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“Intelligent Design Challenge” Challenge

I have a challenge for Ian Musgrave. The sequences provided code for 80 amino acids. That’s almost certainly not a whole protein and not enough information to determine design/non-design. Indeed, none of the six sequences begin with a start codon which means we aren’t given enough information to even frame the sequence into codons.

Ian states:

Determining where a genome has been produced or altered by an intelligent designer is a matter of some importance. Consider the claims that the HIV virus was engineered as a biowarfare weapon, or the concern that virulence genes from other organisms could be inserted into viruses and bacteria to “weaponise” them.

If this were for real we would know the species in which the suspect gene appeared as well as the entire gene sequence rather than a small fragment of it. I challenge Ian to give us the information we’d have to work with in the real world – full gene sequence (framed by start/stop codons!) and the species in which it appears. Fat chance. That would make it a fair test and evolutionists like Ian aren’t interested in a fair test.

I can give him the method ahead of time. We’d compare the suspect gene to a full genome sequence of the closest relatives we could find in the genome database. We’d then take the closest matching gene, apply the principles Mike Behe described in “The Edge of Evolution”, and from the sequence deviations find if the suspect gene goes beyond the edge of evolution or not.

Determining the functionality of a gene from its sequence isn’t within the scope of ID so that’s a red herring.

Addendum 1: Well at least one thing is evolving – Ian’s challenge. He’s saying that researchers trying to determine if some new strain of bug is a bioterror weapon don’t have the luxury of full sequences. Huh? 454 Life Sciences gear can sequence 7 megabases PER HOUR in genomes up to 50 megabases long. Just how long are the genomes we’re talking about here, Ian? Bioengineered terrorist mice? It takes one researcher and one machine a week to sequence a typical bacterial genome. You can bet your bottom dollar in a bioterror scenario it won’t be one researcher and one machine in a 9-5 job with a long lunch break. One thing he’s still failed to acknowledge is that function detection is outside the scope of design detection. Other tools are used for determining the function of any given DNA sequence. ID would sure help speed up the search though by identifying the designed sequences so they can be knocked out and see what changes as a result. Breaking little bits and observing the result is standard operating procedure in black box reverse engineering of everything from integrated circuits to software to genomes.

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56 Responses to “Intelligent Design Challenge” Challenge

  1. “I can give him the method ahead of time. We’d compare the suspect gene to a full genome sequence of the closest relatives we could find in the genome database. We’d then take the closest matching gene, apply the principles Mike Behe described in “The Edge of Evolution”, and from the sequence deviations find if the suspect gene goes beyond the edge of evolution or not.

    Now that’s well said.

  2. The whole concept of the debate is confusing look at it this way they say Darwinism cant hold up But neither can Genisis in either senario the Biodiversity of the world can not be explained even ID either The nature of how life began on Earth can only be explained through thorough research of the facts and a quest for knowledge of those facts in time we may find the answer but not in our lifetime. Darwinism says there is no God.Life began by the right circumstances and evolved through natural selection.

    Genisis says all was created in 6 days but yet it also says that God destroyed the World in the Great Flood.

    So if this is so then how do we explain Biodiversity around the world?

    ID says that life was created then evolved.

    But then ID would have to recognize both Genisis and Darwinism but under ID’s convictions it cancels both out so ID cant be Plausible

    so in my view Science and Theology shouldn’t mix

  3. I’m not sure that approach would work. The basic idea behind ID is that a design agent was involved in some (if not all) aspects of getting life to the point it is right now (which I would assume included DNA sequences).

    Even with full start codons we’d have to allow for the fact we might be comparing a human designed sequence against a non-human designed sequence.

    Unless we find “know it when I see it” sequences that make sense to modern man (who knows? some easily caught encoding that says “go new england patriots” or similar) aren’t we stuck?

  4. How about opposite test? We give him two fully functional protein codes and ask to determine whicn one is Human Designed and which one is Evolved by RM+NS.
    Can Ian provide test for such scenario?

  5. great question shazard. why don’t we try it? give him the two protein codes, and have him explain how the “evolved” one came about step by step.

  6. This is just a case of Darwinists trying to paint us into a “have you beaten your wife lately” corner, and any response will be laughed at — with no response being considered a victory.

    Assuming three of the four sequences are legitimately from the real world, even extended to include codons, they’re possibly designed by some unknown agency.

    The human one was designed by clear definition.

    The issue is not detecting design, but differentiating between human design and non-human design.

    If we throw this back and say “you tell us: how would you determine which was the result of RM + NS, and which was designed” they’ll say “we can’t tell the difference, *that’s the point*”.

    Regrettably it’s up to ID proponents to show the designed sequence, or be clear about why it can’t be done with just this information on its own, or outline how much other information we might need.

  7. Indeed, none of the six sequences begin with a start codon which means we aren’t given enough information to even frame the sequence into codons.

