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“Intelligent Design Challenge” Challenge

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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.

Comments
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? BobBob O'H
February 3, 2008
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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. DaveScot
February 3, 2008
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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. BobBob O'H
February 3, 2008
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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. DaveScot
February 3, 2008
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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.Joseph
February 3, 2008
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"ebola boy"? Can I ask for clarification? I don't understand what that term is supposed to mean or imply.larrynormanfan
February 3, 2008
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Dave, what start state would be used when deciding if the bacterial flagellum was designed? BobBob O'H
February 3, 2008
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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.DaveScot
February 3, 2008
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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. BobBob O'H
February 2, 2008
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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. DaveScot
February 2, 2008
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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.Eric Anderson
February 1, 2008
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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). www.evolutiondebate.info/Brief%20Primer%20on%20Intelligent%20Design.htmEric Anderson
February 1, 2008
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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. Davedgosse
February 1, 2008
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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.JT75
February 1, 2008
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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.interested
February 1, 2008
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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!p.noyola
February 1, 2008
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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?SCheesman
February 1, 2008
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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).Mario A. Lopez
February 1, 2008
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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.DaveScot
February 1, 2008
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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.Patrick
February 1, 2008
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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.p.noyola
February 1, 2008
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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.interested
February 1, 2008
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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?Shazard
February 1, 2008
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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?p.noyola
February 1, 2008
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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 mixsweitzam
February 1, 2008
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"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.Gerry Rzeppa
February 1, 2008
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