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Behe’s Elephant

In Darwin’s Black Box, Michael Behe writes:

Imagine a room in which a body lies crushed, flat as a pancake. A dozen detectives crawl around, examining the floor with magnifying glasses for any clue to the identity of the perpetrator. In the middle of the room, next to the body, stands a large, gray elephant. The detectives carefully avoid bumping into the pachyderm’s legs as they crawl, and never even glance at it. Over time the detectives get frustrated with their lack of progress but resolutely press on, looking even more closely at the floor. You see, textbooks say detectives must “get their man,” so they never even consider elephants.

There is an elephant in the roomful of scientists who are trying to explain the development of life. The elephant is labeled “intelligent design.” To a person who does not feel obliged to restrict his search to unintelligent causes, the straightforward conclusion is that many biochemical systems were designed.

For me, the evidence for design in biology has always seemed so overwhelming, so obvious, that the real question is how so many smart scientists are unable to see the elephant in the room. In Chapter 9 of In the Beginning and Other Essays on Intelligent Design I asked how so many intellectuals could have “lost their minds”:

I think I can explain. 1) When one becomes a scientist, one learns that science can now explain so many previously inexplicable phenomena that one comes to believe that nothing can escape the explanatory power of our science. 2) When one becomes a biologist, or a paleontologist, one discovers many things about the origin of species, such as the long periods involved and the evidence for common descent, that give the impression of natural causes. 3) When one studies history, one may become overwhelmed by the misery and confusion of the human condition, and wonder, why is it so hard to see evidence of the hand of God in human history?

But noticably absent from any list of reasons why intellectuals reject ID is any direct scientific evidence that natural selection of random mutations or any other unintelligent process can actually do intelligent things, like design plants or animals.

So I see three reasons why the elephant in the room, which is so obvious to the unindoctrinated, is ignored by most of our intellectuals, and here is how I would counter each:

  1. Is it possible that this crime could have been committed by an elephant, when all the other crimes the detectives have investigated were committed by humans? Is it possible that we can explain all other phenomena in Nature without invoking design, but we cannot explain the origin and evolution of life without it? Score one point for the other side here, but…of course it is possible, why not? I explained why evolution is so different from other scientific questions that it requires such a different type of explanation, in this video.
  2. Kenneth Miller asked ID advocates to explain why the history of life gives the appearance of evolution, if species were really designed. I answered this with another question in this Evolution News and Views article: “Why does the history of technology give the appearance of evolution, when we know it was the result of intelligent design?” Again, score one point for the other side, but this argument is also not definitive, I gave one possible answer, others are possible.
  3. The presence of evil and misery in our world is an unscientific, but powerful, argument against design. It is unscientific because there is a very simple reply: no one ever claimed that the scientific evidence shows that our designer is good, only intelligent. But it is powerful because neither we nor our critics like this answer. I devoted a chapter in my otherwise scientific book to this objection to design, because it is so powerful, even if it is unscientific. Sometimes my answers there seem convincing, other times they seem naive, even to me. Score 2 points for the other side here, but again their arguments are not definitive.

Despite the above reasons to go after the usual suspects, which seem so powerful to many intellectuals, the evidence implicating the elephant is so overwhelming, so obvious, that the final score is still 1000000 to 4 for the elephant, the way I calculate it.

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61 Responses to Behe’s Elephant

  1. When one is a committed anti-theist, confirmation bias takes care of the rest. All evidence that supports your view is accepted; all evidence that contradicts your view is dismissed. Even the obvious can be denied, if that is the will of the individual.

  2. G.Sewell, only three books left in stock at Amazon. After my visit it is down to two.
    The treatment of your Applied Mathematics Letters paper is an outrage!

  3. It is surprising that argument #2 is not seen more often from the ID side — any biological evolutionary phenomenon for which there is analogous phenomenon in cultural or technological evolutions cannot be used as proof of “randomness” as a mechanism of evolutionary innovation since in the latter instances, randomness is at most a trigger for intelligent creative processes of human designers.

    This argument is especially applicable to microevolution which is largely conceded by ID to be “explained” by “random mutation” (RM) and natural selection (NS), e.g. in antibiotic resistance. Microevolution is quite common phenomenon in evolution of technologies (e.g. service packs, minor tweaks & fixes between the major versions). For example, the ‘antibiotic resistance’ analogue can be easily observed in software malware, which quickly adapts and becomes resilient to the latest anti-malware measures.

    With the bottom-up approaches to intelligent agency, such as Planckian networks (intro post), the designer, the blueprints and the product are all inside the product (like driver inside the car).

    Hence the failure to observe some giant hand coming down fom heavens (i.e. a supernatural phenomenon) to adjust the DNA molecules no more implies the evolutionary novelty was produced by “random mutations”, than the similar absence of heavenly intervention/supernatural implies the randomness as a source of novelty in evolution of technologies.

    For some reason, both neo-Darwinians and ID supporters go along with such unwarranted leap — if something is observed in the lab (e.g. some case of micro-evolution) and no heavenly/supernatural intervention was observed, then they both leap to the conclusion that novelty was produced by random rearrangements of the DNA (random mutation).

  4. nightlight:

    For some reason, both neo-Darwinians and ID supporters go along with such unwarranted leap — if something is observed in the lab (e.g. some case of micro-evolution) and no heavenly/supernatural intervention was observed, then they both leap to the conclusion that novelty was produced by random rearrangements of the DNA (random mutation).

    Maybe some ID supporters do. Definitely not all. My positioon is that if living organisms were designed then they were designed to evolve and evolved by design.

    Then there is “Not By Chance”, which came out in 1997. And one of the UD authors- johnnyb I think- that also has posted about non-random evolution.

    And even James Shapiro’s “natural genetic engineering” is against random rearrangements.

  5. 5
    Granville Sewell

    (Nightlight) We even routinely use the term “evolution” to describe the development of aircraft or operating systems, say. Thus I could say I believe mankind “evolved” from lower animals, in the same sense that Windows 8 evolved from Windows 95 (or whatever went before that, can’t remember back any further!). “Evolution” does not necessarily imply the absense of design, even in common usage. And the similarities between the “evolution” of life and the evolution of technology go even further than that, as pointed out in the above link.

  6. Kenneth Miller asked ID advocates to explain why the history of life gives the appearance of evolution, if species were really designed.

    Today’s species were not really designed. Today’s species are the result of many generations of genetic entropy. They are evolved versions of the original designs.

    The presence of evil and misery in our world is an unscientific, but powerful, argument against design.

    Not if the purpose of the design of the universe was for discovery. Misery, evil and breakdowns all drive us to learn so we can understand and maybe correct some things. The imperfections in our universe give us reason to explore.

  7. nightlight and Joe, regarding the comment Joe quotes @4:

    I think it is true that in the past many evolutionary critics, including ID supporters, have been willing to concede that (i) there is evidence for microevolutionary changes, (ii) some of these are adequately explained by random mutations, and (iii) possibly many, if not all, of them may be explained by random mutations.

    This was a reasonable position to take, both because it was largely consistent with the evidence at the time, and because conceding (iii) does not interfere with the real question of ID, which relates to the origin of complex specified information.

