Talk:Amino acid/GA3

GA Reassessment

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KEPT--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 17:27, 27 August 2009 (UTC)[reply]

Notified: Wikipedia talk:WikiProject Molecular and Cellular Biology, Wikipedia talk:WikiProject Medicine, TimVickers (talk · contribs), DMacks (talk · contribs), Narayanese (talk · contribs), Edgar181 (talk · contribs)--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 21:56, 18 August 2009 (UTC)[reply]

I am reviewing this article as part of GA Sweeps. In order for this article to retain its WP:GA rating, there are several issues that will need to be addressed. The following is a list of my initial concerns:

~~This article needs WP:ALT text according to the alt text checker.~~

I can't see any way of describing molecular images like these in words. I've had a go with the lead image, but this seems a pretty useless exercise. Tim Vickers (talk) 22:20, 18 August 2009 (UTC)[reply]

So basically, your response is "Too hell with all blind people", if I am understanding you correctly.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 00:00, 19 August 2009 (UTC)[reply]

No, you misunderstand me completely. It might be useful to tell you that I'm partially sighted myself. You would be very welcome to improve the alt text of the lead image or produce a better summary of this figure, but I'm not sure if describing molecular structures in this way is actually useful to a blind reader. Tim Vickers (talk) 04:16, 19 August 2009 (UTC)[reply]

Agreed - surely the description can't really add all that much information to the article...and if it does, shouldn't that info be in the article? I would argue otherwise if they were anything but diagrams. Master gopher (talk) 07:12, 19 August 2009 (UTC)[reply]

Currently, the only place where WP:ALT is required to my knowledge is at WP:FAC. I apologize if attempting to raise the image quality of this article toward the level of featured articles is something undesirable to the editors of this page. I have completed 32 GA Sweeps reviews and have for the last ten or so been requesting WP:ALT. No group of editors that was interested in keeping a GA rating has said that they do not want to attempt to raise the quality of their article in this way before. As an example, I will say what a reasonable alt text would be for the main image: This is a molecular diagram of atoms represented by circles and bonds represented straight lines. This diagram has a purple circle with an "N" in the middle on the left with two light blue "H" circles stemming from it. It is linked on the right to a grey "C" circle with a light blue "H" circle above and and a white with black border "R" square below. To the right of this is another grey "C" circle with a double line link to a red "O" circle below and a single line link red "O" circle above that has its own light blue "H" circle linked even further above it.

I have not studied chemistry in 25 years, but that would help me if I had gone blind in those last 25 years. Is this something that is beyond this group of editors.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 13:37, 19 August 2009 (UTC)[reply]

The two optical isomers of alanine, D-Alanine and L-Alanine

We are just unconvinced that that your description above would add anything useful to the article. For another example, what description could you produce of the optical isomerism image to the left? The fact that these are mirror images of each other belongs in the text, not an image caption. You can add this some kind of sphere-by-sphere description to this if you wish, but really I don't think it will increase anybody's understanding of the topic.. Tim Vickers (talk) 14:18, 19 August 2009 (UTC)[reply]

I think you are misunderstanding WP:ALT. This is what a blind person sees instead of the image. Right now he can only read an image caption but can not envision the image. "This is a molecular diagram of atoms represented by circles and bonds represented straight lines. This diagram has a purple circle with an "N" in the middle on the left with two light blue "H" circles stemming from it. It is linked on the right to a grey "C" circle with a light blue "H" circle above and and a white with black border "R" square below. To the right of this is another grey "C" circle with a double line link to a red "O" circle below and a single line link red "O" circle above that has its own light blue "H" circle linked even further above it." is more helpful to a blind person than nothing. As for your example image it would help a blind person to read "This is a dynamic image with two mirror image molecules depicted by grey, red, white, and blue spheres rotating around a central axis." That is the last one I am going to do and I am not going to pass this article if you continue to attempt to ignore the needs of the blind.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 14:25, 19 August 2009 (UTC)[reply]

The issue of alt-text was raised in Wikipedia talk:Good article criteria just last month, where there was clearly no consensus to have that be part of GA standards (and it's not mentioned in the explicit list of image issues on WP:GACR).. Please don't hold a GA nom to standards other than those of GA or conflate it with other quality issues (such as FA). GA-status isn't the end of editing or improvement, it's just a "this meets WP:GACR" stamp--please raise other issues in a section other than the GA review. DMacks (talk) 14:52, 19 August 2009 (UTC)[reply]