    My guess is that Musgrave got lazy and copied and pasted line blocks of the genome as represented by the NCBI Sequence Viewer or some other source. That’s why I noted “overlap with watermark” in the other thread since none of Musgrave’s example sequences exactly lined up with the actual watermarks. The first Vetner portion of the watermark at 84823..84879 is “ttaactag ctaatgtcgt gcaattggag tagagaacac agaacgatta actagctaa” I believe. This is considerably outside my area of expertise and I may have misinterpreted reading the genome so I would appreciate anyone pointing out errors so I can gain more knowledge.

  8. It almost seems like Ian has been reading my email. Last week I wrote to some ID guys doing bioinformatics research suggesting they focus on detecting human intelligent design and patent their methods instead of being automatically rejected in peer reviewed journals due to their connection with ID. There are three criteria for patents that examiners look for: novelty, non-obviousness, and utility. I reviewed over a thousand patent abstracts submitted to me by Dell employees evaluating them for novelty, non-obviousness, utility, and value to the company. I then gave it a thumbs up or thumbs down for pursuing a patent on it. Hundreds of abstracts I approved were granted and none that I know of were rejected. Novelty and non-obviousness of design detection are not a problem. One of the biggest mistakes people with patentable ideas make is thinking it’s not novel or it’s obvious. What’s non-novel or obvious to the inventor is very often novel and non-obvious to the patent office. The inventors are much tougher on themselves than the examiners in those criteria. Utility is covered by linking design detection with bioterrorism and genetically modified foods. It’s a slam dunk for a slew of patents if you know what you’re doing.

  9. I agree with DaveScot.

    By not providing a full sequence, it is like asking whether a round pebble is intended to work as ball bearing designed for a specific purpose. In this sense, modularity is invisible. In the case of the DNA strand, the incomplete sequence tells us nothing. It is incoherent and invisible to design detection.

    Design theory helps to detect design, but it cannot tell you what is not designed! A round pebble may serve as a ball bearing, but we cannot know that without seeing other components that match its intended use.

    Indeed. Design theorists can’t rule out design in non-specifiable components, they can only say that the components are not within the reach of their methods (unless more info. is provided, of course).

  10. Just a suggestion, but perhaps we are over-thinking all this. Maybe Ian provided several “actual” protein sequence segements and a couple of others where the codons actually code for letters in the alphabet and they spell out secret messages. Anyone tried that?

  11. Design theory helps to detect design, but it cannot tell you what is not designed!

    This seems somewhat self-contradictory, but maybe I’m interpreting it wrong.

    Do you have an example of a case where design was accurately detected in some sample set using current design theory? Why couldn’t that have excluded the remainder of the set as un-designed?

    Sounds like a real-world example of that success would be a big event!

  12. p.noyola, maybe i am misunderstading your question, but the design filter has always filtered only for clear cases of design, leaving “lesser” cases undetected. think about pouring ink on the ground and working VERY hard over the next hour to make it look undesigned…..that would not be very difficult and it would be nigh impossible to detect design. any filter that is useful must necessarily ignore simple cases of design in order to be stringent enough to always be correct when it does recognize design.

  13. What would the response be if the challenge were met? It would be seen as an anomaly, niether proving ID nor disproving NDE. The Darwinist is committed to a historical narrative in which vast eons of time are conferred magical powers of creative activity. Until the broader Darwinian narrative is replaced, these particular instances from nature that demand interpretation will recieve opposite ones from Design and Darwinian paradigms.

  14. Hi all

    I am a newbie and not a scientist, so excuse me if I appear a little naive. It occurs to me that DNA is one of the “irreducably complex” artifacts that are evidence of design. It sounds to me as if Mr. Musgrave is challenging you to detect a 2nd level of design hidden in the (obvious) design of DNA.

    Certainly it is his opinion that the 2nd level information that was inserted by an intelligent agent is indistiguishable from the 1st level information allegedly inserted by random chemical events. To my mind his challenge admits the design he is hoping to refute.

    Dave

  15. interested, you are exactly correct. To wit, ID:

    1- Does not claim that it can identify every instance of design.

    2- Cannot detect for certainty that something was not designed.

    This leaves, however, the detection of some things that are designed (focusing particularly on clear-cut cases at the end of the spectrum).

    http://www.evolutiondebate.inf.....Design.htm

  16. This whole “challenge” is a fool’s errand.

    Not only for the reasons stated by DaveScot, but because Ian has stated, has he not, that several of the sequences are real. Thus, to the extent that they are all designed, this becomes like asking someone to choose whether a car or a bicycle was designed (choose only one correct answer, please). We’re dealing with false dichotomies (among all the other problems with the challenge).

    To make this a more rational challenge, we would have to have a number of non-designed sequences (i.e., random sequencing), and one designed sequence. Then the challenge would be to locate the designed sequence. Of course, sufficient length, structure (and potentially some knowledge about function) would be required to make it a rational exercise.

  17. eric

    The background scenario of bioterror is an excellent case for the application of design detection.

    That said, Ian has unrealistically bounded the information we have to work with by denying us a reference point. In the real world we’d have a reference point. Say it was a modified anthrax bacterium. Our reference point would then be previously known strains of anthrax. We wouldn’t have a short snippet of DNA sequence to work with from the new strain. We’d have the entire sequence of the new strain and the entire sequence of the previously known strains.

