Home » Intelligent Design » Responding to Moran – Is “Unguided” Part of Modern Evolutionary Theory?

Responding to Moran – Is “Unguided” Part of Modern Evolutionary Theory?

I am always aghast that in the 21st century people still make the claim that mutations are unguided. This is a hold-over idea from before the discovery of DNA, simply because some mutations were found to occur independently of selection.

However, modern evidence has showed that mutations are actually in large part due to mechanisms geared for adaptive purposes, just like the rest of biology. And, just like hearts have heart attacks, mutation systems can break down, too, and lead to disease. Just like bacteria, we discovered mutations first by noting the ones that were causing disease, but with every closer look we see that these are the exception rather than the rule.

To point to a simple example (and one that is even often used as definitive evidence of the efficacy of random mutations!) let’s look at the somatic hypermutation process in the immune system. When a new bacteria invades the body and causes an infection, the body must generate a new gene. So what does it do? It takes a close-fitting antibody gene and mutates it. Now, first of all, you should notice that the mutations only happen in the correct gene – the antibody gene. That’s 1,200 base pairs out of 3,000,000,000. But that’s not all – it also focuses mutations on the part of the gene that attaches to the antigen, not the part that signals the cell (because otherwise it wouldn’t signal the cell correctly). So, that’s roughly 600 base pairs out of 3,000,000,000. The mutation system is highly selective of the sites that it mutates, skipping over the cell signaling systems and focusing on the part that is specific to the antigen.

So, therefore, in this scenario (which is one of the best-studied), teleology (goal-directedness) accounts for 99.99998% of the specificity of the mutation, and randomness / unguidedness / happenstance accounts for 0.00002% of it. Yet somehow the myth persists that we have good evidence that mutations are random.

For more information on this issue, you might be interested in a UD series I did on the modern synthesis and the video below:

—–

P.S. I originally tried to post this comment on Moran’s blog itself, but was having technical difficulties. So, if it winds up in his moderation queue three or four times under different accounts, I’m sorry, I was just trying to get it posted.

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70 Responses to Responding to Moran – Is “Unguided” Part of Modern Evolutionary Theory?

  1. The Elie Wiesel Foundation for Humanity- Nobel Laureates Iinitiative

    September 9, 2005

    Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.

  2. johnnyb,

    mutations at cause of disease, they are guided?

    sergio

  3. You’re saying that mutation rates vary. Well, yes. We know that. But you’ve shown no evidence that the actual mutations are guided, e.g. that when an organism “needs” a A mutating to a G, it makes this mutation happen.

    BTW, the immune system isn’t a good choice for discussing mutation, as it’s only somatic. Better to chose an example where the DNA gets passed on to the next generation. There are some nice examples, but I’ll let you do the work and find them.

  4. A Gene posted:

    “You’re saying that mutation rates vary. Well, yes. We know that. But you’ve shown no evidence that the actual mutations are guided, e.g. that when an organism “needs” a A mutating to a G, it makes this mutation happen.”

    JohnnyB is easily ghasted.

    It would be very surprising if an organism that is a host to a range of pathogens did not develop an autonomous means of dealing with them within is single generation (organisms without this kind of immunological response are unlikely to survive).

    But where is the teleology? Is JohnnyB arguing that the human immunological system “knows” in advance what biochemical side-step the next infective bacterium is going to present?

    If that is what he means, then he needs to explain the two-way street. To effectively infect a human cell, the bacterium needs to develop the means of side-stepping the host’s existing immunological defences. If it does so, is it imbued with a teleological purpose? If so, what is it and where can we find it?

  5. “You’re saying that mutation rates vary.”

    No, I’m saying that mutations are targeted. Did you read the above? The mutational mechanisms *focus* the mutations on the correct 600 base pairs out of 3,000,000,000.

    “that when an organism “needs” a A mutating to a G, it makes this mutation happen”

    That’s *exactly* what happens. As I said, in this particular case, 99.99998% of the targeting is based on the organism’s need, and 0.00002% of the targeting is haphazard. If one is unable to look at the 99.99998% of the data, and only chooses to look at the 0.00002% of the data that confirms their thesis, I call that willful blindness.

    “the immune system isn’t a good choice for discussing mutation, as it’s only somatic.”

    There are two reasons this is a good choice. First, this is precisely the mutation system that evolutionists use to demonstrate the efficacy of “random mutations”. Therefore, it is a great example in that regard. Second, there is some evidence that even though they are somatic, these changes can get back into the gametes. Blanden and Steele have suggested that somatic mutations can be reverse transcribed back into the germ line. The evidence for this is pretty small at the moment, but not negligible.

    There are other systems which are similar, but for which it is not as easy to see the targeting, such as the SOS system of bacteria, as well as systems which only respond to a much smaller range of issues, such as E. Coli’s responses to the presence of beta glucoside sugars. Thus, it is not a unique situation, but the somatic hypermutation process is uniquely easy to explain to a lay audience.

  6. “If it does so, is it [the bacterial infection process] imbued with a teleological purpose? If so, what is it and where can we find it?”

    Certainly – at the very least for the bacteria. We might at some point find an *ultimate* purpose (which we’ll discuss below), but for the moment, I’m just concentrating on the teleology for the organism itself. I think that’s pretty clear – the teleology (purpose) for the host immune evasion process in bacteria is to infect the host.

    But, to what I think your question was – I also think that the reason we have trouble seeing an ultimate purpose in this is because we are using loaded terms based on outdated ideas of the role of bacteria in the body. “Evasion” and “infection” imply that the bacteria are necessarily doing something bad. However, many human diseases are the result of bacteria having *difficulty* re-infecting the host. Lactose intolerance and even celiac disease have both been linked with the lack of certain strains of bacteria. Celiac is pretty terrible, and I imagine most celiacs would *love* to be “infected” by bifidobacterium if it relieved their issues.

  7. A Gene-

    What, besides our ignorance, demonstrates that all genetic changes are unguided, random, happenstance events?

  8. It is reasonable to propose a Theory that observed changes in living things do not START with a predefined goal. For example: all bears really do NOT want to become whales, but their internal workings are making small changes every day that are gradually turning them into whales, which is why there are so many whales and so very few bears in the 21st century…

    This Theory can of course be flawed. But proposing the Theory, researching facts to support it, and debating the implications of the facts are all normal parts of the game. As is admitting that the Theory does not fit the facts.

    The minor observation that an individual specimen reacts to disease or changes in its environment to survive is not what is generally meant by “guided development”.

    The Theory that there is an External source guiding the overall development of Life in all its variety would explain why individual specimens do not seem to have blueprints embedded in them for changing themselves into something radically different (mice into bats, etc.).

  9. mahuna –

    I’m a bit unclear as to the point you are making. Can you elaborate a little further?

  10. No, I’m saying that mutations are targeted. Did you read the above? The mutational mechanisms *focus* the mutations on the correct 600 base pairs out of 3,000,000,000.

    Are we saying the same thing? The mutation rate in increased in that region.

    “that when an organism “needs” a A mutating to a G, it makes this mutation happen”

    That’s *exactly* what happens.

    Oh, perhaps not. I’m saying that the mutation rate is increased, so there’s a higher chance that the A will mutate, but it could mutate into a T, C or C. Bu you seem to be saying that it will mutate into a G, not a T or C.

  11. JohnnyB said:

    ““Evasion” and “infection” imply that the bacteria are necessarily doing something bad.”

    You may think so, but I certainly don’t.

    Infection and immune responses are survival strategies that, if absent, would likely prevent either the pathogen or the target from surviving to pass on their genes. Note of course that the specific immune response derived from an infection event is not heritable. Unless you are making a case for the ideas of M Lamarck.

    As A Gene pointed out above, several alternative mutational outcomes are possible at any genetic locus, but only one represents a successful immune response. The human immune system has evolved a capability to rapidly shuffle through random mutations in highly variable parts of its antibody genes. Given this ability, we should not be surprised that it eventually hits on the specific mutation that represents success (hint: if it didn’t have this ability, it would probably be dead). No teleology required.

    I must say I like the idea of a teleological bacterium. I thought you were making a joke, but now I see you are serious. Your version of teleology appears to boil down to saying “a particular outcome happened, therefore it must have been intended”. That kind of post-hoc reasoning can be used to justify pretty much any result, which is a polite way of saying it explains nothing.

  12. Whether the Darwinists are being purposely disingenuous to the point that JohnnyB is making I do not know, but if not, it is hard to see how someone could be so blind as to miss the clear point JohnnyB has made.

    The mutational mechanisms *focus* the mutations on the correct 600 base pairs out of 3,000,000,000.

    This clearly is not a truly random mutational process as is required in the theoretical foundation of neo-Darwinism, for a truly random mutational process would have a equal chance of changing any nucleotide in the genome.,,, In fact a few years ago on BioLogos some Darwinists had mistakenly claimed the immune system as proof of ‘evolution in action’. Here are some responses to that mistaken claim:

    Falk’s fallacy – Feb. 2010
    Excerpt: This (the immune system) is one of the most amazing processes ever described.,,, Whatever may be said about it, it is a highly regulated, specified, directed and choreographed process. It is obviously the product of overwhelmingly brilliant design,,,
    http://www.uncommondescent.com.....ks-falacy/

    Response to Kathryn Applegate – Caroline Crocker PhD.- cell biologist and immunologist – October 2010
    Excerpt: Diversity of antibodies generated by B cells is due to deliberate, cell-engineered changes in the DNA sequence, not random mutations. In fact, I have never before heard the process whereby functional antibodies are formed (before they encounter antigen) described as mutation. And it is well-known that the appearance of functionality as a result of a mistake-mutation is extremely rare. Of course, after encountering antigen the hypervariable regions of the antibody DNA do undergo somatic hypermutation, but again this is in particular places and is controlled by enzymes.,,,
    http://www.uncommondescent.com.....-biologos/

    Generation of Antibody Diversity is Unlike Darwinian Evolution – microbiologist Don Ewert – November 2010
    Excerpt: The evidence from decades of research reveals a complex network of highly regulated processes of gene expression that leave very little to chance, but permit the generation of receptor diversity without damaging the function of the immunoglobulin protein or doing damage to other sites in the genome.
    http://www.evolutionnews.org/2.....40661.html

    Evolutionists Are Now Saying That Evolution Created an Optimized Evolutionary Process (For Immunity System) – Cornelius Hunter – July 2012
    Excerpt: This type of problem, known as the calculus of variations, is important in many engineering problems.
    It also applies to our immune system. About ten years ago researchers used Pontryagin’s maximum principle—an important concept in engineering control theory involving the calculus of variations—to predict how our immune system works.
    http://darwins-god.blogspot.co.....-that.html

    In fact, neo-Darwinists tried to use the immune system as evidence for evolution in the Dover trial:

    “A Masterful Feat of Courtroom Deception”: Immunologist Donald Ewert on Dover Trial – audio
    http://intelligentdesign.podom.....1_03-08_00

    In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparitive Immunology, where he realized that the papers published were comparative studies that had nothing to do with evolution at all.

    What Does Evolution Have to Do With Immunology? Not Much – April 2011
    http://intelligentdesign.podom.....9_03-07_00

    Of related note: Immunity bacteria are shown to be species specific (Regardless of the surprising result, Darwinists still insist evolution did it.)

    Our Microbes, Ourselves: Billions of Bacteria Within, Essential for Immune Function, Are Ours Alone – ScienceDaily (June 21, 2012)
    Excerpt: Chung repeated the experiment, only this time populating a third group of mice with microbes common to rats. This new group showed the same immune system deficiency as the humanized mice. “I was very surprised to see that,” Chung said. “Naturally, I would have expected more of a half-way response.”
    http://www.sciencedaily.com/re.....130643.htm

    In fact the deception that neo-Darwinists have tried to pull off with the immune system is very similar to the deception they have tried to pull off with evolutionary algorithms. Here is a very informative interview with Dr. Marks on that whole line of reasoning:

    “Darwin or Design” with Dr. Tom Woodward with guest Dr. Robert J. Marks II – video
    http://www.youtube.com/watch?v=Yoj9xo0YsOQ

    And let’s not forget the waves that Dr. Shapiro is making in this area of ‘random mutations’:

    Revisiting the Central Dogma in the 21st Century – James A. Shapiro – 2009
    Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112).
    http://shapiro.bsd.uchicago.ed.....0Dogma.pdf

    A few comments from the ‘non-Darwinian’ evolutionist, James A. Shapiro PhD. Genetics, on ‘random mutation’:

    Shapiro on Random Mutation:
    “What I ask others interested in evolution to give up is the notion of random accidental mutation.”

    -Comment section
    “Establishing that teleological questions are critical will itself take a considerable effort because we need to overcome the long-held but purely philosophical (and illogical) assertion that functional creativity can result from random changes.” – per Huffington Post

  13. A Gene –

    Modulating the mutation rate is usually meant to imply simply a global increase or decrease in mutagenesis. My point was that this is highly targeted, not just a global increase or decrease in rate.

    “so there’s a higher chance that the A will mutate, but it could mutate into a T, C or C. ”

    I’m not disagreeing with this at all. This is just the 0.00002% of the targeting that is randomized, as opposed to the 99.99998% that is targeted. Perhaps I need to bump that up to 0.00008% randomized, but I don’t think that affects the discussion much.

  14. “Note of course that the specific immune response derived from an infection event is not heritable. Unless you are making a case for the ideas of M Lamarck.”

    There is some evidence for this. Again, Blanden, Steele, and others have done work on this – not conclusive, but certainly interesting. But that is totally beside the point.

    “As A Gene pointed out above, several alternative mutational outcomes are possible at any genetic locus, but only one represents a successful immune response.”

    True. No argument there.

    “The human immune system has evolved a capability to rapidly shuffle through random mutations in highly variable parts of its antibody genes.”

    Actually, to say that it “has evolved” is merely begging the question, and, without a mechanism attached, is pretty much devoid of content. If you look at the genes for this, they are actually formatted, with formatting codes demarcating the beginning and ending of fragments. So, this formatting code would have had to evolve at multiple locations simultaneously at the exact same time that the RAG genes needed to process these evolved. In other words, for this to work, there would have to be hundreds of coordinated evolutionary events!

    “Given this ability, we should not be surprised that it eventually hits on the specific mutation that represents success”

    Yes, that’s basically the definition of having a guided mechanism.

    “(hint: if it didn’t have this ability, it would probably be dead). No teleology required.”

    Where did you remove the teleology? You simply described the teleology, and then said it wasn’t required. Describing something doesn’t make it stop existing. You certainly haven’t showed how natural selection could have done this.

    “Your version of teleology appears to boil down to saying “a particular outcome happened, therefore it must have been intended”. ”

    Quite the opposite. I am using Aristotle’s method of inferring teleology. If the functioning of a part of an organism has a regularly associated benefit to the organism, this is indicative of teleology. So, for the case of bacteria, we see that of all the places where mutations might occur, they happen much more often in locations that help it invade new hosts and adapt to new energy sources than in the housekeeping genes. This is the essence of teleological mutations.

