Talk:Natural product/Archive 2

Archive 1

Archive 2

Archive 3

Archive 4

Opening discussion on future course of article

My history began here when I came to this article in Nov-Dec of last year, where I found an article bearing a "factual accuracy" tag dating to March 2011. Moreover, its concepts were poorly defined, its text content was substantially in either lists or prose lists, and/or it was all but without references to the current preponderance of natural product literature (particularly in chemistry). Its depth was fairly superficial, with emphases on listing natural products (in the context of the class of organisms form which they were isolated, or simply as lists, as in the list of drugs). Traditional medicines was the only subject very developed as prose, and that section was essentially without citations. The historical and contemporary meanings of natural products, their use in Western medicine (e.g., oncology, infectious disease) and natural products chemistry and synthesis were largely absent. Here is the state of article before my initial editing [1].)

I began editing 7 December, beginning with the lede. Before I could complete the addition of citations, a fly-by editor took umbrage with the significant edit (based on my failure to provide an edit summary, which he detected using Huggle). The intent was never to avoid the addition of citations, it was rather to immediately have a reasonable and accurate lede in place, and then to continue developing the long-abandoned article (last substantial edits 8 months prior, no prior editing by editor Boghog identifiable). Here is the version with which the fly-by editor took umbrage, presuming vandalism, which he reverted without discussion; note just the lede and the new cobalamin structure in this version: [2] The reverting editor, I am One of Many, is not a chemist, and has not returned to the article since the fly-by reversion.

In the strident discussion that ensued between the fly-by editor and myself, a third editor, Boghog, a knowledgable organic chemist but one with whom I had an ongoing edit conflict—over what I perceived as a long-standing poor state of the synthetic and overall aspects of the steroid article, especially with regard to lack of referencing—came to the "Natural product" article while I was not editing, and began markedly changing the article. Here were his initial changes (i.e., eliminating my content entirely, returning the article to the poor state it was in before I started): [3].

And here is the final result of his December activities, where he has moved a significant portion of my lede material to a new section on "Impact on chemistry" near the end of the article, and added his own lede, and a new section on "Classes": [4]. At the same time, the the perceived offensive 2011 "factual accuracy" tag was removed, though the bulk of the article (apart from his revised lede and "Classes" section) was largely unchanged.

I think the current lede is in reasonable shape, though it has significantly downplayed chemistry over other meanings and applications of the title term, and removed some subtleties contained in the lede I had created (currently excluding organometallics like cobalamin from mention, omitting the centrality of natural products in the training of chemists and supporting drug discovery, etc.) The more significant issue is elsewhere, see below. Note, first, however, that after working from 8-24 December, and setting in place the defining lede and Class sections, editor Boghog returned to his status prior to December—of doing nothing at this article at all. He has not edited a line in the last 5 months, now going on 6.

I am writing this history into the Talk section, and posting it in the Chemistry project area, because after intending to return to edit at this article, I simply cannot work within the constraints that Boghog has created.

I believe the thrust of the article needs to follow the preponderant understandings of the title term's use in the historic and scientific literature—that while a secondary reference or two can can be found to support a particular obscure perspective, finding such cannot justify giving the obscure perspective equality to or even preeminence over a perspective based on the preponderance of literature opinion.

In particular, two aspects of the article are constraining in ways that prevent my contribution:

• (A) Leading the "Classes" section (in essence, the definition section, the first section to follow the lede), with the following:

"The broadest definition of natural product is anything that is produced by a living organism and this would include organisms themselves.[3][18] Based on this broad definition, natural products include:[3] 1, an entire organism (e.g., plant or animal or a microorganism), 2. part of an organism (e.g., a leaf of a plant or an organ isolated from an animal), 3. an extract from an organism, 4. a pure organic compound isolated from an organism extract A more restrictive definition of a natural product is an "organic compound formed by living systems".[6] These compounds in turn can be divided into the following three classes:[6] Organic substances found in all cells and is [sic.] essential to the survival of those cells and include amino acids, carbohydrates, and nucleic acids . These substances are known as primary metabolites. Polymeric organic materials such as cellulose, lignin, and proteins which form the structure of cells. Unique organic compounds that are found in a limited range of species. These are known as secondary metabolites."

Emphases added. Note that the far-from-common, far-from-preponderant definition of natural products appears first, while the broadly understood, ordinary definition appears fourth in the first set, and that obfuscation returns in the second set, when nucleic acids and proteins are listed before secondary metabolites. This is not a constraining definition to which I can assent, and edit under.

• (B) Also stifling contribution are the large tracts of the "Natural Sources" and "Traditional Medicine" sections—which remain as suspicious as when the 2011 "factual accuracy" tag was placed, for they are substantially without references. These sections are constraining insofar as the last time a major, bold edit was made to this article, it was reverted en masse, and the whole of the text taken over toward the ends described above. However, the only way that these two sections can be moved to first quality content is with aggressive editing, an effort that may in fact have to remove significant chunks of material (e.g., if the structure of the sections cannot be tied to the most reliable sources, and if particular claims cannot otherwise be sourced).

I believe it is prima facie obvious that the current article definitions are not representative of the preponderant thrusts of contemporary and historical natural products research, including that it is a primarily chemical discipline, with its very important contributions to drug discovery (including modern oncology), and its providing the targets that have driven forward the development of nearly all key analytical and synthetic methods being applied in modern chemistry (see my deleted lede, second link above). As well, the importance—societally, historically, intellectually—are simply lost in this current structure and presentation. Where are the Nobels, the tragedies, the intriguing stories like red tide and yew needles? No, for this article to improve, it needs to be opened up.

I look to this community, in Chemistry, to give some attention to the discussion now, so the article is retrieved from a dust-bin its been stuffed into, by virtue of fleeting but ardent attention. Broad opinion and discussion is needed to lead this troubling form of an article forward. Cheers, and looking forward to hearing new perspectives. Le Prof Leprof 7272 (talk) 07:36, 2 June 2014 (UTC)

Discussion on future course of article, 1

Again, focus on the edits, not the editors. In response to issue (A) noted above, what I previously wrote that has been archived equally applies today. Hence I am reproducing it below. Boghog (talk) 08:44, 2 June 2014 (UTC)

Extended content

The spectrum of definitions in the current lead (ranging from anything produced by life to purified secondary metabolites) is not mine, it is the definition used by reliable sources. This article's current description of Gunnar Samuelsson's broad definition is not prooftexting, but rather an accurate summary. If the description were any closer, I would then be accused of close paraphrasing. Within the field of organic/medicinal chemistry, I agree that the definition is usually restricted to mean purified organic substances obtained from natural sources. I have edited the lead to reflect that. Furthermore the predominate definition within these fields is usually restricted to secondary metabolites. It is also clear that natural products can also be prepared by total synthesis as stated in the last paragraph of the current lead. Per WP:UNDUE, each article ... fairly represents all significant viewpoints that have been published by reliable sources, in proportion to the prominence of each viewpoint in the published, reliable sources. In the current lead, there is one sentence that is devoted to the broad definition. The remainder of the lead (paragraphs 2, 3, and 4) are devoted to the narrow definition. Hence each definition in the current lead is proportional to its prominence. What may be debatable is that the article starts out with the broad definition. However I would argue that this is appropriate since it follows a logical progression (from broad to narrow) and also is appropriate for the intended audience (the general public). Boghog (talk) 09:35, 23 December 2013 (UTC) In this edit, I have also explicitly added the "middle of the road" definition used by organic chemists based on language used in a previous version of the manuscript. In summary, there is a spectrum of definitions: anything produced by life – compatible with its use within the field of consumer products primary or secondary metabolites – organic chemistry definition secondary metabolites – medicinal chemistry definition Within the scope of this article, the horse represents natural products while the cart is organic chemistry. The previous version of the lead had definitely put the cart before the horse. Boghog (talk) 13:08, 24 December 2013 (UTC)

The article is about "natural products" but not in the sense that chemists would typically use, at least my colleagues. Wikipedia articles can get jammed into stubborn definitional corners, and maybe we are in that predicament here. One solution is to convert "Natural products chemistry" (currently a redirect to Natural products) into a self-standing article. Within Natural products chemistry, User:Leprof 7272 could focus on a more conventional development of the topic. It is a pity if such a core area (to chemists at least) were poorly represented in Wikipedia. We have on our hands a newish and apparently energetic expert (Leprof 7272), so we should turn him loose and see what happens.--Smokefoot (talk) 16:58, 2 June 2014 (UTC)

No claim was made that Boghog did not adequately paraphrase his sources; rather, the claim is made that the weight of meaning appearing on the title subject as it appears in the vast and vigorous natural products literature is at tremendous odds with the priorities reflected in Boghog's definitions in the Classes section. That is, I specifically deny that his current "Classes" section reflects presentation of ideas "in proportion to the prominence of each viewpoint in the published, reliable sources" as the WP UNDUE policy requires. I state emphatically, that no academic who studies natural products, unless having a commercial interest, describes and publishes on their work as natural products research, if they are reporting about studies of whole organisms, tissues of organisms, whole cells, or even polymeric macromolecules such as proteins and polynucleotides. It is clearly UNDUE, to give these ideas eminence and preeminence (or even anything near equality); at best these deserve closing attention, based on the prominence in usage of distinct other ideas by practicing experts in this area.