    With that information we could apply design detection methodology to determine if the new strain is due to natural or unnatural causes.

    Imagine asking a criminal investigator to determine whether someone who died in a fall from a tall building was accident or homicide by looking at nothing but the hat the person was wearing when he fell. This is what Ian is asking us to do.

  18. DaveScot – on the larger issue of ID, isn’t asking for a reference point a bit like asking for some properties of the designer?

    I have my suspicions that this is part of the reason for the challenge, to see if design detection can get anywhere without assuming knowledge of the designer.

    The lack of data complaint may have weight, but I think progress could still be made by applying the design detection algorithms to the sequences, and seeing if they can be separated into two groups. Even if you don’t get a definite answer, it clarifies the whole design detection process for the rest of us.

    Bob

  19. Bob

    Design detection in an object requires a starting state, ending state, and probabilistic resources available to get from the start to the end. In this case we have an end state (the sequence) and probabilistic resources (random mutation and natural selection) but we have no start state. How can we say whether or not random mutation and natural selection was sufficient to produce the end state when we don’t know what the start state was?

    Of course we’ll have to make more estimations of the probabilistic resources such as how long the period of time rm+ns had to work, how many potential replications (opportunities to produce change), and the mutation rate of the organism.

    We could get all that, or at least a close enough approximation, just by knowing the species from which the sequence came. In the real world we would know the species we were dealing with.

    And no, we don’t need to know anything at all about the intelligent designer. All we need to know is what is reasonably possible absent a designer. If the change we observe goes beyond what we believe is reasonably possible without a designer then we make a design inference in the time honored manner of elimination. ‘When you have eliminated the impossible, whatever remains, however improbable, must be true.’ -Sherlock Holmes

    Is this rocket science or something so complex that it just goes over the heads of Darwin’s faithful so I might as well be trying to teach a hamster how to balance a checkbook as describe how to make a design inference to an ebola boy?

    It’s very frustrating because this is just straightforward, simple problem solving to me.

  20. Dave, what start state would be used when deciding if the bacterial flagellum was designed?

    Bob

  21. 21

    “ebola boy”? Can I ask for clarification? I don’t understand what that term is supposed to mean or imply.

  22. Hey Bob O’H,

    Can you tell me the methodology used to determine that living organisms are the result of non-telic processes?

    Could you demonstrate that any of the sequences Ian provided could arise outside of an organism and without agency involvement?

    Thanks in advance.

  23. Bob

    The start state for the flagellum is a bacteria with no flagellum.

    larry

    “Ebola boy” is short for “Church Burnin’ Ebola Boy” which is an affectionate name I gave to a group of my antangonists who congregate on an ancillary message board attached to the blog “Panda’s Thumb”. I liked it, they liked it, so it’s all in good sport.

  24. Joseph –

    Can you tell me the methodology used to determine that living organisms are the result of non-telic processes?

    It’s called science.

    Obviously the method isn’t perfect, but we haven’t observed any telic processes creating living organisms, other than ourselves.

    Could you demonstrate that any of the sequences Ian provided could arise outside of an organism and without agency involvement?

    No. Why would I want to?

    Dave –

    The start state for the flagellum is a bacteria with no flagellum.

    which bacterium? What did it look like? What genes did it have? Do you allow it to have a Type III Secretory System? What about horizontal gene transfer (which would require you to know about the local gene pool, not just one bacterial species)?

    I guess you can see what I’m driving at – once you start thinking about the problem, the more difficult it becomes to specify the state at the start of the process.

    Bob

  25. bob

    “which bacterium?”

    I should think the mostly closely related bacteria absent a flagellum to one with a flagellum. That happens to be the same modus operandi I suggested be used to discriminate between a naturally occuring variant and a variant that was engineered for bioterrorism use. :-)

    Whether phenotype or genotype or both should be used to determine the most closely related candidate is a question you should ask a bacteriologist.

    By the way, isn’t it fairly well determined that the flagellum preceded the appearance of the type III secretory system in the history of life? Among other things I seem to recall is that the T3SS is a predatory weapon used against other bacteria. The prey must precede the predator. The T3SS would then be a modified flagellum rather than the flagellum being a modified T3SS.

    Also by the way, I don’t care much for the flagellum as a model organelle for chance & necessity to explain. I prefer the ribosome. The start state for something absent a ribosome is inanimate chemicals since there’s nothing known to be alive and free living that doesn’t have one.

    A recent article here talked about using ATP synthease as the model for chance & necessity to explain. The point was made that an energy metabolism must have formed before the ribosome because the ribosome needs an energy source to function.

  26. I should think the mostly closely related bacteria absent a flagellum to one with a flagellum.

    How would you control for any evolution in the rest of the genome? The closest relative will also have undergone quite a bit of change too.

    Also by the way, I don’t care much for the flagellum as a model organelle for chance & necessity to explain. I prefer the ribosome.

    OK, same question – what start state would you use for the ribosome?

    Bob

  27. Can you tell me the methodology used to determine that living organisms are the result of non-telic processes?

    Bob O’H:It’s called science.