  15. sergio -

    For a more in-depth discussion of the relationship between teleology and mutations, you might take look at this paper I wrote a few years ago. It separates out mutations into design-consistent mutations and design-inconsistent mutations, and discusses ways of determining the difference between the two.

  16. JohnnyB- Have you read “Not By Chance” by Dr Lee Spetner?

  17. JohhnyB posted:

    “I am using Aristotle’s method of inferring teleology. If the functioning of a part of an organism has a regularly associated benefit to the organism, this is indicative of teleology.”

    How and why is it indicative of intention?

  18. ““I am using Aristotle’s method of inferring teleology…”

    Biologists have done quite a lot of work in the last 2300 years, you might want to catch up…

  19. wd400 posted:

    “Biologists have done quite a lot of work in the last 2300 years, you might want to catch up…”

    So have baraminologists. To no useful purpose.

  20. A little background on the entire concept of ‘randomness’ is worthwhile to consider. When Darwinists use the word ‘random’ in conjunction with Darwinian evolution they mean that the change was,,,

    Unguided or Not? How Do Darwinian Evolutionists Define Their Theory? Casey Luskin – August 2012
    Excerpt: a review of how mainstream biology textbooks define Darwinian evolution reveals it is defined as a “random,” “blind,” “uncaring,” “heartless,” “undirected,” “purposeless,” and “chance” process that acts “without plan” or “any goals,” where we are “not created for any special purpose or as part of any universal design,” and “a god of design and purpose is not necessary.” This is not simply my opinion–this is a review of biology textbook definitions of neo-Darwinian theory.
    http://www.evolutionnews.org/2.....63191.html

    Yet this metaphysical Darwinian claim of completely unguided ‘random’ processes might rightly strike the Theist as ‘begging the question’ since the Theists believes that even these seemingly random events in the universe are ordained by God:

    Jonah 1:7 “Then the sailors said to each other, “Come, let us cast lots to find out who is responsible for this calamity.” They cast lots and the lot fell on Jonah.”

    1 Samuel 14:42 “Saul said, “Cast the lot between me and Jonathan my son.” And Jonathan was taken.”

    Acts 1:26 “26 Then they cast lots, and the lot fell to Matthias; so he was added to the eleven apostles.”

    Proverbs 16:33 “The lot is cast into the lap, but its every decision is from the LORD.”

    And indeed when one looks for the ultimate source of randomness in the universe, the Theist is found to be correct in his presupposition that even the supposedly random events of the universe are ordained of God. To prove this point, usually when someone builds a random number generator for use in computers, one looks to the maximum source of entropy so as to generate the maximum amount of randomness in his Random Number Generator:

    Cryptographically secure pseudorandom number generator
    Excerpt: From an information theoretic point of view, the amount of randomness, the entropy that can be generated is equal to the entropy provided by the system. But sometimes, in practical situations, more random numbers are needed than there is entropy available.
    http://en.wikipedia.org/wiki/C....._generator

    Yet entropy is found to be, by far, the most finely tuned of initial conditions of the beginning of the universe:

    Roger Penrose discusses initial entropy of the universe. – video
    http://www.youtube.com/watch?v=WhGdVMBk6Zo

    The Physics of the Small and Large: What is the Bridge Between Them? Roger Penrose
    Excerpt: “The time-asymmetry is fundamentally connected to with the Second Law of Thermodynamics: indeed, the extraordinarily special nature (to a greater precision than about 1 in 10^10^123, in terms of phase-space volume) can be identified as the “source” of the Second Law (Entropy).”

    How special was the big bang? – Roger Penrose
    Excerpt: This now tells us how precise the Creator’s aim must have been: namely to an accuracy of one part in 10^10^123.
    (from the Emperor’s New Mind, Penrose, pp 339-345 – 1989)

    This number is gargantuan. If this number were written out in its entirety, 1 with 10^123 zeros to the right, it could not be written on a piece of paper the size of the entire visible universe, even if a number were written down on each sub-atomic particle in the entire universe, since the universe only has 10^80 sub-atomic particles in it. Moreover, if the atheist tries to postulate randomness as the cause for such ‘ordered randomness’ at the beginning of the universe, he winds up in epistemological failure:

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    The Absurdity of Inflation, String Theory & The Multiverse – Dr. Bruce Gordon – video
    http://vimeo.com/34468027

    Here is the last power-point slide of the preceding video:

    The End Of Materialism?
    * In the multiverse, anything can happen for no reason at all.
    * In other words, the materialist is forced to believe in random miracles as a explanatory principle.
    * In a Theistic universe, nothing happens without a reason. Miracles are therefore intelligently directed deviations from divinely maintained regularities, and are thus expressions of rational purpose.
    * Scientific materialism is (therefore) epistemologically self defeating: it makes scientific rationality impossible.

  21. In fact, this ‘lack of a guarantee’ that randomness brings to the epistemological enterprise in science, of trusting our perceptions and reasoning in science to be trustworthy in the first place, even extends into evolutionary naturalism itself;

    Should You Trust the Monkey Mind? – Joe Carter
    Excerpt: Evolutionary naturalism assumes that our noetic equipment developed as it did because it had some survival value or reproductive advantage. Unguided evolution does not select for belief except insofar as the belief improves the chances of survival. The truth of a belief is irrelevant, as long as it produces an evolutionary advantage. This equipment could have developed at least four different kinds of belief that are compatible with evolutionary naturalism, none of which necessarily produce true and trustworthy cognitive faculties.
    http://www.firstthings.com/ont.....onkey-mind

    What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video
    http://www.youtube.com/watch?v=5yNg4MJgTFw

    related notes:

    Epistemology – Why Should The Human Mind Even Be Able To Comprehend Reality? – Stephen Meyer – video – (Notes in description)
    http://vimeo.com/32145998

    Why should the human mind be able to comprehend reality so deeply? – referenced article
    https://docs.google.com/document/d/1qGvbg_212biTtvMschSGZ_9kYSqhooRN4OUW_Pw-w0E/edit

    Alan Turing & Kurt Godel – Incompleteness Theorem and Human Intuition – video (notes in video description)
    http://www.metacafe.com/watch/8516356/

    Moreover, The atheist Ludwig Boltzmann’s story on his work on entropy is very interesting to note and is picked up here at the 29:00 minute mark of this following video

    BBC-Dangerous Knowledge
    http://video.google.com/videop.....4649921614

    Yet what is interesting is that Ludwig Boltzmann, being a materialist/atheist, and him thinking that the ‘random probability’ he had worked out for entropy was the be all end all for his work with entropy (since random chance was his creator in his view of reality) failed to search out the universal constant for entropy. Which is something that the Christian Theist, Max Planck, notes the peculiar omission of here:

    Boltzmann equation
    An important equation in statistical mechanics that connects entropy (S) with molecular disorder (W). It can be written:

    S = k log W
    where k is Boltzmann’s constant.

    The Austrian physicist Ludwig Boltzmann first linked entropy and probability in 1877. However, the equation as shown, involving a specific constant, was first written down by Max Planck, the father of quantum mechanics in 1900. In his 1918 Nobel Prize lecture, Planck said: This constant is often referred to as Boltzmann’s constant, although, to my knowledge, Boltzmann himself never introduced it – a peculiar state of affairs, which can be explained by the fact that Boltzmann, as appears from his occasional utterances, never gave thought to the possibility of carrying out an exact measurement of the constant.
    http://www.daviddarling.info/e.....ation.html

    Thus the Christian Theist is right to ask the atheist, as does the following author:

    Evolution and the Illusion of Randomness – Talbott – Fall 2011
    Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.”
    In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.”
    This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?”
    http://www.thenewatlantis.com/.....randomness

    etc.. etc.. etc..

