Invited responses to my nylonase research and the question of “New Proteins Without God’s Help”

Susumo Ohno (who coined the term “junkDNA”) published a paper in 1984 through the National Academy of Sciences that was used by the NCSE, Ken Miller and Dennis Venema to claim “proteins can evolve without God’s help”. At the request of John Sanford, a courtesy associate research professor at Cornell, I was recruited to write a paper to refute Ohno’s evolutionary hypothesis on nylonases. I wrote it under John’s guidance based on his intuitions about genetics, his life-long specialty of 40 years and for which he became famous as attested by the fact he is one of the few geneticists who had their work featured in the Smithsonian National Museum of American History.

The actual paper is now in review, but it is not intended to be published in any journal, but will be released in a variety of channels shortly. It is hoped the material can be used by others to actually create papers that enter peer review. The motivation for releasing the paper in this way is to counter Venema’s book while it is still hot off the press.

The paper is being also published in this way so as to invite discussion since it isn’t intended to be considered a completely vetted product but one that welcomes improvement. That said, the sentiment among IDists and creationists who’ve seen the drafts is that paper has utterly discredited Ohno’s claims and thus the claims of the NCSE, Ken Miller and Dennis Venema connected to Ohno’s hypothesis of nylonase evolution.

Because the draft paper is a massive VJTorley-sized paper (15 pages in the main section and almost 80 pages of supplemental material) I’m establishing this thread at TSZ to invite review of the some of the themes from the paper that I’m releasing on the nylonase.XYZ website piece by piece in a format adapted for a website.

As I release each webpage, I’ll post in the comment section at TSZ a link to the newly constructed page so as to invite commentary on that page. Thank you in advance to all those willing to participate in this public review of my research on nylonase evolution.

NOTES:

1. “proteins can evolve without God’s help” is a paraphrase of the title of an NCSE article New Proteins Without God’s Help. Thwaites at the NCSE basically framed the debate over nylonase evolution in this way:

We’ve been trying to explain all this to the protein “experts” at ICR for the last seven years. We have told them that new proteins could indeed form from the random ordering of amino acids. We have warned them that their calculations were based on faulty assumptions and soon someone would document the natural formation of a new protein from the random association of amino acids.

Now it has happened! Not one, but two, new proteins have been discovered. In all probability new proteins are forming by this process all the time, but this seems to be the first documentation of this phenomenon. The newly discovered proteins are enzymes that break down some of the byproducts produced during nylon manufacture. Since nylon first came into commercial production in 1940, we know that the new enzymes have formed since that time.

2. The nylonase.XYZ website is under construction, so don’t click around the website too much yet. In the comment section at TSZ I will link to individual pages of the website that can be reviewed individually.

3. The first comments by me at TSZ will be more technical, not for the beginners regarding Ohno’s work. The beginner and introductory stuff will be added later to the website.

174 thoughts on “Invited responses to my nylonase research and the question of “New Proteins Without God’s Help”

  1. I also find it odd that you say your paper is so long, because so far it doesn’t seem to be saying much that requires great length.

    It’s of great length so as to curtail Venema, Ken Miller and their defenders. It’s nice that you’re knowledgeable enough to see Ohno was wrong with so little persuasion, most aren’t as smart as you and need to have it spelled out for them.

    I know the kind of stuff Ken Miller writes, and many paragraphs are oblique responses to what he wrote in his book “Only a Theory”.

    BIOSIS is the standard database of journal citations. Used to be printed, but I don’t know if that happens any more. Sanford didn’t know about it?

    Well if he didn’t, then it’s obvious God sent you to us to help us prosecute our case. Obviously if such a paper exists, then Dennis Venema and Ken Miller have some splainin’ to do. It reflects just as badly on them, wouldn’t you agree. 🙂

  2. I should point out the circumstantial evidence suggests Venema seems to be aware of the X-ray crystallography results that Rumraket mentioned:

    Additionally, the three-dimensional structure of the protein has been solved using X-ray crystallography, a method that gives us the precise shape of the protein at high resolution. Nylonase is chock full of protein folds – exactly the sort of folds Meyer claims must be the result of design because evolution could not have produced them even with all the time since the origin of life.

    Dennis Venema

    So why then would Venema swear by Ohno’s results in view of the fact that the X-Ray crystallographers actually gave strong evidence Ohno was wrong? Venema’s got some splainin’ to do.

