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Ian Musgrave’s “Intelligent Design Challenge”

I received the following email dated 1.31.08 from Ian Musgrave:

Dear Dr. Dembski

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. For example the engineered mouse pox virus that turned lethal (Nature. 2001 May 17;411(6835):232-5 see also Nat Genet. 2001 Nov;29(3):253-6) and limits on the sequencing of the 1918 strain of the flu to stop flu from being weaponised (Fed Regist. 2005 Oct 20;70(202):61047-9,). A method that could reliably detect the action of human intelligent design in the genomes of microorganisms would be of significant advantage.

Thus we issue the “Intelligent Design Challenge”. Below are 6 gene sequences. At least one of them has been produced by a human designer. All you have to do is to determine which one(s) have been acted on, what the designed sequence does, and explain the method you used to determine this (in sufficient detail to replicate your determination eg. if you used an approximation of Chaitin information, a brief description of the algorithm you used [not the entire program]). Given your interest in design, you may wish to participate. You migght also like to pass this on to your colleagues.

The first successful determination of the designed sequence(s) and their function will win a copy of OpenLab 2007, the best of Science Blogging. You may wish to Reminding everyone again, the comments will be opened at 10:30 pm Australian Central Daylight Savinng Time (GMT +10:30), 1 February.

Sequence 1:
attatcacaa aatggtgtga tcttatcaat
agcactactt gcttaactag ctaatgtcgt
gcaattggag tagagaacac agaacgatta
actagctaat ttttttagtt ggatggcaat
tgttggaatt cacagctttt tagttggaat
tttagttaat catcaaacac ttaaaataag
taaaaagtat gttattttag gttcgatttt
tccaattatg gcattaacaa atactcttgt

Sequence 2:
gatagtagtg ggtggaatag tgaagaaaac
gaagctaaaa gtgatgcgcc cctaagtaca
ggagggggtg cttcttctgg aacatttaat
aaatacctca acaccaagca agcgttagag
agcatcggca tcttgtttga tggggatgga
atgaggaatg tggttaccca actctattat
gcttctacca gcaagctagc agtcaccaac
aaccacattg tcgtgatggg taacagcttt

Sequence 3:
attatcacaa aatggtgtga tcttatcaat
agcactactt gcttttttta gttggatggc
aattgttgga attcacagct ttttagttgg
aattttagtt aatcatcaaa cacttaaaat
aagtaaaaag tatgttattt taggttcgat
ttttccaatt atggcattaa caaatactct
tgtaattaga aaaaaattaa aagctttatt
aggagagggt aaggttcaaa aaggactcaa

Sequence 4:
agtagtgggt ggaatagtgt taactagcta
agtagaaaac accgaacgaa ttaattctac
gattaccgtg actgagttaa ctagctaaaa
gaaaacgaag ctaaaagtga tgcgccccta
agtacaggag ggggtgcttc ttctggaaca
tttaataaat acctcaacac caagcaagcg
ttagagagca tcggcatctt gtttgatggg
gatggaatga ggaatgtggt tacccaactc

Sequence 5:
ttttatttgt ttaatagtta aaaaaagcgt
taactagcta atgcataaac gacatcgcta
atgactgtct ttatgatgaa ttaactagct
aatgggtcga tgtttgatgt tatggagcag
caacgatgtt acgcagcagg gcagtcgccc
taaaacaaag ttaaacatca tgttatgttt
tatctatttt attagttaaa aaagttttga
atttttatct atttttagtt aataaaagtc

Sequence 6:
ggagggagat catcagatca aagtaataaa
ttcaccaagt acctcaacac caagcaagca
ttggaaagga tcggcatctt gtttgatggg
gatggaatga ggaatgtggt tacccaactc
taccaaccca acaaggtgaa aagtggtcaa
tatcaacaaa ataacaccta caacaggtta
attgagcctg acaatgcaac aagtgcagcg
agcagcatga ccagcttgtt aaagctgttg

Yours sincerely
Ian Musgrave

========================================
Ian F. Musgrave Ph.D, [email protected]
Senior Lecturer, Discipline of Pharmacology, School of Medical Sciences
Co-convener, Healthy Aging Research Cluster
University of Adelaide, SA, 5005, Australia

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41 Responses to Ian Musgrave’s “Intelligent Design Challenge”

  1. This was on Pandas Thumb and referenced on Fark.

  2. The amusing thing is, the best that Ian Musgrave can hope to prove is that nature may fundamentally be designed, yet we may not be aware of it. Somehow, I don’t think that’s quite the point he wishes to make.

