Is the evidence concerning the Nylon bug being exaggerated

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... 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... And yet the Ohno paper I mentioned previously says in its conclusions... 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

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... The important part of this is of course the word 'might'. Or the Figure legend containing this phrase.. Where the important word is 'assume'. With particular relevance to your argument the author goes on to say... 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 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... 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

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

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,WKThis message has been edited by Wounded King, 11-17-2004 02:27 AM

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

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