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Author Topic:   Is the evidence concerning the Nylon bug being exaggerated
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 1 of 20 (159632)
11-15-2004 6:19 AM


Dear All,
I initially posted the main body of this post in the 'Directly observed mutation' thread. I would like to make it a topic in its own right as that thread is fairly old and abandoned and Steen, to whom I was replying, doesn't appear to have been back since.
In the original thread Steen said...
Steen writes:
Well, the nylon bug was DOCUMENTED to have a frameshift mutation that lead to completely new traits.
Is this actually the case? Certainly the Ohno (1984) paper makes a convincing argument that the existence of an alternative 400+ amino acid sequence coding ORF which would be formed by the removal of a single nucleotide which forms a termination codon in that longer ORF.
As I say, the argument is convincing but is it a documented frameshift mutation? Is there a plasmid or a gene identified in the wild corresponding to the alternative long ORF?
One site which discusses the frame-shift origin is here, I dont know if this is a site you've seen or where you got your information concerning the fame-shift from but this site is one I have often seen referenced for this claim. The site says...
Detailed examination of the DNA sequences of the original bacterium and of the nylon-ingesting version show identical versions in the gene for a key metabolic enzyme, with only one difference in over 400 nucleotides.
And yet the Ohno paper I mentioned previously says in its conclusions...
Indeed, the very basic former totally lacking Trp and Asn residues is not likely to function as an enzyme of any sort,
And produces absoloutely no comparison with any original plasmid sequence but rather a hypothetical alternative open reading frame. If this is the source of the 'Detailed examination' showing only 'one difference in over 400 nucleotides' then it is a phantasm caused by a misreading of the original paper.
I want to make clear that I have no reason to doubt that this is most likely how the nylon digesting genes have arisen, I just don't know if you could say that it is really a documented case of a frameshift mutation leading to a new trait.
It may just be that there is subsequent research of which I am unaware which has identified an ancestral form of the gene with the alternative ORF still functional, if so I would be obliged if someone could provide it.
I think that it is vital that those of us who argue in favour of evolution should ensure that our evidence is of the highest standard and not fall into the sort of lazy habits we so often bemoan in our creationist interlocutors, such as presenting misinterpretations from a web site as if it were evidence from the primary literature.
TTFN,
WK

Replies to this message:
 Message 3 by Loudmouth, posted 11-15-2004 1:34 PM Wounded King has replied

  
AdminJar
Inactive Member


Message 2 of 20 (159670)
11-15-2004 10:07 AM


Thread moved here from the Proposed New Topics forum.

  
Loudmouth
Inactive Member


Message 3 of 20 (159739)
11-15-2004 1:34 PM
Reply to: Message 1 by Wounded King
11-15-2004 6:19 AM


quote:
As I say, the argument is convincing but is it a documented frameshift mutation? Is there a plasmid or a gene identified in the wild corresponding to the alternative long ORF?
From the Ohno paper that you reference:
{abstract} . . .Analysis of the published base sequence residing in the pOAD2 plasmid of Flavobacterium Sp. K172 indicated that the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein
The difference between the wild type and the nylC gene is the insertion of one nucleotide that caused a reading frame shift. Before the mutation, there was a 472 amino acid protein that had no acitivity. The insertion of one nucleotide resulted in a new reading frame, a different amino acid sequence, and an active enzyme. We already know that random insertions of nucleotides occurs naturally in bacteria. Therefore, assuming that this mutation occured randomly and naturally is supported by the data. Also, when they claim that "the 392-amino acid-residue-long bacterial enzyme 6-aminohexanoic acid linear oligomer hydrolase involved in degradation of nylon oligomers is specified by an alternative open reading frame of the preexisted coding sequence that originally specified a 472-residue-long arginine-rich protein" they had to have the original sequence available, otherwise they could not make such a statement.

This message is a reply to:
 Message 1 by Wounded King, posted 11-15-2004 6:19 AM Wounded King has replied

Replies to this message:
 Message 4 by Wounded King, posted 11-16-2004 2:55 AM Loudmouth has not replied
 Message 6 by Wounded King, posted 11-16-2004 8:04 AM Loudmouth has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 4 of 20 (160016)
11-16-2004 2:55 AM
Reply to: Message 3 by Loudmouth
11-15-2004 1:34 PM


