of how IT happened, so lets just say what we wish happened and call it a day. But, does that charge fit Abel’s work? Abel’s “Three Subsets” paper is not a quantitative assessment in its fullest form, instead it is qualitative. It’s asking the question of fitness to the observed effect for the mechanisms currently assumed to be the cause. It is asking: are the artifacts of chance and necessity mechanisms apparent (indicated, specified, inferred by what is available to us) in the sequencing of nucleic acids.

    So the immediate question is “do we know anything about chance and necessity that would give us any reasonable footing whatsoever to make such a qualitative assessment? Your answer, as the basis of your charge, is “no” we do not. But the answer is YES, we know a GREAT DEAL about how chance and necessity function.

    Do you think that chance and necessity have not been studied rigorously? Please explain the basis of your claim. It would seem that we had to know a thing or two for Einstein to craft the Theory of Relativity – and I hear that Newton, Déscartes, Gödel, and La Place were fairly competent mathematicians. Didn’t we find the quark and the photon? Is it too much to say that we don’t know enough about our physical world to even venture an assessment of what can happen by means of chance working within physical law? Are we expecting that under the proper conditions nitrogen and carbon will spring into action by expressing themselves in ways that we had no idea was under our noses – like forming with other elements and starting to record their existence in a conventional code of digital information that is proofread and error-corrected, but isn’t contingent on physical need?

    In fact, let’s turn your argument around and see how it drives: “We expect that there is an unknown quality of chance that explains why inanimate elements begin to record their existence.” “We expect that electromagnetism and quantum mechanics will soon explain why inanimate chemicals organize themselves and begin demonstrating a drive for survival.”

    - – - – - – - – - -

    Now that we are down here at the bottom of your religious God of the Gaps argument, how does it feel? “We have an unknown force that we invoke in defense of observations we cannot explain by chance and necessity alone; it is the God of the Unknown.” Is this your solid rationale? Please allow me to highlight something about history and human nature that you may not be aware of; your rationale has an unmistakable face on it. It’s the kind of rationale that only exists by power, not by argument.

    So what is left on the table? It is the virtually unmistakable evidence of an agent. It is the only cause that is capable of the non-determinant, non-random, non-ordered, physically-inert, foresighted coordination that is the absolute and undeniable hallmark of nucleic sequencing. That is the exact point of the research that you refuse to address. Despite your mockery, David Abel and the others are not lowly thinkers. Your argument is exactly why I asked you to provide a single paragraph that you could challenge. You failed to do so. In failing to do so, you’ve only deepened your position that the God of the Unknown is mighty and should command the respect of those who look at the evidence instead. You might find the role reversal distasteful, but at least you’ve earned it.

    Now if you’d like to address the issue instead, please be my guest:

    Random Sequence Complexity (RSC)
    A linear string of stochastically linked units, the sequencing of which is dynamically inert, statistically unweighted, and is unchosen by agents; a random sequence of independent and equiprobable unit occurrence.

    Ordered Sequence Complexity (OSC)
    A linear string of linked units, the sequencing of which is patterned either by the natural regularities described by physical laws (necessity) or by statistically weighted means (e.g., unequal availability of units), but which is not patterned by deliberate choice contingency (agency).

    Functional Sequence Complexity (FSC)
    A linear, digital, cybernetic string of symbols representing syntactic, semantic and pragmatic prescription; each successive sign in the string is a representation of a decision-node configurable switch-setting – a specific selection for function.

    Conclusions
    In summary, Sequence complexity can be 1) random (RSC), 2) ordered (OSC), or functional (FSC). OSC is on the opposite end of the bi-directional vectorial spectrum of complexity from RSC. FSC is usually paradoxically closer to the random end of the complexity scale than the ordered end. FSC is the product of nonrandom selection. FSC results from the equivalent of a succession of integrated algorithmic decision node “switch settings.” FSC alone instructs sophisticated metabolic function. Self-ordering processes preclude both complexity and sophisticated functions. Self-ordering phenomena are observed daily in accord with chaos theory. But under no known circumstances can self-ordering phenomena like hurricanes, sand piles, crystallization, or fractals produce algorithmic organization. Algorithmic “self-organization” has never been observed [70] despite numerous publications that have misused the term [21,151-162]. Bone fide organization always arises from choice contingency, not chance contingency or necessity.

    Reduced uncertainty (misnamed “mutual entropy”) cannot measure prescriptive information (information that specifically informs or instructs). Any sequence that specifically informs us or prescribes how to achieve success inherently contains choice controls. The constraints of physical dynamics are not choice contingent. Prescriptive sequences are called “instructions” and “programs.” They are not merely complex sequences. They are algorithmically complex sequences. They are cybernetic. Random sequences are maximally complex. But they don’t do anything useful. Algorithmic instruction is invariably the key to any kind of sophisticated organization such as we observe in any cell. –Trevors & Abel

  177. Upright Biped:

    Your argument is exactly why I asked you to provide a single paragraph that you could challenge.

    I don’t disagree with Trevors and Abel that there are gaps in our knowledge. I see nothing in the paper that shows that nature cannot produce “algorithmic instruction”.

    Now that we are down here at the bottom of your religious God of the Gaps argument, how does it feel? “We have an unknown force that we invoke in defense of observations we cannot explain by chance and necessity alone; it is the God of the Unknown.”

    Why does it require an unknown force for chemical evolution to produce “FSC”? What laws of physics would that process break?

    What is unknown is the chemistry of the OOL, and the chemistry of the evolution of the genetic code.

    There are enormous gaps in our knowledge of biology all over the place. It’s in its infancy, compared to what could be known. But it doesn’t require any unknown forces so far as I know. Isn’t that your claim rather than mine?

    Are Trevors and Abel suggesting that the sophisticated organization that empirical observation tells us is required in intelligent designers cannot come about naturally? Or just that we don’t yet know the full story of how it could happen?

    If the latter, I agree. If the former, we’ll start discussing the impossibility of the existence of intelligence (according to I.D. arguments) or empirical evidence for the non-natural (a brief discussion, inevitably).

    From the paper: But under no known circumstances can self-ordering phenomena like hurricanes, sand piles, crystallization, or fractals produce algorithmic organization.

    Note the “no known”. Why should I disagree?

    Would you agree that there are, inevitably, lots of unknown circumstances in the history of this planet?

    What we’ll get into here is that I’ll be accusing I.D. of “God of the gaps”, and you’ll be accusing me (correctly) of “nature of the gaps”.

    Expect the response “which do we have the most empirical evidence for, an invisible interventionist intelligent designer, or nature”?

    You say:

    It is asking: are the artifacts of chance and necessity mechanisms apparent (indicated, specified, inferred by what is available to us) in the sequencing of nucleic acids.

    As you know, I always infer natural processes for natural phenomena.

    If we both google “research nucleic acids” and spend a few days reading around, we might find out some of what’s “available to us”. We’d certainly find that it’s an area of ongoing research. If you want to conclude “design” on the basis of current knowledge, go ahead. It would be good to see I.D.ers united in common concrete views, like “bacterial flagella cannot evolve” (is there unity there?).

    If I.D. already has a measured way of detecting design, how soon will we see a general agreement amongst I.D.ers on what evolves naturally, and what is designed? Surely all brains of all species must be designed considering the amount of species specific complex information they seem to contain?