  3. Hmph…my immediate reaction is that only 480 informational bits are required to encode each of those sequences. Oops?

  4. 4

    If the “non-designed” ones are in nature, then they’re all designed! Where’s my book?

  5. At least one of them has been produced by a human designer.

    This appears a little ambiguous. This could refer to recreating a genome, or adding a watermark to it as by Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome Gibson et al. The J. Craig Venter Institute.

    Of particular interest is their “signing” the genome:

    Gene pioneer signs his synthetic DNA creation

    New Scientist, 31 January 2008, #2641

    Artists usually sign their work – and genomics pioneer Craig Venter is no exception. Written into the sequence of the synthetic bacterial genome unveiled last week is his name, his institute’s, plus those of other key researchers involved. . . .
    To make their marks, the team took the one-letter abbreviations for amino acids – “C” for cysteine, “R” for arginine, “A” for alanine, and so on – and included the corresponding DNA sequences in their synthetic genome (Science, DOI: 10.1126/science.1151721).

    These “watermarks” also have a serious purpose. . . .”

    Another example of human design is forming purely synthetic topologies from DNA. e.g.
    New Motifs
    In DNA Nanotechnology

    ————-

    All you have to do is to determine which one(s) have been acted on, what the designed sequence does, and explain the method you used to determine this.

    This suggests looking for a modification of an existing DNA sequence.

  6. Well at least we know that ID has some people very scared. You don’t issue challenges to those you don’t fear.

  7. I was expecting a dishonest question but come on…. Musgrave does not seem to realize that design detection does NOT happen in a void; thus the spurious set of directions to determine “what the designed sequence does” based upon the sequences alone by themselves without being allowed to take into account the greater context of the items in question. In short, by limiting our reach to the mere list of sequences he’s creating a set of constraints by which to funnel our actions toward his desired result.

    http://blog.wired.com/wiredsci.....titut.html

    http://www.ncbi.nlm.nih.gov/en.....=166078610

    Sequence 1 is in there. 84781 – 84961. Overlap with watermark
    Sequence 2 is not.
    Sequence 3 is not.
    Sequence 4 is. 169021 – 169201. Overlap with watermark.
    Sequence 5 is. 314101 – 314281. Overlap with watermark.
    Sequence 6 is. 315061 – 315241. No overlap with watermark.

    And, yes, Musgrave will probably attempt to make the argument that since I used an alternative method for detecting design that somehow invalidates ID-based methods.

    Here is a quick use for the EF: did Musgrave purposely pull these sequences from the Venter sequences, an instance of design? 1. No law is known to be capable. 2. A minimum of 1920 informational bits seems to say so. 3. The specification is the marked overlap with the watermark along with Musgrave’s designation that the source of some of the information would be human. So using the EF we can be perfectly clear that Musgrave did intentionally pull from Venter.

    But let’s say for the moment we limit ourselves to just Musgrave’s email and do not allow ourselves to do any research to discover the functionality for the sequences (why are Darwinists always trying to prevent ID proponents from doing research? ;) ). So… 1. Again, no law. 2. 480 informational bits, thus the complexity does not exceed the UPB. 3. The specification cannot be known, since we’re not allowed to determine functionality by examining the organism that contains the sequence. Thus we’re forced to conclude that none of the sequences are designed, which results in at least one false negative (some of the sequences might have been gibberish for all we know). At this point Musgrave would probably try to make his point that “the EF is useless”. Well, of course it is! The Designer, Musgrave, rigged the question to get just that result: we were purposefully not given the ability to gather enough information about the objects in question. Musgrave may also try to claim that ID theory is useless for the practical application of human design detection. Kept within its scope, of course that’s the case, but combined with DesignER Detection methods I don’t see why that’d be the case.

    But let’s bring up a hypothetical scenario where I knew nothing of Vetner and his watermarks. I’m given a sample of Mycoplasma genitalium not knowing its origins. **Musgrave claims a portion of its sequence is a watermark, but does not give examples. Knockout tests are used to find non-functional sequences (presumably the watermark would not be functional). Cryptographic programs would be applied to discover the cypher. Note the purposeful misspelling of “Institvte”. Applying the cypher to other sequences should result in mostly gibberish. At this point we’d have enough to apply the EF to validate whether the particular sequence is the watermark, since it’s possible that among the gibberish of DNA-to-English there might be some other actual words.

