Home » Intelligent Design » Will Texas Face Court Challenges to the New Science Standards?

Will Texas Face Court Challenges to the New Science Standards?

Now that the moaning and hand-wringing are over, there’s talk of mounting some legal challenges to the new science standards in Texas. At issue aren’t the standards themselves, but the personal motivations of some of the Board members who advocated for these standards.

Now the issue is whether there is enough prima facie evidence to challenge the Constitutionality of the wording now, or wait for the textbook review process in two years.

“They have shown clear religious motivations that certainly raise some questions,” Quinn said. “But if the board requires phony religious arguments in the science textbooks, I can’t imagine somebody won’t challenge it.” Publishers may end up producing a textbook for Texas and other conservative states and a separate version for other states—because under the new guidelines, a Texas textbook “will be poison in states that value education,” [Dan Quinn, a spokesman for the Texas Freedom Network].


I guess Quinn isn’t bothered at all by the motivations of atheists or philosophical naturalists who want to teach students that no matter how complex and specified biological systems might appear, the design is only apparent and not actual because nature posses all the creative power to produce it through chance and/or necessity. If Quinn is really concerned about motivations, he ought to check the philosophical and worldview motivations of those who want to promote naturalism as science in science classrooms. He has nary a peep about any of that.

So here’s a few questions for Mr. Quinn and anyone else sweating bullets over the “religious” motivations of those who question the way science is taught in public school classrooms: What does a worldview free science classroom look like? How do you sucessfully divorce science from any and all philosophical underpinnings? And if you can’t do that, how do you decide which philosophical considerations are necessary for science and which aren’t?

While we’re on the subject of motivations, perhaps Mr. Quinn might take note that William Wilberforce fought for over 20 years in the early 1800′s to end the slave trade in England motivated almost entirely by his “religion” (Christianity). Should England have repealed the anti-slave trade act because of those “religious” motivations? Or can we only call motivations into question when it involves how we teach science? If so, Mr. Quinn, what’s your specific criteria for determining those motivations and deciding that no matter how good the standards might be, if they were inspired by the “wrong” motivations, we just can’t let them stand.

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193 Responses to Will Texas Face Court Challenges to the New Science Standards?

  1. “But if the board requires phony religious arguments in the science textbooks, I can’t imagine somebody won’t challenge it.”

    What if the board just requires sound scientific arguments in those science textbooks, but those arguments dispute the mainstream PoV?

  2. To add some context, readers should understand that the motivations behind the Texas standards are relevant because of the United States Supreme Court’s so-called “Lemon test,” developed in the 1971 case of Lemon v. Kurtzman.

    The first prong of that test is whether legislation has a “legitimate secular purpose.” If the purpose is to advance religious ideas, it violates the first amendment under the Lemon test.

    For a thorough discussion of Lemon and an example of its application, curious readers can consult the federal district court opinion in Kitzmiller v. Dover Area School Dist. (E.D. Pa. 2005), which concluded that the purpose of the school board’s policy of referring students to the ID textbook Of Pandas and People was to “advance religion,” running afoul of the Lemon test.

    The opinion can be easily found via any Internet search engine.

  3. Dan Quinn, a spokesman for the Texas Freedom Network

    You have to love this. The “Freedom Network” is fighting against the freedom of students and teachers to challenge, on purely scientific grounds, a “theory” that is in a state of evidential collapse.

    This reminds me of the “People’s Republics,” which are universally run by vicious dictatorial thugs, and in which “the people” have no voice.

    The nicer the name, the more you should be suspicious. If a country had the name, “Republic of Altruistic Personal Enhancement,” you could probably guess what you would get.

  4. 4

    “The nicer the name, the more you should be suspicious.”

    Hmm. So many names to consider: “Discovery Institute,” “IDEA clubs” . . .

  5. “Discovery Institute,” “IDEA clubs”

    I believe that they are interested in discovery and ideas. The “Texas Freedom Network” is not interested in freedom by any stretch of the imagination. It is interested in the suppression of freedom, ideas, and discovery that might cause young students to question Darwinian dogma.

  6. But Gil discovery and ideas are terrifying things for the anti-ID crowd.

  7. Since we’re on the topic of philosophical underpinnings of science, I’d be interested in getting a better explanation of how an empirical science that includes non-naturalistic entities is supposed to operate *and* be superior to a naturalistic science. This is a fairly grand claim, but don’t recall seeing much detailed information on the topic in the standard info on ID.

  8. 8

    Gil: “Republic of Altruistic Personal Enhancement”

    I think I can guess what I would get. Lots of junk email. :D

  9. This is a fairly grand claim, but don’t recall seeing much detailed information on the topic in the standard info on ID.

    You have mysteriously missed the entire point. ID is not a theory of mechanism, as is materialistic evolutionary theory. ID is a theory of design detection.

    Darwinian theory is a theory of mechanism, and it is hopelessly vacuous in light of modern science and information theory.

    The “grand claim” is that the Darwinian mechanism can create highly sophisticated computer programs and human consciousness, with hopelessly inadequate probabilistic resources.

  10. tragic mishap:

    Gil: “Republic of Altruistic Personal Enhancement”
    I think I can guess what I would get. Lots of junk email.

    Nice try, but look again.

  11. Ludwig

    To add some context, readers should understand that the motivations behind the Texas standards are relevant because of the United States Supreme Court’s so-called “Lemon test,” developed in the 1971 case of Lemon v. Kurtzman.

    The first prong of that test is whether legislation has a “legitimate secular purpose.” If the purpose is to advance religious ideas, it violates the first amendment under the Lemon test.

    Well let’s see, would teaching students how to analyze and evaluate scientific evidence serve a secular purpose or advance a “religious” agenda? Regardless of the motives, the new standards in Texas clearly advance a secular purpose. It only those who want to advance their own agenda that don’t want students to learn how to analyze and evaluate scientific evidence…even though that’s what real scientists do every singel day.
    The Lemon test is irrelevant to the Texas standards, all the weeping, moaning and hand-wringing from the anti-ID crowd not-with-standing.

  12. 12

    Gil, I’ve been trying to ask you a question for a while, but I think it keeps getting lost in the shuffle. If you have time, I’d love a response.

  13. GilDodgen wrote:

    You have mysteriously missed the entire point. ID is not a theory of mechanism, as is materialistic evolutionary theory. ID is a theory of design detection.

    Perhaps, but perhaps not. If ID claims itself to have a superior explanation for the diversity of life on this planet, then simply stopping at “Eureka, we think we’ve found something” is not going to build a better model, and in fact is not really that compelling a model at all in explaing how life developed. Assuming we’ve found a designer, how did the designer create a new species? How long did it take? What energy/material was needed? Why haven’t we seen it happen in recent history? Can we make it happen on command?

    I’ve read repeatedly in this forum that “Darwinism is in ruins”, yet your quote above suggests that ID is not really interested in forming an alternative theory, merely detecting the possible presence of something that may or may not become the basis of an explanation at some point in the future.

  14. David Kellogg:

    Gil, I’ve been trying to ask you a question for a while, but I think it keeps getting lost in the shuffle. If you have time, I’d love a response.

    To the best of my knowledge, my father is completely unaware of ID theory. He is 87 and this is a subject that would not be of interest to him, so we have never discussed it.

    By the way, so far no one has guessed the acronym.

    Who gets the prize?

  15. 15

    Thanks.

    The acronym is obvious (and implied in the term “acronym”).

  16. mikev6,

    If neo-Darwinism is in such ruins that it cannot realistically ever become anything more than what it currently is, that is, a theory in ruins, then it should be rejected. Even if there were to be no alternative ideas/theories in play, it would be more honest and better the furthering of science and discovery if we simply ventured off into new territory for explaining life. That such a venture is even opposed is quite unfortunate and detrimental. Talk about a science stopper.

    Whether neo-Darwinism is really even in ruins would be obviously up for debate, but even if it wasn’t alternative ideas and theories should always be welcomed. And especially welcomed if they better explain the data.

  17. 17

    Gil, if your father has no interest in ID, does he have any views on evolution? Looking back, I see I asked the question in both ways.

  18. Mr GilDodgen,

    The “grand claim” is that the Darwinian mechanism can create highly sophisticated computer programs and human consciousness, with hopelessly inadequate probabilistic resources.

    I’m wondering how you explain the success of Darwinian mechanisms in papers such as human competitive results in finite algebra. The Darwinian mechanism found results in 2 hours that uninformed search would be expected to take 10 billion years to find. The results are far better than the results produced by any human mathematician.

    This is not a case where anyone can say the programmers knew the answer, or coded it into the program.

  19. Domoman commented:

    Even if there were to be no alternative ideas/theories in play, it would be more honest and better the furthering of science and discovery if we simply ventured off into new territory for explaining life. That such a venture is even opposed is quite unfortunate and detrimental. Talk about a science stopper.

    Except that ID doesn’t appear to have any explanatory power, other than to suggest the possible existence of some shadowy unknown entity. The most obvious next question (“how does this entity operate?”) has never been addressed AFAIK, and the sole research direction always seems to be directed back at “Darwinism” under the assumption that there are only two possible explanations for life’s diversity rather than looking for direct empirical evidence for one’s own theory. Rather than being “opposed” by some external force, it almost seems to me that ID is limiting itself (Oh – we only *detect* design); a kind of passive-aggressive approach to science that seems totally at odds with my experience of how science normally works.

    alternative ideas and theories should always be welcomed. And especially welcomed if they better explain the data.

    I doubt that most readers of the UD forum would think that *all* alternative ideas are equally valid, or that *all* ideas should be presented to students. An alternative theory gets a certain level of leeway as a hypothesis, but eventually the expectation to pony up the data happens, and it has to stand on its own. Again, as an outside observer, ID seems more “anti-Darwin” than “pro-ID”, and even taking controversies into account, ID does not seem to have the explanatory breadth to better fit the current data without raising more questions than it answers.

  20. GilDodgen @ 9:
    “You have mysteriously missed the entire point. ID is not a theory of mechanism, as is materialistic evolutionary theory. ID is a theory of design detection.”

    But ID is a theory that can’t detect design!

    First it said that specified complexity was an indicator of design, but that’s exactly what Darwinian evolution produces.

    Then it was the Explanitory Filter, but if you feed the Designer into it, it says the Designer was designed. And you CAN’T feed Darwinian evolution into the EF because the EF can only handle something that’s either random OR something that’s determined. There is literally no way to feed standard two step random variation and natural selection into it.

    So Behe suggested Irreducible Complexity, but it turns out that Darwinian Evolution can produce that too!

    ID has nothing left but “That looks designed to me.”

  21. Gil,

    If a country had the name, “Republic of Altruistic Personal Enhancement,” you could probably guess what you would get.

    This has to be hands down the funniest statement I’ve seen on this website. Well done Haha.

    Something tells me Dawkins would be the most appropriate candidate for sitting at the throne of the Darwinian R.A.P.E. committee. After all he’s king of philosophically justifying altruistic and humanitarian purpose. Oh wait, or was it called archeo-purpose? …neo-purpose? ….anti-purpose? pentagonal arachno-purpose? Bah. Either way, he’s a really cool guy, and he’s smart, so everyone needs to listen to him.

  22. 22

    PaulN says:

    Something tells me Dawkins would be the most appropriate candidate for sitting at the throne of the Darwinian R.A.P.E. committee.

    PaulN: keeping it classy.

  23. 23

    Gil: Nice try, but look again.

    I did, but it hasn’t gotten any bigger. I want my money back :(.

  24. DK:

    PaulN: keeping it classy.

    I only aim to be as classy as PZ or Dickie D.

  25. Besides, you don’t think Dawkins would properly represent the Republic for Altruistic Personal Enhancement?

  26. Though I support ID I am not sure if schools are the right place to have this battle. Do we really think that High School students are capable of analysing all the data when we can’t yet convince the establishment?

    Consider another recent science paradigm shift in Plate Tectonics, that idea didn’t gain acceptance because it was in school text books. The establishment was convinced and that is what we have to do.

    Peer reviewed papers are the way to go and I am glad Dr Dembski (and others of course) are choosing that approach.

  27. 27

    mikev6,

    In the ’60′s, the Grateful Dead did a song called “The Eleven” (lyrics by Robert Hunter). One line was -

    No more time to tell how, this is the season of what.

    Perhaps it is not really possible to abandon the hope that we will be able to explain the “How?”, but, with all the constant surprise at the complexity that is being discovered seemingly daily in nature, and especially biological life forms, wouldn’t it be better to look at these things with the assumption that they are, in fact, designed, and try and understand the “What”?

    Certainly it can’t help to intone the Crick mantra (it’s not designed, it’s not designed). I’m not a researcher, but I can’t see how that could possibly help.

  28. DonaldM

    Regardless of the motives, the new standards in Texas clearly advance a secular purpose.

    I probably could have been clearer. We can’t analyze the constitutionality of the standards “regardless of the motives” behind them because those motives are part of the Lemon analysis. Even if the standards are facially secular, if the motives for passing them are religious, they’re suspect. If the YECs on the Texas board understood that, they would keep their mouths shut.

    The Lemon test is irrelevant to the Texas standards . . . .

    Justice Scalia might agree with you about that. But it’s not the law of this country as it stands. If the Texas standards are scrutinized by a federal court, evidence of the religious motivations of the board members will almost certainly be considered. (The Fifth Circuit has never discussed the Lemon case as far as I can tell. I suppose it’s possible a rogue district court judge could refuse to apply it.) If it does consider those motivations, the YECs on the board–particularly McLeroy–have given the plaintiffs plenty of ammunition.

  29. Ludwig, thank you for the Lemon test background. I believe you are mistaken in applying the first prong to any alleged religious motivations for the action.

    From http://www.firstamendmentcente.....index.aspx,

    Using the Lemon test, a court must first determine whether the law or government action in question has a bona fide secular purpose. This prong is based on the idea that government should only concern itself in civil matters, leaving religion to the conscience of the individual.

    A “bona fide secular purpose” is sought for in the law or action NOT in the motivations of the proponents of the law.

    It is backward thinking to say that the apparent bona fide secular purpose in the action should be called into question because of any alleged religious motivations of the proponents of the action.

    Oh crud, DonaldM has beat me to it in #11! I’m posting anyway!!

  30. Tim,

    That issue was addressed in Kitzmiller, specifically at 90-132, available here: http://www.pamd.uscourts.gov/k.....er_342.pdf

    For example, in footnote 20:

    with regard to Defendants’ contention that we should exclude individual Board members’ statements from the legislative history on the ground that they are not full pronouncements by the Board, the Supreme Court has consistently held not only that legislative history can and must be considered in ascertaining legislative purpose under Lemon, but also that statements by a measure’s sponsors and chief proponents are strong indicia of such purpose. McCreary, 125 S. Ct. at 2734 (although courts do not engage in “psychoanalysis of a drafter’s heart of hearts,” they routinely and properly look to individual legislators’ public statements to determine legislative purpose); Edwards, 482 U.S. at 586-88 (reliance upon a statute’s text and the detailed public comments of its sponsor when determining the purpose of a state law requiring creationism to be taught alongside evolution).

    The court also rejected the “plain language” approach you guys seem to be advocating. The “purposes” that are intended by the rulemakers are relevant.

    Of course, Kitzmiller isn’t binding law in a district court in Texas, but a Texas district court would have to give it serious consideration and find some really good reasons to get around it in order to avoid reversal on appeal to the Fifth Circuit.

  31. Ludwig,

    Thank you for the clarification. I would only add that the rulings you cited may have been wrongly applied in Kitzmiller.

    The ruling in Kitzmiller apparently allowed that statements concerning proponent’s motivations somehow inhered in the measure in question rather than simply informing it.

    More to the point, if one of the Texas proponents is a dyed in the wool YEC, that remains irrelevent in terms of legislative history.

    . . .statements by a measure’s sponsors and chief proponents are strong indicia of such [legislative]purpose”

    I added “legislative” because I believe it to be the antecedent. The strong indicia of the statements are (or I say, should be) only concerned with legislative purpose, and legislative purpose can only be located in the law. Such statements are helpful in providing context and theoretical applicability of the measure in question, but that should be where the story ends.

  32. Sure, I understand your position there, Tim. We could imagine, for example, a hypothetical where a legislator sponsors an indisputably secular law, maybe an environmental bill of some kind, on religious grounds.

    The sponsor might say something in the legislative history like “I sponsored this bill because I believe the Bible directs us to take care of the environment.” The legislator’s purpose is clearly religious, but no reasonable court would say it’s a first amendment violation. I think that’s because the legislator did not intend for the legislation to “advance religion,” as Kitzmiller put it.