Smoke, TY for perspective; note here that per the long, ongoing discussion with PP, the consensus of the larger community seems to be just what I am asking—that the preponderance of meaning in the relevant scientific literatures has to drive the scope, priorities, and preponderance of attention in the article. Boghog's biannual return to defend what have otherwise been dead-end edits do not persuade me, but his green block should be allowed to stand to try to persuade others. I stand by my argument that the definitions he has introduced are clearly not the mainstream, though he has indeed found the rare reference to support his unconventional priority in definition.

Boghog, I ask you, please, do not rush back to make a flurry of edits, and thereby cloud this discussion. I know it is hard for you to help yourself. But please, now, show good faith and respect, and allow this discussion to proceed without large new edits that confuse the ongoing discussion. I call on you publicly, a priori, to show good faith here. Le Prof Leprof 7272 (talk) 18:12, 2 June 2014 (UTC)

Smokefoot made the following constructive suggestion: One solution is to convert "Natural products chemistry" (currently a redirect to Natural products) into a self-standing article. which echoes what I have stated before:

Extended content

Perhaps what is needed is a new article on natural product chemistry (which is currently a redirect to this article). However before creating a new article, I suggest that we develop this one further before splitting out a new article. Boghog (talk) 18:27, 7 December 2013 (UTC) In summary, I think it would be a mistake to restore to the previous version. The present version of the lead is carefully source, balanced, and appropriate. If you still disagree, I think it would be appropriate to create a separate article on natural product chemistry. Boghog (talk) 20:33, 7 December 2013 (UTC) For what it is worth, I have re-added most of LeProf's previous contributions to the lead to a Natural_product#History section where I think it is more appropriately placed. As I have suggested above, this material could eventually be split out into a new natural product chemistry article. Boghog (talk) 22:48, 7 December 2013 (UTC)

Le Prof, what are you waiting for? Boghog (talk) 19:15, 2 June 2014 (UTC)

An end to obfuscation, and to half an argument well heard, the other half passed over. First, no work has proceeded on this article following the December edits you performed and defend, and the attack on restoring any previous edit is a straw man. (No proposal has been made to restore; the question is the thrust/direction of the whole article, which one editor singlehandedly and fleetingly came on board to change.) This eloquent, historical sleight of hand obscures the actual point of the foregoing, which is to move the article in the direction of reflecting the preponderance of sourcing and scholarly information on the subject. This, rather than having it reflect one or a few source handpicked to make the title subject's focus seem less chemical than it clearly is, in the bulk of reliable, non-commercial sources. We are not "thought leaders" here, we are "thought reporters". In this article's current shape, and content of its Class section, we do not accurately reflecting the content of this subject area's thought leaders.

Second, however inviting it may seem, there is no general support at Wikipedia for "my article, your article" thinking (which is what underlies encouraging disagreeing editors to focus on different, closely related articles). Instead, this article needs to come to a consensus of the editing communities with interest; no interested editor should be encouraged to go off and create a separate article, just so their perspective can see light of day. In the same sense, this article needs to not be held hostage to the definitions and structure favored by one. To test whether this is the case, this discussion needs to continue, to see how the Boghog-believes-it-fine vs. article-is-about-"'natural products' but not in the sense that chemists would typically use" (Leprof, Smoke) debate plays out when the larger community has their say. As well, my comments regard the course and content of this article, the capstone article of what may ultimately be a series of articles. I'll not sidestep the issues of this article, even though socially easier to do so, by moving to another not-yet-extant article on the most significant subset of this article's content. In the long term, after this article presents a consensus on the preponderance of verifiable, non-POV, non-commercially driven, and especially scientific content on this title subject—which is, I argue, more than 95% scientific in its reliable sourcing, and of that, similarly, having a large majority in chemistry aspects—I may indeed move on to the more specialized article.

Finally, though some editors seem to take different sides of the same issue in different venues (see Steroids discussion over dexamethasone facts being common knowledge), I strongly agree that this capstone article needs to be a general audience-directed effort. The issue is not a general versus specific debate; it is accurate vs. inaccurate—I will say again—relative to not one or even a few citations, but to the clear preponderance of scholarly information available on the title subject. And the preponderance of scholarly general scientific information does not support the prioritization and therefore bias of the limited authors' work that appears in the Class section. Le Prof Leprof 7272 (talk) 17:50, 3 June 2014 (UTC)

*Adding a gray background (C0C0C0) to highlight comments coming from parties other than Le Prof or Boghog. This needs to be your discussion, natural products community. Le Prof Leprof 7272 (talk) 18:57, 3 June 2014 (UTC)

Mountain, mole hill. Cart, horse. The focus of this article should be on the natural products themselves and not specifically the synthesis of natural products. The synthesis of natural products is an important subject in its own right supported by an extensive literature and therefore deserves its own article. At the same time, this article should retain a synthesis section that start with a {{main}} tag redirecting interested readers to an article that covers the synthesis of natural products in more depth. Neither the parent nor daughter subject is controversial. Hence the proposed natural product chemistry article is a WP:SPINOFF and not a WP:POVFORK. Boghog (talk) 19:38, 3 June 2014 (UTC)

I have no further discussion-cluttering comments/replies. I have challenged your content, and the community has been invited to reply. The question is, how to we shape a watching world's understanding via the question, "What is a natural product?", and whether to inform them of the prevailing view, or to reshape them toward a broader view that is uncharacteristic of the thought leaders in the field. It is not about what you or I think, but about what the thought leaders think, and now, about what the rest of the community thinks about the tack you have taken. Le Prof Leprof 7272 (talk) 20:07, 3 June 2014 (UTC)

"What is a natural product?" – yes, I totally agree that is the key question that should determine the focus of this article. More specifically, the focus should be on where do natural products come from, why they are important, the major classes of natural products, a general description of their structures and properties. How they are made in the laboratory does not define a natural product. Their synthesis (both biosynthetic and laboratory) are important subtopics that should be included but not made the main focus. Boghog (talk) 20:52, 3 June 2014 (UTC)

Unfortunately for your perspective, there is no such thing as the title subject, as it is really used in the literature, without the chemistry you are trying to marginalize—no natural products without the spectroscopy to determine their structures, or the synthetic chemistry to provide substantiation (termed "proof by synthesis", a phrase that I do not support, but nevertheless use, because a preponderance of the thought leaders in the field do so). Please see attached, impartially searched and impartially selected quotes, from [5]. Now, our opinions are abundantly clear. Let's hear from others, shall we? You and I, no comments for a month, or until the discussion dies down? Shall we? Le Prof Leprof 7272 (talk) 22:54, 3 June 2014 (UTC)

Here are the two preeminent hits that appear when searching the latest online version of Encyclopedia Britannica for the phrase "natural product", [6]; please, feel free, all readers, to reproduce this search, and or to review further hits from the search at that web site.

"LEAD COMPOUNDS FROM NATURAL PRODUCTS from the article pharmaceutical industry

Another very important way to find new drugs is to isolate chemicals from natural products. Digitalis, ephedrine, atropine, quinine, colchicine, and cocaine were purified from plants. Thyroid hormone, cortisol, and insulin originally were isolated from animals, whereas penicillin and other antibiotics were derived from microbes. In many cases plant-derived products were used for hundreds or thousands of years by indigenous peoples from around the world prior to their “discovery” by scientists from industrialized countries. In most cases these indigenous peoples learned which plants had medicinal value the same way they learned which plants were safe to eat—trial and error. Ethnopharmacology is a branch of medical science in which the medicinal products used by isolated or primitive people are investigated using modern scientific techniques. In some cases chemicals with desirable pharmacological properties are isolated and eventually become drugs with properties recognizable in the natural product. In other cases chemicals with unique or unusual chemical structures are identified in the natural product. These new chemical structures are then subjected to drug screens to determine if they have potential pharmacological or medicinal value. There are many cases where such chemical structures and their synthetic analogs are developed as drugs with uses unlike those of the natural product. One such compound is the important anticancer drug taxol, which was isolated from the Pacific yew (Taxus brevifolia)." Link: [7]

