3
$\begingroup$

Context

This relates to a post including the compound FADH2, in a sentence within the main text (technically ‘in-line’), set as I have here, using HTML ‘sub’ markup to render the subscript, and thus in the same default sans-serif typeface as the rest of the text. I noticed that someone had edited this using LaTeX so that it was rendered in a larger size, in italic (since removed), and in a serif face (i.e. visually different from the rest of the text): $\ce{FADH2}$. I felt that this was not only unnecessary, but inferior to the original, and so reverted it, commenting on the fact that I had done so and the reason why. The person who had made the edit replied with the statement:

“LaTeX has been the preferred mode for both Mathematical as well as Chemical equations/formulae on SE; and its italic by default.”

The purpose of this post is both to question this assertion and suggest recommendations for users wishing to sub- super-script in chemical formulae.

Proposal

  1. Ideally SE would be asked to provide an edit option to set subscript and superscript within text, as for word processors rendering it through the HTML sub and sup tags. However the version of Markdown used by SE does not support this, and I imagine the request has been made before. Hence it seems unlikely that they will agree.

  2. Thus, in the absence of support in Markdown I propose the following guidelines for SE Biology users.
    (i) For in-text chemical formulae either HTML tags or LaTeX may be used.
    (ii) HTML tags are preferred as they do not change the typeface, producing the most standard apparance. [An explanation of the two tags would follow].
    (iii) For chemical equations LaTeX is appropriate, although graphics of equations obtained using GUI-based methods are also acceptable.

Technique for achieving subscripts and superscripts: Current Policy

Contrary to what I have quoted above, the reference to LaTeX in the SE Biology Advanced Editing Help is:

LaTeX
Biology Stack Exchange uses MathJax to render LaTeX. You can use single dollar signs to delimit inline equations, and double dollars for blocks

That’s it. Nothing about being the preferred mode for anything, and reference solely to equations.

As far as HTML goes:

Inline HTML
If you need to do something that Markdown can't handle, use HTML.

Note the reference to Inline HTML.

Desired appearance of in-line chemical formulae: Policy of Chemical publications

Clearly, if SE allows you to achieve an effect by two alternative methods, the key to which is preferable is the effect they produce. That is what is important to the reader.

The arbiter of this is surely printed publications — both books and journals — in the area of chemistry and biological chemistry, and their on-line versions

The universal agreement for in-line chemical formulae (not equations) is to render them in the same typeface as the rest of the text. Examples shown below are from The Journal of the American Chemical Society and the text book Biochemistry, by Berg et al.. (The text here is in a serif face, as is normal in printed publications. The point is it is in exactly the same style as the rest of the text.)

JACS example of chemical formulae face

Berg et al. example of chemical formulae face

And the reason publications follow this convention is easy to see. If you set something in the text in a different face or weight or style you are drawing attention to it. Drosophila melanogaster is in italics because it is Latin species name. In other cases italics or bold are used for emphasis or perhaps to indicate something is a specific technical name rather than its normal English meaning. Although it is not customary to set chemical equations in a different typeface, one might justify that by saying that it helps them stand out from the surrounding text, like an illustration.

Can LaTeX be tamed?

I notice since my comment that the answer to the question using LaTeX for chemical names has had the italics removed. I do not use LaTeX myself, so I do not know if it is also possible to have the compounds rendered in the default face. I somehow doubt it, because that presumably goes against the mathematical conventions that LaTeX was designed to follow. However if it is possible, perhaps it can be explained to users.

Otherwise, anyone who can follow the arcane markup of LaTeX (dollar, backslash, ce, curly bracket, text, close bracket, dollar) can surely manage sub and sup HTML tags. One suspects that it is ‘religious’ thing. If so, I doubt whether it will find many converts among contemporary biologists.

$\endgroup$
  • 1
    $\begingroup$ I agree HTML super- and subscripts are better than latex for most cases. Some drawbacks for proposal 2.iii: images are not searchable and they increase page loading time (though perhaps negligibly). $\endgroup$ – canadianer May 16 '18 at 17:41
  • $\begingroup$ @canadianer — You found me out. As a web designer I am acutely aware of web accessibility problems and gritted my teeth as I made this suggestion. The problem is that SE support for advanced HTML is limited, and few biologists use LaTeX. My generation threw away our BBC micros when the Mac came in. MathType (bought later by Microsoft) made setting equations in documents a dream. Certainly the younger generation of biologists would think you mad if you asked them to learn LaTeX. And I'm not sure it would help. Unless LaTeX converts to MathML and that is supported in users' browsers... $\endgroup$ – David May 16 '18 at 18:08
  • $\begingroup$ @canadianer — It strikes me that your point about images in posts needs to be the subject of a separate question, because it is really a general one. Questions or answers (especially my own) that have diagrams of metabolic pathways pose accessibility problems. When I have a moment I'll post another question, perhaps on the pan-Meta, because you even get questions or answers on English Language & Usage that are scans of dictionary entries. $\endgroup$ – David May 22 '18 at 12:42
1
$\begingroup$

I agree, and dont think that LaTeX-use should be "mandatory". I like and often use LaTeX for equation, but one additional problem, besides the formatting you mentioned, is that it is often rendered incorrectly on mobile devices . For instance, in the answer to the Q you link to I see this (Xperia/Chrome):

enter image description here

$\endgroup$
  • $\begingroup$ In chrome it is rendered correctly. I think the page is not fully loaded in your case. $\endgroup$ – user237650 May 13 '18 at 7:46
  • 1
    $\begingroup$ @Mesentery No, that is not it. The page is fully loaded, and I've encountered the same issue several times with LaTeX at Bio-SE on my mobile. Maybe it differs between version/devices. $\endgroup$ – fileunderwater May 13 '18 at 18:12
  • $\begingroup$ The rendering of an NCBI Bookshelf page on a particular mobile phone and browser is a problem of its own. I gave the link so everyone can see it, but could have posted a screen shot of the book. The more general question here is what sort of support SE has for mobile devices and for sophisticated modern HTML. $\endgroup$ – David May 16 '18 at 18:02

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .