The Nylon Bug

Discussion in 'Creation vs. Evolution' started by Helen, Jul 23, 2003.

  1. Helen

    Helen
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    A nylon digesting bacteria has been presented as evidence of natural evolution. I was curious about that. Lee Spetner has a good response as follows:

    The Nylon Bug

    Comments by Lee Spetner, November 19, 2002


    It's interesting, first of all, that the URL you pointed to picked the "nylon bug" as an example of a random mutation yielding a gain of information. (The short answer is, the mutation does yield an increase of information, but was it random?) It's interesting because the "nylon bug" is exactly what I used in my letter #7 to Jim Crow (of which you got a copy) as a possible example of a nonrandom mutation triggered by the environment. To respond to your query, I shall have to elaborate on this more than I did in that letter, which was not polemical.

    Let me point out two important facts that the URL ignores. First, there are two altered enzymes, not just one. Both these enzymes are needed to metabolize the 6-aminohexanoic-acid-cyclic-dimer (6-AHA CD) found in the waste water of the nylon factory. Neither of these enzymes alone is effective. Both are needed. The first enzyme, which I shall call enzyme 1, is 6-aminohexanoic-acid-cyclic-dimer hydrolase (6-AHA CDH) and catalyzes the conversion of 6-AHA CD to 6-aminohexanoic-acid-oligomer (6-AHA LO). The second enzyme, which I shall call enzyme 2, is (6-aminohexanoic-acid-oligomer hydrolase (6-AHA LOH) and catalyzes the conversion of 6-AHA LO to 6-amino-hexanoic acid [Kinoshita et al. 1981]. Only enzyme 2 is the product of a frame shift. Enzyme 1, whose DNA sequence I have not seen, is probably the product of only point mutations. [Okada et al. 1983, Ohno 1984]

    Second, enzyme 2 is not just the product of a frame shift, it is also the product of 140 point mutations. Many of these mutations are silent, but many are not. 47 amino acids out of 392 of the enzyme have been changed.

    It seems to me that many of these altered amino acids are essential to the catalytic effect of the enzyme. How many, I don't know. In my above cited letter to Jim, I calculated the probability of getting multiple random mutations in the 30 years it took to evolve these enzymes. If the evolution of this enzyme had to rely on random point mutations, it could have never evolved. Thus, if only 6 of these 47 mutations were essential for the evolution, the probability of achieving it in 30 years is about 3 x 1035. So, if the evolution could not be random, then it would have to be nonrandom, and as I have suggested in my book, they would be triggered by the environment. That is, the capability is built into the bacterium and the environment triggers the mutations.

    I have ignored the evolution of enzyme 1, and the random evolution of that enzyme makes for an even less probable event.

    Now, why should there be a built-in capability to metabolize nylon, which did not exist until 1937 or so? The answer is there shouldn't be. But there could have been a built-in capability to metabolize some other substrate. Kinoshita et al. (1981) tested enzyme 2 against 50 possible substrates and found no activity, but that does not mean that it doesn't have activity on some substrate not tested. The activity of enzyme 2 was small, but enabled the bacteria to metabolize the nylon waste.

    References

    Kinoshita, S., T. Terada, T. Taniguchi, Y. Takene, S. Masuda, N. Matsunaga, & H. Okada (1981)) Purification and characterization of 6-aminohexanoic-acid-oligomer hydrolase of flavobacterium sp. K172. Eur. J. Biochem. 116: 547-551

    Ohno, Susumu. (1984). Birth of a unique enzyme from an alternative reading frame of the pre-existed, internally repetitious coding sequence Proceedings National Academy of Sciences, USA 81: 2421-2425

    Okada, H., S. Negoro, H. Kimura, & S. Nakamura, (1983) Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature 306: 203-206.


    from here: http://members.tripod.com/aslodge/id89.htm
    The emphasis is from me.

    I would be interested in comments.
     
  2. Peter101

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    &gt;&gt;&gt;&gt;&gt;&gt;So, if the evolution could not be random, then it would have to be nonrandom, and as I have suggested in my book, they would be triggered by the environment. That is, the capability is built into the bacterium and the environment triggers the mutations.&lt;&lt;&lt;&lt;&lt;&lt;&lt;

    I am not sure that this guy knows what he is talking about. What is a nonrandom mutation and how is it triggered? How does a nonrandom mutation differ from an random one? Seems to me that if there is a mechanism for triggering a nonrandom mutation, then the effect is still the same regardless of whether it is random or nonrandom. How does this help the creationist?

    What does it mean that the "capability is built into the bacterium"? If the capability was not there before the mutation, then it is not built into the bacterium.
     
  3. Helen

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    It's his field of expertise, and obviously not yours, Peter101.
     
  4. Paul of Eugene

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    There is one sense in which there is an environmental cause for mutations. That is when the environment stresses a cell so that the normal error correction methods are comprimised, allowing more mutations to get through.

    This can work to the advantage of a population, allowing the cells to evolve more quickly in an environment that they are not well suited for, and once the evolution succeeds, they are less stressed, and the error correction mechanisms again are restored to full efficiency.

    But the important thing to note here is there is no control over any particular mutation itself. That is still a random event. It is the natural selection afterwards that determines whether the mutation is "good" or "bad" for the population.
     
  5. Paul of Eugene

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    PETER101, it would appear this line you quoted is an echo of the creationist mantra that living things never invent anything new, they only exploit potentials they already had.