    Science hasn’t determined that living organisms are the result of non-telic processes.

    That is a dishonest “answer”.

    Could you demonstrate that any of the sequences Ian provided could arise outside of an organism and without agency involvement?

    No. Why would I want to?

    Because that is something that would support your position.

    But I understand your avoidance.

  28. OK, same question – what start state would you use for the ribosome?

    An organism without at least one.

  29. Joseph: Could you demonstrate that any of the sequences Ian provided could arise outside of an organism and without agency involvement?

    Bob O’H: No. Why would I want to?

    I am not sure why Bob O’H is tolerated on this blog. He’s obviously a Darwinist and an atheist who considers ID advocates to be stupid. His only purpose here is to trip up an IDer and go claim bragging rights on antievolution.org or PZ Myers’s blog. Bob O’H does not really contribute anything constructive to this forum. I personally find his posts offensive, dishonest and condescending. This is not a public forum and, in my opinion, Dr. Dembski should not tolerate the enemy in our midst. Sorry for this outburst, I always tell it like I see it.

  30. I am not sure why Bob O’H is tolerated on this blog.

    Entertaiment. He also provides a good gauge for ID ignorance.

  31. 31

    “He’s obviously a Darwinist and an atheist who considers ID advocates to be stupid.” Of these, I’d say he’s obviously a Darwinist. I don’t know his religious views, which are irrelevant to these issues. But he’s a very smart person who treats others on this blog respectfully and who has published seriously in the scientific literature on mathematics and biology – precisely the focus of ID. (I won’t link to his home page, which is not in the U.S., but it’s easy enough to find.)

  32. larrynormanfan: he’s a very smart person who treats others on this blog respectfully and who has published seriously in the scientific literature on mathematics and biology – precisely the focus of ID.

    His respect for others here is hypocritical since he goes on other forums to disparage what is being discussed on this blog. And as far as his being smart and having published in scientific literature is concerned, I don’t see the importance of that. That’s an appeal to authority, in my opinion. I admire people like Dr. Dembski and Dr. Behe for their honesty and well-reasoned philosophies, not their titles. I have no respect for PZ Myers and Richard Dawkins in spite of their titles.

  33. I found another example of an apparent candidate for irreducible complexity in cellular subsystems, the catalytic core of the photosystem II photosynthetic machinery, where “water splitting” in plants occurs. This catalytic core is the same in all plants, algae and cyanobacteria. The exact arrangement of atoms and the exact series of steps is critical to its functioning at all. Change it in any way and it loses its powers. The catalytic core comprises four manganese ions, a calcium ion, several oxygen atoms and at least two water molecules, all held in place by a protein scaffold. The catalytic core starts at a resting state, then moves through several successive states in response to the absorption of four photons of light by the system. After three steps of +1 volt each, a further sequence of several more unique steps are required to finish and restart the cycle.

    The reason for the steps is to accumulate enough “electron stripping power” or redox potential to extract electrons from water. Each step can only raise redox potential by +1 volt and by itself is useless since the redox potential of water is +2.5 volts. Each of these steps is finely tuned to depend on the exact configuration of the atoms in the catalytic core.

    This system appears like a candidate for an IC machine. This is not only in the intricate critically balanced series of steps but in the structure and atomic composition of the catalytic core, which apparently is so critically specific that it has not changed since the evolution of cyanobacteria. Could the catalytic core have been arrived at by a series of steps? If so, there is no trace in extant organisms, and it doesn’t seem likely anyway because the catalytic action is so critically determined by that exact structure.

    Reference, New Scientist, May 1 2004 (vol. 182 issue 2445), article on research at Imperial College London by J. Barber and S. Iwata, at http://sci.tech-archive.net/Ar...../0260.html

  34. Bob O’hara has been a valued member of this blog for a long time. He’s a biologist who is quite well informed on the issues and willing to listen to views he doesn’t share. More importantly, as far as scientist critics of ID go, he’s the epitomy of civility. I expect he be treated in a like manner. If I see anyone unduly harrassing him someone will get the boot and it won’t be Bob.

    His respect for others here is hypocritical since he goes on other forums to disparage what is being discussed on this blog.

    He’d be expelled by his peer group on those other forums if he didn’t is my guess. Very few of them are allowed to be members here because they’re almost all either ignorant or asshats or both.

  35. Mapou: His respect for others here is hypocritical since he goes on other forums to disparage what is being discussed on this blog.

    DaveScot: He’d be expelled by his peer group on those other forums if he didn’t is my guess. Very few of them are allowed to be members here because they’re almost all either ignorant or asshats or both.

    Dave, my personal opinion of O’Hara is that he is an asshat and probably worse. Now if you think I’m harassing him and you feel that I should be booted on account of it, so be it. I’ll just leave. I just tell it like I see it. This isn’t my blog after all and I don’t make the rules here. I enjoyed it while it lasted.

  36. I found another example of an apparent candidate for irreducible complexity in cellular subsystems, the catalytic core of the photosystem II photosynthetic machinery, where “water splitting” in plants occurs.