  3. stcordova: It reflects just as badly on them, wouldn’t you agree.

    I’d say it reflects equally badly on both of you. But yes, it’s a black eye for both Miller and Venema. Still, they’re generally much better on facts and much more willing to consider the bulk of the data than you are, so don’t crow too loud.

  4. stcordova: The paper is a monstrosity, and Dr. Sanford said he wanted feedback on it’s accuracy before trying to go to something more formal like a journal paper.

    Translation: “I don’t have time to locate and correct all Salvador’s mistakes.”

  5. stcordova: “Part of the reasoning for Dr. Sanford and I writing the paper is to clarify and codify our own thoughts on the matter. The writing process is an extension of our own thought process.”

    There’s the problem.

  6. Davemullinex:

    There’s the problem.

    Well, our thought process was waaaaaay better than Ken Miller’s, the “expert” witness at the Kitzmiller vs. Dover trial.

    Miller was gullible enough to believe Ohno’s theory, but our skepticism and careful consideration of actual facts demonstrated Ohno’s theory was all a fantasy.

  7. stcordova: our skepticism and careful consideration of actual facts

    It’s easy to apply those to things you don’t want to believe. The hard part is applying them to things you do want to believe. For good exercise, you could try using them on YEC.

  8. stcordova: Well, our thought process was waaaaaay better than Ken Miller’s, the “expert” witness at the Kitzmiller vs. Dover trial.

    Miller was gullible enough to believe Ohno’s theory, but our skepticism and careful consideration of actual facts demonstrated Ohno’s theory was all a fantasy.

    Add conceit to the long list of your character defects.

  9. stcordova,

    our skepticism and careful consideration of actual facts

    So, turning that skepticism towards the carbon content, inorganic + organic, of limestones …

  10. So, turning that skepticism towards the carbon content, inorganic + organic, of limestones …

    All for it! Which is more than I can say for the attitudes of Darwin defenders here who blindly believe, yet pretend what they have is skeptical science.

  11. Regarding UNIPROT, I believe I’ve discovered how they infer similar protein structure without actually resorting crystallography in every case. It follows along the Hidden Markov detection systems.

    I was blessed to talk to one of the heads of the NIH GenBank yesterday. Why? Because that person is professor of my graduate-level BioInformatics class at the NIH. Bwahaha! I was told to look at Psi BLAST and its use of Hidden Markov modeling. It appears something similar is used by UNIPROT/SWISS PROT. Bwahaha!

    https://www.ncbi.nlm.nih.gov/books/NBK2590/

    The iterative profile generation process makes PSI-BLAST far more capable of detecting distant sequence similarities than a single query alone in BLASTp, because it combines the underlying conservation information from a range of related sequence into a single score matrix. In the evolution, three-dimensional (3D) structures of proteins may be conserved even after considerable erosion of their sequence similarity. PSI-BLAST has been demonstrated to be useful in detecting such relationships via sequence searches, which were previously only detected through direct comparison of the 3D structures

    Bwahaha!

    God could embed a Hidden Markov signature. No need of phylogenetic processes if you God is the designer. As I said, Theobald totally ignores the the problem of orphan systems, and a smooth evolutionary common descent model collapses in the face of orphan systems. Therefore the Hidden Markov signatures were created by God, not by random processes. Praise Be!

    So this explains now UNIPROT apparently inferred the nylB gene without much sequence similarity.

  12. stcordova,

    All for it! Which is more than I can say for the attitudes of Darwin defenders here who blindly believe, yet pretend what they have is skeptical science.

    So, you dodge the question by pointing out the behaviour of others?

  13. stcordova: God could embed a Hidden Markov signature.

    God could in principle do all sorts of things. God could also not embed a “hidden markov signature” somewhere. So merely suggesting that he could is worth a fart in a pigsty.

  14. So, you dodge the question by pointing out the behaviour of others?

    I say, “I don’t know, there’s a chance you could be right. Maybe wait and see. If I’m right, bad for you because then there is a God. If I’m wrong, we’re even, because we both meet equal ends. You’re playing your wager poorly, and you are wagering with your soul.”