    What do you think?

    I’ll have a look at the research on sequencing of nucleic acids when I’ve got time, to show that I’m taking I.D. arguments seriously.

  178. Evidence of agency can be found in irreducible complexity and complex specified information.

    Now to refute that inference all one has to do is demonstrate that nature, operating freely, can account for it.

    Are you serious?

    Yes Alan that is how science operates.

    I take it that you don’t understand science.

    All we have to do to refute irreducible complexity and CSI, which you have so far not defined and which rationalists suggest is an empty set, is to demonstrate they occur naturally?

    Both CSI and IC are more rigorously defined than ANYTHING your position has to offer.

    As a matter of fact your position doen’t define anything.

    As for Del’s book, read the whole thing.

    Then maybe you will have a clue.

    Ya see “natural” isn’t the issue.

    UNGUIDED is.

  179. UB, 176:

    Very well said.

    Especially:

    Is it too much to say that we don’t know enough about our physical world to even venture an assessment of what can happen by means of chance working within physical law? Are we expecting that under the proper conditions nitrogen and carbon will spring into action by expressing themselves in ways that we had no idea was under our noses – like forming with other elements and starting to record their existence in a conventional code of digital information that is proofread and error-corrected, but isn’t contingent on physical need? . . . . what is left on the table? It is the virtually unmistakable evidence of an agent. It is the only cause that is capable of the non-determinant, non-random, non-ordered, physically-inert, foresighted coordination that is the absolute and undeniable hallmark of nucleic sequencing . . . . FSC results from the equivalent of a succession of integrated algorithmic decision node “switch settings.” FSC alone instructs sophisticated metabolic function. Self-ordering processes preclude both complexity and sophisticated functions. Self-ordering phenomena are observed daily in accord with chaos theory. But under no known circumstances can self-ordering phenomena like hurricanes, sand piles, crystallization, or fractals produce algorithmic organization. Algorithmic “self-organization” has never been observed [70] despite numerous publications that have misused the term [21,151-162]. Bona fide organization always arises from choice contingency, not chance contingency or necessity.

    Can anyone here present a known counter-example — observed not theoretical or speculative — to Bona fide organization always arises from choice contingency, not chance contingency or necessity?

    There are many, many observed supportive instances; starting with the software on your PC.

    So in the absence of serious counter example, we have good reason to confidently conclude that we have a best explanation of such organisation: namely, design.

    And, BTW, that is one reason why design thought adds significantly to our ability to observe, describe, analyse, understand, explain and act into our world.

    GEM of TKI

    PS: I have now summarised my thoughts on where failing to understand the crucial difference between [a] chance [ = stochastic, undirected contingency], [b] necessity [= mechanical forces acting in accordance with low-contingency dynamics] and [c] rational choice [= design] leaves us, here and here. {The latter focuses on how intelligently designed foresighted target seeking programs came to be presented as in effect significantly analogous to spontaneous, undirected random variation and competition among functioning entities for survival and reproduction; through a question-begging contrast between “single step” and “cumulative” selection.)

  180. iconofid says he? doesn’t see evidence for design yet he? cannot support his position.

    What part of that don’t these guys understand?

    Support your position as opposed to arguing, from ignorance, against ID.

    Also it is a bit ironic that icon says that “we don’t know” out of one side of his? mouth but out of the other comes “but we know it wasn’t via a designer”.

    Just about the entire theory of evolution equates to “we don’t know”.

    Do chimps and humans share a common ancestor? We don’ know is the ONLY honest answer.

    Did whales evolve from land animals? Again we don’t know is the only honest answer.

    And again both design and intelligence are NATURAL.

    We can and do make determinations of agency involvement on a daily basis.

    And guess what?

    Reality has demonstrated that it matters to any investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.

    And the people who refuse to understand tat basic fact have no business conducting an investigation.

  181. iconof id,

    YOu don’t seem to understand ID.

    ID does NOT say that the bacterial flagellum could not have evolved.

    The debate is all about the mechanisms-

    Was it designed to evolve- ie evcolved by design or did it evolve via an accumulation of genetic accidents?

    And in the end “nature” had a beginning- tat is according to science- and seeing that natural processes exist oinly in nature they cannot account for its origin.

    IOW YOU also requiore the non-natural.

    Deal with it.

  182. uoflcard:

    Because even demonstrating a possible pathway would refute that argument for intelligent agency, regardless of whether it actually happened that way.

    I diodn’t say anything about a possible pathway.

    They have to demonstrate it can arise without agency involvement.

    Period.

  183. iconofid:

    As I pointed out to Joseph, what we don’t know at any particular time does not = intelligent design.

    Science allows us to make inferences given our current state of knowledge.

    Science does not and cannot wait for what the future may of may not uncover.

    And as I said above if we listen to icon then the theory of evolution amounts to “we don’t know”.

    Now, be positive, and devise an experiment which will demonstrate your mechanism in action, the mysterious designer designing.

    Design is a mechanism.

    So if Dr Behe went into a lab and designed a bacterial flagellum would that “prove” ID?

    This can be done for mutation, selection and drift, as you know.

    1- Not all mutations are unguided- IOW mutation could very well be part of the design- evolved by design

    2- Mutation, selection and drift have NEVER been observed to do anything except slight, oscillating variations.

    IOW you don’t have anything to support your position.

    So how about it- can you provide an experiment that demonstrates the true powers of yourt proposed mechanisms?

    Or is confirming the Creation model of evolution the best you can do?

  184. Alan, did you miss this (164)?

    Before I give you a definition do you agree that (design) is something that exists? . . . Why so coy?

    Nothing coy, just trying be keep the discussion clear: For instance:

    The word “design” exists as a noun and a verb. People design and build things . . .But just having a word does not give something existence. How can I agree something exists before you tell me what that something is?

    You seem to be saying design exists and you describe it then you say you can’t agree that it exists until I tell you what it is despite it being something you apparently know.

    So to get to the point, we agree that design exists, right?

  185. I am not sure design has a hard definition. Does anyone have one? We use it here mainly to indicate that some entities were the result of purposeful activity. We can point to human activity and various animals and some of their activity and we know what are the elements of design by the results of this activity.

    No one would point to non life and things produced by nature and call it design even though we have all seen various things in nature that we say make nice designs because of the order and the arrangement of the various parts. I still get a sense of wonderment at Yosemite Valley which I consider the prettiest place on earth. It seems that all the elements were placed just right to give the sense of awe whether you are looking at the valley from its entrance, standing in the middle of it or on top of Glacier Point. We talk of God’s design as a metaphor for such a place but we all know it was produced by law and chance as the glacier first carved out the valley and then receded to allow the trees to grow and the water to flow.

    But here in the discussion of evolution and the origin of life we tend to use the term as more one of purpose in contrast to the wondrous array of nature. And when confined to this, we can often distinguish between the sort of random effects that life’s activity has and the purposeful parts.

    We also tend to use the term design to apply to those entities outside the life form that are left due to the activity of the life form. I am not talking about the space ship, the skyscraper, the works of Michaelangelo etc but unconscious activity that indicates that life was once there. As such it is murky whether a foot print or the mark of something dragged or some other indication that the life form was there is design or not. We can compare a beaver dam to the indentations in the ground due to the dragging of the log. Is one design and the other not. Most would say the indentation is not design so we are left with consequences that mostly have some purpose or function which we call design.

