Talk:Malacidin

Sourcing

This article reports on breaking news of research, based only on early studies. Those sources, although reliable, are not sufficient to support statements of biomedical efficacy, as stated at WP:MEDRS:

Ideal sources for biomedical information include: review articles (especially systematic reviews) published in reputable medical journals; academic and professional books written by experts in the relevant fields and from respected publishers; and guidelines or position statements from national or international expert bodies. Primary sources should generally not be used for medical content – as such sources often include unreliable or preliminary information, for example early in vitro results which don't hold in later clinical trials.

This is certainly "preliminary information" and the article runs close to falling foul of WP:NOTNEWS:

Wikipedia should not offer first-hand news reports on breaking stories. ... While including information on recent developments is sometimes appropriate, breaking news should not be emphasized or otherwise treated differently from other information.

It's possible that secondary sources may review these preliminary findings and give us good sources to work from, but until they do, it is inappropriate to claim that these compounds have particular antibiotic properties. --RexxS (talk) 18:24, 13 February 2018 (UTC)

I agree with this, but I'm confused about whether popular media sources count as secondary sources for MEDRS. They just summarize what the original research says. They aren't evaluating it or verifying its accuracy. Natureium (talk) 19:18, 13 February 2018 (UTC)

Given that we are talking about a compound that has never been used in humans, isn't generally available, and is years away from being tested in humans, my personal opinion is that it is a bit of a stretch to consider most of this article biomedical information at this moment. In other words, at this point the applicability of MEDRS isn't entirely clear to me. There is no medical treatment right now, or even a generally available compound that could be abused in untested medical activities. Obviously the hope is to eventually develop a medicine, but at the moment that is so far in the future, that I inclined to give a somewhat higher degree of latitude right now and treat this article as mostly a microbiology topic rather than a medicine one. Dragons flight (talk) 20:29, 13 February 2018 (UTC)

the "excitement" here is exactly because we need new classes of chemistry for antibiotic drugs. It is kind of interesting from the standpoint of how some bacteria try to kill other kinds, but nobody really cares about that. The excitement is about the medical potential. And part of why MEDRS matters is keeping out all kinds of prelimnary hype, be that from pharma or medical devices, or this kind of thing which is hype driven by successful university PR. Jytdog (talk) 20:43, 13 February 2018 (UTC)

@Natureium: of course popular media sources aren't considered as useful for biomedical information. Hello magazine is fine for celebrity gossip, but we're not going to use it as a source for the latest cure for cancer. Similarly, the Independent has a decent reputation for reporting news, but for the claim that a particular chemical is usable as an antibiotic, we're going to need a review or meta-analysis in a decent medical journal, or a description in a widely-used textbook, etc. to sustain the claim. If those don't exist we ought to be very suspicious about news reports based on single studies, such as in this case. Merely reporting a primary study in a newspaper doesn't transform it into a secondary source for our purposes.

@Dragons flight: "Given that we are talking about a compound that has never been used in humans, isn't generally available, and is years away from being tested in humans," I'd have to ask why should we have an article in an encyclopedia about it? As soon as you start talking about use as an antibiotic, you're making medical claims, so MEDRS applies. In fact the whole thrust of the Nature article is that these compounds are being toted as a solution to bacterial resistance in humans. You can't simply pretend that this is nothing to do with a potential for human use, and you mislead our audience when these sort of claims are being made despite not a shred of evidence existing of their efficacy in treating MRSA, for example, in people. I'm inclined to give no latitude at all to such speculative hype, and I'll be removing the disputed content soon if better sources don't show up. --RexxS (talk) 21:46, 13 February 2018 (UTC)

I really think calling this a medicine related article is far too premature, given how the paper authors discuss it. While "antibiotics" generally are related to drugs, there is a non-drug related definition which is what I read the paper using; they are certainly not stating that it is a drug right now. This would put it immediately out of being under MEDRS concern.

As for notability (RexxS's point), I'd equate this (A discovery of a new class of antibiotics) as equivalent to a new chemical element. There are a clear finite element number of classes that we know about, and the former ones all appear to have appropriate coverage to pass the GNG. Even if we take the Nature MB as the primary source, the news coverage putting the discovery in light would qualify as initial secondary sourcing that we can presume the notability at this point. That could be proven wrong in the future and deletion or merging would make sense, likely in the case if this discovery is reported wrong. But in the current situation, it seems fully appropriate for an article. --Masem (t) 21:58, 13 February 2018 (UTC)

@Masem: The Nature article begins "Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide". In what sense could anyone call that a "non-drug related definition"? Are you sure you're reading the same paper? Of course they are pitching it as a medical application. --RexxS (talk) 22:04, 13 February 2018 (UTC)

In any scientific paper, you want to frame the problem to explain the research goals. That quote seems a very simple way to explain why they wanted to take these soil samples. They are clearly doing research to aid in medical application, but they are also clearly not stating the work as it stands as published has any immediate medication application; they know there's a long road before they can consider this medically applicable. --Masem (t) 22:08, 13 February 2018 (UTC)

Of course they are implying that the research will have medical application, and that's their sales pitch. Without that, there would be interest and no notability. You can't have it both ways. As for the "new chemical element" analogy, we'd want some confirmation that the new substance was indeed an element, wouldn't we? Just like all the chemical elements, all the other antibiotics that have articles are attested in quality, reliable sources meeting MEDRS. What's so special about this compound that it should be an exception? --RexxS (talk) 22:12, 13 February 2018 (UTC)

If you are doing funded research, you need to make a sales pitch of sorts to get funding. That's the unfortunate truth of science today. We need to recognized that this doesn't seem to be the case of "big pharma"-backed research which could spin COI issues or the like. I see no issue with them spinning this as a step towards an antibiotic for dealing with drug-resistant species to explain the direction their research took. There is no indication that this story has any immediate commercial angle driving to create hype. It appears as a valid discover that has a potentially great end result for the medical community, though they're nowhere close to that point yet. Also, I'm not seeing any major naysayers here doubting the discovery. They're being bullish if it can be made human-safe, but as a new class of antibiotics, they seem to agree. That's another good sign that there's proper science behind this and not just a commercial play.

Now yes, I would agree that there needs to be third-party confirmation, and a bunch of other factors to affirm their results, much less drive towards a potential drug. We don't want a cold fusion situation here (but that was a case where the researchers also hyped it up a lot more than what this paper provided). And those third-party confirmations are probably still months if not years from publication. If we frame it within WP's notability and not#news standards, which is a valid case, notability as a new antibiotic discovery (not a new "miracle cure") is clearly there - several stories from mainstream are explaining the significance of this should it be found safe for human use; they're framing the primary source (the Nature MB article) in secondary terms. As a minimum, the GNG is met. not#news is a bit more questionable, but from what I'm seeing in other articles, this new class should have the field's attention as they attempt to duplicate and confirm the properties. It likely does have enduring notability, though it will take time for those articles to come about; otherwise we just have the burst of news coverage today. But unlike an event, which is generally what NOT#NEWS is meant to avoid, this is a new piece of human knowledge that just needs to be tested further. It is the same type of coverage that we see when a new major published work is announced in contemporary media - as long as we can generally talk about it more than just a press release (or here, the journal article), we allow for an article, with the presumption that if the work is cancelled (here, the science invalided) we can then delete it. That's why the minimal tests for notable are met, but this does not mean this article can never be deleted, but we should give it time until it gets there. Still, even if the antibiotics fail to be all they think they might be, we still have a new class of antibiotics to include; here, a negative result would not change the encyclopedic appropriateness for us.