    So I have to ask, why then do you wager your soul on evolutionary theory if there is the possibility of Creator God who may call you into judgement one day. The God who designed the wasp larvae who kills the caterpillar is able to do far more horrendous things to those who oppose him. Darwin could not comprehend why God would make such a cruel work of nature. I suggest it is a warning sign.

    You’re the one who looks to me like the one dodging far more weighty dangers. What danger is there to me a million years from now if I’m wrong?

  15. stcordova: As I said, Theobald totally ignores the the problem of orphan systems, and a smooth evolutionary common descent model collapses in the face of orphan systems. Therefore the Hidden Markov signatures were created by God, not by random processes.

    This literally makes zero logical sense.

    Your “therefore” in that sentence has no place in it. No single thing in that last sentence follows from your first one, and your first one is outright nonsensical.

    Please, please try to derive your “therefore….” from the statement above with a proper syllogism.

  16. stcordova,

    Sal, enough with Pascal’s Wager. It’s been done to death, literally, because it’s been shown to make no sense. If that’s the foundation for your belief, you have built a house on sand.

    If you want to believe in an evil god, I’m OK with that. But I can’t imagine why you suppose that your evil god is also a god of love, worthy of admiration or worship, and various other mutually inconsistent properties you attribute to it.

  17. stcordova: Theobald totally ignores the the problem of orphan systems, and a smooth evolutionary common descent model collapses in the face of orphan systems.

    What you call “orphan systems” are in some cases things whose origin we don’t know and in other cases things whose origin we do know but you choose to ignore. In neither case does “it was poofed into existence in a large number of species a few thousand years ago” make any sense as an explanation. Why do these “orphan systems” organize into groups consistent with groups formed from other data? Why do their characteristics vary in a nested hierarchical manner within groups, and in the same manner as determined from other data? Why do they vary at all, if they were poofed recently?

  18. stcordova: Bla bla bla worst delivery of pascal’s false dichotomy ever

    Why do you waste so many words on a complete irrelevancy when they have no bearing on what is actually true? It really is diagnostic of your thinking that this is what you go to in every discussion. You are so deeply afraid of what the facts might be, you’d much rather jump to conclusions and try to give yourself some peace of mind than you would want to find out if you are wrong about what you already believe.

    You really don’t get this. I’m not like you at all. I want to know what is actually true, and what is most plausibly implied by the evidence we have. I literally could not care any less about what you think will happen to people who accept other interpretations than you do. Also, there are tens of thousands of interpretions of christianity and creationism alone, so this whole judgement gibberish that you have been taught to regurgitate to scare your fellow creationists away from information that threatens their worldview, is a false dichotomy. Not to mention all the other religions.

    I want to relay to you the degree to which I take your “threats” seriously. Here goes: Try to explore for a second how it makes you feel if I tell you that the the Galactic Empire from Star Wars will come and arrest you and have you tortured by Darth Vader if you don’t stop talking about creationism. Notice how entirely unaffected you are. Imagine how little sleep you will lose over this possibility. I imagine you’re sitting behind your monitor reading this, and smiling at how ridiculous it is. That feeling you have there, that’s me. That’s how much your threat of hellfire moves me. I smile and think “what a dolt”.

    Now, can we just get back to the facts and the logic please? Your emotional state is not a guide to truth or history. Thank you.

  19. stcordova,

    So I have to ask, why then do you wager your soul on evolutionary theory if there is the possibility of Creator God who may call you into judgement one day. The God who designed the wasp larvae who kills the caterpillar is able to do far more horrendous things to those who oppose him. Darwin could not comprehend why God would make such a cruel work of nature. I suggest it is a warning sign.

    How can I oppose something that doesn’t exist? You think I should suck up to God because he’s the kind of guy who might lay an egg in my brain?

    Anyway, I’m treating Pascal’s Wager like an eBay ‘sniping’ exercise. Repent on me deathbed, up I go, job’s a good ‘un. Win-win.

    You’re the one who looks to me like the one dodging far more weighty dangers. What danger is there to me a million years from now if I’m wrong?

    None. But if you are interested in science, surely the question ‘where did all the carbon come from?’ is a good one? And relevant to the YEC/something else choice that means so much to you.

    What you are pinning your hopes on is not so much Pascal’s Wager per se, but a variant in which you ignore inconvenient reality in the hope that the operator of this stupid bet will be pleased by your stubbornness. But the operator of such stupid, whimsical bets seems just as likely to lay an egg in your brain for wasting what He gave you.