"ORGANIC CHEMISTRY from the article chemistry

Organic compounds are based on the chemistry of carbon. Carbon is unique in the variety and extent of structures that can result from the three-dimensional connections of its atoms. The process of photosynthesis converts carbon dioxide and water to oxygen and compounds known as carbohydrates. Both cellulose, the substance that gives structural rigidity to plants, and starch, the energy storage product of plants, are polymeric carbohydrates. Simple carbohydrates produced by photosynthesis form the raw material for the myriad organic compounds found in the plant and animal kingdoms. When combined with variable amounts of hydrogen, oxygen, nitrogen, sulfur, phosphorus, and other elements, the structural possibilities of carbon compounds become limitless, and their number far exceeds the total of all nonorganic compounds. A major focus of organic chemistry is the isolation, purification, and structural study of these naturally occurring substances. Many natural products are simple molecules. Examples include formic acid (HCO2H) in ants, ethyl alcohol (C2H5OH) in fermenting fruit, and oxalic acid (C2H2O4) in rhubarb leaves. Other natural products, such as penicillin, vitamin B12, proteins, and nucleic acids, are exceedingly complex. The isolation of pure natural products from their host organism is made difficult by the low concentrations in which they may be present. Once they are isolated in pure form, however, modern instrumental techniques can reveal structural details for amounts weighing as little as one-millionth of a gram. The correlation of the physical and chemical properties of compounds with their structural features is the domain of physical organic chemistry. Once the properties endowed upon a substance by specific structural units termed functional groups are known, it becomes possible to design novel molecules that may exhibit desired properties. The preparation, under controlled laboratory conditions, of specific compounds is known as synthetic chemistry. Some products are easier to synthesize than to collect and purify from their natural sources. Tons of vitamin C, for example, are synthesized annually. Many synthetic substances have novel properties that make them especially useful. Plastics are a prime example, as are many drugs and agricultural chemicals. A continuing challenge for synthetic chemists is the structural complexity of most organic substances. To synthesize a desired substance, the atoms must be pieced together in the correct order and with the proper three-dimensional relationships. Just as a given pile of lumber and bricks can be assembled in many ways to build houses of several different designs, so too can a fixed number of atoms be connected together in various ways to give different molecules. Only one structural arrangement out of the many possibilities will be identical with a naturally occurring molecule. The antibiotic erythromycin, for example, contains 37 carbon, 67 hydrogen, and 13 oxygen atoms, along with one nitrogen atom. Even when joined together in the proper order, these 118 atoms can give rise to 262,144 different structures, only one of which has the characteristics of natural erythromycin. The great abundance of organic compounds, their fundamental role in the chemistry of life, and their structural diversity have made their study especially challenging and exciting. Organic chemistry is the largest area of specialization among the various fields of chemistry." Link: [8]

Le Prof Leprof 7272 (talk) 23:09, 3 June 2014 (UTC)

You and I, no comments for a month, or until the discussion dies down? Shall we? – that was a short month ;-) Boghog (talk) 23:57, 3 June 2014 (UTC)

The EB paragraphs are not an argument, they are data, from a competing high quality encyclopedia, that contains both information supporting my argument (clear movement away from your overly broad) and information requiring me to yield a bit (reference to macromolecules). As a fellow scientist and educator you should wish to see real, relevant data of this sort. Feel free to have the last word. Le Prof Leprof 7272 (talk) 15:32, 4 June 2014 (UTC)

Attention banners

Concerning the current {{expert}} banner with the following explanatory text:

article static and with significant historical deficiencies, constraining definitions and structure, and limited participation of knowledgable or expert editors

• article static – not static, anyone is free to edit it. Recent modifications include these edits
• significant historical deficiencies – matter of opinion. The issue raised in the expert banner apparently is this article doesn't restrict itself to a narrow definition of natural products. However to put the subject of this article in context, it is important to include both broad and narrow definitions.
• constraining definitions and structure – quite to the contrary, limiting the definition of natural products solely to primary and secondary would be constraining. The current broad definition encompasses the more narrow definition and in no way constrains or limits further expansion of this or related articles to cover primary and secondary metabolites in more depth.
• limited participation of knowledgable or expert editors – the same could be said of most articles in Wikipedia. Too many subjects and too few editors.

Concerning the {{unbalanced}} banner – I agree that the synthesis section should be somewhat expanded, but it should not be the main focus of this article. It would be appropriate to create a new article that covers the synthesis of natural products in more depth.

Hence I think both the {{expert}} and {{unbalanced}} banners are inappropriate and should be taken down. Boghog (talk) 07:47, 8 June 2014 (UTC)

Per the foregoing discussion, first, the reason to invite outside opinion is to resolve the dispute that now stagnates the article, that is, the disagreement that exists over the course prescribed for the article by its definitions ("Classes" section). Contrary to your argument, I for one cannot edit boldly in the areas that I wish to, including in the Classes section and the downstream content that they influence, and there is no reason to expect someone else might be allowed to significantly revise your definitions; you have made this "hands off" clear through past responses to bold change. Second, after months of no activity by anyone at this article (excepting me, including you), the fact that you personally come on today and make a few edits—this is what you are referring to with the "these edits" link—this evidence proves precisely nothing about the article being non-static, and everything about your inability to submit to reasonable requests from other editors (in this case, my request that you and I not edit the article while we wait for this discussion to proceed). These are the only things in your statement worth responding to; the rest of what you bullet are the crux of the disagreement, and the focus of the foregoing proposal-cum-argument (and so are senseless to cover again). Again, please stop editing this article; please change nothing (tags or anything) until there is a discussion to resolve my claims. Le Prof Leprof 7272 (talk) 02:50, 9 June 2014 (UTC)

Your overly long talk page posts are driving away the very editors that you are try to attract. The one editor, Smokefoot, who has responded made a suggestion that I support. It has been a week since your request for comment has been made and no additional editors have responded. You have written above or until the discussion dies down. I think we have now reached that point. Hence your request to wait additional time before editing is not reasonable. It is also not a reasonable to insist that the definition of natural products be narrowed to only include primary and secondary metabolites. I repeat, the current broad definition of natural products encompasses the more narrow definition and in no way constrains or limits further expansion of this or related articles to cover the synthesis of natural products in more depth. What is the problem? Boghog (talk) 05:33, 9 June 2014 (UTC)

Your interpretation of Smokefoot's response was self-serving, ignoring the obvious, for a point that allows you to leave this article unchanged. And you have argued clearly, and forcefully at Steroid, A week is nothing at Wikipedia. You have not done anything here in months; beginning to work further now is a further statement that you do not care to have an honest settlement of the issue by the community, but rather wish to muddy matters. Leave off. Let the community have a chance to respond. Please. And your continuing harassment regarding length of postings ignores months of work at steroids, and many other places, where, absent an argumentative editor who insults and selectively WP: bashes, the entries remain rather short. Cheers, and have a good rest of week. My request for an abeyance here stands. Le Prof Leprof 7272 (talk) 04:11, 11 June 2014 (UTC)

Quite to the contrary, ignoring Smokefoot's suggestion is self-serving. Furthermore, how do the definitions in current Natural_product#Classes section prevent you from expanding Natural_product#Synthesis? Boghog (talk) 19:23, 11 June 2014 (UTC)

Not replying to any further Talk here, until the community can have a say. Cheers. Le Prof Leprof 7272 (talk) 08:49, 12 June 2014 (UTC)

@Leprof 7272:: The community is unlikely to respond if you are unresponsive to simple questions such as the one I asked above and the one Doc James asks below. I repeat, how do the definitions in current Natural_product#Classes section prevent you from expanding Natural_product#Synthesis? Please answer the question. Boghog (talk) 20:27, 13 June 2014 (UTC)

Discussion on future course of article, 2

Natural products community, feel free and add comments here. Le Prof Leprof 7272 (talk) 15:39, 4 June 2014 (UTC)

A couple of comments

1. There was way too many tags. I removed a bunch.
2. To which viewpoint is this article unbalanced and which are missing? What high quality secondary source are you proposing to use to support the missing viewpoint? Doc James (talk · contribs · email) (if I write on your page reply on mine) 09:43, 12 June 2014 (UTC)

I am writing, @Doc James, so that it does not appear that your two questions went unanswered, and so the gist of our conversation about this article and your involvement also appears here. Other readers, the questions were already answered above, here in Talk, and received further direct response at Doc's talk page. This can serve as a guide to the questions and answers; in the following, I will abbreviate "natural product" as "NP".

I have long regarded this Administrator with esteem, and and have posted at times to his talk page to solicit involvement in medical and pharmcologic discussions. In this case, the timing of his appearance here seemed odd (as an Admin, entering into this discussion), so I reviewed Talk pages. There, it became clear that this Admin has a close working relationship with the editor that is the other party in the NP content dispute, Boghog (17 Talk entries between them, from Jan. to May 2014, search "Doc" e.g., here [9] and here [10]).

After learning of this, I asked him to revert his removal of the lead "Expert needed tag", and to recuse himself from further involvement here. In response, he accused me of being unwilling to answer his questions, the two above, and a further, which was, "substantiat[e] why you added the tags in question", of which the "Expert needed" and "unbalanced viewpoint" tags were the one remaining under discussion. (Though he also removed citation tags from sections clearly bereft or weakly supported, I did not ask for reversion of these edits.) I responded to each of these requests, and I will summarize this responses here.

Substantiation of the Expert needed tag. Responded thus:

the substantiation regarding the single tag in question (the one you were asked to revert), is contained in [A] the content of the Expert request tag, saying that the "article [is] static and with significant historical deficiencies, [with] constraining definitions and structure, and [with] limited participation of knowledgable or expert editors", [B] in the Section at NP Talk entitled "Opening discussion on future course of article" which explains and defends the identified issues, here [11], and [C] in a pointed rebuttal to Boghog's counterclaims to the tag's points (static, historical deficiencies, constraining definitions, limited participation), here, in the paragraph beginning "Per the foregoing discussion" at [12].

This quoted answer can be found in its context, in the last paragraph here, [13].

Answer, in which viewpoints article is unbalanced. Responded thus: First, I called attention to Talk already in place here above, containing substantial explanation of the issues (see point [B] just given, immediately above). This content was available to him, and is readily available to the reader here, see bright green highlighted text with nested quote, in Talk above.

Second, though I asked that we discuss content matters only after his COI question was answered, I nevertheless provided him with:

• (1) list of the sections of the article, indicating that in addition to the problematic sections presented above, there were at least two major areas where whole sections were absent, leading to bias (e.g., traditional medicine had a section, but no prose section discussing use of NPs and NP-derived drugs in evidence-based medicine). In addition, I provided
• (2) a list of all natural products journals from the American Society of Pharmacognosy, which makes the clear point that the emphasis of contemporary, non-commercial, and non-fringe natural products research is on small molecule agents isolated from natural sources (<95% content, from a quick survey). (Had he reviewed Talk, above, he would have also see this point made by the content appearing from Encyclopedia Britannica, see large block quotes above.) Then, I provided
• (3) a literature analysis of about 3500 citations at Pubmed, which indicated that none of them reflected the prioritization displayed in the current, opening "Classes" definitions section of the article. (A liberal upper limit of < 2% of the articles present organisms, organs, tissues, polypeptides or polynucleotides, cellulose, or lignans as natural products; >98% refer to small molecules, and to chemistry, including substantial on synthesis and bioassay of synthetic products).

Doc disparaged the journal representation because I arrived at them via Google, and argued that the presence of primary source in the Pubmed search analysis invalidated the approach, instead suggesting that I needed to provide to him a secondary source for each area that I believed was unbalanced. I declined to submit to this, on principle, but did offer the following:

the answer to your questions is nested in the foregoing analysis and other data I have gathered. (It should be clear, if near 100% of available primary literature focuses on natural products as small molecules isolated from natural sources, and studied using the tools and practices of chemistry and pharmacology, the secondary literature, which is derived therefrom, follows suit.) I am using the clear statistics of the matter, because they make the prima facie case plainly, and give anyone unbiased in perspective somewhere to have a quick look (having part of the work done for them).

Here is the section continuing the analysis and discussion, [14].

Answer as to what high quality secondary source was proposed to support missing viewpoint. Responded thus: As already noted, I declined, with this Admin, to enter into a detailed review of secondary literature for each of the problem areas (as being impractical with respect to time, because it was focusing on minutiae rather than the pressing problem setting a course for the article, etc.), and because the COI matter had still been avoided in his answers. I did however respond further, in this way:

It should be absolutely clear that I am strongly committed to sound, secondary sourcing (see my User page, review my articles and edits, or just return in the article's Edit history, to see what the tags you removed were about). It should also be clear here that the matters at hand are not about one citation, but about tens of reviews and book chapters needed to address the many issues of the article, which appear above in the links I gave you (which you have in fact had access to, and certainly should have consulted before you began to edit anew at this article). There is not one issue; there is not one book chapter. You are arguing your premise reductio ad absurdum.

To this I would only add the following brief entry regarding my devotion to secondary sources in scientific editing:

• first, I had joined an argument at his Talk page, supporting him in demanding secondary sourcing, see [15]
• second, I regularly coach beginners in the same, and am affirmed for it, see [16] and [17] (the thanks and barnstar in response to the secondary sourcing guidance of the first); more available like this, on request; then
• third, for the articles I am working on, see [18] ("Structural: Cleaved…" subection only, vis-a-vis referencing), and [19] (note no refs. in lede, because all material mirrored and ref'd in main body), and for an article in process (6 of 13 secondary, remaining primaries take from secondaries, and no bare URLs, etc., [20].
• fourth and finally, for a long history of citation review work, much invited by others, see [21] and [22] (citation analysis at request of another editor, followed by 30 day wait since not my area of expertise, then by posting of tags), and [23] and [24], etc. ) (critiques of articles at request of editors/colleagues, resulting in tags, including for reliance on primary sources).

Bottom line on this matter, there is no real issue between Doc and I, vis-a-vis commitment to secondary sourcing. This all will work itself out, once the overarching issues of the article are settled.

Finally, I have to note again in closing, that I have stated/asked…

For sake of appearance, if not substance, I assert that [Doc James], you are not the Adminstrator to adjudicate this [NP content matter], and ask (i) you provide the reversion [of the Expert needed tag] I request, and (ii) recuse yourself from further participation, per [25], except as participating as a future committed editor of this article, in a discussion overseen by a separate Admin who has not a prior strong relationship with one or other of the editors [in the conflict]. Please. You have a position of authority and confidence. I respect you, and that office.

In re: the referenced WP:INVOLVED in the WP:ADMIN that is linked: Please, note that I find very distasteful the idea of using WP's as clubs. In every case, there are two sides, and generally more than one WP that applies. I'd rather, generally, rely on shared values and common sense. And common sense, as much as the WP's, suggest (for instance) that a judge should recuse themselves in presiding over actions involving friends, family, etc. The aim is to avoid not only actual corrupt practice, but also any appearance of mixed motivation in adjudicating matters… is it not?

So, I again point to these two requests, (i) and (ii) immediately above, and as I did yesterday, ask Doc to respond clearly and directly to them. And as I have asked before, if he wishes to make a clear statement regarding arrival at the article at this time, and relationship with Boghog, I would be welcome that as well. But the point is not a mea culpa; rather, it is unbiased, COI-free fair actions and decisions on the part of this Admin. Cheers. I await a response and decision, here. Le Prof Leprof 7272 (talk) 04:48, 14 June 2014 (UTC)

I am unclear if there is a response to my questions in there. I am wanting a two sentence reply. Doc James (talk · contribs · email) (if I write on your page reply on mine) 00:44, 17 June 2014 (UTC)

Discussion on future course of article, 3

Natural products community, feel free and add comments here. Le Prof Leprof 7272 (talk) 15:39, 4 June 2014 (UTC)

@Leprof 7272:

Be concise and keep discussions focused.
— WP:EXHAUST

Doc James asked a simple, straightforward question that deserves a simple, straightforward response. Boghog (talk) 06:59, 14 June 2014 (UTC)

Per prior statement made to Boghog, here and at his Talk, the purpose of opening communication is to resolve a long-standing difference in the courses he and I see for the Natural Products article. As such, unless in the context of unbiased community, I will not reply to his statements, apart from again presenting this prepared statement. If someone other that this editor has asked a question, it either has been, or will be answered promptly. "...Friede auf Erden den Menschen guten Willens." Le Prof Leprof 7272 (talk) 07:27, 14 June 2014 (UTC)

@Leprof 7272: The above conflict of interest charges are absurd. Doc James and I have collaborated from time to time on improving articles within the scope of WP:MED and WP:PHARMA projects (e.g., substituting {{cite doi}} templates and populating {{infobox drug}} templates with data). Both of these activities were carried out with the consensus of the wider Wiki project communities (see this and this discussion). Please limit the discussion on this talk page to improving the natural products article. Also please keep your posts concise. If they are not concise, no one will read them. Boghog (talk) 07:40, 15 June 2014 (UTC)

Per prior statement made to Boghog, here and at his Talk, the purpose of opening communication is to resolve a long-standing difference in the courses he and I see for the Natural Products article. As such, unless in the context of unbiased community, I will not reply to his statements, apart from again presenting this prepared statement. If someone other that this editor has asked a question, it either has been, or will be answered promptly. "...Friede auf Erden den Menschen guten Willens." Le Prof Leprof 7272 (talk) 08:47, 15 June 2014 (UTC)

@Leprof 7272: Of the two other editors that have responded, you have ignored the suggestion of the first and inappropriately questioned the motives of the second. And you still have not have supplied an answer to the question I have asked above. This is not a court of law. If you have a disagreement with an another editor, you have an obligation discuss it on the article's talk page. Boghog (talk) 10:20, 15 June 2014 (UTC)

Per prior statement made to Boghog, here and at his Talk, the purpose of opening communication is to resolve a long-standing difference in the courses he and I see for the Natural Products article. As such, unless in the context of unbiased community, I will not reply to his statements, apart from again presenting this prepared statement. If someone other that this editor has asked a question, it either has been, or will be answered promptly. "...Friede auf Erden den Menschen guten Willens." Le Prof Leprof 7272 (talk) 08:47, 15 June 2014 (UTC)

@Leprof 7272:

The prime values of the talk page are communication, courtesy and consideration.
— Wikipedia:Talk page guidelines

Boghog (talk) 05:21, 16 June 2014 (UTC)

Discussion on future course of article, 4a

Natural products community, feel free and add comments here. Le Prof Leprof 7272 (talk) 15:39, 4 June 2014 (UTC)

In separate places, @User:Jmh649, has asked/stated the following:

I have edited more than 10,000 of Wikipedia health related articles. I have interacted with most of those who edit in this topic area and get on with most of them most of the time relatively well. I was not invited by Boghog to comment or become involved in any way. I had one simple question: what text do you want to add with what reference to improve the situation / article in question. This question needs a 2 sentence answer " I want to add X using Y". It never was and I remain confused thus went off to work on other stuff. Doc James (talk · contribs · email) (if I write on your page reply on mine) 23:02, 16 June 2014 (UTC)

and

I am unclear if there is a response to my questions in there. I am wanting a two sentence reply. Doc James (talk · contribs · email) (if I write on your page reply on mine) 00:44, 17 June 2014 (UTC)

and

This behavior is in my opinion unacceptable. [26], [27], [28] [Note, Leprof 7272: replying repeatedly to another user with a prewritten statement.] Neither is your overly long "non response" to a very simple question [29]. You need to keep your responses much shorter and assume good faith of others. To clarify I will not take admin action against you but if this continues further input from admins may be needed. Best Doc James (talk · contribs · email) (if I write on your page reply on mine) 00:46, 17 June 2014 (UTC)

Answer:

• (1) Please note that the context for the folowing discussion is a Wikiproject Chemistry and Wikiproject Alternative Medicine article. This speaks to both the issue of the unbalancedness of the article (absence of medical vs. alt. medical participation, absence of major chemistry content areas), and to which expert tag was placed (Chemistry), and why (because it is the obvious, and vis-a-vis the literature, the foremost relevant category).

• (2) I apologize, @Doc James (talk · contribs · email) (if I write on your page reply on mine), in part, for suggesting that you came here in response to another editor's invitation, the editor with whom I have the content conflict here, Boghog. As an emergency physician without history at this or related articles and 17 interactions with Boghog between Jan and May, and with you arriving to perform an edit that Boghog had asked of me that I declined (Chem expert tag deletion), it was a reasonable for me to ask whether he had then asked this or any participation of you instead. Your declining to diffuse the matter by answering the question of being invited, when it was first (and second, etc.) asked, contributed to the matter not coming to a brief and amicable close (as one might have expected based on your clearly greater level of experience here). Still, I respect your pharmacol and medical editing, and now that you have answered the question, and state no invite, direct or indirect from Boghog, I accept your word, and apologize for my part in the length and intensity of questioning that followed.

• (3) To be clear, here, at my talk, and at your talk, you have not asked "one simple question", you have asked several different ones, in different places at different times, and I have given you answers each time. I will not, as I did above, repeat earlier answers, because I will be accused of giving overly long answers. Your answers were already given, in summary, again, here, [30]; read down, and skipping the parts about the COI matter that we have laid to rest.

As for the problem, that I do not provide answers your way, and in particular, your demand that my answers be nearly shorter than the markup language required for your signature to appear — this will not happen, because: (1) The matter does not regard adding a proposed sentence and a proposed citation, it is rather to address a broad complex matter of the direction of the article as a whole, with larger subject matter-expert issues to be resolved, and (2) there is no policy that says any one editor can can frame the course of the debate by insisting on progress through the issues in their own way, or with two sentence answers.

• (4) I have been relating to you here as a fellow editor, a non-specialist entering into a thorny subject matter content issue with two experts that are specialists. I do so, despite knowledge that you are an Adminsitrator, because others who have reviewed the NP talk page counsel that, with your entry and removal of tags (editorial work) you have assumed a role you have every right to, alongside all of us here, the role of any WP editor. Their further counsel is that it is acceptable for you have one, or the other, role at an article, but not both. Entering it as an editor, the playing field is level; we are both in the same role, and should display mutual patience, forbearance, AGF, and respect. If you have inclination to switch gears, as you suggest in your closing sentence above, wishing to oversee this process as an Adminstrator: then again, I have to ask, based on your prior significant relationship with one of the parties in conflict, that you recuse yourself, and you let any higher level activity ("blocking, page protection, setting edit restrictions, imposing sanctions, etc.") proceed by third parties, so it may be unbiased.

• (5) Finally, I am also counseled that, given the long history of mutual poor treatment, each at the hands of the other, my using a cordial pre-written statement in response to the goadings of another editor is a perfectly acceptable response.

That is all from me on this. If after reading the long answers I provided, you have followup questions, please feel free to ask them, and I will respond. But I will not again speak to the same questions, or the accusation that I have not answered something, where I have repeatedly provided links and content to do just that. Please, again, read here, ([31]). Cheers. Le Prof Leprof 7272 (talk) 05:14, 17 June 2014 (UTC)

You mean this was your answer "As already noted, I declined, with this Admin, to enter into a detailed review of secondary literature"

By the way I have never stated that I was becoming involved with this article as an admin. A diff of mine that you interpreted to mean this would be helpful to maybe clarify things. Thus the comments made about COI did not really need a reply. Doc James (talk · contribs · email) (if I write on your page reply on mine) 05:29, 17 June 2014 (UTC)

No, I did not highlight or emphasize that quote. I provided this link, [32], twice above. You apparently have not read it, and until you do, carefully and completely, you will not understand, you will not be able to speak to any of this fellow editor and subject matter expert's concerns, and so I can have nothing further to reply to you. I am still AGF, but the more you refuse to engage my concerns and answers, detailed though they are (as they might be if I were in one of your medical articles), the more it looks like you enter into the article with bias.

Vis-a-vis editor or admin roles, no "diff" is needed. I am referring to your implied threats, above: "This behavior is... unacceptable. Neither is... You need to... To clarify I will not take admin action against you but if this continues further input from admins may be needed." In these statements you are not relating like an editor, and even if an editor were to say such things, it looms large from you because of the added control you can exert over others as an Admin. Again, I am waiting for you to read my answers, AT THE LINK, and to reply to them. Le Prof Leprof 7272 (talk) 05:54, 17 June 2014 (UTC)

Per "I am waiting for you to read my answers, AT THE LINK, and to reply to them". I have read what you have written and am unsure what you are getting at.

It appears that you feel because I have edited with Boghog I should not edit this article. This is not how Wikipedia works and no I will not recuse myself.

Second that because I am not an expert in the chemistry of "natural products" I should not edit this article. Also not how Wikipedia works. Doc James (talk · contribs · email) (if I write on your page reply on mine) 06:15, 17 June 2014 (UTC)

I also read the post at the link provided and the entry of Doc James as an admin was initiated by Le Prof 7272. I'm sorry to come at this from an accusatory bend and I'm not looking to get into conflict. I have noted Le Prof 7272 being overly concerned with who people are and not as concerend with what they are adding to the article. To this end I also see others defending themselves rather than direct conversation to the article (admittedly difficult to do from one side). Can we please drop any and all reference to editors and start talking about edits? Padillah (talk) 14:31, 17 June 2014 (UTC)

Sorry, the "who" matter is settled, as far as I am concerned, with the apology above. No more to say on that. Otherwise, I perceive either a lack of commitment to deal with the issues laid out, clearly and repeatedly above, or a lack of expertise on the title subject. I will answer specific questions about the content issues I have raised, but will not be led away from the points already made. If I am unclear on something that I have said, ask a specific question about it. (I will not restate them yet again.) The conclusions that should be drawn are obvious to experts other than the one who wrote the original material, e.g., another chemistry editor, responding to the same opening material said:

The article is about "natural products" but not in the sense that chemists would typically use, at least my colleagues. Wikipedia articles can get jammed into stubborn definitional corners, and maybe we are in that predicament here. One solution is to convert "Natural products chemistry" (currently a redirect to Natural products) into a self-standing article. Within Natural products chemistry, User:Leprof 7272 could focus on a more conventional development of the topic. It is a pity if such a core area (to chemists at least) were poorly represented in Wikipedia. We have on our hands a newish and apparently energetic expert (Leprof 7272), so we should turn him loose and see what happens.--Smokefoot (talk) 16:58, 2 June 2014 (UTC)

[see this entry above, and my response to it]. One expert, @User:Boghog, continues to defend content he placed that is unrepresentative of the title article sources. That is the issue. See here [33] and here [34], and find me one source where a whole organism or a plant leaf (an organ of an organism) is the preponderant subject in a secondary source on natural products. Not that someone mentions it, as a sidebar, but that it is a preeminent definition, covering the whole of the content of the source, such that it should be given first prominence among the definitions at the Wikipedia article. Passing points are not to be given undue prominence; stray sources are not to be added to proof text an idea that an editor prefers. We are to reflect the clear preponderance of opinion—including definitions and classes—from valid scientific sources. That is not being done in the article. If you are experts, speak to this point. If you are not, put back in the "Expert needed" tag, and/or invite experts to enter the debate. Enough on all the stray matters. Points are long and well-enough made. One person with understanding has spoken to the issues. Others are invited to as well. Le Prof Leprof 7272 (talk) 23:27, 17 June 2014 (UTC)

@Leprof 7272: The subject matter of this article is broader than chemistry. Hence it is appropriate to include both broad and narrow definitions of natural products both in the lead and in the classes section. Furthermore the broad definition is supported reliable sources. Finally you still have not explained how the current Natural_product#Classes section prevents you from expanding the Natural_product#Synthesis section.

We are to reflect the clear preponderance of opinion—including definitions and classes—from valid scientific sources. That is not being done in the article. – False. The article does contain the more narrow definitions that are used within organic and medicinal chemistry. Boghog (talk) 05:41, 18 June 2014 (UTC)

I do not need to answer the "You have still not explained…" because you have no authority to assign which sections another editor can and cannot edit. It is the direction of the whole article, as defined by the Classes section, the lede, and the overarching structure of the article, that is in question. I stand by the fact that the order and content of the Classes section is clearly unrepresentative both of the citations appearing throughout, and of the broader total array of all reliable secondary sources available on the title subject. Please, there is nothing new in your arguments; lets just agree to disagree, and leave it to other experts to decide this. Le Prof Leprof 7272 (talk) 05:52, 18 June 2014 (UTC)

:@Boghog: I think you hit on the main point of contention. I know Leprof has a hard time restating his point but I think his contention is that this article should not be broader than chemistry. How or why did the subject get defined as "broader than chemistry"? Can you provide a source that mentions "Natural Products" as being broader than "chemical substances derived from natural sources"? [User:Padillah]

Here is a source (reference #4 in the current article) that contains a range of definitions from broad to narrow:

Samuelson G (1999). Drugs of Natural Origin: A Textbook of Pharmacognosy. Taylor & Francis Ltd,. ISBN 9789186274818.{{cite book}}: CS1 maint: extra punctuation (link)

Products of natural origins can be called “natural products”. Natural products include:

1. an entire organism (e.g., plant or animal or a microorganism)
2. part of an organism (leaf or isolated animal organ)
3. an extract of an organism
4. a pure compound

An entire organism is comprised of chemicals, but life is greater than the sum of its parts. If one accepts this broad definition, I think it fair to say that the scope of natural products is wider than chemistry, it also incorporates biology.