    Could the catalytic core have been arrived at by a series of steps? If so, there is no trace in extant organisms, and it doesn’t seem likely anyway because the catalytic action is so critically determined by that exact structure.

    The following freely available article may help to judge your claims:
    Samuilov VD.(2005):
    Energy problems in life evolution. Biochemistry (Mosc)70(2):246-250

  37. Dave,

    Whatever happened to great_ape? He was one of the few civil Darwinists and also a great source for the current state of technical information in evolutionary biology. I learned a lot from his posts.

  38. Joseph @ 27 (sorry about the lack of formatting) –

    Can you tell me the methodology used to determine that living organisms are the result of non-telic processes?

    Bob O’H:It’s called science.

    Science hasn’t determined that living organisms are the result of non-telic processes.

    That is a dishonest “answer”.

    I’s object (mildly and respectfully!) about “dishonest”. Now, “glib” I would admit to.

    The problem is that the way we decided that teleology was unnecessary in evolution was through a long process, taking in several strands of evidence (and at least one shave). So, the slightly less glib answer is “read an evolutionary biology textbook”, and the really long one is an evolutionary biology textbook.

    Evolutionary biology provides us with a perfectly adequate framework for explaining the real world without invoking teleological processes. So why add them on?

    Could you demonstrate that any of the sequences Ian provided could arise outside of an organism and without agency involvement?

    No. Why would I want to?

    Because that is something that would support your position.

    But I understand your avoidance.

    I don’t see how that would help – I don’t know of any claims that modern day sequences have arisen outside of an organism and without agency involvement. The assumption is that they arise within organisms.

    Joseph @ 28 -

    OK, same question – what start state would you use for the ribosome?

    An organism without at least one.

    Quite. You’ll have to search for a long time to find one. :-)

    Bob

  39. Bob

    Intelligent design provides us with a perfectly adequate framework for macroevolution.

    Since macroevolution happens so slowly that it has no practical application and cannot be observed almost any just-so story is an adequate framework.

    It isn’t so much about what’s an “adequate” framework for a historic narrative it’s about which framework is actually true.

    I mean come on. We have a chance & necessity theory and we can’t observe that producing a flagellum. We have a God of Abraham hypothesis and we can’t observe Him creating a flagellum either. Both are equally unobservable. I prefer to just admit we don’t know. Clearly -something- designed the flagellum and if it wasn’t chance & necessity, which we can’t verify, what’s left? We do know for sure that intelligent agency can design things that are out of reach for chance & necessity. You won’t ever see a space shuttle or laptop computer created by chance & necessity. We know for sure that the universe contains at least one instance of intelligent agency and no physical laws prohibit there being more than one or others in forms not based on carbon chemistry. Intelligent design, suitably denuded of any specific religious deities to satisfy constitutional neutrality, deserves study as a possible mechanism behind organic evolution just as much as chance & necessity is deserving.

  40. Bob OH

    I have a challenge for you. If you’ll agree to carefully read Dembski and Wells’ new book, which I’m in the process of doing, you and I can parse it out bit by bit.

    You have my word I’ll be objective. I’m up to about page 80 and haven’t yet examined the CD with all the notes and references.

    I have a few minor reservations so far mostly about what IMO are hasty conclusions. In a specific instance I wrote to Dembski and Wells saying that “epigenetics” wasn’t mentioned anywhere in the book and most notably in the part where Wells offers evidence that DNA doesn’t control evo-devo programs. I considered that a major oversight. A horse is a horse not so much because of its DNA but rather because the rest of the egg cell is configured to produce a horse and the DNA is just the specifications for building blocks some of which are found in all forms of life and few which are unique to the horse. If you use nuclear transfer to stick a cat nucleus into a horse egg development will proceed toward a horse until some incompatibility between the cat DNA and the horse egg causes it to abort. I pointed out that neo-Darwinists don’t have a particular problem with that and it’s studied under the rubric of epigenetics.

    A common theme that seems to run through ID books I’ve read is they seek to conclusively disprove chance & necessity in every single category of evidence – molecular, anatomical, fossil, information theory, and sundry others. In general I don’t believe that any single class of evidence falsifies chance & necessity in macroevolution but rather it’s the weight of all of the problems added together that tip the scales.

    In any case if you agree I’ll restrict the commentary to just you and I and the authors if they care to chime in with clarifications. This should be slotted for some months in the future as it’ll be that long before I finish a careful study of it. Don’t ask about using a forum other than UD because if I’m going to spend time adding content to a blog I want it to benefit this blog.

    What say you?

  41. Jerry

    Great_ape comes and goes as he pleases. You’re right about him being the kind of critic welcomed here – a scientist in a relevant field who remains civil even when provoked and gives careful consideration to views he doesn’t agree with.

  42. The problem is that the way we decided that teleology was unnecessary in evolution was through a long process, taking in several strands of evidence (and at least one shave). So, the slightly less glib answer is “read an evolutionary biology textbook”, and the really long one is an evolutionary biology textbook.–Bob O’H

    I have read several biology/ genetic textbooks and THAT is why I am an IDist.

    There isn’t ANY scientific cdata that supports the non-telic PoV.

