Wikipedia talk:WikiProject Molecular Biology

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WikiProject Molecular Biology Archives: 1, 2, 3

Taskforce archives:

MCB: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
Genetics: 1, 2, 3, 4
Computational Biology: 1, 2
Gene Wiki: 1, 2, 3, 4

Biophysics (inactive): 1, 2
Metabolic Pathways (inactive): 1
Cell Signaling (inactive): 1
RNA (inactive): 1

Good article reassessment for Catalytic triad

Catalytic triad has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Z1720 (talk) 17:04, 6 November 2024 (UTC)

Discussion at Wikipedia:Redirects for discussion/Log/2024 November 11 § Ro (antigen)

 You are invited to join the discussion at Wikipedia:Redirects for discussion/Log/2024 November 11 § Ro (antigen). Shhhnotsoloud (talk) 10:00, 11 November 2024 (UTC)

"In enzymology, a dihydroxyphenylalanine ammonia-lyase (EC 4.3.1.11, entry deleted) is a non-existing enzyme that catalyze"

Dihydroxyphenylalanine ammonia-lyase says it doesn't exist and the KEGG entry agrees. What is the normal protocol for such articles? JoJo Eumerus mobile (main talk) 19:09, 16 November 2024 (UTC)

This isn't a difficult decision. Delete the entire article. Genome42 (talk) 15:43, 17 November 2024 (UTC)

And done. Jo-Jo Eumerus (talk) 16:24, 17 November 2024 (UTC)

TNIK

I have been reading some fairly remarkable reports regarding TNIK inhibitors in late stage clinical trials, and thought I might ask some of the article authors with greater technical understanding of the field to expand on this. Looking at the article history, I was surprised to find that this article was created by a bot, and almost every edit to the article has been expansion or maintenance by another bot, or by a passing-by gnoming editor. It would be nice to see some real work done by some actual human hands, before we get to the point where AI takes over writing everything anyway. BD2412 T 18:48, 11 December 2024 (UTC)

I'm sorry to report that what you've uncovered is the norm rather than the exception. It's exactly as you suggested, not enough hands here to cover the huge topics of molecular biology. There are many genes/proteins that have attracted 10+ times more coverage than TNIK and yet we have just a lousy little article (e.g. B7-H3, TROP-2, CLDN18, Nectin-4, all of which are the targets of dozens of drugs in clinical trials and some FDA approved). Apologies for using the opportunity to whine, but I suppose I'd suggest (A) hold your molecular biologists tightly; we should make a concerted effort to recruit folks who show up at AfC, student projects, et al., and (B) you could try posting at WT:MED, perhaps someone interested in pulmonary fibrosis would be willing to take a stab at it. I'll add it to my list, but I'm on a cancer kick right now, so I might not get to it for a while. Ajpolino (talk) 21:16, 11 December 2024 (UTC)

Fair enough, although I understand that this is also being looked at in the cancer space (though perhaps everything is). BD2412 T 23:10, 11 December 2024 (UTC)

I'd like to offer another perspective. I don't think there should be a Wikipedia article on TNIK or on hundreds of other genes. Wikipedia is not the place for such detail; besides, there are much more important tasks that need to be accomplished in order to clean up the mess of biology articles on Wikipedia. Let's concentrate on fixing articles on the fundamentals so that they are up-to-date and easy to understand.

If the article on TNIK really is AI generated then I recommend deletion. The current versions of AI are incapable of generating scientifically correct information. They are heavily influenced by misinformation and disinformation on the internet. In fact, we (molecular biologists) are partly responsible for some of that misinformation since we haven't been correcting existing articles on Wikipedia. Genome42 (talk) 16:14, 12 December 2024 (UTC)

@Genome42: The article was bot-generated — in 2008 — rather than "AI"-generated. Basically, we used to have a lot of bots that scraped public-domain databases and created articles from information in those databases. Wikipedia has hundreds of thousands of articles that were made this way, mostly about athletes, remote villages, obscure species, and the like. For the record, though, I tend to think that we should have articles on genes, as these are fundamental to our existence. BD2412 T 16:29, 12 December 2024 (UTC)

Are you defending BOT-generated articles on human genes that were created from public information dating back to 2008? Why?