    So one of the characteristics of a lot of design is purpose. Even an idle doodling often has a purpose or a lot of other apparent unconscious activity. But a supposedly random scribble or foot dragging is a lot different than an automobile.

    Design detection does not attempt to determine all design since that would be impossible but it tries to determine if a specific entity was part of the subset of design. That is what the explanatory filter is trying to do. It wants to include only things that are designed with the understanding that a whole lot of designed things will be left out but no undesigned items get included. Since it tries not to include anything that may be not designed, it constantly is assessing whether something can be due to the work of law and chance and even if there is only the smallest possibility that it could be due so. It will not declare a lot of entities designed even they were.

    An aside, Dembski’s EF is an attempt to be very general and include items from a wide range of activity as designed and as such the attempts get a little bit murky as to the reasoning because of the generality. But we should not confuse these designed items that may be a little bit vague with other items are so obviously designed that the rationale is simple and straightforward.

    Now one of the things we notice about a lot of design, though not all, is that it has a function. It accomplishes something for a larger purpose and often it accomplishes it because it is necessary for several interdependent parts to work in unison. We can point to a sub part and say that this along with other sub parts leads to an eventual result that is good for the entity. A computer, water system, farming, art, etc. This is not hard to see as we are all familiar with the multitude of purposeful activity and machines in our world. We can also see that the same phenomena also happens within life. In fact some of the more sophisticated processes we know about are within life forms and cells in particular.

    So is life designed. Someone can come along and say no it is not but then do they have any knowledge that shows that it is not designed. It obviously has function and interacting sub parts with function. All the essential elements of a complicated machine. Then we learn that the basis of this coordination is a sophisticated computer like process using incredibly complicated code to make and control the parts and processes.

    For most of human life it was noticed that life was incredibly coordinated and nearly everyone thought it was designed. This was before anyone knew any biology and knew about the sub-systems and how they worked together or the incredibly sophisticated code that is necessary to control it. It seems like the more sophisticated we know the system of life is the more adamant a sub group seems to be saying it was all just an accident. Each new discovery must be accompanied by the obligatory phrase it evolved or it was selected for. Like these incredibly complex interacting machines just arise out of nowhere all the time.

    The person who says that life is not designed has an obligation to show how such a thing that has all the interconnecting functional processes with the incredibly complex code could have arisen by law and chance. They must be able to point to a process in nature that leads to such entities. They cannot just make the claim and defy you to show otherwise. They have to show you the way.

    We get a lot of unsophisticated voices here who just assert it happened without showing the way. The sophisticated do not do this because they know there is no known way it could have happened. They are commenting in some journal about the difficulty of showing the way and discussing the possibilities on how it might have happened.

    So it gets a little tiresome to see the comments that it must have happened naturally because it is here and only nature is allowed to do it. Or another argument is to make sarcastic comments about an unknown designer like it was a thief in the night. Argument by sarcasm and assertion seems to be a necessary technique. One thing they cannot do is argue for their position. All they do is assert it.

  186. 186

    Icon,

    Firstly, let me thank you for actually trying to address the evidence – it is a rarity.

    “I don’t disagree with Trevors and Abel that there are gaps in our knowledge. I see nothing in the paper that shows that nature cannot produce “algorithmic instruction”.

    The paper makes the point that algorithmic instruction are only known to exists by means of an agent, and such instructions have never in the history of science been caused by “nature” (as you say it) acting without agency input. So the question becomes: On what grounds do we justify ignoring agency as a natural force today?

    Why does it require an unknown force for chemical evolution to produce “FSC”? What laws of physics would that process break?

    ID does not posit broken laws of physics – it posits that based upon the evidence 1) the only known cause for the observed effects is agency, and 2) that neither chance nor necessity have ever been observed creating these effects. This is not a trivial distinction; these effects are clearly defined, just as the glaring dissimilarity between a crystal and a compact disc. This leads to two straigtforward questions: Can a compact disc come about by “natural” causes? Are there any laws of nature broken by the existence of a compact disc?

    What is unknown is the chemistry of the OOL, and the chemistry of the evolution of the genetic code.

    This is simply a return to the failed God of the Unknown argument. Again, do you think science is actually expecting an unknown property of chance to come forth and explain why formerly inanimate chemicals would self-organize into three-dimensional energy-metabolizing structures driven by highly-coordinated information processing systems that spontaneously initiate the recording of their existence by means of a conventional code of digital information that is proof-read and error-corrected but is not contingent on material need? Will neutrinos explain the empirically detectable drive for survival?

    There are enormous gaps in our knowledge of biology all over the place. It’s in its infancy, compared to what could be known. But it doesn’t require any unknown forces so far as I know. Isn’t that your claim rather than mine?

    Again, ID does not make claims for unknown forces, to the contrary, ID claims that the cause of the observable effects in nucleic sequencing (and other aspects of biology) is very well known – it is the result of an Agent. What ID cannot say is who/what the Agent is. Why? Because ID appropriately stops at the line of what is knowable by the evidence itself. Some may find this lacking, but it is completely harmonious with what is science is supposed to be. As an empirically-based program, what else could it do?

    Are Trevors and Abel suggesting that the sophisticated organization that empirical observation tells us is required in intelligent designers cannot come about naturally? Or just that we don’t yet know the full story of how it could happen?

    This is once again an appeal to the God of the Unknown. Ask yourself (once again) is science expecting to discover the explanation for life within an unknown property of chance and necessity? If you say “yes”, then please provide some conceptual thoughts about what this might be – or, simply admit to an argumentative dependence on the God of the Unknown and all of its ideological baggage.

    Of course the answer is NO, science is not expecting this. It’s a shell game providing blind support to an ideological priori that was established long before the advent of molecular biology. It’s a stance that cannot withhold the force of molecular biology. It’s a stance that is becoming more and more untenable. To be clear, there is a pattern that has emerged; the more we know, the less we can explain.

    Now, ask yourself a manifest question. Under what conditions could such a pattern exists – this relationship between vastly increased technical knowledge and a dwindling applicability of ideological assumptions (as clearly evidenced by the continuous expansion and rewriting of those assumptions). I suggest this pattern exist because the priori assumptions were established without technical merit.

    We have often been our own fools, the advent of the microsope was hardly the end of it.

    If I.D. already has a measured way of detecting design, how soon will we see a general agreement amongst I.D.ers on what evolves naturally, and what is designed? Surely all brains of all species must be designed considering the amount of species specific complex information they seem to contain?

    This is a point in another long post where the discussion starts to drift off into the weeds. If one understands that the difference between inanimate material and functioning living tissue is the prescribed instructions written into nucleic sequencing, then why would I think a big toe is a result of that information, but a gall bladder is not?

    I’ll have a look at the research on sequencing of nucleic acids when I’ve got time, to show that I’m taking I.D. arguments seriously.

    Thank you.

  187. —-Upright Biped: “If you say “yes”, then please provide some conceptual thoughts about what this might be – or, simply admit to an argumentative dependence on the God of the Unknown and all of its ideological baggage.”

    Yes, indeed. If those wedded to the idea that naturalistic forces can actually create information or its equivalent, they should at least be able to conceive of some imaginative scenario whereby such things are possible.