    In any case, Kitzmiller–and the cases cited in Kitzmiller, including Edwards (with regards to the “public statements” of the sponsor of the law at issue in that case)–appear to have rejected the “plain language” approach.

    I can appreciate what you’re saying, though. Thanks for your comments.

  33. 33
    CannuckianYankee

    GilDodgen: “The nicer the name, the more you should be suspicious. If a country had the name, “Republic of Altruistic Personal Enhancement,” you could probably guess what you would get.”

    They’re called “euphemisms.” The Nazi’s were masters of the euphemism in order to convince their victims that they intended good. So “showers” were actually gas chambers; “special treatment” was actually imprisionment in concentration camps and eventual murder, which was called “liquidation.”

    Of course I’m aware that this is an extreme example, and I’m not using this to suggest that the use of euphemisms is necessarily evil.

  34. Nakashima:

    The Darwinian mechanism found results in 2 hours that uninformed search would be expected to take 10 billion years to find. The results are far better than the results produced by any human mathematician.

    Darwinian mechanisms and genetic algorithms are highly efficient at locating solutions in well-behaved and mostly-continuous fitness landscapes. You can trace the path it takes from the starting conditions to the final solution like a string of pearls selected from a near-infinite collection of possible solutions and paths. That is why the search is so efficient, and why a machine can vastly outperform “clever” humans when dealing with a multitude of variables with unpredictable (except to a mathematical processor) interactions. No new information is created, it is discovering by clever search algorithms what already exists.

    Useful genetic code “solutions”, on the other hand, are like dark moons, separate by light-years drifting through solution space, while the rest of space is filled with non-functional junk. There is no helpful gradient, and one cannot in general (and except in the extremely limited form found in cases like bacterial resistance) reach out and hope to find another nearby that’s functional in a usefully different way.

    Real, complex, specified information is like that.

  35. djmullen:

    First it said that specified complexity was an indicator of design, but that’s exactly what Darwinian evolution produces… So Behe suggested Irreducible Complexity, but it turns out that Darwinian Evolution can produce that too!

    Surely you jest.

    David Kellogg:

    Gil, if your father has no interest in ID, does he have any views on evolution?

    When I was growing up my parents talked about Haeckel’s embryos, the horse sequence, bacterial antibiotic resistence, etc. To the best of my knowledge, they never evolved beyond that, or demonstrated any further interest in the topic.

  36. Mr SCheesman,

    That’s an interesting position. Just as I’ve heard several people on this site say, “Oh, we all accept micro-evolution, it is macro-evolution that is impossible!”, it seems you are claiming that Darwinian processes work fine in areas outside biology, but fails in dealing with organic chemistry. If so, I really don’t understand why so many words have been wasted on Weasel on other threads, or why Mr Dodgen made the claim he did to which I responded. It would seem that several influential people in the ID community, including Dr Dembski and Dr Marks, believe either that Darwinian evolution cannot work at all, even in computational settings, or that investigating the conditions for success/failure informs the nature of what Darwinian evolution can do in biological settings.

    I am reminded of how success by AI researchers has always been met by the reply that ‘real intelligence’ is something else than what they just showed a machine can do. Computer checkers and chess were examples of ‘machine intelligence’ until they beat us, then they were ‘brute force search’. :)

    Mr Dodgen, you did work in this area. Could your programs play better checkers than you could?

  37. Mr Dodgen, you did work in this area. Could your programs play better checkers than you could?

    Yes, and a calculator adds, multiplies, takes square roots, and does trigonometric calculations far more efficiently and accurately than I. But this is not intelligence or creativity.

    My checkers program is not much different. It searches more than a million moves per second, while a human searches perhaps three or four. The program also includes a vast human-generated opening book, and an endgame database which is flawless and includes billions of positions, which required more than 16,000,000,000,000,000 CPU clock cycles over a period of several months to compute, and which can be accessed instantaneously with highly efficient database access algorithms.

    Humans can no longer compete with this, because sooner or later they overlook something that the computer program does not. The same is now true in the game of chess.

  38. GilDodgen @ 35:
    “djmullen:

    First it said that specified complexity was an indicator of design, but that’s exactly what Darwinian evolution produces… So Behe suggested Irreducible Complexity, but it turns out that Darwinian Evolution can produce that too!

    Surely you jest.”

    I do not jest and stop calling me Shirley ;) I see you don’t mention the EF. Have you given up on it too? Smart move. I know Dembski gave up on it, which was a smart move for him, but then he tried to take it back later which was a very dumb move.

    While I’m telling unpleasant truths to UD about ID, I’ll add these:

    ID is not a new, upstart idea that’s revolutionizing science. It’s a very old idea, older than Jesus, that started to fall apart in the 19th century and was killed dead by Darwin in 1859 and many others before (Darwin’s Grandfather, for instance) and since (just about every biologist in the world).

    After about ten years of following ID, here, on ARN, on a few other ID websites and after reading three books by Dembski, both books by Behe, Johnathan Well’s terrible book, Gonzalez’s Privileged Planet and a few others whose titles don’t come to mind at this moment, including that terrible book by that late Australian, Broome, that Denyse loves so much, I have yet to find even one ID advocate who understands how evolution is supposed to work. I’m not just saying they don’t believe evolution works, I’m saying that no ID advocate I’ve seen even understands how it is claimed to work. (Which explains a lot about ID right there.)

    ID is not a mechanistic theory because it has no mechanistic theory nor any idea of what one would even look like. You say a designer created life as we know it? How? When? Evolution can answer those questions, at least in part, and is actively filling in the blank spaces in our knowledge. ID isn’t even trying.

    Nobody in ID can even propose an experiment that might confirm or falsify ID. How could they if an intelligent designer can account for any possible result?

    Gil, you hang glide so I won’t question your courage and I’ve played your checkers game so I won’t question your intelligence or programming ability, but when it comes to ID, you have a fixed idea in your head and it twists your thinking and blinds your eyes to any evidence that contradicts ID.

    This idee fixe makes you think that hundreds of thousands of biologists are either stupid, ignorant or dishonest and that they have all joined together in a vast centuries long conspiracy to fool the world, apparently so they can deny God.

    This is nonsense. Test me. TRY to describe ID to your father. Just try to put your beliefs into words once and explain ID to him as best you can and see what he thinks.

  39. Jack Golightly said:

    Perhaps it is not really possible to abandon the hope that we will be able to explain the “How?”, but, with all the constant surprise at the complexity that is being discovered seemingly daily in nature, and especially biological life forms, wouldn’t it be better to look at these things with the assumption that they are, in fact, designed, and try and understand the “What”?

    If ID and the Discovery Institute were content to explore this concept in the arena of science – publish papers, hold conferences, etc – I would be happy to participate. I’d be highly skeptical, but I actually enjoy exploring ideas that I don’t fully accept as part of my own learning process.

    However, this is a political issue, not a scientific one. Currently, ID seems to add almost nothing to our understanding of things, yet there are those who want to teach it to my child in school. I object to this on the same grounds that I would for teaching astrology – there is insufficient evidence and accepting things without evidence is not how we teach science correctly. No matter how weak we may say parts of evolution are, ID hasn’t even gotten past the first rung of the evidential ladder. I can’t help but infer that ID is being foisted on my child to further a social agenda – “we can’t convince the parent so we’ll target the child instead.”

    It is the political agenda that changes my stance from “hmm – interesting idea” to “where’s the ACLU on speed dial?”.

  40. M6:

    Please cf here. (Topics 1 – 7 just above the linked point will also help.)

    GEM of TKI

  41. SCheesman @34 : Stochastic search features in genetic algorithms allow solutions to jump past ‘local peaks’ as you suggest and find the global peak. Basically, randomly jumping around the ‘solution landscape’ and then reattempting to climb the peak, to truly find the best answer, and not just a small peak in the shadow of a better solution.

    Genetic algorithms have been used to create new Theories in Math, finding solutions in datasets far larger and complex than any human can work with.

    I think you’d be surprised by what solution a genetic algorithm can produce!

    mikev6 @38

    Bravo friend! Yes, it should not be a political issue, but only a scientific one! The fact that ID has no science, it relies on politics, but then people ignorant of the science say ‘but with all this politics, surely it’s a science issue!’ and ‘why would such a solid science foundation need such a political defense’ without realising that their is no science issues, ID is only politics, politics to convince us that the science destroying religion is wrong!! (I don’t personally have a religious issue with anything that emerged from Darwin’s theory, but apparently some people do)

    I say ID should pretend that no other theories exists, and just use ITSELF to explain everything it sees. (I’d also like to see politicians saying the same, explaining how they make things better, without attacking their opponents).

    By the way, I say this with the understanding that ID does no explaining, it has no hypothesis it tests, it only postulates that things MAY be designed.

  42. A footnote or two:

    1] Wilberforce’s struggle against the slave trade was from the 1780′s – 1807, when it was abolished. (The battle against the slave system in the British empire hotted up across the 1820′s and culminated in abolition after the Jamaican Baptist War uprising of 1831 — which started as a sit down strike for pay. The key leadership were in specific and major part motivated by the Christian Bible’s teachings on liberty and equality and mutual duty in community under God. That history says something to those who seemingly can only construct the Christian faith as being oppressive. (Cf here for some historical pointers.)]

    2] I like Gil’s key observation: The “grand claim” is that the Darwinian mechanism can create highly sophisticated computer programs and human consciousness, with hopelessly inadequate probabilistic resources. {Prezactly. And, FYI, DK et al, I have put up my after-exchange summary on this general theme here, joining other remarks on the capacity and limitations of chance, necessity and agency here. I think these give enough for people to make up their minds for themselves on the main and secondary issues; so I will not take up further attempts to debate the matter, especially given the poisonous atmosphere that has developed at Anti Evo etc. In short, some serious lines of no return have been crossed; lines that cannot be un-crossed.]

    3] Science is — by inescapable epistemic constraints and irrefutable Q-theory and relativity-shaped historical fact — provisional and partial knowledge of the world based on observation, experiment and theorising etc. It is therefore astonishing that the need for citizens in training [aka high school students] to be aware of the provisionality of science should even be an issue. So, studying “strengths and weaknesses” and/or critical assessment of the strength or limitations of and issues surrounding scientific knowledge claims in general, of scientific theories is not even an issue, properly.

    4] When it comes to the point that those theories and models that try to reconstruct a remote, unobserved and unrepeatable past are even more limited than those which deal with the ongoing operations of our currently experienced world, it ALMOST is not necessary to underscore the contrast. [And that is one reason why the theory of Macroevolution and OOL models simply cannot be compared with say the theory of gravitation, Newtonian or Relativistic forms.]

    Just a few thoughts.

    GEM of TKI

  43. Nnoel,

    You say that ID has no science but what does YOUR position have?

    It has absolutely nothing.

    And your ignorance of ID is not a refutation.

    The theory of evolution is a thjeory of “we don’t know”:

    Do chimps and humans share a common ancestor? We don’t know is the only honest answer.

    Did the vision system/ eyes evolve from a population that didn’t have either? We don’t know.

    Can the bacterial flagellum evolve from a population that never had one? We don’t know.

    Heck how can we test those premises?

    We can’t test them objectively.

    Ya see the truth is if YOU could support your claims then ID would go away.

    But anyway:

    Supporting ID- be sure to follow the links provided.

  44. mikev6-

    The theory of evolution adds nothing to our understanding.

    “Evidence”(?) for the evolution of the vision system

    Andrea Bottaro said the following over at the panda’s thumb:

    Eyes are formed via long and complex developmental genetic networks/cascades, which we are only beginning to understand, and of which Pax6/eyeless (the gene in question, in mammals and Drosophila, respectively) merely constitutes one of the initial elements.

    IOW 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!

    I say the above because if Dr Bottaro is correct then we really have no idea whether or not the vision system could have evolved from a population or populations that did not have one.

  45. mikev6

    However, this is a political issue, not a scientific one. Currently, ID seems to add almost nothing to our understanding of things, yet there are those who want to teach it to my child in school. I object to this on the same grounds that I would for teaching astrology – there is insufficient evidence and accepting things without evidence is not how we teach science correctly. No matter how weak we may say parts of evolution are, ID hasn’t even gotten past the first rung of the evidential ladder. I can’t help but infer that ID is being foisted on my child to further a social agenda – “we can’t convince the parent so we’ll target the child instead.”

    Whether or not ID adds anything to our understanding of things is part of (a very large part) the issue. Merely asserting that it doesn’t is begging the question. Additionally, rejecting ID on evidential grounds (“insufficient evidence” or “not gotten past the first rung of the evidential ladder”)requires explaining why certain observations of data and phenomenon in nature can not be taken to be evidence for ID. The claim of “no evidence” only means that there is nothing you accept as being evidence for ID, which is very different from the claim of “no evidence”.

    The real question is what background principles give warrant to rejecting ID as a proper explanation for certain observations of data and phenomenon in nature?

  46. Nnoel:

    I saw your comment on GA’s.

    What happens when we are dealing with a fitness landscape that is a huge [>> 10^180,000+ configs . . . that's just for DNA for credible first life] sea of non function that has in it isolated islands of function?

    What happens when to get to major body plans beyond the very first one, you have to, de novo — dozens of times over — create 10′s – 100′s of megabits of new functional information?

    Functionality that is not simply bridged by handy isthmuses?

    Climbing up to hilltops within Isle Improbable, and hopping form one mountain top to another is only relevant AFTER the real challenge has been dealt with.

    GEM of TKI

    PS: 1,000 bits of info specifies a space of ~ 10^301 configs, ten times the SQUARE of the credible number of quantum states of our observable cosmos across its lifespan. Isolated islands in such a toy-sized space are not credibly findable by random walks, and unless you are on a shore of function you cannot hill climb by differential performance, nor can short hops credibly land you on handy nearby hill slopes. Long random hops will overwhelmingly splash you down anywhere in the sea of non-function, i.e back to square 1. but, intelligent designers routinely produce artifacts that are on islands of function, but by just that: directed, purposeful contingency. [And, GA's themselves are illustrative: where do you think the program and its underlying databases, rules, knowledge base, principles functionality etc and the machine it runs on come from?]

  47. Off topic comment: I notice that comments on the Simulation Wars thread were closed without explanation. That seems odd, as some significant new material had just been posted.

    I’m wondering why this was done?

    Can anyone in management explain?

  48. Nnoel:

    Stochastic search features in genetic algorithms allow solutions to jump past ‘local peaks’ as you suggest and find the global peak. Basically, randomly jumping around the ’solution landscape’ and then reattempting to climb the peak, to truly find the best answer, and not just a small peak in the shadow of a better solution.

    It is precisely the “jumping” around function that I was referring to in my ‘moons separated by light-years’ analogy. Kairfocus makes the point in a similar way. If your local maxima are not too far enough, then random search is sufficient to cross over the “junk” to find new fitness paths, and eventually you find the right way home. But if viable solutions are too widely separated, then random search fails due to the lack of probabilistic resources; there is simply not enough time to find an alternate solution path once you have reached a local maximum. The problem is not with the search algorithm, it is the character of the solution space.

  49. SCheesman @34

    Darwinian mechanisms and genetic algorithms are highly efficient at locating solutions in well-behaved and mostly-continuous fitness landscapes. You can trace the path it takes from the starting conditions to the final solution like a string of pearls selected from a near-infinite collection of possible solutions and paths. That is why the search is so efficient, and why a machine can vastly outperform “clever” humans when dealing with a multitude of variables with unpredictable (except to a mathematical processor) interactions. No new information is created, it is discovering by clever search algorithms what already exists.

    Useful genetic code “solutions”, on the other hand, are like dark moons, separate by light-years drifting through solution space, while the rest of space is filled with non-functional junk. There is no helpful gradient, and one cannot in general (and except in the extremely limited form found in cases like bacterial resistance) reach out and hope to find another nearby that’s functional in a usefully different way.

    I agree with you that this is probably the case, but it is by no means proven. This is exactly why I consider Dr. Behe’s work to be a more likely route to reaching a scientific theory of ID from the various current hypotheses. If we can show that there is no way for the known mechanisms of modern evolutionary theory to have produced the “endless forms most beautiful” that we observe, if, in other words, we can find the “edge of evolution,” then ID will have made a positive, testable prediction.

    Unfortunately, we’re not there yet. Claiming that the many dimensional biological fitness landscape does consist of separated islands is, in my view, likely but definitely unproven.