  20. John:

    Sal, enough with Pascal’s Wager. It’s been done to death, literally, because it’s been shown to make no sense. If that’s the foundation for your belief, you have built a house on sand.

    It was Allan who accused me of dodging. I wasn’t. I don’t worry to much about things that won’t destroy me, but I find it ironic Allan seems not to care one iota about something that could destroy him. Me being wrong about limestones doesn’t cost my soul, but me being right about C14 might cost him his.

    I was just pointing out the irony that he should be throwing a lot more skepticism about his understanding of science given he has far more to lose by being wrong. So, from my perspective, he’s the one really dodging the weighty issue for him. He should be trying to make a more informed decisions about where he is betting his soul.

    Otherwise, these discussions are not of much personal value, but just an intellectual amusement.

    I’ll give you all some amusement, but I have to admit, I get amused by the collective folly and blind uncritical belief in the unproven theory of Universal Common Ancestry.

    So I found out a good explanation for how UNIPROT infers NylB. Any objections. Do you all agree Hidden Markov actually detects protein structure without X-ray crystallography or cryo electron microscopy or even chemical testing?

    It’s you and Allan who wanting to throw in talk of limestones in a thread about NYLONASES!

  21. stcordova: I’ll give you all some amusement, but I have to admit, I get amused by the collective folly and blind uncritical belief in the unproven theory of Universal Common Ancestry.

    I get amused by the colossal irony of you counterfactually asserting that the theory of universal common ancestry is “unproven” yet is believed “uncritically”. And even preposterously, that the detection of structural homologous for a protein in uniprot is somehow a problem for common descent. This is both ironic, hilarious and said at the same time.

    What happened, you’ve learned to regurgitate the phrase “Hidden Markov” and now it has to find a place in everything you write and must also in some way you have yet to explain, also constitute a falsification of common descent?

    So I found out a good explanation for how UNIPROT infers NylB. Any objections. Do you all agree Hidden Markov actually detects protein structure without X-ray crystallography or cryo electron microscopy or even chemical testing?

    Why would we not and how is this in any way a problem for the inference of common descent?

    The detection of structurally similar NylB enzymes using protein blast implies it exists in many species – therefore common descent is false. <- Doesn't look like valid logic to me. Can you elaborate what your thinking is even like here, Sal? Do you even know, or this just another of your completely illogical knee-jerk brainfarts?

  22. Rumraket: I get amused by the colossal irony of you counterfactually asserting that the theory of universal common ancestry is “unproven” yet is believed “uncritically”.

    Even keiths can’t prove it. Instead he has to refer me to some paper by some other guy. Then, when the paper is called into question, keiths vanishes.

  23. stcordova: So I have to ask, why then do you wager your soul on evolutionary theory if there is the possibility of Creator God who may call you into judgement one day

    I think you underestimate the pettiness of the version of God you worship, all scientific theories ignore the necessity of God’s intervention. Would you risk your soul on the theory of relativity?

    Jesus when He healed the sick used only faith, why do you risk your soul on a MRI?

    Greedy activities are condemned in the Bible, why do you risk your soul on greedy endeavors such as gambling for money and even worse gambling that the appearance of belief for personal gain will satisfy such a God?

    Let’s not even get into pride and where that get’s one soul.

    The God who designed the wasp larvae who kills the caterpillar is able to do far more horrendous things to those who oppose him

    You poor ,poor child.Your God does horrible things to those who do not oppose Him.He wants only blind faith, inquiry is forbidden.

    Darwin could not comprehend why God would make such a cruel work of nature. I suggest it is a warning sign.

    The devout are subject to the same cruel work of nature and they heeded the “warning”. Sounds more like the Stockholm Syndrome

  24. Mung: Even keiths can’t prove it. Instead he has to refer me to some paper by some other guy. Then, when the paper is called into question, keiths vanishes.

    Sounds like a win win

  25. stcordova,

    So in response to a request for enough of Pascal’s Wager already, your response is to double down on Pascal’s Wager. Do we really have to discuss, once more, why it’s invalid? What if your god isn’t the true god, and the true god wants to torture forever anyone who doesn’t accept evolution? Hey, all of a sudden you’re betting your soul against that guy.