    Heck Bob you can’t even account for the physiological and anatomical differences observed between chimps and humans- that is no one has been able to link the genetic differences to physiology and anatomy.

    Evolutionary biology provides us with a perfectly adequate framework for explaining the real world without invoking teleological processes.

    Evolutionary biology has failed miserably. We don’t even know whether or not the transformations required are even possible with any amount of accumulated mutations.

    I don’t see how that would help – I don’t know of any claims that modern day sequences have arisen outside of an organism and without agency involvement.

    You should just say that you don’t know of ANY nucleotide sequences arising outside of an organism and without agency involvement.

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

    ID will not go away because some people just refuse to understand it.

  43. The problem is that the way we decided that teleology was unnecessary in evolution was through a long process, taking in several strands of evidence (and at least one shave). –Bob O’H

    The problem is there isn’t any evidence that living organisms arose from non-living matter via non-telic processes.

    As you noted with the ribosomes living organisms are irreducibly complex.

    Reading biology and genetic textbooks we read of the processes of transcription and translation.

    That alone should be enough to refute the notion that non-telic processes gave rise to living organisms.

    Next the best you can offer is one new protein-to-protein binding site and that was found in a virus.

    Yeah Bob, that is really convincing stuff.

    If you handed a biology textbook, void of all the biased nonsense, to a student taking biology for the first time, that student would most likely reach a design inference from the data presented.

    That is what I am looking for in public schools- present the data without the unnecessary and untestable biased assumptions. Then have open discussions, come up with hypotheses, and test them.

  44. on the larger issue of ID, isn’t asking for a reference point a bit like asking for some properties of the designer?

    I have my suspicions that this is part of the reason for the challenge, to see if design detection can get anywhere without assuming knowledge of the designer.

    Besides actual specimens to use as references, or copies of the entire object and surrounding details, I believe the major reference point is the Specification.

    “Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. In virtue of their function, these systems embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specification criterion.”

    For the flagellum it’s easy; it functions like an outboard rotary motor. We don’t need to know anything about the Designer(s) in that case. But Musgrave’s challenge provided an extra obstacle since the Specified information in English words was encoded using a cypher. So in this case we did need to know properties about the Designer since finding the cypher relies on knowing English. The watermark was also not functional in itself in regard to the organism it was encoded into, thus we’d generally get false negatives.

    Now if instead of encoded English words the Venter watermark had been a particular functional feature exceeding the UPB then we’d at least could have detected the design without knowing properties of the Designer(s). Then at point we’d employ DesignER Detection methods outside of ID and I’d assume we’d match the functional object to details provided by Venter.

    But let’s say we’re not certain about the type of Designer and the designed object is still an encoded message. So in our search we’d not only include English but other languages. I’m certainly not an expert on cryptography but since the Venter cypher was relatively simple I’m sure there is a way of brute forcing its discovery. We’d also look for repeating patterns. Personally I’d find it interesting if we found a sequence like this:

    aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa tttttttttt tttttttttt tttttttttt tttttttttt
    gggggggggg gggggggggg gggggggggg gggggggggg cccccccccc cccccccccc cccccccccc cccccccccc aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa tttttttttt tttttttttt tttttttttt tttttttttt
    gggggggggg gggggggggg gggggggggg gggggggggg cccccccccc cccccccccc cccccccccc cccccccccc aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa tttttttttt tttttttttt tttttttttt tttttttttt
    gggggggggg gggggggggg gggggggggg gggggggggg cccccccccc cccccccccc cccccccccc cccccccccc aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa tttttttttt tttttttttt tttttttttt tttttttttt
    gggggggggg gggggggggg gggggggggg gggggggggg cccccccccc cccccccccc cccccccccc cccccccccc

    Multiple even blocks of 4 repeated on various scales. There’s other mathematical expressions that could be encoded as a watermark by corporations. So we could use the EF to find that Design then DesignER Detection methods to see if we know of any human who uses such watermarks. Now if these watermarks were done secretly and the person(s) responsible did not admit to the deed and no one else used such watermarks it’s possible that the DesignER Detection would fail and falsely attribute the Design to some non-human source.

  45. Dave – I’m intrigued by your suggestion, but give me a few of days to think about it. I’m coming towards the end of a hectic time at work, and I’ll need to take stock (and work through all of those things I should have done last week etc.).

    Bob

  46. All quotes are from Bioinformatics, Genomics, and Proteomics: Getting the Big Picture part of a “Biotechnology in the 21st Century” series:

    It is important to note that the proteins made by an organism determine all of the characteristics that “nature” provides for that particular living thing. The enzymes allow other molecules, including proteins, fats, and carbohydrates to undergo chemical reactions, such as being put together or taken apart inside living things.
    … (skipping surface receptors and other structural elements)
    Other proteins bind DNA, the molecules of heredity, and determine which codes are going to be used to make proteins- at which time and in which type of cell.

