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PZ Myers throws down a gauntlet to ID

Yesterday, Intelligent Design critic and creationist basher, P.Z. Meyers, posted what he considers to be a real scientific challenge for ID proponents on his Pharyngula blogsite. The main thrust of his challenge is outlined in this Youtube video:

embedded by Embedded Video

YouTube Direkt

So, has Myers indeed stumbled upon a true significant challenge for ID?  Or, has he simply stumbled, as he so often does, over his own misconceptions and metaphysics?  I vote for the latter.
First off, he stumbles into what Phillip Johnson called Berra’s Blunder referring to Darwinist Tim Berra’s book Evolution and the myth of creationism,1990, pg 117-119, where Berra writes “If you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people.” As Johnson points out, Berra completely misses the point that similarities between cars are still the result of common design.

“Of course, every one of those Corvettes was designed by engineers. The Corvette sequence – like the sequence of Beethoven’s symphonies to the opinions of the United States Supreme Court – does not illustrate naturalistic evolution at all. It illustrates how intelligent designers will typically achieve their purposes by adding variations to a basic design plan. Above all, such sequences have no tendency whatever to support the claim that there is no need for a Creator, since blind natural forces can do the creating. On the contrary, they show that what biologists present as proof of “evolution” or “common ancestry” is just as likely to be evidence of common design.”
P. Johnson, Defeating Darwinism by opening minds, 1997, pg 63.

In other words, homolgy doesn’t necessarity imply evolution, or exclude design. In his challenge, Myers is relying on the same sort of blunder, as he is assuming that any homology automatically eliminates design. My challenge back to him would be to show scientifically why that is the case.

ID proponent and Darwinism critic, Cornelius G. Hunter points out the hidden metaphysical blunder Myers is making as well. On his Darwin’s God blogspot, Hunter writes “While there are several problems with the challenge, the disguised religion comes around the 1:15 mark, [in the Youtube video], where the criterion of homology is explained. Don’t worry if you are not familiar with the concept of homology. The bottom line is that the challenge uses random design as a test for whether a structure evolved. Specifically, if there is any non random pattern detectable, then it must not have been designed; instead, it must have evolved.” Hunter goes on to say “This is today’s version of a test that dates back to Daniel Bernoulli and Immanuel Kant in the eighteenth century. The idea is that God would not design according to a gratuitous pattern.” In other words, this yet another version of the old “God wouldn’t have done it this way” argument. It would be interesting to see Myers scientific explanation for how he knows what God would or would not do.

Then there’s Myers’s implied Philosophical Naturalism, as he writes in the blog “The argument has long been highly asymmetric. Scientist find a gene, and what do they do? Figure out what it does, and dig into the databases to find its relatives within that organism or in other species. Creationists claim genes can’t be created without the intervention of a designer, and what do they do? Nothing.” In other words, Myers merely assumes evolution is the only explanation for homology, and his criticism of ID is that they aren’t busy digging into databases looking for those homologies, that is to say a naturalistic explanation for the data. Thus, according to Myers, doing “nothing”, means “not looking for only undirected, natural causes” as opposed to actively trying to understand the information content of the genetic code, tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about. All that, per Myers, is doing “nothing”.

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150 Responses to PZ Myers throws down a gauntlet to ID

  1. Have you got any examples of:

    “actively trying to understand the information content of the genetic code, tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about.”

  2. Ok, lets take on the challenge head-on. My understanding is that there are about 50 recognized orphan genes in the human genome. The only thing needed to prove that these meet his requirements is if any of them have significant function.

    Further, I understand that there are two orphan genes in the flagellum. Both of these should fully meet his challenge.

    What’s the problem here. I know he is the evil PZ Myers, I know he presents his challenge in a very mocking way. But it would be painfully cool if we could respond to his challenge within a week.

    So what are the names of the two orphan genes that make up the bacterial flagellum?

  3. I looked at that Pharyngula post and the comments. Wow, what a place THAT is. It looks to me like they are saying that looking at cars you could see evidence of design that they claim you don’t see in biological evolution. For instance, some of the commenters mentioned the seat belt, or air bags, which they claim appeared out of nowhere in the car “fossil record.” So it may be that they are not saying that the homology is proof of evolution, but that something appearing out of nowhere is evidence of design, and they want to see evidence of design. So I think ID should take up the challenge, and show them the seat belt gene. They also claim that any gene homologies will fall into a so-called “nested heirarchy” that, say, seat belts won’t fall into. But, so far as I can tell, Joseph is teh resident expert on nested heirarchy, and he assures that evolution does not produce them.
    For all I know, people used to strap ropes around themselves and the car seat in the early days of the car, so maybe even seat belts have “homology” with prior car structures.

  4. Just saw bfast’s comment. Very cool indeed. Someone find those two orphan genes!

  5. feebish

    Someone find those two orphan genes!

    Um, are these the ones? yab3 and yab4? See
    http://www.pubmedcentral.nih.g.....id=1899503

    Please scroll down to the section on “Gene evolution rate” and also the Discussion. I won’t reproduce it here, since it’s rather long, and I’m not qualified to assess it, as I’m not a scientist.

  6. feebish,

    They also claim that any gene homologies will fall into a so-called “nested heirarchy” that, say, seat belts won’t fall into. But, so far as I can tell, Joseph is teh resident expert on nested heirarchy, and he assures that evolution does not produce them.

    I’d pay money to see Joseph wade in over there and set a few people straight re: nested hierarchies. ^-^

    Doesn’t Meyers also claim to dabble in marine biology as well? Looks like a perfect matchup.

  7. Creationists claim genes can’t be created without the intervention of a designer, and what do they do? Nothing.”

    A extraordinarily ironic statement considering that Mendel was a creationist.

    Here is a very interesting link with regard to Mendel: Mendel’s Opposition to Evolution and to Darwin from Oxford Journals “Journal of Heredity”

    Another great irony is that it now seems PZ is trying to falsify ID — which some evos like to claim can’t be falsified.

  8. It looks to me like they are saying that looking at cars you could see evidence of design

    The classic example is is Professor John McDonald’s attempt to show the evolution of the mousetrap.

    Apparently he is trying to disprove the existence of James Henry Atkinson

  9. DonaldM:

    In other words, homolgy doesn’t necessarity imply evolution, or exclude design. In his challenge, Myers is relying on the same sort of blunder, as he is assuming that any homology automatically eliminates design. My challenge back to him would be to show scientifically why that is the case.

    Exactly. PZ Myers is completely missing the point here. Sequence homology can tell you nothing about how a system could have evolved by numerous, successive, slight modifications. By assuming that sequence homology implies (naturalistic) evolution, PZ Myers is assuming what he’s trying to prove. It’s a completely circular argument.

  10. N.b. One needs to calculate the probability that these genes would evolve (and their proteins assemble into nanomachines) in order to determine whether evolution is a plausible explanation of homology.

  11. * naturalistic evolution that is.

  12. 12

    Donald M suggests that Paul Myers has stumbled over his own feet, which is both obvious and expected.

    The question of gene homologies is certainly relevant to the study of biology, but it has nothing whatsoever to do actual causes (which is the answer he wishes it would represent). It’s the very presence of the sequence itself that is the issue.

    There is absolutely nothing in the field of physics (or biology) that says matter should organize itself into energy metabolizing structures that begin recording their existence in a (randomly emergent) digitally encoded language based on a (randomly emergent) symbol system that uses a code convention (which is not contingent on physical laws) as a means to communicate vital information and meaning between discrete physical objects within the structure.

    It’s the very existence of recorded language, information, and meaning that is the real reason for such meaningless challenges.

    After all, a dramatic challenge is far more profitable than dealing with the actual evidence.

  13. 13

    Notice how quickly P.Z takes transgenic organisms off the table. Why can’t these serve as postive controls? We know it is possible for genes to be moved from one organism to another by design. Why isn’t that evidence of intelligent design? We already know the mechanisms by which a desinger could do this.

    Arrgh

  14. vjtorley, I don’t think your link provides for the two orphan genes in the bacterial flagellum.

  15. 6
    herb
    05/16/2009
    10:37 am

    I’d pay money to see Joseph wade in over there and set a few people straight re: nested hierarchies. ^-^

    I don’t know. It looks like kind of an echo chamber over there, where dissent is quickly pounced on. I don’t think someone like Joseph would last long there without being banned. Maybe he is already banned there.

  16. feebish,

    I don’t know. It looks like kind of an echo chamber over there, where dissent is quickly pounced on. I don’t think someone like Joseph would last long there without being banned. Maybe he is already banned there.

    I think you’re probably right. It looks like they have no concept of free and open discussion over there, unfortunately.

  17. “So, has Myers indeed stumbled upon a true significant challenge for ID? Or, has he simply stumbled, as he so often does, over his own misconceptions and metaphysics? I vote for the latter.”

    I as well.

    “In other words, homolgy doesn’t necessarily imply evolution, or exclude design. In his challenge, Myers is relying on the same sort of blunder, as he is assuming that any homology automatically eliminates design. My challenge back to him would be to show scientifically why that is the case.”

    It’s merely an assumtion on his part. Homologies imply both common descent AND common common design(er(s)). But the assertion that design requires the introduction of a new protein is fallacious, and in a nutshell, here is why.

    The automobile (and/or TV, computer, appliance et al) analog to biologic design is valid in some ways, but not in others, and the analogous exception I will detail here is used by the evo crowd to discredit ID, but is without merit.

    While both entail common elements, the assertion that new proteins would of necessity follow design intervention, is based on an assumption that design activity conforms to the ‘poof’ scenario, i.e. “let there be’. While that may be true at certain point in time, incremental design alterations show evidence of using what is there, but with modification. I even accept exaptation on occasion, but due in most cases to fortuitous opportunism, rather than to contingency, or that change was needed, so it eventuality happened via natural selection.

    In sum, if true speciation (not alopatric or symatric speciation), as well as the addition of complex organs has occurred via intervention, it could well be by the method of ‘moving the furniture’, rather than poofing in new genes.

    Remember, that when adding seat belts or GPS devices to a car we have the option of bringing them in from another workbench, which is not necessarily an option with biologic progressions.

    Bottom line: Homologies do not prove naturalistic evolution, nor does design require non homologous additions.

  18. “Another great irony is that it now seems PZ is trying to falsify ID — which some evos like to claim can’t be falsified.”

    Has PZ given the store away inadvertently?

    Vivid

  19. I wonder if this one might be relevant:

    http://mednews.wustl.edu/news/.....11349.html

    Although I agree with DonaldM and many of the commenters that the challenge is a false one, it may also be interesting to find a gene that meets the challenge…

  20. 20

    feebish (#3) wrote: “For all I know, people used to strap ropes around themselves and the car seat in the early days of the car, so maybe even seat belts have “homology” with prior car structures.”

    No ropes, and no homology. While seat belts for cars were discussed earlier, the first car with seat belts as standard equipment was the 1958 Saab. This was a “gene” grafted from aircraft – SAAB means “Swedish Airplane Limited.” They had seat belts in their aircraft and thought they were a good idea in cars – a very intelligent design.

  21. Interestingly, his challenge is to find one single gene that is exclusively designed. Is this a subtle suggestion that ALL other genes are not?

    PZ, what evidence can YOU present that ALL genes do not have evidence of design?

  22. The consensus here is that PZ’s suggestion doesn’t, in fact, test ID because apparent homologies can be reconciled as “common design.”

    So, what would?

  23. 23

    Diff,

    Something that actually adresses the molecular evidence of non-physically-dependant symbol system emerging in any material object whatsoever. That would, at least, be something to ponder.

    Without it, there is absolutely no non-ideology based reason to ignore agency as a natural cause operating within natural law.

  24. Diffaxial @22:

    The consensus here is that PZ’s suggestion doesn’t, in fact, test ID because apparent homologies can be reconciled as “common design.”

    So, what would?

    Ask yourself the following question: what would test an alien race’s assumption that a Corvette was designed?

    It all comes down to probabilities, some say. The reasoning is that there must be a sufficiently low probability of natural causes to assume intelligent design. In this light, one could then say that the probabilty of a Corvette being the product of natural processes is so astronomically low that we can categorically conclude that it was intelligently designed. Some use the probability hypothesis to claim that the entire physical universe was designed.