    JJ

  50. Hi mikev6,

    I’m curious how you were able to make the leap from this:

    In all fields of science, analyze, evaluate, and critique scientific explanations by using empirical evidence, logical reasoning, and experimental and observational testing, including examining all sides of the scientific evidence of those scientific explanations so as to encourage critical thinking by the student.

    to this:

    ID is being foisted on my child to further a social agenda

    Seems like juuuust a bit of a stretch, but I’m willing to listen.

  51. Regarding Joseph @42 :

    I am not responding to Joseph himself, but to those that have read his remarks and re-inforced their view that ToE is a ‘theory in crisis’. This is NOT TRUE, plain an simple, his ignorance on this topic is not truth. All he has done is try to refute ToE with what? nothing. my previous point proved I believe. His comments are part of the ‘politics and progaganda’, not the sceince

    In Joseph’s next comment he concludes ToE adds nothing to our understanding. In my humble opinion, I for MYSELF understand organsims and the part they play in the larger scheme of things based on ToE, it’s how everything fits together. For those interested, Panda’s thumb has an illuminating article on this exact topic :

    http://pandasthumb.org/archive.....eason.html

    SCheesman @ 47

    I appreciate that the landscape may be empty space (in my mind I think of it as ‘non-solution space’ nested amongst ‘solution space’), but for me that would correlate to harmful mutations, and nobody would argue that those don’t exists, but a random search is limited by the population that is producing offspring (each offspring is a [possible] stochastic jump), and the length a generation takes to produce offspring, hence bacteria are so well suited to evolving.

    I fail to find the problem you see with the ‘solution space’ as described, but perhaps the ‘initial setup’ is bothering you, in which case I’d say invoke your god all you like, evolution doesn’t deal with beginnings, only what happened after.

    If the problem is with x turning into y where x is not abiotic, well then that’s irreducible complexity, and reasonable evaulation has shown that all cases of IR do have a solution space, and claiming the stochastic search couldn’t possibly navigate the landscape is just religiously motivated thinking that ‘god must have helped’, and in that case, you’d be admitting that the improbable answer WAS reached, it was just done so with the Flying Spagetti Monster using his noodly appendages in manners we do not and could not understand.

    My reference to FSM is not meant as insult, just as always, trying to show typical example without pinning down which higher intelligience ‘dun it’

    I’m at work, almost home time, this may be my last post for a while.

    Love you all like your me

  52. Just a quick note about how ToE improves my (amatuer) knowledge of things (if anyone is interested [and doubts what I say])

    Basically, the study of biology will find HOW something lives (like it’s life cycle, it’s feeding patterns) or HOW it functions (how it’s limbs work, how it moves, how it interacts with it’s own species).

    The ToE kicks in almost automatically when the HOW of many different types of creatures are placed in the same ‘knowledge space’ (hehe, just cause ‘solution space’ above). When that happens, the correlations, similarities and patterns infer what is related to what, knowing everything about tigers and lions would lead you to conclude they are related in some way. Some people would say the relation is because ‘they were both designed by the same god’, but evolution would lead you to conclude that they both evolved from a common cat-like creature.

    ToE explains the WHY questions, once biology has answered the HOW questions, and surprisingly enough, knowing the WHY helps you answer more HOW questions. And thats how ToE helps.

    With this in mind, I’d recommend the article at Panda’s thumb I mention above.

  53. Nnoel,

    I have read many books, scientific articles, text books and just about everything I can find on biology and evolution.

    There isn’t anything which demonstrates that genetic accidents can accumulate in such a way as to give rise to new body plans requiring new protein machinery and body parts.

    The ToE is mere speculation based on the assumption.

    However it does provide for a good bedtime story…

  54. BTW Nnoel,

    The day that Musgrave demonstrates any understanding of his opposition will be a day he stops writing so many misrepresentations about them.

    Also there wasn’t anything in that essay which would demonstrate the changes required are even possible.

    Tell me-

    How can one test the premise that the bacterial flagellum arose from a population that never had one via an accumulation of genetic accidents?

    Your attempt to answer that question should point out the weakness of the theory.

    Your avoidance of the question will prove my point.

  55. Nnoel,

    No one and I mean no one from Richard Dawkins on down to the entire evolutionary biology community on the planet has give a coherent explanation for the naturalistic explanation of macro evolution. It is either micro evolution or speculation they propose.

    You can make all the assertions you want but no one in any book or on any internet site or in any journal has ever provided a coherent explanation. If they had then one would point to it. There is lots of speculative writings out there starting with Darwin’s OOS which have the ability to convince gullible minds but nothing that holds up to scrutiny.

  56. On-topic update. It appears that the Texas Senate Education Committee may have lost its patience with the YECs on the board. Excerpt below from here: http://www.marshallnewsmesseng.....board.html

    “All I hear is that the Republicans want to push their religious views into the curriculum, and the Democrats want to teach our children how to masturbate,” [Senator, R-Waco] Averitt said during the committee hearing Tuesday.

    Senate Bill 2275 would give the state’s education commissioner, who is appointed by the governor, the authority to approve the curriculum standards and textbooks based on the recommendations of a group of educators. The board members, however, could override the commissioner’s decision with a four-fifths vote.

    State Board of Education Chairman Don McLeroy, R-College Station, said that under the proposal, only the “education establishment” would shape curriculum and textbook decisions and that the board would simply become a rubber stamp.

    Maybe litigation won’t be necessary after all.

  57. Mr SCheesman,

    The problem is not with the search algorithm, it is the character of the solution space.

    If so, why complain about Weasel, ev, Avida et al.?

  58. Nnoel,

    jerry’s hyperbole notwithstanding, here is a very coherent explanation of macroevolution, by three of the best evolutionary biologists in the business:

    Charlesworth B, R Lande & M Slatkin (1982). A Neo-Darwinian commentary on macroevolution. Evolution 36(3): 474-498

  59. DonaldM wrote:

    Whether or not ID adds anything to our understanding of things is part of (a very large part) the issue. Merely asserting that it doesn’t is begging the question. Additionally, rejecting ID on evidential grounds (”insufficient evidence” or “not gotten past the first rung of the evidential ladder”)requires explaining why certain observations of data and phenomenon in nature can not be taken to be evidence for ID. The claim of “no evidence” only means that there is nothing you accept as being evidence for ID, which is very different from the claim of “no evidence”.

    The real question is what background principles give warrant to rejecting ID as a proper explanation for certain observations of data and phenomenon in nature?

    Two points on this:

    1) I don’t think there are any background principles forcing rejection of ID as an explanation. My objection to ID is that I don’t feel there is sufficient positive empirical evidence at this point to raise it to the level where it should be included in a school science curriculum. I feel the same about astrology.

    2) I would rather not assert anything. I would prefer that someone show me the extensive reading list on how new species are created by a designer or other aspects of how ID explains the diversity of life. Evolution at least puts a stake in the ground, says “we think it happened this way”, and one can argue pro/con and search for/evaluate evidence. It doesn’t seem that ID has reached that point, but if you have research links to this type of material, I will be more than willing to read more.

    -m

  60. Ludwig in #56. Thanks for the update. Wow, this whole thing just has everyone in an uproar doesn’t it? I love this last bit:

    University of Texas biology professor David Hillis said the result of that decision is: “Texas students now have a weakened science curriculum, and the science reputation of the state has been seriously injured.” This bill will “keep the focus of education on education, rather than on politics,” Hillis said.

    Weakened curriculum? What nonsense!! If anything, the new standards in Texas are among the strongest in the Nation! What I’ve said all along is proving true. What the Darwinian establishment fears most that students who learn how to analyze and critique the evidence for a scientific theory just might realize the real problems with a lot the evolutionary hypotheses. Not to mention the fact that analyzing and critiquing evidence for a theory is exactly what ordinary scientists due on every ordinary day of the week in their labs and in the field. Why on earth would anyone NOT want students to learn how to do that properly? Hillis’s statement here is a croc! Gimme a break.

  61. Now Christopher Hitchens has weighed in on Texas in an editorial in Newsweek. The article appears replete with photos from Dayton, TN in 1925 and a book table from the “Anti-Evolution League”….not that one should read any bias in that!

    Hitchens writes,

    It’s not just that the overwhelming majority of scientists are now convinced that evolution is inscribed in the fossil record and in the lineaments of molecular biology. It is more that evolutionists will say in advance which evidence, if found, would refute them and force them to reconsider. (“Rabbit fossils in the pre-Cambrian layer” was, I seem to remember, the response of Prof. J.B.S. Haldane.) Try asking an “intelligent design” advocate to stipulate upfront what would constitute refutation of his world view and you will easily see the difference between the scientific method and the pseudoscientific one.

    I have no idea what Hitchens is talking about in that last sentence. I doubt if he does either. Now if he had substituted “evolution” for “Intelligent Design”, then it might have made sense!

  62. NNoel,

    I would add Sean Carrol’s “Endless Forms Most Beautiful”, James Valentine’s “Origin of the Phyla” and Lynn Margulis’ “Acquiring Genomes: A Theory of the Origins of Species.” THe first is a nice summary of evo-devo research that shows how macroevolution occurs through changes in regulatory genes. The second is by a paleontologist but is truly an integrative work, bringing in fossils, genetics, morphology, etc. into a coherent theory of the evolution of body plans. It’s a slow read, but worth it. The third argues that symbiosis, rather than mutation, is the primary source of innovation and variation that natural selection can work on. jerry by his own admission uses a lot of hyperbole, so take statements like this

    You can make all the assertions you want but no one in any book or on any internet site or in any journal has ever provided a coherent explanation.

    with a grain of salt.

  63. Dave Wisker,

    How come it never gets into the textbooks or the biology classes? I have several textbooks and have videos of classes at Berkeley and MIT and a course by the Teaching Company.

    Hyperbole or not, we are still waiting and why don’t you present the evidence in the article? The hyperbole is on purpose because first it is true. No one has ever presented a coherent explanation for macro evolution here and we have evolutionary biologists on record that there is no model for it or that it has to be taken on faith. And second, it is meant to get people’s attention and see if they can deliver.

    So I suggest you be the first and lead the way. That the UD challenge (present a coherent discussion on the origin of macro evolution) and we can see what happens. We are eager to learn.

  64. Dave Wisker,

    I just noticed one of the authors of your article. It is Monty Slatkin and he teaches the evolution course at Berkeley which I claim does not present a coherent discussion of macro evolution. I have seen him twice and it was the same both times and was not able to support any explanation for macro evolution.

  65. Jerry,

    How come it never gets into the textbooks or the biology classes? I have several textbooks and have videos of classes at Berkeley and MIT and a course by the Teaching Company.

    What texts? Have you ever taken an actual course in Evolution or Genetics?

  66. ” I don’t feel there is sufficient positive empirical evidence at this point to raise it to the level where it should be included in a school science curriculum. I feel the same about astrology.”

    Then you agree with us that macro evolution should be removed from the textbooks and classrooms because there is no evidence that any particular theory can explain it. Let is be explained to students that science is still working on it but as of this time there is no theory than can explain it.

  67. jerry,

    Ijust noticed one of the authors of your article. It is Monty Slatkin and he teaches the evolution course at Berkeley which I claim does not present a coherent discussion of macro evolution. I have seen him twice and it was the same both times and was not able to support any explanation for macro evolution.

    Slatkin is the head of the Integrative Biology Dept at Cal. My undergraduate Genetics degree is from there. What exactly is ‘incoherent’ about Slatkin’s work?

    I’m sorry, but your claiming it’s incoherent doesn’t cut much ice with me.

  68. Khan,

    Carroll’s books are full of nothing but speculation.

    Also as you have been told several times now the definition of “macro-evolution” that you are using is NOT even being debated.

    That you refuse to understand that fact just further exposes your agenda of bait-n-switch deception.

  69. mikev6,

    There isn’t any sufficient positive empirical evidence for the theory of evolution.

    All the evidence points to a wobbling stability and nothing shows that new body plans with new protein machinery and new body parts can arise.

    The ONLY hope left is evo-devo which is very similar to hocus-pocus.

    Now perhaps you are OK with your kids being taught hocus-pocus but when my kids get to that age I will put up a fight that will put Maureen O’Hare to shame.

  70. Joseph,

    Carroll’s books are full of nothing but speculation.

    that sounds exactly like a statement from someone who hasn’t read them.

    Also as you have been told several times now the definition of “macro-evolution” that you are using is NOT even being debated.

    and that sounds exactly like a statement from someone who didn’t read my post.. or does “evolution of body plans” sound like just more microevolution to you?

  71. Jerry asked:

    Then you agree with us that macro evolution should be removed from the textbooks and classrooms because there is no evidence that any particular theory can explain it. Let is be explained to students that science is still working on it but as of this time there is no theory than can explain it.

    Nope. I would present it as the best current explanation that we know at this time given the available data. I would use it (as well) to talk about the difficulties inherent in scientfic inferences from past events, the role of weight of evidence in science, and the importance of being able (as you suggest) to say “we don’t know” rather than automatically fill that void with a minimally tested and analyzed explanation until such time as it can start to compete with the current best solution.

  72. mikev6,

    The theory of evolution doesn’t explain anything.

    There aren’t any predictions to be made from the proposed mechanisms.

    The whole theory can be summed up as “we don’t know”.

  73. Dave Wisker,

    You don’t seem to have a clue about the debate or else you would not have made some of your comments. Especially bringing up genetics. The silly question about whether I took a course in evolution is an indication of this lack of understanding. I watched what they provide at Berkeley for their biology course. I have read several pro Darwin books of evolution. I have textbooks by several popular authors and a textbook on evolutionary biology. I have seen what people say at various sites on the internet and when they come here, including evolutionary biologists.

    Slatin was very good but he never, and I mean never, provided support for any mechanism that explains macro evolution. So yes, he did not provide a coherent theory for macro evolution only that it happened. He is a geneticist and probably a very good one but genetics is micro evolution, not macro evolution.

    Maybe your are confusing the fact of evolution with the mechanism for evolution. I suggest you read the standard ID disclaimer I wrote before you go further with this debate.

    http://www.uncommondescent.com.....ent-296129

    For example, ID accepts all of genetics but genetics is not macro evolution. The question is where did the variation come from for complex novel capabilities and the information necessary to produce it and control it. The debate is over the origin of variation.

  74. “Nope. I would present it as the best current explanation that we know at this time given the available data.”

    This is farcical because there is no explanation at the current time. There is no evidence to support any mechanism only speculation and a fair amount of evidence to question the Darwinian paradigm. So what you want is to present speculation rather than an admission that we do not know and to suppress any information that suggest that what is being presented is not correct but only speculation. The result will be that the student will not know what is being presented is not true. That is a helluva attitude for teaching anything. I suggest you ask the students if that is what they want to know.

  75. Joseph @ 54 :

    Show macro-evolution ? Why well it’s just micro-evolution, just over a longer time period, any fool can see that! lol. Micro-evolution is an established fact, and everyone agrees, but only those that let their theology get in the way and refuse to see how millions of years of micro-evolution can lead to macro-evolution.

    With the time periods involved, even when taking about the [not so] dreaded Cambrian [not so sagely named] explosion, the ‘explosion’ took millions and millions of years (70 or 80 million years [go wikipedia!]), and considering humans arose in the last 200 000 thousand years (a fifth of a million years), why can you not imagine how different things would evolve?!

    And also, their is probably good evidence in the books mentioned previously by Dave Wisker [go Dave, he rocks!]. Complicated things can be simply explained, but asking for 500 millions years of evidence… not much of a few line answers

  76. DonaldM @61 :

    I am GODSMACKED by your comments, first you quote hitchens (good find by the way) :

    [the last line]
    ‘Try asking an “intelligent design” advocate to stipulate upfront what would constitute refutation of his world view and you will easily see the difference’ between the scientific method and the pseudoscientific one.

    and then unbelievable say this :

    ‘I have no idea what Hitchens is talking about in that last sentence. I doubt if he does either.’

    My previous comment written before I read this. I now understand that you do not understand science. Yay! I can help !

    Gather Round.. Science is all about stating what you believe to be true and then formulating what facts would be true if your theory was to be incorrect. In this way, know what ISN’T true is one of the few types REAL facts. Therefore anything in science that is considered ‘true’, can always be discovered to be false based on further evidence. People often talk about the way science can predict future test cases, which leads scientists to presume them to be correct, but when evidence is present that doesn’t follow the known facts, then those facts are reconsidered, could possibly be rejected, but most often just reformulated with the new test cases in mind.