Also relevant is reference #6 Natural products are represented by a wide array of consumer goods that continue to grow in popularity each year. These products include natural and organic foods, dietary supplements, pet foods, health and beauty products, "green" cleaning supplies and more. Generally, natural products are considered those formulated without artificial ingredients and that are minimally processed.

The bottom line is that natural products have different definitions in different fields. Which of these definitions is correct? I would argue all of them. Boghog (talk) 20:20, 18 June 2014 (UTC)

@Leprof 7272: I understand that, to you, it may seem like we are asking you to repeat yourself, but we are not. Sometimes a restatement hits on a phrase or is presented in a way that "clicks" with the other party and simplifies the communication. Or, it may simply be looked at as "we didn't understand the text you put up before can you rephrase it in hopes of breaking through this miasma". Padillah (talk) 19:25, 18 June 2014 (UTC)

@Padillah (and @User:Jmh649 and @Smokefoot), I do not deny that there should be acknowledgment of broader use of the NP term. Boghog's argument is again selective in presentation, and straw man in argument. I defy him to support that "his [Le Prof's] contention is that this article should not be broader than chemistry". In fact, I say, it should be broader than chemistry: in a sentence that Boghog deleted (see this Talk, Archive 1), I said "Natural products play essential or important roles in their organisms of origin, for instance as biosynthetic intermediates and cofactors, agents of coloration and fragrance, and internal and external chemical signals (i.e., semiochemicals)." To this I would add all biological categories that are contained repeatedly, such as to establish preponderance of scientific opinion: we should say further on chemical ecology, natural harvesting or cultivation of medicinal organisms, aspects of the biotechnology of production of natural products, etc. No, as a pharm scientist, I am a foremost fan of good bioscience description. (My latest argument at a chemistry drug article was to give biologists as well as a synthetic chemist credit for drug's discovery.) What I do resist is misrepresentation of marginal definitions and fringe/commercial definitions, see below. So, one last time: we agree that "the scope of natural products is wider than chemistry, it also incorporates biology"; this is a straw man issue, pure and simple, and to continue saying this will (certainly at this stage) be to attempt to misrepresent me and sidetrack the discussion.

Regarding the specific issue, the content of the Classes section: Yes, there will always be a small minority of scientific writers that do not hold close to the mark contained in the hundreds of natural products secondary sources.

• One group will do so out of ignorance: they will use the word natural as an adjective, and the word product as a generic noun, and afix the two together as "natural product", in a general way to mean any product that is produced by nature. A stone outcropping is rightly described as a "natural product", in this way. This term will appear so, occasionally, in the literature, and so in this sense, a leaf, or a bacterium can indeed be considered natural products.

However, its use in this way ignores (hence its description as ignorant) the fact that the two words appearing together have—post 1913 Websters, certainly—taken on a new meaning, independent of the two terms, a meaning that is decidedly a reference to small molecules and about chemistry. Please look again at this, and do further searching yourself, [35]. There is no question here; see also the Smokefoot quote above.

Now, when a person writes "reformation in England" or "reformation England", using the first noun adjectivally, they are within their rights to use it, as a writer, to mean reforms of the England's National Health Service under Prime Minister Blair, or the reforms in managing English football, or any other general application. This does not mean that an encyclopedia should ignore the vast preponderance of scholarly and historical uses of the term, to mean something very specific, and other. (An expert in chemistry would not need the reformation England example, but I am trying hard to make the case absolutely plain, even to those not involved in natural products work.)

• The second group that misuses the term does not do so out of ignorance; rather, they are very well informed—but are commercial. With their information they seek to broaden the use of the term for their own gain. The definitions of the term arise because the group of individuals marketing products want anything they market to be able to bear the imprimatur of "natural product". Again, see here [36], and click on the first hit, and skim the images. There are two connotations for the term, competing. One is the small molecule definition, preponderant, and the second has to do with labeling from manufacturers in the "natural products" industry. This is also not an encyclopedic use of the term, and a reason that definitions that include leaves and whole organisms, etc., should not be given first priority (as they are now).

Now, otherwise, Boghog states his case well, and provides his two central citations. The two citations he picks do indeed support his wider view, and the priorities contained in the current Classes section. (No one has argued that he is not technically faithful to the specific text bits in the sources he chooses.)

• About one of the two source, Samuelson, two rebuttal points:

• first, that while it is a reputable source, its definition is in the minority, rather than majority, both in its listing whole organisms and parts of organisms (e.g., leaves), but also in the priority it gives these minority cases — relatively speaking, how many of these examples are in the last link I gave, and if so, from what type of source? In the vast majority of NP citations, these two entries do not appear at all, see earlier Pubmed analysis. This is proof texting an editor's idea (finding the one or few source that prioritize/present things the way you prefer), and not accurately representing the way most experts present the idea.
• Second, and more critically (regarding Boghog's choice and prioritization): Please, actually check his reference, [37] (Table of Contents tab), or click Edit of this Talk section to see the following collapsed list in easily read form. Bottom line, the vast, vast, vast proportion, of even this, the best source he can muster, talks not about organisms and leaves; rather, essentially the whole of the book is about small molecules (skim the ToC). His excerpting this definition does accurately reflect the page of its source, but, in his presentation, he clearly sidesteps the clear thrust of the rest of the book. This, in my view, misses the forest for a tree. So, while it's true that this one source indeed says what Boghog has placed in the Classes section, the WP reader does not have the rest of the book in hand for context. The book proceeds to talk not about whole organisms and leaves as NP's, but nearly exclusively about small molecules, the last of Boghog's listed class entries on both lists. We as editors reading the reference know that the mention of organisms and leaves is a passing mention, perhaps for reasons of academic thoroughness. It is our obligation to accurately reflect the real content thrust of Samuelson, and not over represent something he presents on essentially a very few pages (at most) of a 776 page book (!). No, the book is about small molecules, and their sources, biosynthesis, isolation, structural characterization, testing, human preparation, and human biomedical uses (especially). It needs to be accurately represented as being so.