    Personally, I am not altogether satisfied with the probability-based ID hypothesis because the exact probability is hard to calculate. In my opinion, ID needs at least one falsifiability criterion that completely eliminates the probability of naturalistic causes for certain objects and or phenomena. This is what Drs. Behe, Dembski and others have tried to formulate in their work (e.g. irreducible complexity, the conservation of information principle, etc.). It is up to you to decide whether or not to accept their conclusions.

  25. Without it, there is absolutely no non-ideology based reason to ignore agency as a natural cause operating within natural law.

    One reason to ignore agency is exemplified by the above responses to Myers’ challenge. Some advocates of ID writing here argue that agency can build genes (proteins, etc.) de novo, such that we will sometimes fail to observe homologs due to the saltational impact of the injection of information. Yet above many argue that agency may also build genes utilizing “common design” in a manner yielding observations similar to those predicted by standard evolutionary scenarios. Because the postulate of agency is consistent with either observation, it generates no testable dispositive prediction, and is therefore scientifically empty.

    What would? We need a prediction arising from the postulate of agency that doesn’t fail in the same way Myers’ does – one that places ID at risk of disconfirmation.

    The empirical observation of natural processes yielding information processing systems in nature (particularly those amenable to description in purple prose) would certainly render ID superfluous, but is not really a formal test of ID, in that it would remain possible that intelligence operates in parallel with natural processes, producing similar results for particular purposes. Nor would the failure to articulate such processes within the current framework confirm the ID hypothesis – both theories may be wrong.

    Therefore we need a test that succeeds where Myers’ fails.

  26. Mapou @ 24:

    Ask yourself the following question: what would test an alien race’s assumption that a Corvette was designed?

    Were I such an alien I’d look for evidence that a design process had been employed, evidence that is independent of the objects (Corvettes) in question. Certainly evidence of the existence of organisms capable both of the process of representation entailed in design, as well as the fabrication techniques required actualize those representations, would increase my confidence in my design hypothesis. Perhaps I’d look for a design center containing preliminary sketches, engineering plans, prototypes and so forth – representations of the object being designed – as well as evidence for the manufacturing and assembly processes required to form a Corvette. I’d look for these things because the only instance of design activity with which I am intimately familiar (the techniques we aliens employ) are best described as a distinct process, not simply an abstract quality of the objects designed. I’d therefore predict indicia of a similar processes, and hope to find them.

  27. I know I’m primarily just cheerleading lately, but that’s a darn good post, and so was the one before it. :)

  28. First off, he stumbles into what Phillip Johnson called Berra’s Blunder referring to Darwinist Tim Berra’s book Evolution and the myth of creationism,1990, pg 117-119, where Berra writes “If you compare a 1953 and a 1954 Corvette, side by side, then a 1954 and a 1955 model, and so on, the descent with modification is overwhelmingly obvious. This is what paleontologists do with fossils, and the evidence is so solid and comprehensive that it cannot be denied by reasonable people.” As Johnson points out, Berra completely misses the point that similarities between cars are still the result of common design.

    What Berra is offering is an argument from analogy similar to that of the watch on the heath by William Paley in his Natural Theology. As far as I am aware Johnson has not referred to ‘Paley’s blunder’ so it is hard to see why Berra’s argument should be singled out in this way.

    An argument from analogy is not a fallacy as such but it depends for its rhetorical force on the extent to which the two cases being compared are similar. What Berra is arguing is that, if we were shown all the Corvette variants, even if we knew nothing else about that particular model, we would infer that they were related. If we knew nothing else it might be difficult to decide whether they were designed simultaneously or sequentially but if we had some sort of chronological data then we could infer descent with modification. That the cars were designed is simply not relevant to Berra’s point. The key is that even the design of things like cars changes over time in response to environmental pressures.

    ID proponent and Darwinism critic, Cornelius G. Hunter points out the hidden metaphysical blunder Myers is making as well. On his Darwin’s God blogspot, Hunter writes “While there are several problems with the challenge, the disguised religion comes around the 1:15 mark, [in the Youtube video], where the criterion of homology is explained…

    It is ironic that Hunter is quoted here in light of the previous lengthy discussion of the Law of Non-Contradiction (LNC). One of his theses appears to be that atheism is as much a religion as any other faith. This is like arguing that something can be both itself and its negation, that not collecting stamps is as much a hobby as collecting stamps. Religion involves belief in deities, supernatural domains, transcendental and spiritual realms amongst other things. Atheism is at least a total lack of belief in such things. In apparent violation of the LNC Hunter is arguing an equivalence between belief and its negation not-belief.

    The idea is that God would not design according to a gratuitous pattern.” In other words, this yet another version of the old “God wouldn’t have done it this way” argument. It would be interesting to see Myers scientific explanation for how he knows what God would or would not do.

    Perhaps I missed something in the video but I saw no attempt to argue against the existence of God on the grounds of imperfection in the world so this counter-argument is irrelevant to the case at hand.

    Then there’s Myers’s implied Philosophical Naturalism, as he writes in the blog “The argument has long been highly asymmetric. Scientist find a gene, and what do they do? Figure out what it does, and dig into the databases to find its relatives within that organism or in other species. Creationists claim genes can’t be created without the intervention of a designer, and what do they do? Nothing.” In other words, Myers merely assumes evolution is the only explanation for homology, and his criticism of ID is that they aren’t busy digging into databases looking for those homologies, that is to say a naturalistic explanation for the data. Thus, according to Myers, doing “nothing”, means “not looking for only undirected, natural causes” as opposed to actively trying to understand the information content of the genetic code, tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about. All that, per Myers, is doing “nothing”.

    …all of which neatly sidesteps the central challenge of the video which is for the Discovery Institute to identify just one gene for which there is clear evidence of design rather then evolutionary descent. In fact, the original post reads as a skilfull example of what I believe is known in stage magic as misdirection aimed at distracting attention from that point.

  29. atheism is obviously a faith. its a worldview, and it requires faith in the atheist creation fable, evolution. you have faith there is no God…no proof, just as you have faith in evolution, which you cannot prove. So you believe that all that you see just happened, that evolution explains why giraffes are tall, and skunks are small. evolution is all in all..and atheism is nothing more than another faith. a rather absurd one at that.

    I didn’t know genes showed evolutionary descent…guess you just take it on faith.

  30. In the opening post, Donald writes, and Severesky quotes,

    Thus, according to Myers, doing “nothing”, means “not looking for only undirected, natural causes” as opposed to actively trying to understand the information content of the genetic code, tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about. All that, per Myers, is doing “nothing”.

    Hmmm. I’m not sure that I know of any ID advocate that is try to do the part I bolded above. In fact, I’m pretty sure I’ve read quite a bit from ID advocates that say the bolded part is not necessary, or even possible.

    So, Donald, could you point to some examples of where ID advocates are “tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about”?

    Doing the above would be a part of identifying a gene that has been designed, I would think. If ID advocates are really doing something rather than nothing in regards to the things Donald mentioned, could someone point to that work and/or summarize it here?

  31. 31

    Well first of all the first questions is inane. Why would any one particular gene be designed? Design is the some total of multiple parts or processes working towards a whole. That is like saying “show me one dot of paint on the mona lisa that is deisgned. You cant go by that because you are comitting the fallacy of false comparasion.

    Put it like this…

    Q.When one is doing a puzzle, what is the most IMPORTANT piece?”

    A. The picture.

    He is trying to use a red herring argument about some kind of singled out “detail” which he thinks he has already set up so that IDists- or the theory of ID cant win. But there is a multiplicity effect of not “one gene” but all of the genes necessary for a particular function to exist which need to be taken into account.

  32. 32

    Not to mention their probabilistic relationship to a fitness landscape.

  33. Hazel #30 and myself #1 both asked for examples of:

    “tracing the informational pathways and/or trying to determine when, where and how the information was imparted into the system and how an intelligence may have been involved to bring this about”

    Any offers? If not, a description of how you might set about this task?

  34. Why is it that when scientists come up with evidence of evolution, the ID crowd say; “this is not possible because…”. Why not come up with evidence of design instead, as a counter argument? That is, instead of trashing the other sides evidence, discover some of your own, that is tangible, arguable, or at least serious.

  35. 35

    rvb6, evidence for design is everywhere. Design was the scientific paradigm before non-teleological evolution monopolized the education establishment. The goal of ID is to lay out in scientific terms exactly how we know if something is designed. If is no secret that we are talking about things like living creatures. The evidence is in the improbability of such creatures ever raising without an intelligent guiding force. The digital code of DNA, the molecular machines within the cell- not to mention the fact that the origin of life flys in the face of physical principles of thermodynamics.

    There is plenty of evidence for design everywhere. Where ID is now is that stage where it is formulating and articulating the specifics of the theory and trying to present that along with negative critical analysis of non-teleological evolution to sway the establishment and the people as a whole that ID- as an engineering science – could be a more fruitful scientific template.

  36. My answer to Myers is that they all are designed. Out.

    There exist no evidence of any gene arising by naturalistic processes thus, the conclusion is they all arose by design. Now I am being a little bit facetious but not much. The ID challenge has always been show us the money. Until the naturalists can, then the burden is on them. We know that intelligence can create the genes. We do not know that naturalistic processes can. Show us naturalistic processes creating the genes.

    That does not say that genes do not get modified over times and will not vary by different species or that some genes will produce proteins that behave somewhat differently from organism to organism or may in fact take on a new use. But it does say that most if not all arose by design.

    If I am wrong and I do not think I am, then why in all these years and in all the books on evolution and in all the snide comments made about IDiots are there not any examples. So let’s discuss why they are not all designed and see if we can find any examples. If no answers are forthcoming, then they are all designed.

    I expect we will find a couple but even if we do that does not a summer make.

  37. ” The goal of ID is to lay out in scientific terms how we know if something is designed”: Really?
    And if you are ‘scientifically’ sucessful, and come to the conclusion that something, or some physiology is designed, what then? Stop and move on to prove that some other thing is designed and then stop, and move on; wonderful, and when all is proved designed stop all together?
    Marvellous ‘science’ this!

  38. Folks:

    UB has put his finger on the money:

    There is absolutely nothing in the field of physics (or biology) that says matter should organize itself into energy metabolizing structures that begin recording their existence in a (randomly emergent) digitally encoded language based on a (randomly emergent) symbol system that uses a code convention (which is not contingent on physical laws) as a means to communicate vital information and meaning between discrete physical objects within the structure.

    It’s the very existence of recorded language, information, and meaning that is the real reason for such meaningless challenges.

    We know, per direct observation and experience, that intelligent agents do create complex, specifically functional digital information-processing entities.

    We know as well, that trial and error to get to initial functionality, is a most unlikely to succeed mechanism. (And, we have many calculations, simple or complex that show why. In effect a random walk that starts at an arbitrary configuration — for an entity requiring 1,000+ bits of information storage capacity — is far too weak a strategy to be probabilistically plausible on the gamut of the observed cosmos. And, life forms as observed start out at ~ 600,000 – 1 million bits.)

    As to Berra’s blunder, it’s point is obvious.

    Berra lined up a sequence of changes that showed a progressive family resemblance, and claimed that such homologies showed evolution; in a context hat suggested that the explanation was spontaneous, random change plus natural selection. But in fact, he chose an example of a known designed sequence.

    This suffices to show that the logic of homology fails, unless we know in advance that here was no designer present.

    That is, there is an issue of question-begging at work so soon as homologies and “progress” are used as evidence that design was not necessary to produce such evident progress. Worse, the case is a demonstration that intelligent agents are known to be capable of creating a sequence of information-rich functional structures that show homologies.

    Has an unambiguous case of spontaneous change per random variation plus natural selection producing such complex entities requiring 1,00+ bits of information storage capacity been demonstrated?

    Plainly, not.

    And so, Mr Myers’ “challenge amount”s to an attempt to shift the unmet burden of proof.

    One that has been unmet for 150 years.

    GEM of TKI

  39. “wonderful, and when all is proved designed stop all together?
    Marvellous ’science’ this!”

    What a marvelously stupid comment. First there will never be an “all proved.” Second, it never stopped thousands of ID believing scientists from continuing on in the past.