  22. As well, it is interesting to note where the maximum source of entropic randomness in the universe is centralized:

    Thermodynamics – 3.1 Entropy
    Excerpt:
    Entropy – A measure of the amount of randomness or disorder in a system.
    http://www.saskschools.ca/curr.....rgy3_1.htm

    Evolution is a Fact, Just Like Gravity is a Fact! UhOh! – January 2010
    Excerpt: The results of this paper suggest gravity arises as an entropic force, once space and time themselves have emerged.
    http://www.uncommondescent.com.....fact-uhoh/

    Entropy of the Universe – Hugh Ross – May 2010
    Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated.
    http://www.reasons.org/entropy-universe

    “But why was the big bang so precisely organized, whereas the big crunch (or the singularities in black holes) would be expected to be totally chaotic? It would appear that this question can be phrased in terms of the behaviour of the WEYL part of the space-time curvature at space-time singularities. What we appear to find is that there is a constraint WEYL = 0 (or something very like this) at initial space-time singularities-but not at final singularities-and this seems to be what confines the Creator’s choice to this very tiny region of phase space.”
    Roger Penrose – How Special Was The Big Bang?

    further notes:

    Blackholes – The neo-Darwinian ‘god of entropic randomness’ which can create all things (at least according to them)
    https://docs.google.com/document/d/1fxhJEGNeEQ_sn4ngQWmeBt1YuyOs8AQcUrzBRo7wISw/edit

    Is Randomness really the rational alternative to the ‘First Mover’ of Theists?
    https://docs.google.com/document/d/1pSSfbR2QFZ5JAJTOsrEXQDqkJ_6zPTvYNGwcI4YDvRY/edit

    Verse and music:

    Romans 8:18-21
    I consider that our present sufferings are not worth comparing with the glory that will be revealed in us. The creation waits in eager expectation for the sons of God to be revealed. For the creation was subjected to frustration, not by its own choice, but by the will of the one who subjected it, in hope that the creation itself will be liberated from its bondage to decay and brought into the glorious freedom of the children of God.

    Creed – Six Feet
    http://www.youtube.com/v/aQ9Gr.....autoplay=1

  23. wd400:

    Biologists have done quite a lot of work in the last 2300 years, you might want to catch up…

    And they STILL haven’t found any evidence that supports evolutionism.

    How much longer are we going to have to wait before they realize evolutionism is a worthless heuristic?

  24. corrected link:

    Creed – Six Feet – music
    http://www.youtube.com/watch?v=qnkuBUAwfe0

  25. I probably shouldn’t ask this but…

    Joe, what is evolutionism? Do you just meant evolutionary biology?

  26. Evolutionism is the premise that all of life’s diversity owes it collective common ancestry to some unknown populations of prokaryotic-like organisms via accumulations of genetic accidents.

  27. “How and why is it indicative of intention?”

    It is indicative of begin *purposeful*. I don’t mean to claim that the organism itself has intentionality (though it is possible – many microbiologists have been moving in this direction). Think about a machine – its actions are purposeful but not intentional – the machine is merely constructed to bring about its end, but doesn’t know anything about it. In life, since organisms are reproducing, their actions can be viewed as purposeful if they contribute towards their own ends. It is in that specific way that mutational mechanisms were thought of as purposeless by the modern synthesis – they didn’t contribute towards function as an intrinsic part of their operation, but the ones that happened to not cause the organism to die collected to produce design-looking things.

  28. “I am using Aristotle’s method of inferring teleology…”

    Biologists have done quite a lot of work in the last 2300 years, you might want to catch up…

    So what modern method of inferring teleology would you like me to use? First of all, the notion that ongoing research immediately invalidates anything written before the 1850s is simply ludicrous. Good ideas last – if you have a problem with them, you should cite the problem, not the age of the idea. But in any case, this is precisely the notion of teleological that Ernst Mayr uses, for instance. He claims that evolution is a non-teleological process precisely because mutations are not oriented in a way that contribute to the adaptation of the organism. He is wrong on mutations, but his use of criteria of teleology is precisely the same one used by Aristotle.

    But if you want a more modern way of inferring teleology, you can use Active Information, which compares the efficacy of a search process to the likely efficacy of that same search if it did not have intentionality. An overview of the concept is here, and the theoretical reasoning why a more teleological search process cannot be created by a non-teleological one is here.

    Now, if only we had a good way of applying this to biology. Oh wait. We do. It turns out that the hypothesis that mutations are random with respect to function in the somatic hypermutation system is wrong by at least 10 orders of magnitude (22.7 bits). It’s actually more like 66 bits (30 orders of magnitude) because the average number of mutations required for creating a match is 3 (going from memory), and the orders of magnitude are additive for every mutation.

    So, (a) yes, Aristotle’s definition is still in use, and (b) it has been made more rigorous by others, and (c) with the more rigorous definition, we can see just how ludicrous is the idea that the mutational process is haphazard.

  29. Joe –

    No, I haven’t read “Not by Chance”, but I’ve read a lot of Spetner’s online stuff. It’s on my reading list.

  30. Please do yourself a favor by taking it off the list, putting it in your hands and (start) reading it.

    Just sayin’…

  31. Johnnyb,

    This is ridiculous. Evolutionary biology tells us how we can get apparent purpose as an a postori result of selection, without the requirement for goal-seeking by an organism or a designer. Just going from apparent purpose to design is begging the questions

    The somatic mutation system is not directed. That’s like saying the krebs cycle is teleological because it knows it’s going to get sugars at some stage.

  32. wd400 -

    “Evolutionary biology tells us how we can get apparent purpose as an a postori result of selection”

    No it doesn’t. It presents a speculation on this, but the evidence is lacking. There is evidence of *change*, but not evidence of purpose coming as a result of selection. In nearly every case where we have beneficial mutations, what we find are specific mechanisms which generate them. Thus, the idea that these are the a posteriori result of selection is falsified, because as we can see in this particular example, it is the mechanism doing 99.99992% of the work, and mutation/selection doing 0.00008% of the work. It’s important, but it’s a relatively minor part of the process.

    “Just going from apparent purpose to design is begging the questions”

    No, it isn’t. It might, perhaps, not be sufficient for proof, but apparent purpose is in fact direct evidence for design. Begging the question would be that we had no evidence for design, so we just assumed it. But apparent design *is* evidence for design. Darwinism was *thought* to be a defeater for this argument, but as modern mutation experiments show, it fails miserably in that regard, by many orders of magnitude.

    Can you present either (a) direct evidence that haphazard changes coupled with natural selection can produce something? Or (b) can you at least present a model to validate your claim?

    I’ve pointed out experiment and mathematical reasons why fully mechanized processes do not work. Additionally, there are computational reasons as well. In other words, design is required in the causal chain.

    If you would like to propose evidence for your idea, I encourage you to do so!

    “That’s like saying the krebs cycle is teleological because it knows it’s going to get sugars at some stage”

    Again, you are confusing teleology with consciousness. See again my comment about machines. Just to point out, Ernst Mayr would have viewed the Krebs cycle as teleological. He just mistakenly thought that evolution had the power to produce teleological mechanisms from non-teleological ones, which the No Free Lunch theorem and Active Information show mathematically to be a non-starter.

  33. 1. Look up what begging the question means.

    2. The somatic mutations you are talking about are not directed.

    3. You really don’t get the maths if you NFL has anything to say on evolution (although, you’re with Dembski on that one).

  34. OT: JohnnyB, you may appreciate this video:

    Evolution Impossible! – video
    http://www.youtube.com/watch?v=uIae8PPg-fE

  35. wd400:

    Evolutionary biology tells us how we can get apparent purpose as an a postori result of selection, without the requirement for goal-seeking by an organism or a designer.