    But it got me to thinking. Could it be that the original task that the bacteria faced, in the plant wastewater stream, was how to dispose of the excess nylon precursor chemicals in the water? That in the original evolutionary path was better waste elimination, and that incidentally a way was developed to use the resulting degraded nylon components for energy?

    This would be a possible line of research.
     
  6. The Galatian

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    My undergraduate degree is in bacteriology, and he's spouting hooey. The reason that the frameshift mutation worked (they are usually devastating) is because the gene happened to be on a plasmid, and so the frameshift didn't affect the whole genome.

    The fact that the enzyme, once evolved, was repeatedly refined by further mutations is not surprising. Barry Hall's work on E. Coli showed the same thing occuring.
     
  7. Helen

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    Let me see, Galatian. Spetner had a fellowship in Biophysics at Johns Hopkins in 1962-63 and has been studying organic evolution ever since.

    You're on a roll! You are smarter than Spetner, more correct than "Evolutionary Biology", ...

    and,ummmm, you teach jr. hi. Right?
     
  8. The Galatian

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    Hmm.. I took biophysics. Not much in evolution in most biophysics courses.

    And I've been studying evolution as long as Spetner has.

    But there's a difference. He's shackled to his religious assumption of creationism. And so he has to find excuses, instead of dealing with the evidence.

    The fact that he didn't understand what a "plasmid" was, tripped him up this time. Sometimes, when talking about bacteria, it helps to know something about them.

    It's why frameshift mutations are so often successful in bacteria: plasmids are transferred by conjugation, and rarely are necessary to the survival of the bacterium.
     
  9. Peter101

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    &gt;&gt;&gt;&gt;&gt;It's his field of expertise, and obviously not yours, Peter101.&lt;&lt;&lt;&lt;&lt;&lt;

    Well maybe you and your reference know more about the subject than I do. But still I repeat my question and specifically ask you for a response, Helen. The question is this. Suppose your reference is correct that the mutations that produce nylon eating organisms are in fact non-random mutations. How does that help the creationist position? Does it make evolution any less likely? If so, how?
     
  10. Peter101

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    &gt;&gt;&gt;&gt;&gt;Let me see, Galatian. Spetner had a fellowship in Biophysics at Johns Hopkins in 1962-63 and has been studying organic evolution ever since.

    You're on a roll! You are smarter than Spetner, more correct than "Evolutionary Biology", ...

    and,ummmm, you teach jr. hi. Right?&lt;&lt;&lt;&lt;&lt;&lt;
    .............................................
    Helen, let me make sure I understand you. You are implying that credentials are important?
     
  11. Travelsong

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    Only when they are held by someone who supports a young earth model. All those scientists in the majority are crazy despite their credentials, so they can be discounted.
     
  12. Helen

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    No, guys. What I am saying is that Galatian is talking from his own authority against those in fields who have expertise. Spetner does not have the degree Galatian does, but he has been studying in this area for almost 40 years now. Nor are degrees given to journals to the best of my knowledge.

    Galatian is making is a point to disagree with anyone who doesn't agree with him as though they were totally ignorant. It is one thing to disagree respectfully, and another to claim your opponent is ignorant; doesn't know what he is talking about; is full of it, etc. -- on your own authority.

    I know from experience that when I have asked Galatian for references, he pulls out either nothing, one or two that have little or nothing to do with the subject at hand, or the same two or three he has been using for years now.

    I prefer people who know what they are talking about. Peter, I prefer you in the C14 area because, if you are who I think you are, you have expertise in this area. Barry wants to check some more data first before he makes any changes, as I already mentioned. But you don't know beans about biology from what I can tell.

    Travelsong, I don't know who you are, but you have had the courtesy to consider points individually and speak your own mind instead of just rattling off some standard responses.

    But Galatian just denies what he wants to deny -- perhaps for his own purposes. And in doing so, is deceitful about what other Christians believe and Christian doctrine itself -- all the while claiming that religion and science must be kept separate.

    I don't give credence to much of anything he says now after watching him for so many years.
     
  13. Paul of Eugene

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    Helen, it's not possible to be "deceitful" about what other christians believe, because christians are such a diverse group that some christian somewhere is going to believe anything you could possibly specify!

    Galatian's ideas generally seem sound. If you don't like them, attack the science. Uncover evidence, for example, that frame shifting in plasmid dna really is fragile instead of robust like he asserted and show it to the world.
     
  14. The Galatian

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    The Barbarian actually earned a degree in bacteriology, unlike Spetner, who did not. His lack of expertise is obvious to anyone who understands bacteria. I'm not saying that because my credentials are better than Spetners (they are), but because he doesn't understand the issue.

    I've been studying in this area for almost 40 years now, and I have a degree in the field.

    I didn't say he was totally ignorant. I'm merely pointing out why a frameshift mutation in a bacterial plasmid is generally not harmful.

    Sorry. If Spetner is saying what you seem to be implying that he is, then he's ignorant about framshifts in bacterial plasmids. And that was the question.

    Giving the same answer to the same question is not considered a bad thing in science. But I've given you on this board, a great deal of information that is well-documented. I'm not sure what you think assailing me personally is going to do to help Spetner.

    Actually having earned a degree in bacteriology, I assure you that I do know about this subject.

    Most folks deny what they want to. For their own purposes. Why would they deny what they don't want to, for purposes they didn't intend?

    No. There are indeed some Christians who believe in creationism. But that doesn't make it a Christian belief, any more than "no dancing" is a Christian belief.

    As you've seen, mixing supernatural and science gives you unworkable science and worse religion.

    It's good to be skeptical. I encourage you to check my assertions on your own. You'll find that they are correct.
     

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