Extended content

1'Introduction Definitions The history of natural products in medicine Natural products as modern drugs Production of drugs based on natural products The role of natural products in drug discovery Plants used in traditional medicine Ethnopharmacology Natural products from marine organisms Combinatorial biosynthesis Screening of randomly chosen organisms Chemoinformatics and phylogenetics Systems biology Application of the systemic biology approach to the study of naturl products used in medicine Pharmacognosy as a research subject Further reading Plant derived Crude drugs and Herbal Remedies Nomenclature Production of crude drugs from medicinal plants Cultivation of medicinal plants Propagation of plants Plant breeding Collecting and harvesting medicinal plants Preservation of plant material Storage of crude drugs Quality control of crude drugs Sterilization of crude drugs Preparations of crude drugs Grinding of crude drugs Herbal “Teas” Extracts Herbal remedies Definitions and trade regulations Side effects Interactions Information sources Isolation of pure compounds from extracts of crude drugs and other organisms Isolation of compounds with known properties Bioassay-guided isolation Industrial high-throughput screening of extracts Further reading Biotechnological Drug Production Production of Antibiotics The growth curve of microorganisms Energy metabolism and production of metabolites in microorganisms Technical aspects on the producton of antibiotics Plant tissue and cell culture (Plant Biotechnology) Callus cultures Suspension cultures Organ cultures and regeneration of plants Environmental factors of importance for plant tissue and cell culture Tissue and cell culture in plant breeding Industrial production of natural products by plant tissue and cell cultures Future prospects for plant biotechnology in the production of drugs Further reading Formation of Pharmacologically Active Compounds in Plants – Biosynthesis Photosynthesis Light reactions and dark reactions Dark reactions Photorespiration C3 Plants CAM and C4 plants Biosynthetic pathways Glycolysis and the citric acid cycle Investigation of biosynthetic pathways Transporters of secondary metabolites Classification of natural products Further reading Carbohydrates Monosaccharides Disaccharides Polysaccharides Gums and mucilages Reduction products of carbohydrates: sugar alcohols 5 Natural products related to carbohydrates Glycosides Aminoglycoside antibiotics Acarbose Ethyl alcohol, C2H5OH Further reading Natural Products Derived Biosynthetically from Shikimic Acid Shikimic acid Localization of the shikimic acid pathway The enzymes of the shikimic acid pathway Biosynthesis of shikimic acid Gallic acid and tannins The aromatic amino acids phenylalanine, tyrosine and tryptophan Biosynthesis of tyrosine and phenylalanine Biosynthesis of tryptophan Phenylpropanes Typical phenylpropanes Adaptogens Coumarins and furanocoumarins Substances formed from phenylpropanes by shortening of the side-chain Further reading Natural Products Derived Biosynthetically from Acetate The acylpolymalonate pathway Fatty acids Saturated fatty acids Unsaturated fatty acids Other derivatives of fatty acids Fats and waxes Fats Waxes Phospholipids Eicasonoids Prostaglandins Thromboxanes Leukotrienes Lipstatin Polyketides Polyketides derived from acetate or propionate Macrolides Erythromycins Avermectins Spiramycins Polyene macrolide antibiotics Epothilones Griseofulvin Aflatoxins Mevastatin and lovastatin Leptospermone and Nitisinone Mupirocin Tetracyclines Anthracyclines Enediynes Anthraquinones Polyketides of mixed biogenetic origin Flavonoids Kava pyrones Flavonolignans Mycophenolic acid The ansamycin group of antibiotics Rapamycin Tacrolimus (FK-506) Rotenoids Khellin Sodium cromoglycate Further reading The isopentenyl diphosphate pathway Isoprenoids Mevalonic acid and isopentenyl diphosphate The non-mevalonate pathway for the biosynthesis of isoprenoids Monoterpenes Biosynthesis of monoterpenes Hydrocarbons Alcohols Aldehydes Ketones Phenols Iridoids and secoiridoids Other oxidized monoterpenes Sesquiterpenes Biosynthesis of sesquiterpenes Diterpenes Biosynthesis of diterpenes Triterpenes and steroids Biosynthesis of triterpenes and steroids Biosynthesis of pentacyclic triterpenes Biosynthesis of tetracyclic triterpenes and steroids 38 Triterpenes Saponins Modified triterpenes Steroidal hormones Cardiac glycosides Glycosides from Digitalis purpurea Glycosides from Digitalis lananta Other cardiac glycosides Vitamin D Tetraterpenes Biosynthesis of tetraterpenes Further reading Amino acids 2-oxoglutaric acid group Pyruvic acid group Oxalacetic acid group Serine group Histidine Aromatic amino acids Essential amino acids Toxic, non-proteinogenic amino acids Further reading Natural Products Derived Biosynthetically from Amino Acids Peptides and proteins Symbols for the amino acids in primary structures of peptides and proteins Proteolytic enzymes Ribosome inactivating proteins (RIP toxins) Lectins Amanita toxins Snake venoms Lizard toxins Ziconotide Mistletoe toxins Cyclotides Non-ribosomal polypeptides Glycopeptide antibiotics Streptogramin antibiotics â-Lactam antibiotics Other â-lactams Vitamines derived from amino acids Cyanogenic glycosides Glucosinolates (mustard-oil glycosides) Further reading Alkaloids General aspects Amino alkaloids Pyridine and piperidine alkaloids Tropane alkaloids Pyrrolizidine alkaloids (Senecio alkaloids) Quinolizidine alkaloids (Lupinus alkaloids) Isoquinoline alkaloids Protoberberine alkaloids Benzylisoquinoline alkaloids Bisbenzylisoquinoline alkaloids Amaryllidaceae alkaloids Benzophenanthridine alkaloids Terpenoid tetrahydroisoquinoline alkaloids Indole alkaloids Simple indole alkaloids Terpenoid indole alkaloids Quinoline alkaloids Imidazole alkaloids Steroidal alkaloids Aconitum alkaloids Guanidinium alkaloids Further reading Purines and Pyrimidines Purine derivatives Biosynthesis ATP Nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+) Coenzyme A (CoA) Guanosine 5´-triphosphate (GTP) Riboflavin Flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) 5,6,7,8-Tetrahydrofolate (THF, Vitamin B9) Caffeine, theobromine and theophylline Pyrimidine derivatives Uridine triphosphate (UTP) Cytidine triphosphate (CTP) Cytarabine (Ara-C) Thiamin (Vitamin B1) Further reading Appendix I Index

• Regarding the only other source he presents, reference #6: Here I will spend almost no time. Editor Boghog was already asked to remove this source. The case for the removal is simple: The source (and sourced definition) are from a commercial trade and lobbying group. Here are some other statements from elsewhere on their web pages, that I also think do not belong on WP and in the NP article:

• "The Natural Products Foundation is organized exclusively to stimulate and support research, education and knowledge regarding dietary supplements, nutritional foods, and related products, with the overall objective of advancing the knowledge of the public, and thereby, improving the public health." [38]
• "The mission of the Natural Products Foundation is to promote and facilitate research and education related to natural products for the benefit of consumers and industry." [ibid.]
• "Naturalproductsinfo.org is a part of the Natural Products Foundation, your source for science-based vitamin and supplement information." [39]
• "Board of Directors / David Brown / Chairman / David Brown is the current Chairman of the NPF Board of Directors. Mr. Brown was most recently President of the LifeVantage Network. Prior to LifeVantage, Mr. Brown had been Managing Director and Co-Founder of Nutritional Business Advisors, President and CEO of Metabolife International, and President of Natural Balance, International. Mr. Brown earned his Juris Doctor degree from Cornell University, and began his career as a corporate attorney at the law firm Kindel & Anderson." [40]

This source is simply inappropriate as a guiding source of this article. When I introduced this citation at the start of this controversy (and it was I that originally did), I did so for completeness, for a very specific and different purpose. Here is how the reference appeared in a closing introductory sentence (that Boghog deleted):

"The term natural product has also been extended for commercial purposes to refer to dietary supplements and related products, and indeed to particular foods,[3] a lexicographic use that will not be the covered directly in this article."

where "[3]" was citation of the NP Foundation website. (This was all the validity I gave them, here.) You can see Archive 1 of this Talk page, for rejection of this one of several of my statements, and for Boghog's ultimate selective omission of other mentioned "classes" (e.g., foods, probiotics) from the same cited definitions. These are a few of an extensive array of failed attempts on my part to persuade Boghog to steer closer to the mark of the preponderance of all reliable natural products secondary sources, dropping this and other inappropriate sources (except from minor roles acknowledging their existence). My argument has always been to give first word to the preponderant best material, and last word to the marginal and least, both in the biology and the chemistry.

To close, I will say again, the direction of the whole article, as defined by the Classes section, the lede, and the overarching structure of the article... is in question. I stand by the fact that the order and content of the Classes section is clearly unrepresentative both of the citations appearing throughout, and of the broader total array of all reliable secondary sources available on the title subject. Le Prof Leprof 7272 (talk) 22:24, 18 June 2014 (UTC)

Discussion on future course of article, 4b

OK, great. Now, @Boghog, can you defend the weight of your sources? And what of the assertion that "Drugs of Natural Origin" in fact weighs more on the "natural products as small-molecule" side and not so much on the "everything that's natural is a natural product"? While I don't have the text I was able to peruse the ToC and there was a single chapter about plants (and even that looked to be mostly about getting compounds out of plants), the rest appeared to deal with chemical compounds and there application. Padillah (talk) 13:05, 19 June 2014 (UTC)

That being said, Le Prof, what do you propose as changes to the article to bring it more in line with the appropriate weight of topics? I must say, while I don't think it should go in the lede, I think a mention of the use (or should we call it re purposing?) of the term for marketing should be mention if only for completeness. Padillah (talk) 13:05, 19 June 2014 (UTC)

And what of the assertion that "Drugs of Natural Origin" in fact weighs more on the "natural products as small-molecule" side and not so much on the "everything that's natural is a natural product"? – That depends on the field. As already made clear by the present lead, within the fields of organic and medicinal chemistry, natural products are by definition small molecules. Other fields have different definitions. As I have already explained elsewhere, the present lead has a range of definitions, each portional to its importance. Le Prof has already stated that I think the current lede is in reasonable shape.

The main issue appears to be the classes section, and in particular, only the first two bullet points. The two subsections "Classification according to biological function", and "Classification according to chemical structure" deal almost entirely with small molecules. Hence in the current Classification section (including the two subsections), each definition is also treated in portion to its weight. What may be debatable is the order in which the definitions are introduced. I would argue that the current order follows a logical progression (from broad to narrow) and also is the order in which the definitions are listed in the source I have cited. This entire argument could go away if the classification section were expanded to included more details about small molecules, but nevertheless, I think it is important to retain the broad definition in addition to the more narrow definitions. The broad definition helps to put the more narrow definitions in context. Hence I see the two definitions not as in conflict with each other, but instead complementary. Boghog (talk) 14:37, 19 June 2014 (UTC)

I don't think you answered my question, you just walked around it. How do you respond to the assertion that even the source you presented, "Drugs of Natural Origin" only passively accepts the broad definition of the term?