    Argument by stupidity is all that is available for the anti ID proponents. First, Myers stupid challenge and then, this inane comment.

  40. Frost122585 @ 31:

    Why would any one particular gene be designed? Design is the some total of multiple parts or processes working towards a whole. That is like saying “show me one dot of paint on the mona lisa that is deisgned. You cant go by that because you are comitting the fallacy of false comparasion.

    Jerry @ 36:

    My answer to Myers is that they all are designed. Out.

    There exist no evidence of any gene arising by naturalistic processes thus, the conclusion is they all arose by design. Now I am being a little bit facetious but not much.

    Frost says that single genes aren’t designed. Jerry says nearly all were designed.

    Again the emptiness of “design” and “agency” vis the generation of testable predictions is apparent.

    Tribune7 @ 7:

    Another great irony is that it now seems PZ is trying to falsify ID — which some evos like to claim can’t be falsified.

    The real irony is that your collective responses illustrate why they are correct.

  41. Corvettes! Score another metaphor for Chatty PZ.

    The inability of Darwinoids to produce anything but colorful analogies reminds us of a certain famous ratiocinator and his complaint that theory produces “nothing but metaphors.” The same force of unifying resistance that makes simple, elegant theories like NS possible also divides them from the complex realm of actual experience, where manmade metanarratives have no meaning.

    Sorry, PZ—the train has already left the station (to use your kind of lingo). The real research in the life sciences today—where real men simply look at how nature works and don’t try to force any kind of ideology on it or stamp their feet—all indicates design. Evolution never shows up except to make a rare appearance in the discussion session wearing its pajamas and seeming out of place.

    Evolution is never found in the methods of these reports for one very simple reason: it cannot be proven.

  42. Diffaxial,

    I answered the question of what ID predicts and what it would take to disconfirm the design inference.

    That you choose to continue to ignore that just further expoases your agenda of willfull ignorance.

    Now if we do determine design- IOW once the design inference is given a “Go” then we set out to TRY to answer the questions a design inference produces- the who, how, where, when.

    And the ONLY way to do that is by studying the design in question.

    That is how it works in forensics. That is how it works in archaeology and that is how it works with SETI.

    1- determine design

    2- study it so that you can understand it.

    3- understand it so that you can try to answer those new questions.

    That said experience has taught us that it does matter to an investigation whether or not that which is being investigated arose via agency involvement or nature, operating freely.

    And as for “nature, operating freely”, well that cannot account for the origin of nature…

  43. Is there any scientific data which demonstrates that a gene can arise via undirected processes where there wasn’t any genes before?

    Why isn’t the following paper the “death knell” for undirected evolution?

    Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution

    With new genes you also need a new binding site for that gene. The above paper talks about getting two mutations- what aboput building a new binding site from scratch?

    Is it even possible? I am sure it is but how much time would be required?

    And not only is a new binding site required but so are a promoter, enhancer, repressor, etc.

    And even then if the new gene starts pumping out another protein that protein has the potential of getting in the way of an already existing and functioning system.

  44. Joseph writes,

    Now if we do determine design- IOW once the design inference is given a “Go” then we set out to TRY to answer the questions a design inference produces- the who, how, where, when.

    It seems to me that finding evidence about “who, how, where, [and] when” is part of trying to determine whether something was designed in the first place. It’s not just “first determine design, and then answer those questions.

    Also, Joseph writes,

    2- study it so that you can understand it.

    3- understand it so that you can try to answer those new questions.

    As I and others have asked, can you provide examples of ID advocates studying life in order to determine ““who, how, where, [and] when” the designing was done?, or if not, provide examples about what types of investigation one would do to answer those questions?

  45. hazel:

    It seems to me that finding evidence about “who, how, where, [and] when” is part of trying to determine whether something was designed in the first place. It’s not just “first determine design, and then answer those questions.

    I take it that you don’t have any investigative experience.

    Ya see in the absence of direct observation or designer inpuet, the ONLY possible way to make ANY scientific determination about the who, how, when or where, is by studying the design in question.

    But FIRST you must determine design is present.

    As I and others have asked, can you provide examples of ID advocates studying life in order to determine ““who, how, where, [and] when” the designing was done?, or if not, provide examples about what types of investigation one would do to answer those questions?

    hazel YOU need to focus on the claims of YOUR position.

    I am sure IDists will start taking on those questions once ID is accpeted and the resources are expanded.

    IOW it is a bit nonsensical to ask IDists to answer all the questions BEFORE allowing ID the resources required to answer them.

    After all your position doesn’t answer squat and it has all the resources it needs.

  46. “Again the emptiness of “design” and “agency” vis the generation of testable predictions is apparent.”

    An empty comment. Again argument by stupidity.

    Suppose the comments about which genes were designed were contradictory, does that make ID empty? First, one could be right and one could be wrong or secondly, they both could be right and it is just the context of the argument that has to be understood. I stand by my argument and please if you want to refute it try offering empirical evidence instead of empty rhetoric. It is ID that uses science to put forward its claims, not fatuous words which is what we get from anti ID proponents.

  47. ” It seems to me that finding evidence about “who, how, where, [and] when” is part of trying to determine whether something was designed in the first place.”

    These are interesting by ancillary questions. They are not needed to determine a high probability of design. But they are certainly interesting questions which belies the stupidity of rvb8′s comment at #37. The probability of design could be close to one and the answers to some of these questions could move it almost to one but they are not necessary to make it a high probability in the first place.

  48. Joseph writes, “hazel YOU need to focus on the claims of YOUR position.”

    My position on what? I was just making a remark on the issue of determining design.

    As an example, suppose I find a rock that looks like it might be an arrowhead. (I did a little bit of archeology work as an undergraduate, for what it’s worth.) If I found this in a jumble of rocks in a creek I wouldn’t have much to go on. But what if I found the rock in a cave where there was evidence of campfires dating to 1500 years ago . some pottery shards, and some striking stones known to be used for creating arrowheads. Then I would have some evidence about when, who and how, and that would add quite a bit to a possible determination of design.

    Do you agree with this analysis of this situation.

    Similarly, when the fire investigator works to determine arson he doesn’t determine arson first and then look for gas cans. Looking for evidence of who, when, and how is an integral part of trying to determine design in fields like archeology and forensic science.

  49. hazel:

    As an example, suppose I find a rock that looks like it might be an arrowhead.

    Suppose you do.

    If I found this in a jumble of rocks in a creek I wouldn’t have much to go on. But what if I found the rock in a cave where there was evidence of campfires dating to 1500 years ago . some pottery shards, and some striking stones known to be used for creating arrowheads. Then I would have some evidence about when, who and how, and that would add quite a bit to a possible determination of design.

    Yes hazel investigators use all the evidence at their disposal.

    But let’s say you found your arrow-head in that cave.

    Could that arrow-head be from an attacking enemy which would mean all the evidence in the cave is useless as it did not belong to the arrow-toting person?

    So if we took your approach we would be attributing stuff to the arrow-maker that was not even part of his/ her life.

    Similarly, when the fire investigator works to determine arson he doesn’t determine arson first and then look for gas cans.

    What happens when there aren’t any gas cans?

    Ya see fire investigators try to find out if the fire could have started unintentionally. And then once they have exhausted that possibility do they then turn to a possible arson.

    IOW they try to figure out if nature, operating freely can account for the fire.

    Looking for evidence of who, when, and how is an integral part of trying to determine design in fields like archeology and forensic science.

    That is false for the reason provided. One may NEVER know who, how, when or where but one canb still dtermine design from nature, operating freely.

  50. Diffaxial– Another great irony is that it now seems PZ is trying to falsify ID — which some evos like to claim can’t be falsified. . .The real irony is that your collective responses illustrate why they are correct.

    Are you referring to the non-PZ evos or our collective responses?

  51. jerry,

    Suppose the comments about which genes were designed were contradictory, does that make ID empty? First, one could be right and one could be wrong or secondly, they both could be right and it is just the context of the argument that has to be understood.

    Good point. And based on the comments so far, it sounds like individual genes could be a borderline case—maybe they could come about naturally, maybe not. How about throwing specified complexity at this problem? That’ll give those Meyersbots something to chew on.

  52. #35, Frost122585:

    rvb6, evidence for design is everywhere. Design was the scientific paradigm before non-teleological evolution monopolized the education establishment. The goal of ID is to lay out in scientific terms exactly how we know if something is designed.

    We are all waiting for that to happen, how far off is it? In the meantime, to what extent is it appropriate to refer to ‘design’ as a scientific paradigm before modern scientific methodology began to be used? Going back a couple of centuries, the teleological paradigm used to be that the world was created in six days and the planets orbiting in perfect spheres around the sun. When scientists began to view the world objectively they found a disorderly universe working according to universal laws instead of idealized divine order.

    Against fierce resistance from proponents of the teleological worldview, the modern scientific view eventually became universally accepted and I presume very few people today subscribe to the antiquated teleological, heliocentric paradigm.

    Maybe we are in a similar situation today except the subject is origins of the species instead of whether the physical universe mirrors a perfect, divine order?

    Is it possible that as the now abandoned, antique cosmology was founded on the teleological paradigm, the application of a teleological paradigm on biology eventually also may be found to be in error?

    Evidence for design is claimed to be everywhere so I guess there is something wrong with my brain since I am unable to see it. Is there any cure for that?

  53. Joseph,

    it is a bit nonsensical to ask IDists to answer all the questions BEFORE allowing ID the resources required to answer them.

    What resources are required? One thing is detecting design in mechanical devices; it is obvious. But how do we detect design presumably having taken place millions of years, thousands of generations back in time? Is it possible, have you got any suggestions?

  54. Cabal:

    What resources are required?

    Money, people, time- for starters.

    “On the Origin of Species…” was published 150 years ago. Yet the evidence for the (alleged) evolution of the eye/ vision system is the same today as it was then.

    And that is even though we know much, much more about eyes and vision systems than Darwin did.

    The evidence is the same- that is we observe varying degrees of eyes/ vision systems in living organisms and we “know” the original population9s) didn’t have either.

    One thing is detecting design in mechanical devices; it is obvious.

    What about in non-mechaniscal devices?

    What is it that prevents glaciers from depositing the massive stones that form Stonehenge?

    But how do we detect design presumably having taken place millions of years, thousands of generations back in time?

    Knowledge gained via experience.

    That is we have observed nature, operating freely and we have also observed what designing agencies can do with nature.

    We take that knowledge and apply it to what we are investigating.

    Then we form an inference.

    And as with ALL scientific inferences it can either be confirmed or refuted with future knowldge.

    However the science of today does not and cannot wait for what the future may or may not bring.

    As for the utility of ID- as I have been saying for years- under the ID premise:

    Living organisms are NOT reducible to matter, energy, chance and necessity. They are NOT reducible to their chemical make-up.

    The “genetic information” is NOT the sequence. The sequence is just necessary to carry out the instructions. Those instructions that are NOT visible via a microscope (just as the information on a computer disk is not visible by a microscope).

    And only under an ID framework would scientists even start to look for such a thing.

    “Nothing in biology makes sense except in the light of Intelligent Design.”

  55. Sorry, I wrote heliocentric instead of geocentric…

  56. Cabal,

    Copernicus, Galileo, Newton and Kepler all understood that science was a way to understanding “God’s” Creation.

  57. Joseph @ 42:

    I answered the question of what ID predicts and what it would take to disconfirm the design inference.
    That you choose to continue to ignore that just further expoases your agenda of willfull ignorance

    I don’t recall that any of your responses have satisfied the request for a prediction arising from a necessary entailment of ID, such that ID is put at risk of disconfirmation. Something analogous to what PZ Myers attempted, but (by your collective lights) failed to achieve.
    However, I tend to ignore your posts due to your preference for argument by bald declaration and frequent use of personal insults (such as the above), so I may have missed it.

  58. Diffaxial,

    The prediction thta arises from ID is the SAME that arises from archaeology, forensic science and SETI- Intelligent agencies tend to leave behind traces of their involvement.

    If we fail to see such traces or the traces we do observe are demonstrated to be obtainable via nature, operating freely, the design inference is disconfirmed.

    As for bald declarations- that is all your position is.

    Ya see as I have said many times you cannot even account for the evolution of eyes/ vision systems beyond some simplified narrative.