  188. I am not sure design has a hard definition. Does anyone have one?

    This works for me:

    1: to create, fashion, execute, or construct according to plan : devise, contrive

  189. Upright Biped

    Thanks for the lengthy reply.

    You say:

    The paper makes the point that algorithmic instruction are only known to exists by means of an agent, and such instructions have never in the history of science been caused by “nature” (as you say it) acting without agency input. So the question becomes: On what grounds do we justify ignoring agency as a natural force today?

    Yes, I understood the point of the paper. As I said, I see no evidence in it for I.D. Let me explain.

    12,000 years ago, the cavemen Iconofid and Upright Biped are sitting by the fire near the mouth of their cave, watching “fire” erupting from a volcano on the horizon during a storm. A bolt of lightning strikes a tree just a few hundred yards away, and it bursts into flames.

    “I wonder what fire is, and where it comes from”, Iconofid muses.

    “Well”, says Upright the Wise, “the only times we know the source of fire is when we make it, so it’s reasonable to assume that the volcano fire and the lightning fire are the products of other agents.”

    And so great was the influence of this early philosopher and others like him that still to this day there are people who make offerings to volcano gods (Bali), and the gods of lightning are renowned far and wide.

    If this caveman had a strong argument, then so do the authors of your paper, Upright the Wise.

    ID does not posit broken laws of physics – it posits that based upon the evidence 1) the only known cause for the observed effects is agency, and 2) that neither chance nor necessity have ever been observed creating these effects. This is not a trivial distinction; these effects are clearly defined, just as the glaring dissimilarity between a crystal and a compact disc. This leads to two straightforward questions: Can a compact disc come about by “natural” causes? Are there any laws of nature broken by the existence of a compact disc?

    None whatsoever. A few billion years of evolution in negative entropy could certainly produce creatures that could make them, for example.

    This is simply a return to the failed God of the Unknown argument. Again, do you think science is actually expecting an unknown property of chance to come forth and explain why formerly inanimate chemicals would self-organize into three-dimensional energy-metabolizing structures driven by highly-coordinated information processing systems that spontaneously initiate the recording of their existence by means of a conventional code of digital information that is proof-read and error-corrected but is not contingent on material need?

    There is no “unknown property” required. Think of it like cosmologists figuring out how the solar system formed over the last century or so. They didn’t know how it happened, now they pretty much do.

    As for your characterization of what’s at the base of modern organisms, that would have to be the result of a lengthy evolutionary process. There’s absolutely nothing to prevent evolutionary processes increasing complexity and what you call information. I’m not saying anything that I couldn’t get thousands of physicists, biologists and chemists to agree with. And they certainly wouldn’t all share the same philosophy, religion or ideology.

    It’s a stance that cannot withhold the force of molecular biology.

    Perhaps you should spend more time communicating with molecular biologists and less time with people who think molecules are computer components.

    I’d be genuinely interested to know when you would predict the downfall of methodological naturalism, and what folks around here call “materialism” in science. I can find you quotes from people predicting the downfall of “Darwinism” from the late nineteenth century onwards.

    Do you think it’s a matter of years, or decades? (A question for all I.D.ers, not just UB).

    Cheers.

  190. JAD:

    Is the adult organism capable of any further differentiation? No, is my answer.

    What about dichogamy? You may ask Nemo if you should find him. What about budding in Hydra What about adult plants? Isn’t there something like vegetative reproduction, rhizomes, stolons, tubers, etc.?

  191. tribune7,

    “to create, fashion, execute, or construct according to plan : devise, contrive”

    Your definition may be useful for the evolution debate. At first I didn’t think it would be. It has in it the phrase, “according to a plan.” I initially thought you might get yourself into trouble in this debate because you will be asked for the plan. However, there is a plan and the plan is the coding part of the DNA. So there is in fact a physical plan. No where else in the world except life and human activity is there such a plan

    However, for some other non evolutionary items, the plan underlying the design would not be so obvious. Such as a sculpture or a painting or an arrow head or a set of tools where the only plan was in someone’s mind and never took physical shape. And to use this definition to assess something found in the world as either design or not may be problematic in such cases.

  192. At first I didn’t think it would be. It has in it the phrase, “according to a plan.” I initially thought you might get yourself into trouble in this debate because you will be asked for the plan.

    The one problem I would have with the definition is in its use of synonyms to define each other i.e. “plan” and “design”. I toyed with “a designed object or event is one that came into existence through desire guided by thought” but I felt safer with the dictionary one.

    Not having the plan doesn’t make design any less real. Remember with design detection, the expectation is that one won’t have the plan in front of him. The goal is to determine design without the plan. Was the fire arson or accident? Is the noise signal or static? etc.

    However, for some other non evolutionary items, the plan underlying the design would not be so obvious. Such as a sculpture or a painting or an arrow head or a set of tools where the only plan was in someone’s mind and never took physical shape.

    Remember the definition (or reality) of design is not the ID process. All those things are designed as per the definition. Would the hyper-rigorous ID method be able to detect design in them?

    Maybe not.

  193. Alan, did you miss this (164)?

    Life intervened. A friend crashed her car, in hospital , pets to sort out. Will try find time later to respond.

  194. You seem to be saying design exists and you describe it then you say you can’t agree that it exists until I tell you what it is despite it being something you apparently know.

    People design things. So I know what human design is. I don’t know if intelligent beings exist elsewhere in the universe. I don’t know if they design things and have no idea what these things might look like or do. I can only imagine in extrapolating from human experience.

    Are the honeycombs of bees deigned? do termites plan their mounds? Do beavers plan their dams?

    It is hard for me to see what the concept of design means without qualifying it in some way. Can you define design in the abstract?

    So to get to the point, we agree that design exists, right?

  195. So to get to the point, we agree that design exists, right?

    For the purpose of argument, yes.

  196. 196

    sparc in #190.

    In forms capable of vegetative growth and reproduction, the individual becomes a vague entity, but even there I know of no proven instance of true speciation occurring through those means. Neither does anyone else as far as I know.

    I insist that all real evolution was through instantaneous events exactly as Otto Schindewolf insisted. While there have been “stepping stones” there have been no gradual transformations of one species or taxon to another. To claim otherwise as the Darwinians still insist is a scandal.

    Furthermore, I see no evidence that there remains a single extant organism capable of leaving descendents significantly different than itself. In short -

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

    That does not mean that one could not hy experimental intervention achieve that which Nature can no longer manage to bring about.

    In 2004 I published my paper “Is Evolution Finished?” available on the side bar here at Uncommon Descent. On my weblog I have rearranged the words in the thread “Evolution is finished.” My challenge to the Darwinian fantasy has remained unanswered both in the professional literature and on internet forums. It has always been the habit of Darwinians to pretend they have no critics. That won’t wash any more. They are finished!

    I hope this helps.

  197. 197

    I think a problem in using the term “design” in the Intelligent Design movement is that for believers, all things are designed (I am taking for granted that design is part of creation). Del Ratzsch describes a hundred-meter, perfect titanium cube on Mars (Nature, Design and Science, p12). He says we would not think it was “natural,” using that as an example of an obvious artifact, implying design. However, what he misses is that the planet Mars is also designed: it is designed as a planet. The discovery of fine-tuned physical constants which make the universe the way it is has given us the idea of the Anthropic Principle. The laws of the universe are designed. Even random movements of molecules are a necessary part of the design of the world, very useful in things like the atmosphere and diffusion.