I have never met a group of editors who said that it is too troublesome for me to add stuff like "This is a dynamic image with two mirror image molecules depicted by grey, red, white, and blue spheres rotating around a central axis." to my images and that there is even debate that gives me an out not to help the blind people understand the article's images. I would prefer not to pass an article that refuses to make such simple changes, but yes if you want to "hide" behind the GA talk page debate, I probably would be overruled for delisting solely on that basis. There is just no reason not to add stuff like this for the blind.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 15:55, 19 August 2009 (UTC)[reply]

Exactly. It's an important accessibility issue that should be raised and addressed outside the scope of GAR. DMacks (talk) 16:12, 19 August 2009 (UTC)[reply]

Perhaps it would solve the problem if, instead of just describing the images as collections of spheres and lines of various colors (which is totally uninformative) we instead use the alt text to describe the important point that the reader would take from the image if they could examine it? I've had a go at this approach in the section on "Occurrence and functions in biochemistry". Tim Vickers (talk) 17:16, 19 August 2009 (UTC)[reply]

I want to be clear that I don't think we shouldn't have alt-text in this article; I'm just not sure how to make it helpful to the blind. Perhaps it would be more useful to describe the structure of the molecule depicted rather than describing the diagram itself? E.g. for the very first image: "This image depicts the typical structure of an amino acid, consisting of a central carbon atom with four bonds: one to the functional group, one to a hydrogen atom, one to the amino group and one to the carboxyl group". This might be better as it focuses on the information in the image, whereas saying that (for example) 'the amino group is on the left' doesn't really give useful information, it just says how that particular diagram was drawn. Thoughts? Master gopher (talk) 10:03, 20 August 2009 (UTC)[reply]

That's very true. A blind reader has no use or need for information about colors, orientation or if something is rotating or not - that kind of information is irrelevant. As you say alt text might be useful if it says what the diagram is meant to illustrate, rather than describing an image line by line, sphere by sphere. Tim Vickers (talk) 15:41, 20 August 2009 (UTC)[reply]

I agree with Master gopher and Tim Vickers: the point is to convey to the visually impaired reader the gist of the image: what a sighted reader takes away from that image, info that is not already conveyed by the caption or by adjacent text. For Image:AminoAcidball.svg the current alt text is pretty good, but I have two suggestions to improve it. First, the phrase "This image depicts the typical structure of an amino acid, consisting of" repeats the caption and should be removed. Second, the current alt text assumes that the reader knows the formula for an amino group and for a carboxyl group, which is typically not the case, and it would be helpful to describe that in the alt text (since it's obvious from the image), at least as something like "NH2" and "COOH". Similar comments apply to most of the other alt text: briefly describe what info the visual appearance of the image gives to the reader, omitting info that's already in caption or adjacent text. For Image:D+L-Alanine.gif the current alt text is OK, but I would mention that an invisible mirror plane separates the two molecules, and that the axis of revolution is within this plane. It might not hurt to add that the two molecules are nearly touching. Eubulides (talk) 08:01, 21 August 2009 (UTC)[reply]

I've added explanatory alt text, rather than descriptive alt text, to all the images. Tim Vickers (talk) 16:40, 21 August 2009 (UTC)[reply]

It seesm one image has been neglected (the polypeptide bond). See the alt text checker mentioned above.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 05:51, 24 August 2009 (UTC)[reply]

That link isn't working (toolserver down again?). Which image do you mean? Tim Vickers (talk) 17:04, 24 August 2009 (UTC)[reply]

File:Protein-primary-structure.png .--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 19:07, 24 August 2009 (UTC)[reply]

Diff, alt text was there, but the alt tag wasn't. Tim Vickers (talk) 19:24, 24 August 2009 (UTC)[reply]

Made a slight change to this one, I think it is clearer; Diff Master gopher (talk) 02:52, 25 August 2009 (UTC)[reply]

~~Please address the dablinks~~

The self-link is in a template common to multiple articles. Tim Vickers (talk) 22:20, 18 August 2009 (UTC)[reply]

~~The article has three suspicious links~~

I've replaced one, removed one and the third works fine for me. Tim Vickers (talk) 22:20, 18 August 2009 (UTC)[reply]

~~Please check WP:CAPTION#Wording as it relates to use of periods.~~

Added a few full stops.

Please reread.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 00:03, 19 August 2009 (UTC)[reply]

Addressed. Dabomb87 (talk) 00:28, 19 August 2009 (UTC)[reply]

The images all seem to be PD and the citation is very thorough.
The following verbiage needs copyediting:

~~"Some other amino acids found early were cystine in 1810[5], its monomer, cysteine, was only discovered in 1884,[6][4] and glycine and leucine in 1820.[7]" is runon it seems.~~

Reworded.