You say that we should have articles on genes because they are fundamental to our existence. I assume you only mean human genes, right? There are close to one million different genes in the biosphere - do you really think we need a Wikipedia article for every one?

As for human genes, there are about 19,500 protein-coding genes. What's the point of having outdated, possibly incorrect, articles for each one since hardly anyone is ever going to read them?

We don't know how many non-coding genes there are but what we do know is that there are far more speculative non-coding genes (especially for lncRNAs) than genuine genes. The number of such speculative genes exceeds 100,000. What about those? Genome42 (talk) 22:54, 12 December 2024 (UTC)

I see no reason why we could not have an article on each of 19,500 protein-coding genes. I am dubious of the assertion that 2008 databases are automatically "outdated, possibly incorrect"; I would be interested to know if you have examples of errors stemming from them, or are just assuming. You are, of course, welcome to nominate TNIK for deletion, if you think it should be deleted. BD2412 T 23:31, 12 December 2024 (UTC)

I think we should have articles on genes that are well-covered in reliable sources (there are several recent reviews focusing on TNIK); we just need the manpower to keep those articles up-to-date (not sure how we get there). I don't think we should have articles on genes that aren't well-covered in reliable sources (arbitrary example GLB1L3); these can redirect to an article on the gene family if needed. There's a large grey area in-between those two groups that I don't have a strong opinion on. Ajpolino (talk) 19:48, 12 December 2024 (UTC)

I'm a biochemist/molecular biologist and I've been working in this area for 56 years. I've never heard of TNIK. I don't care about TNIK.

Who's going to make the decision that a given gene is "well-covered"? I agree that there are some genes in some species that deserve a Wikipedia article of their own but let's not get carried away. It's pretty easy to decide on the genes that we absolutely need to cover. We should ignore all the others unless there's someone who wants to put in the time and effort to write a decent article.

Let me give you an example of the mess we're in. Pyruvate dehydrogenase is a very important metabolic enzyme but the article doesn't even come close to informing readers about its importance and it completely ignores the evolutionary history of this crucial enzyme. The important enzymes that share a common ancestor aren't mentioned. I suspect the article was created by a BOT - there's only two references from the last 17 years.

The human version of this enzyme is encoded by eight genes; PDHA1, PDHB, DLAT, PDHX, PDP1, PDPK1, PDK2, and PDK4. The last two are the only ones with their own article; for the others you have to look up the name of the enzyme they encode. None of the genes (human or otherwise) are mentioned in the pyruvate dehydrogenase article.

What's the point of having separate articles for each of the subunits/genes?

There's a whole lot of work that needs to be done before we start devoting time and effort to TNIK. Let me remind everyone that a separate article on junk DNA was only created last year and that's a very important topic. Genome42 (talk) 23:51, 12 December 2024 (UTC)

I came here at all because I happened to see coverage of TNIK — and specifically, of the potential for TNIK inhibitors to treat human diseases. Whatever other genes may exist in the genome, the potential for inhibition of a specific gene to treat a specific disease is certainly worth covering. The same reasoning would apply to something like USP1 (which currently contains no information on investigative efforts), or CD47 (which is reasonably well-covered in this respect). BD2412 T 00:09, 13 December 2024 (UTC)

You say, "Whatever other genes may exist in the genome, the potential for inhibition of a specific gene to treat a specific disease is certainly worth covering."

Why? An online encyclopedia is not required to cover everything under the sun. Surely there has to be some limits to what's on Wikipedia, especially since there are only a handful of editors who are capable of checking molecular biology articles for accuracy.

Wikipedia is already full of inaccurate and misleading articles on molecular biology. Let's concentrate on fixing those instead of looking for excuses to add more.