    The opposite of design, like the opposite of Creation, is not randomness but nothingness. I believe God gives us the innate ability to sense design, and also the revelation in the Bible that He made all things.

    The ID movement is important in showing the discrepancy between chemical and physical laws acting on molecules and the facts of biological laws. Though some may be confused by the differences, they do exist. Molecules are subject to chemical and physical laws, not biological laws like neo-Darwinian selection. You will not (or should not) find “survival of the fittest” in any index of a chemistry book. The probabilities of usable combinations of atoms are sources of information for ID Theory.

  198. UB, 186:

    ID does not posit broken laws of physics – it posits that based upon the evidence 1) the only [directly] known cause for the observed effects is agency, and 2) that neither chance nor necessity have ever been observed creating these effects. This is not a trivial distinction; these effects are clearly defined, just as the glaring dissimilarity between a crystal and a compact disc. This leads to two straigtforward questions: Can a compact disc come about by “natural” causes? Are there any laws of nature broken by the existence of a compact disc?

    Excellent summary.

    Let us now cf. Mr Fox — hope your friend turns out okay — at 194:

    People design things. So I know what human design is. I don’t know if intelligent beings exist elsewhere in the universe. I don’t know if they design things and have no idea what these things might look like or do. I can only imagine in extrapolating from human experience.

    1 –> Now, of course, that we are familiar with human intelligent designers and their artifacts immediately means that we can identify major characteristics of what we mean when we use the terms intelligence, design and artifacts, etc. (Cf a good dictionary.)

    2 –> Thus, we have identified a cluster of concepts, and we have identified concrete exemplars; i.e. what we need to identify other instances [and, perhaps counter-instances] on a family resemblance basis; and, key example and close family resemblance thereto is legitimate as a definition; indeed it is the basis for other definitions. (Cf, for instance how we have to deal with life, the subject matter of biology: we cannot put together a neat and clean one size fits all precising necessary and sufficient conditions or genus-difference definition. Denotative or taxonomical definition and/or quantification are not necessary conditions of science. So let us not indulge selective hyperskepticism.)

    3 –> that also grounds ideas like the explanatory filter, which give decision rules for dealing with cases: mechanical necessity gives rise to low-contingency regularities of nature, undirected stochastic contingency is distinguishable form directed and purposeful contingency. the criteria of specification, functionality and complexity are relevant to these and may be quantified.

    4 –> From this, we have a well tested rule: functionally specific complex information [cf FSC etc] is a known artifact of agency and on inductive reasoning, we see that in every known case, its source is intelligence. Further, we see that stochastic processes will be overwhelmed by the search space challenge to arrive at shores of islands of function, absent intelligent direction. [Indeed that is the key point of failure of the Weasel program. (Cf my summary discussion here that now joins my always linked.)]

    5 –> Someone has recently challenged the idea that functionality exists in isolated islands (and archipelagos) in large config spaces. Let that one do the experiment of trying to compose a functioning algorithm and program by random chance, or of trying to improve it substantially (more than 1,000 bits worth of new code) by random variation of its instructions.

    6 –> Nor, do we know that humans exhaust the list of intelligent designers.

    7 –> Nor, do we know that such candidate designers are confined to being embodied within the cosmos. (Indeed, we have a contingent, complex, massively fine-tuned cosmos that is indeed on an island of local function in the parameter space of physics, and it is credibly contingent, thus at least possibly designed by an intelligence that is extracosmic.)

    8 –> What we do know is that on principles of inductive reasoning, we have good and reliable signs of intelligent design. So — pace selectively hyperskeptical objections — we are entitled and well-warranted to infer inductively from such signs to the signified.

    9 –> And, such signs can therefore be used to support the inference that such an agent is/was present, even where we have no other indication.

    GEM of TKI

  199. PS: WTW: pardon, one may as a worldview accept that design is the foundation of reality. That is a different project (and under a different head, philosophy) from the scientific case that per signs of intelligence, design is empirically detectable on evidence, for certain important cases. [Christians inclined to support ID tend to see that say Jn 1, Ac 17, Rom 1 - 2, Col 1 etc expect that the design of the universe and specific items in by him who is Reason Himself it will be empirically evident and intelligible to the eye of reason, to a point where one has to resist or even suppress the conclusion if one finds it uncomfortable to one's worldview. (Thus, at these points the Christian worldview is subject to empirical test and potential falsification. You may find the FAQ's 1 - 8 helpful, esp when they deal with Logos theology.)]

  200. Alan, sorry to hear about your friend.

    OK, assuming design exists, would it have unique traits? Sure. It’s a word we use successfully in communication and it’s a concept we use internally to help us understand life.

    Are these traits objectively describable? There is no reason to think they wouldn’t be.

    Does ID succeed in describing them? That’s a fair debate.

    People design things. So I know what human design is. I don’t know if intelligent beings exist elsewhere in the universe. I don’t know if they design things and have no idea what these things might look like or do. I can only imagine in extrapolating from human experience.

    You believe in evolution. Presumably that means you see Man as having naturally evolved the ability to design. Presumably that would mean that you leave open the possibility of some other life form –an earthly one — also acquiring such an ability.

    Which means it would be beneficial to seek an objective means of determining design. There is nothing wrong with using human experience as a starting point.

    Are the honeycombs of bees deigned? do termites plan their mounds? Do beavers plan their dams?

    ID would not say yes. Of course it wouldn’t say yes to the parquet floor of the Boston Gardens. The examples are patterns which are an indication of design. Their complexities, however, do not reach such a level that you could ascertain it.

    It is hard for me to see what the concept of design means without qualifying it in some way. Can you define design in the abstract?

    I gave this one to Jerry: a designed object or event is one that came into existence through desire guided by thought

    That would mean design is thought guiding desire which would not become evident until action.

    The bees and beavers wouldn’t be designers with this definition in the same sense that a laserprinter wouldn’t be a designer when it prints out a colored chart. The hives and dams would be built according to instinct rather than thought and desire.

  201. womanatwell–I think a problem in using the term “design” in the Intelligent Design movement is that for believers, all things are designed

    ID is a scientific methodology, and it is a rather limited one. It is incapable of detecting design in all things. It is also falsifiable, and if it should be falsified it shouldn’t affect your faith.

  202. Alan Fox:

    Are the honeycombs of bees deigned? do termites plan their mounds? Do beavers plan their dams?

    So I take it that you did NOT read Del’s book.

    I say that because if you had vread it you would NOT be asking those questions.

    So is arguing from ignorance the best you can do?

  203. 203

    There is no such thing as a “fair debate.” Debates are meant never to be resolved. That is why they always start off with the words -

    “Resolved that etc, etc.”

    I defy anyone, here or elsewhere, to name a single issue, scientific or otherwise that was ever “resolved” through “debate.” I think 24 hours ought to prove sufficient. I’ll check back tomorrow morning, supremely confident there will be no answer.

  204. Resolution (policy debate):

    In policy debate, a resolution or topic is a normative statement which the affirmative team affirms and the negative team negates.

    In this sense “resolved” would mean to separate- divide into two distinct groups.