    Because each protein has an important job to do, it is crucial that proteins be made to precise specifications, just like the precision parts of an expensive sports car. In fact, the blueprints for some proteins have been so good, they have been preserved through millions and even billions of years of evolution.—page 5

    The importance of these precise structures and hence functioning of protein machines like these channels cannot be understated. Potassium channels, like other channels that pass other ions from one side of the cell membrane to the other, have a particular architecture that allows them to open and close upon command. We now know that intricately designed and mechanically fine-tuned ion channels determine the rhythm and allow an electrical impulse initiated when we stub our toe to be transmitted to the brain.- page 19

    Wet electricity. Whereas the electricity that powers our computers is comes from the flow of electrons through solid wire and “hates” water, the electricity that runs our bodies is designed for a wet environment and uses pumped ions to convey differing messages to our command center.

    That pretty much should clinch it right there for the ID side, but there is more to be learned by reading biology textbooks:

    Transcription:

    You start with a tightly wound piece of DNA. Enzymes called RNA polymerases begin the process by unwinding a portion of DNA near the start of a gene, which is specified by sequences called promoters. Now there are two strands exposed. One strand is the coding strand- it has the correct sequence information for the product- and the other strand is the non-coding strand. That strand contains the complimentary layout.

    At this point decisions have to be made. Where to start, where to stop and although it may seem counterintuitive the mRNA goes to the non-coding strand in order to reconstruct the proper codon sequence (nucleotide triplets which code for an amino acid) for the protein to be formed.

    This process is unidirectional (5’-3’). There is only one start codon which also codes for an amino acid (met) and therefore all amino acid sequences start with methionine. The stop codons don’t code for an amino acid. Transcription actually starts before the “start” codon and continues past the stop codon. Before the mRNA leaves the nucleus any/ all introns are cut out and the remaining exons spliced together. A chemical cap is added to the 5’ end, the non-coding stuff at the end is cut off by a special enzyme (endonuclease) and a string of A’s is added in its place. You now have a processed mRNA.

    So now we have this piece of processed mRNA which leaves the nucleus and has to rendezvous with a ribosome-the protein factory within the cell.

    A ribosome consists of over 50 proteins and 3-4 different kinds of rRNA (ribosomal), plus free-floating tRNA (transfer). Each tRNA has a 3 nucleotide sequence- the anti-codon to the mRNA’s codon plus it carries the appropriate amino acid molecule for its anti-codon. To attach the appropriate amino acid to the correct anti-codon an enzyme called amino-acid synthetase is used.

    There, large workbenches made of both protein and nucleic acid grab the mRNA so the correct amino acids can be brought up to the mRNA. Each amino acid is escorted by a module called tRNA or transfer RNA. It is important to note that the escort molecules have three bases prominently exposed on their backsides and that these molecules also use the base U instead of T. The kind of amino acid is determined precisely by the tRNA escort’s anticodon, or triplet set of bases on the escort’s backside. pg 23

    The amino acid attachment to the tRNA is temporary. When not being assigned to build a chain the tRNAs float around without amino acids attached (and the amino acids are also “free-floating”).

    Are you understanding this so far? Do you really think that blind, mindless processes can account for even this part of protein synthesis?

    Data vs decree. The data points to ID but the decree prevents a design infernce.

  47. Joseph #42:

    ‘Heck Bob you can’t even account for the physiological and anatomical differences observed between chimps and humans- that is no one has been able to link the genetic differences to physiology and anatomy.’

    That’s a bit much to ask at the moment. An initial sequence of the chimpanzee genome is around since september 2005 (nature 2005, vol. 437, 69-87). They found ‘… approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements …’. To work out how this huge number of genetic differences is then linked to physiological and anatomical difference might take just a tiny bit longer then two and a half years. however, there are some interesting examples suggesting connections between genetic differences in chimps and humans and physiological differences as e.g. in the case of the Fox2p gene (Genetics, vol. 162, 2002, 1825-1835), the MHC genes, CMP-sialic acid hydroxylase etc. …. However, even for the well studied genes there is often still not a complete functional description even for one variant. To characterize differences in the function of human and ape variants or just different human alleles will take a long time.

  48. Spark (#36), according to my search the Samuilov article isn’t freely available – it has to be purchased, a typical cost $42.

  49. rna,

    Thanks but I am well aware of FOX2P. That doesn’t help any as there are many physiological and anatomical features that no one can account for.

    And we still don’t even know whether or not any amount of accumulated mutations can account for thos differences.

    IOW there isn’t any way (yet) to test the premise.

    ALL that is doen is to assume common ancestry and then seek what one would consider as confirming that assumption.

    However if one first assumes a common design then the SAME data can be used to support that position!

    The bottom line is no one knows what it takes to make a human other than two humans (male & female) successfully mating.

    So how long do we have to wait? And shouldn’t it be that until we can confirm this that we teach precaution about universal common decsent?

  50. Fox2P- 3 amino acid difference between humans and mice. 2 of the three allegedly occured after the chimp-human split.

    Conserved genes sound like a case of common design to me.

  51. “Conserved genes sound like a case of common design to me.”

    I love the study of conserved genes. Many of them are all but identical in all living organisms. 500 such were recently discussed on Telic Thoughts very recently.