    The fact that (iii) is becoming less clear in many cases, in that we are learning that many previously-thought “random” mutations are actually directed or at least under the higher control of a “mutation” system, certainly should allow opponents of evolutionary theory to take a stronger stance, but it probably can’t fundamentally affect the structure of the argument.

    It is still the case that many microevolutionary events are observed and it is still the case that some of them can occur through random natural processes. Specific disputes could be raised in particular instances, but battling about how many, what percentage and so forth — while an important nuance and a meaningful discussion in its own right — does not change the overall engagement. The primary battle to be waged still lies with the macroevolutionary events and the infusion of large amounts of information into the biosphere.

  8. 8
    Granville Sewell

    Joe,

    Not if the purpose of the design of the universe was for discovery. Misery, evil and breakdowns all drive us to learn so we can understand and maybe correct some things. The imperfections in our universe give us reason to explore

    Your conclusions are pretty similar to mine, in the book chapter (Epilogue) I referred to.

  9. Dr. Sewell:

    Thanks, as always, for your post.

    However, I’m having a hard time seeing any “points scored by the other side” in anything you wrote. All the things you listed as objections to design are readily dealt with, manifesting that the objectors’ attempts have missed the mark, gone into foul territory, ended wide of the goal, been stopped at the 1-yard line, bounced off the rim . . . To the objective arbiter watching from the sidelines, no points have been scored, only a myriad of errant attempts made.

    This one in particular, which has been addressed in detail so many times in the past (including by you):

    The presence of evil and misery in our world is an unscientific, but powerful, argument against design.

    It is not a powerful argument. It is a naive, philosophically-motivated, and poorly-thought-through argument. It is a terrible argument.

    I suppose it may be “powerful” in the sense of swaying lots of people, in the sense of appearing convincing to those who have only superficially thought through the issues or who come to the table with deep a priori religious or philosophical biases.

    But it is not powerful in any rational or logical sense.

  10. 10
    Granville Sewell

    Eric,
    I did mean, as you said, that it is powerful in the sense of swaying lots of people. It is primarily an emotional argument, but a very powerful emotional argument.

  11. Another unfortunate event that has shaped the biased attitudes towards ID of modern thinkers is the confusion of the methods of science with the concept of what reality is. It is in this light that men of faith and science ( Newton, Pascal, Planck ) practiced science and believed in God.

    A. By the mere fact that scientific experiments insist on reproducibly, the practice of the scientific method must assume methodological naturalism.

    What should be understood by all, ( and is ignored by fools ), is that point A is a statement about the limitations of science. It has no bearing about what the reality looks like. The questions that science can not answer are simply the question that science can not answer.

    People who do not see science as a tool of humanity, but instead have made it their god, unfortunately must insist on a reality which is limited to the small portions of reality that can be investigated by science. No wonder they reject the true and living God.

  12. About argument #3:
    “If you think of this world as a place intended simply for our happiness, you find it quite intolerable: think of it as a place of training and correction and it’s not so bad.”
    CS Lewis, God in the Dock, page 52

  13. #5 Granville Sewell: “Evolution” does not necessarily imply the absence of design, even in common usage. And the similarities between the “evolution” of life and the evolution of technology go even further than that, as pointed out in my link.

    That’s a very powerful argument and it’s a pity that it is not often used by the ID side to counter noe-Darwinian claims such as, that microevolution observed in the lab (or even in nature) is result of “random mutation” + NS, especially when that is allegedly “proven” via reverse engineering in the lab of the DNA changes behind the phenotypic adaptations.

    I think the underlying reason that substantial fraction of ID side routinely concedes RM+NS as sufficient mechanism behind such lab observed microevolution is that they, along with neo-Darwinians, imagine that somehow any actions of intelligent agency must come from heavens, as it were, and since lab observations failed to detect any such heavenly (‘supernatural’) intervention, and have even uncovered molecular basis behind phenotypic effects, then they concede defeat and accept the gratuitous “randomness” claims by the neo-Darwinians which doesn’t follow from any such observations.

    While one may still temporarily cling on the non-observation of ‘macro-evolution’ or of ‘origin of life’, that’s a very fragile position to hold in case the intelligent agency is acting from inside (like driver controlling the car from inside), rather than coming down to intervene from heavens (supernaturally). It’s only a matter of time before a live organism is synthesized from scratch in the lab, and what then? The origin of life will be conceded, and this faction of ID will have to retreat to its last castle, the fine tuning of the physical constants (which may not last too long either). In other words, such position of expecting heavenly interventions such as violations of laws of physics, is a recipe for defeat.

    Fundamental laws of physics (quantum theory) are statistical, e.g. like statistical laws or regularities of traffic flows, that still leave plenty of room for intelligent control of each car by the driver from inside without any violation of the coarse grained statistical laws of the traffic flows. Hence, there is plenty of room for intelligent action which doesn’t require any violation of the statistical laws of fundamental physics.

    However, if one takes a more coherent (principled) view and assumes that intelligent agency that created universe and life in all its forms is active at all times, from within every particle and up, continuously upholding their very existence and all their behaviors, then one would challenge neo-Darwinian claim of “randomness” as generator of novelties the same way one would challenge it in evolution of technologies.

    Just because the gigantic hand didn’t come down through the ceiling of the lab to tweak the E. Coli DNA in the famous 1988 Cairns’ experiments, that doesn’t mean that the same intelligence behind life didn’t actually figure out very quickly how to design and build an efficient cellular lactase factory via suitable DNA modifications out of the materials given in the experiment (E. Coli on a lactase substratum).

    The only way to distinguish “random” vs non-random (intelligent) generator of novelty would be to probabilistically model event space, enumerate all possible alternate DNA configurations consistent with the laws of physics & chemistry (under given initial & boundary conditions), compute their probabilities, them compute the odds of given number of bacteria in a given time randomly picking out the correct one which yields that E. Coli lactase factory (as illustrated in this dice calculation example).

    Since such odds calculations (quantum theory of molecules) are out of question at present for any large molecule such as DNA, one should reject neo-Darwinian attribution of novelty to random mutation, even if they show exact DNA change that occurred.

    Accepting these claims based on such observations would be like accepting fairness claim in that dice example as soon as someone shows what the obtained dice pattern is (such as getting triple one in 10 or fewer tries). Just seeing 3 dice come out with 3 ones, without anyone reaching down and turning them around by hand, doesn’t imply the dice tosses were fair (“random”).

    Yet, in microevolution observed in the lab, such as evolution of bacterial resistance or new metabolic pathways, neo-Darwinians get away with such “randomness” claims without almost any opposition from the ID side, especially when the exact DNA changes were uncovered.

    In short, biological evolution (micro and macro) is the best ally of ID (better even than the Behe’s irreducible complexity or Dembski’s CSI), not the enemy as commonly perceived, since updating and improving existent designs takes lot more intelligence then producing single version one of a product and then running out of creative juices. The evolution of technology analogy illustrates this perfectly — the smarter the company the quicker and better it will keep up with the market by evolving new designs.

  14. 14
    Chance Ratcliff

    nightlight @13,

    #5 Granville Sewell: “Evolution” does not necessarily imply the absence of design, even in common usage. And the similarities between the “evolution” of life and the evolution of technology go even further than that, as pointed out in my link.