This is still runon as "Some other amino acids found early were cystine in 1810[5], its monomer, cysteine, was only discovered in 1884."

I would rearrange as Some other amino acids found early were cystine in 1810[5] as well as Glycine and leucine in 1820.[7] Cystine's monomer, cysteine, was only discovered in 1884.[6][4]--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 13:52, 19 August 2009 (UTC)[reply]

Reworded more, cysteine and cystine do need to be together though.

~~"as in lysine on the right," would probably be more grammatical as "such as lysine, which is shown to the right" or "such as lysine (see image to the right)"~~

Reworded.

I don't like "as in". How about "such as" and then add a comma after the parenthesis.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 13:52, 19 August 2009 (UTC)[reply]

Having a comma and a parenthesis seems a bit redundant, but you're right that "such as" is probably better.

~~I believe "and hydrophobe if they are nonpolar." should be "or hydrophobe if they are nonpolar." unless it behaves as several of these at the same time.~~

Reworded.

~~Rephrase "are catalogued in the article, proteinogenic amino acid." to WP:ASR. Find a way to link the term more naturally.~~

Reworded.

"but this is not correct in the current nomenclature.[10]" Explain why.

Reworded.

Here is what I am looking for "Proline has sometimes been termed an imino acid because of its XX property, but is classed as an amino acid in the current nomenclature since it is simply a YY-type structure.[10]"--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 13:52, 19 August 2009 (UTC)[reply]

You can call it either, I've modified the text to explain why you can call it an imino acid, but I don't know why this isn't followed by IUBMB numenclature (historical reasons I suspect). The Oxford Dictionary of Biochemistry and Molecular Biology refers to it as an "N-alkylated alpha-amino acid", which comes partway between the two!

I would try to be more NPOV on this issue. I would name sources that call it Imino, sources that call it amino and this middle of the road source should be added to educate the reader as to the possible points of confusion.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 01:17, 20 August 2009 (UTC)[reply]

I've added a source for "imino" and the third alternative name, but going into this in more detail is difficult as I can't find any sources that actually discuss the various options - people just choose one of the other and don't explain themselves. I could synthesise this literature and discuss this myself, but that would be inserting my own opinions. Tim Vickers (talk) 17:21, 20 August 2009 (UTC)[reply]

I will add further prose comments in time.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 03:15, 19 August 2009 (UTC)[reply]

"the number of protonated ammonium groups with a positive charge and deprotonated carboxylate groups with a negative charge are equal" seems ungrammatical. If I am correct this should be "the number of protonated ammonium groups with positive charges and deprotonated carboxylate groups with negative charges are equal"

Reworded.

~~I would explain that unbranched means that of the four bonds to the carbon atom no more than two of them are to other carbon atoms.~~

Reworded.

~~What is a "stop codon"?~~

Linked.

The "In human nutrition" needs expansion. I am a former competitive weightlifter and credit any success I had to lysine, arginine and ornithine. Younger weightlifters now use creatine, which sounds like an amino acid and has become quite controversial. I feel a WP:GA on this topic should explain how particular aminos are important in muscular development. I should be able to come to this article and find something out about that topic.

See the daughter article protein in nutrition. Unfortunately creatine is not an amino acid, so we can't discuss it in this article. Tim Vickers (talk) 14:37, 19 August 2009 (UTC)[reply]

~~Where are the H and A essentials for the PVT TIM HALL thingy?~~

"Essential" is a slippery idea, as the rest of the text in this section explains, so I don't think any mnemonic can be accurate. I've cut this entirely.

~~At one point you use the term building units and another building blocks. I recall the latter being familiar. I think the article should be consistent.~~

Reworded.

~~"either forming part of their main chains, or bonded as side chains" does not seem to need a comma to me.~~

Reworded.

I will finish this later.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 14:18, 19 August 2009 (UTC)[reply]

~~Again "and are discussed in the articles dealing with each specific type of amino acid" should be restated to avoid WP:ASR.~~

Reworded.

~~"while integral membrane proteins tend to have outer ring of hydrophobic amino acids that anchors them into the lipid bilayer," is currently ungrammatical in its person agreement.~~

Reworded.

I have edited this.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 07:41, 27 August 2009 (UTC)[reply]

The copyedit is done.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 01:34, 20 August 2009 (UTC)[reply]

The article is in pretty good shape. I will monitor progress on addressing my concerns and evaluate the article after a week.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 21:50, 18 August 2009 (UTC)[reply]