As a counter example, in light of the MEDRS concerns, if this was a Big Pharma company announcing a new drug that they were about to enter voluntary clinical tests but that there were no reported results on the drug from third-parties, that would be a place where MEDRS needs to be upheld and potentially eliminating the article on that drug until its validity is confirmed by appropriate third-parties. --Masem (t) 23:14, 13 February 2018 (UTC)

I'd say that the article as it is today is sufficiently clear that this is a first, not a reproducing study. The study was financed with grants from Gates and NIH. NIH have a lot of employees who will no doubt be interested in writing those secondary sources quickly. Twang (talk) 05:52, 14 February 2018 (UTC)

There are already confirmations by uninvolved scientists confirming this, e.g.: The US team behind the malacidin discovery are "right to call it a new class of antibiotics", molecular biologist Dr Luke Alderwick told The Independent, "They've used a clever approach to mine for antibiotics," said microbiologist Kim Lewis, who directs Northeastern University's Antimicrobial Discovery Center and wasn't involved in the work. Per WP:SCHOLARSHIP, "Articles should rely on secondary sources whenever possible". While in other cases searching for secondary sources is reasonable, here when the first secondary source appears, the news will naturally become stale, so waiting in the absence of substantiated doubts is moot. Brandmeister^talk 10:22, 14 February 2018 (UTC)

Between here and discussion at WP:ITN/C, its clear this article is not a "medicine" topic, but "microbiology". As such, tryng to apply the stricter MEDRS to the sourcing is far too early, so I have remove said tags that had been previously removed but readded. If this starts getting into any type of clinical trial, then MEDRS would apply. --Masem (t) 13:49, 14 February 2018 (UTC)

Just jumping in late in the game here.... Anyways I support removal of MEDRS and Masem's reasoning. Yilloslime ^T_C 16:06, 14 February 2018 (UTC)

FWIW, I've started a discussion at WT:MEDRS related to how MEDRS should apply to microbiology vs biomedical topics. --Masem (t) 16:56, 14 February 2018 (UTC)

• Coming here from the MEDRS posting. One can say MEDRS applies here, but I think people are getting too hung up on the human medicine aspect. What's more important is the idea that we rely on secondary sources to establish the importance of this work, which the more broad WP:SCIRS explains as well. Wikipedia is by definition behind the ball (i.e., NOTNEWS). Whether it's human medicine or not, we typically want secondary sources to outline how accepted a study is in the scientific community. At the end of the day, it's still early-stage research whether it's for the fields of human medicine, animal medicine, plant health, or even soil microbe interactions. The concepts of MEDRS still apply regardless. I would be surprised if there wasn't some secondary commentary soon, so there's no harm in waiting for MEDRS/SCIRS appropriate sources for that. Kingofaces43 (talk) 17:06, 14 February 2018 (UTC)
  • Secondary sourcing is important, no question. And I agree the Nature MB article is primary for all purposes; if that was the only source, there shouldn't be an article. However, the mainstream news coverage of this does include secondary commenting on the topic from other noted microbiological researchers talking both about the importance of the discovery and the "mining" approach used to potentially discover more classes. From strictly a GNG/NOT#NEWS standpoint, this has sufficient coverage for presumed notability to be kept as a standalone article. That could be challenged in the future. But whereas MEDRS is very important to avoid junk health-related topics and needs that secondary-sourcing scrutiny (specifically to make sure any health-related information is corroborated), taking the few of a non-health related topic here doesn't require the same scrutiny. --Masem (t) 17:48, 14 February 2018 (UTC)

Those news sources are not reliable secondary sources for scientific content. In order to have true secondary sources for scientific content, you need it in the published literature, etc. While that is often a confusing point for editors new to scientific topics on Wikipedia (I write about it on my userpage because even some scientists aren't taught how the publishing process is really intended to work), that really isn't an idea that's appropriate to continue arguing. This is the kind of stuff we usually try to keep out of Wikipedia articles even outside medicine, but this kind of microbiological research is also a branch of medicine. Kingofaces43 (talk) 19:37, 14 February 2018 (UTC)