    This is the stage ToE is at, it is literally evolving with all new discoveries, and this evolution builds on the strength of the fact of evolution.

  77. jerry @ 66 :

    You’ve misquoted :

    ” I don’t feel there is sufficient positive empirical evidence at this point to raise it to the level where it should be included in a school science curriculum. I feel the same about astrology.”

    Then you agree with us that macro evolution should be removed from the textbooks and classrooms because there is no evidence that any particular theory can explain it. Let is be explained to students that science is still working on it but as of this time there is no theory than can explain it.

    Lying for Jesus you naughty boy, I thought that quote above was about ID, look how you turned it around and made it sound like he was talking about evolution. you naughty naughty boy !

  78. jerry,

    Are you defining a very limited area you want ‘explained’ and then claiming the ToE to be void when it does not have an answer?

    What about the explanatory power of the ToE? I wouldn’t be surprised if you claim ‘it doesn’t have one’, but then as we’ve seen, lying for Jesus isn’t beyond you! Every creature can be placed somewhere on the tree of life, which is VERY strong evidence that everything is related, there is no creature that doesn’t fit. Whatever designed everyting went to a lot of effort to make it look like everything is just one big happy family!

    Adding to this the fact that by examining the ‘creation’ we are unlikely to find a real explanation of what the ‘creator’ is (can you tell what a authors voice sounds like by the words they write?) With the understanding of the requirements of ID [a deity of some sorts], one sees the search for ID can only ever be a theological quest until some new research technique is discovered.

  79. 79

    Nnoel @ 74:

    You say macro-evolution is just micro-evolution working over a longer time – “any fool can see that!” I think your wording is wrong there. Should be “only a” not “any”.

  80. Jerry mentioned:

    This is farcical because there is no explanation at the current time. There is no evidence to support any mechanism only speculation and a fair amount of evidence to question the Darwinian paradigm. So what you want is to present speculation rather than an admission that we do not know and to suppress any information that suggest that what is being presented is not correct but only speculation.

    Well, if you re-read my original comment I suggested that it would be important to discuss the limitations of any scientific analysis of historical events, which perhaps covers the “speculation” part; as to “not correct”, we may have to agree to disagree on that.

    However, I’m now curious. Can I take it then that you would not support teaching ID in the classroom for your original reasons? It doesn’t appear to have any firmer foundation than macroevolution.

  81. mikev6,

    I have no desire to teach ID in the classroom. My objective is to teach science. And right now the only honest answer to macro evolution is that it is a mystery.

  82. 82

    jerry every Darwinist out there always falls back to this position, which is why they must continually spread the lie that ID is based on political slight of hand. Darwinists ask us to read their book and textbooks, but refuse to read a single paragraph if it refutes their last ditch fallback position.

    http://www.discovery.org/csc/t.....tionPolicy

  83. Nnoel,

    I want to thank you for making the ID case so easy. Usually most of the commenters here are not so transparent. You are looking kind of foolish if I happen to be Jewish, or maybe Buddhist or maybe an agnostic or a Deist. You have no idea what my religious beliefs are if any.

    If we want to see how someone who opposed ID can get absurd just read your comments. Where does Jesus come into it? This is a frequent tactic used by someone who has no basis for what they are saying. They will turn the discussion towards religion because they cannot win the science argument. The Darwinian case for macro evolution is baseless so this has been a fairly common maneuver for years. However, it just confirms that you or no one has anything or else you would present it. But you obviously cannot.

    Again thank you for making our case so easy. And I suggest if you want to be taken seriously, drop the religious arguments. The debate is over science.

  84. Nnoel

    My previous comment written before I read this. I now understand that you do not understand science. Yay! I can help!

    Spare me. You clearly missed the entire sarcasm of my comment. Look at the entire comment from Hitchens that I referenced:

    It’s not just that the overwhelming majority of scientists are now convinced that evolution is inscribed in the fossil record and in the lineaments of molecular biology. It is more that evolutionists will say in advance which evidence, if found, would refute them and force them to reconsider. (”Rabbit fossils in the pre-Cambrian layer” was, I seem to remember, the response of Prof. J.B.S. Haldane.) Try asking an “intelligent design” advocate to stipulate upfront what would constitute refutation of his world view and you will easily see the difference between the scientific method and the pseudoscientific one.

    Now, notice how in talking about evolution, Hitchens is clearly referencing what might falsify evolutionary theory (or at least parts of it). Laying aside for the moment all the problems inherent with falsification itself, at least it references something fairly common to scientific practice. But then notice that in discussing ID, he very cleverly changes the terms from falsification in scientific terms to refuting a worldview. (It is also worth noting that he uses the word “refute” in talking about evolution, too – though there he clearly means ‘falsify’ in the common scientific understanding of the term). In other words, he’s changing discussion categories: scientific falsification for evolution; philosophical refutation for ID. (Why else would he use the term “worldview”?) So, per Hitchens, evolution is science, but ID is just a worldview.

    But if that’s what he thinks (and clearly that is what he thinks), then why juxtapose the question this way? If Hitchens were being honest, he would have said something like “try asking an ID proponent what evidence might falsify ID in biological systems?” or something similar. Instead, in trying to be clever, he’s being disingenous.

    Now, we could take it at face value and assume he’s comparing apples to apples. Well, that would imply either that both evolution and ID are merely worldviews (to keep them both in the same category); or that they are both scientific. The first route denies evolution as wholly scientific; the second admits that ID is science after all. Hitchens doesn’t want to go either route, so opts instead to compare apples to oranges: science to worldview, and then make it appear as if they amount to the same thing. This is classic bait and switch!

    Thus in my comment I am being sarcastic (while also being truthful): Hitchens comment is utter non-sense — he has no idea what he’s trying to say, or if he does, he’s being completely dishonest in how he presents it. So, thanks but no thanks with your explaining to me how science works! Explain it Hitchens instead — he’s the one who seems to need the remedial course!

  85. Hi jerry,

    You don’t seem to have a clue about the debate or else you would not have made some of your comments. Especially bringing up genetics.

    I asked that question to find out just how much you actually know about this subject. The college Evolution courses I’ve taken usually are upper division and have Genetics as a prerequisite (for what I think are perfectly obvious reasons), so I’m puzzled by your remark. Knowing your level of understanding helps me in my responses. For example, if I were to reference Wright’s Shifting-balance theory (discussed in the paper I cited) without accompanying explanation, would you know what I was talking about without having to first scramble over to Google? I’d rather spare you the effort.

    The silly question about whether I took a course in evolution is an indication of this lack of understanding.

    I see.

    genetics is micro evolution, not macro evolution.

    I read your missive in the link you provided. I suppose this part was the relevant one for this discussion:

    The driving force for most of the diversity of life on the planet seems to be due to Darwinian processes. Darwin’s original ideas have been considerably changed since Darwin’s time but the theory today generally hypothesizes that the appearance of new minor variation in species is driven by environmental factors but modified by a whole host of genetic and epigenetic processes that tend to produce gradual changes in species over time.

    Who says the “appearance of new minor variation is driven by environmental factors?” Could you point out what environmental factors drive DNA polymerase’s base error rate, for example, or drive the meiotic process of crossing over?
    Also, there was this:

    However, this process has never been to shown to be able to produce new complex functional capabilities but only minor changes probably creating at best a new genera. We remain skeptical of its ability to completely explain what Ernst Mayr called megaevolution.

    So, the differences between genera of mice (Peromyscus vs Mus, say) are within reach of so-called microevolutionary processes, but the differences between families of rodents (mice vs squirrels, for example) are not?

  86. mikev

    1) I don’t think there are any background principles forcing rejection of ID as an explanation. My objection to ID is that I don’t feel there is sufficient positive empirical evidence at this point to raise it to the level where it should be included in a school science curriculum. I feel the same about astrology.

    Well this sort of proves my point. What you are really saying is that you don’t accept any principle that justifies connecting the data (what we observe in biological systems) with the explanation of intelligent cause. The postivie empirical evidence is contained in all of biology. Your rejection, therefore, is not really on evidential grounds, but on background principles that justify connecting the empirical evidence to the explanation of ID. We’re all looking at the very same data: biological systems. So, I don’t find your claim of lack of sufficient evidence to be all that convincing. You just don’t take any of this data to be sufficient evidence for ID. The question, then, is what would you need to see or know in order for the data to rise to a sufficient level (for ID to be warranted) for you?

    2) I would rather not assert anything. I would prefer that someone show me the extensive reading list on how new species are created by a designer or other aspects of how ID explains the diversity of life. Evolution at least puts a stake in the ground, says “we think it happened this way”, and one can argue pro/con and search for/evaluate evidence. It doesn’t seem that ID has reached that point, but if you have research links to this type of material, I will be more than willing to read more.

    Here you introduce a separate albeit interesting question. One can infer the need for design without knowing how it was accomplished. Indeed this is precisely what we see with evolution. Evolution, we are told, can explain the entire diversity of life, including the complex, specified information we observe at the cellular level. But to date, no one can explain how evolution did all this. Natural selection, the supposed mechanism of evolution, is very little understood. So, the data is, according to you, sufficient to accept evolution, even though we don’t know how it happened, but insufficient for ID because we don’t know how a designer could have done it. The stake that evolution has put in the ground, as you put it, is based on the very same data set as ID.

  87. DonaldM @ 84 :

    As you are an ID proponent what evidence might falsify ID in biological systems?

    (you say this is what hitchens should have asked, so i’m asking it!)

    Please answer. Your answer could define ID as a scientific theory instead of a philosophical worldview. At this point, to the best of my knowledge, ID IS NOT SCIENCE, but it is trying to play on the same playground. All the ‘bait and switch’ you refer to is the fault of ID not being science, it is NOT science. Repeat the mantra ‘ID is not Science’ and re-read your comments, complete that exercise honestly and you’ll have answered all your own mis-understandings.

    “Hitchens doesn’t want to go either route, so opts instead to compare apples to oranges”.

    And? you cant call orange apples, or apples oranges! when oranges are oranges and apples are apples, how else to compare them???? lol. Arg! (much hand waving and gesturing as I say this)

  88. jerry @ 83 :

    The ToE or anybody supporting the ToE CANNOT affect the status of ‘Intelligent Design’. I may be as religious hating as I like, I may think all proponents of ID are raving crazies, but when ID starts MAKING PREDICTIONS, all. my. opinions. would. count. for. naught!

    You don’t know my religious convictions, and I doubt I even fit anywhere in your world view. How exactly am I making the case easy for ID. AS I’ve said before, ID is leaning on the ToE, trying to ‘overthrow’ it without realising it cannot stand on it’s own.

    I’d like to hear ID described as a scientific theory that makes no mention of evolution. I think I’ll be waiting a long time!

    from this link :
    http://www.discovery.org/csc/t.....tionPolicy

    ‘it does believe there is nothing unconstitutional about discussing the scientific theory of design in the classroom’

    ID IS NOT SCIENCE, (remember that mantra?), and the discovery Institute either knows that and is.. wait for it… lying for jesus, or they don’t know that ID is not science, and then they are fools trying to do science and just getting it very wrong. But as I’ve said, lying for Jesus is the over-arching theme I can see. As most Christians are suppose to follow the ten commandments, I don’t understand why it is allowed.

    Regarding your comments that I am assuming all ID proponents are Christians, and I should just concentrate on ‘the science’, well ID IS NOT SCIENCE, and therefore if you follow your own advice you wouldn’t be arguing for the deity!

  89. Ello!

    Just read the posts above and I come out sounding a bit frustrated and impatient, and for that I’m sorry. I am not trying to discourage anybody from ID, but I would like ID to define itself in a scientific manner.

    All discussions attacking the ToE when ID is not yet scientifically defined only promote the belief that ID is a religiously motivated attempt to attack science for disproving god. (and the usual disclaimer, the ToE only disproves god or gods if you let it, I dont think it does)

    I sound frustrated because I am frustrated by people not admitting that ID is not YET science. I have a sneaky suspicion (as many ID proponents themselves do) that ID will never be science, but more like a ‘assistant teacher’ in the science classroom whispering in all the religious kids ears that they need not believe god is dead just because evolution can be true.

    Honesty and compassion are the most important values I cultivate in my life, and it is compassion that drives me to engage in the ID discussion to further ID’s cause. As it stands, the propaganda against ToE is only convincing those that are already convinced. A scientific theory of ID is what is needed to play ball in science circles.

    Love you like your me.

  90. David Wisker,

    I will repeat, micro evolution is not under debate and genetics is micro evolution so whatever complicated theories that are subsumed by genetics are not under debate. No, I cannot quote the theories and their details because they are not relevant. What happens as a result of sexual reproduction is irrelevant.

    The debate is over how variation appears in the gene pool not how the variation is reshuffled after it appears there. And yes, basic Darwinian theory assumes the selection of the elements of the gene pool is primarily driven by the environment. It is called natural selection. Now as you must know having had these upper level courses, there are other factors that affect the frequency of alleles and other genetic elements. But the shrine at which the Darwinist worship the most is natural selection.

    We often make a point that in the evolution debate that natural selection is really a minor factor not because it doesn’t work but because it doesn’t do much in terms of the debate. The essence of the debate is over the source of new variation to the gene pool not what happens to it after it appears.

    You do not come here very often or else you would not be making the comments you do. An evolutionary biologist from Cornell named Allen MacNeill is a frequent contributor here and has a website in which he lists what he calls the engines of variation. He lists 50+ sources of variation from SNP’s to elaborate transpositions. Allen maintains and rightfully so that this is where the evolution debate is really centered. Natural selection and genetics are a side show.

    This does not say that genetics are not important because medicine, ecology, energy and food production, are major areas where genetics plays a role and are very important to our society. But they are not relevant to the evolution debate.

    Actually there are some elements of genetics that are part of the debate. Namely, how fast a change in the gene pool can become fixed in a population. For example, there is the never ending discussion of chimps and humans and their descent from a common ancestor and if in fact the differences could have happened as quickly as it supposed to have happened through normal genetic processes.

    Since you have a degree in genetics then you are quite familiar with the information content of the genome and the debate is essentially over how this information could have changed over time to effect the morphological changes seen in the fossil record and in the suite of species on earth at the moment. Allen MacNeill says it is due to his engines of variation. ID says it is not possible and the debate is over probabilities and complexity changes in the genome which produce new capabilities and the time it would be necessary for these changes to take place.

    So this is why I say you didn’t have a clue over the debate. Now that you know, you can direct your questions elsewhere in this discussion. If you have access still to Berkeley’s library then I suggest you go to Paleobiology in 2005 and there was an issue devoted to macro evolution. It was made into a book by Vrba and Eldredge on macro evolution but all the chapters are in Paleobiology so you can download them. Read the first chapter by a guy name Jurgen Brosius. This is the essence of the debate. Brosius assumes it is a slam dunk that naturalistic evolution caused all the changes but not through Darwinian processes so I am not sending you to an ID person but to a virulent anti ID one.

  91. The theory of evolution does NOT make any predictions based on the proposed mechanisms.

    None, nada, zip, zilch, zero.

    ID is science because it can be empirically tested.

    ID makes predictions- one being that agencies (usually) leaves traces of their involvement behind.

    Those traces are evinced by IC and CSI.

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

    And if all you have is to throw eons of time at something then you don’t have a science.

    Also EVOLUTION is NOT being debated.

    EVOLUTION has several meanings.

    ID is NOT anti-evolution.

    At best ID can be considered to be anti- blind watchmeker having sle dominion over evolutionary processes.

    IOW it appears that yu guys don’t even know what it is you are arguing against.

    Par for the course…

  92. Carroll’s books are full of nothing but speculation.

    that sounds exactly like a statement from someone who hasn’t read them.- Khan

    I read “Endless forms…” and “Making of..”. I read every page.

    Now you could refute what I said by posting the relevant passages that do so.

    Also as you have been told several times now the definition of “macro-evolution” that you are using is NOT even being debated.

    and that sounds exactly like a statement from someone who didn’t read my post.

    How so? Please be specific as I am tired of your continued vague accusations.

    or does “evolution of body plans” sound like just more microevolution to you?

    There isn’t any evidence for such a thing.

    If there was you would have posted it.

  93. Dave Whisker,

    Instead of asking questions why don’t you guys just post the scientific data which supports your claims?

    For example- Show us the data that demonstrates that a mouse-like organism (population) can evolve into a squirrel-like organism.

    Or show us the data which would demonstrate the small bones in a reptilian jaw can morph into ear-bones of a mammal.

    Hoiwever it is obvious that ALL you have is slight variations to an already existing body plan.