    That’s a very powerful argument and it’s a pity that it is not often used by the ID side to counter noe-Darwinian claims such as, that microevolution observed in the lab (or even in nature) is result of “random mutation” + NS, especially when that is allegedly “proven” via reverse engineering in the lab of the DNA changes behind the phenotypic adaptations.

    A few points. First, ID is not incompatible with common descent or change-over-time evolution. This should be clear to anyone familiar with ID. Second, ID specifically takes issue with the RM+NS mechanism for producing formal novelty of sufficient complexity. However, it does not rule out the potential influence of random mutations in principle, nor should it. Third, ID does *not concede* that any changes which occur, in the lab or outside it, are the necessary result of random mutations.

    I think the underlying reason that substantial fraction of ID side routinely concedes RM+NS as sufficient mechanism behind such lab observed microevolution is that they, along with neo-Darwinians, imagine that somehow any actions of intelligent agency must come from heavens, as it were, and since lab observations failed to detect any such heavenly (‘supernatural’) intervention, and have even uncovered molecular basis behind phenotypic effects, then they concede defeat and accept the gratuitous “randomness” claims by the neo-Darwinians which doesn’t follow from any such observations.

    ID is about design detection, not supernatural causation.

    While one may still temporarily cling on the non-observation of ‘macro-evolution’ or of ‘origin of life’, that’s a very fragile position to hold in case the intelligent agency is acting from inside (like driver controlling the car from inside), rather than coming down to intervene from heavens (supernaturally).

    What specifically about ID denies that intelligence might be acting “from the inside”? Who among prominent ID proponent makes any claims about how biological design must be implemented?

    It’s only a matter of time before a live organism is synthesized from scratch in the lab, and what then? The origin of life will be conceded, and this faction of ID will have to retreat to its last castle, the fine tuning of the physical constants (which may not last too long either).

    This is profoundly mistaken. If life is synthesized in the lab it will demonstrate that life is capable of being intelligently designed. This can hardly undercut ID. If instead you mean that we might discover self-organizational properties of matter under specific conditions, it’s a risk worth taking, since all evidence indicates otherwise. In addition, because ID is interested in empirical evidence, it would welcome the actual demonstration of the principle, instead of the uncritical belief that such a self-organizational process must exist.

    In other words, such position of expecting heavenly interventions such as violations of laws of physics, is a recipe for defeat.

    Have you read any books by Meyer, Behe, Dembski, Wells, Denton, etc? If so, it’s a great opportunity to present specifics, and discuss what ID proponents actually say.

  15. Chance @14:

    Good points, particularly your last two.

    Design of life in the lab will demonstrate that life can be designed. It will also eliminate the oft-made, but absurd, objection to ID that because we don’t “know” life can be designed, then we can’t infer it.

    I personally would welcome knowing that life can come about through purely natural processes if it is true. However, such an idea is preposterous the evidence points strongly the other direction.

  16. 16
    Chance Ratcliff

    Eric @15, thanks much. Nightlight should also reference your post #7, which makes similar points eloquently.

    It should also be noted that even if we hypothesize a bottom-up intelligent causal mechanism operating through physical laws to organize matter into biologically relevant configurations, why do we not see such processes in action today? Behe’s The Edge of Evolution looked at changes in malaria and in the populations which it infects and found that, if memory serves, it took 10^20 generations for malaria to stumble upon chloroquine resistance conferred by two substitutions. He did this giving the benefit of the doubt that evolutionary processes have been in operation the whole time; so whether mutation, selection, drift, gene duplication, horizontal gene transfer, etc., all were free to operate in whatever capacity they could to produce chloroquine resistance. Since the result was empirical, we can substitute any putative hypothetical process we want, and still find that it takes malaria about 10^20 generations to develop the trait. If intelligent processes are guiding everything from the bottom up, they don’t appear to be doing much of anything today that isn’t already part of a given organism’s internal configuration. I think it’s likely we’ll find that, for such instances of “evolution” such as the podarcis sicula lizards on Pod Mrcaru (see here) the changes most likely resulted from a reconfiguration of existing genetic material via a signalling process triggered by something like dietary changes. This would be explicable by reference to the organism’s existing configurational makeup, with no need of smuggling information from external sources, whether random accumulations or bottom-up intelligent processes.

  17. 17
    Chance Ratcliff

    I’d like to ask a semi-OT question about random mutations that perhaps somebody would be willing to address or correct me on.

    How likely is it for a truly random mutation to stumble upon a beneficial change more than once? Let’s presume a hypothetical prokaryote with a genome consisting of three-million base pairs. Let’s also stipulate that any site along the genome can be mutated by a replication error with equal probability, that any substitution can be made, and that the error rate is such that a mutation occurs about once every replication, given whatever reasonable replication time one sees fit. Suppose a selective advantage could be introduced by a single substitution mutation conferring antibiotic resistance by modification to a protein binding site. Should we expect that the same replication error could be discovered twice? With a genome that size, there are one-million codons with 64 possibilities each, for a grand total of 64^1,000,000 possible variations. How is it that the same random mutation could occur twice at the same codon? What am I missing? By my assumption of the sequence space, even for a much-smaller genome, we shouldn’t expect to see a single point mutation occur by random twice in the entire age of the universe.

  18. ID makes no judgments about the designer–for all we know, among the “billions and billions” of planets in the universe, there are likely to be some clever aliens who seeded the Earth. If that were indeed true, many of the arguments used by Darwinists would sound silly:

    If superior aliens brought life to Earth . . .

    1. Why are their designs imperfect? After all, I know a perfect design when I see one!

    2. Why is there so much suffering and misery? Not that I cause any myself.

    3. It invalidates Science. Why must you invoke the “Aliens of the Gaps?” By extrapolation, we can easily predict that ALL questions will have terrestrial explanations. We don’t need aliens to explain anything even if they were the designers.

  19. It’s just stumbling change. If it happens to be beneficial then so be it.

    3 million base pairs- that’s a small sample space. So given a large population, I would say it is very likely.

    It’s the lottery- high odds but many players.

  20. Chance @16:

    It should also be noted that even if we hypothesize a bottom-up intelligent causal mechanism operating through physical laws to organize matter into biologically relevant configurations, why do we not see such processes in action today?

    Good point. The typical response is: it takes too long, so we can’t see it in action. Could be. But it might also be that it isn’t happening at all. Another one I’ve heard is that, with respect to OOL at least, because the conditions on earth today are different than on the pre-biotic earth, the newly-formed nascent polymers are quickly eaten up/absorbed/destroyed by all the biotic reactions going on now. Indeed, that was Darwin’s thought too in his “warm little pond” musing. Nevertheless, those “explanations” ring rather hollow and it remains an reasonable question why we don’t see these newly-formed biological systems emerging at least somewhere on occasion.

    This would be explicable by reference to the organism’s existing configurational makeup, with no need of smuggling information from external sources, whether random accumulations or bottom-up intelligent processes.

    I understand your point, but I would argue that in such a situation at least some information has been preprogrammed into the system in order for it to narrow the search space and come up with a workable solution. If it is not something that occurs purely by the force of chemistry and physics, and is not directly guided, then something still has to provide the organism with the ability to narrow the search space to something that can be realistically achieved.