If you think it's really, really important to add something on TNIK then why not put it in the article on signal transduction or the one on kinase or the one on wnt signalling pathway? All of those articles could use some serious atrention. Genome42 (talk) 21:47, 13 December 2024 (UTC)

I should qualify that if reliable sources cover the potential for inhibition of a specific gene to treat a specific disease, that is what (by Wikipedia standards) makes it worth covering. I am not a molecular biologist, nor a pathologist or epidemiologist, although my work brings me into contact with these fields once in a while. When I come across a source that says that there is a development with respect to the study of inhibition of a specific gene, it's really not going to occur to me (or, I think, to the average editor) to add this to signal transduction or kinase or wnt signalling pathway, rather than the article on the gene being directly studied. BD2412 T 22:02, 13 December 2024 (UTC)

BD2421 says, "I am not a molecular biologist, nor a pathologist or epidemiologist ..."

and, "... it's really not going to occur to me (or, I think, to the average editor) to add this to signal transduction or kinase or wnt signaling pathway, rather than the article on the gene being directly studied."

That pretty much sums up one of the main points I've been making. I realize that the Wikipedia culture is skeptical of experts and wants to encourage amateurs to add content based on the latest popular science articles but I think it's time to push back against this culture.

We need to recognize that this culture has created a horrible mess of articles in the fields of molecular biology, genetics, evolution, biochemistry, and genomics. What this means is that Wikipedia is full of misinformation and misleading information. This may have been (barely) tolerable in the past but no longer. Now that AI is relying on Wikipedia for accurate information we need to step up an fix the problem. Genome42 (talk) 16:21, 14 December 2024 (UTC)

This xkcd comic comes to mind. Wikipedia is written for the average reader, not the average molecular biologist. BD2412 T 02:47, 15 December 2024 (UTC)

Exactly. That's why we don't need articles on every detail (e.g. every gene) that might be of interest to molecular biologists and why we need to concentrate on explaining the fundamentals to the average reader.

But here's the problem. You need to be an expert on molecular biology in order to explain the fundamentals correctly. Genome42 (talk) 15:32, 15 December 2024 (UTC)

That's why we rely on sources written by experts. BD2412 T 16:32, 15 December 2024 (UTC)

But Wikipedia editors DO NOT rely on sources written by experts. The policy of Wikipedia is to place more emphasis on secondary sources written for the general public. Genome42 (talk) 21:08, 16 December 2024 (UTC)

Are you suggesting that experts do not write secondary sources? BD2412 T 21:20, 16 December 2024 (UTC)

Most secondary sources are not written by experts. They are often cobbed from press releases written by publicists. Some science writers are very knowledgeable about their subjects but most are not. One of the main issues on Wikipedia is the proper identification of "reliable sources." Genome42 (talk) 17:14, 17 December 2024 (UTC)

Secondary sources include academic journal articles evaluating the work of other academics, and textbooks for teaching in the field. All of these are generally written by experts. To the extent that an author is not writing about their own personal research or experiments, the source is a secondary source. BD2412 T 18:52, 17 December 2024 (UTC)

You are correct. Sources from the scientific literature (e.g. reviews) or authoritative textbooks should be acceptable reliable sources. Articles in the New York Times and popular science magazines should not. However, it still takes an expert to figure out which reviews and which textbooks represent the scientific consensus.

I've had to fight other editors when I used a textbook definition (of allele and junk DNA) that conflicted with the Oxford dictionary definition. That's a problem. Genome42 (talk) 15:40, 18 December 2024 (UTC)

Requested move at Talk:Zoonotic origins of COVID-19#Requested move 14 December 2024

There is a requested move discussion at Talk:Zoonotic origins of COVID-19#Requested move 14 December 2024 that may be of interest to members of this WikiProject. TarnishedPath^talk 14:24, 15 December 2024 (UTC)

Good article reassessment for Protein

Protein has been nominated for a good article reassessment. If you are interested in the discussion, please participate by adding your comments to the reassessment page. If concerns are not addressed during the review period, the good article status may be removed from the article. Z1720 (talk) 17:49, 18 December 2024 (UTC)