    That is the evidence-free propaganda, anyway.

  36. JohnnyB posted this:

    “It is indicative of begin *purposeful*. I don’t mean to claim that the organism itself has intentionality (though it is possible – many microbiologists have been moving in this direction).”

    Let us leave aside the question of who these microbiologists are, and what are their published research papers. JohnnyB then posted this:

    “But if you want a more modern way of inferring teleology, you can use Active Information, which compares the efficacy of a search process to the likely efficacy of that same search if it did not have intentionality.”

    Well which is it? Defined as you do it, “purposefulness” is simply an attribute of a system that is apparently “fit to its purpose”, which is precisely what evolutionary biology predicts about systems selected by their environment (system components that reduce an organism’s purposefulness will be selected out, those that increase it will be selected in).

    But then (18 minutes later) you claim to be able to identify “intentionality”, which seems to imply that you think that the agent involved (the actual biological organism) is able to predict (pre-dict before the event) the appropriate system response to a future challenge.

    It is probably just me, but I am confused about what you are actually claiming.

  37. wd400 claims:

    The somatic mutations you are talking about are not directed.

    and yet:

    Response to Edward Max on TalkOrigins Immunity Article
    Donald L. Ewert – PhD. immunologist
    Excerpt: In contrast to neo-Darwinism, the process of introducing un-programmed changes in the DNA during SHM (somatic hypermutatio) is tightly regulated. Unless one is willing to accept that the entire process of evolution was pre-programmed (orthogenesis), as Applegate may, there is no room for teleology in modern evolutionary theory. The fallacy of the argument is that both the computer in Dawkins’s scenario and the process of hypermutation show evidence of a design which permits the mutations to achieve a defined objective. Chance is bounded by the limits of the system in which it operates.

    Furthermore no significant new information is being generated by SHM. The nucleotide changes are limited to replacing amino acids that alter the electric forces between two proteins. The specificity of the antigen receptor must remain unaltered or the B cell would be destroyed by cell-suicide or apoptosis.
    http://www.evolutionnews.org/2.....40661.html

    Thus wd400 you have highly sophisticated machinery of the cell making tightly regulated changes to the DNA, moreover no significant information is created. Thus there are two problems with your claim that the SHM are random (not directed). 1. SHM ARE directed! and 2. Even if they were truly random and undirected mutations in the Darwinian sense (i.e. randomly caused by replication error, radiation, entropic decay, etc.. instead of imposed by the sophisticated machinery of the cell) you still have not demonstrated that what you claim are purely Darwinian processes can generate any non-trivial functional information above that which is already present in the system.

    Notes:

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
    http://www.ncbi.nlm.nih.gov/pubmed/15321723

    Correcting Four Misconceptions about my 2004 Article in JMB — May 4th, 2011 by Douglas Axe
    http://biologicinstitute.org/2.....le-in-jmb/

    ID Scientist Douglas Axe Responds to His Critics – June 2011 – Audio Podcast
    http://intelligentdesign.podom.....9_43-07_00

    Doug Axe Knows His Work Better Than Steve Matheson
    Excerpt: Regardless of how the trials are performed, the answer ends up being at least half of the total number of password possibilities, which is the staggering figure of 10^77 (written out as 100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000). Armed with this calculation, you should be very confident in your skepticism, because a 1 in 10^77 chance of success is, for all practical purposes, no chance of success. My experimentally based estimate of the rarity of functional proteins produced that same figure, making these likewise apparently beyond the reach of chance.
    http://www.evolutionnews.org/2.....35561.html

    Evolution vs. Functional Proteins – Doug Axe – Video
    http://www.metacafe.com/watch/4018222

    Moreover wd400, even if you could explain the origination of a single novel functional protein domain by Darwinian processes, you still have not even scratched the surface of ‘body-plan information’:

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    Dr. Stephen Meyer comments at the end of the preceding video,,,

    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ – Stephen Meyer – (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate – 2009)

    Epigenetics and the “Piano” Metaphor – January 2012
    Excerpt: And this is only the construction of proteins we’re talking about. It leaves out of the picture entirely the higher-level components — tissues, organs, the whole body plan that draws all the lower-level stuff together into a coherent, functioning form. What we should really be talking about is not a lone piano but a vast orchestra under the directing guidance of an unknown conductor fulfilling an artistic vision, organizing and transcending the music of the assembly of individual players.
    http://www.evolutionnews.org/2.....54731.html

    The Mysterious Epigenome. What lies beyond DNA – video
    http://www.youtube.com/watch?v=RpXs8uShFMo

  38. This video may be of ‘random’ interest to some:

    “Random: A Carefully Selected Word” Dr. Michael Behe – video
    http://www.youtube.com/watch?v=x-MuGUVWeFs

  39. BA, that quote doesn’t say the mutations are directed… because they aren’t.

  40. timothya –

    My side note about intentionality was just that – a side note. It is *irrelevant* to this discussion whether or not organisms have intentionality. My definition of purpose was exactly what I had said before – that it was fit to a function.

    Defined as you do it, “purposefulness” is simply an attribute of a system that is apparently “fit to its purpose”, which is precisely what evolutionary biology predicts about systems selected by their environment (system components that reduce an organism’s purposefulness will be selected out, those that increase it will be selected in).

    You are conflating several things – first of all, the purposefulness of the organism and the purposefulness of the evolutionary process. My point was that, contra the modern synthesis, the evolutionary mechanism itself is purposeful. As Larry Moran points out for us, the modern synthesis excludes purpose from the evolutionary process itself.

    The conjecture of many evolutionists is that natural selection allows evolution to create purposeful structures without having a purpose itself. However, the key link that is used to defend this conjecture – that the mutation process is haphazard – is simply incorrect. There are stochastic pieces to it, and some mutations do come in that are haphazard, but mostly it operates purposefully just like the rest of the organism.

    In addition to the experimental evidence that has been pointing against the conjecture that the evolutionary mechanism is haphazard, no evolutionary biologist that I am aware of has proposed a model that would make even the idea that natural selection could produce purposeful mechanisms plausible.

    Prior to natural selection, purposeful mechanism was indicative of design. The only reason why anyone doubted this line of reasoning was because it was thought that Darwin produced a mechanism which could mimic purpose without design. However, now that we see that he hasn’t, then there is no evidence left against the original intuition. Note that it is still true that purposeful mechanisms may have evolved, but, given the nature of the evolutionary process, it is likely that if they evolved, they evolved according to their programmed directions.

  41. JohhnyB posted this:

    “You are conflating several things – first of all, the purposefulness of the organism and the purposefulness of the evolutionary process. My point was that, contra the modern synthesis, the evolutionary mechanism itself is purposeful. As Larry Moran points out for us, the modern synthesis excludes purpose from the evolutionary process itself.”

    I certainly do not conflate the two concepts. Evolution, if true, will select mechanisms that are “purposeful” precisely because those mechanisms improve the fitness of the organism in relation to the environmental challenges it faces. If you want to assign that “purpose” to a pre-existing “intention” then it is up to you to provide the evidence.

    And then posted this:

    “Prior to natural selection, purposeful mechanism was indicative of design.”

    Presumably you mean that people believed this. So what? People in history have believed many things that are now evidently unture. To whit: the authors of the Christian Old Testament.

  42. wd400,that article does say the SHM are ‘tightly regulated’ which permits the mutations to ‘achieve a defined objective’ and ‘Chance is bounded by the limits of the system in which it operates’. Thus despite you assertion that the article does not say that the mutations are directed, the article is very clear that the mutations are ‘tightly regulated’ ‘to ‘achieve a defined objective’. Clearly you are defending a a-priori philosophical commitment to materialism rather than letting the evidence speak for itself. Why???