Dear Loudmouth,
I don't know if you actually read the paper, since the quote you use is from the abstract, but if you have you must have noticed certain things such as sections entitled...
R-IIA Coding Sequence for 6-AHA LOH Embodies an Alternative, Longer Open Reading Frame That Might Have Been the Original Coding Sequence
The important part of this is of course the word 'might'. Or the Figure legend containing this phrase..
I assume that the longer open reading frame identified as PR.C. was the original coding sequence of this stretch of plasmid DNA until several decades ago.
Where the important word is 'assume'. With particular relevance to your argument the author goes on to say...
In particular, I suggest that the RS-IIA base sequence was originally a coding sequence for an arginine-rich polypeptide chain 427 or so residues long in its length and that the coding sequence for one of the two isozymic forms of 6-ALA LOH arose from its
alternative open reading frame.
So we see that what you take as a definitive statement of fact and from which you infer that they have done a sequence comparison with a wild type gene which they themselves only ever put forward as a hypothetical and which if they had isolated they would surely have documented.
So to rebut your
they had to have the original sequence available, otherwise they could not make such a statement.
They could make such a statement without the original sequence available, although they might be wrong in doing so. As I suggested earlier, you are inferring that they have the sequence but there is no evidence to back up your inference.
Abstracts are hardly the best source of data, though obviously highly preferable to potentially partisan websites, I would direct your attention to...
Pitkin RM, Branagan MA, Burmeister LF.
Accuracy of data in abstracts of published research articles.
JAMA. 1999 Mar 24-31;281(12):1110-1.
CONTEXT: The section of a research article most likely to be read is the abstract, and therefore it is particularly important that the abstract reflect the article faithfully. OBJECTIVE: To assess abstracts accompanying research articles published in 6 medical journals with respect to whether data in the abstract could be verified in the article itself. DESIGN: Analysis of simple random samples of 44 articles and their accompanying abstracts published during 1 year(July 1, 1996-June 30, 1997) in each of 5 major general medical journals (Annals of Internal Medicine, BMJ, JAMA, Lancet, and New England Journal of Medicine) and a consecutive sample of 44 articles published during 15 months (July 1, 1996-August 15, 1997) in the CMAJ. MAIN OUTCOME MEASURE: Abstracts were considered deficient if they contained data that were either inconsistent with corresponding data in the article's body (including tables and figures) or not found in the body at all. RESULTS: The proportion of deficient abstracts varied widely (18%-68%) and to a statistically significant degree (P<.001) among the 6 journals studied. CONCLUSIONS: Data in the abstract that are inconsistent with or absent from the article's body are common, even in large-circulation general medical journals.
Although I realise that this only covers a small sample of medical journals it is not unwarranted to expect similar incongruities in the wider biological sciences field.
Thank you for answering, I thought no-one was ever going to say anything about it.
TTFN,
WK

This message is a reply to:
 Message 3 by Loudmouth, posted 11-15-2004 1:34 PM Loudmouth has not replied

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 Message 5 by Wounded King, posted 11-16-2004 7:30 AM Wounded King has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 5 of 20 (160033)
11-16-2004 7:30 AM
Reply to: Message 4 by Wounded King
11-16-2004 2:55 AM


Dear Loudmouth,
I just reviewed some of the other threads on this topic, in particular the Debate Help Required
thread. Clearly you have read the primary literature on this subject previously.
TTFN,
WK

This message is a reply to:
 Message 4 by Wounded King, posted 11-16-2004 2:55 AM Wounded King has not replied

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 Message 7 by Loudmouth, posted 11-16-2004 3:57 PM Wounded King has not replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 6 of 20 (160038)
11-16-2004 8:04 AM
Reply to: Message 3 by Loudmouth
11-15-2004 1:34 PM


Dear Loudmouth,
Do you think the existence of anti-sense non-stop frames (NSF) around the GC rich sequences, such as that on which the nylB genes are located, would predispose the regions to show ORFs on the sense strand which may not represent any functional or expressed gene. Perhaps the most important issue for the gene is not the frame shift but the gaining of a start site.
I don't think the gene in question is the nylc gene since the Ohno paper was published in 1984 and nylc was only discovered in 1992 (Negoro, 1992).
TTFN,
WK
This message has been edited by Wounded King, 11-17-2004 02:27 AM

This message is a reply to:
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Loudmouth
Inactive Member


Message 7 of 20 (160161)
11-16-2004 3:57 PM
Reply to: Message 5 by Wounded King
11-16-2004 7:30 AM


quote:
Dear Loudmouth,
I just reviewed some of the other threads on this topic, in particular the Debate Help Required
thread. Clearly you have read the primary literature on this subject previously.
TTFN,
WK
It seems like a decade ago, but yeah I have read the primary lit. I am reviewing some of it now and will get back to you later.

