Template:Did you know nominations/AlphaFold

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AlphaFold

  • Comment: Note: I am one day over in submitting this, because it was previously up for consideration at WP:ITNC (discussion), and only fell off the page there at midnight this morning. So any leeway you could give it would be appreciated.
  • Reviewed: The Adults Are Talking

Converted from a redirect by Ktin (talk), Jheald (talk), and My very best wishes (talk). Nominated by Jheald (talk) at 18:36, 8 December 2020 (UTC).

  • Symbol voting keep.svg The article is new enough and long enough. The rationale for the two nonfree images is perfectly argued. I had some doubt for the first image, but searching in google-images didn't show the same image anywhere else. The article is neutral and well sourced. The "Earwig's Copyvio Detector" don't show any copyvio (it just marked the quoted part). You have done a great job, congratulations. Alexcalamaro (talk) 20:03, 9 December 2020 (UTC)
  • Comment: in spirit of MOS:PEACOCK, I suggest the following blurb: ... that AlphaFold 2 won the 14th biannual CASP competition achieving 92% accuracy, essentially solving the decades-old protein folding problem. --bender235 (talk) 01:26, 10 December 2020 (UTC)
  • Template:Re While claims such as "In a serious sense the single protein single domain [prediction] problem is largely solved" have been widely made (that quote is from conference chair John Moult's closing presentation to the conference), were very widely featured as a top line in media coverage, and have also been supported in thoughtful commentary by eg Mohammed AlQuraishi [1], they have also met with opposition; and so we are not currently running them on the article. (Though this could be changed). See article talk page for extended discussions. That is why I submitted the DYK text as above.
Note also that while AF2 has made a very significant advance in the protein structure prediction problem, this is a different question to the question of how protein folding develops in nature, so caution should be taken not to confuse the two. — Preceding unsigned comment added by Jheald (talkcontribs) 09:43, 10 December 2020 (UTC)
  • Symbol question.svg Returning to WP:DYKN until review is settled. I personally find the ALT0 wordy and difficult to understand. Yoninah (talk) 21:28, 12 December 2020 (UTC)
  • Folks Template:Ping, this one has been open for sometime now, let's go ahead and drive this one to closure. I think the below text is the best that someone on homepage would be able to follow; anything more and we run the risk that folks find it Template:Tq or Template:Tq. Let's move ahead, if you are good. Also Template:Ping I do not want to presuppose your background but can you read the below two hooks as a layperson and let me know if you a) find it interesting b) generally get the gist of this one? If you are not a layperson for this topic, I am happy to go chase down some laypersons for this topic. Cheers.Ktin (talk) 22:42, 14 December 2020 (UTC)
ALT 3.0.... that DeepMind's protein-folding AI AlphaFold 2 has solved a 50-year-old grand challenge of biology? (source: MIT Technology Review).
OR
ALT 4.0 .... that DeepMind's AI AlphaFold 2 can predict the shape of proteins to within a width of an atom? (source: MIT Technology Review).
  • Template:Ping I am a layperson, and I really like ALT 3.0. ALT 4.0 is also more understandable than ALT0. Thanks, Yoninah (talk) 22:35, 14 December 2020 (UTC)
  • Thanks Template:Ping. Wonderful. Template:Ping -- if one of you have a moment, please can you review the above two hooks per the standard WP:DYK hook review guidelines? Cheers. Ktin (talk) 22:42, 14 December 2020 (UTC)
  • I agree with Template:U, ALT 4 blurb is very catchy. Probably the best choice. --bender235 (talk) 23:04, 14 December 2020 (UTC)
  • Template:Ping I prefer ALT 3.0, I think fits better with the achievement and is more attractive for "the layperson" ;-) . Alexcalamaro (talk) 23:07, 14 December 2020 (UTC)
  • Wonderful. Thanks both of you Template:Ping. Please can one of you review the hooks per our guidelines and approve both the hooks, we can choose one from the two post that or empower the posting Admin to make a choice. But, first step, lets approve the hooks. Cheers. Thanks again folks. Ktin (talk) 23:14, 14 December 2020 (UTC)
  • Lua error: expandTemplate: template "y" does not exist.
Passing the baton over to you Template:U to take it from here. I am good with either of the hooks (ALT3 or ALT4). I know you had prefered ALT3 and Template:U had prefered ALT4. Template:U -- do you want to cast the tie-breaker vote? ;) Ktin (talk) 18:54, 15 December 2020 (UTC)
I vote for ALT 3.0 option (after all, we are talking about folding proteins). Alexcalamaro (talk) 19:24, 15 December 2020 (UTC)
Thanks much Template:U. Passing the baton to Template:U. Over to you now for next steps :) Thanks everyone. I want to specially thank Template:Ping who have done and continue to do lots of good work on the article. Genuinely thank you folks. Ktin (talk) 19:27, 15 December 2020 (UTC)