  43. timothya –

    “Evolution, if true, will select mechanisms that are “purposeful” precisely because those mechanisms improve the fitness of the organism in relation to the environmental challenges it faces.”

    You say it will “select” them, but that assumes they are being generated. How do you know that evolution will generate them? This is precisely my point. For evolution to work, it must generate complex adaptations. Simply saying it will “select” them is silly – of course it will select them. But will it generate them? My contention, and what the evidence indicates, is that to the extent that it generates them, it is generated by predominantly purposeful mechanisms of mutations, not predominantly haphazard ones.

    “Presumably you mean that people believed this. So what? People in history have believed many things that are now evidently unture.”

    But you missed my point. The reasons for thinking it untrue are no longer valid. Until you can re-establish their validity, common, uniform experience tells us that purposeful mechanisms are generally indicative of design.

  44. 44

    Hello Timothya,

    Evolution, if true, will select mechanisms that are “purposeful” precisely because those mechanisms improve the fitness of the organism in relation to the environmental challenges it faces.

    Evolution requires the existence of heritable recorded information, as well as the existence of a mechanism to transfer that information. Recorded information is properly disambiguated as form (i.e. the form of a thing) instantiated in a material medium. As such, it demonstrates material requirements. Our confidence in the existence and validity of these material requirements is supported by both their logical necessity, as well as their direct observation during the transfer.

    These physical requirements include two arrangements of matter; one acting as a representation of form in order to evoke an effect within a system (where the arrangement is necessarily arbitrary to the effect it evokes), and the second arrangement which serves as a transfer protocol (to materially establish the otherwise non-existent relationship between the representation and the effect). These two arrangements of matter form an (empirically and logically validated) irreducibly complex core which is fundamentally required in order to transfer recorded information (i.e. one is entirely useless without the other). These physical requirements also include the dynamic relationship between the two material arrangements just mentioned; that is, neither of them becomes the effect (i.e. the necessarily arbitrary relationship between the representation its material effect is preserved within the transfer by the protocol). Finally, the requirements include the production of unambiguous function in order to be identified (i.e. an arrangement of matter that does not produce a functional effect cannot be validated as ‘containing information’). People can say that such an irreducibly complex system (one that produces every single instance of biofunction observed on Earth) “does not have a purpose”, but then again, people can say anything. They do what profits them.

    Regarding your comment, the long and short of it is this: This system is not the product of evolution because evolution itself requires the system in order to exist. To say that evolution produced this system is to say that a thing that does not yet exist can cause something to happen – which is obviously false.

  45. The post is talking about the location of the mutations – they’re focused to particular places. They aren’t directed in the sense that the changes being made are the ones that are needed, which is what is meant by directed mutation in this thread.

  46. wd400 –

    “The post is talking about the location of the mutations – they’re focused to particular places. They aren’t directed in the sense that the changes being made are the ones that are needed, which is what is meant by directed mutation in this thread.”

    You have missed the point – in the adaptive immune system, the place where the mutations are focused *is* the place where it is needed. They are not only focused on the correct gene, but the correct *half* of the correct gene. In other words, if the mutations were focused merely somewhere else in the same gene, the necessary evolution would not happen.

    Now, if you are simply saying that the mutations are 99.99992% directed rather than 100% directed, then I agree totally. I just have to really wonder about an idea that disregards the 99.99992% and makes grandiose statements about the 0.00008% as if they were the main focus.

  47. No, I get your point, I just think it’s, and this is really something, probably the stupidest argument I’ve ever heard for ID.

  48. BTW, re “the necessary evolution would not happen”, you do know that somatic mutations can’t contribute to evolution… yes?

  49. johnnyb,

    Until you can re-establish their validity, common, uniform experience tells us that purposeful mechanisms are generally indicative of design.

    So HIV is designed is it? It has a purposeful mechanism, wikipedia descirbes it as follows:

    HIV enters macrophages and CD4+ T cells by the adsorption of glycoproteins on its surface to receptors on the target cell followed by fusion of the viral envelope with the cell membrane and the release of the HIV capsid into the cell.[35][36]
    Entry to the cell begins through interaction of the trimeric envelope complex (gp160 spike) and both CD4 and a chemokine receptor (generally either CCR5 or CXCR4, but others are known to interact) on the cell surface.[35][36] gp120 binds to integrin ?4?7 activating LFA-1 the central integrin involved in the establishment of virological synapses, which facilitate efficient cell-to-cell spreading of HIV-1.[37] The gp160 spike contains binding domains for both CD4 and chemokine receptors.[35][36]
    The first step in fusion involves the high-affinity attachment of the CD4 binding domains of gp120 to CD4. Once gp120 is bound with the CD4 protein, the envelope complex undergoes a structural change, exposing the chemokine binding domains of gp120 and allowing them to interact with the target chemokine receptor.[35][36] This allows for a more stable two-pronged attachment, which allows the N-terminal fusion peptide gp41 to penetrate the cell membrane.[35][36] Repeat sequences in gp41, HR1, and HR2 then interact, causing the collapse of the extracellular portion of gp41 into a hairpin. This loop structure brings the virus and cell membranes close together, allowing fusion of the membranes and subsequent entry of the viral capsid.[35][36]
    After HIV has bound to the target cell, the HIV RNA and various enzymes, including reverse transcriptase, integrase, ribonuclease, and protease, are injected into the cell.[35] During the microtubule-based transport to the nucleus, the viral single-strand RNA genome is transcribed into double-strand DNA, which is then integrated into a host chromosome.

    Complex stuff, no? Too complex to have evolved?

    And it’s mutational strategy is to evade the human immune system and so far it’s done a fantastic job. So that strategy is obviously designed, as you show in this thread!

  50. johnnyb

    In other words, if the mutations were focused merely somewhere else in the same gene, the necessary evolution would not happen.

    Um, perhaps at one point they were and that organisms failed, leaving the fitter with the current configuration to survive.

    Otherwise you get into the argument “well, why did the designer make things to infect you in the first place?”, as it seems a bit silly to give you an immune system that can’t cope with 100% of what’s thrown at it (or people would never die of infections or AIDS) and to keep inventing new things (directed mutations in HIVS) to throw at it.

    Not sure I like the sound of your “designer” so much TBH.

  51. JohnnyB posted:

    “You have missed the point – in the adaptive immune system, the place where the mutations are focused *is* the place where it is needed.”

    I have to say that I think this idea is braindead. It should be obvious that if a genome has an ability to hyper-mutate, then that ability will be expressed somewhere in the genome.

    The “where” is irrelevant to explaining why and how it arose. As a minimum, you have to explain why the capability to hyper-mutate inside somatic cells, and thereby generate non-heritable immune responses, is evidence of design. Or more to the point, to demonstrate why this capability cannot arise via natural evolutionary pathways. You haven’t done so, armwaving about Aristotelean “inferences” notwithstanding.

  52. mphillips –

    “So HIV is designed is it? It has a purposeful mechanism, wikipedia descirbes it as follows:”

    I think it is, or at least the descendent of something designed (corrupted design is not problematic to ID, for instance).

    “And it’s mutational strategy is to evade the human immune system and so far it’s done a fantastic job. So that strategy is obviously designed, as you show in this thread!”

    Exactly – glad you are catching on.

    Your more serious point is here:

    In other words, if the mutations were focused merely somewhere else in the same gene, the necessary evolution would not happen.

    Um, perhaps at one point they were and that organisms failed, leaving the fitter with the current configuration to survive.