    **(Modified scenario)Now, let’s say instead, like the original email, we are given sequences to examine but we’re not told it’s a watermark nor that human design is involved. There are no more constraints to the challenge and the sequences are all well beyond the UPB. The sequences listed would be examined to discover the specification and whether the system produced by the sequence is IC. Not knowing we are supposed to look for a watermark, we may overlook the “non-functional” sequences and not look for a encrypted message. At this point, using ID theory we’d identify the “truly functional” sequences that require design. Some of the sequences may be within the limits of Darwinian processes. So at this point we’d have at least one false negative since the human-designed watermark is encrypted and thus appears like noise (designers can purposefully design something to appear natural and/or by chance, which is why I earlier put “truly functional” in quotes). Musgrave does not reveal there is human design, but now that we’ve identified sequences as designed he demands we find the Designer(s). At this point we’ve gone beyond the current scope of ID and we’re using DesignER detection methods. ID theory is still useful for verifying the results but unless we look for a cypher we may never discover the specification for the human watermark sequence and might spend fruitless time reexamining the “functional sequences” again for clues to their origin.

  8. Partick – Congratulations on locating four of 6 sequences that were “produced by a human designer” as either synthetically sequenced or including watermarks.

    Purpose: the description given is:
    “Mycoplasma genitalium synthetic DNA”
    The “overlap with watermark” provides a digital signature or evidence of copyright:
    “VENTERINSTITVTE
    CRAIGVENTER
    HAMSMITH
    CINDIANDCLYDE
    GLASSANDCLYDE”

    For further functions see: Mycoplasma genitalium Proteome Overview

    For further details see NCBI’s taxonomy browser for
    Mycoplasma genitalium

  9. I don’t understand which way this challenge is supposed to be an “intelligent design challenge”. Is it a human design challenge or an ID challenge? I guess what I’m asking is, if the challenge is solved, what does that prove? Does it prove anything with regard to ID the theory? Or is it just an exercise to see if a reliable method can be developed to detect gene modification by humans?

    Is it a challenge to ID proponents or a challenge to bio-geneticists in general? Help me out.

  10. Yes, Mapou, that is what I considered all along. Musgrave isn’t providing a ‘challenge’ in the typical contest-orientated-way, but ‘challenge’ in the call-to-battle variety.

    He is an author of the ‘Why Intelligent Design Fails’ book – he believes that ID is just grandiose claims without scientific rigour.

    He would not submit a challenge such as this, knowing it would be posted to the web, without having carefully assessed how it may be dealt with and how he can respond to the findings. The ‘challenge’ is certainly designed …!

  11. AussieD,

    So what you saying is that it’s a trap designed to throw eggs in the faces of ID proponents. Am I reading this right?

  12. Let me first say that I have my doubts that this challenge was issued in good faith. AussieID makes a good point. But let’s be charitable and assume for the moment that it was issued in good faith:

    If I understand Dr. Musgrave’s challenge correctly, he is asking you to discriminate between naturally occuring biological gene sequences, and gene sequences that were designed by humans.

    Dembski’s methods of design detection can discriminate between informational patterns that are produced by chance/law, or alternatively were produced by intelligence. When there is real design to be detected, Dembski’s methods of design detection can work regardless of whether the designer was human or non-human.

    But Dr. Musgrave’s challenge seems to only allow intelligent design when it is human design. If we assume that Dr. Musgrave’s challenge was issued in good faith, then it seems the challenge has an inappropriate assumption: namely, that naturally occuring gene sequences were not designed.

    Dr. Musgrave may think that the correct “answer” is that only certain sequences were designed, because he knows they were designed by humans. But someone applying rigorous methods of design detection might find that other sequences were designed as well.

    Dr. Musgrave might then proclaim that the ID proponent is wrong, when in fact he is the one who is wrong because he assumed from the beginning that no naturally occurring gene sequence was designed. This is something to keep in mind if anyone submits analyses here.

  13. #9 Patrick

    Excellent post both for the content and for what it implies: that IM’s challenge is really pathetic and unfair (but after all what could you expect from a guy with students such as AS …).

    I would only focus again our attention to the fact that, in absence of contextual information (and this is just the way it has been stated by his author!), IM’s challenge is a ridiculous one. From a computer science point of view the DNA sequence can be compared to sequence of highly compressed information, such as for example MP3 or JPEG sequences. But, in absence of any reliable information about the encoding/decoding algorithms “nature” put in function to use them, simply there’s no way to recognize other “non-natural” encoding/decoding algorithms.
    So, the question is. Did Mr. Musgrave understand this point before throwing his challenge?

    If the answer is NO I’m sorry to say that the challenge does only prove his deep ignorance about CS problems.

    But if the answer is YES I’m sorry to say that the challenge does only prove something that is much ethically worse. Tertium non datur

  14. #17 Casey

    then it seems the challenge has an inappropriate assumption: namely, that naturally occuring gene sequences were not designed.