    As for PZ all he has to do is start supporting his position and ID will fall.

    It is that simple.

  59. Jerry:

    My answer to Myers is that they all are designed. Out.

    Ha ha. Take that, PZM! This is the best answer I’ve seen in this discussion so far.

  60. Joseph:

    Now if we do determine design- IOW once the design inference is given a “Go” then we set out to TRY to answer the questions a design inference produces- the who, how, where, when.

    Given that ID allows for any type of designer (including supernatural omnipotent ones), how would one do that? From an ID point of view, wouldn’t “the-designer-did-it” always be the most parsimonius explanation?

  61. Hoki:

    Given that ID allows for any type of designer (including supernatural omnipotent ones), how would one do that?

    As I said- by studying the design in question- all the available evidence that led to the inference.

    However questions would be addressed in the order of importance.

    For example knowing the Wright brothers won’t tell me how to fly nor fix an airplane.

    From an ID point of view, wouldn’t “the-designer-did-it” always be the most parsimonius explanation?

    ID is not religious so parsons have nothing to do with it. :)

    Once the design inference is reached it opens up new questions. And given our nature we will do what we can to answer them.

  62. 62

    Once the design inference is reached it opens up new questions. And given our nature we will do what we can to answer them.

    What are your plans?

  63. Joseph @ 58

    The prediction thta arises from ID is the SAME that arises from archaeology, forensic science and SETI- Intelligent agencies tend to leave behind traces of their involvement.
    If we fail to see such traces or the traces we do observe are demonstrated to be obtainable via nature, operating freely, the design inference is disconfirmed.

    These analogies are indeed useful, although not in the way you imagine.

    Take the forensic investigation of arson, which concerns the origins of fires. The occurrence of a fire within a structure, in and of itself, is not evidence for the action of an agent. The “traces” of arson to which you refer are quite specific, and our knowledge of them reflects long experience with the manner in which people typically intentionally start fires within structures: evidence of the use of accelerants, multiple points of origin, and so on. These are understood in light of equally long experience with fires that arise absent agency, which lack such indicators and are typically traceable to a handful of causes: overloaded electrical circuits, untended candles, lightning strikes, etc., causal pathways which leave their own well known traces. In short, the detection of arson – of agency as the origin of structural fires – requires experience both with the typical indicia of agency, against a background of equally long experience with fires that arise inadvertently, and indicia of the causation of such accidental fires.

    You would like to construct an analogy to determination of the origins of complexity in biology. For the analogy to hold, a complex biological structure, in and of itself, cannot be regarded as evidence for the action of an agent (just as a fire is not prima facie evidence of arson). The traces of agency in biology should be quite specific, reflecting long experience with the manner in which agents intentionally originate biological structures. Again, to continue the analogy, that experience takes on its significance only against a background of experience with the origination of biological complexity by non-intentional (natural) means. Similar reasoning informs other forensic investigations.

    It should be easy to see that your analogy fails when extended to biology and ID. We have no experience with the origination of complexity in biology at the hands of intelligent agents from which to derive knowledge of the typical “traces” of such agents as they go about their biological arson. Indeed, we have no candidate agents at all, much less any knowledge of the means employed by any such agent, and the traces left by such means. Moreover, because you don’t acknowledge origination of biological complexity by natural means at all, you therefore cannot contrast whatever traces you imagine “must” reflect agency within biology with indications of the instances of the origins of biological complexity absent agency.

    It follows that, whatever means you claim is capable of detecting agency within biology, it is decidedly NOT analogous to the detection of arson. Your analogy to forensics fails, as above. Therefore the logic of your assertion that ID predicts “traces” of the action of agency in a manner similar to that predicted by forensic science also fails.

  64. Re “Who, How, Where, When”

    The following link shows one example of how ID proponents might go about answering some of these questions:

    http://designmatrix.wordpress......us-system/

    I would like to point out in passing that from a front-loading perspective, P. Z. Myers’ deliberate exclusion of genes with homologs is 100% wrong. These are precisely the genes we should be looking at.

  65. 65

    @60 Hoki

    “From an ID point of view, wouldn’t “the-designer-did-it” always be the most parsimonius explanation?”

    I wold have to say the answer would be no less than “nothing did it”.

    This is after all what it all boils down to isn’t it? At least as far as OOL is concerned.

    Either someone Intelligent introduced information to get the ball rolling, or nothing introduced information to get the ball rolling.

    Take your pick. At least that’s how I see the thing from the outside.

  66. I think everyone is getting twisted out of shape here.

    If such genes were found, its not a smoking gun that kills Evolution (or validates ID), its just a piece of concrete evidence that provides some small support for ID. Thats it. I think the point of the challenge is that, so far, ID hasnt been able to provide such concrete evidence. A lot of hand waving and moaning about probablilities, but no concrete evidence.

    Another minor point, I dont think its PZM that is ‘mounting the challenge’. He provided a link to youTube (and presumably supports it), but I watched the video and it doesnt look like PZ. I couldnt tell who is pushing it, but I dont think its PZ.

  67. Diffaxial:

    These analogies are indeed useful, although not in the way you imagine.

    What I presented is a fact not an analogy.

    So I can see where your “refutation” fails.

    Take the forensic investigation of arson, which concerns the origins of fires.

    First arson has to be determined.

    So it starts out as a fire investigation.

    And yes as I have already stated numerous times our inferences depend on our current state of knowledge- usually gained via experience.

    You would like to construct an analogy to determination of the origins of complexity in biology.

    Complexity is NOT being debated.

    So no, I would not like to construct such an analogy.

    However we do have experience with information-rich systems.

    So we can use that experience to form inferences about information-rich systems in which the origins are not known.

    Therefor when we observe the information-rich systems in living organisms we infer design.

    Now to refute that inference all one has to do is demonstrate they can arise via nature, operating freely.

    And BTW all of our experience demonstrates that only life begets life.

    IOW there aren’t any reasons or evidence to support your position.

    I take it you still don’t understand the significance of the “Waiting for Two Mutations…” paper.

  68. Graham,

    The point is that there is little evidence that any gene arose naturally. If they did not arise naturally then what is the option?

    So we can discuss the validity of sentence 1 in the preceding paragraph and examine the absoluteness of the claim or what exceptions that may exist. And we can discuss the implications of sentence 2 given that sentence 1 is generally correct.

    Whoever did the video hasn’t a clue on what the debate is about. ID just says show us the evidence. We can show you why we believe it cannot happen and we ask for empirical data to counter the ID assessment. So far neither PZ Myers, Richard Dawkins, Jerry Coyne or any other of the naturalist elite have complied.

    So what are the ID people to think. Maybe that our assessment is correct.

  69. jerry,

    there is little evidence that any gene arose naturally

    Surely, thats the whole point, there is such evidence, in that genes tend to show similarities to earlier genes in other/earlier forms. Thats what evolution is all about, descent with modification. Its why all those biologists out there accept evolution and laugh at ID.

    The challenge is asking ID to provide some evidence of a designer, because a designer could just introduce a brand new gene with no evolutionary precursor. I realise a designer need not do this, (God could do whatever he plaeses), but if he did, it would provide some evidence for ID. So far, and ID is over 10 years old, all weve got are popular books, and wailing about probabilities.

  70. Surely, thats the whole point, there is such evidence, in that genes tend to show similarities to earlier genes in other/earlier forms.

    No, the point was that such similarities do not provide evidence of a purely naturalistic origin. Or do the similarities between a Toyota station wagon and one made by Mitusubushi prove they both arose with no intelligent input?

  71. 71

    For prime example of the shoddy “similarity evidence”, most materialists are adamant that Darwinian evolution is proven true when we look at the supposed 98.8% similarity between certain gene segments of the DNA in a Chimpanzee and compare them with the same gene segments of the DNA in a Human. Though suggestive, the gene similarity, even if true, is not nearly good enough to be considered “conclusive” scientific proof. But this is beside the point since the oft quoted 98.8% similarity is not even true in the first place. To show how flimsy this evidence is, other recent comparisons of the genes, between chimps and Man have yielded a similarity of only 96%. Whereas, the December 2006 issue of PLoS ONE reported that human and chimpanzee gene copy numbers differ by a whopping 6.4% (Hahn). Even more realistically, Dr. Hugh Ross states the similarity is closer to 85% to 90% when taking into account the chimp genome is actually about 12% larger than the human genome. A recent, more accurate, Human/Chimp Genome Comparison Study in 2008, which honestly took into account the fact that the ENCODE study has implicated 100% functionality across the entire human genome, and is thus not to be limited to just the biased “gene comparisons” of materialists, has found that when they compared the entire genomes of Chimpanzees and Humans side by side, they found that the true similarity of the genomes is slightly below 70%!

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs
    …Therefore the total similarity of the genomes could be below 70%.
    http://www.refdag.nl/artikel/1.....anzee.html
    The author of the paper is a research geneticist at the University of Florida.

    The Unbearable Lightness of Chimp-Human Genome Similarity
    excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. “Relative differences: The myth of 1%,” Science 316: 1836.). Part of the reason for this is if one decides to take into account the plethora of species-specific DNA insertions and deletions (“indels”) that are present along any segment compared between chimp and human, the percentage of identity drops. Another reason is that duplications, inversions, translocations, and transpositions at all scales uniquely characterize the two genome sequences — these have to be untangled before aligning the sequences in order to measure their similarity. Also, the 99% identity figure is often derived from protein-coding regions that only comprise about 1.5% of the two genomes. Many mammalian protein-coding regions are highly conserved, however. We also have to consider that a detailed comparison of certain “heterochromatic” chromosome regions between chimps and humans has yet to be made. In short, the figure of identity that one wants to use is dependent on various methodological factors.
    http://www.evolutionnews.org/2......html#more

    As well, there are several hundred genes that are completely unique to humans that are completely ignored in the biased similarity studies of evolutionists:
    Among the approximately 23,000 genes found in human DNA, scientists currently estimate that there may be as few as 50 to 100 that have no counterparts in other species. (Contract) that comparison to include (only) the primate family known as hominoids, and there may be several hundred unique genes.
    http://mednews.wustl.edu/news/.....11349.html

    Secondarily, at the protein level only 29% of genes are found to code for the same exact amino acid sequences in proteins in chimps and humans (Nature, 2005), but this evidence is just brushed aside as insignificant by evolutionists, even though the protein structures themselves are now shown to be extremely sensitive to any random point mutations imposed on them, and have been shown to have a “Feedback Control Loop” mechanism which works to correct the integrity of the precise protein structure from the random mutations imposed on them to try to change their structure.

    Proteins with cruise control provide new perspective:
    “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/.....topstories

    Cruise Control?!?.. Last time I checked, cruise control is very limiting thing for a car that prevents any change from happening! Thus, the burning question is, Why are proteins working so hard to correct random mutations imposed on them to protect their structural integrity, since random mutations incurred by protein structures are suppose to be the primary driving force for the morphological change of evolution? Though the authors of the paper try to put a “evolution friendly” spin on the “cruise control” evidence, finding a “advanced Feedback Control Loop” at such a base molecular level, before natural selection even has any chance to select for the morphological change, is screaming Design, and is, in fact, a very constraining thing to the amount of variation we can expect from the stable protein structures of the cell, and is thus, a very constraining thing to the variability of species that we can expect, and is thus, a very constraining thing for what we can expect from evolution in general.

    As well, using materialists very biased and misleading “only similar Genes count” methodology, our DNA is 92% similar to mice as well as 92% similar to zebrafish (Simmons PhD., Billions of Missing Links). So are we 92% mouse or are we 92% zebrafish? Our DNA is 70% similar to a fruit fly; So are we therefore 70% fruit fly? Our DNA is 75% similar to a worm; So are we therefore 75% worm? No, of course not! This reasoning that evolutionists have used to try to scientifically prove humans evolved from a chimp-like anscestor, is simply minded in its approach, and is severely contradicted by many other, more concrete lines, of evidence that refute it.