    But there are 3,000,000,000 base pairs, leaving 3,000,000,000 places to target. Perhaps you could get as small as 5,000,000 (since the target area is 600 base pairs wide – it would at least have to overlap the target region somewhat). In addition, it has to be timed right. In other words, mutating that region at the wrong time leads to failure as well. Finally, it is a conglomeration of multiple genes and introns and even DNA secondary structures that all contribute to this targeting. So, you would need all of these pieces simultaneously. Without them all simultaneously, the whole mechanism would be selected against. This is the problem of incipient structures which was first pointed out by Mivart.

    Otherwise you get into the argument “well, why did the designer make things to infect you in the first place?”, as it seems a bit silly to give you an immune system that can’t cope with 100% of what’s thrown at it (or people would never die of infections or AIDS) and to keep inventing new things (directed mutations in HIVS) to throw at it.

    Here you are getting beyond the bounds of current ID theory. ID can detect the design present in Stonehenge, but can’t tell you why it was built. In addition, it can’t tell you how many designers there are (perhaps HIV and other organisms had different designers?)

    But as a provisional answer, if you are indeed needing one, is that over and over again, most bacteria and viruses that cause disease are either (a) out of place ecologically (in other words, there is an ecological place where they function in a mutualistic situation), or (b) a descendent of an organism that wasn’t disease-causing. In other words, the design is deteriorating.

    So why isn’t the immune system 100%? Perhaps the same reason everything isn’t 100% – because the design is deteriorating. This de-evolution is actually a much more empirically sound version of evolution that the Darwinian evolution which is often proposed.

    As I said, just like hearts have heart attacks, it doesn’t mean that hearts don’t have functions in the organism.

  53. timothya –

    It should be obvious that if a genome has an ability to hyper-mutate, then that ability will be expressed somewhere in the genome.

    The “where” is irrelevant to explaining why and how it arose. As a minimum, you have to explain why the capability to hyper-mutate inside somatic cells, and thereby generate non-heritable immune responses, is evidence of design.

    See my response to mphillips above. Also, the “something had to happen, why not this?” argument is simply ignoring a large part of what we see – that what *did* happen correlates very heavily with function. In fact, you state at the outset that you are going to ignore the data:

    The “where” is irrelevant to explaining why and how it arose.

    The “where” is precisely what is both interesting and useful about the system, yet you think that it should be ignored in explanations of how it arose? I guess Darwinism turns ignoring evidence from an accident into a habit.

  54. wd400:

    Johnnyb,

    This is ridiculous. Evolutionary biology tells us how we can get apparent purpose as an a postori result of selection, without the requirement for goal-seeking by an organism or a designer. Just going from apparent purpose to design is begging the questions

    If organisms are not goal seeking why are you posting here?

    Going from apparent purpose to no purpose is begging the question.

    wd400:

    The somatic mutation system is not directed. That’s like saying the krebs cycle is teleological because it knows it’s going to get sugars at some stage.

    The Krebs cycle is teleological.

    You’re probably mistaken about WHY it is teleological. No surprise there.

  55. wd400:

    Biologists have done quite a lot of work in the last 2300 years, you might want to catch up…

    I’m sure you’ll be able to fill us in on the last 2300 years of progress by biologists.

  56. wd400:

    3. You really don’t get the maths if you NFL has anything to say on evolution.

    Huh?

    In formal terms, there is no free lunch when the probability distribution on problem instances is such that all problem solvers have identically distributed results.

    http://en.wikipedia.org/wiki/N.....timization

  57. wd400 @33:

    2. The somatic mutations you are talking about are not directed.

    This has of course been established via empirical methods which you can cite.

  58. Mung,
    Mutations being directed are the provenience of ID.
    Therefore it would be more relevant were you to show that they are directed, rather then placing the onus on others who are not making that claim. If you are genuinely interested on why it is generally accepted that mutations are random with respect to fitness then there is plenty of reading material out here.

    Furthermore, I would ask you how you would test a set of dice to see if they were “fair”?

    Is there any test that you can perform on the dice that would unequivocally show that they are not being directed?

    In your world, Maus, is there such a thing as a set of provably fair dice?

  59. johnnyb,

    I think it is, or at least the descendent of something designed (corrupted design is not problematic to ID, for instance).

    Why is it that it has to be corrupted design? Is your method of telling “corrupted design” simply that the organism does something which you don’t like?

    Perhaps you could give a few examples of designs that are still as the designer intended them to be and some which are not?

    Finally, it is a conglomeration of multiple genes and introns and even DNA secondary structures that all contribute to this targeting. So, you would need all of these pieces simultaneously. Without them all simultaneously, the whole mechanism would be selected against.

    But this is an argument that HIV is designed in it’s current form. Given the difficulty that evolution has (as has been detailed here over the years) making even the simplest of changes I find it hard to understand from an ID perspective how a harmless organism could acquire the complex molecular machinery to become a deadly virus that can evade the immune system and medical technology.

    (b) a descendent of an organism that wasn’t disease-causing. In other words, the design is deteriorating.

    Not a very good design in the first place was it then? And if that’s really the case then can this rate of deterioration be calculated? How?

    Note that it is still true that purposeful mechanisms may have evolved, but, given the nature of the evolutionary process, it is likely that if they evolved, they evolved according to their programmed directions.

    Why “is it likely”? So you want to have it both ways, even if it can be shown to have evolved then it evolved that way due to programmed directions.

    Given that we have the complete DNA sequences of many organisms now perhaps you could make a start on finding those “programmed directions”?

    Or you could say why you feel these “programmed directions” even exist all all other then to save your version of ID from irrelevance?

    Perhaps the same reason everything isn’t 100% – because the design is deteriorating. This de-evolution is actually a much more empirically sound version of evolution that the Darwinian evolution which is often proposed.

    Then demonstrate it empirically! If we look at the fossil record we don’t see a pattern of deterioration. If we look at a bacteria over many generations we don’t see a pattern of deterioration. The only “pattern of deterioration” we see is the one you invent to explain why HIV etc exists. Other then that, it’s invisible.

    The “where” is precisely what is both interesting and useful about the system, yet you think that it should be ignored in explanations of how it arose? I guess Darwinism turns ignoring evidence from an accident into a habit.

    I quite agree. Please explain the origin of *anything* from an intelligent design perspective without using the phrase “it was designed”.

  60. “Why is it that it has to be corrupted design?”

    It doesn’t have to be corrupted design. It is funny that my every side note of options is being interpreted as a dogmatic statement. Whether or not the design is original or corrupted is not part of ID, at least at the present moment.

    “Perhaps you could give a few examples of designs that are still as the designer intended them to be and some which are not?”

    Again, I could list things that *I* think are corrupted, but that is not part of ID proper. I will refrain from listing them because you have trouble distinguishing between when I am conjecturing and presenting reasoned arguments.

    “But this is an argument that HIV is designed in it’s current form”

    It’s an argument that the mechanism you mention is designed in it’s current form. Also note that one form of corruption is simply being out-of-place. Of course, I shouldn’t say any of this, because you will think that I’m telling you an established ID position.

    “Why “is it likely”? So you want to have it both ways, even if it can be shown to have evolved then it evolved that way due to programmed directions.”

    Which two ways do I want to have it?

    The reason why it is likely is because

    (a) there is no empirical evidence that natural selection acting on random mutations alone can build the sort of structures needed,

    (b) there is theoretical reasons to think that it can’t (see here and here),

    (c) there is empirical evidence to show that interesting mutations do happen as the result of prior information being present in the genome (see this post, and also this book)

    (d) Shannon’s channel capacity theorem, as shown by Yockey, provides a theoretical basis for understanding information transfer over many generations, and why evolution can work if it starts with an information-rich starting point rather than an information-poor starting point.