    I agree; the challenge is invalidated from the fact that IM put as a starting assumption what instead is the issue to be solved. However, as I stated in my previous post, IM’s challenge can be discarded also in its weaker form of simple discrimination about “natural” (i.e. non human) and “non natural” processes

  15. I second Casey Luskin’s analysis. Musgrave appears to be assuming that “not produced by a human designer” means “not designed”. Unless, of course, all of the given sequences that he knows were “not produced by a human” are simply random.

    I also agree with Patrick that “design detection does NOT happen in a void; thus the spurious set of directions to determine ‘what the designed sequence does’ based upon the sequences alone” is an unreasonable constraint.

    And I personally think Dr. Musgrave is asking too much: a cryptographic technique that can decode some but not all messages may still be a useful tool; and just because I can’t spot an intentionally camouflaged soldier in a thickly wooded area – at night – doesn’t mean I’m blind.

  16. Bravo, Patrick. That was an impressive performance. Venter clearly knew his watermarks were inarguably beyond the edge of evolution – their appearance in any organism would prove beyond reasonable doubt that his artificial genome was the source. Without explicit admission Venter applied the principles of ID in the very act of inserting those designed sequences.

  17. Yes, Mapou, I believe that Musgrave – a fellow Aussie, I’m disappointed to say – did ‘design’ a trap to “throw eggs in the faces of ID proponents.”

    The question will be, after all the testing of this hypothetical idea, was the egg fresh, hard boiled or rubbery? I hope that there is an element of bounce … right back at him.

    Patrick: thank you for employing the rigour of scientific investigation. Your response was candid and quite powerful. I am always quite pleased how so many of the bloggers @ UD are able to use their inherent/earned skills to evaluate the issues. ID continues to bubble along and grow in momentum.

    Thank you to all who continue to use the tools of science to work scientifically, although the Thumbsmen will of course ignore such obviousness.

  18. Gentlemen:

    Well done!

    The catches that IM chose sequences below 500 bits of information storage capacity, and also went on to implicitly beg the question by assuming that sequences not designed in the recent past by human agents were not created by agents at all, are sadly telling on the level of ID critics.

    But, we may make an observation or two:

    1 –> Absent an argument that the sequences come form an original life form, we are looking at sequences that arguably originated here on earth [and in a highly contingent situation (we are not simply dealing with natural regularities originating in mechanical necessity), the sequences are from origin by design or by chance -- and that could include use of chance or pseudo-chance techniques by intelligent designers; cf my remarks on tumbling dice], so we can identify an Earth life-form probabilistic resources bound, off say a measure of the available number of Carbon atoms on the surface down to the deep crust of the earth.

    2 –> That restricted scope of matter would at once shift the balance dramatically in favour of holding that the sequences — if shown to be biofunctional* — are (at least in part) designed one and all by some UNSPECIFIED — agent.
    ________

    * Notice, Professor Musgrave, the relevant conditionalities: I am speaking of detected bio-function as a particular form of specification.

    3 –> That leads to the issue highlighted above, that the EF detects design, not specific designER(s). [Ever heard of a coroner's verdict on autopsy that there was murder by an unknown party?]

    4 –> I would therefore also observe the following, from my always linked, section A, following from here:

    we all intuitively and even routinely accept that: Functionally Specified, Complex Information, FSCI, is a signature of messages originating in intelligent sources. [Compare the text of the challenge -- chance or necessity or agency or a combi of the three?]

    Thus, if we then try to dismiss the study of such inferences to design as “unscientific,” when they may cut across our worldview preferences, we are plainly being grossly inconsistent.

    Further to this, the common attempt to pre-empt the issue through the attempted secularist redefinition of science as in effect “what can be explained on the premise of evolutionary materialism – i.e. primordial matter-energy joined to cosmological- + chemical- + biological macro- + sociocultural- evolution, AKA ‘methodological naturalism’,” is itself yet another begging of the linked worldview level questions.

    For in fact, the issue in the communication situation once an apparent message is in hand is: inference to (a) intelligent — as opposed to supernatural — agency [signal] vs. (b) chance-process [noise]. Moreover, at least since Cicero, we have recognised that the presence of functionally specified complexity in such an apparent message helps us make that decision. (Cf. also Meyer’s closely related discussion of the demarcation problem here.)

    More broadly the decision faced once we see an apparent message, is first to decide its source across a trichotomy: (1) chance; (2) natural regularity rooted in mechanical necessity (or as Monod put it in his famous 1970 book, echoing Plato, simply: “necessity”); (3) intelligent agency. These are the three commonly observed causal forces/factors in our world of experience and observation. [Cf technical, peer-reviewed, scientific discussion here. Also, cf. Plato's remark in his The Laws, Bk X, excerpted below.]