Could the Classes section could be reformed as prose thus eliminating the numbered list and any hint at a hierarchy? It looks like the controversy stems around the conflict between the opposing hierarchies. How can we best eliminate this? Padillah (talk) 17:00, 19 June 2014 (UTC)

IMHO, I did directly answer your question. The key is "each proportional to its importance". The definition is field specific and both in the lead and in the classification sections, the amount of text devoted to each definition is appropriate. Furthermore the broad definition is explicitly stated in the source. The hierarchy is instructive and is also used in the source. The hierarchy also parallels the historical development of natural products and how they are isolated: first organisms, then extracts, then purified chemical substances. Boghog (talk) 17:19, 19 June 2014 (UTC)

I don't think the argument is about opposing hierarchies, but rather the breadth of the hierarchy. There is broad agreement that item #4 and probably #3 is should be included. The disagreement is whether the first two bullet points should be included. Boghog (talk) 17:43, 19 June 2014 (UTC)

Most importantly, how does including the hierarchy prevent expansion of the rest of the article to cover small molecules in more depth? The lead already defines the scope of the article. The classification section discusses the scope in more detail and as I have already indicated, should be expanded to include more details about small molecules. Boghog (talk) 17:29, 19 June 2014 (UTC)

I am going to hold on answering your question, @Padillah, until your discussion with @Boghog winds down, so that things don't get too confusing. I will make a couple of brief comments regarding the ongoing discussion, soon, to keep matters on point and accurate (from my perspective). Cheers. Le Prof Leprof 7272 (talk) 18:58, 19 June 2014 (UTC)

Feel free to chime in whenever you see a point you want to make. I'd rather have small, easy to follow blurbs than walls of text as we reply to one thing after another. Padillah (talk) 19:48, 19 June 2014 (UTC)

Ok, maybe I don't see it the same way. I was asking specifically about the book you cite. I don't see how the subject of the book you cite has to do with what field of study I am adhering to. Either the book mentions Natural Products as entire organisms or it does not. This has nothing to do with what field I am interested in. The question remains, how do you defend the use of the book "Drugs of Natural Origins" to support entire organisms as Natural Products when it only mentions this use in passing? Padillah (talk) 19:48, 19 June 2014 (UTC)

While only mentioned in passing, the definition nevertheless is specifically mentioned in the book to put the subject of natural products in context. For the exactly the same reason, it is appropriate to include the same definition in this article. Perhaps we could rephrase it to down play it as a definition. Boghog (talk) 20:55, 19 June 2014 (UTC)

In addition to your unanswered point, @Padillah, which has now been clearly stated twice, there is the matter of the second inappropriate non-scientific citation that I responded to after it was raised by Boghog, the citation from the commercial/trade and lobbying group. Its challenge has also been ignored. Le Prof Leprof 7272 (talk) 20:40, 19 June 2014 (UTC)

What's with this talk page?

Pardon me for speaking out of turn; I happened to see this discussion come up on a user talk page on my watchlist and it piqued my curiosity. I have to admit that on looking at the rest of this page, my first reactions were

• Where did all this highlighting come from? Different text colors? Bolded/italic/boxed text? What does it mean? Why is it important? Are the editor(s) doing this aware that background shaded text on Wikipedia discussion pages is usually part of 'closed' or 'completed' discussions?
• Why do so many sections start out with the same bolded header text: "Natural products community, feel free and add comments here"? Aren't all talk page sections supposed to welcome comments about the article, particularly from subject matter experts?
• Why do so many discussion threads have uselessly generic titles: "Discussion on future course of article"? Aren't all article talk page discussions, on any article talk page, supposed to be about the future course of an article? Are these subsequently numbered sections for continuation of the same discussion, or are they unrelated, or what?

I assume that somewhere under all this formatting mess is a statement of actual article content discussions and disputes, but they're very difficult to pick out of the clutter. TenOfAllTrades(talk) 22:18, 19 June 2014 (UTC)

Welcome to the page. What aspect of the content dispute do you wish to weigh in on? All comers welcome. But the Wikiprojects are clear above, with Chemistry being the lead, and the tag removed earlier (under protest) was this:

Here is a starting point, for top down: [41]. Here is a starting point, for bottom up [42]. Others may suggest starting elsewhere.

To take your questions in mishmash order (assuming you are sincere in wanting answers, and not just miffed at us for being different): There exists a substantive, longstanding content issue here, between two principle individuals (I am one). Too much of the spate of Talk is taken up by a never progressing discourse between the two. Invites and headings are intended to move the Talk away from the endless debate of the two, into broader areas and other hands, esp. from Nat Prod experts especially with chem and biol backgrounds (see here for why, [43]). Numbered, similarly titled sections are indeed continuations of an ongoing discussion (broken up by me, to make referencing of particular subtopics easier). The shaded boxes are a mixed, mostly failed experiment, again to make particular segments of the debate easier to access. Boghog my opponent likes to use green text for his quotes of others; I introduced the gray boxes to accentuate contributions from editors other than the two disputing, though this seems to be failing, because Boghog believes it marginalizes his contributions. The bright green box was added, in particular, because the question kept coming up, what is this about, and that box captures the core issues.

Any other questions, feel free to ask. Cheers, AGF, and look forward to your constructive questions. Le Prof Leprof 7272 (talk) 23:32, 19 June 2014 (UTC)

Thanks, but I'll pass. This talk page is too much of a mess, and the fact that you've managed to drive off Jmh649 already suggests that my patience wouldn't last much longer. TenOfAllTrades(talk) 00:35, 20 June 2014 (UTC)

Good editor, he, and am sorry to see you both go. Le Prof Leprof 7272 (talk) 01:07, 20 June 2014 (UTC)

@TenOfAllTrades:, Thanks for your input. I am trying to address some of the issues here and in the article. I implore you not to abandon me to my fate. Especially if you have any expertise in Chem or Bio. That being said, this does provide a definitive entry into the "Talk about the Talk" that needs to happen. I would like to archive some of this page to help clean up the place and to reduce the appearance to others that we have collectively lost our minds. We would need to leave the recent progress to allow it to continue and we would produce a link at the top to the archive with the understanding that it can be referred back to at any point. I hope that this, combined with the addition of new editors, will help get contributions to this article up. (Now I just have to remember how to do an archive...) Padillah (talk) 12:39, 20 June 2014 (UTC)

Thanks for continued presence, Pad, and I too ask continued outside participation. No progress will be made without it. However, we need expert chem/biol attention, as it is primarily a Chem wikiproject article. Hence the Chem expertise tag I placed, that a non-expert removed. This put us back to square one, and it needs reverting. Through that means or another, what we then need are further natural products editors in these sciences (NP chem, pharmacognosy, secondary metabolism, drug discovery, etc., as laid out here [44]). I am one of these, but I cannot stand alone. Granted, Boghog is an OChem expert; but his promotion of trade/lobbying web pages like this [45], and its definitional components, is not mainstream in the preponderance of natural products study. (Thankfully, he has admitted this is not a good source, see above—but only after 6 mos. span of argument, and only after your/outside attention.) I say again, there is no comparable set of valid secondary sources supporting the commercial connotation, that even begins to compare to this, [46]. I invite editors other than Boghog (who has wasted weeks of my life on this simple, clear academic question) to show me that I am wrong in this. Le Prof Leprof 7272 (talk) 14:06, 20 June 2014 (UTC)

Discussion on future course of article, 5

Natural products community, feel free and add comments here. Le Prof Leprof 7272 (talk) 15:39, 4 June 2014 (UTC)

* this is a very complex discussion and I arrive late in the game. I would hesitate to classify an entire organism as a natural product. Before continuing on this article though may I alert people to a bigger issue. Articles like chemical compound should ultimately derive from matter but this article is not decent. We could divide everything up into compounds and materials but the material article does not exist (composite material on the other hand does exist) Chemical compounds could then be divided up to synthetic compounds (synthetic compound is now a redirect to chemical synthesis) and natural compounds which would be a better name for the natural product article. We then also have natural materials such as silk and synthetic materials such as concrete. Even then I would not know how to fit in biological lifeforms. In lifeform, a lifeform is a kind of entity but not a form of matter. Perhaps worthwhile to look into this bigger issue before deciding what the content of this page should be V8rik (talk) 21:10, 18 June 2014 (UTC)

TY for your perspective. I look forward to the discussion that it stimulates. Le Prof Leprof 7272 (talk) 22:08, 18 June 2014 (UTC)

@V8rik, after rereading your comment, and doing some thinking... I take from your comment two points:

• (1) need to reexamine overarching structure of this article relative to other related articles,
• (2) hesitance to "classify an entire organism as a natural product". No comment on this point.

On the first point, one prior overarching structure for multiple articles has been proposed (Boghog, Smoke):

• Natural Products

• Natural Products Chemistry

You seem to be proposing the following overarching structure (yes?):

• Materials

• Natural Materials
• Synthetic Materials

• Chemical Compounds

• Natural Compounds
• Synthetic Compounds

My first reactions to this: First, mostly for the compounds categories, I note the predicament that while brevetoxin is a "natural compound", the question would be, what is it after Nicolaou and Crimmins groups succeed in preparing representatives in the laboratory? And what is artemether, really, since it is two very simple bench chemistry steps away from a very complex "natural chemical"? Second, there is the "Houben-Weyl" conundrum: losing readership via the oddity of organization that might have been gained in the thoroughness of coverage. In particular, I think it problematic to try to rename the NP area of study, with 1,860,000 hits Google, in the direction of "natural compound", with < 1/3 the number, where many of even those fewer hits simply appear as synonyms of NP, and many of the rest are "reformation England" appearances (incidental, see above).

Bottom line: (1) Natural Materials is a fine idea for an article, with the caveat that "natural" applies to original source, and that placing semisynthetic materials will be an eventual issue. (2) I otherwise think I have to stand by the NP/NPC structure of Boghog and Smoke, as more easily representing the actual ways in which practitioners refer to their subject. (Though, the Germanic part of me was pleased by the symmetry of your attempt at a systematic approach.)

So, unless you object, I propose tabling this broader restructuring, and focusing on getting the existing NP article in order, where thereafter we can i, consider renaming if we choose, and ii, create more specialized related articles like the proposed NP Chemistry. Cheers, Le Prof Leprof 7272 (talk) 05:33, 19 June 2014 (UTC)

Along with LeProf's well-reasoned argument I offer WP:NC which asks that articles be titled as they are referred to in the sources. Padillah (talk) 12:53, 19 June 2014 (UTC)