    Therefore, given the empirical these facts, you see that there are two possibilities – either evolution happens in a very limited fashion, evolution happens in a downward fashion primarily (de-evolution), or evolution happens according to pre-existing information.

    “Then demonstrate it empirically!”

    Oh, goodness. That’s pretty much every experimental and theoretical study on selection. While the beneficial mutation rate is much higher than previously assumed (it was assumed to be lower because the idea of a teleological mutational mechanism never occurred to them), it turns out that selection against slightly deleterious mutations is problematic – it isn’t strong enough to remove them.

    Kondrashov, for instance, points out that deleterious mutations which cannot be selected against represent a range of 4 orders of magnitude! In other words, in any reasonable population genetic scenario, you are going to primarily get de-evolution rather than evolution. To get beyond these results, you would have to propose a mutational system more radically teleological than what I’m suggesting. There’s even a software system that allows you to test this at home.

    “Please explain the origin of *anything* from an intelligent design perspective without using the phrase “it was designed”.”

    Why? Please explain the thermodynamics of *anything* without using terms such as “heat” and “energy”. The point of ID is that agency is a fundamental, not a derived, cause (at least in relation to the other commonly-used fundamental causes).

    However, for a mathematical look at what design is (which might be what you are looking for), see this conference presentation.

  61. mphillips-

    Mutations being undirected are the provenience of the theory of evolution.
    Therefore it would be more relevant were you to show that they are undirected, rather then placing the onus on others who are not making that claim.

    If you are genuinely interested on why it is generally accepted that mutations are random with respect to fitness then there is plenty of reading material out here.

    LoL! They have to random, period. Mutations can be random wrt fitness and still be directed.

    So what do YOU have besides your belligernece towards ID?

  62. Joe,

    Mutations can be random wrt fitness and still be directed.

    Of course. And many other things might be true as well. The point is what you can demonstrate.

    You should, however, be able to understand this:

    http://evolution.berkeley.edu/.....berg.shtml

    In 1952, Esther and Joshua Lederberg determined that many of the mutations for antibiotic resistance existed in the population even before the population was exposed to the antibiotic — and that exposure to the antibiotic did not cause those new resistant mutants to appear.

    So if mutations were indeed “directed” as you claim Joe then the results would have been different. Or perhaps this is just a special case and the designer knew it was an experiment and did not do what it usually does?

  63. johnnyb,

    In other words, in any reasonable population genetic scenario, you are going to primarily get de-evolution rather than evolution.

    So why don’t we see bacteria “de-evolving” over the many thousands of generations we are able to observe them over?

    Where can I see this “devolution” in action, in near-real time? If it’s as ubiquitous as you claim….

  64. Joe,

    Therefore it would be more relevant were you to show that they are undirected, rather then placing the onus on others who are not making that claim.

    The mechanics behind directing every mutation rules out your position as impracticable, if for no other reason. We’d have noticed by now!

    Are you really proposing that “the designer” reaches in and directed every single mutation?

    That’s laughable. I’d suggest you search google scholar for “spontaneous mutations” but then you’d simply reply “there’s nothing there that proves the mutations are not really directed after all” or perhaps “you can’t use what you are trying to explain to explain the origin of the thing you are talking about”. You seem to use those two alot.

  65. The mechanics behind directing every mutation rules out your position as impracticable, if for no other reason.

    Nice strawman.

    Are you really proposing that “the designer” reaches in and directed every single mutation?

    Nope, never said nor implied such a thing.

  66. The point is what you can demonstrate.

    Well it is clear that you cannot demonstrate anything beyiond ignorance and belligerence.

  67. mphillips falsely believes:

    If we look at the fossil record we don’t see a pattern of deterioration. If we look at a bacteria over many generations we don’t see a pattern of deterioration.

    Yet the truth is:

    Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory – Cornelius Hunter – July 2012
    Excerpt: Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time.
    http://darwins-god.blogspot.co.....badly.html

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.”"From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.” University of Chicago paleontologist Mark Webster; article on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.
    http://www.terradaily.com/repo.....s_999.html

    In fact, the loss of morphological traits over time, for all organisms found in the fossil record, was/is so consistent that it was made into a ‘scientific law’:

    Dollo’s law and the death and resurrection of genes:
    Excerpt: “As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo’s law, after its propounder, and is taken as a general statement that evolution is irreversible.”
    http://www.pnas.org/content/91.....l.pdf+html

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    as to ancient bacteria:

    The Paradox of the “Ancient” (250 Million Year Old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland’s work:

    “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
    http://www.physicsforums.com/s.....p?t=281961

    In reply to a personal e-mail from myself, Dr. Cano commented on the ‘Fitness Test’ on the ancient bacteria, I had asked him about:

    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.

  68. ba77,

    a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains.

    Seems to me the opposite. Modern strains have a better or just different diet. Therefore they have evolved.
    Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria.
    In that specific example, perhaps. And so?

    The point is that every human is “infected” by more then 200 strains of bacteria, adults have between 11,000 (forearm) and 1.5 million (scalp) bacteria per square centimeter of skin.

    So if your claim was true, then nobody as told all these bacteria as they seem to be filling their ecological niches quite well indeed.

    If we can have many generations of bacteria how many will have to pass before we notice any sign at all of this inevitable deterioration you claim is happening?

  69. mphillips you claim that there is no evidence of deterioration and yet the fitness test conducted by Dr. Cano showed a loss in ‘fitness. But when shown this evidence you state: “Seems to me the opposite”,,, Perhaps you should take a closer look at exactly what ‘the fitness test’ measures so that your ‘seems to’ misconception can be corrected:

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    As to your quote ,,, ‘filling their ecological niches quite well’,,, nothing like assuming your conclusion into the very question being asked so as to insure you get the answer you want, is there mphillips???

    i.e. Immunity bacteria are shown to be species specific (Regardless of the surprising result, Darwinists still insist evolution did it.)

    Our Microbes, Ourselves: Billions of Bacteria Within, Essential for Immune Function, Are Ours Alone – ScienceDaily (June 21, 2012)
    Excerpt: Chung repeated the experiment, only this time populating a third group of mice with microbes common to rats. This new group showed the same immune system deficiency as the humanized mice. “I was very surprised to see that,” Chung said. “Naturally, I would have expected more of a half-way response.”
    http://www.sciencedaily.com/re.....130643.htm

    As to calculating varying rates of genetic entropy for different forms of life, which I hold large populations of bacteria to be extremely resistant to, you can use this computer program to get a ballpark figure:

    Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load:
    Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space.
    http://bioinformatics.cau.edu......aproof.pdf
    MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE
    http://mendelsaccount.sourceforge.net

    Also of note:

    DNA Degeneration: Top Population Geneticists agree neo-Darwinism is not supported by the data – John Sanford
    http://www.youtube.com/watch?v=tYEkqwOXE5U

    Genetic Entropy – Dr. John Sanford – Evolution vs. Reality – video (Notes in description)
    http://vimeo.com/35088933

    further notes:

    AMBER: THE LOOKING GLASS INTO THE PAST:
    Excerpt: These (fossilized bacteria) cells are actually very similar to present day cyanobacteria. This is not only true for an isolated case but many living genera of cyanobacteria can be linked to fossil cyanobacteria. The detail noted in the fossils of this group gives indication of extreme conservation of morphology, more extreme than in other organisms.
    http://bcb705.blogspot.com/200.....st_23.html

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

  70. mphillips

    Mutations being directed are the provenience of ID.

    Hardly. Are you certain you’re using the word provenience correctly?

    Living organisms are themselves the source of directed mutations. Catch up on the latest science please.

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