  94. jerry,

    Your reply is somewhat puzzling to me.You wrote:

    The debate is over how variation appears in the gene pool not how the variation is reshuffled after it appears there.

    This seems to me that you are saying the debate is only on the origin of the genetic information. itself. Is that right?

    And yes, basic Darwinian theory assumes the selection of the elements of the gene pool is primarily driven by the environment.

    But that isn’t what you wrote. Your link clearly states:

    appearance of new minor variation is driven by environmental factors?

    So which is it?

    Now as you must know having had these upper level courses, there are other factors that affect the frequency of alleles and other genetic elements. But the shrine at which the Darwinist worship the most is natural selection.

    More hyperbole. Natural selection is believed to be responsible for adaptation, but many biological features do not possess immediate adaptive value (positive or negative), though that may change as the environment changes.

    We often make a point that in the evolution debate that natural selection is really a minor factor not because it doesn’t work but because it doesn’t do much in terms of the debate. The essence of the debate is over the source of new variation to the gene pool not what happens to it after it appears.

    So… if the essence of the debate is what you say, then genetics is at the heart of it. And since the debate, in your eyes, is not about what happens to the variation after it has appeared, then adaptation is irrelevant to the debate as well. So how exactly, does macroevolution fit in here?

    You do not come here very often or else you would not be making the comments you do. An evolutionary biologist from Cornell named Allen MacNeill is a frequent contributor here and has a website in which he lists what he calls the engines of variation. He lists 50+ sources of variation from SNP’s to elaborate transpositions. Allen maintains and rightfully so that this is where the evolution debate is really centered. Natural selection and genetics are a side show.

    What are SNP’s and transpositions, if not genetic phenomena? Students certainly learn about these in Genetics and Molecular Genetics courses. Perhaps you have a different definition of genetics than I (and most of my colleagues, apparently) do.

    This does not say that genetics are not important because medicine, ecology, energy and food production, are major areas where genetics plays a role and are very important to our society. But they are not relevant to the evolution debate.

    Are you saying ecology is not central to evolutionary theory?

    Actually there are some elements of genetics that are part of the debate. Namely, how fast a change in the gene pool can become fixed in a population. For example, there is the never ending discussion of chimps and humans and their descent from a common ancestor and if in fact the differences could have happened as quickly as it supposed to have happened through normal genetic processes.

    Im confused. First you say the essence of the debate is about how variation appears, and has nothing to do with what happens after it does. Now you say how variation becomes fixed in a population is part of the debate, which contradicts what you said earlier. Which is it?

    Since you have a degree in genetics then you are quite familiar with the information content of the genome and the debate is essentially over how this information could have changed over time to effect the morphological changes seen in the fossil record and in the suite of species on earth at the moment.

    So let me get this straight. The debate is about how variation appears, not about what happens to variation after it is there. But the debate is about how variation becomes fixed in a population after it has appeared, and how it changes over time after it has appeared.

    This sounds self-contradictory.

    So this is why I say you didn’t have a clue over the debate.

    Assuming your incoherent summary of the debate is actually accurate, you might be right.

    Now that you know, you can direct your questions elsewhere in this discussion.

    I’m fine here, thanks. You haven’t convinced me, based on the above, that you actually understand enough about this debate to be taken seriously.

    If you have access still to Berkeley’s library then I suggest you go to Paleobiology in 2005 and there was an issue devoted to macro evolution. It was made into a book by Vrba and Eldredge on macro evolution but all the chapters are in Paleobiology so you can download them. Read the first chapter by a guy name Jurgen Brosius. This is the essence of the debate. Brosius assumes it is a slam dunk that naturalistic evolution caused all the changes but not through Darwinian processes so I am not sending you to an ID person but to a virulent anti ID one.

    I’ll check it out, thanks.

  95. Hi joseph,

    Dave Whisker,

    Instead of asking questions why don’t you guys just post the scientific data which supports your claims?

    For example- Show us the data that demonstrates that a mouse-like organism (population) can evolve into a squirrel-like organism.

    How qualitatively different from a mouse is a squirrel? jerry says ID is cool with microevolutionary forces producing new genera at best. I’m simply asking what’s so different between squirrels and mice (which are in different families, which are higher taxa than genera) that precludes microevolutionary forces from generating them?

    By the way, there is no “h” in my last name. Thanks.

  96. Note to all:

    I seem to be on perpetual moderation, so there may be delays in seeing my comments.

  97. Mr Nnoel,

    I think that if you restricted your use of the phrase “lying for Jesus” to your opinion of Don McLeroy you would be on safer ground in this thread. As it is, applying the phrase at random to your co-discussants is just going to put you on the short road to bannination. Whatever your point is, you are dulling it.

  98. Mr Joseph,

    I think the most celebrated recent prediction of evolutionary biology has been the discovery of Tiktallik Roseae. It was found in just the age and kind of rock that was predicted. No rabbits were discovered in the same strata.

  99. Nakashima @ 94 :

    Thanks for the warning? lol, but I call it as I see it, and if I’m wrong I’m happy to be told why.

    jerry @ 90 :

    My understanding of ‘how new information arises’ in the genetic information an orgamism carries is based on the fact that the ‘container’ for information grows, and it does this through duplication. When an ‘instruction’ is duplicated, it is often the equivalence of ‘junk dna’, with the disclaimer that junk dna is a bad name as if implies this has no purpose (no purpose is speculation on the ‘unknown’ purpose).

    Once the ‘container’ has been enlarged, mutation etc kick in, basically different types of copy errors. Of course we cannot ignore that copy errors are mostly bad, but thank copy errors when they are not :)

    That is my view of the ToE, natural selection kicks in after birth, genetics happen at birth, natural selection is what demands a solution, genetics is what blindly tries to answer (with the assumption that as it IS answering, the previous answer wasn’t half bad)

    Is that not a sufficient answer when you throw in a few eons of time? How else without relying on time could you answer?

    Would love to hear thoughts on my opinion :)

    Love you like your me.

  100. Nakashima,

    Thank you for demonstrating that the theory of evolution does not have any predictions based on the proposed MECHANISMS.

    Tiki is not a prediction based on any mechanism and all it is is a fish with different characteristics than fish we think are “normal”.

  101. Mr Jerry,

    I am also very interested in discussing macro-evolution. However, I think it would be more useful to avoid confrontation and hyperbole to advance that discussion.

    Here are some of my initial thoughts on the subject. I freely admit that I have not thought about this subject as long as some others, and certainly don’t know the literature completely.

    The operators of micro-evolution, i.e. variation, selection, time, and scarcity, are insufficient to explain the diversity of life. To explain this diversity we must appeal to other historical and ecological concepts, and see how they push or pull the micro-evolutionary engine in certain directions.

    Part of the historical context includes
    – the distance of the earth from the sun
    – changing solar radiation
    – plate tectonics
    – axial tilt
    – existence of the moon (tides)

    I believe the last three are very important to understanding macro-evolution. What this adds to micro-evolution is a distribution in space as well as time, and a dynamism to that distribution which helps keep life from falling into a stable equilibrium.

    The other major context is ecology, the recognition that other life forms a significant part of the environment.
    – competitors for resources
    – source of energy and organic chemicals
    – source of information
    – source of niche (Co-evolution)

    Even more than the dynamic physical environment, the dynamic ecological environment drove macro-evolution.

    In outline, these are the things that I think have operated historically, and operate today, to drive macro-evolution. To these could be added very basic issues of physics such as the cube square law and the properties of materials that form fundamental constraints on variation.

    Micro-evolution itself does not predict the tension between reproductive success from isolation (not having to share resources) and reporductive success from closeness (neighbors are resources). In our world, the balance is tipped towards success from closeness, which has led to biofilms, bacterial signalliing, the evolution of predation, arms races, and cooperation, the preference for self similarty, sex, and multi-cellularity, symbiosis and parasitism.

    So that is my thesis, that the engine of micro-evolution, combined with physical and ecological dynamism over long periods of time, is sufficient to explain the level of biodiversity that exists today and the pattern of biodiversity shown in the fossil record.

    I would be happy to discuss it further with you.

  102. Mr Joseph,

    The characteristics of Tiktallik were exactly those predicted by the mechanisms of evolution. THe mechanisms of evolution predicted characters intermediate between those of forms immediately prior to and after, in chronological sequence. The mechanisms of evolution predicted no saltational leap. There was none.

  103. kairosfocus:

    intelligent designers routinely produce artifacts that are on islands of function, but by just that: directed, purposeful contingency.

    This directed, purposeful contingency sounds quite amazing. Let’s give it a test run:

    Can you find a 32-character (capital letters and spaces) string with an MD5 hash of cb6ba5a8daf75b7d50fef95cecae78d7? There are millions of solutions, and the search space is a measly 2^152, which should be a piece of cake compared to 2^1000.

    If you can’t do it, you might ask yourself why your directed contingency can successfully search some large spaces but not others. In fact, you might ask yourself whether the solutions it can find really are sparse and functionally isolated when you model the problem with all of the pertinent information taken into account.

    [And, GA's themselves are illustrative: where do you think the program and its underlying databases, rules, knowledge base, principles functionality etc and the machine it runs on come from?]

    Coins are made and flipped by humans. Do coin flips fall in the category of directed, purposeful contingency?

  104. 104

    Mr Nakashima,

    It would be nice if you would spell Tiktaalik correctly.

    http://en.wikipedia.org/wiki/Tiktaalik

    Mr Joseph,

    How do your know that it’s a ‘fish’?

  105. Mr DiBagno,

    Thank you for the correction. I trusted Google to suggest the correct spelling to me, which apparently was not safe!

  106. Dave Wisker, you have asked a bunch of questions. Here are my answers.

    “the debate is only on the origin of the genetic information. itself. Is that right?”

    Yes, as a couple of evolutionary biologists have said that here. It is mainly not over what happens to it afterward of how something is inherited. Though there is another debate and I am sure there are others over the speed at which some things can happen but the main debate is over the appearance of information that can drive novel complex capabilities. Maybe some of these capabilities will not be selected for and will disappear from the gene pool over time. But that is what the debate is about and genetics in the sense of heredity has nothing to do with the main part of the debate. There are two sides of this process, the origin of new variation in the gene pool and second the eventual expression of this variation or not through heridity. The second aspect is not as controversial but there are issues that can generate heated debate. The first is what interests us most of the time and what we refer to as macro evolution.

    I wrote “appearance of new minor variation is driven by environmental factors?” As I said in the comment I wanted input and here you are providing input. Make it “appearance of new minor variants is driven by environmental factors” Does that make you happy? Thank you for the correction. You are the first one to pick this up.

    “More hyperbole. Natural selection is believed to be responsible for adaptation, but many biological features do not possess immediate adaptive value (positive or negative), though that may change as the environment changes.” I am not sure what your point is here. I do not deny other factors are involved in the fixing of a genetic element or the percentage of genetic elements but natural selection is the one that is at the root of Darwin’s theory. I read a book on evolution a year or so ago and every other page seemed to have the term “was selected.” The hyperbole is on the naturalistic evolution side which has promoted natural selection as a major driver in evolution for 150 years. Are you denying that Darwin is primarily identified with the concept of natural selection.? If I have to debate this with you then it says what you are about and where this discussion is going. Interesting choice to make to try and catch me on something like this.
    “So… if the essence of the debate is what you say, then genetics is at the heart of it. And since the debate, in your eyes, is not about what happens to the variation after it has appeared, then adaptation is irrelevant to the debate as well. So how exactly, does macroevolution fit in here?” I am sorry but this does not make sense. I said genetics is not at the heart of it and by this I mean how various elements are inherited that are already in the gene pool and the changes in the frequencies of these elements. Adaptation happens but adaptation does not produce new variation to the gene pool. It is essentially a reshuffling. Adaptation may produce new variants which are using different combinations of the gene pool or it may produce a different percentage of certain alleles. You tell me since you are the genetics major. The gene pool hasn’t expanded. Most likely it has narrowed with adaptation.

    “What are SNP’s and transpositions, if not genetic phenomena? Students certainly learn about these in Genetics and Molecular Genetics courses. Perhaps you have a different definition of genetics than I (and most of my colleagues, apparently) do.” Well maybe we do have a problem of definition here. I look at genetics as heredity and all the factors that change the percentage of the genetic elements in the gene pool. When I am referring to genetics I am referring to things that happen to the organism as a result of the reproductive process using the genetic elements already in the gene pool not changes to the gametes prior to reproduction. Now if you want to include cell division, gene duplication, reverse transpositions as part of genetics, then be my guess, but in the past discussions these have been separated. So you are welcome to establish a different delineation.

    “Are you saying ecology is not central to evolutionary theory?” – To micro evolution. There is no coherent theory of macro evolution which is essentially the appearance of novel complex capabilities. That is what we are having the debate about. So yes and no. Once the novel complex capabilities appear then they are subject to micro evolution and all that it involves and ecology is part of that.

    “Im confused. First you say the essence of the debate is about how variation appears, and has nothing to do with what happens after it does. Now you say how variation becomes fixed in a population is part of the debate, which contradicts what you said earlier. Which is it?” This is a silly question which makes me doubt your sincerity. Can’t you understand that there could be separate issues not of the same magnitude that do not involve each other.

    “So let me get this straight. The debate is about how variation appears, not about what happens to variation after it is there. But the debate is about how variation becomes fixed in a population after it has appeared, and how it changes over time after it has appeared.” This comment has definitely said to me that you are not serious and only interested in a gotcha. If you were sincere, then you would have expressed it quite differently. As you express it, it could be contradictory but as I said it here there is more than one single issue and one is more important than the other.

    “Assuming your incoherent summary of the debate is actually accurate, you might be right.” My summary is coherent and accurate but I appreciate that I have to be extra careful with some people who are looking for anything they can to impugn someone. You are falling into a pattern that has happened here many times before. I am sorry to see it because you obviously have a lot of knowledge but your choice how to use it is revealing.

  107. 107

    jerry, this may be a good time to point out that you have never adequately answered me on the question of punctuated equilibrium. I said your representation of PE on another thread was completely inaccurate. You replied by claiming it was accurate but otherwise merely provided a lot of bluster (nonspecific references to Allen MacNeill etc). I pointed out that your reply was not responsive. Let me quote from that:

    To recap, your claims is that PE involves “changes that happen out of sight in unused parts of the genome.” You write that in PE, “[a] very small number of these changes suddenly become functional and this is when a new species or genera are born.” You even write that “This is the essence of punctuated equilibrium.”

    Can you provide a quote from Gould or Eldredge that supports this? Can you even provide a quote from MacNeill that supports this? I think you can’t. It shouldn’t be hard. The original PE paper is available online, along with a number of other of Gould’s works on PE.

    Please don’t just tell me that everybody knows this is what the theory says. It isn’t.

    Why ask it on this thread? Because this thread is where you seem to be paying attention, because others have questioned (and you have defended) how much you know about evolution, and because PE is a theory about macro-level changes. If you’ve got that wrong — as I think you do — it may be relevant.

  108. Mr. Nakashima, you said

    “I am also very interested in discussing macro-evolution. However, I think it would be more useful to avoid confrontation and hyperbole to advance that discussion.”

    I have been commenting here for about 3 1/2 years and in that time there have been about 300-500 people who have commented here who are anti ID and who have come here to challenge us. Few have been polite and interested in having an open dialogue. Most challenge us almost immediately. Invariably, we ask them to defend what they understand as macro evolution. Which we define as the origin of complex novel capabilities. This may not be the best definition but it can serve till one better comes up. Not one person has been able to do so. Most decline to try to answer the question. A few have made an attempt but all have resorted to micro evolutionary examples. So is it hyperbole to say that no one has a coherent theory of macro evolution.

    Allen MacNeill who teaches evolutionary biology at Cornell has said there is no model for macro evolution. There are some theories or speculations but no adequate model. The current one that seems to be getting favor is that part of the genome is not subject to selection and thus can mutate away and for a very small number of genomes there will develop a functional element which then can be added to the coding area of the genome and then subject to selection. This process could take millions of years but it seems to be the theory that is gaining favor as opposed to the Darwinian model which hypothesizes an ongoing series of changes to the coding region of the genome due to adaptation.

    So when you say it is hyperbole or confrontation, you have to take everything in context. It is not hyperbole that no one has ever provided a coherent explanation of macro evolution. All they produce is speculation. Also nearly everyone who is anti ID who comes here confronts us first and often without politeness. We very often treat someone with politeness and try to inform them about what we believe and why but it quickly turns into a confrontation started by the anti ID people who are not here to learn but to prove us wrong or that we are ignorant or that we are blinded by religious beliefs.