• it is very unlikely that the community would agree to delete this now although it really is WP:TOOSOON. I have gone through and removed or toned down medical claims (for example, it kills bacteria, it doesn't "treat infections"). i have also added that it will be years and many dollars before we know if this will be a drug, and that the scientists aren't planning to try. I also removed "antibiotic" from the first sentence and replaced that with a wikilink to secondary metabolite, which is what these are from a microbiological standpoint. Jytdog (talk) 19:51, 14 February 2018 (UTC)

I am inclined to agree. Based on past AFDs I've seen any attempt to delete this would be SNOW closed; GNG usually overrides NOTNEWS (TOOSOON is an essay and after having actually read it would not apply in this context anyway) in practice since GNG is a fairly clear cut criterium while NOTNEWS is a very vague policy that can be interpreted a dozen different ways, and seldom carries the day in a deletion discussion. Jo-Jo Eumerus (talk, contributions) 10:46, 17 February 2018 (UTC)

Related discussions

Just so folks have them, related discussions are occurring at WT:MED Wikipedia_talk:Identifying_reliable_sources_(medicine)#Distinguishing_"microbiology_topics_that_may_lead_to_medical_applications"_from_"biomedical_information" (argh, quotation marks screw up links) and ITN here: [[Wikipedia:In_the_news/Candidates#[Posted]_Malacidins]]. Jytdog (talk) 20:27, 14 February 2018 (UTC)

Another bacteria

"another bacteria" should either be "another bacterium" (singular) or "other bacteria" (plural). Art LaPella (talk) 14:57, 16 February 2018 (UTC)

fixed, thx Jytdog (talk) 19:25, 16 February 2018 (UTC)

Great. Any suggestions for {Chembox}?

Hi you all who created this article -- it is on Main page now ;-).

I maintain the {{Chembox}} (doing template improvement &tc.). My question is: did you meet issues that {{Chembox}} could do better? Troubles entering data? Considering {{Infobox drug}}? -DePiep (talk) 22:33, 18 February 2018 (UTC)

user:DePiep i am not a big fan of edits like this the chembox. that is unsourced and i have no idea if it is even accurate, as i am not a chemist.

btw this molecule It looks remarkably like a lawnmower to me if you orient the macrocycle horizontally :) I have no other comment to your question, sorry... Jytdog (talk) 18:46, 20 February 2018 (UTC) (tweaked a bit Jytdog (talk) 21:56, 20 February 2018 (UTC))

All ;-) fine.

I am not a chemist either. But why do you doubt the JSMol image? Apart from being unsourced, I cannot judge. Also, the structure section additions -- what's the problem? Being unsourced?

But really, my OP question was: are there any "general" improvements you editors of this hot new article, can suggest for {{Chembox}} (that is: template improvements, not article improvements). -DePiep (talk) 20:19, 20 February 2018 (UTC)

How did you get lawnmower from a ring and a stick? Natureium (talk) 20:22, 20 February 2018 (UTC)

Question seconded. -DePiep (talk) 20:29, 20 February 2018 (UTC)

I am (or was) a chemist, and this edit[1] was almost certain wrong. (And it was certainly unreferenced.) At any rate, thinking about the chembox, "Point group" links to Point group, but it would probably be more useful to have it link to Molecular symmetry, since that article actually discusses point groups in the context of chemistry. Yilloslime ^T_C 20:39, 20 February 2018 (UTC)

 Done, see [[Template_talk:Chembox#{Chembox_Structure}:_'Point_group'_target_link_change]]. -DePiep (talk) 21:52, 20 February 2018 (UTC)

I don't know how you came to think I doubt the Jsmol image. I like those.

3D Malacidin

About the lawnmower thing, see pics to the right. if you don't see it i of course can't help you. Thick round base, handle = old fashioned simple lawnmower in my mind. Just tossed off silliness.