  21. 21
    Chance Ratcliff

    Joe @19, yes 3 million sounds reasonable at first blush, because if a mutation is likely to occur at some codon, then the probability is 1/1,000,000 or 10^-6. Then multiply by 1/64 for the probability of selecting the right codon. That’s only 1/64,000,000 probability. This sounds pretty likely for a replication error to be able to find it twice or more. But that doesn’t square with the calculation for the sequence space of that hypothetical genome, which by my reasoning would be 64^1,000,000. One of those numbers is wrong, and it must be the first one — that probability calculation assumes independent events, and doesn’t cover the search space.

  22. 22
    Chance Ratcliff

    Eric @20,

    “I understand your point, but I would argue that in such a situation at least some information has been preprogrammed into the system in order for it to narrow the search space and come up with a workable solution. If it is not something that occurs purely by the force of chemistry and physics, and is not directly guided, then something still has to provide the organism with the ability to narrow the search space to something that can be realistically achieved.”

    Absolutely, but I’m suggesting that the changes observed in podarcis sicula may not have been some sort of targeted search, but a preprogrammed environmental response that could have been dependent on a preexisting mechanism for such a display of plasticity. I’m not sure we know what causes that sort of rapid morphological change. Is this distinction making sense? Features of the immune system look like targeted searches, but certain displays of phenotypic plasticity might be a little more concrete with regard to cause and effect, I suppose.

  23. Chance @17:

    Suppose a selective advantage could be introduced by a single substitution mutation conferring antibiotic resistance by modification to a protein binding site. Should we expect that the same replication error could be discovered twice? With a genome that size [3M bp], there are one-million codons with 64 possibilities each, for a grand total of 64^1,000,000 possible variations. How is it that the same random mutation could occur twice at the same codon? What am I missing? By my assumption of the sequence space, even for a much-smaller genome, we shouldn’t expect to see a single point mutation occur by random twice in the entire age of the universe.

    I’m not sure I’m following your math. Are you talking about nucleotide substitutions in DNA or amino acid substitutions in proteins? I’ll focus on nucleotide substitutions just for sake of simplicity.

    The mutation rate of an organism like c elegans is around 2.1 x 10^-8 mutations per base per generation. (Incidentally, the human mutation rate is pretty similar. It depends primarily on the age of the father at the time of conception and varying for other factors, but it is a decent working number.)

    If we use a similar mutation rate in your hypothetical organism with 3M bases, the odds of getting a mutation each generation is 0.063 (taking a single DNA strand and ignoring for a moment the complementary DNA strand). Therefore, after 16 generations you will get one mutation. Put another way, if you had 16 individuals in the population, the population would experience one mutation every generation.

    Now we also have to factor in your generation time. C elegans has a generation time of about 4 days. Let’s call it 3.65 days, just to make the math easy. So every year, we go through approximately 100 generations. Thus, following a single individual’s line, we would have about 6.3 mutations/year. Obviously if we are looking at the entire population, the number of mutations in the population would go up commensurately.

    Anyway, I’ll stop there for now as I’m not sure whether your real question relates to:

    (A) the odds of (i) a particular pre-specified mutation occurring, or (ii) any mutation occurring,

    multiplied by

    (B) the odds of the mutation occurring again (i) in a single lineal descent line, or (ii) in the entire population.

  24. 24
    Chance Ratcliff

    Eric @23, thanks for engaging my question. It doesn’t appear as straightforward as I imagined when I wrote it down.

    Let me try and simplify. For a 3 million base pair genome, where a codon is comprised of 3 base pairs, there are 1 million codons. Each codon can be one of sixty-four words. That gives a sequence space of 64^1,000,000 at the codon level, correct? Or am I missing something?

    However I just discovered the error in my reasoning while typing this response. A single mutation doesn’t imply a single sequence, so the probability is indeed 1/64,000,000 in my hypothetical, not 64^-1,000,000 for an entire sequence.

    Joe was correct at #19, it’s not too difficult for a single substitution to be conferred multiple times in a genome of that size in a population of prokaryotes. Thanks to both of you. :)

  25. 25
    Chance Ratcliff

    Joe @19, you are correct sir, my #21 was ill-conceived, and the result of a mental block! ;)

  26. Also, there aren’t really 64 codon-produced words, due to redundancy. 20 + start and stop (if we assume there is truly no difference in the amino acids built under redundancy — probably true, although we haven’t really gotten into the construction details yet or examined all the quantum features in biology).

    But let’s keep it simple and say 22, rather than 64.

  27. 27

    Eric @26, yes indeed, but considering a mutation that effects a single base, such would need to search through far more than 22 combinations to find a specific amino, correct? Depending on the target amino, the target space could be anywhere from two, to six codons out of sixty-four possible words I believe. Regardless, I ended up answering my own question while trying to clarify, becoming aware of the flaw in my reasoning. It was a silly mistake. The probability of a specific point mutation, given one occurs in uniform distribution at the codon level is, I believe, between 2/64 (phenylalanine for instance) and 6/64 (leucine) multiplied by one over the size of the genome in codons. My initial mental collapse wrt post #17 is noted and appreciated. :P

  28. 28
    Chance Ratcliff

    “such would need to search through far more than 22 combinations to find a specific amino, correct?”

    Sorry Eric, I suppose this is overstated.

  29. I have a follow-up question about mutations – nucleotide substitutions in DNA.
    Isn’t it true that even a beneficial mutation isn’t beneficial at all without corresponding epigenetic mechanisms in place? The transcription of the new code has to be regulated. This involves all sorts of mechanisms that have to be finely tuned. Let’s assume that we are talking about a new potentially beneficial protein. It is only beneficial for the cell in the right amount in context with different stages in the cell’s life.

    ‘The essence of cellular life is regulation: The cell controls how much and what kinds of chemicals it makes; when it loses control, it dies’, Michael Behe, Darwin’s black box, p.191.

    So just a beneficial DNA mutation is not enough. There has to be a synchronized change in epigenetic factors as well, otherwise the cell loses control and dies.

  30. A few notes as to ‘beneficial’ mutations. It is now found that proteins are ‘context dependent’, in that the ‘whole’ of the protein structure takes precedence over how the parts of the amino acids are used thus further severely constraining the ‘evolvability’ of proteins.

    (A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics – 2012
    Excerpt (Page 4): The Probabilities Get Worse
    This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.
    http://powertochange.com/wp-co.....Myers_.pdf

    Proteins with cruise control provide new perspective:
    Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.”
    http://www.princeton.edu/main/...../60/95O56/

    Why Proteins Aren’t Easily Recombined, Part 2 – Ann Gauger May 17, 2012
    Excerpt: In other words, even if only 10% of non-matching residues were changed, the resulting hybrid enzyme no longer functioned. Why? Because the substitution of different amino acids into the existing protein structure destabilized the fold, even though those same amino acids worked well in another context. Thus, each protein’s amino acid sequence works as a whole to help generate a proper stable fold, in a context-dependent fashion.
    http://www.evolutionnews.org/2.....59771.html

    “Why Proteins Aren’t Easily Recombined, Part 2″ – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    As well, the ‘beneficial mutations’ that are found to ‘naturally’ occur in protein sequences are found to be ‘designed errors’:

    Cells Defend Themselves from Viruses, Bacteria With Armor of Protein Errors – Nov. 2009
    Excerpt: These “regulated errors” comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed,
    http://www.sciencedaily.com/re.....134701.htm

    Moreover the Genetic Code is also ‘designed’ to resist the harmful effects of mutations:

    DNA – The Genetic Code – Optimal Error Minimization & Parallel Codes – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4491422

    Deciphering Design in the Genetic Code – Fazale Rana
    Excerpt: Sixty-four codons make up the genetic code. Because the genetic code only needs to encode 20 amino acids, some of the codons are redundant. That is, different codons code for the same amino acid. In fact, up to six different codons specify some amino acids. Others are specified by only one codon.,,,
    Genetic code rules incorporate a design that allows the cell to avoid the harmful effects of substitution mutations. For example, six codons encode the amino acid leucine (Leu). If at a particular amino acid position in a polypeptide, Leu is encoded by 5? (pronounced five prime, a marker indicating the beginning of the codon). CUU, substitution mutations in the 3? position from U to C, A, or G produce three new codons, 5? CUC, 5? CUA, and 5? CUG, all of which code for Leu. The net effect produces no change in the amino acid sequence of the polypeptide. For this scenario, the cell successfully avoids the negative effects of a substitution mutation.
    Likewise, a change of C in the 5? position to a U generates a new codon, 5?UUU, that specifies phenylalanine, an amino acid with similar physical and chemical properties to Leu. A change of C to an A or to a G produces codons that code for isoleucine and valine, respectively. These two amino acids also possess chemical and physical properties similar to leucine. Qualitatively, the genetic code appears constructed to minimize errors that result from substitution mutations.,,,
    The genetic code’s error-minimization properties are actually more dramatic than these results indicate. When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution.18 Researchers estimate the existence of 10^18 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of 10^18 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature.
    http://www.reasons.org/biology.....netic-code

    Though the DNA code is found to be optimal from a error minimization standpoint, it is also now found that the fidelity of the genetic code, as to how a specific amino acid is spelled in the sequence, is far greater than had at first been thought:

    Synonymous Codons: Another Gene Expression Regulation Mechanism – September 2010
    Excerpt: There are 64 possible triplet codons in the DNA code, but only 20 amino acids they produce. As one can see, some amino acids can be coded by up to six “synonyms” of triplet codons: e.g., the codes AGA, AGG, CGA, CGC, CGG, and CGU will all yield arginine when translated by the ribosome. If the same amino acid results, what difference could the synonymous codons make? The researchers found that alternate spellings might affect the timing of translation in the ribosome tunnel, and slight delays could influence how the polypeptide begins its folding. This, in turn, might affect what chemical tags get put onto the polypeptide in the post-translational process. In the case of actin, the protein that forms transport highways for muscle and other things, the researchers found that synonymous codons produced very different functional roles for the “isoform” proteins that resulted in non-muscle cells,,, In their conclusion, they repeated, “Whatever the exact mechanism, the discovery of Zhang et al. that synonymous codon changes can so profoundly change the role of a protein adds a new level of complexity to how we interpret the genetic code.”,,,
    http://www.creationsafaris.com.....#20100919a

    Throw on top of all that the multiple mechanisms of DNA repair and perhaps now even Darwinists can start to see the insurmountable problem that this presents to neo-Darwinian evolution:

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.

    Repair mechanisms in DNA include:

    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass

    etc…

  31. Moreover, besides the ‘context dependency’ as to how proteins are constructed from amino acids, it is now found that proteins are also dependent on the specific context of the particular cellular environment that they may be in. Thus, the sheer brick wall that neo-Darwinian processes face in finding ANY novel functional protein in the first place, (Axe; Sauer), to perform any specific single task in a cell, is only exponentially exasperated by the fact that many proteins are multifunctional and, ‘serendipitously’, perform several different ‘context dependent’ tasks within the cell:

    Human Genes: Alternative Splicing (For Proteins) Far More Common Than Thought:
    Excerpt: two different forms of the same protein, known as isoforms, can have different, even completely opposite functions. For example, one protein may activate cell death pathways while its close relative promotes cell survival.
    http://www.sciencedaily.com/re.....134623.htm

    Genes Code For Many Layers of Information – They May Have Just Discovered Another – Cornelius Hunter – January 21, 2013
    Excerpt: “protein multifunctionality is more the rule than the exception.” In fact, “Perhaps all proteins perform many different functions by employing as many different mechanisms.”

    Explaining how a protein can perform multiple roles – Cell Biology – December 18, 2009
    Excerpt: It’s been known for more than a decade that some cell proteins can carry out multiple functions. For example, it was discovered in 1999 that the protein TyrRS (explained shortly) participated not only in the building of enzymes, but also could function to stimulate the growth of blood vessels. Discovering that the same protein could perform very different roles opened one of the great new chapters in molecular biology.
    http://scitechstory.com/2009/1.....ple-roles/

    Moreover, protein-protein interactions and domain-domain interactions for proteins are tentatively found to be very different in different species

    A Top-Down Approach to Infer and Compare Domain-Domain Interactions across Eight Model Organisms
    Excerpt: Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them.,,, Our results show that only 23% of these DDIs are conserved in at least two species and only 3.8% in at least 4 species, indicating a rather low conservation across species.,,,
    http://www.plosone.org/article.....ne.0005096

    Yet, as with functional proteins, protein-protein interactions (domain-domain interactions) between proteins are very hard to achieve by neo-Darwinian processes of mutation and selection:

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    - Michael Behe – The Edge of Evolution – page 146

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.html

    Supplemental notes as ‘top down’ control of proteins:

    Watching a protein as it functions – March 15, 2013
    Excerpt: When it comes to understanding how proteins perform their amazing cellular feats, it is often the case that the more one knows the less one realizes they know. For decades, biochemists and biophysicists have worked to reveal the relationship between protein structural complexity and function, only to discover more complexity.,,,
    A signaling protein usually responds to a messenger or trigger, such as heat or light, by changing its shape, which initiates a regulatory response in the cell. Signaling proteins are all-important to the proper functioning of biological systems,
    http://phys.org/news/2013-03-p.....tions.html

    An Electric Face: A Rendering Worth a Thousand Falsifications – September 2011
    Excerpt: The video suggests that bioelectric signals presage the morphological development of the face. It also, in an instant, gives a peak at the phenomenal processes at work in biology. As the lead researcher said, “It’s a jaw dropper.”
    http://darwins-god.blogspot.co.....usand.html

    The (Electric) Face of a Frog – video
    http://www.youtube.com/watch?v=ndFe5CaDTlI

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

    Quote and music:

    “Too often, we envision the cell as a “factory” containing a fixed complement of “machinery” operating according to “instructions” (or “software” or “blueprints”) contained in the genome and spitting out the “gene products” (proteins) that sustain life.
    Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this “factory,” many if not most of the “machines” are themselves constantly turning over — being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle…is one of the best-known examples, but there are many others.
    Funny sort of “factory” that, with the “machinery” itself popping in and out of existence as needed!,,,”
    - James Barham

    Eric Church – Like Jesus Does (Acoustic)
    http://www.youtube.com/watch?v=wuG1rLPjVkk

  32. Follow-up thoughts on my previous post #29:
    I can see how genetic knock-out experiments – reverse engineering – can be successful. One amino acid is removed (or replaced), but the conforming epigenetic system is left in place!
    So when the DNA code is somehow recovered it will be ‘welcomed’ by the good old fitting epigenetic environment.
    My point is: this will not be the case for new DNA code. New DNA code is like an unconnected part in a car engine. At best meaningless, but likely detrimental.