    If you want to discuss macro evolution, then you are certainly welcome. But I doubt if you will find anyone here or anywhere who can provide a coherent explanation for it. Macro evolution certainly happened but the question is how. You mentioned Tiktaalik but as far as I know this fossil has no predecessor or successor for about 10 million years. But even besides that, various versions of ID predict such organisms as well as other naturalistic methods of evolution. So what is the point of it?

    One way of analyzing macro evolution is the same as was done with the Abel paper on the thread started by Salvador Cordova a couple weeks ago. The answer is in the origin of information in the genome. Not only just the origin of the DNA for new proteins but the coordination of that information with other pieces of information to produce complex novel capabilities. It is an issue of probabilities and whether the proposed processes for altering the genome have the time or resources to produce the new information.

    You can hypothesize all the factors you have named as the cause for macro evolution but in the end you will have to show how they lead to the information changes that are necessary to drive macro evolution.

  109. David Kellogg,

    You have been answered several times. I pointed you to a specific article in a book that is a tribute to Stephen Gould. Allen MacNeill confirmed it before he unconfirmed it. Does that make him like a certain senator from Massachusetts.

    Are you getting tired of debating the cosmological argument and atheism and want to get in on the action here. With your typical flair you could turn this into at least a 300 comment thread about nothing. Invite Hazel or some of the other obfuscators and everyone can have a ball.

    If your library cannot get Paleobiology then have one of your academic buds from Harvard or MIT get it for you. Read the Brosius article which was selected to go first and then come back. It is from 2005.

    Adios. Time to watch hockey which I know is your favorite game.

  110. 110

    My library has Paleobiology, thanks.. I’ve read the article (“Disparity, adaptation, exaptation, bookkeeping, and contingency at the genome level,” Paleobiology 31(sp5):1-16. 2005. You can’t get enough of recommending that article. The problem is that it isn’t even really about punctuated equilibrium, and it doesn’t describe PE as you say it does.

    It mentions PE (though it never uses the phrase) but it’s really about whether certain genetic data are consistent with PE, not about PE itself. It’s not a review of PE or anything of the sort. The closest thing I can find to what you have to say is this: “Conversely, punctuated retropositions can take several if not tens of millions of years to become exaptations, ‘awaiting’ additional small changes that, for example, create a functional splice site or an open reading frame.” That’s a minor sentence with a word (awaiting) in scare quotes. Is that sentence really what you want to claim is “central” to PE?

  111. 111

    Jerry, it really doesn’t matter if MacNeill recommended the book (or the article, which is pretty good actually) or if the issue of Paleobiology is dedicated to Gould. What matters is whether you can characterize the PE position adequately. Thus far, I’d say, meh, not so much.

  112. Mr Jerry,

    You are correct, the references to Tiktaalik are not paricularly relevant to a discussion of macro-evolution. They were only a response to Mr Joseph’s request for information.

    Since we are offering each other source material, I would like to recommend to you this book chapter.

    As a further motivation to the ideas I have shared, I would point out that genetic algorithm researchers have used similar approaches, in the form of island models (demes) to acheive or maintain diversity.

    As you say, gene duplication, viral insertion and other micro-evolutionary mechanisms may be creating variety nearly constantly, but what suddenly brings it to the forground? It may truly be functional advances, or it may simply be environmental variation leading to different selection pressures. We know the environment is constantly changing, and that needs to be recognized in our models.

  113. DonaldM@86 said:

    Well this sort of proves my point. What you are really saying is that you don’t accept any principle that justifies connecting the data (what we observe in biological systems) with the explanation of intelligent cause. The postivie empirical evidence is contained in all of biology. Your rejection, therefore, is not really on evidential grounds, but on background principles that justify connecting the empirical evidence to the explanation of ID. We’re all looking at the very same data: biological systems.

    I don’t quite agree here, but I’ll forge ahead because I’d really like to hope that I can learn something about ID in the process. My concern here is that this seems a hugely broad definition of evidence – it sounds like you’re saying “look at all of creation around you – it has to be designed”. (If I’ve missed the point, let me know.) However, a definition this broad is largely useless for science – why bother researching if you already have an explanation that covers everything?

    So, in an attempt to impose some structure for further debate on what seems to be an intractably amorphous concept, I try proposing specific questions (as in my second point): e.g. How does the designer create a new species? Evolution says “small incremental changes governed by natural selection mechanisms lead to larger changes over time to create a new species”. I’m not trying to defend that particular statement, but I would expect ID as a model of the development of life to have at least an explanation of the same end-result (species) that can be analyzed and form the basis for further research. It seems the current ID explanation is that an unknown entity goes “poof”, and this isn’t satisfying for either of us – it just leads to endless circular arguments.

    So, to answer your question about what would sufficient evidence to accept ID, I don’t think we can even address that until ID has imposed some structure and generated hypotheses in a variety of these questions.

  114. David Kellogg,

    Like the hamburger ad said many years ago. Have it your way. I would think that an unchanging genome for maybe as long as tens of millions of years and then the appearance of a novel characteristic out of no where would ring a bell some how. But if it doesn’t then, pass the ketchup.

  115. ” it sounds like you’re saying “look at all of creation around you – it has to be designed” ”

    Nope. Though that is what many have done for thousands of years. It is an intuitive position to take but that is not ID. I am surprised that you believe that given the discussion that has gone on just on this thread.

    “a definition this broad is largely useless for science – why bother researching if you already have an explanation that covers everything?”

    This is not the ID position so portraying it as such is not relevant. Closer to the ID position is the paper by Abel discussed in a thread starting two weeks ago.

    http://www.uncommondescent.com.....d-article/

    I would not recommend reading the thread though you can if you want. Look at the paper referred to in the post at the top. Some of it is difficult but a lot of it is accessible. It is about the nature of information in the genome and its possible origin. That is what the main ID debate is about.

    “. How does the designer create a new species? Evolution says “small incremental changes governed by natural selection mechanisms lead to larger changes over time to create a new species””

    There is a couple problems here. First of all the designer if he/she/it existed was not here some time a couple months ago but billions of years ago and so the how is obviously very speculative. But there exists a discipline called Synthetic Biology which claims it is within years of creating a functioning cell. So it is obviously possible. Second you use the word evolution to mean a specific mechanism for changes in life over time and that is not the proper use of the term. Small incremental changes subject to natural selection is just one mechanism hypothesized for the mechanism of evolution.

    “It seems the current ID explanation is that an unknown entity goes “poof”, and this isn’t satisfying for either of us – it just leads to endless circular arguments.”

    The use of word “poof” is a loaded word intended to mock the idea. Suppose you changed it to “seed” instead so that an unknown entity seeded the earth at one or more times with various life forms, maybe only once according to front loaders. Why is this circular? It may not be satisfying to you but what if it actually happened this way. What would be different than what you see and why?

    “I don’t think we can even address that until ID has imposed some structure and generated hypotheses in a variety of these questions.”

    If you see the name John Davison on the comments list, he has a whole theory with hypotheses and lots of discussion on how it happened. Other are generating different hypotheses. Behe has some on the ability of mutation and reproduction to be able to create meaningful new proteins. Abel and others have hypotheses on the ability of natural processes to be able to create the information to produce functional proteins. Dembski and others have hypotheses on the ability of search processes in the form of new mutations and reproduction to find new functional proteins. It may all turn out to be a bust but it is not like nothing is going on. This idea is in its infancy and the one common theme seems to be in the ability or inability to find usable proteins for use in life.

    By the way there is a similar program going on by those in favor of a naturalistic process to show that mutations along with other genomic processes can produce useful proteins.

  116. 116

    Hi jerry,

    I read the Brosius paper as well., and agree with David Kellog that the only place punctuated equilibria is really talked about is in the passage he cited. It seems what Brosius was trying to say was that retronuons could accumulate gradually until they suddenly became adaptive, giving the appearance of a “saltatory event”, a “punctuation”, if you will. But that isn’t the essence of punk eek, as any reading of Gould and Eldredge’s papers will tell you.

    What confuses me is your insistence on this paper being concerned with non-Darwinian processes. Brosius clearly states that retronuons are, for the most part, “transcriptionally dead on arrival” when they are inserted into the genome, because they often lack promoters . He says they can be reshuffled and recobbled by recombination and subsequent mutation to where they might acquire the right sequences in the right place and then become adaptive:

    Only later did some authors recognize the advantages of retroposed genes, namely that, although the odds of generating a functional gene are low, genes duplicated via transposition can recombine with alternative regulatory elements

    As an aside, perhaps now you can sense my confusion when you insist that processes such as recombination and gene duplication aren’t part of this debate, when they are central to a paper you say is about the essence of the debate.

    But I digress. What Brosius is saying is entirely consistent with the neo-Darwinian view. Retronuons arrive in the genome via retrotransposition, and almost always are non-functional as genes or regulatory elements. Their frequencies in the population are primarily determined by genetic drift, since they are, for all practical purposes, neutral alleles. However, once they are in the genome they are subject to gradual mutation, and recombination (recombination is also responsible for gene duplication). In some cases, mutation and/or recombination can produce a functional gene or regulatory element, which may change it from selectively neutral to having a selective advantage (or disadvantage), as well as a sudden appearance. After that, its frequency becomes primarily determined by selection. I fail to see how this is radically different from processes under the neo-Darwinian paradigm.

    In a post some time ago I mentioned how new, functional genes can appear suddenly via recombination of non-coding elements (T-urf13 in maize is one example). Recent genomic work in Drosophila has suggested 10-12% of its genes may have arisen this way. Brosius’s paper is concerned with essentially the same thing.

    One final note: since much of our misunderstandings seem to be over definitions, I suggest dialing back on the “you don’t have a clue about what the debate is about” stuff until those misunderstandings are ironed out. It might make for more amicable discussions.

  117. Nakashima:

    The characteristics of Tiktallik were exactly those predicted by the mechanisms of evolution.

    1- There is no way to predict what mutations will ocur at any point in time

    2- There is no way to predict what will be selected for at any point in time

    So what mechanisms, exactly, predict Tiki?

    THe mechanisms of evolution predicted characters intermediate between those of forms immediately prior to and after, in chronological sequence.

    Nonsense. The PREMISE that land animals evolved from fish may make that prediction but that is NOT based on any mechanisms.

    The mechanisms of evolution predicted no saltational leap. There was none.

    How do you know?

    And what is the genetic data which would demonstrate that a bone-less fin could give rise to a fin with robust bones?

    IOW how can we test the premise that Tiki evolved from a non-tiki-like fish?

  118. Adel:

    How do your know that it’s a ‘fish’?

    I am taking the word of the scientists who reviewed it.

  119. Dave Wisker:

    How qualitatively different from a mouse is a squirrel?

    If you think they are so similar then it shouldn’t be any prolem pointing out the genetic differences and tying those to the physiological and anatomical differences.

    However no one knows what makes a mouse a mouse nor a squirrel a squirrel.

  120. mikev6:

    How does the designer create a new species?

    Mutation and selection- the mutations would be directed by the organisms internal programming and the selection could be artificial.

    The design hypothesis- ID- states that designing agencies (usually) leave traces of their activity behind.

    IC and CSI are examples of those traces.

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

  121. 121

    Hi joseph,

    You wrote:

    How qualitatively different from a mouse is a squirrel?

    If you think they are so similar then it shouldn’t be any prolem pointing out the genetic differences and tying those to the physiological and anatomical differences.
    However no one knows what makes a mouse a mouse nor a squirrel a squirrel.

    I think you are missing my point, which could very well be due to the way I expressed it. Let me elaborate.

    Jerry’s link says that microevolutionary processes can account only for the differences between genera “at best”. Presumably then, according to ID, the differences between higher taxa of organisms, such as families or orders, can only be explained by macroevolutionary processes consisting of novel complex adaptations. I am taking jerry’s premise at face value, and asking: what differences between these two families of rodents, the Muridae (mice) and Sciuridae (squirrels) require novel, complex adaptations to explain them that cannot be just as easily explained by microevolutionary processes? This doesn’t require any fine genetic detail to answer, that’s why I said “qualitative differences” originally.

    I’m not asking what makes a mouse or a squirrel. I’m asking what makes a mouse different from a squirrel, and do those differences require novel, complex adaptations to explain them.

  122. Hi joseph,

    You wrote (regarding differences between mice and squirrels):

    Hoiwever it is obvious that ALL you have is slight variations to an already existing body plan.

    Exactly, although an evolutionary biologist would say it was minor variation on the body plan of the common ancestor of the two families. ;) Since we all know microevolutionary processes can bring about minor variations, doesn’t this fact call jerry’s statement that differences between higher taxa can only be explained by novel complex adaptations (or capabilities) into question?

  123. Mr Joseph,

    From the work of Spector, et al, which I referenced earlier, here is one of their results.

    ((((((((x*(y*x))*x)*z)*(z*x))*((x*(z*(x *(z*y))))*z))*z)*z)*(z*((((x*(((z*z)*x)* (z*x)))*x)*y)*(((y*(z*(z*y)))*(((y*y)*x )*z))*(x*(((z*z)*x)*(z*(x*(z*y)))))))))

    What is the CSI of this result? Is it IC? Does the answer change if the result is attributed to Spector, who is not an algebraist but is good at writing cool programs, or the program, which is also not an algebraist bus is good at searching algebra shaped spaces?

  124. David Kellogg,

    “Why ask it on this thread? Because this thread is where you seem to be paying attention, because others have questioned (and you have defended) how much you know about evolution, and because PE is a theory about macro-level changes. If you’ve got that wrong — as I think you do — it may be relevant.”

    A very, very interesting comment and is it one where a tiger reveals his stripes or is it a leopard that reveals its spots. Or is it the leopard lost its spots. But I think we know about your stripes or spots already. Whatever, the comment is enlightening especially the “it may be relevant.” If I am wrong and you seem to want this desperately does that mean that anything else I say can probably be discounted or ignored. That is quite a compliment that you want me to be ignored. However, there is a problem.

    I also want to be proven wrong. Which is why I push. And when I push and no one pushes back except to imply I am stupid or ill informed and not with substance then I learn something. I have pushed David Wisker and look how he has responded. Like you, he wants to bury me with my ignorance but in the process I may learn something new which is my hope. So far he hasn’t provided much. Nakashima is being polite and has referred me to a unknown book for me and by the way I just ordered it from Amazon. Part of the first chapter is on line and I have read a few pages of it and do not know when I will have the time to read more of it, but at least I will have it to peruse. I pushed Hazel and the thread ran over 700 comments.

    One of the first things we learned in Business School was some of the sociological things about innovation. That is, you learn more about the world from weak ties than strong ties. Strong ties tend to repeat what you already know but weak ties can open up new possibilities. So I often look for people who would be classified as weak ties. Which is why I read more of the pro Darwin literature than the anti Darwin stuff. I learn a lot from reading these books, and one thing is that they never present anything conclusive. Interesting finding.

    Now back to the issue at hand. Do you really think that I am/was unaware of the basis for punctuated equilibrium? Based on the fact that I have read a lot of stuff on naturalistic evoluition. Has my rant about the new basis for it been any longer than Allen MacNeill’s suggestion that we read the Vrba and Eldredge book which was a result of pushing on macro evolution and the revealing post by Allen where he resorted mainly to micro evolution.

    Q. What is the book about? A. – Stephen Gould and his ideas. Q. What is Gould known for? A. – Many, many thing but one is punctuated equilibrium and the editor of the book is his co-author on this topic. Q. Does punctuated equilibrium have any theory behind it other than wishful thinking to hide the problems with Darwinian evolution and the gradualism of adaptation. A. – no, it assumes that a sub population goes off into some isolated place where the small numbers can mutate away from the stabilizing effect of the original population (did you miss my sarcastic remark about going off in secret is so out of date.) Highly, speculative at best. So along comes the first article in a tribute to Gould which suggests that there is another possibility for the sudden appearance of new characteristics and it does not take an Einstein to connect the dots.

    If you and others prefer not to connect the dots so be it. I was just trying to help everyone along. But there is something about a cow and water. And I said elsewhere Michael Lynch has similar ideas.

    The whole thing is an academic exercise for me since I do not believe in efficacy of punctuated equilibrium or Brosius’ theories so I have nothing at stake here. I am just pointing out what current thinking is and I find your reactions fairly predictable which is why I dubbed you Mr. blue sky/grey sky. I frequently leave comments here to bait you but after the catch you are thrown back in to be caught again. I am sure you will be back.