Thanks for reviewing and reverting the addition of the content I asked about, Yilloslime, which is what matters. Content. Jytdog (talk) 20:53, 20 February 2018 (UTC)

(LOL the fun is, Jytdog: you linked to a 3D *interactive* image. When I opened it, is did not look like a lawnmower at all. More like a tennis racket to me, or a spine-less sea animal. That's what 3D-interactive does. OK? -DePiep (talk) 00:58, 21 February 2018 (UTC))

Somebody should respond to Depiep's OP. Jytdog (talk) 20:53, 20 February 2018 (UTC)

Jytdog, are you saying that the specific 3D structure--bond lengths, angels, conformation, etc--as depicted in the chembox/chembox links, is not cited and is presumably WP:OR? 'Cuz if that's what you are saying, I suspect that you are right. I haven't read the entire paper and supplemental material, but there's no crystallography or discussion of bond lengths and angles and dihedral angles, etc--nothing from which one could generate the 3D structure that you liken to a lawnmower. So I could see removing it, but I also don't see that it does any damage. Yilloslime ^T_C 00:01, 21 February 2018 (UTC)1

No i asked only about a specific diff which you took care of. My comment about jsmol image was only goofing around. I like them. the image is fine. Fine. Perfectly OK. Great. Wonderful. Jytdog (talk) 01:01, 21 February 2018 (UTC)

Why on main page when ...

Why is this on the front page when it still hasn't been tested on humans, and the study authors have a clear conflict of interest? --124.150.79.29 (talk) 08:58, 20 February 2018 (UTC)

It is interesting basic science and it makes no health claims; it is good to have basic science on the front page from time to time. Jytdog (talk) 14:51, 20 February 2018 (UTC)

• user:Masem remember when I wrote this (A lot of the hoopla was about their method, and I wouldn't be surprised if they set up a company to discover more interesting chemicals using the method, but that is a different business.)? I hadn't looked at the COI disclosure in the paper at that time. When I did, finally, I added this to our article. I am wondering - would your approach to any of the ITN or other matters changed, had you been aware of this while those discussions were ongoing? (real question; for me the answer is i think "no"... although the article sure does appear now to be selling Lodo's approach to natural products discovery....) Jytdog (talk) 18:40, 20 February 2018 (UTC)

I don't consider it a conflict of interest yet in terms of research. There's no financially-viable product right now. Lots of basic and advanced research is funded by commercial entities alongside academics, and even if it meant as a long-term run to get a profitable product by the commercial entity, the basic research here still seems completely valid (based on external experts from those news reports). It would be very different if this was research at the start of commercial trials. That said, I think the wording re: Lodo's involvement could be better to make it less like an ad. --Masem (t) 18:53, 20 February 2018 (UTC)

Oh Masem. What Lodo sells now, is the promise of its method. It will need people to believe in the method to get further rounds of investment. I am very curious what you would change about the Lodo wording. The somewhat promotional part of the article as it stands now, in my view, is the long description of the discovery method and emphasis on the people who did it. Jytdog (talk) 19:03, 20 February 2018 (UTC)

I'm not sure what I would change immediately, something sounds "off" in the NOR aspect. For example, the C&EN article notes Lodo got funding from the Gates Foundation for treating overlooked diseases. I'd actually include a bit more about that founding and that the goal was to find antibiotics from soil samples. Now as for how they discovered it, I see no issue again restating Lodo, but to me, how they came about it, even if this was how Lodo was founded, is rather interesting and news reports from other microbiologists suggested that this is a novel approach that others can replicate to find even more (eg Lodo may have a head start but don't seem to have anything blocking other research, which would also be triggering a COI issue). We do have to be careful here of the NCORP-related issues, but that's wording to be adjusted. --Masem (t) 03:27, 21 February 2018 (UTC)

wow you went deep into the weeds there. i think the article is current okish but i read it again after reading the IP's remark and i see how they got there. Jytdog (talk) 04:49, 21 February 2018 (UTC)