    Each of these forces, clearly, stands at the same basic level as an explanation or cause, and so the proper question is to rule in/out relevant factors at work, not to decide before the fact that one or the other is not admissible as a “real” explanation . . . .

    Then also, in certain highly important communication situations, the next issue is whether the detected signal comes from (4) a trusted source, or (5) a malicious interloper, or is a matter of (6) unintentional cross-talk. (Consequently, intelligence agencies have a significant and very practical interest in the underlying scientific questions of inference to agency then identification of the agent — a potential (and arguably, probably actual) major application of the theory of the inference to design.)

    5 –> Dr Musgrave’s artful design has backfired, especially once additional empirically anchored techniques have helped commenters above to provisionally identify certain of the relevant sequences, and watermarks in them.

    6 –> That is the sequences as presented were designed, as a part of a message, intended to discredit the design inference. But the message itself shows how chance, necessity and agency can be combined to form a particular outcome that manifests FSCI, so is per reliable inference, designed as a whole. For, reliably, FSCI is an artifact of agency in action in all cases where we directly know the causal process, and on good statistical thermodynamics-related principles as say are discussed at introductory level in my always linked, APP 1 point 6.

    7 –> This wider conclusion is independent of whether or not the particular sequences used were modified in the recent past by human agency or not. The purposeful SELECTION of the sequences and their being embedded in a message is itself a substantiation of the empirically anchored point of the design inference.

    GEM of TKI

  19. Casey Luskin wrote (13):

    “Dr. Musgrave might then proclaim that the ID proponent is wrong, when in fact he is the one who is wrong because he assumed from the beginning that no naturally occurring gene sequence was designed. This is something to keep in mind if anyone submits analyses here.”

    Surely the answer, then, is to call him on it. Do the ID analysis, see which sequences drop out as having been designed (whether by human or other agency). If he then says that ID got it wrong, and some of the sequences are natural, respond with the ID results to point out that, in fact, ID predicts that these “natural” sequences were actually designed.

  20. I take it Musgrave doesn’t understand that ID does not stand or fall on his challenges.

    IF (big if) Ian really wanted to refute ID all he has to do is to demonstrate that stochastic processes can account for living organisms and the IC structures they contain.

    THAT would be a challenge- for ID to stay unfazed in the light of such data.

    And great job Patrick!

  21. Something else to ponder-

    When conducting research- ie to determine design or not- the researchers must have a first-hand look at that which is being investigated.

    With Ian’s “challenge” all we have is what he provided. And we have very good reasons to not accept what he provides- he is a proven anti-ID zealot.

    It would also be interesting to see how the sequences Ian says are not designed arose via purely stochastic processes.

  22. For us non-latin readers, Kairos #14
    Tertium non datur =
    “there is no third (possibility)”.
    See: Law of the excluded middle.
    and False dilemma

  23. Joseph
    “When conducting research- ie to determine design or not- the researchers must have a first-hand look at that which is being investigated.”
    Yes that would help, but is it “required”? e.g., Patrick was able to identify some of the strings based on published information. In cryptography, even if the message itself cannot be deciphered, tracking the source and destination can show that the strings were intelligently sourced, and give clues to its content. etc.

  24. “When conducting research- ie to determine design or not- the researchers must have a first-hand look at that which is being investigated.”

    Yes that would help, but is it “required”? –DLH

    I guess you could count on others but do you really want to do that?

    e.g., Patrick was able to identify some of the strings based on published information.–DLH

    Then he is relying on their expertise. And that is OK as long as that expertise can be trusted.

    What would have been the case if Patrick hadn’t been so smart or the data wasn’t published?

    In cryptography, even if the message itself cannot be deciphered, tracking the source and destination can show that the strings were intelligently sourced, and give clues to its content. etc.–DLH

    One of my areas of expertise is in cryptography. I got to travel around the world providing secure communications to businesses and militaries. But anyways, by tracking the encrypted message you are doing so first-hand. However even knowing its source will not give you any clues to the content.

    The only way to do that is to ask the sender and hope the answer is truthful or try to decipher the message.

    All that said I do understand your point. My point is is it is better to do the investigation first-hand or at least get the data from a trusted source.

    Musgrave isn’t a trusted source. Or perhaps he can be trusted to be misleading…

  25. Can I just ask for a clarification from Patrick – are you claiming that sequences 1, 4, 5, and 6 are all designed (by humans)?