    Decoding the dogma of DNA similarity
    http://creationontheweb.com/content/view/5111

    This article has a totally different conclusion on what comparing genes proves about evolution:
    “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009)
    Excerpt: Even among higher organisms, “the problem was that different genes told contradictory evolutionary stories,” leading Syvanen to say, regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” A recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “despite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” Likewise, Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”
    http://www.evolutionnews.org/2......html#more

    This following article shows that the “same exact genes” have actually been shown to produce “completely different” adult structures:
    A Primer on the Tree of Life (Part 4)
    “In sharks, for example, the gut develops from cells in the roof of the embryonic cavity. In lampreys, the gut develops from cells on the floor of the cavity. And in frogs, the gut develops from cells from both the roof and the floor of the embryonic cavity. This discovery—that homologous structures can be produced by different developmental pathways—contradicts what we would expect to find if all vertebrates share a common ancestor. … To summarize, biologists have made two discoveries that challenge the argument from anatomical homology. The first is that the development of homologous structures can be governed by different genes and can follow different developmental pathways. The second discovery, conversely, is that sometimes the same gene plays a role in producing different adult structures. Both of these discoveries seem to contradict neo-Darwinian expectations.”— from the textbook Explore Evolution http://www.evolutionnews.org/2......html#more

    A recent article in Trends in Ecology and Evolution concluded, “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows. W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7), pgs. 270-274 (July 7, 1998).

    So did their very philosophically biased methodology of establishing genetic similarity, between man and chimps, help establish Darwinian evolution as true once more solid evidence came in? No, of course not!! From the very beginning, that type of reasoning, used by materialists, was simple minded in its approach and clearly flawed in establishing a solid scientific foundation on which to draw valid inferences from. Especially since they blatantly ignored the second law in order to make their case. Clearly, it must be found if the DNA is flexible enough to accommodate any type of random mutations happening to it in the first place before we can infer whether materialistic evolution is even viable as a hypothesis. This one point of evidence, the actual flexibility of DNA to any random mutations, must be firmly established, first and foremost, before we can realistically draw any meaningful inferences from the genetic data we gather from organisms. Fortunately we, through the miracle of science, can now establish this crucial point of DNA flexibility. The primary thing that is crushing to the evolutionary hypothesis is this fact. Of the random mutations that do occur, and have manifested traits in organisms that can be measured, it appears that at least 999,999 out of 1,000,000 (99.9999%) of these mutations to the DNA have been found to produce traits in organisms that are slightly deleterious, harmful and/or fatal to the life-form having the mutation. (Gerrish and Lenski, 1998, Bataillon, 2000, Elena et al, 1998).

    “I have seen estimates of the incidence of the ratio of deleterious-to-beneficial mutations which range from one in one thousand up to one in one million. The best estimates seem to be one in one million (Gerrish and Lenski, 1998). The actual rate of beneficial mutations is so extremely low as to thwart any actual measurement (Bataillon, 2000, Elena et al, 1998). Therefore, I cannot …accurately represent how rare such beneficial mutations really are.” (Sanford; Genetic Entropy page 24)

    The fate of competing beneficial mutations in an asexual population (Philip J. Gerrish & Richard E. Lenski)
    “Clonal interference is not the only dynamic that inhibits the progression of beneficial mutations to fixation in an asexual population. A similar inhibition may be caused by Muller’s ratchet (Muller, 1964; Haigh, 1978), in which deleterious mutations will tend to accumulate in small asexual populations. As shown by Manning and Thompson (1984) and by Peck (1994), the fate of a beneficial mutation is determined as much by the selective disadvantage of any deleterious mutations with which it is linked as by its own selective advantage.”
    http://myxo.css.msu.edu/lenski.....Lenski.pdf

    Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? (Thomas Bataillon)
    Abstract……It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.
    http://www.nature.com/hdy/jour.....7270a.html

    High Frequency of Cryptic Deleterious Mutations in Caenorhabditis elegans ( Esther K. Davies, Andrew D. Peters, Peter D. Keightley)”In fitness assays, only about 4 percent of the deleterious mutations fixed in each line were detectable. The remaining 96 percent, though cryptic, are significant for mutation load…the presence of a large class of mildly deleterious mutations can never be ruled out. ”
    http://www.sciencemag.org/cgi/...../5434/1748

    “Bergman (2004) has studied the topic of beneficial mutations. Among other things, he did a simple literature search via Biological Abstracts and Medline. He found 453,732 “mutation” hits, but among these only 186 mentioned the word “beneficial” (about 4 in 10,000). When those 186 references were reviewed, almost all the presumed “beneficial mutations” were only beneficial in a very narrow sense- but each mutation consistently involved loss of function changes-hence loss of information.” Sanford: Genetic Entropy

    A Quantitative Measurement of the Human Somatic Mutation Rate (2005)
    Our demonstration that µ is elevated in patients with cancer predisposition syndromes provides experimental support for the notion that the (elevated) mutation rate of individuals is associated with their risk of cancer.
    http://cancerres.aacrjournals......65/18/8111

    Trying to find an actual “hard” number for the “truly” beneficial mutation rate is, in fact, what Dr. Behe tried to do in his book “The Edge of Evolution”.

    Dr. Behe states in Edge of Evolution on page 135.
    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would explain the generation of the stunning complexity of molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.” That order of difficulty is put at 10^20 replications of the malarial parasite, by Dr. Behe. Thus, the actual rate for “truly” beneficial mutations, that would account for the machine-like complexity we see in life, is far in excess of one-hundred-billion-billion mutational events. Thus, this one in a thousand to one in a million number, for “truly” beneficial mutations, is actually far, far, too generous for the evolutionists to be using for their hypothetical calculations. In fact, from consistent findings such as these, it is increasingly apparent that the principle of Genetic Entropy is the overriding foundational rule for all of biology, with no exceptions at all, and that the belief in “truly” beneficial mutations is nothing more than wishful speculation on the naturalists part that has no foundation in empirical science whatsoever:

    Evolution vs. Genetic Entropy – video
    http://www.tangle.com/view_vid.....99f4016636

    The foundational rule of Genetic Entropy for biology, which can draw its foundation in science, semi-directly, from the Second Law of thermodynamics and the Law of Conservation of Information (Dembski, Marks), can be stated something like this: “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment,
    will always come at a loss of the original complex information in the parent species genome.”

    Professional evolutionary biologists are hard-pressed to cite even one clear-cut example of evolution through a beneficial mutation to the DNA of humans that would violate the principle of genetic entropy. Although evolutionists try to claim the lactase persistence mutation as a lonely example of a beneficial mutation in humans, lactase persistence is actually a loss of a instruction in the genome to turn the lactase enzyme off, so the mutation clearly does not violate genetic entropy. Yet at the same time, the evidence for the detrimental nature of mutations in humans is clearly overwhelming, for doctors have already cited over 3500 mutational disorders (Dr. Gary Parker).

  72. tsmith @ 29

    atheism is obviously a faith. its a worldview, and it requires faith in the atheist creation fable, evolution. you have faith there is no God…no proof, just as you have faith in evolution, which you cannot prove. So you believe that all that you see just happened, that evolution explains why giraffes are tall, and skunks are small. evolution is all in all..and atheism is nothing more than another faith. a rather absurd one at that.

    No, atheism is not a faith. As an atheist, I can say that I do not believe in a god because I know of no compelling evidence to support the existence of such a being. But neither do I worship the non-existence of any god. I feel no compelling need worship anything. In fact, the whole concept of religious worship has me slightly puzzled since I cannot conceive of a god vain enough to need people to worship it that would actually be worthy of such adoration. I do not pray to the void where a god might be if it existed. There are no churches where fellow atheists gather to sing the praises of nothing and hear readings from The God Delusion.

    I have faith, yes. I have faith that the Sun will rise in the east each morning and set in the west each evening. But I do not worship it as a deity. I have faith in the honesty and integrity of the scientists who tell us what they have discovered about the world. That does not mean I revere them as some kind of priesthood or their writings as Scripture.

    I have a view of how the world is that does not include a god. That view is limited, parochial, imperfect and is always open to improvement but I see no reason to believe I am overlooking the presence of deity.

    So, yes, like everyone else I have faith but that does not mean I belong to a faith. I can see that there are many that do belong to a faith and that it is very important to them. I can see that it brings them great comfort and strength, that it inspires some to do great good and others to do great evil. I would not deprive believers of their belief, even if I could, but neither do I believe that their belief licenses them to force it on me or others.

  73. Graham,

    The theory of evolution is how old and all we’ve got is a colorful narrative.

    But anyway say you get a duplicated gene.

    That gene also needs a binding site.

    It needs to be activated.

    It needs to be controlled.

    So I would say that gene duplication followed by rapid integration and mutation to allow for a differing function, would be a sign of evolution by design- What Dr Spetner calls the “non-random evolutionary hypothesis”.

    As for “descent with modification”, what , exactly, got “modified” to get vertebrates on a planet that never had one- ie populations of invertebrates?

  74. StephenA @70:

    No, the point was that such similarities do not provide evidence of a purely naturalistic origin. Or do the similarities between a Toyota station wagon and one made by Mitusubushi prove they both arose with no intelligent input?

    Thank you. I guess it is not enough to refer to Berra’s blunder in an argument against Darwinism. We must beat the dead mule into a pulp and then some.

  75. 75

    Diffaxial says:

    The traces of agency in biology should be quite specific, reflecting long experience with the manner in which agents intentionally originate biological structures.

    That’s an unnecessary restriction on a design inference, Diff. Detection of design traverses domains. When one sees a billions-long encoded instruction and nano-machinery in one cell that is more complex than all human machines combined on the planet, it screams design. Ask Antony Flew and James Le Fanu.

    If your statement were true, SETI is meaningless.

  76. Adel:

    What are your plans?

    1- Get a (another) new ACL for my right knee

    2- Recover

    3- Rehab

    4- Get the medial meniscus tear in my left knee taken care of

    5- Recover

    6- Rehab

    7- Go back to school in September

    8- From there I plan to get my degree, come out of retirement and open a business

  77. Joseph @ 67

    However we do have experience with information-rich systems.

    So we can use that experience to form inferences about information-rich systems in which the origins are not known.

    THERE is the analogy you hope for: the analogy from information rich human artifacts, and their origins, to information rich biological systems, and their origins.

    But it is that very analogy that is at issue. That an analogy can be constructed itself establishes nothing, and inferences are not warranted until the aptness and empirical usefulness of the analogy has been established.

    Here is how to do that: Employ the analogy as an heuristic to generate hypotheses about the intelligent design of biological origins that, in turn, lead to unique testable predictions (“inferences” is too strong, but “hypotheses” is just right). Testable empirical hypotheses that place the theory that entails them at risk of disconfirmation. Under those circumstances, confirmation of observations predicted from your model will indeed increase our confidence that ID has gotten something right.

    You argue that intelligent activities leave traces, and the prediction of such traces satisfies this request for predictive test. Unfortunately, that is far too general to guide actual research. The traces one expects from one design activity are not necessarily at all similar to those of another. To cite two recent examples, traces enabling the forensic detection of arson (accelerants, multiple points of origin) are entirely dissimilar to and have no relevance for the detection of the design of Corvettes (art work, engineering plans, clay models and prototypes). Nor is knowledge of one sort of trace much help in predicting the those that arise from another entirely different design activity, however much intelligent agency accounts for both. Knowledge of the design activities themselves, and the materials upon which designs are imposed, is required. That, of course, is what is painfully lacking vis the hypothesis that organisms were designed.

    So, WHAT traces do you predict necessarily arise from the design activities that yielded living organisms? What specific traces do you predict, such that failure to observe them places your theory in jeopardy of disconfirmation?

    Vis your linked paper, I find an abstract only, one that promises results that cast doubt upon Behe’s conclusions regarding the limits of Darwinian processes. Pointedly enough to have provoked a reply from Behe in all his himselfitude.

    That doesn’t sound promising for your position. However, absent the paper itself it is impossible to say more.

  78. No, atheism is not a faith. As an atheist, I can say that I do not believe in a god because I know of no compelling evidence to support the existence of such a being

    of course just because you know of no evidence, of course does not mean there is none. so you have faith that there is no god, because surely you would have to admit you do not know enough to make a definitive statement on the existence of non-existence of God.

    But neither do I worship the non-existence of any god.

    I would submit you do, you are your own god, deciding good from evil, right from wrong. and of course all atheists bown down to darwin.