    I still think that my favorite is the HAR1F rna gene (it doesn’t code to protein). It is ultra-conserved in all mammals, but differs by 18 mutations in humans. It seems to relate to brain development.

    According to NDE, conservation is caused by necessity. If a gene is ultra-conserved, then it must be both clearly necessary, and totally disabled by any mutation. Yet there are at least 8 cases where ultra-conserved genes have been deleted from organisms (mice, I think) and the organisms have shown no detrimental effects. This makes no neo-Darwinan sense at all!

    (Some have suggested that as long as a gene’s function requires a very specific form, the gene may not need to be all that necessary. I would suggest that if this hypothesis is true, we should periodically find species that are devoid of genes that are ultra-conserved in all of their cousins. For instance, if we found a shrew that didn’t have a gene that was ultra-conserved in all vertibrates, well, that would support that the gene is not all that necessary, or is not necessary in certain environments, but must have an exact configuration to have any use at all. I have not heard of such a phenomenon — not that my hearing on the subject is, well, professional.)

    Conserved genes that aren’t essential wreak if a different conserving agent than natural selection is. Non-essential conserved genes leave one with the impression that variation is not random.

    Now, does conserved genes support the hypothesis of common design. Yes, the common design hypothesis would definitely predict conserved genes, even ultra-conserved genes with no essential purpose. Yet, a designed common descent would also predict the same.

    The strongest case I can see that challenges ex-nihilo creation of lineages is the existance of common disease-causing mutations accross species, including between chimps and humans. The best explanation I can find for such is common dessent.

  52. 52

    Joseph,

    The bottom line is no one knows what it takes to make a human other than two humans (male & female) successfully mating.

    I’m not sure I understand you here. We know a lot of the basic requirements :-). I think we can also exclude things such as the movement of the stars or the shape made by tea leaves at the bottom of the cup. What are you suggesting we add to the picture that we don’t have now? And won’t anything we add boil down to material (that is, physical, chemical, biological, environmental, etc.) processes? Surely there isn’t a design intervention during a normal gestation!

  53. The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”–geneticist Giuseppe Sermonti in “Why is a Fly Not a Horse?”

    When scientists took a gene from a mouse that enables eye development (Pax6) and inserted it into a fly genome lacking the fly version, the fly developed fly eyes. IOW no one knows where the info for the type of eye resides.

    Infomation doesn’t boil down to material.

  54. Joseph #49:

    My objection is that you used the fact that the connection between genetic differences and physiological differences is not clear (yet) as an argument against a nontelic point of view.

    One could make a similar argument that the idea of common design is around for centuries and say:
    ‘Heck, Joseph, you can’t even account for the physiological and anatomical differences observed between chimps and humans- that is no one has been able to link the genetic differences to physiology and anatomy.’

    We only have an exhaustive list of the differences for only a very brief period of time. It took seventy years to realizes that genes are made of DNA. So this is not a good argument against either a non-telic view nor common descent.

    Common descent has been a tremendously fruitful hypotheses in modern biology and lead to dramatic novel insights. it explains very well why we have an fundamental unity of biochemical processes in all kingdoms of life and why it is possible to translate findings made in bacteria or archaebacteria to humans. So why not teach this if it is so successful. Assuming common design and design interventions at several stages one could have a similar unity of biochemistry due to commonly used parts but there would be no requirement for that. It is a less stringent concept.

  55. Common descent has been a tremendously fruitful hypotheses in modern biology and lead to dramatic novel insights. -rna

    Nonsense. Seeing that it can’t even be objectively tested it is easy to see that is a bald assertion.

    it explains very well why we have an fundamental unity of biochemical processes in all kingdoms of life and why it is possible to translate findings made in bacteria or archaebacteria to humans.

    Umm UCD does not predict this. There isn’t anything thta says the code for living organisms has to be universal. The fact that it is should be evidence for design because if there is only one then blind searches is unlikely to find it.

    However with a common design this would be expected.

    My objection is that you used the fact that the connection between genetic differences and physiological differences is not clear (yet) as an argument against a nontelic point of view.

    That is only part of the issue.

    One could make a similar argument that the idea of common design is around for centuries and say:
    ‘Heck, Joseph, you can’t even account for the physiological and anatomical differences observed between chimps and humans- that is no one has been able to link the genetic differences to physiology and anatomy.’

    Design doesn’t attempt to do that because design isn’t making claims about the differences.

    However UCD is making claims about the differences by saying that accumulated genetic accidents can account for them.

    The reality hits and the only thing can account for is wobbling stability.

    No one has ever observed any examples of mutations accumulating in such a way to give rise to a useful novel structure.

    We only have an exhaustive list of the differences for only a very brief period of time. It took seventy years to realizes that genes are made of DNA. So this is not a good argument against either a non-telic view nor common descent.

    How long do you need? And why, if you don’t have the answers, is it taught as fact to the exclusion of ID?

    And why is it that we see people leave the non-telic position and embrace ID but not the other way around?

  56. rna- as far as UCD is concerned, there isn’t any evidence for universal common descent tha cannot also be used as evidence to support alternative scenarios.

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