    As in there are (at least) two sides to every issue.

    In that sense then every issue brought up for debate is “resolved”.

  205. tribune7:

    The bees and beavers wouldn’t be designers with this definition in the same sense that a laserprinter wouldn’t be a designer when it prints out a colored chart. The hives and dams would be built according to instinct rather than thought and desire.

    Any living organism has the ability to be a designer.

    “Instinct” is just a word for “we don’t know”.

    Nature, operating freely would not and could not build a beaver dam.

    Nature, operating freely would not and could not build a bee-hive nor a termite mound.

    tribune7- have you read “Nature, Design and Science” by Del Ratzsch?

    You should.

  206. OK, JAD. We will make it a “legitimate point of contention”

  207. Any living organism has the ability to be a designer.

    Joseph, I disagree. I don’t think a spider puts a moment of thought in designing it’s web. Can a house spider build an orb web? It’s all in the programming.

    “Instinct” is just a word for “we don’t know”.

    It means in this case 2 a: a largely inheritable and unalterable tendency of an organism to make a complex and specific response to environmental stimuli without involving reason b: behavior that is mediated by reactions below the conscious level

  208. tribune7:

    Joseph, I disagree. I don’t think a spider puts a moment of thought in designing it’s web.

    Good luck with your research trying to confirm such a premise.

    Can a house spider build an orb web? It’s all in the programming.

    Can my six-year old program a computer?

    I bet if someone could teach the spider how to build something different it could.

    However one first has to figure out how to communicate with it.

    Can nature, operating freely create a spider web?

    If the answer is “No” then it is clear that a spider is an agency and its involvemnet with nature can be detected.

  209. 77 Pav
    The change in head morphology is puzzling. I don’t see why the lizards with smaller heads would have a tendency to die before reproducing compared to the ones with larger heads, especially if food was abundant.

  210. 210

    I am very much aware of the dual meaning of the word “resolved.”
    I still be back tomorrow morning to see if thare is any answer to my challenge. I am betting there won’t be, because there never has been!

  211. uoflcard 169
    I’m still trying to figure out why a rodent that had mutated webs between it’s digits would have an evolutionary advantage. Furthermore, the webs and digits would have to enlarge through succeeding generations, along with the attendant muscular and vascular changes, until the animal became aerodynamically capable.

  212. 212

    In the meantime I offer some light reading below.

    http://www.iscid.org/boards/ub.....p-108.html

    April 16, 2009,8:40

  213. 213

    Icon,

    Well, it seems by your last post that any promise of addressing the actual issues will have to be put on hold. You’ve returned to the safety of fuzzy logic.

    You start off your post by quoting me when I ask “On what grounds do we justify ignoring agency as a natural force today?” and then you say:

    “I understood the point of the paper. As I said, I see no evidence in it for I.D.”

    This statement of yours is referring to a peer-reviewed paper in which the authors clearly state:

    The fundamental contention inherent in our three subsets of sequence complexity proposed in this paper is this: without volitional agency assigning meaning to each configurable-switch-position symbol, algorithmic function and language will not occur. The same would be true in assigning meaning to each combinatorial syntax segment (programming module or word). Source and destination on either end of the channel must agree to these assigned meanings in a shared operational context. Chance and necessity cannot establish such a cybernetic coding/decoding scheme [71]. (emphasis added)

    In making this statement the authors draw defensible conclusions from an observation-based analysis of the qualitative cause and effect relationship between known causes (chance, necessity, and agency) and their known effects in our natural world. And somehow you take from that paragraph the idea that there is no inference to ID being suggested. It is this kind of reasoning that proponents of ID have to contend.

    The authors are saying that the pattern in nucleic sequencing is physio-dynamically inert – leading to a conceptual and logical impossibility that physio-dynamics lead to the pattern observed in nucleic sequencing. What part of this do you disagree with? And if you do disagree, then please provide at least some conceptual thoughts as to why the authors are wrong and you are right.

    The authors are also saying that the algorithmic complexity of the sequencing requires a coordination of disparate systems that is beyond the reach of chance mechanisms given that chance mechanisms operate with equal-probable results at each decision-node along the nucleic chain (the exact opposite of complex coordination). What part of this do you disagree with? And if you do disagree, then please provide at least some conceptual thoughts as to why the authors are wrong and you are right.

    Further, the authors are saying that the algorithmic instruction in nucleic sequencing are, in fact, imbedded in a conventional code and are therefore subject to a non-physical coordination of symbol meaning between the receiver and the transmitter. What part of this do you disagree with? And if you do disagree, then please provide at least some conceptual thoughts as to why the authors are wrong and you are right.

    - – - – - – - – -

    The point you want to return to are the historical mistakes that man has made in the discovery of his world. This is a point that I have already addressed:

    “…the corrective measure to the historical context you raise is to stop seeing agency where agency is not empirically inferred. It’s been a couple hundred years and several million thinkers since that became clear. Mission accomplished. On the other hand, the irrational corrective measure is to hide our eyes from the evidence and simply say that we must not see agency even under the strongest possible inference to it, and (at the same time) operate with the complete lack of inference to either chance or necessity being able to accomplish what is observed. Now how smart are we?”

    I still stand by this statement. If you disagree that this is not the appropriate corrective measure, then please be specific in what the corrective measure should be.
    Also, regarding your cavemen, you have their names wrong. There names are Upright Lemaitre and Icono Hoyle. Now replay your tape and see if it means the same.

    The same goes for your appeal to consensus power.

  214. 214

    I am no longer allowed to comment on scordova’s thread. I have kept a record of all my accepted comments on my “Why Banishent?” thread on jadavison.wordpress.com

    By comparing that record with the subsequent fate of those comments represents a revealing testimony on the tactics of one “author” here at Uncommon Descent.

    The most galling aspect of scordova’s actions is his insistence that he is “protecting me from myself.”

    I have been quite able to protect myself all by myself all my adult life.

  215. Joseph –Can my six-year old program a computer?

    That’s sort of the point. Spiders aren’t taught how to spin webs.

  216. Aren’t court cases resolved via debate?

  217. Upright Biped:

    And somehow you take from that paragraph the idea that there is no inference to ID being suggested. It is this kind of reasoning that proponents of ID have to contend.

    It must be difficult. I think I said before that I do not know how “chance and necessity” can account for the systems that they’re discussing in that paper, and I certainly can’t contradict anything but their final conclusion without searching through hundreds of papers. They, like you, have concluded that every other possibility has been exhausted, and design is required. So, I think I said before that I.D. should definitely claim that intelligent design is required, just as Michael Behe did for the bacterial flagellum.

    I think it’s an ongoing area of research. I think that’s what you call “the God of not knowing”, but no-one informed me that science would be complete this year.

    As for the history, the caveman was saying exactly what they’re saying in their conclusion in that paper.

    The same goes for your appeal to consensus power.

    I think you’re referring to my comment that there’s no reason why evolutionary processes can’t increase complexity and “information”. If you disagree, what is that reason?

  218. 218

    Court cases are indeed sometimes resolved by debate and often prove to be in error. Lawyers are not scientists and neither are politicians, or the captains of debating teams.

    “If you tell the truth, you can be certain, sooner or later, to be found out.”
    Oscar Wilde

    It is as simple as that.