    Now, some of us think that the evidence of a claim is what we should judge truth by, and not our prospects for punishment. It certainly seems more honest to do it that way. If you value anything similar to truth or honesty and not just avoidance of punishment, consider that others may weigh the first more heavily than the second.

    I have no idea how UNIPROT infers NylB. But you’re arguing that whatever it is, that’s evidence for creation. You’re the one who brought up creationism.

  26. Rumraket:

    that the detection of structural homologous for a protein in uniprot is somehow a problem for common descent.

    I never said detection of homologies through hidden markov models is evidence against common descent. In fact it would be persuasive evidence of common descent if that was the only data point. You are not representing what I actually believe. You making fun of a position I don’t hold. Laugh away at something of your own fabrication, but don’t pretend what you’re laughing at was something I actually said.

    I was pointing out, however, Theobald suffers from cherry picking since his model falls apart because of Orphan Systems. Cherry picking is junk science.

    But in any case, the first public version of my nylonase paper is about to be rolled out.

    It’s fair game to criticize anything in the paper if they are constructive criticisms so as to improve the way I and John Sanford’s arguments are communicated.

    Some reviewers of our public document have already flagged weaknesses in the formatting and grammar, etc. but not the substance. Maybe in a week it will be out. Dr. Sanford wants it out in short order.

  27. Mung,

    What could you possibly repent of?

    I’ll think of something. It seems de rigueur to adopt the persona of a miserable penitent.

  28. stcordova,

    It’s you and Allan who wanting to throw in talk of limestones in a thread about NYLONASES!

    Sal Cordova complains about a derail. Fffft-whirr-KERBLANG! There goes another one.

  29. Addendum:

    After collecting public criticisms, we will re-write the paper and submit it to an open access journal.

    My understanding is that many open access journals don’t consider something published if it is dumped on archives like Arxiv at Cornell or any other public repository.

    If we can get our paper in present form published, we can re-write it or extract important sections that are worthy of separate papers. For example, confirmation of the UNIPROT Hidden Markov models in the form of experiments that confirm enzymatic activity of predicted proteins ought to be of interest to someone somewhere!

  30. stcordova: we will re-write the paper and submit it to an open access journal.

    What journal are you thinking of? Given that there are quite a few open-access online journals whose entire purpose is to make money by publishing anything they are sent, it shouldn’t be hard to find one. A legitimate open-access journal might be more difficult. I don’t think publishing the same thing twice, first at once and then in pieces, is a morally defensible way of increasing your publication count.

  31. stcordova: I never said detection of homologies through hidden markov models is evidence against common descent. In fact it would be persuasive evidence of common descent if that was the only data point. You are not representing what I actually believe.

    If that is the case then I apologize, but you’re not being very clear.

    You wrote this earlier:

    God could embed a Hidden Markov signature. No need of phylogenetic processes if you God is the designer. As I said, Theobald totally ignores the the problem of orphan systems, and a smooth evolutionary common descent model collapses in the face of orphan systems. Therefore the Hidden Markov signatures were created by God, not by random processes.

    This makes no sense, and seems to imply that you think Hidden Markov signatures are better explained by God, rather than evolution. Which is another way of saying you think they’re evidence for creationism, and against evolution.

    But okay, you meant to imply something else. Let’s look at that then.

    I was pointing out, however, Theobald suffers from cherry picking since his model falls apart because of Orphan Systems. Cherry picking is junk science.

    Oh so the whole Hidden Markov signature-thing was irrelevant. Your complaint is that you think Theobald has cherrypicked something somewhere. Can you elaborate? What did he cherry pick, where did he do so, and what should he have picked instead? And how would that have changed his results?

  32. John,

    What makes you think we’re trying to increase publication count. We want the truth out.

    John Sanford is my co-author, he’s in this to tell the truth, not to make money or increase his reputation. Heck, he’s one of the few if not the only geneticist to have his work featured in the Smithsonian National Museum of American History. He doesn’t need to do this except for the sake of setting the record straight.

    We aren’t publishing the same thing twice. I double checked some journals with Open Access policies whether they count dumping a paper in an archive like the Cornell Arxiv as publication, and they don’t. There is a good reason for this.