    And just an observation – you found the sequences by looking for them in the synthetic Mycoplasma genitalium, i.e. you used your knowledge of possible designers. I suspect part of point of the challenge is to see if design detection can be done without using that sort of knowledge.

    Bob

  26. Bob

    It was Venter himself who employed the concept of intelligent design detection. What’re the odds of those watermarks showing up by way of random mutation and natural selection? Just say “close to zero” Bob – don’t waste any time trying to figure out precisely how close to zero. Instead envision a courtroom scenario where Venter is accusing someone of stealing his artificial genome. Can the accused plausibly make an argument that the Venter watermarks showed up in a different organism by chance mutations? Would Judge Jones of Dover fame need coaching from the NCSE to make that call? This is funny stuff. It’s okay to laugh.

  27. What will Ian Musgrave send next, letters from the zodiac?

  28. I think an important aspect has been sadly neglected in the above responses:

    Did Patrick win a copy of ‘OpenLab 2007, the best of Science Blogging’?

    IF Patrick did a sterling job at answering this challenge, will he be in ‘OpenLab 2008, the best of Science Blogging’?

    It is all about winning, no? In this case anyway???

  29. will he be in ‘OpenLab 2008, the best of Science Blogging’?

    Considering the entries that made it into the previous compilation, I kind of doubt that…

  30. Ah well, Patrick, it might have to be retitled:

    ‘OpenLabToEveryoneButIdists 2008′

    That may have some issues with typesetting the title though … and that thing about ID. You know, that elephant in the room that no one notices.

    I hope Musgrave autographs a copy of the book for you!

  31. Joseph 25
    Thanks for the clarification and highlighting the importance of direct analysis. Appreciate your expertise.

    By “clues to content” I was inferring from news of volume of terrorist channel “chatter” related to inferring something major was developing. Similarly, encrypted transmissions between financial facilities. This is not direct inference, but gives some higher probability based on past associations. Similarly the use of anonymizers to reroute emails by rerouting to avoid associative detection.

    Patrick’s reference to finding the sequence in the NIH web site states: “This Genbank entry is for the designed molecule”. That appears a reliable source for the data and evidence of human design, (without relying on the analysis which identified the watermarks.)

  32. [...] Comments DLH: Joseph 25 Thanks for the clarification and highlighting the importance of direct analysis. [...]

  33. DLH,

    My point is that in some biological warfare emergency the scientists would have the whole infecting organism to work with.

    What Patrick did was awesome but just think what could have been accomplished if he had the whole organism to work with.

  34. Joseph 34
    I agree. See my post regarding
    The 1000 Genomes project
    “The 1000 Genomes Project will involve sequencing the genomes of at least a thousand people from around the world.”

    and the
    Archon X Prize for Genomics

    “$10 Million to the First Team to Sequence 100 Human Genomes in 10 Days”

  35. Just for the record, here are decodings in the three different possible reading frames, with “watermarks” highlighted:

    Sequence 1:
    attatcacaaaatggtgtgatcttatcaatagcactacttgcttaactagctaatgtcgt
    gcaattggagtagagaacacagaacga
    ttaactagctaatttttttagttggatggcaat
    tgttggaattcacagctttttagttggaattttagttaatcatcaaacacttaaaataag
    taaaaagtatgttattttaggttcgatttttccaattatggcattaacaaatactcttgt
    0: IITKWCDLINSTTCLTSXCRAIGVENTERLTSXFFXLDGN
    CWNSQLFSWNFSXSSNTXNKXKVCYFRFDFSNYGINKYSC
    1: LSQNGVILSIALLAXLANVVQLEXRTQNDXLANFFSWMAI
    VGIHSFLVGILVNHQTLKISKKYVILGSIFPIMALTNTL
    2: YHKMVXSYQXHYLLNXLMSCNWSREHRTINXLIFLVGWQL
    LEFTAFXLEFXLIIKHLKXVKSMLFXVRFFQLWHXQILL

    Sequence 2:
    gatagtagtgggtggaatagtgaagaaaacgaagctaaaagtgatgcgcccctaagtaca
    ggagggggtgcttcttctggaacatttaataaatacctcaacaccaagcaagcgttagag
    agcatcggcatcttgtttgatggggatggaatgaggaatgtggttacccaactctattat
    gcttctaccagcaagctagcagtcaccaacaaccacattgtcgtgatgggtaacagcttt
    0: DSSGWNSEENEAKSDAPLSTGGGASSGTFNKYLNTKQALE
    SIGILFDGDGMRNVVTQLYYASTSKLAVTNNHIVVMGNSF
    1: IVVGGIVKKTKLKVMRPXVQEGVLLLEHLINTSTPSKRXR
    ASASCLMGMEXGMWLPNSIMLLPASXQSPTTTLSXWVTA
    2: XXWVEXXRKRSXKXCAPKYRRGCFFWNIXXIPQHQASVRE
    HRHLVXWGWNEECGYPTLLCFYQQASSHQQPHCRDGXQL