    There are no churches where fellow atheists gather to sing the praises of nothing and hear readings from The God Delusion.

    but you have your high holy day, Darwin day, and the holy sacrament of atheists, and the left in general…abortion. I find it interesting that all atheists have the same world view, the same ideology, the same sort of faith…so by all I can tell, its a religion. and if I am not mistaken, the supreme court has held it as such..

  79. Joseph:

    what did you do to mangle your knees so? I will keep you in my prayers…I tore a bicep tendon..and the pain of recovery was FAR worse than the injury itself…it took almost a year to recover…little things like flossing my teeth were an agony at first…and I didn’t want to take pain pills for fear of re-injuring it…

  80. Surely, thats the whole point, there is such evidence, in that genes tend to show similarities to earlier genes in other/earlier forms. Thats what evolution is all about, descent with modification. Its why all those biologists out there accept evolution and laugh at ID.

    yeah if they didn’t bow down to darwin they’d be unemployed.

    ok then give me the exact mutations, in order, that led to the eye.

  81. tsmith,

    but you have your high holy day, Darwin day, and the holy sacrament of atheists, and the left in general…abortion.

    Ouch—that’s a bit inflammatory.

    Even though I’m not an atheist myself, I agree with Seversky that atheism is not a faith. Here’s a somewhat trivial but relevant analogy: I personally do not believe that Bigfoot exists, simply because of the lack of credible evidence. Would you call that lack of belief a faith?

  82. My comment at 37 was ridiculed by Jerry at 39. “Stupid”; apparently asking ID what is to be studied once design has been inferred, or proved is, well, unaskable! Why?
    When ‘design’ is detected, what in universes, is the point of going further?
    Jerry, as an anti-theist (I go one better than atheist, along with Dawkins, whom I believe coined the term) I must say your science sounds barren and dull. It appears to be mired in answers, not questions. If you know the answer why raise the question? This appears to be the guiding motivation of ID, that is,work backwards from a known, ‘design’, to an unknown, ‘the designer’, whom, of course you can never know, wonderful chicanery; how in universes, do you and your supporters see anything marvellous (in creation?) at all

  83. No, atheism is not a faith. As an atheist, I can say that I do not believe in a god because I know of no compelling evidence to support the existence of such a being.

    I suppose it’s to the degree to which you take it. Being skeptical of claims is obviously not a faith.

    Feeling obliged to defend one’s worldview by attacking those held by others, however, a la Dawkins or Madalyn Murray O’Hair, is solidly expressing a faith.

  84. apparently asking ID what is to be studied once design has been inferred, or proved is, well, unaskable! Why

    Because ID can’t do it. An ammeter will tell you the electric current in a circuit. It won’t tell you why there is or isn’t a current. You have to figure that out using other means.

  85. rvb8,

    You should refrain from commenting since you do not seem to understand the debate. There is little if any research on the face of the earth that people who espouse ID would refuse or not be interested in doing. They may come to different conclusions than others on some studies but then again they may not. Because of a more open minded approach to research they would actually expand the topics considered.

    So given that, how can the research ID would do be barren or dull. No I think that it is those who criticize ID who are barren and the dullards.

    I would stay in the background for awhile till you are up to speed otherwise you will continue to make these marvelously stupid comments.

  86. 86

    jerry,

    —-”I would stay in the background for awhile till you are up to speed otherwise you will continue to make these marvelously stupid comments.”

    Is that necessary jerry?

  87. rvb8,

    You need to explain your logic that made you to conclude that finding design inevitably leads to a cessation of science.

    Do you really think that if the SETI actually do find ETI, that they will stop their efforts to find out more? Why would anyone that find design in the building blocks of biological life stop their investigation?

    Since you seem to be very sure of this “magical end to science” once design has been detected, I think you can answer my questions above… they are not rhetorical.

    I can formulate a counter question for you and your professed anti-theistic view. Why would any anti-theist bother to do any science, if there is no purpose to any action in our reality? Why so sure about your mindless method if you have no reason for it?

    You see… it is very easy to profess an irrational world view, but it is not that easy to act according to irrational convictions. Maybe it is because we humans are meant to FIND truth not to MAKE truth.

    Regards,
    Michael
    P.S. Science cannot bare the burden of naturalistic myth making much longer.

  88. Clive,

    rvb8 has made some ill informed negative comments (stupid comments) about ID. There is no intent to learn from rvb8 only to sling stuff.

    I am pointing this out to rvb8 in words he used, “marvelously,” “barren” and “dull.” I use the word stupid as a synonym for ill informed and it refers to his comments. He should not be making his comments since as I said he is extremely ill informed and thus giving him advice to stay out of things till he understand the issues.

    If rvb8 had good intentions he would ask questions not pontificate on our ignorance.

  89. 89

    Just thought I’d chime in that the real reason it’s not a fair test is because even if we found a gene that fit his criteria, PZ would find a way to say that it doesn’t, and he has many options for doing so. In other words, the proctor of the exam has already determined every grade will be an F before anyone has taken the test. If this test were offered more honestly, maybe there would be a reason to talk. Since it’s obviously not, it’s all showbiz. As if you couldn’t tell by listening to the narrator. Sounded like the intro to a horror movie or something, lol.

  90. I personally do not believe that Bigfoot exists, simply because of the lack of credible evidence. Would you call that lack of belief a faith?

    no because belief in bigfoot is not an all-encompassing view of the world…from dictionary.com the defnition of religion:

    re?li?gion??/r??l?d??n/ Show Spelled Pronunciation [ri-lij-uhn] Show IPA
    –noun 1. a set of beliefs concerning the cause, nature, and purpose of the universe, esp. when considered as the creation of a superhuman agency or agencies, usually involving devotional and ritual observances, and often containing a moral code governing the conduct of human affairs.
    2. a specific fundamental set of beliefs and practices generally agreed upon by a number of persons or sects: the Christian religion; the Buddhist religion.
    3. the body of persons adhering to a particular set of beliefs and practices: a world council of religions.

    atheist have a shared set of beliefs ‘concerning the cause, nature, and purpose of the universe’

    so yes it is a religion.

  91. Jerry,
    I’m not angry, or even all that argumentative, but I do seem to have touched a raw nerve; namely research and the lack thereof from ID.
    Just that this simple fact is undeniable is hardly cause to call me ‘stupid’, I would not do this to you inperson and I retain that simple morality while posting.
    mullerpr: Why would an anti-theist bother to do science? To gain an insight into how things came to be, minus a designer, or any other outside force. Curiosity, a very evolved function. Because without a designer the “how?”, becomes infinately more interesting, and infinately less easily explained away, that’s why.

  92. Diffaxial:

    So, WHAT traces do you predict necessarily arise from the design activities that yielded living organisms? What specific traces do you predict, such that failure to observe them places your theory in jeopardy of disconfirmation?

    Irreducible complexity and/ or complex specified information.

    Both have been defined far more rigorously than anything evolutionists have to offer.

    So all you have to do is to demonstrate that IC and CSI can arise via nature, operating freely and ID falls.

    And that is what I have been telling you for months and everyone else for years.

    Vis your linked paper, I find an abstract only, one that promises results that cast doubt upon Behe’s conclusions regarding the limits of Darwinian processes. Pointedly enough to have provoked a reply from Behe in all his himselfitude.

    The promise made has been soundly refuted.

    The jest of the paper is that if something requires two specified mutations then that would take about 25 million years in a fast reproducing organism such as the fruit fly.

    And that is only if no deletrious mutations occur during that same time frame.

  93. tsmith,

    Balad, Iraq March 2004.

    I think I was trying to prove one can outrun an RPG :)

  94. Tragic @ 89

    Just thought I’d chime in that the real reason it’s not a fair test…

    So, what would be?

  95. At 92:

    The jest of the paper is that if something requires two specified mutations …

    Yes, many people did think it was a joke. :)

  96. 96

    Diffaxial [77]:

    Vis your linked paper, I find an abstract only, one that promises results that cast doubt upon Behe’s conclusions regarding the limits of Darwinian processes. Pointedly enough to have provoked a reply from Behe in all his himselfitude.

    That doesn’t sound promising for your position. However, absent the paper itself it is impossible to say more.

    A free pdf of the full paper is available here:

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

    Yes, it is critical of Behe’s claims.

  97. 97

    Joseph,

    We are all in your debt for your service to our country.

    A debt we can never repay.

  98. hazel,

    It is a peer-reviewed paper.

    Adel,

    Dr Behe has throroughly refuted the premise of the paper- that his “edge” has been sought and found.

    You can read Behe’s responses here- just scoll down to “Waiting Longer for Two Mutations, Part 1″

  99. P.S. on 95: Sorry, I couldn’t resist the joke. I don’t even know what paper you were talking about.

    For the record, the word wanted is “gist”.

  100. rvb8-Just that this simple fact is undeniable is hardly cause to call me ’stupid’

    He didn’t call you stupid, rvb8. He called your comment stupid. There is a big difference.

    For instance, calling our science “barren and dull” is not the same as calling us “barren and dull”, do you agree?

    And “when ‘design’ is detected, what in universes, is the point of going further?” is a pretty stupid comment. Einstein presumed a design to the universe. Do you think he wanted to quit?

  101. Adel DiBagno
    Once the design inference is reached it opens up new questions. And given our nature we will do what we can to answer them. . . What are your plans?

    With regard to attempting to find the identity of the designer maybe we just put that on hold — at least with regard to using a naturalistic methodology.

    With regard to understanding the universe, once design is presumed we can focus our study as to how the forces of the universe work and use this knowledge for our benefit, materially and philosophically.

    If you want to consider a “science-stopper” suppose the universe is designed and we insist on working from the assumption that it is not.

  102. tsmith @ 98:

    atheist have a shared set of beliefs ‘concerning the cause, nature, and purpose of the universe’

    so yes it is a religion.

    I may be ill informed and ignorant about what religion is, but I have been living under the assumption that it is essentially about salvation of man’s soul?

    As far as I can tell, beliefs relating to cosmology, astronomy, geology and many other scientific issues are irrelevant wrt salvation, which is about dying and resurrecting with Christ?

    That is at least how I understand Christianity. Other religions probably have other criteria but as far as I know they are more about spiritual matters (for instance man’s relation to the deity) than about beliefs regarding the material world.

  103. No, atheists don’t have a “shared set of beliefs concerning the cause, nature, and purpose of the universe.

    Atheists have all sorts of beliefs about these things, with the only common feature being that there is no God involved.

  104. Graham: Thats what evolution is all about, descent with modification. Its why all those biologists out there accept evolution and laugh at ID and and wailing about probabilities.

    Graham – are you laughing as well? and who are “all those scientists” – how much hand waiving, how many assumptions, how many straw-men and as if these probabilities have no weight. Are you able to understand StephenA’s point at all? Do you ignore so you can obfuscate on purpose? Seems you live your life on the laws of chance yet distain probabilities. Well that is par for the materialist.

    From Wesley on Rom. 1:20 “For those things of him which are invisible, are seen – By the eye of the mind. Being understood – They are seen by them, and them only, who use their understanding”

    Please don’t interpret this post as being in the same spirit as your. i.e. I am not laughing at you, but would ask you one question – would you WANT to know the/a “Creator” anyway?

    “There was a time before the past
    When things to come were clearly cast”

  105. The author of the OP seems to have misinterpreted a couple of things.
    First, that was not PZ’s challenge, he simply embedded the video on his site.

    Second, the challenge has nothing to do with homology, it is asking for unambiguous evidence for a designed/created gene.

    As it is the position of the ID community, or so I infer, that genes, being the primary carriers of “information”, such information by definition being of an Intelligent source, it seems a reasonable challenge.

    Joseph – As an aside, what unit were you with in Iraq? What was your MOS?

  106. As another aside, Behe’s post on 2-mutation evolution is mentioned. Is there any evidence that evolution requires such specific, sequential mutation accumulation?

  107. No, atheists don’t have a “shared set of beliefs concerning the cause, nature, and purpose of the universe.

    Atheists have all sorts of beliefs about these things, with the only common feature being that there is no God involved.

    Could you not say the same thing about religious people from all different faiths, with the exception of the belief that there is a god involved?

