Talk:EPSP synthase

comment

I have edited the page to include the fact that the shikimic acid pathway is found in microbes in animal gut microbiomes, because i think it's not fully accurate to state that the pathway is not found in animals and it needs this qualifying additional statement to be complete. This is in a paragraph that provides background knowledge about the shikimic acid pathway, and contains other assertions and no references. I could provide references to the fact that microbes in the animal gut contain EPSPS and the shikimic acid pathway, but it's general knowledge, on the same level with the other statements in that paragraph. I added this, and then noted in the history that i had already added it before and it was removed by Jytdog. I have been having problems with this user removing my edits consistently and aggressively in relation to the glyphosate article, as well. I think there is something wrong with the nature of his/her editing, as it seems to be unfairly biased against my edits in which i simply want to make the basic science of glyphosate clear. I wanted to state that i am not engaged in an "edit war" over this point, but i added this a second time without even noticing that i had changed it previously, and i am writing this comment prophylactically, because i can foresee that Jytdog is going to come around and remove my edit, most likely, and then i will have to find a way to get third-party refereeing about this. Wikipedia is supposed to be the people's domain, providing quality knowledge without special vested interest types of bias as is found in other sources of knowledge like mainstream media. If i cannot edit a scientific article to include a relevant fact, then that openness is a chimera. SageRad (talk) 11:07, 5 May 2015 (UTC)

tagged it for citation needed. please read WP:OR and WP:VERIFYJytdog (talk) 14:17, 5 May 2015 (UTC)

I added a citation to support the statement in response to Jytdog's "citation needed", and Jytdog then removed it, and changed the section's text to omit any reference to the presence of EPSPS within the microbes who inhabit the gut microbiome. SageRad (talk) 14:55, 9 May 2015 (UTC)

see below. Jytdog (talk) 14:58, 9 May 2015 (UTC)

Here is a review-level paper that states:

Animals do not contain the herbicide molecular target site (EPSPS) of glyphosate. Intestinal flora of some animals do contain the EPSPS, but in studies with sheep, glyphosate had no significant effect on rumen fermentation parameters and in sacco degradation of grass hay and corn grain (Huther et al., 2005).

References

SageRad (talk) 09:03, 14 May 2015 (UTC)

new content

about this edit and about the source: Rossi, Maddalena, Alberto Amaretti, and Stefano Raimondi. "Folate production by probiotic bacteria." Nutrients 3.1 (2011): 118-134. and the quote from it: Quote: "all the sequenced lactococci and streptococci, with rare exceptions, possess all the genes for both shikimate pathway and chorismate conversion into pABA". neither Streptococcus nor Lactococcus are gut bacteria. i removed this and replaced the content with the language we developed at the glyphosate article, in this dif. Jytdog (talk) 13:27, 9 May 2015 (UTC)

The article that i cited reported that EPSPS is in probiotic microbes. So if i find another reference that supports the presence of EPSPS in the microbes that are known to be in the gut microbiome, would you support the fact of its presence in animals in that form being in the article? Or do you think it does not belong here, and why? You see, its not true that EPSPS is not found in animals, and the article seems to be currently reporting that in a strange coded workaround language. Just because i have yet to find a source that states this explicitly, it seems odd to report a false fact as truth. It's knowing that gasoline is in cars that are on a ferry, and yet saying "The ferry runs on diesel. There is no tank in the ferry's design plans for gasoline storage." But if i found a source in a secondary review article that said "Gasoline is in cars on the ferry," then you'd let it be reported perhaps? But having the clearly accepted facts that gasoline is in cars, and that cars are on the ferry, is not enough verification? I guess you'd call that synthesis? SageRad (talk) 15:06, 9 May 2015 (UTC)

the article is about EPSPS in bacteria used in probiotics, yes. Not about endogenous microflora. Those are two different things. And yes, you need a source that supports the content. If you continue to edit in ways that violate WP:VERIFY you are going to get blocked; that is WP policy. please do read Wikipedia:Verifiability, not truth -- Jytdog (talk) 15:26, 9 May 2015 (UTC)