  219. 219

    Icon,

    If you don’t know the cause, and they don’t know the cause, and no one else knows the cause, then how do we know that agency isn’t the cause?

  220. 220

    …and Icon, I hope you won’tgo back to your cavemen to make your next comment. Its an insult.

    You might want to remember – language, information, and instructions were around and driving life long before there was a caveman to observe it. It is that which must be explained.

  221. Icon,

    If you don’t know the cause, and they don’t know the cause, and no one else knows the cause, then how do we know that agency isn’t the cause?

    I agree entirely. We don’t. Don’t mistake Joseph putting words into my mouth further up the thread for anything I’ve actually said.

    He said:

    Joseph: Also it is a bit ironic that icon says that “we don’t know” out of one side of his? mouth but out of the other comes “but we know it wasn’t via a designer”.

    I doubt if Joseph’s fantasies are the origin of your comment, but my position is that we can never know if agency isn’t involved in some way in pretty much everything, even if we appear to have very good “non-agency” explanations, let alone in the area we’re discussing.

    I think I said somewhere above that you would be correct in saying that I do “nature of the gaps” in the same way you do “unknown agency” of the gaps.

    You might want to remember – language, information, and instructions were around and driving life long before there was a caveman to observe it. It is that which must be explained.

    I don’t want to get into semantic arguments, because I’m personally happy with the use of those words in relation to chemical processes, and indeed, I use them. However, the strict traditional use of “language” was only for human languages, although it’s recently been extended to other animals and elsewhere.

    All uses are valid, but I’ve noticed that some I.D.ers will use the modern sense in which, for example, the chemical messages of ants are language, then associate this with the traditional meaning, and the intelligent design side of our own languages, and start to see sentience in chemical communication and reaction.

    That point made, I agree with your comment, including the caveman bit.
    Chemical “codes” appear to be a prerequisite for intelligence, so far as our present empirical observations of the fossil record can tell us, not the other way around. But if we found a large skull of some kind at the ~4 billion year period, I’d consider it direct evidence for I.D.

    I don’t think you should complain that my cavemen are an insult (and they’re not intended to be). When someone claims that the only known cause of something is our own volition (and that was the case for the cavemen in relation to fire) then I’m correct to illustrate why that means nothing.

    If you don’t like it, always remember that no-one outside I.D. is forcing I.D.ers to make weak arguments. Because the only time we can be sure of the cause of nuclear fusion is when we do it doesn’t mean that the sun was designed. As we already have a reasonable explanation for the formation of stars, few I.D.ers would make that argument, but there are the remains of a natural “power station” where fusion took place in Australia, so, perhaps someone might like to try the I.D. argument there.

    It won’t work.

  222. 222

    It is important to recognize thst it is impossible to reason with ideologues. That does not mean one can’t communicate with them.

    P.Z. Myers has an interesting feature at Pharyngula. While I have been banished from that forum and am now a permanent resident of his “Dungeon,” I am still able to reach Myers because I can transmit messages to him. I think anyone can. All you have to do is use your valid email address, compose your message and push the send button. He recognizes your message proving that he received it which is all that matters.

    279. John A. Davison – April 18, 2009[Edit]
    I just sent the following message to P.Z. Myers on Pharyngula. It was accepted but of course will never appear.

    There are plenty of scientists living and dead who were evolutionists but certainly never Darwinists. Darwinism is dead P.Z. Get used to it as many other evolutionists already have. There is no longer any doubt that evolution WAS a guided process now finished.

    I love it so!

    ___________________________________

    It is great sport. I recommend it highly.

  223. 223

    I see no point in continuing on this particular thread so I will retire from it now, confident that I have left my convictions behind for others to accpt or reject as they choose. That is all that matters to me anyway.

    There are matters far more important to me than the mystery of phylogeny.

    Spring comes to Vermont earlier each year, leaving little doubt in this investigator’s mind that we are witnessing what Martin Rees has called “Our Final Century.”

    I hate being right!

  224. Can my six-year old program a computer?

    That’s sort of the point. Spiders aren’t taught how to spin webs.-tribune7

    And you know that how, exactly?

  225. iconofid,

    Once it is shown that agency involvement is NOT required then ID falls. Period, end of story.

    Science operates via our existing state of knowledge.

    Scientific inferences of today cannot and do not wait for what the future may or may not reveal.

    That said if EVERY time we observe CSI or IC and know the cause it is ALWAYS via agency involvement, then when we observe CSI or IC and don’t know the cause, agency involvement is a safe scientific inference.

    Why does it matter?

    Experience with reality demonstrates that it matters a great deal to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.

    So until you have evidence tat nature, operating freely can bring about CSI or IC all you are doing is whining.

    But somehow I am sure that you don’t care.

  226. 226

    Icon,

    As chameleons go, Icon, you’ve dodged the ball well. All that’s left for you to deny now is that (S)cience disregards agency as a legitimate cause with evidence to support its consideration.

    Oddly enough this is exactly where you came into this discussion. I had asked another commenter on the thread if he would “be joining materialists everywhere calling for an end to the current default assumption that life began by chance and necessity?”

    You then took exception to this question by suggesting that ID lacked any real evidence and commented that you “haven’t personally seen any evidence for design in biology” and indeed that you would have “thought that “agency” is readily accepted”.

    It’s been a shell game of parsed meanings throughout.

    I’ve repeatedly asked you to be specific and repeatedly you’ve bounced out to “non-natural”, and to “cavemen”, and now to whatever Joseph said. Indeed, you may very well be the perfect example of a materialist ideologue – an enabler of a failed paradigm in the face of overwhelming evidence to the contrary.

    - – - – - – - – - –

    Science celebrates positive and parsimonious descriptions of presumed objectivity. But we must never forget that our knowledge is only “best thus far.” Even the most fundamental laws of physics technically must be viewed as “tentative.” We rightly eschew diatribes of metaphysical pontifications. Science proceeds through open-mindedness and the falsification of null hypotheses, not through the rhetorical pronouncement of dogmas. Popper and many since have exposed the problems associated with trying to prove any positive hypothesis [176, 177]. Neither induction nor deduction is foolproof. Theses that cannot be proven ought not to be proclaimed as positive statements of fact.

    At the same time, we have spent much of the last century arguing to the lay community that we have proved the current biological paradigm. Unfortunately, very few in the scientific community seem critical of this indiscretion. One would think that if all this evidence is so abundant, it would be quick and easy to falsify the null hypothesis put forward above. If, on the other hand, no falsification is forthcoming, a more positive thesis might become rather obvious by default. Any positive pronouncement would only be labeled metaphysical by true-believers in spontaneous self organization. Those same critics would disingenuously fail to acknowledge the purely metaphysical nature of the current Kuhnian paradigm rut [178]. A better tact is to thoroughly review the evidence.
    Let the reader provide the supposedly easy falsification of the null hypothesis. Inability to do so should cause pangs of conscience in any scientist who equates metaphysical materialism with science. On the other hand, providing the requested falsification of this null hypothesis would once-and-for-all end a lot of unwanted intrusions into science from philosophies competing with metaphysical materialism.