    Are atheists not just as faithful in purely naturalistic processes explaining the cause, nature, and purpose of the universe as religious people are toward God or gods? Does deep time and limitless chance not serve the same purpose in a naturalistic world view to explain the “illusion” of design? Atheism is a faith on many fronts, while not explicitly religious, there certainly are many religious implications following philosophical naturalism.

  108. Cabal: 102 Correct – Belief about the Creator revels who you are spiritually. And yes, the “religion” (a true Christian would not refer to the Revelation as a religion – religion being what men think about things including atheism) of Christianity is about the Evidence provided for its confirmation and revealed to be True by God into to New Resurrected Soul imparted. This is WHY the natural man can not understand or even want to know God as 1 Cor. 2:14 points out.

    This is why the anti-ID persons use argument such as Graham did in #69 did to (intentionally or not) obfuscate the real science. Its hand waiving. Pay no attention to the man behind the curtain.

  109. 109

    jerry,

    —-”If rvb8 had good intentions he would ask questions not pontificate on our ignorance.”

    Fair enough.

  110. PaulN:

    Are atheists not just as faithful in purely naturalistic processes explaining the cause, nature, and purpose of the universe as religious people are toward God or gods?

    I think you are conflating “faith” with “Faith” in addition to adding some unnecessary baggage to what an atheist may or may not ‘believe.’

    For example, I am pretty suire that the typical atheist does not SEE ‘purpose’in the universe, so ascribing their ‘faith’ in naturalism to explain ‘purpose’ is a strawman, it seems to me.

    As an atheist, I have “faith” that natural processes and mechanisms are sufficient to explain the phenomena that we can investigate in any real way, in large part because of the track record of such investigations, therefore, I do not need to have “Faith” in this.

  111. 111

    derwood [105]:

    Second, the challenge has nothing to do with homology, it is asking for unambiguous evidence for a designed/created gene.

    Still waiting for a candidate after a hundred posts.

    But I’m not convinced that lack of homology is ruled out, at least as a place to start. bfast in #2 mentioned orphan genes – open reading frames with no homology to any known gene. There might be a lot of them worth examining – assuming one had some clear criteria for distinguishing the designed from the evolved.

  112. Interesting that bfast referred to them as ‘orphan’ genes, rather than ‘orfan’.

    Anyway, yes, they seem interesting, however, I came across a recent paper which looked at orfans in E.coli and concluded that they are likely the products of phage activity:

    “Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions.”

    from Bacterial Genomes as New Gene Homes: The Genealogy of ORFans in E. coli. It will be interesting to see what comes of it, but I agree that even if these genes end up being enigmas, how that counts as “design” remains to be established.

  113. derwood @110,

    I’m terribly sorry, but can you explain to me the difference between “faith” and “Faith” please? I’ve never been familiar with such a distinction before.

    As an atheist, I have “faith” that natural processes and mechanisms are sufficient to explain the phenomena that we can investigate in any real way, in large part because of the track record of such investigations, therefore, I do not need to have “Faith” in this.

    How can you be so sure that these natural processes themselves aren’t designed? Also are you implying that designed systems cannot be investigated in any “real” way because they don’t follow methodological naturalism? It sounds to me like you’re defining the terms and conditions in which anything should be “truly” investigated according to a naturalistic mindframe. Answer me one question please, how would you find the truth using this methodology if the universe really is designed?

  114. PaulN:

    derwood @110,

    I’m terribly sorry, but can you explain to me the difference between “faith” and “Faith” please? I’ve never been familiar with such a distinction before.

    Hi Paul,
    Sorry – I meant to explain that and failed to do so.
    For me, small ‘f’ faith refers to more of an expectation, while capital ‘F’ Faith refers to what I suppose we can refer to as ‘religious faith’, as in belief without the need for evidence.

    Me:
    As an atheist, I have “faith” that natural processes and mechanisms are sufficient to explain the phenomena that we can investigate in any real way, in large part because of the track record of such investigations, therefore, I do not need to have “Faith” in this.

    PaulN:
    How can you be so sure that these natural processes themselves aren’t designed?

    Because it is turtles all the way down? For my part, I do not and rationally cannot deny the possibility of some ‘higher power’getting the ball rolling, so to speak, but at the same time, I see no reason TO believe that. Not understanding something for me is no reason to adopt a ‘designer did it’ position.

    Also are you implying that designed systems cannot be investigated in any “real” way because they don’t follow methodological naturalism?

    In a snese, I am concluding that premised on some of the things I have read, written by ID advocates themselves. For example, when design advocates use ‘good design’ arguments to support their position, they reject examples of ‘bad design’ as an argument against it, claiming that the designer’s motives are unknown, so what we might see as bad design really isn’t. But how then to determine the designer’s motives? Seems that the supernaturalistic mindset sets up, by definition, an unfalsifiable position.
    If I am incorrect, perhaps you can give an example of valid research into the supposed ‘intelligent design’ of a structure/entity that does NOT rely on contrived probability calculations, analogies, and the like?

    It sounds to me like you’re defining the terms and conditions in which anything should be “truly” investigated according to a naturalistic mindframe.

    Perhaps you can correct me, then. How, using a supernaturalistic (?) mindframe would one investigate the natural world and identify evidence for supernatural/Intelligent intervention?

    Answer me one question please, how would you find the truth using this methodology if the universe really is designed?

    We are constantly told that that WAS the mindframe of all the great scientists of old, and yet these folk did not seem able to find any concrete evidence that the universe was designed.

    Using a naturalistic mindframe to study the natural world seems reasonable to me, and it seems to me that unless this designer used what we might refer to as “magic” that evidence for a non-natural creation might be forthcoming.

    I am aware of many philosophical arguments surrounding this issue, but philosophical arguments, to me, are the arguments employed when one cannot muster evidence.

    I find it somewhat sad that ID advocates are forced to try to find ‘Design’ in bacterial flagella and the like using what amount to math tricks and semantics when they believe that this ‘designer’ had the power to create the entire universe and everything in it. It seems like it should be a bit more obvious.

    Using a supernaturalistic mindframe, tell me – what do reearch programs look like?

  115. derwood–As an atheist, I have “faith” that natural processes and mechanisms are sufficient to explain the phenomena that we can investigate in any real way, in large part because of the track record of such investigations, therefore, I do not need to have “Faith” in this.

    Are you saying these investigations have never provided incorrect answers, or are you saying that while this method routinely gives wrong answers its ability to self-correct inevitably leads to the right one and that you have the faith that through this method all will be known?

    Using a supernaturalistic mindframe, tell me – what do reearch programs look like?

    Why would you use a “supernaturalistic” research program to investigate nature?

  116. Seversky @72

    “No, atheism is not a faith. As an atheist, I can say that I do not believe in a god because I know of no compelling evidence to support the existence of such a being.”

    I respectfully disagree.

    I think you have made Chance your god. You must believe that all that exists, is simply by Chance, that our universe won the lottery of potential universes that (also by chance) have remarkably fine-tuned parameters for life. You may not worship Chance, but your world view crumbles without it. As well, without positive evidence that the universe began by Almighty Chance, you must excercise faith that ALL the other explanations are less plausible. That takes a lot of faith. Unfortunately, Chance does not “do” anything, is not a causal agent. I’m afraid you have put your faith in something….that does nothing.

    I think there are is a reasonable alternative. What do you think?

  117. 117

    Diffaxial @94

    Well I have no doubts that you actually read my post, but to make it more clear a fair test would at least include the possibility of the proctor allowing you to pass it.

  118. Alan (see #104),

    Sorry, I just got back.

    As I understand it, (Im not a scientist), evolution claims that we have descended from earlier forms, by many small changes. Thus evolution predicts that we would find precursors to our genes in earlier forms. This seems to be obvious. If we found an entirely new (human) gene that had no precursors in earlier forms (monkeys etc), it would be a problem for evolution, and a comfort to ID.

    Im not suggesting that ID cannot ever have any precursors. The car analogy demonstrates this. Im merely making the simple point that an entirely new gene with no precursors would be a problem for evolution and of interest to ID, thus I would have thought that the ID crowd would like to take up the challenge.

    (And the Bible quotes dont help).

  119. “Still waiting for a candidate after a hundred posts.”

    Anyone have any doubts about what drives this frivolous comment. This is why it is so easy to read the anti ID people here. They are so so very transparent.

    The answer was provided far above. They all are designed. Each gene encodes proteins through a process only known to exist through intelligence. Now it is possible and that the new paradigm coming into ascendancy, which is trying to replace Darwinian gradualism, will show where unused areas of DNA mutate into a usable gene or two and are then exapted to be functional could end up explaining some examples. However, current examples are thin.

    That is what the whole discussions about searches is about, the possible finding of these genes by serendipity and Allen MacNeill’s 50+ engines of variations. If it could show that thousands or even a few hundred genes arose this way or maybe even a couple dozen or so, ID would be on the run. However, even if this process was able to show genes arising naturally, it begs the question of the transcription and translation process necessary to make the information specified. The genes only become specified by the elaborate process of producing proteins that have function. Now where did that process come from?

    So the stunt published on PZ Myers site is a desperate attempt to cover up the inadequacy of current evolutionary biology to explain macro evolution. Do you think they would waste all this time let, alone a nano second, trying to discredit ID if they could point to how all the genes developed naturally.

    I think folks around here need to look at human nature a little more to understand what is going on. The anti ID crew haven’t got anything or else they would be acting quite differently. Does anyone remember the Visa commercial where the artist was trying to impress his girl friend that his blank white canvas represented a new level of art and her astute reply was that the art supply store wouldn’t take his check. So the selling point was that he should use a Visa card. I don’t think anyone around here should start cashing the anti ID people’s checks let alone take their credit cards. They are bankrupt.

    Hey, this isn’t to say that some genes or maybe several arose through nature but then they must climb the next hurdle and that is the creation of specified information. Ribosome et al., here we come.

  120. Before continuing a debate about what is a religion and what is not, what about going to the roots:

    http://en.wikipedia.org/wiki/Religion#Etymology

    The English word religion has been in use since the 13th century, loaned from Anglo-French religiun (11th century), ultimately from the Latin religio, “reverence for God or the gods, careful pondering of divine things, piety, the res divinae”.[5]

    It strikes me as somewhat contradictory to say what amounts to:

    Belief in God is religion.
    Non-belief in God is religion.

  121. “non-belief” is a belief. But hey, this thread has nothing to do with religion and in the past 6 weeks some have spent nearly a couple thousand comments of belief on their non beliefs.

  122. Tragic @ 117:

    Well I have no doubts that you actually read my post, but to make it more clear a fair test would at least include the possibility of the proctor allowing you to pass it.

    Fine. You get to be the proctor. Describe your test, and the proctoring by means of which you would decide the outcome.

    What test?

  123. 123

    jerry [119]:

    The answer was provided far above. They all are designed. Each gene encodes proteins through a process only known to exist through intelligence.

    Is that The Answer, or jerry’s answer? Does everyone in the ID movement agree?

    How does jerry’s special creation of every gene square with Behe’s The Edge of Evolution: The Search for the Limits of Darwinism?

    It was my understanding, subject to correction, that Behe granted naturalistic mechanisms the ability to generate a whole lot of biological variation up to his edge. In 2007, Behe said,

    I would suggest that Richard Dawkins re-read my book. In it I clearly state that random evolution works well up to the species level, perhaps to the genus and family level too. But at the level of vertebrate classes (birds, fish, etc), the molecular developmental programs needed would be beyond the edge of evolution.

    http://calitreview.com/260

    And if I recall correctly, hasn’t jerry himself characterized a whole lot of examples of biological variation as “microeveolution, which is no threat to ID”?

  124. derwood,

    I was a technical advisor in Iraq (and Colombia, Saudi, Egypt, Ireland, Mexico- well a lot of different countries- but that is another story).

    I have worked with companies that supply technology to militaries around the world.

    And that means I have also worked with militaries around the world.

    But anyway the point of Behe’s claim is that not any mutations will do the trick.

    With gene dupication that new gene needs a binding site. And not just any binding site will do- it has to be specific to that gene.

    Also that gene needs to activated and/ or repressed and at specific times. Then there are enhancers which dictate how many times that gene is transcribed and translated.

    All of that has to be specific to that gene.

    Then there needs to be something for that new product to do such that it does not arbitrarily bind to already functioning cellular systems and mess them up.