This message is a reply to:
 Message 5 by Wounded King, posted 11-16-2004 7:30 AM Wounded King has not replied

  
Loudmouth
Inactive Member


Message 8 of 20 (160189)
11-16-2004 4:54 PM


Wounded King,
Ok, I found the problem. The Ohno 1984 paper involves the EI, EII, and EII' activities. These enzymes are coded by nylA, nylB, and nylB'. nylB and nylB' are derivatives of the same polypeptide repeat, according to Ohno. nylC is not mentioned anywhere in the paper which is designated as EIII in the literature.
I'll do some further research for references on nylC in order to find the premutation sequence.

Replies to this message:
 Message 9 by Wounded King, posted 11-17-2004 3:05 AM Loudmouth has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 9 of 20 (160337)
11-17-2004 3:05 AM
Reply to: Message 8 by Loudmouth
11-16-2004 4:54 PM


Dear Loudmouth,
Why should nylC have any particular relevance? The New mexicans for Science and Reason site is clearly talking about the sequence analysis of nylB from the Ohno (Ohno, 1984) paper. Why do you suppose that there exists a pre-mutation sequence for nylC when there is not one for the other genes?
The Negoro (Negoro, et al., 1992) paper which first identifies nylC is not documenting the origin of a totally novel gene but simply the identification of a previously undiscovered one. The only sequence comparison they do is between the K172 and K17251R strains from which they find the nylC gene sequences are identical.
The origin of the pOAD2 plasmid does not seem to be well documented enough that ancestral non-nylon degrading sequences can actually be identified in the wild, only inferred.
TTFN,
WK

This message is a reply to:
 Message 8 by Loudmouth, posted 11-16-2004 4:54 PM Loudmouth has replied

Replies to this message:
 Message 10 by Loudmouth, posted 11-17-2004 11:43 AM Wounded King has not replied

  
Loudmouth
Inactive Member


Message 10 of 20 (160510)
11-17-2004 11:43 AM
Reply to: Message 9 by Wounded King
11-17-2004 3:05 AM


quote:
Why should nylC have any particular relevance? The New mexicans for Science and Reason site is clearly talking about the sequence analysis of nylB from the Ohno (Ohno, 1984) paper.
You are absolutely correct. I feel a little embarassed. All this time I thought the NMSR site was referring to the nylC gene. Oops. More research is needed, I will get back to you.

This message is a reply to:
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AdminNosy
Administrator
Posts: 4754
From: Vancouver, BC, Canada
Joined: 11-11-2003


Message 11 of 20 (175590)
01-10-2005 5:25 PM


Thread moved here from the Biological Evolution II forum.

  
coffee_addict
Member (Idle past 477 days)
Posts: 3645
From: Indianapolis, IN
Joined: 03-29-2004


Message 12 of 20 (175599)
01-10-2005 5:44 PM


Dear all, please talk in normal English for us biology-deprived mortals can understand.

Replies to this message:
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 Message 14 by Wounded King, posted 01-11-2005 2:22 AM coffee_addict has replied

  
Nighttrain
Member (Idle past 3994 days)
Posts: 1512
From: brisbane,australia
Joined: 06-08-2004


Message 13 of 20 (175713)
01-11-2005 1:28 AM
Reply to: Message 12 by coffee_addict
01-10-2005 5:44 PM


What I want to know is, are my fishing lines safe? Or do I have to coat them with a nucleotide bug-spray?

This message is a reply to:
 Message 12 by coffee_addict, posted 01-10-2005 5:44 PM coffee_addict has not replied

Replies to this message:
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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 14 of 20 (175723)
01-11-2005 2:22 AM
Reply to: Message 12 by coffee_addict
01-10-2005 5:44 PM


What didn't you understand? It's a pretty technical topic so explaining everything would take a while. You can ignore the discussions of exactly which gene it is as that was pretty much an unproductive deviation from the main point.
From my point of view you would understand it bestby reading the NMSR website on the subject and then reading my objections to their account.
TTFN,
WK

This message is a reply to:
 Message 12 by coffee_addict, posted 01-10-2005 5:44 PM coffee_addict has replied

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Loudmouth
Inactive Member


Message 15 of 20 (175859)
01-11-2005 12:27 PM
Reply to: Message 13 by Nighttrain
01-11-2005 1:28 AM


quote:
What I want to know is, are my fishing lines safe? Or do I have to coat them with a nucleotide bug-spray?
Yeah, your fishing lines are safe, as are women's pantyhose, climber's ropes, etc. The nylon bug eats short polymers of nylon that are in solution (ie in water). I'm not sure, but I think these enzymes are only found within the bacteria so the nylon derivatives need to be transported inside the bacteria before they are digested.

This message is a reply to:
 Message 13 by Nighttrain, posted 01-11-2005 1:28 AM Nighttrain has not replied

  
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