I am reading Wikipedia:Verifiability, not truth -- which is an essay, not a guideline. The policy itself is Wikipedia:Verifiability. I'd like to ask a question that may highlight an issue. You have issues with Seneff, for example, as do i. You've made a point to include a special section on Seneff on a page about sources in attempt to disqualify her papers on the topic as a reliable source, right? I don't like her papers and haven't even read more than a few paragraphs of any of them before heading off to more solid research articles. The only reason i might cite her if allowed is to be able to include a relevant fact such as the presence of microbes that contain EPSPS in the human gut microbiome, if i could find no other source to "verify" it, as per rules of verifiability, even though it's well known that microbes in the human gut microbiome do contain EPSPS. But you seem to have defined Seneff preemptively as unreliable. On the other hand, you seem willing to allow statements supported by citation of research reports from the industry and their allies about their own products, when they report the opposite sorts of things, claims to the absolute safety of glyphosate based on research that i know is not comprehensive. Couldn't i also add a section on the page about sources that reflects my concern about the reliability of those sources, and then hold in contention claims made from such sources? Of course verifiability does not guarantee inclusion, I know. But it seems that verifiability simply means that the statement is published by an acceptable source, and academic journal articles are typically considered reliable enough, or quality enough. It's the first gate, and relevance for inclusion is another level of decision-making done by consensus. I think i have all this correct. Please correct me if i am wrong. SageRad (talk) 15:54, 9 May 2015 (UTC)

her papers are not reliable sources. we cannot source WP content to unreliable sources. there is no WP:NODEADLINE here. the gut microbiome is a newish focus of research and there will surely be reliable sources out on this in the near future. there just aren't any now. Jytdog (talk) 15:55, 9 May 2015 (UTC)

also. please discuss content, not contributors, per WP:TPG and WP:NPA. thanks. Jytdog (talk) 15:58, 9 May 2015 (UTC)

and with regard to: "Couldn't i also add a section on the page about sources that reflects my concern about the reliability of those sources, and then hold in contention claims made from such sources?" no, you cannot. WP articles are about their subjects, they are not places for meta-discussions. If there is substantial controversy about research on X that is discussed in reliable sources, there can be a section about that. (There is a section on scientific publishing in Genetically_modified_food_controversies#Scientific_publishing by the way.) That is different than what you are proposing - a section like that would be WP:OR about your concerns. Jytdog (talk) 16:03, 9 May 2015 (UTC)

You said "Her papers are not reliable sources" about Seneff, but my question is, couldn't i claim that a source is too closely allied with the industry on which it reports and is therefore unreliable? That's the heart of my question: if it's good for the goose, is it not good for the gander? Claims of unreliability can go in any direction, can they not? By the way, i think you may have misunderstood my question, as when i said, "Couldn't i also add a section on the page about sources that reflects my concern about the reliability of those sources," i was referring to adding a section where you've written a note about Seneff papers. Where was that, again? Would you refresh my memory, as i saw it in passing but i can't remember what title it was under. SageRad (talk) 16:23, 9 May 2015 (UTC)

this Talk page is for discussing content and sources about this article. is there some specific source or content in this article that you have a question about? Jytdog (talk) 16:30, 9 May 2015 (UTC)

Ok, then, i would like to propose that we state that EPSPS is in many microbes in the human gut microbiome, and use a Seneff paper as a source. Would you be okay with that? If not, why not? I would prefer another paper to Seneff if i can find one that states the obvious, but it seems that people fail to state obvious things that everyone knows in papers because they're obvious. SageRad (talk) 16:39, 9 May 2015 (UTC)

seneff paper is not a reliable source. see here. Jytdog (talk) 16:48, 9 May 2015 (UTC)

Regarding this edit, the paper that i cited also states, "all the sequenced bifidobacteria possess the entire set of the genes for the shikimate pathway and are expected to produce chorismate" and this does include Bifidobacterium adolescentis, who is an inhabitant of a healthy human gut microbiome, and therefore, i think that the source supports the statement that i added to the article. SageRad (talk) 01:52, 11 May 2015 (UTC)

That is WP:SYNTHESIS with respect to tying the quoted statement to the microbiome thing again. Without that issue, we are not in a position to currently be splitting hairs in an encyclopedia about kinds of bacteria having the pathway. We don't have the weight telling us why that's important. Maybe if research related to glyphosate shows something important on the topic, but the scientific community isn't there yet. It doesn't matter if one of us thinks it's important, so until that time, we wait. Kingofaces43 (talk) 02:49, 11 May 2015 (UTC)

I deny that it is synthesis to make sure that statements are accurate. Note that i had a problem with an inaccurate statement that was in the article before, and that's why i made the original change. Your last sentence seems kind of pushy / dictating. I would suggest reading WP:SYNTHNOT to get some perspective on what is considered synthesis and what is not, as well as some tempering about the nature and purpose and use of the guideline. SageRad (talk) 09:03, 11 May 2015 (UTC)