    So I would say that gene duplication followed by rapid integration and mutation to allow for a differing function, would be a sign of evolution by design- What Dr Spetner calls the “non-random evolutionary hypothesis”.

  125. Graham,

    Small changes to what, exactly, led to the evolution of vertebrates from invertebrates?

    That seems to be the million dollar question. And so far the ONLY answer I have ever receieved is “the DNA gets modified” (or the genome).

    However the people who accept that answer are not interested in science.

  126. Mr DiBagno,

    I hadn’t read that statement of Dr Behe’s before, and I find it surprising. I thought he accepted that birds are special kind of fish? :)

    I’m not sure why Dr Behe thinks this level of diversity is beyond the scope of evolution. Back in the Mississipian era, when some amniote differentiated into amniotes with 0, 1, or 2 holes in the skull, the developmental changes to create holes wasn’t that great, was it?

  127. 127

    I don’t know, Mr Nakashima, you’ll have to ask Dr Behe…

  128. I base nearly all my conclusions on Behe’s Edge of Evolution. To me that is the definitive work so far. I also base a lot of my conclusions on Sherlock Holmes and the story of Silver Blaze and one of the most famous insights in history. Namely, of the dog barking in the night.

    Both these works support/prove my conclusions about the design of genes.

  129. Cabal: simple – religion, belief, faith: the BEST definition is what it actually is – what one thinks is true which automatically is what one puts ones faith, trust, belief in – right
    forget the dictionary

  130. 130

    This article by Koga and Morii contains info on 3 ORFan enzymes in Archaea which regulate ether-type lipid biosynthesis:

    http://www.pubmedcentral.nih.g.....d=17347520 .

    These enzymes are part of the pathway that makes cell membrane lipids different in Archaea than other domains (bacteria and eukaryotes). One mentioned is: sn-Glycerol-1-phosphate dehydrogenase, from Methanocaldococcus janaschii, found at Uniprot # Q58122 at:

    http://www.uniprot.org/uniprot/Q58122 .

    Picture of protein is at Swiss Model Repository, enter Q58122 and search (it’s worth the trouble) here:

    http://swissmodel.expasy.org/repository/ .

    Gene number is NC_000909.1, sequence of 1,664,970 nucleotide bases found:

    http://www.ncbi.nlm.nih.gov/nu.....;flip=true

    Online book discussing criteria for Comparative Genomics,
    Sequence-Evolution-Function: Computational Approaches in Comparative Genomics
    by
    Eugene V. Koonin
    Michael Y. Galperin found here:

    http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=sef

    Discussion of non-orthologous genes,
    “Chapter 7. Evolution of Central Metabolic Pathways: The Playground of Non-Orthologous Gene Displacement,” found:

    http://www.ncbi.nlm.nih.gov/bo.....hapter.371 .

    A very interesting paper by Koonin and Wolf about the emerging data of comparative genomics is “Genomics of bacteria and archaea” found here:

    http://nar.oxfordjournals.org/.....36/21/6688 .

    Many genes are unique to one or a few species.

  131. 131

    jerry: In “Silver Blaze” The dog did nothing in the night…

    ps: Please pm Erasamus ASAP!

  132. 132

    GeneID (ncbi) for sn-Glycerol-1-phosphate dehydrogenase is 1451590:

    http://www.ncbi.nlm.nih.gov/si.....rm=1451590

    and covers 645966-644959 .

  133. Scot.David,

    So you understand my point completely.

  134. “Is there any point to which you would wish to draw my attention?”

    “To the curious incident of the dog in the night-time.”

    “The dog did nothing in the night-time.”

    “That was the curious incident,” remarked Sherlock Holmes.

    …”Before deciding that question I had grasped the significance of the silence of the dog, for one true inference invariably suggests others.

    So what do we conclude by the silence of the Darwinists here and in the press both popular and academic. A curious incident. What are the inferences?

  135. 135

    Correction & clarification of my previous entries @130 & 132: the genome number (not gene number) of the archea, M. janaschii, is NC 000901.1 and the organism has 1,664,970 nucleotide bases. The GeneID number 1451590 is for the enzyme I mentioned and has about 1000 nucleotide bases.

    For comparison, another Methanocaldococcus janaschii GeneID is # 1451939 for one protein segment of RNA polymerase RNA polymerase copies DNA to RNA. (The protein sequence is at Uniprot #Q58445):

    http://www.uniprot.org/uniprot/Q58445

    The gene is sequenced at:

    http://www.ncbi.nlm.nih.gov/nu.....port=graph

    from 974406 to 978834 (over 4000 nucleotide bases). Press the sequence button on top left of toolbars to see the sequence.

  136. Ms Womanatwell,

    If you are proposing genes that meet the challenge stated in the video, post them in the comments on the original YouTube video. The creator of that video (C0nc0rdance) will reply.

    This video was created by C0nc0rdance, then a beginning and ending were added by Thunderf00t, then it was blogged about on Pharyngula, then here at UD.

    Please copy us on any reply you receive! Thanks!

  137. 137

    Diffaxial @ 122:

    If a protein requires more than two non-selectable mutational steps from any other functioning protein, it was designed. That would be a test to apply to nature.

    If you want a single all-encompassing test to determine forever if ID is true or false, you won’t find it because science doesn’t work that way. As you guys are so fond of reminding us, evolution has 150 years of science behind it. If your definition of a scientific theory is that it has passed a fair test, then what test did evolutionary theory pass that led to its acceptance? Perhaps if you show me how this process works by giving examples, I can answer your question better. Until then, I’m not willing to discard all scientific knowledge other than that which pertains to this so-called “test”, which actually sounds more like a taunt from some professional wrestler.

    Besides which, there probably are genes which will pass the test as any sensible person would be willing to admit. But PZ Myers is not such a person, and therefore I reject his little test.

  138. If a protein requires more than two non-selectable mutational steps from any other functioning protein, it was designed. That would be a test to apply to nature.

    Your test smuggles its conclusions, secreted in the word “non-selectable” (and “functioning.”)

  139. To tragic mishap

    sounds more like a taunt from some professional wrestler

    No, it sounds like every test that every piece of science has faced (and passed). True, it is expressed in a melodramatic way, but it is basically asking to dig into the evidence and see if the evidence supports ID or evolution, or maybe neither. This is exactly what scientists do all the time, challenge science with difficult questions.

    Assuming that the resources were available to pursue it, what possible objection could you have ?
    The worst case seems to be an inconclusive result, but it is possible that it may support ID and refute evolution.

  140. Graham,

    ID does not even attempt to refute evolution.

    All ID says about that is that non-telic processes are NOT the sole driver.

    IOW ID argues against the blind watchmaker as having sole dominion over the variation and diversity.

  141. Joseph:
    derwood,

    I was a technical advisor in Iraq (and Colombia, Saudi, Egypt, Ireland, Mexico- well a lot of different countries- but that is another story).

    I have worked with companies that supply technology to militaries around the world.

    And that means I have also worked with militaries around the world.

    Sure, but you claimed to have been injured seeing if you can ‘outrun an RPG’in March, 204, near Balad Iraq. I did some searching and found that in 2004 in or near Balad the only non-military injuries were from vehicle attacks – one an RPG attack in which all the occupants of the vehicle were killed, one in which the vehicle was hit by a roadside bomb. Neither took place in March.


    But anyway the point of Behe’s claim is that not any mutations will do the trick.

    In terms of the specific issue he was looking at. Did Behe establish that this two-sequential -mutation requirement is widespread?


    With gene dupication that new gene needs a binding site. And not just any binding site will do- it has to be specific to that gene.

    During gene duplication events, it is quite common for the binding sites to be duplicated as well. In the beta globin cluster, for example, where in humans there are 5 duplicates, all of the duplicates retained their promoter and enhancer sites.
    Did Behe address any actual cases?


    Also that gene needs to activated and/ or repressed and at specific times. Then there are enhancers which dictate how many times that gene is transcribed and translated.

    That is not exactly what enhancers do, but see above.


    All of that has to be specific to that gene.

    Transcription factor binding sites are actually pretty common, even in noncoding DNA. Not that it matters, since as I indicated, in the instances in which gene duplications have been investigated, such sequences are partof the duplicated region.


    Then there needs to be something for that new product to do such that it does not arbitrarily bind to already functioning cellular systems and mess them up.

    In a new duplicate, the product would be the same as the old, at least initially. Additional product can, in some cases, produce phenotypic or physiological change.


    So I would say that gene duplication followed by rapid integration and mutation to allow for a differing function, would be a sign of evolution by design- What Dr Spetner calls the “non-random evolutionary hypothesis”.

    So, everything and anything count as pro-ID ‘evidence.’

    Spetner’s hypothesis is fairly weak, even when it was first concocted.

  142. Jerry:
    The answer was provided far above. They all are designed. Each gene encodes proteins through a process only known to exist through intelligence.

    I was unaware that it was a human’s ability to ‘know’ something that rendered it the product of ‘intelligence.’ A rather odd definition/application, to be sure.

  143. “I was unaware that it was a human’s ability to ‘know’ something that rendered it the product of ‘intelligence.’ A rather odd definition/application, to be sure.”

    If I had a clue what you were talking about, I might respond to this.

  144. 144

    Diffaxial:

    “Your test smuggles its conclusions…”

    Really? So you are saying the test is unfair because it smuggles in its conclusions? Huh. Sounds almost exactly like the objections to Myers’ test from ID proponents, that it smuggles in the conclusion that homology refutes design.

    Graham:

    “No, it sounds like every test that every piece of science has faced (and passed).”

    Really? “Every piece of science” has passed tests like this? Anything that has failed these “tests” does not qualify as a “piece of science”? Than you should not have trouble letting us in on these “tests” that ultimately validated evolution. Please help a poor student understand this concept.

  145. tragic mishap:

    letting us in on these “tests”

    Yes, thats pretty much it. If the evidence doesnt support an idea, the idea is discarded. This is how science works.

    Evolution is no exception. Poking into the genetic makeup shows all the similarities/differences that have been described over & over and which support the evolutionary model.

    The use of the word ‘test’ is figurative. Its not a formal process like a school test, just a constant accumulation of evidence that supports an idea. This is why the biology community supports evolution and mocks ID.

  146. 146

    Nakashima,

    The gene I put in my post has to do with lipid metabolism in an Archaea. For a while, biologists thought Archaea were direct ancestors of bacteria. Then they found that their cell membranes are composed of phospholipids with different composition than those of bacteria. So this type of lipid metabolism proved Arachaea are not direct descendents of bacteria. This is in contrast to the challenge of this post that wants to prove evolution through genes.

    I again put the link to this article “Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world,” by Eugene V. Koonin* and Yuri I. Wolf of the National Center for Biotechnical Information (NCBI). It was published October 2008.

    http://nar.oxfordjournals.org/.....36/21/6688

    The article is very important. It talks about how a vast majority of genes being found in the newly sequenced whole genomes are unique to one or, more often, a very small number of organisms. Several paragraphs from this article include:

    Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.

    The paradox of today’s state of the art is that, despite the tremendous progress—but also owing to these advances—the emerging complexity of the prokaryotic world is currently beyond our grasp. We have no adequate language, in terms of theory or tools, to describe the workings and histories of the genomic network. Developing such a language is the major challenge for the next stage in the evolution of prokaryotic genomics.

    Please see the graphs of genes from sequenced organisms (they are very colorful). They show how the genes sit separately in isolated islands.

    I do not understand why the standards of the NCBI are inadequate for the challenger or for many posters in this website.

    Also, Casey Luskin has spoken for Discovery Institute at:

    http://www.evolutionnews.org/2......html#more .

  147. 147

    Correction to previous post: …this type of lipid metabolism proved Archea are not direct ancestors of bacteria (or, for that matter, direct descendants either–they are looking for a Last Unknown Common Ancestor).

  148. “If I had a clue what you were talking about, I might respond to this.”

    I know the feeling.

  149. “I know the feeling.”

    Then maybe you should ask. Essentially I asked what your statement was about and you failed to provided an answer.

  150. Thunderf00t replied to this post on YouTube.

    Challenging the Discovery Institute to Discover: Part 2
    http://www.youtube.com/watch?v=Sq3mKJxxZgg

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