    So prove me wrong and then you can be happy that I am some ignorant misguided troglodyte who should be ignored. As I said I like be proven wrong because I like learning.

  125. 125

    “How do your know that it’s a ‘fish’?”

    I am taking the word of the scientists who reviewed it.

    From http://en.wikipedia.org/wiki/Tiktaalik

    Tiktaalik is a transitional fossil; it is to tetrapods what Archaeopteryx is to birds. While it may be that neither is ancestor to any living animal, they serve as proof that intermediates between very different types of vertebrates did once exist. The mixture of both fish and tetrapod characteristics found in Tiktaalik include these traits:

    Fish
    fish gills
    fish scales

    “Fishapod”
    half-fish, half-tetrapod limb bones and joints, including a functional wrist joint and radiating, fish-like fins instead of toes
    half-fish, half-tetrapod ear region

    Tetrapod
    tetrapod rib bones
    tetrapod mobile neck
    tetrapod lungs

    It doesn’t seem so clear-cut.

  126. 126

    jerry, you say such delightful things. No wonder there is an active discussion (at After the Bar Closes) as to whether you are really a deep cover anti-ID operative.

  127. jerry,

    since you like to be proven wrong, I can help you. you are wrong about both punctuated equilibrium and the founder effect.

    PE has nothing to do with the origin of “novel traits”: it is specifically about the lack of transitional fossils between species, i.e. what you would call microevolution. Gould pointed out hat there were plenty of transitional fossils between higher taxonomic orders, including those that contain in the transition the acquisition of novel traits. for example, feathers began as simple hollow tubes in early dinosurs, then branched off to become “fuzzy” feathers useless for flight then branced off again to allow interlocking barbuless and hence some flight ability. this is a classic case of slightly beneficial intermediates producing a new novel trait. PE has nothing to do with what you could call macroevolution (origin of novel complex traits), and indeed all of the examples Gould talks about are at the species level and do not involve novel traits.

    Second, the founder effect does not postulate that organisms go off in secret and mutate; it states that a sub-population gets isolated from the larger population. if just a few individuals in the sub-population have “weird” (relative to the main population) alleles, then those alleles will quickly spread through the sub-population as it grows, causing them to rapidly differentiate from the main population. this is hardly speculation; it is currently being used in HIV research:
    http://www.sciencemag.org/cgi/...../5818/1583
    the founder effect also probably allowed the island lizard population to rapidly evolve its new digestive system, although that remains to be shown.
    in any case, you appear to once again be arguing w yourself using definitions that no one else agrees with.

  128. 128

    The paper I mentioned earlier by Charlesworth et al, “A Neo-Darwinian commentary on macroevolution” discusses the arguments by advocates of punctuated equilibria against the neo-Darwinian model of evolution, and its treatment of macroevolution. They write:

    A central problem for evolutionary theory has always been to account for complex adaptations (Darwin, 1859, Ch. 6). Furthermore, because most of the features distinguishing higher taxonomic categories are recognizable as adaptations to different modes of life (Simpson, 1953 p 171-181), the problems of explaining the origin of higher categories can largely be reduced to that of explaining the emergence of a new adaptation or set of adaptations.

    They also point out that, while the evolution of higher taxa may appear rapid or sudden in the geologic record, from a genetic or ecological point of view, such a transitions can still require up to thousands of generations to complete. In other words, there is nothing in the fossil record that demands or requires a saltational (sudden) explanation for adaptations. Richard Dawkins has pointed this out in The Blind Watchmaker. They also argue against the prevalence of advantageous morphological mutations of large effect, pointing out that these kinds of mutations often have deleterious pleiotropic (multiple) effects, and mention Fisher’s famous argument that small, gradual changes have a better chance at achieving adaptation overall than single, large changes.

    For a neo-Darwinian example of the evolution of a novel, complex adaptation, they use mimicry in butterflies:

    A remarkable test case is, however, provided by the ecological genetic studies of Clarke, Sheppard, Turner and colleagues on Batesian and Mullerian mimicry in butterflies (reviewed by Turner, 1977, 1981). These have led to convincing reconstructions of the sequences of genetic events involved in the evolution of complex mimetic phenotypes built up of numerous distinct elements. Despite the fact that Batesian mimicry is often associated with polymorphisms for different mimetic forms, apparently controlled by alternative alleles at a single locus, it has been possible to exclude the saltatory interpretations of Punnet (1915) and Goldschmidt (1945). It is now clear that the polymorphic mimicry loci in in species of Papilio are actually complexes of closely-linked loci (supergenes), each controlling different elements of the mimetic character complex. The evolution of this close linkage has been discussed by Sheppard (1959), Charlesworth and Charlesworth (1975b) and Turner (1977), and fits in well with the concept of stepwise incorporation of mutations at separate loci, each of which has a net selective advantage on the background established by previous evolution. Furthermore, it is certain that the effects of the major mutations incorporated into the supergenes have been considerably enhanced by the selection of minor modifiers that interact with them in very specific ways to perfect the mimetic patterns…This is in accord with the theoretical predictions of Fisher (1927, 1930 Ch 7) and Nicholson (1927), made long before the genetic studies were carried out.

  129. David Kellogg,

    The best thing ever produced for television is Tinker, Tailor, Soldier, Spy and George Smiley is one of my all time favorite characters. A friend lent me the VHS tapes several years ago. The DVD cut some of the original production which was on the VHS. You need to see it at least 2 or 3 times before you understand it all. I watched it 10 or more times and still find something new each time. I love the language.

    Sorry, no intrigue. The fine tuning of the universe is a non negotiable ID event despite 700+ comments on the cosmological argument. Hazel can go off proud while ignoring the 8000 pound gorilla staring at her. OOL looks out of reach for naturalistic processes and so does some of evolution. So I am a committed anti materialist. But I am also a committed anti creationist though I personally have met a few and really like them. You do not find too many in the New York area.

  130. Well khan has just said that punctuated equilibrium has nothing to do with macro evolution. So we will cross that off our list and I can quote khan in the future. Thank you khan. While you are doing that, maybe khan and everyone interested in punctuated equilibrium should read

    http://www.stephenjaygould.org.....f-age.html

    And let us know how they use the term macro-evolution in Gould’s paper on punctuated equilibrium. Is it khan’s definition or our definition? One of paragraph headings is

    Punctuated equilibrium and macroevolution

    However, on the founder effect which khan describes as

    ” the founder effect does not postulate that organisms go off in secret and mutate; it states that a sub-population gets isolated from the larger population.”

    Sounds like the same thing to me. I wasn’t implying that they were hiding their behavior on purpose.

    So khan, I will go with the first one unless there are readers out there that disagree with khan. On the second one I believe we are saying the same thing.

  131. jerry,
    it is obvious in the article that they are referring to the standard definition of macroevolution as evolution at the species level and above, and not the special UD definition of evolution of novel complex traits. PE has nothing to say about that bc Gould rcognized that there is abundant evidence for the origin of novel complex traits through transitional stages; e.g. feathers and the ear bones of mammals.

    as for the second, you quotemined me. read the 2nd part

    if just a few individuals in the sub-population have “weird” (relative to the main population) alleles, then those alleles will quickly spread through the sub-population as it grows, causing them to rapidly differentiate from the main population

    this is to differentiate reality from what you said, i.e. that founder populations mutate away from the rest of the population; the founder effect has nothing to do w mutation. this is the 2nd time you have quotemined me recently. I do not appreciate this as I am trying to have a civil conversation.

  132. jerry@115:

    I suspect I’m reaching the limit on this topic, but a followup query – if a designer is required for a new species, why is a “couple of months ago” not a possibility? joseph@120′s comment suggests a more continuous engagement by the designer, for example. Is there anything to suggest that the designer cannot be present even when a species is *not* being created, or has other impacts such as creating mutations as needed?

  133. GilDodgen, sorry to more or less unload on you in @ 38. I don’t mean to imply that you’re the only ID enthusiast who has those problems. They are endemic in the ID field.

    I do recommend that you formulate your beliefs and try them on somebody you trust and respect who is also a part of main stream science.

  134. khan,

    I stand corrected. I understand what you are saying and that it is just micro evolution. It was my impression that more than just an unusual combination of alleles arose when the population was separated but that novel complex capabilities could also arise. So we are getting some place here and the ID and anti ID people are coming together on some stuff.

    Thank you, khan. I am sincere in that thank you and am glad you proved me wrong. So punctuated equilibrium is a little like artificial selection.

    There was no attempt to quote mine but just a misunderstanding on what you meant on your understanding of what I meant (sounds confusing). This is an interesting development because I bet few here have this understanding of punctuated equilibrium.

  135. Adel,

    The wikipedia article is wrong.

    There wasn’t any functional wrist found nor any lungs present.

    And it could just be a mosaic- ya know like the duck-bill platypus.

    There isn’t any genetic data which would demonstrate a bone-less fin can evolve into a fin with robust bones.

  136. mikev6,

    Young Earth Creationists accept speciation.

    They say that all living organisms are descended from the originally Created Kind.

  137. Khan:

    it is obvious in the article that they are referring to the standard definition of macroevolution as evolution at the species level and above, and not the special UD definition of evolution of novel complex traits.

    And as you have been told that standard definition is useless regarding the debate.

    Also it is NOT the UD definition that is used to differentiate but the Creation definition.

    Ya see “species” is an ambiguous concept.

    Therefor saying variation leading to a new species or at or above the level of species, is macro-evolution, is nonsensical.

    Then you say you are trying to have a civil conversation- more nonsense.

    If you were interested in a civil conversation you would start supporting the claims of your position.

  138. Joseph,
    if the wikipedia article is wrong then the original scientific article is wrong too.:

    http://www.nature.com/nature/j.....04639.html

    Although the body scales, fin rays, lower jaw and palate are comparable to those in more primitive sarcopterygians, the new species also has a shortened skull roof, a modified ear region, a mobile neck, a functional wrist joint, and other features that presage tetrapod conditions.

    did you examine tiktaalik yourself? if so, you should write a follow-up paper to Nature.

  139. 139

    Another way of describing the founder effect is to say small samples of populations often do not represent the gene pool of the population as a whole. For those familiar with statistics, it is the equivalent of sampling error.

  140. mikev6,

    As far as evolution is concerned the evidence seems to point to nothing major happening during current times. That is one of the ID objections to the Darwinian process leading toward macro evolution. While micro evolution happens all the time, there does not seem to be any evidence that there is any progression to new complex capabilities anywhere on the planet.

    An interesting discussion of this is by John Davison who wrote an essay or paper on it called “The Blind Alley.” Here is the link to this article

    http://www.uncommondescent.com.....ind-alley/

    The Darwinian process predicts thousands of steps along the way to new and better capabilities each of which would be a viable species and there should be evidence of this but there isn’t. So why has this process stopped. Maybe it never happened the way they hypothesize.

  141. David Wisker,

    ID has no problem with the founder effect or any of the other ways that populations generate new variants. I personally never associated the founder effect with punctuated equilibrium. My impression was that in these isolated populations, something more than micro evolution within a limited gene pool was going on. Otherwise why make a big deal about punctuated equilibrium and why did it take so long to convince evolutionary biologists about it. That’s why I though it had to do with much more than micro evolution. It seems simple to understand.

  142. jerry,

    it really is difficult to know where to begin. i really think the problem is in your vague, poorly formulated definitions that seem to be shared exclusively by you. for example,in 140, what is “nothing major” and what is “current times”? and why does this statement completely contradict what you say in the end, that there should be “thousands of steps.” you seem to simultaneously want small steps and major changes at the same time. in other posts you seem to agree that there are plenty of examples of “small steps”, i.e. speciation events that we can observe. this is what you (mistakenly) call microevolution. each of these speciation events might (or might not) be a step towards something else (a novel complex function, for example). what that something is we have no way of knowing. so how can you say that we are not on the way to “new and better capabilities” when we don’t know what those capabilities may be? and what, exactly, do you expect to see in”modern times” (besides Charlie CHaplin)? small steps or major changes?

  143. Hi jerry,

    I was just suggesting another way of looking at the founder effect that might help others understand it. The founder effect, however, does play a role in punk eek, since it contributes to allopatric speciation. To Gould and Eldredge, punk eek was an explanation of the patterns allopatric speciation could be expected to show in the fossil record.

  144. Khan,

    What is the genetic data which demonstrates that fish without such bones in their fins can evolve into fish with such bones?

    How can we test such a premise?

  145. Joseph (144),

    we can test for the genetic bases of this transition by comparing expression of conserved genes like homeoboxes during fin and limb development. Differential expression of Hoxa-11 and Hoxd-13 in tetrapods and fish during development appear to at least be partially responsible for the fin-limb difference. the next step is to see how the regulatory genes that control hox expression differ between fish and tetrapods (no easy task). this
    would give us some idea of the mutations that would be necessary to cause the change in expression, and hence fin-limb transition. given that regulatory sequences are frequently quite small (sometimes just 6 nucleotides) it may not take many mutations to cause this change. but we will have to eagerly await those results. in the meantime you can read this nice article for a summary of work on the genetic bases of fin-to-limb transition.

    http://www.sciencedirect.com/s.....83bc98139b

    does that help?

  146. 146

    Joseph [118]

    “How do your know that it’s a ‘fish’?”

    I am taking the word of the scientists who reviewed it.

    Joseph [135]

    The wikipedia article is wrong.

    I sense a double standard regarding how you evaluate evidence.

    There isn’t any genetic data which would demonstrate a bone-less fin can evolve into a fin with robust bones.

    So?

  147. 147

    If I wanted a fin without bones I’d have to use a fillet knife.

  148. joseph@136 commented:

    Young Earth Creationists accept speciation.

    They say that all living organisms are descended from the originally Created Kind.

    That’s my understanding as well; I’m not quite getting the connection here though – could you add a little more context?

  149. mikev6,

    You were talikng about speciation.

    YEC accepts speciation.

  150. Khan,

    That is a start but they have a long, long way to go.

    I do find it amusing how they start with the conclusion that said evolution occurred.

    But hey if they can take a fish embryo- one without those robust bones in its fins- add the missing genes- or whatever- and get a fish with those robust bones then you will have something.

    However we still do not know what makes a fish a fish.

    You know what else would be helpful for your position?

    Demonstrating that the HOX and other regulatory genes arose via an accumulation of genetic accidents.

    Ya see I think that the transition would require more than two specified mutations.

    And if that is the case there wouldn’t be enough time on this planet for your scenario to work.

  151. Tiki’s “wrist”-

    Tiki only has a “wrist” if one redefines the definition of a wrist.

    Evolution news and Views has a good article”

    An “Ulnare” and an “Intermedium” a Wrist Do Not Make: A Response to Carl Zimmer

    IOW Tike has a “wrist” only because it has been deemed a transitional from water to land.

    Which is basically what happened to whales- there have been claims of a femur found in whales. But the claim of a “femur” is just because it is assumed that whales evolved from land animals.

  152. 152

    I’m impressed by how every transitional form produces two new gaps. The more transitional forms, the more gaps between them!

    Also: Joseph, can you explain who claims that “a bone-less fin can evolve into a fin with robust bones”?

  153. 153

    Tiki only has a “wrist” if one redefines the definition of a wrist.

    Evolution news and Views has a good article”

    An “Ulnare” and an “Intermedium” a Wrist Do Not Make: A Response to Carl Zimmer

    IOW Tike has a “wrist” only because it has been deemed a transitional from water to land.

    That’s exactly how it’s supposed to work. The theory of evolution is a hypothesis. It predicts that transitional forms exist. Tiktaalik has features expected of a transitional form. Therefore, it confirms the hypothesis.

    Which is basically what happened to whales- there have been claims of a femur found in whales. But the claim of a “femur” is just because it is assumed that whales evolved from land animals.

    Again, you have it correct, except you need to substitute “it is hypothesized” for “it is assumed.” (Since all assumptions in science are tentative.)

    So, if them bones ain’t femurs, what are they? What does Intelligent Design theory have to say on that issue?

  154. Adel,

    Tiki could just be a mosaic- not a transitional.

    There isn’t any genetic evidence that would demonstrate those changes are even possible.

    As for the bones in whales- they are bones. They certainly do not match any definition of “femur” we currently use.

  155. David Kellogg,

    Until YOU can start producing

    1- That mysterious definition of nested hierarchy tat some few evolutionary scientists use

    AND

    2- Those rigorous definitions that evolutionary scientists use

    Don’t bother asking me anything as it is clear that YOU are beyond reasoning.