• In fact, i would say that to state it how it originally was, i.e. that EPSP synthase is not in animals [in somatic cells, but this part remained unstated] and therefore that glyphosate does not act on humans, is in *itself* the real act of synthesis that *i* was opposing here. The way it was written originally ipmlied incorrectly that animals do not contain EPSP synthase, and therefore, how silly to think that glyphosate could possibly affect human beings, as they don't contain the EPSP synthase in their organism! But actually, they do, and the very careful sidestepping sort of wording that is in the article *now* is more of a synthesis toward a probably false conclusion, and based on false implications, than what i wanted to change it to. I wanted to leave the field open, with accurate facts in the article, and definitely never advocated for the article to read "It is possible that glyphosate affects humans because it may affect the microbes in the human gut microbiome" -- although this *is* true as best known by science right now, that this dynamic is possible. It's not disproven by any study, and it's seen to be likely by many people. However, this is *not* what i wanted the article to say, clearly. I simply wanted the article not to be implying a verifiably false fact. SageRad (talk) 09:09, 11 May 2015 (UTC)

is the content now acceptable to everybody based on what we can say now, based on currently available reliable sources? Jytdog (talk) 12:49, 11 May 2015 (UTC)

I'm not fully happy with it, but i am accepting it as a compromise. Please take note that i do compromise, Jytdog, on editorial decisions, as long as the factors are fully hashed out and clearly understood and the inherent conflict is made plain, so it's an honest compromise. At least an incorrect statement no longer stands within the article. SageRad (talk) 15:36, 11 May 2015 (UTC)

great. Jytdog (talk) 15:47, 11 May 2015 (UTC)

"Enough of this" ?

User Jytdog reverted my edit here with the reason "enough of this!" I had removed the sentence here because it was not supported by the source. What is wrong with that? Using sources reliably and verifiably is what we're about here. I went to the paper to verify the statement. It does *not* establish that humans and other animals don't have the EPSPS enzyme, and it especially does not make the statement that glyphosate does not inhibit aromatic amino acid production in humans nor does it refer to the human diet supplying those amino acids. If you want to include that, you'll have to support it with a source that does in fact support it. I don't think "enough of this!" is a good reason for a revert. I'm doing my job, reading papers, fact-checking, centering the sourced text on what the paper actually says. The sentence that i removed was WP:SYNTHESIS -- the statement was not made by the paper itself. The statement that i removed was also about human health and therefore ought to be subject to WP:MEDRS. The statement i removed is also not in the natural flow of the logic of the section, and therefore is salient as WP:ADVOCACY, for the only reason it would be there is advocacy for the product glyphosate. How was the revert an acceptable edit, and not disruptive? SageRad (talk) 14:01, 20 August 2015 (UTC)

we worked out the exact issue at the Glyphosate article. Instead of implementing that here, you just deleted it, just like you did at the Glyphosate article originally. If we work something out, we work it out; we don't need to rehash the same issue across the whole encyclopedia. I inserted the language we already to, in this difJytdog (talk) 16:42, 20 August 2015 (UTC)

I think you're conflating things. We never worked out whatever you're supposing we worked out. Please pay attention to the exact language in the diff that i provided. What we worked out at "Glyphosate" is the language that is in there now, which is "EPSPS is produced only by plants and micro-organisms; the gene coding for it is not in the mammalian genome. Gut flora of some animals contain EPSPS." This is far frmo what you reverted back into this article here. SageRad (talk) 17:02, 20 August 2015 (UTC)

Ok, as per what i think you intended, i did use the language that we'd worked out on the glyphosate page. Also re-ordered the text in that section so it flows well. Thanks. SageRad (talk) 18:25, 20 August 2015 (UTC)

Recent edits

Recent edits by Jytdog look good to me so far. I appreciate all the hard work and thoughtfulness. The only thing i'd differ with is that i think the para that begins with "EPSP synthase has been divided into two groups according to glyphosate sensitivity..." would fit better under the section on glyphosate. SageRad (talk) 16:04, 22 August 2015 (UTC)

Reverted one edit, explanation

I did revert an edit by Wuerzele, here, as i think the original sentence was better. I don't see how it was a tautology, but was a simple statement. Gut flora is a defined term that has a good Wikilink. I appreciate all your hard work and edits, and i am certainly open to discussing this further. SageRad (talk) 12:57, 6 October 2015 (UTC)

Reference 8 seems irrelevant to the point.

How come reference [8] (Gut flora of some animals contain EPSPS.[8]), which is supposed to provide evidence for EPSP Synthase being applicable to some Gut Bacteria actually links to a an irrelevant study when there are various other papers supporting strong impact on the GIT microbiota in various species? here are few ones.

• The influence of glyphosate on the microbiota and production of botulinum neurotoxin during ruminal fermentation.
  https://www.ncbi.nlm.nih.gov/pubmed/25407376

• The effect of glyphosate on potential pathogens and beneficial members of poultry microbiota in vitro.
  https://www.ncbi.nlm.nih.gov/pubmed/23224412

• Glyphosate suppresses the antagonistic effect of Enterococcus spp. on Clostridium botulinum.
  https://www.ncbi.nlm.nih.gov/pubmed/23396248

Alain Pannetier (talk) 19:08, 3 October 2017 (UTC)