    While proof may be evasive, science has an obligation to be honest about what the entire body of evidence clearly suggests. We cannot just keep endlessly labeling abundant evidence of formal prescription in nature “apparent.” The fact of purposeful programming at multiple layers gets more “apparent” with each new issue of virtually every molecular biology journal [179-181]. – The Capabilities of Chaos and Complexity (D. Abel) International Journal of Molecular Sciences. 2009, 10, 247-291

  227. JohnADavison 203 -
    “I defy anyone, here or elsewhere, to name a single issue, scientific or otherwise that was ever “resolved” through “debate.””

    JohnADavison 218 -
    “Court cases are indeed sometimes resolved by debate…”

  228. 228

    I see that “Davem” (#227), whoever that is, waits until I am gone to introduce an incomplete statement in an attempt to denigrate me. That is characteristic of the sort of tactic that typifies internet communication and it invariably comes from some “mighthavebeen” who hasn’t the integrity to identify himself.

    I recommend leaving this sleeping dog alone. If I ever find out who “Davem” is I will expose him to the world as I hope to do with every anonymous blowhard who clutters up internet forums with spiteful, mindless drivel.

    As David Springer used to say -

    “Got that? Write that down!”

    Besides, court cases are not really resolved by debate. If they were there would be no appellate courts, no district courts and no Supreme Court. Even after things finally get “resolved” they are still subject to repeal.

    The truth has never been subject to repeal.

    “If you tell the truth, you can be certain, sooner or later, to be found out.”
    Oscar Wilde

    “Truth is incontrovertible, malice my attack it, ignorance may deride it, but in the end, there it is.”
    Winston Churchill.

    There is not a word in the entire Darwinian fantasy that ever had anything to do with an ascending, goal directed phylogeny which is no longer in progress – not a single word!

    “Here I stand. I can do no otherwise.”
    Martin Luther

    He also said -

    “When I pass wind in Wittemburg they can smell it in Rome.”

    That is exactly what I have been doing for quite some time.

    I love it so!

  229. 229

    Since Davem woke me up, I might as well show you what scordova did with my last three messages.

    379

    JohnADavison

    04/17/2009

    4:39 am
    e i o. y ai y eae, ooa ai e i oei e o ye. y e ae ei a oe o oi e ae i? I i e you y. ey ae o aei o aiia, a’ y.

    I i a o eiee i’ i?

    380

    JohnADavison

    04/17/2009

    8:28 am
    a

    I i you ou aao i ae o e a “i iuee” ui you ae oee you auae uie. oee, I o’ ee o you oiy a ae e ie o i.

    381

    JohnADavison

    04/17/2009

    1:07 pm
    .tfel dna thgir em gniteled erew uoy nehw em ot ti tup uoy sa “flesruoy morf uoy tcetorp ot” gniyrt ylno ma I .laS em natsrednusim t’noD

    That is the sort of thing one expects at After The Bar Closes. The last one can at least be read, so please do!

  230. #182 Joseph -

    I diodn’t say anything about a possible pathway.

    They have to demonstrate it can arise without agency involvement.

    Period.

    If all they have to demonstrate is that it can arise without agency, ID is already defeated. Saltation is physically possible. It is POSSIBLE, that thousands or millions of genetic mutations occur correctly in a single specimen, creating an entirely new species. It is astronomically improbable, but still possible. The improbability is why no one believes that actually happened. This is why I say possibility (“can”) should be considered along with probability.

    The example of saltation is an extreme, and not believed by any rational person, but it demonstrates the point.

  231. 231

    uoflcard, whoever that is.

    Saltation WAS a reality and is believed by this very rational person.

    There is absolutely no need for any intervention, supernatural or otherwise, in a goal seeking mechanism such as the Prescribed Evolutionary Hypothesis proposes.

    Where is there intervention in ontogeny? There isn’t any.

    I had planned to abandon this silly “debate” but I cannot abide idiotic statements such as the one that led to this exchange between joseph and yourself.

    There is no need for any allelic mutations to have a occurred to explain evolution. Allelic mutations never had anything to do with evolution except to ensure extinction.

    Everything we know pleads for a planned phylogeny now finished.

    I have presented my case and I might just as well have been talking to the wall.

    This entire thread has been dominated by a half dozen or so unknowns who would rather “debate” with each other than consider an alternative to Darwinian mysticism presented by a real human being. I hope they know whom they are “debating.” I sure don’t and don’t care to find out. Comments from anonymous sources contribute NOTHING, never have and never will.

    It is hard to believe isn’t it?

    Not at all. Look around. That is exactly all that you see.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  232. uoflcard:

    If all they have to demonstrate is that it can arise without agency, ID is already defeated.

    Why? Such a thing has NOT been acomplished.

    It is POSSIBLE, that thousands or millions of genetic mutations occur correctly in a single specimen, creating an entirely new species.

    YEC accepts speciation.

    What’s your point?

  233. I am wondering why Bill did not bold or comment on this:

    Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed.

    I also noted the title of the paper:

    Exceptional Convergent Evolution in a Virus

    I’m not sure what Dembski =meant when he wrote:

    The actual phylogenies here were experimentally known and yet standard evolutionary theory drew completely wrong conclusions. Oh, but it was a small population, small genomes, and intense selection pressure. Spare me.

    So, do fasle positives and false negatives in the EF falsify ID?

    Perhaps if the paper had relied on analogies and bogus probability calculations and unsupported assertions, he would have been more impressed?
    Heck – maybe we could send a copy to the boys in the ISCID Princeton Office and they could take a look at it…

  234. …but scientists try to gloss their dogma in the language of probability

    So, apparently, do DI Fellows.

  235. Jehu:

    Phylogenetic trees ultimately fail because the real pattern of life is a mosaic or a web, not a tree.

    Were it the case that ALL phylogenetic reconstructions sought ot recontruct the entire history of life, then you might have a point.
    Let us look at a more manageable scale – look at your family tree going back, say, ten generations.

    Is it a web, or a tree?

    So, the phylogenetic trees always end up containing inconclusive and contradictory data.

    Always? Really?

    The DNA that leads to one tree could just as easily be used to construct an entirely different tree.

    This is true, but very misleading. You can constrain tree reconstruction software to produce arrangements contrary to what the data indicate, and in come software packages you can sort of ‘cut and paste’ brnaches to rearrange trees. However, in doing so, the reliability scores for the tree drop significantly. I have seen this done in creationist publications, where programs are constrained to prevent humans from grouping with other apes, since the ‘researhcers’ know that humans and apes are not related. This produces ridiculously low bootstrap values for species that even creationists acknowledge as being related via descent, because it throws the whole tree off, as it were.
    Simply letting the program produce the tree as indicated by the data will NOT produce any old tree. To claim so is to admit ignorance of the entire field.

    Therefore, in order to make the DNA fit the original assumption that a tree even exists in the first place a procrustean bed is fashioned for the data using the twin excuses of horizontal gene transfer and convergent evolution to cover up the contradictions.

    The only instances in which this sort of thing needs ot be done is, again, in the case of creationsit baraminological analyses in which outcomes are constrained to reflect Scriptural criteria.
    Please do not assume that all researchers engage in such manipulation.

    A third excuse, mutational hot spots can also be used to defend the tree. However, the mutational hot spot explanation must be handled with care because it is a double edge sword that effectively threatens the very assumptions upon which the tree was built in the first place.

    A series of largely unsupportable assertions and a misleading claim. Interesting.

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