  33. OT: The Latest Buzz on Bumblebees – April 8, 2013
    Excerpt: We report a formerly unappreciated sensory modality in bumblebees (Bombus terrestris), detection of floral electric fields. These fields act as floral cues, which are affected by the visit of naturally charged bees. Like visual cues, floral electric fields exhibit variations in pattern and structure, which can be discriminated by bumblebees. We also show that such electric field information contributes to the complex array of floral cues that together improve a pollinator’s memory of floral rewards. Because floral electric fields can change within seconds, this sensory modality may facilitate rapid and dynamic communication between flowers and their pollinators.
    http://www.evolutionnews.org/2.....70911.html

  34. Chance, 17

    Personally I am skeptical that any beneficial mutations are truly random. I think they are part of a genomic plasticity system… where certain regions are made more available for alteration in stressed environments.

    There is emerging research on the non-random quality of mutations, particularly those occurring in stressed cells of bacteria. Also, it has been demonstrated that Recombination enzymes can repair DNA perfectly without causing mutations… meaning mutations are not necessarily random errors.. Susan Rosenberg is doing research on this.

    I have put together some more references here when I was researching it awhile back.
    http://www.youtube.com/watch?v=qTChu5vX1VI

  35. 35
    Chance Ratcliff

    lifepsy @34, thanks for that video, very informative. I agree that most beneficial mutations are likely non-random, and plasticity seems to be the source of quite a bit of phenotypic change. It looks to leave neo-Darwinism helpless to account for anything substantial with regard to beneficial changes. It’s been presumed for so long that “evolution” was occurring anytime change was observed, it’ll be interesting to see how long the notion persists that RM+NS is the primary source of phenotypic novelty. By the way, I also watched your video on podarcis sicula a while back, so thanks for putting that together. Interestingly, there’s nothing about podarcis sicula on Wikipedia’s phenotypic plasticity page.

  36. The presence of evil and misery in our world is an unscientific, but powerful, argument against design.

    I don’t see this as a powerful argument at all. We live in a yin-yang reality. There can be no such thing as health without sickness, beauty without ugliness, or happiness without sadness.

    The argument about evil is certainly a religious one. As a Christian, I would say it is illogical for the following reason. Evil is not a physical concept. It is a spiritual entity and, as such, is neither created nor destroyed. It just is. God could not create evil even if he wanted to. Our spirits, good or evil, are our own. They are eternal and transcendental. We cannot blame God for them. God only created the physical body.

  37. 37
    Granville Sewell

    Mapou,
    If you remember that this list was my attempt to explain why so many otherwise intelligent people are unable to see (or pretend to be unable to see) what is so obvious to the rest of us, maybe you will then agree that this item should in fact have been at the top of the list.

  38. Ratcliff @14:

    A few points. First, ID is not incompatible with common descent or change-over-time evolution. This should be clear to anyone familiar with ID.

    True but ID should certainly be incompatible with common descent. It is a mistake to restrict Intelligent Design to design detection. ID should encompass everything about intelligent design. Design is an integral part of human civilization and we can deduce powerful principles from observing what human designers do.

    So why should ID be incompatible with common descent? Because, from what we know about design, the evolution of complex designed objects always follow a mostly nested hierarchy peppered with instances of lateral inheritance. This is what is also observed in living organisms. My understanding is that horizontal inheritance is not evidence for common descent. It is evidence for the intelligent reuse of previous designs.

    As a Christian, it bothers me that Darwinists are claiming that the tree of life was their idea. I beg to differ. The book of Genesis was several millenia ahead of them.

  39. Sewell @37,

    You are probably right but I am not sure that these things are really obvious to the rest of us. This is the reason that they keep popping up everywhere, in my opinion. We need to forcefully put those arguments out to pasture, once and for all.

  40. 40
    Chance Ratcliff

    Mapou @38,

    “So why should ID be incompatible with common descent? Because, from what we know about design, the evolution of complex designed objects always follow a mostly nested hierarchy peppered with instances of lateral inheritance. This is what is also observed in living organisms. My understanding is that horizontal inheritance is not evidence for common descent. It is evidence for the intelligent reuse of previous designs.”

    Interesting thoughts. I agree that what’s termed, convergent evolution, is good evidence for design, but I’m not willing to make the leap that it falsifies common descent. Don’t get me wrong, I don’t think UCD from a “simple” organism occurred, and I wouldn’t be opposed to a methodology which could reliably falsify common descent, but I’m not sure one exists presently. I don’t think that lateral inheritance alone falsifies common descent, because it’s possible to imagine a scenario where both UCD and design are compatible. In other words, they are not mutually exclusive.

  41. Ratcliff:

    I don’t think that lateral inheritance alone falsifies common descent, because it’s possible to imagine a scenario where both UCD and design are compatible. In other words, they are not mutually exclusive.

    Unfortunately, I cannot imagine such a scenario. What do you have in mind?

  42. 42
    Chance Ratcliff

    Mapou, I’ll take a stab at it.

    An engineer builds a single-celled self-replicator and wants a population of around a million, so he will let the creatures replicate for twenty generations. Since we want to track ancestry in the tree, in the genome of each offspring the engineer introduces a mechanism for storing two identifiers, one uniquely for the current offspring and one for its parent’s identifier. This is just a way for introducing an evolutionary component and a way to track ancestry back to the root organism.

    At generation ten he takes two creatures from disparate parts of the tree and adds a new function, let’s say bioluminescence. After ten more generations we have a one-million population master tree with two subtrees consisting of a thousand members each. Both subtrees have the common feature of bioluminescence, but each one traces ancestry from separate parts of the master tree, where neither of their parents have the trait. The engineer could have even taken two specimens from different generations and introduced bioluminescence.

    So in that example there is both universal common descent and convergent evolution by the injection of design in distantly related creatures. Nope, I don’t really buy it either in regards to actual history, but I think it shows that there’s no logical exclusivity between common descent and design where we see a horizontal introduction of features across distantly related specimens.

    If ID can accommodate both front loading and the incremental infusion of information over time, then it’s possible to imagine common descent and common design both being true at the same time. For a front loading scenario, we can imagine a genome loaded with information constituting a developmental program which allows for pre-programmed responses to environmental cues. This would allow for different organisms to develop similar features because of similar stressors or environmental conditions. In an incremental infusion of information scenario, the designer is free to add a heritable feature at any time to a specimen, allowing for similar features in unrelated organisms according to his goals and preferences. In both cases common descent has still occurred.

  43. Ratcliff,

    For some reason, I was under the impression that common descent, as understood by Darwinists, assumes that the entire genetic material that make up every living organism came about via an uninterrupted succession of procreation events. Thus lateral inheritance would violate this rule. But no matter. Intelligent design does not forbid (probably predicts) the creation of parallel descent lines, some of which could have been merged into single lines at an early stage or could have borrowed features laterally via genetic engineering rather than procreation.

    That being said, I think the biggest problem with convergent evolution is that it is just another mediocre so-so story that will not stand the test of time. Similarities in design do not mean much. The (big?) ID hypothesis predicts that huge and complex identical genetic code segments will be found to be identical in distant species, codes that could not possibly have evolved independently. Why? Because, by its very nature, evolution guarantees that no independently evolved genetic code segments of high complexity could be identical in two different species.