Symbol question.svg I think all these versions of hooks, including ALT3 and ALT4 misinform a reader. No, the "50-year-old grand challenge of biology" has not been solved. There will be many future CASP meetings to assess further progress in this direction. Just saying that it "predicts the shape of proteins to within a width of an atom" is also wrong. No, it does not. AlphaFold-2 makes sufficiently precise predictions only for 2/3 of proteins, according to CASP assessors. But even in these good cases it does NOT predict protein structure with such precision for all atoms, as a reader would assume. Actually, such claim is simply ridiculous because there is protein dynamics and there is no such thing as width of an atom. There are only atomic radii, but but this is not a single number; they are very different for different types of atoms. Also, this is not "shape", but a three-dimensional structure. The referencing is to a misleading opinion piece. Author does make a claim that AlphaFold can predict the shape of proteins to within the width of an atom, but he apparently does not have a slightest idea what he is talking about. Let's not multiply the misinformation in Wikipedia. Please see the hook I suggested above (it can be shortened if needed). My very best wishes (talk) 19:51, 15 December 2020 (UTC)

  • All, very good points Template:U, but, this gets very close to WP:OR unless substantiated with a clear note from WP:RS. For now, the statements are sourced perfectly from WP:RS, and I think they meet the layperson's needs on the homepage. My suggestion is let's move forward with ALT3 as discussed above. Ktin (talk) 20:12, 15 December 2020 (UTC)
  • Yes, there are indeed WP:News sources about it (some of which claim nonsense like predicting "the shape of proteins to within the width of an atom"). However, this is an extraordinary and exceptional claim about solving a fundamental scientific problem, and not everyone agree (some similar WP:News type sources claim the opposite). I think we do need some WP:MEDRS quality sources here, such as serious independent scientific reviews. There is none. The method (AlfaFold-2) has not been published. The official assessment on CASP has not been published in any peer reviewed journal.
For example, as this article tells, "DeepMind’s press release trumpeted “a solution to a 50-year-old grand challenge in biology” based on its breakthrough performance on a biennial competition dubbed the Critical Assessment of Protein Structure Prediction (CASP). But the company drew criticism from academics because it made its claim without publishing its results in a peer-reviewed paper. ... “Frankly the hype serves no one,” and so on. I just do not think we should multiply this "hype" in WP. My very best wishes (talk) 20:29, 15 December 2020 (UTC)
  • Template:Ping in a literal sense the protein folding problem is not "solved," since we can obviously always move the goalposts regarding the necessary precision (≥90% accuracy? ≥99%? ≥99.99%?). The jump in precision at this year's CASP certainly deserves to be called a "breakthrough." I agree that the catchy "width of an atom" is not a precisely determined length (just as the even more popular "width of a human hair" is not); the press release said less than two angstrom, which we could use, too. --bender235 (talk) 21:31, 15 December 2020 (UTC)
  • In the spirit of serving our homepage readers, I will still recommend that we go with either of ALT3 or ALT4. Sufficient backing form WP:RS to move ahead. Ktin (talk) 00:00, 16 December 2020 (UTC)
  • Maybe we could change the "problematic" word solve by crack (also used in the MIT review), so we keep the catchy hook for the "layperson", without multiplying the "hype". What do you think of this one ? :
ALT 3.1.... that DeepMind's protein-folding AI AlphaFold 2 has cracked a 50-year-old grand challenge of biology? (source: MIT Technology Review).

Alexcalamaro (talk) 04:06, 16 December 2020 (UTC)

Template:Ping I am good with this hook (i.e. ALT 3.1). Ktin (talk) 06:30, 16 December 2020 (UTC)