    Sequence 3:
    attatcacaaaatggtgtgatcttatcaatagcactacttgctttttttagttggatggc
    aattgttggaattcacagctttttagttggaattttagttaatcatcaaacacttaaaat
    aagtaaaaagtatgttattttaggttcgatttttccaattatggcattaacaaatactct
    tgtaattagaaaaaaattaaaagctttattaggagagggtaaggttcaaaaaggactcaa
    0: IITKWCDLINSTTCFFXLDGNCWNSQLFSWNFSXSSNTXN
    KXKVCYFRFDFSNYGINKYSCNXKKIKSFIRRGXGSKRTQ
    1: LSQNGVILSIALLAFFSWMAIVGIHSFLVGILVNHQTLKI
    SKKYVILGSIFPIMALTNTLVIRKKLKALLGEGKVQKGL
    2: YHKMVXSYQXHYLLFLVGWQLLEFTAFXLEFXLIIKHLKX
    VKSMLFXVRFFQLWHXQILLXLEKNXKLYXERVRFKKDS

    Sequence 4:
    agtagtgggtggaatagtgttaactagctaagtagaaaacaccgaacgaattaattctac
    gattaccgtgactgag
    ttaactagctaaaagaaaacgaagctaaaagtgatgcgccccta
    agtacaggagggggtgcttcttctggaacatttaataaatacctcaacaccaagcaagcg
    ttagagagcatcggcatcttgtttgatggggatggaatgaggaatgtggttacccaactc
    0: SSGWNSVNXLSRKHRTNXFYDYRDXVNXLKENEAKSDAPL
    STGGGASSGTFNKYLNTKQALESIGILFDGDGMRNVVTQL
    1: VVGGIVLTSXVENTERINSTITVTELTSXKKTKLKVMRPX
    VQEGVLLLEHLINTSTPSKRXRASASCLMGMEXGMWLPN
    2: XWVEXCXLAKXKTPNELILRLPXLSXLAKRKRSXKXCAPK
    YRRGCFFWNIXXIPQHQASVREHRHLVXWGWNEECGYPT

    Sequence 5:
    ttttatttgtttaatagttaaaaaaagcgttaactagctaatgcataaacgacatcgcta
    atgactgtctttatgatgaa
    ttaactagctaatgggtcgatgtttgatgttatggagcag
    caacgatgttacgcagcagggcagtcgccctaaaacaaagttaaacatcatgttatgttt
    tatctattttattagttaaaaaagttttgaatttttatctatttttagttaataaaagtc
    0: FYLFNSXKKRXLANAXTTSLMTVFMMNXLANGSMFDVMEQ
    QRCYAAGQSPXNKVKHHVMFYLFYXLKKFXIFIYFXLIKV
    1: FICLIVKKSVNXLMHKRHRXXLSLXXINXLMGRCLMLWSS
    NDVTQQGSRPKTKLNIMLCFIYFISXKSFEFLSIFSXXK
    2: LFVXXLKKALTSXCINDIANDCLYDELTSXWVDVXCYGAA
    TMLRSRAVALKQSXTSCYVLSILLVKKVLNFYLFLVNKS

    Sequence 6:
    ggagggagatcatcagatcaaagtaataaattcaccaagtacctcaacaccaagcaagca
    ttggaaaggatcggcatcttgtttgatggggatggaatgaggaatgtggttacccaactc
    taccaacccaacaaggtgaaaagtggtcaatatcaacaaaataacacctacaacaggtta
    attgagcctgacaatgcaacaagtgcagcgagcagcatgaccagcttgttaaagctgttg
    0: GGRSSDQSNKFTKYLNTKQALERIGILFDGDGMRNVVTQL
    YQPNKVKSGQYQQNNTYNRLIEPDNATSAASSMTSLLKLL
    1: EGDHQIKVINSPSTSTPSKHWKGSASCLMGMEXGMWLPNS
    TNPTRXKVVNINKITPTTGXLSLTMQQVQRAAXPACXSC
    2: REIIRSKXXIHQVPQHQASIGKDRHLVXWGWNEECGYPTL
    PTQQGEKWSISTKXHLQQVNXAXQCNKCSEQHDQLVKAV

    And for ease of reference, here’s the key for decoding the sequences:

    Amino Acid | Letter | Corresponding Codons
    Alanine | A | GCT, GCC, GCA, GCG
    Arginine | R | CGT, CGC, CGA, CGG, AGA, AGG
    Asparagine | N | AAT, AAC
    Aspartic acid | D | GAT, GAC
    Cysteine | C | TGT, TGC
    Glutamic acid | Q | CAA, CAG
    Glutamine | E | GAA, GAG
    Glycine | G | GGT, GGC, GGA, GGG
    Histidine | H | CAT, CAC
    Isoleucine | I | ATT, ATC, ATA
    Leucine | L | TTA, TTG, CTT, CTC, CTA, CTG
    Lysine | K | AAA, AAG
    Methionine | M | ATG
    Phenylalanine | F | TTT, TTC
    Proline | P | CCT, CCC, CCA, CCG
    Serine | S | TCT, TCC, TCA, TCG, AGT, AGC
    Threonine | T | ACT, ACC, ACA, ACG
    Tryptophan | W | TGG
    Tyrosine | Y | TAT, TAC
    Valine | V | GTT, GTC, GTA, GTG
    (Inapplicable) | X | TAG, TGA, TAA

  36. WOW J…

    Do we have a winner here?

  37. Where can one find studies that apply specified complexity analysis to real-world phonomena to show the presence or absence of design?

  38. j,

    Thanks for posting that complete reference! When I wrote my first hypothetical scenario I assumed that the surrounding characters would not form English words and mostly be gibberish. So your comment bares that assumption out.

    As an interesting study a program could be written to convert entire genomes using Venter’s cypher. Then this information could be searched for any legible English words, taking into account substitutions due to the limited 20 character set. I’d assume that at most we’d find words like “can” and “as” and whatnot. Assuming other groups adopt the Venter cypher for watermarks, this should allow people to find other watermarks and other genomes.

    Also, the other major thing to note is that since Musgrave only challenged us with 3 out of 5 parts of the entire watermark the amount of informational bits would NOT exceed the UPB of 500 informational bits. The 3 portions are only 117 characters, thus 234 informational bits. I find it hard to believe that Musgrave knows so little of ID that he’d contrive a challenge where the only result could be a false negative based upon the limitations of the EF.

    But here is the complete sequence for the entire watermark:

    http://www.telegraph.co.uk/ear.....ome101.xml

    TTAACTAGCTAATGTCGTGCAATTGGAGTAGAGAACACAGAACGATTAACTAGCTAA

    TTAACTAGCTAAGTAGAAAACACCGAACGAATTAATTCTACGATTACCGTGACTGAGTTAACTAGCTAA

    TTAACTAGCTAACATGCAATGTCGATGATTACCCACTTAACTAGCTAA

    TTAACTAGCTAATGCATAAACGACATCGCTAATGACTGTCTTTATGATGAATTAACTAGCTAATGGGTCGATGTTTGATGTTATGGAGCAGCAACGATGTTACGCAGCAGGGCAGTCGCCCTAAAACAAAGTTAAACATCATG

    TTAACTAGCTAAGGTCTAGCTAGTAGCGCGAATGACTGCCTATACGATGAG TTAACTAGCTAA

    That’s 380 characters and 760 informational bits, thus the Explanatory Filter would be able to detect the design.

  39. Patrick,

    Thanks for recognizing (@8) that the “Challenge” incorporated Venter’s work.

    By the way, it seems that the sequences for the watermarks that you just gave include extra leading and trailing characters. Here are the codings for the actual watermarks themselves, with quantity of characters in brackets:

    TGTCGTGCAATTGGAGTAGAGAACACAGAACGA [33]

    (CRAIGVENTER)

    GTAGAAAACACCGAACGAATTAATTCTACGATTACCGTGACTGAG [45]

    (VENTERINSTITVTE)

    CATGCAATGTCGATGATTACCCAC [24]

    (HAMSMITH)

    TGCATAAACGACATCGCTAATGACTGTCTTTATGATGAA [39]

    (CINDIANDCLYDE)

    GGTCTAGCTAGTAGCGCGAATGACTGCCTATACGATGAG [39]

    (GLASSANDCLYDE)

    So there are only 33 + 45 + 24 + 39 + 39 = 180 characters = 360 bits.

    Also by the way, the code isn’t Venter’s invention. It’s just the common representation of codons in the genetic code.
    __________

    jpark (37),

    Thanks, but I was only confirming what Patrick pointed out at comment (8). I was also curious to see what the non-watermark characters looked like when converted into text, and what resulted from using alternate reading frames.

  40. heh, that’s what I get for not doublechecking a news media source…never mind being lazy and using such a source in the first place. :D

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