  156. 156

    Joseph,

    Thanks for responding to my posts.

    You said,

    Tiki could just be a mosaic- not a transitional.

    It could also be a transitional form. How does Intelligent Design theory help us decide, based on the available evidence?

    There isn’t any genetic evidence that would demonstrate those changes are even possible.

    See Khan #45. To which you replied,

    That is a start but they have a long, long way to go.

    Nevertheless, there is genetic evidence for the possibility of such changes.

    As for the bones in whales- they are bones. They certainly do not match any definition of “femur” we currently use.

    So, you agree that they are bones, but their nature is a mystery to you. Does Intelligent Design theory provide an explanation for why the designer put those bones there?

  157. Adel,

    Intelligent Design is NOT anti-evolution.

    And yes Tiki could be a transitional. But until there is some genetic data that can account for the changes there isn’t any way to test the premise.

    The genetic data that Khan posted is speculative- meaning it needs to be TESTED.

    So if imagination is evidence then there is evidence. However imagination is not evidence.

    As for whales and that bone- it is obvious that you don’t understand ID.

    Oh well, not my problem…

  158. 158

    Thank you, Joseph, for your non-answers to my questions about how Intelligent Design theory explains the evidence.

    As for whales and that bone- it is obvious that you don’t understand ID.

    Evidently, you don’t understand it either.

  159. Joseph,

    Here is a new transitional for you to agonize over.

    Enjoy!

  160. mauka

    Maybe it is, maybe it isn’t. The age of the fossil has it co-existing with modern seals, so the researchers are forced to say it must be a “living fossil”. That puts it in the same category as many other “modern” creatures with some “ancestral” characteristics. I think, before you can call something transitional, you actually have to locate it at the correct time. Maybe both it and modern seals evolved from a different common ancestor.

    Still, even if it is transitional, what of it? ID doesn’t deny that forms evolved, and there obviously has to be a gradation and transitional forms, even in ID. The point is that discoveries like this remain exceptional; evolution has not left the countless numbers and smooth parade of forms that Darwin hoped for. Evolution as observed in the fossil record happens in leaps and bounds. This discovery, though very interesting, does not change that.

  161. SCheesman writes:

    Still, even if it is transitional, what of it? ID doesn’t deny that forms evolved, and there obviously has to be a gradation and transitional forms, even in ID.

    SCheesman,

    You apparently aren’t aware that ID’s “big tent” includes creationists, such as Joseph. That’s why I directed my comment specifically to him.

  162. Adel,

    ID does NOT deal with trivial questions about any specific bone.

    The theory of evolution doesn’t either.

  163. mauka,

    I am not a christian and believe the Bible is nothing more than a collection of stories.

    As for your alleged transitional- it doesn’t cause me any agony because you cannot demonstrate that any amount of mutational accumulation can account for such an organism “evolving” from a purely land animal.

    BTW I was a staunch evolutionist until I started looking more closely at the scientific data while studying to be a zoologist/ marine biologist.

  164. Joseph,

    I didn’t say that you are a Christian. I said that you are a creationist.

    Do you disagree?

  165. Regarding your marine biology studies, I take it your career took a different turn? What happened?

  166. BTW I was a staunch evolutionist until I started looking more closely at the scientific data while studying to be a zoologist/ marine biologist.

    *steps back in amazement*

    Just out of curiosity, Joe, was this for long, and was it at a recognized academic institution?

  167. 167

    Three novel, complex adaptations in arthropods (wings, tracheae, spinnarets) that most likely have a common origin as variations of ancestral gills:

    Changing conditions of life impose new requirements on the morphology and physiology of an organism. One of these changes is the evolutionary transition from aquatic to terrestrial life, leading to adaptations in locomotion, breathing, reproduction, and mechanisms for food capture. We have shown previously that insects’ wings most likely originated from one of the gills of ancestral aquatic arthropods during their transition to life on land [[1]]. Here we investigate the fate of these ancestral gills during the evolution of another major arthropod group, the chelicerates. We examine the expression of two developmental genes, pdm/nubbin and apterous, that participate in the specification of insects’ wings and are expressed in particular crustacean epipods/gills. In the horseshoe crab, a primitively aquatic chelicerate, pdm/nubbin is specifically expressed in opisthosomal appendages that give rise to respiratory organs called book gills. In spiders (terrestrial chelicerates), pdm/nubbin and apterous are expressed in successive segmental primordia that give rise to book lungs, lateral tubular tracheae, and spinnerets, novel structures that are used by spiders to breathe on land and to spin their webs [[2]]. Combined with morphological and paleonntological evidence [[3 9]], these observations suggest that fundamentally different new organs (wings, air-breathing organs, and spinnerets) evolved from the same ancestral structure (gills) in parallel instances of terrestrialization.

    Damen WGM, T Saridaki & M Averof (2002). Diverse adaptations of an ancestral gill: a common evolutionary origin for wings, breathing organs,and spinnarets. Current Biology 12:1711-1716

  168. Define creationist.

    Ya see I think the living organisms on this planet were brought here as a colony- or several colonies.

    Why did I leave biology?

    Once I figured out the the theory of evolution was BS, I started challenging my professors only to learn that they only cared about defending the orthodoxy.

    I went to school to learn not to be indoctrinated.

    So I returned to my number one passion of electronic technology & electricty.

    Engineering is far more challenging and rewarding than being a research scientist- and yes I have done both.

    And I got to travel the world- every continent except Antartica and Austrailia- more countries than we have states.

  169. Alan Fox:

    Just out of curiosity, Joe, was this for long, and was it at a recognized academic institution?

    Was what for long?

    And I doubt you would recognize any academic institution of higher learning.

  170. SCheesman says:

    “Still, even if it is transitional, what of it? ID doesn’t deny that forms evolved, and there obviously has to be a gradation and transitional forms, even in ID.”

    Why do there have to be “gradation and transitional forms even in I.D.”?

    I wouldn’t expect such things if designers were designing life. You could have 100,000 planets with designed life, and there’s no reason why there should be any appearance of transition in form or nested hierarchies.

    The only possibility of design on this planet seems to involve designers who are deliberately trying to give the impression that naturalistic evolution is responsible. There is no reason to design on an evolutionary timescale and within the parameters of evolutionary possibility.

    If we have designers, they’re certainly weird, and appear to be trying to conceal their presence.

  171. Engineering is far more challenging and rewarding than being a research scientist- and yes I have done both.

    Well, I for one had no idea you had any formal training in biology. And yet you were a research scientist.

    Wow!

    Any published stuff?

  172. Could a fossil-like otter be a fossilized otter?

    Yes it could, especially seeing that there isn’t any genetic data that would demonstrate a leg could “evolve” into a flipper.

  173. iconofid:

    The only possibility of design on this planet seems to involve designers who are deliberately trying to give the impression that naturalistic evolution is responsible.

    There isn’t any evidence that naturalistic evolution can do anything other than slight, oscillating variations.

    If we have designers, they’re certainly weird, and appear to be trying to conceal their presence.

    Only to people like you who don’t have a clue.

    Ya see IF you could support your position ID would go away.

    But you cannot and that is why ID is here to stay.

  174. Alan Fox:

    Just out of curiosity, Joe, was this for long, and was it at a recognized academic institution?

    Was what for long?

    The time you spent studying to be a marine biologist.

    And I doubt you would recognize any academic institution of higher learning.

    But I could write to them asking they improve their teaching on nested hierarchies.

  175. Alan,

    Ypu don’t know anything about nested hierarchies.

    So what coulod you write?

  176. Ah c’mon Joe, tell me where you studied marine biology and I’ll tell you about nested hierarchies.

  177. Alan,

    YOU cannot tell anyone anything about nested hierarchies because you don’t know anything about them.

    And if you want to know about me then meet me and I will tell all.

  178. In the meantime,

    Where did you study marine biology?

  179. There isn’t any evidence that naturalistic evolution can do anything other than slight, oscillating variations.

    Really? Which of your ancestors have you “oscillated” back into?

    Actually, nature produces constant novelty, unique creatures with unique genomes.

    As for evidence of definitely non-oscillating change, why don’t you try “gene duplication novelty” on google scholar, and have a look around?

    Only to people like you who don’t have a clue.

    Ya see IF you could support your position ID would go away.

    I.D. doesn’t go away for the same reason that young earth creationism doesn’t go away. Desire does not recognise evidence.

    “But you cannot and that is why ID is here to stay.”

    But where is I.D.? Sweeping the scientific world and replacing methodological naturalism? Or just attacking education systems, mainly in the U.S.?

    Aren’t you aware that people criticise I.D. in relation to its possible effects on public understanding of science, not because of any effects on science itself?

  180. Sorry, italicised quotes above from “Joseph”.

  181. Alan I have been all over the world- France included.

    I have spent quite a bit of time in Central and South America.

    IOW I would bet I have been exposed to more cultures and values (as if you have any) than you have.

  182. iconofid:

    Actually, nature produces constant novelty, unique creatures with unique genomes.

    In your dreams.

    As for evidence of definitely non-oscillating change, why don’t you try “gene duplication novelty” on google scholar, and have a look around?

    Been there done that and found nothing tat would indicate that A) gene duplications are random events and B) that they do what you think they do.

    And it is very telling that YOU cannot produce ANY evidence to support your position.

    None, nada, zip, zilch, zero.

    All you have is minor oscillating variations as seen in the beak of the finch, the peppered moth, anti-biotic resistance and every other example of “evolution”.

    As for science I doubt you even know what tat is…

  183. iconofid,

    What part of transcription and translation- complete with proof-reading, error-correction and editing, strikes you as being cobbled together via an acumulation of genetic accidents?

    And

    How can we test the premise that a bacterial flagellum, for example, arose from a population that never had one via an acumulation of genetic accidents?

    The point is that YOUR position doesn’t have anything to offer besides “it evolved”.

  184. Joseph says:

    “In your dreams.”

    You don’t agree that you have a unique genome? Then I repeat, which of your ancestors have you oscillated into?

    “Been there done that and found nothing tat would indicate that A) gene duplications are random events and B) that they do what you think they do.”

    Really? In reference to A, what did you find out about how gene duplications happen? And which of these processes would you perceive as being non-random?

    And it is very telling that YOU cannot produce ANY evidence to support your position.

    My position that gene duplications can produce novelty?

    You asserted that “There isn’t any evidence that naturalistic evolution can do anything other than slight, oscillating variations.”

    I pointed you to the literature, and you assert that there’s no evidence that gene duplications can do “what I think they can do”.

    Is this position (that there’s no evidence that gene duplications can produce novelty) one that all I.D. supporters hold?

    In the post after the one I’m replying to, you seem to want to change the subject. I’d be happy to address the points you’re raising there, but after we’ve finished with this subject.

    So, I want a strong commitment before I discuss specific research. Is it the I.D. position that there’s no evidence that gene duplication can produce novelty?

  185. Alan I have been all over the world- France included.

    I have spent quite a bit of time in Central and South America.

    IOW I would bet I have been exposed to more cultures and values (as if you have any) than you have.>/blockquote>

    That’s nice.

    BTW, you overlooked to mention where you studied marine biology.

  186. Oops!

    Messed up tags.

  187. iconofid,

    What literature demonstrates that gene duplication can produce new body plans complete with new body parts and protein machinery?

    What litertaure demonstrates that mutation and selection can produce something more than slight oscillating variations?

  188. iconofid,

    What part of transcription and translation- complete with proof-reading, error-correction and editing, strikes you as being cobbled together via an acumulation of genetic accidents?

    And

    How can we test the premise that a bacterial flagellum, for example, arose from a population that never had one via an acumulation of genetic accidents?

    I need a strong commitment before I discuss anything else with you.

  189. iconofid:

    Is it the I.D. position that there’s no evidence that gene duplication can produce novelty?

    It is not.

    It is the position of ID that not all mutations are random. And perhaps the ONLY mutations that are random are point mutations that occur as copying errors.

    IDist understand that with a duplicated gene that new gene also requires a binding site.

    And even then all that could be hoped for is another transcription of an already existing component.

    So you would have this extra protein floating around ready to get in the way of the existing system.

    So if a gene duplication leads to novelty I would say we should take a closer look because it may be directed by some underlying program.

  190. Joseph writes :

    It is the position of ID that not all mutations are random. And perhaps the ONLY mutations that are random are point mutations that occur as copying errors.

    Gene duplication is the result of unequal crossing over. There is no evidence suggesting unequal crossing over is anything other than random with regard to fitness.

    IDist understand that with a duplicated gene that new gene also requires a binding site.

    This is trivially true. Not all unequal crossing over events result in gene duplications—only those that involve the promoters will result in genes that can be immediately transcribed.. Further recombination, however, can result in the cobbling together of new genes from non-transcribable fragments produced by unequal crossing over and promoter sequence fragments.

    And even then all that could be hoped for is another transcription of an already existing component.
    So you would have this extra protein floating around ready to get in the way of the existing system.

    It’s not the duplication itself that leads to novelty, but subsequent mutation to the copy resulting in neofunctionalization or escape from adaptive conflict. Neofunctionalization is discussed in this paper:

    Lynch M, M O’Hely, B Walsh & A Force (2001). The probability of preservation of a newly arisen gene duplicate. Genetics 159(4): 1789- 1804

    Escape from adaptive conflict is discussed here:

    Des Marais DL & MD Rausher (2008). Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454: 762-765

    From the abstract:

    Gene duplications have been recognized as an important source of evolutionary innovation and adaptation since at least Haldane1, and their varying fates may partly explain the vast disparity in observed genome sizes2. The expected fates of most gene duplications involve primarily non-adaptive substitutions leading to either non-functionalization of one duplicate copy or subfunctionalization3, neither of which yields novel function. A significant evolutionary problem is thus elucidating the mechanisms of adaptive evolutionary change leading to evolutionary novelty. Currently, the most widely recognized adaptive process involving gene duplication is neo-functionalization (NEO-F), in which one copy undergoes directional selection to perform a novel function after duplication4. An alternative, but understudied, adaptive fate that has been proposed is escape from adaptive conflict (EAC), in which a single-copy gene is selected to perform a novel function while maintaining its ancestral function5, 6. This gene is constrained from improving either novel or ancestral function because of detrimental pleiotropic effects on the other function. After duplication, one copy is free to improve novel function, whereas the other is selected to improve ancestral function. Here we first present two criteria that can be used to distinguish NEO-F from EAC. Using both tests for positive selection and assays of enzyme function, we then demonstrate that adaptive evolutionary change in a duplicated gene of the anthocyanin biosynthetic pathway in morning glories (Ipomoea) is best interpreted as EAC. Finally, we argue that this phenomenon likely occurs more often than has been previously believed and may thus represent an important mechanism in generating evolutionary novelty.

    Joseph concludes:

    So if a gene duplication leads to novelty I would say we should take a closer look because it may be directed by some underlying program.

    Or may just be due to RM& NS.

  191. Dave Wisker:

    Gene duplication is the result of unequal crossing over. There is no evidence suggesting unequal crossing over is anything other than random with regard to fitness.

    IOW our ignorance sez it is random.

    And seeing that variation provides fitness- see the plight of bananas because tey lack variiation- what does one mean by “random with regards to fitness”?

    IDist understand that with a duplicated gene that new gene also requires a binding site.

    This is trivially true.

    Without said binding site the new gene is useless- so it is hardly trivial.

    Perhaps you guys should read “Not By Chance” by Dr Leee Spetner.

    That would help you understand the telic position.

    As studies have shown just to get two specified mutations would take more time than evolution has.

    And even then the change is so subtle that it doesn’t help you.

    But I do understand that all your hopes rest with evo-devo and more magical mystery mutations.

  192. I find it curious that Joseph declined to ever answer Alan’s questions regarding Joseph’s claim to have been a research scientist and to have studied marine biology.

    One has to wonder why that is.

    As for Spetner’s book, I read it some time ago and was not impressed in the least. He dealt only with enzymes and enzyme specificity, as if all proteins are enzymes. Beyond that, it was the usual IDcreationist boilerplate.
    His discussion with Gert Khortof was very enlightening – for one thing, Spetner was forced to admit that information-increasing mutations do in fact occur.

    As studies have shown just to get two specified mutations would take more time than evolution has.

    Well, that is not exactly what ‘studies’ have shown. Seelke – a YEC, not an ID advocate – in his high school-level ‘experiments’ found that you it takes an inordinate amount of time to get two specific sequential mutations. Claiming that this is relevant to evolution is to set up a rather unsophisticated strawman.

    Sorry.

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