    In my opinion, this is the sort of things that ID experimenters should be searching for. A good starting place to look is in the genomes of echo-locating bats and whales. An intelligent designer would certainly reuse tried and tested code rather than reinvent the wheel.

    Not that any of this matters much in the evolution/creation debate because it is not a scientific debate but a political and religious one. Otherwise, Darwinian evolution would be a forgotten folly by now, not even worthy of a footnote in the history of science.

  44. 44

    Mapou @43, not much to disagree with there, and your comments are thought provoking. I’ll offer more thoughts tomorrow.

  45. 45
    Chance Ratcliff

    lifepsy @34,

    I just revisited your video linked in your comment at #34 and I have to say that not only is your choice of material excellent, your commentary is insightful. This is important information, thanks much. I took the time to really listen to your presentation here and it’s quite good. I recommend your video heartily.

  46. I would like to add to Sewell’s reason 1 & 2 that the force of authority comes into play. Scientists are authorities and their adherence to naturalism is hard for students and laymen to brush aside. Whenever self-doubt sets in there is immediately the problem that the vast majority of scientist adhere to naturalism. IOW one has to be self-confident in order to believe one’s own eyes and see the elephant in the room – despite the fact that everyone else (people with more experience and of higher intelligence) assures you the elephant does not exist.
    I can relate to Sewell’s third reason in a slightly different way. Theistic believe has a certain fairy tale quality. For instance many NDE reports have a ‘too good to be true’ ring to it; something so far distanced from good old harsh reality that believing them feels naive. Reconciling heaven and Auschwitz is a real problem indeed.

  47. 47
    Chance Ratcliff

    Mapou, I’m just offering some additional thoughts about the comments in your post #43.

    “For some reason, I was under the impression that common descent, as understood by Darwinists, assumes that the entire genetic material that make up every living organism came about via an uninterrupted succession of procreation events.”

    While Darwinists like to think that common descent implies Darwinian evolution, this is problematic because under this logical relationship, no Darwinian evolution implies no common descent. But clearly this isn’t the case; I think the converse is instead true. While it’s understandably convenient for Darwinists to suggest that we get common descent if and only if Darwinian evolution is true, it falls to us to repeatedly make the distinctions clear. At least some Darwinists don’t make the distinction, as every so often somebody has to remind a Darwinist interlocutor here that common descent doesn’t falsify ID. The same is true with the term “evolution” denoting both micro and macro varieties, and often the prebiotic version as well. ID proponents are constantly needing to untangle the definitions because the equivocation is advantageous to the pro-Darwinian side of the debate.

    “Thus lateral inheritance would violate this rule.”

    Yes indeed, hence the term “convergent evolution” used to label homoplasy. Here’s the google search for homoplasy. Notice the Wikipedia entry that comes up at or near the top. With the events surrounding the lizard species podarcis siclua that I’ve been so fascinated with lately, this phenomenon gets labeled, Rapid Evolution. Just never mind the oxymoron implied in that title! :) Hence, evolution covers violations to its rule quite easily, by appending “evolution” at the end of a word or phrase.

    That being said, I think the biggest problem with convergent evolution is that it is just another mediocre so-so story that will not stand the test of time.

    With regard to the attempt to make exceptions to the rule appear to be confirmations, “convergent evolution” is certainly a just-so story. But it seems we agree that homoplasy itself is very suggestive of design.

    Because, by its very nature, evolution guarantees that no independently evolved genetic code segments of high complexity could be identical in two different species.

    I believe evolutionists would say that an unexpected result, “sheds new light on evolution”. ;)

    In my opinion, this is the sort of things that ID experimenters should be searching for. A good starting place to look is in the genomes of echo-locating bats and whales. An intelligent designer would certainly reuse tried and tested code rather than reinvent the wheel.

    By the way, I think bats and whales echolocation is a documented case of homoplasy. Echolocation in Bats. From the article, ” In any event, echolocation in bats provides some remarkable examples of evolutionary convergence.”

  48. 48

    Mr Sewell makes the best point at the top that evolutionists didn’t and don’t have scientific evidence backing up their claims about evolution.
    It has always been the issue of methodology behind the claims of evidence that evolutionism has slipped under the radar.
    Thats the equation to break the code here.
    a false idea should not be a existing theory where the scientific method is king.
    either there is no evidence for the great claims of evolution or creationists are missing it!
    Therefore is the ‘evidence” evolutionists present actually biological scientific evidence??
    Nope!

  49. “While Darwinists like to think that common descent implies Darwinian evolution, this is problematic because under this logical relationship, no Darwinian evolution implies no common descent. But clearly this isn’t the case; I think the converse is instead true. While it’s understandably convenient for Darwinists to suggest that we get common descent if and only if Darwinian evolution is true, it falls to us to repeatedly make the distinctions clear.”

    If the homonids didn’t descent from Australopithicus, where did the the homonids come from? They just appear fully formed in the fossil record out of thin air while the A.cines just disappear. I know that ID can include common descent but how does ID explain this for those who don’t accept common descent? I know creationism says “poof, there it is”.

  50. 50
    Chance Ratcliff

    “If the homonids didn’t descent from Australopithicus, where did the the homonids come from?”

    Where did life come from, and what observable mechanism gives it the ability to produce novel functionality and form?

    I know creationism says “poof, there it is”.

    Actually that’s what Darwinism says. ;) The magical force that supposedly makes apparent design illusory is completely missing. Design implicates a designer. “Poof” is when you suggest that goal-directed processes arise out of nothing for no particular reason. It’s a non-starter.

  51. Ratcliff @50,

    LOL. I just love the way you turn the table on the false prophets. Darwinists are indeed the real magicians. Amazing how they can so easily accuse others of what they are guilty of.

  52. 52
    Chance Ratcliff

    Mapou @51, :D

  53. Ratcliff is right. Darwinian atheists are the only ones who have a problem with the fossils suddenly appearing in the fossil record as they do.

    Three (or Four) Reasons Everyone Should Read Darwin’s Doubt
    Casey Luskin – April 9, 2013
    http://www.evolutionnews.org/2.....71001.html

    As far as science itself is concerned, the fact that the entire material universe ‘poofed’ into existence from a higher dimension means that there is no known barrier, scientifically speaking, that would prevent anything within this universe from ‘poofing’ into existence from a higher dimension subsequent to that initial ‘poofing’. In fact Eugene Koonin, an evolutionist, tried to appeal to a ‘Many Worlds’ mechanism a few years back to explain at least the Origin of Life:,,,

    The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life – Eugene V Koonin – 2007
    Excerpt: Recent developments in cosmology radically change the conception of the universe as well as the very notions of “probable” and “possible”. The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.
    http://www.ncbi.nlm.nih.gov/pm.....MC1892545/

    The Biological Big Bang model for the major transitions in evolution – Eugene V Koonin – 2007
    Background: “Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life’s history, the principal “types” seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate “grades” or intermediate forms between different types are detectable;
    http://www.biology-direct.com/content/2/1/21

    Biological Big Bangs – Origin Of Life and Cambrian – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4284466

    The trouble of “Many Worlds” for Koonin is that #1 there is no evidence for it/them, and #2 once you let the multiverse/Many Worlds cat out of the bag all insanity breaks out:

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: What is worse, multiplying without limit the opportunities for any event to happen in the context of a multiverse – where it is alleged that anything can spontaneously jump into existence without cause – produces a situation in which no absurdity is beyond the pale.
    For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    “If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.”
    Michael Behe – “Edge of Evolution”

    Yet, though atheists have no evidence for ‘Many Worlds’ so as to try to ‘explain away’ the sudden appearance of different kinds of fossils in the fossil record (or of the sudden appearance of life on earth), Theists do have empirical evidence for ‘higher dimensions’ above this temporal dimension:

    The ‘Top Down’ Theistic Structure Of The Universe and Of The Human Body
    https://docs.google.com/document/d/1NhA4hiQnYiyCTiqG5GelcSJjy69e1DT3OHpqlx6rACs/edit

    Music, Quote, and Verse

    Jeremy Camp – “†There Will Be A Day†”
    http://www.youtube.com/watch?v=le-TG4sRRiQ

    “There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy.”
    William Shakespeare – Hamlet

    Job 19:26
    And after my skin has been destroyed, yet in my flesh I will see God;

  54. 54
    Granville Sewell

    Box:

    I would like to add to Sewell’s reason 1 & 2 that the force of authority comes into play. Scientists are authorities and their adherence to naturalism is hard for students and laymen to brush aside. Whenever self-doubt sets in there is immediately the problem that the vast majority of scientist adhere to naturalism. IOW one has to be self-confident in order to believe one’s own eyes and see the elephant in the room – despite the fact that everyone else (people with more experience and of higher intelligence) assures you the elephant does not exist.

    Exactly. The average person would never believe a theory as absurd as Darwinism unless he were constantly told that ALL competent scientists believe it, then he begins to think ‘maybe they see something I can’t see.’ But if even a handful of biologists/biochemists start to question the theory, most of them will revert back to common sense.

    That is why, of course, bullies like the NCSE feel such a need to ostrasize this handful, and call into question their motives and credentials.

  55. Semi related: Marvellous molecular machines– CMI LIVE – video
    http://www.youtube.com/watch?v=-GNmaB-zFW4

  56. While I know what you are saying, I might be somewhat less generous and award the other side only half a point on #1, because, as shown by cosmological ID (fine tuning of the laws of physics, design in mathematics, etc., as described, for example, in Chapter 2 of your book), we can’t really explain all other phenomena in Nature without ultimately invoking design. The difference, as I understand, is just that, while all other phenomena can probably be explained using the same set of design parameters, which were presumably all present from the Big Bang, the origin and development of life requires additional design specifications (or information sources) which probably (though not necessarily) were not all present from the beginning of the universe. So, actually elephants also initiated all the other crimes the detectives have investigated, just perhaps less directly (though of course many of the detectives may still not admit that an elephant was really behind the other crimes).

    To go one step further, as Behe writes in Chapter 10 of The Edge of Evolution, “Rather than supporting randomness, a consilience of relatively recent results from various branches of physical science – physics, astronomy, chemistry, geology, molecular biology – actually points insistently toward purposeful design in the universe…Merely intriguing when considered in isolation, when taken together the results from the disparate disciplines strongly reinforce each other. They paint a vivid picture of a universe in which design extends from the very foundations of nature deeply into life.” So I think the nature of all the other “crimes” should really be more points on the side of ID, although of course many on the other side don’t see it that way, so it is still a good reason to help understand why they have “lost their minds” with respect to the origin and development of life.

  57. JLAfan2001

    If the homonids didn’t descent from Australopithicus, where did the the homonids come from?

    From Intelligence, JLAfan. They came from Intelligence. If you don’t know what that means then just ask yourself:
    Where did your car come from? – Intelligence

    Where did your computer come from? – Intelligence

    Where did the international space station come from? – Intelligence

    Ok, now where did homonids come from? __________

  58. GS #54 : The average person would never believe a theory as absurd as Darwinism unless he were constantly told that ALL competent scientists believe it, then he begins to think ‘maybe they see something I can’t see.’

    In an ideal world our beliefs are based on rationality – deliberate dr. Spock-like weighing of pros and cons -, but being social beings seems to render this impossible. Believes are socially grounded and this implies all sorts of factors correlated with self-esteem.
    Speaking strictly for myself, my belief in the afterlife can become rather feeble when I lose a game of chess. These kind of social intrusions into beliefs are bizarre, I know. The fact that so many competent scientists adhere to Darwinism weighs in heavily when self-esteem (defense) is down. In order to regain my balance I have to seek support from authoritative figures on the ID site. So reading Meyer, Berlinski, Behe and Sewell(!) strengthens my beliefs, but admittedly a well-played chess game works even better …
    Our beliefs are not separate from other parts of our lives and are in need of constant nurturing. The good news – at least for some of us – is that it keeps the momentum for book sales.

  59. Semi OT:

    Clinging to crevices, E. coli thrive – April 10, 2013
    Harvard research reveals the role of the flagellum in helping biofilms colonize rough surfaces
    Excerpt: A team of materials scientists and microbiologists studied the gut bacterium Escherichia coli, which has many flagella that stick out in all directions. The researchers found that these tails can act as biological grappling hooks, reaching far into nanoscale crevices and latching the bacteria in place.,,,
    E. coli are equipped with two types of appendages: pili, which are short, sticky hairs, and the whip-like flagella, which are often twice as long as the bacterium itself. Pili had previously been recognized as playing a critical role in the formation of biofilms. These short hairs, up to only a micron in length in E. coli, can stick to surfaces temporarily, while the bacteria secrete a thick slime that holds them permanently in place.
    Flagella, on the other hand, typically play a propulsive role, helping bacteria to swim and steer in liquid environments. As it turns out, though, when it’s time to settle in one place, flagella also contribute to adhesion on rough surfaces, where the pili would have access to fewer attachment points.
    https://www.seas.harvard.edu/news-events/press-releases/flagella

  60. Taking on Behe’s Challenge: Evolve Me a Cilium – April 15, 2013

    Excerpt: “Once upon a time, a complete, working cilium with all the correct components, and with all the right genetic assembly instructions, just “emerged” in some mythical common ancestor. Maybe evolution “repurposed” some protein-coating genes after a mistake duplicated them. However it happened, all those parts were “conserved” the rest of the way, from simple one-celled Chlammy to complex trillion-celled Sammy. During evolution, some branches of the eukaryotic tree lost some parts, but the ones that didn’t die are getting along OK. ”
    http://www.evolutionnews.org/2.....71121.html

  61. Quote of Note:

    LIFE: WHAT A CONCEPT!
    Excerpt: The ribosome,,,, it’s the most complicated thing that is present in all organisms.,,, you find that almost the only thing that’s in common across all organisms is the ribosome.,,, So the question is, how did that thing come to be? And if I were to be an intelligent design defender, that’s what I would focus on; how did the ribosome come to be?
    George Church
    http://www.edge.org/documents/.....index.html

    The Ribosome of the cell is found to be very similar to a CPU in a electronic computer:

    Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems – 2012
    David J D’Onofrio1*, David L Abel2* and Donald E Johnson3
    Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,,
    An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,,
    The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm.
    It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive.
    http://www.tbiomed.com/content.....82-9-8.pdf

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