    Many government funded outfits are required to essentially make available the research to the public. They will do this by dumping stuff to archives and repositories. They may or may not publish in a journal. Since a journal’s publishing decision is up to the editors, researchers funded by the government could be in violation of their contracts if they sit on their data without releasing it somewhere first. Saying they can’t get a journal to publish their data can’t be an excuse. Hence these facts have changed the way journals do business, especially open access journals. The allow exactly the sort of thing I described, including Nature’s Open Access journals.

    Besides, you’ll see for yourself if what we say is true. If it is true, it stands on its merits. The journal is only a means of getting the truth out.

  33. I have money. See, that proves I don’t want money.

    Of course, If I did have more money I could buy out all those lying Darwinist propaganda “journals” and replace them with real science journals.

  34. So we’d fault a study that’s trying to get to the bottom of the ‘universal’ question because it doesn’t include sequences that are restricted to a single species? That doesn’t seem a sensible criticism.

  35. Mung,

    Of course, If I did have more money I could buy out all those lying Darwinist propaganda “journals” and replace them with real science journals.

    You could burn a load of books while you were at it. In fact, don’t you have some?

  36. stcordova:
    What makes you think we’re trying to increase publication count.We want the truth out.

    That disagrees with your statement that you’re mainly interested in escaping eternal torment, and questions of truth are purely secondary.

    John Sanford is my co-author, he’s in this to tell the truth, not to make money or increase his reputation.Heck, he’s one of the few if not the only geneticist to have his work featured in the Smithsonian National Museum of American History.He doesn’t need to do this except for the sake of setting the record straight.

    Or is he, like you, making Pascal’s Wager? And again, your credential-inflation is not necessary or useful. Being featured in the National Museum of American History isn’t even a credential.

    We aren’t publishing the same thing twice.I double checked some journals with Open Access policies whether they count dumping a paper in an archive like the Cornell Arxiv as publication, and they don’t.There is a good reason for this.

    I was taking about your claim that you would publish once and then abstract pieces to publish again. If all you meant was that you would archive the whole thing, then I wouldn’t count that as publishing.

    Since a journal’s publishing decision is up to the editors, researchers funded by the government could be in violation of their contracts if they sit on their data without releasing it somewhere first.

    I’ve been funded by the government. What you say there is nonsense. You’re expected to publish. You’re expected to make your data available after publication.
    Archiving is making available, but it isn’t publication.

    Besides, you’ll see for yourself if what we say is true.If it is true, it stands on its merits.The journal is only a means of getting the truth out.

    So far we have no evidence that truth is one of your concerns. Pascal’s Wager isn’t about truth.

  37. John:

    Archiving is making available, but it isn’t publication.

    Ok, then your accusations of double publishing are baseless since we aren’t published. We can shop for a journal.

    Thanks for your editorial review when I started posting on this topic way back in March. It helped us assemble a credible case against Ohno and Okada’s theories, so much so, even you John Harshman agreed we were right, which means Ken Miller and Dennis Venema and the NCSE and lots of other people were wrong about nylonase. Thank you very much.

  38. stcordova: Ok, then your accusations of double publishing are baseless since we aren’t published. We can shop for a journal.

    You said “If we can get our paper in present form published, we can re-write it or extract important sections that are worthy of separate papers.” What did you mean by that?

  39. Allan Miller:

    Sal Cordova complains about a derail. Fffft-whirr-KERBLANG! There goes another one.

    You want off topic, here is off topic. The following is a video of boxer Usman Ammed “Uzzy” dancing before he gets knocked out in the ring.

    Uzzy’s dancing moves remind of the Mung’s attempts at humor:

    https://youtu.be/ZUKXSbX_oWk

  40. It’s amusing that someone like Sal, who boasts endlessly of his gambling prowess, would fall for Pascal’s Wager.

  41. You said “If we can get our paper in present form published, we can re-write it or extract important sections that are worthy of separate papers.” What did you mean by that?

    Exactly what I meant except I failed to write “can’t” not “can”. Sorry for the misunderstanding caused by me and my typos. Apologies.

    You just said our paper isn’t considered published, yet you threw around accusations that I’m attempting to double publish. The word “publish” in this case means “journal published” not “dumping on the net”. Now that I admitted my typo and you know my intended meaning you can drop your false accusations.

  42. stcordova: Now that I admitted my typo and you know my intended meaning you can drop your false accusations.

    Correct, since my false exaggerations were based entirely on what you actually said but didn’t mean to say.

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