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I made the mistake of trying to author a scientific paper in org-mode. Big mistake. I should have just stuck with LaTeX, because what ended up happening is that

I made the mistake of trying to author a scientific paper in org-mode. Big mistake. I should have just stuck with LaTeX, because what ended up happening is that all my problems and difficulties had to do with me navigating org-mode wrappers around LaTeX, when I could just have dealt with LaTeX directly. I'm sure there will be plenty of people to tell me that I'm wrong.

danShumway 6y ago
I don't think Org-mode's export features are particularly great. I'm finding that when I do want to export something, it's sometimes easier to grab a parser in a language where I'm more comfortable rather than trying to mess around with Lisp and templates. I'm sure if I was better at Lisp my opinion would be different. But if I was writing something and wanted to target LaTeX or pure HTML, I'm not sure I would use Org-mode as the source unless I was writing the converter myself. I think I'd just write in HTML/LaTeX directly. That being said, I would probably still stick all of my notes, references, and TODOs for a scientific paper in Org-mode, and then use LaTeX just for the final paper. The fact that Org-mode can do text references like * TODO Find facts about bees Need more details at file:~/final.tex::And another thing about bees References checklist: - [ ] https://google.com - [X] https://duckduckgo.com - [ ] https://wikipedia.com means that Org-mode ends up being more useful for me as a surrounding 'notebook' around my projects rather than as the core format I'm authoring everything in.
sqrt17 6y ago
What pain points would it have saved to write the scientific paper in org-mode? Usually there's a dozen dirty little corners where you want fine-grained control and the org-mode-to-latex converter isn't giving you that by default. I once wrote a short report that I (probably) could also have written in (any equivalent of) Word or LyX/TeXmacs, or some random WISYWIG editor. Very little finetuning of the layout required or necessary, people still liked it better than plaintext (it had some headlines and tables and stuff, but nothing too fancy). So, nice output yes but be careful if what you need is actual LaTeX document preparation.
- na85 6y ago
  >What pain points would it have saved to write the scientific paper in org-mode? For me, latex is the pain point. I don't want to have to read through pages of inscrutable error messages about overfull mboxes and then read dozens of contradictory stack overflow answers for outdated versions that only half-address the problem I'm having.
why-el 6y ago
I think you are correct. I do everything personal in org-mode, but I switch to manual if the doc ends up being shared. Heck, I even elect to use google doc if I have at least one collaborator.
- eigenhombre 6y ago
  This for me is the biggest pain-point about Org Mode -- most of my colleagues won't touch it, so it's off to Google Docs we go....
dan-robertson 6y ago
I think that’s probably reasonable. Fortunately, AUCTEX mode works well for latex so the main loss is org’s document structure management and maybe syntax. I don’t know if there’s a way to get that in AUCTEX
eigenhombre 6y ago
I've written a few hundred Org mode docs, and a doctoral thesis in LaTeX. I would not write a complex technical paper in Org Mode, other than just to get my thoughts together initially to eventually copy/paste into LaTeX. But, Org Mode is good enough for most of my writing over the last several years. It is more readable as plain text, and exports to HTML or PDF trivially (the latter via the LaTeX export hook). I like it enough that I use it as the basis of my blog, exporting each article to HTML and then massaging the HTML programmatically to generate static files styled and cross-linked the way I want. This approach gives me math formulas via MathJax, still images, tables, code snippets... basically everything I want for a somewhat tech-y blog. But, yeah, if you're going to just write a full-on technical paper for publication, I'd go right to LaTeX.
- _emacsomancer_ 6y ago
  I agree with this. I often write up notes in Org mode, but, after trying for a while to have all of my 'sources' in Org, I also came to the conclusion that for actual papers, it's far better just to write them directly in LaTeX (other than initial notes).
alxlaz 6y ago
IMHO (15+ years of Emacs and counting) you are not wrong. First, Emacs already has excellent LaTeX support. Unless org-mode brings you any major advantage over plain LaTeX (which I doubt it is when you're writing a paper, that's not exactly 400 pages of loosely-coupled ideas) the extra headaches of dealing with one more intermediary language and set of packages isn't useful. If hacking on org-mode is your hobby, then yes, it's an enjoyable experience. But if you're just using it, then it's one of those cases where knowing you can is not enough, and you should maybe stop for a second and think if you should. Second, I don't think anyone ever intended for org-mode to be used (as a wrapper) for authoring scientific papers. It's great that you can export your notes to LaTeX because it allows you to easily integrate them with existing manuscripts, it allows you have formulae embedded in them and so on. It just so happens that it's so good, and so flexible, that you can do it -- but there's no world in which a simple (no matter how flexible!) export engine for/wrapper around a language will ever be able to deal with complex matters that even said language can barely deal with. It's one thing to use it for authoring simple documents (like blog posts), that works great. But when it takes hours of fiddling just to get the editor-supplied template to play nice with your text and figures, the last thing you need is one more moving piece.
bachmeier 6y ago
I'd never author a paper directly in latex. That would suck. I'd author in Pandoc markdown, convert to latex, and then add tables and whatever using latex around it. It's pretty painful IMO to write documents in latex vs markdown.
- ArneBab 6y ago
  In that case you have a perfect example of starting with org-mode instead: Then you can already add tables and images and all the stuff and have much less finetuning to do: - create draft in org - export to LaTeX - polish for publication
Myrmornis 6y ago
Plug: I've been working on a new LaTeX-editing minor mode to use in conjunction with auctex: https://github.com/dandavison/xenops https://github.com/dandavison/xenops It's basically a replacement for preview-latex: it renders math/TikZ/table fragments automatically and asynchronously. If any emacs-lisp programmers who are interested in LaTeX editing would like to help out please get in touch!
ArneBab 6y ago
I authored my PhD in org-mode, where the planning and re-structuring provided huge benefits. But for the shorter paper I just used LaTeX.
kindahero 6y ago
Oh I know the pain, I did the same back in 2015. That was my first scientific paper ever. Then "never again" said to myself. Now I use pure latex. org-mode is only good for quick exports should not think it as an alternative to latex.

danShumway 6y ago

I don't think Org-mode's export features are particularly great. I'm finding that when I do want to export something, it's sometimes easier to grab a parser in a language where I'm more comfortable rather than trying to mess around with Lisp and templates. I'm sure if I was better at Lisp my opinion would be different. But if I was writing something and wanted to target LaTeX or pure HTML, I'm not sure I would use Org-mode as the source unless I was writing the converter myself. I think I'd just write in HTML/LaTeX directly. That being said, I would probably still stick all of my notes, references, and TODOs for a scientific paper in Org-mode, and then use LaTeX just for the final paper. The fact that Org-mode can do text references like * TODO Find facts about bees Need more details at file:~/final.tex::And another thing about bees References checklist: - [ ] https://google.com - [X] https://duckduckgo.com - [ ] https://wikipedia.com means that Org-mode ends up being more useful for me as a surrounding 'notebook' around my projects rather than as the core format I'm authoring everything in.

sqrt17 6y ago

What pain points would it have saved to write the scientific paper in org-mode? Usually there's a dozen dirty little corners where you want fine-grained control and the org-mode-to-latex converter isn't giving you that by default. I once wrote a short report that I (probably) could also have written in (any equivalent of) Word or LyX/TeXmacs, or some random WISYWIG editor. Very little finetuning of the layout required or necessary, people still liked it better than plaintext (it had some headlines and tables and stuff, but nothing too fancy). So, nice output yes but be careful if what you need is actual LaTeX document preparation.

na85 6y ago
>What pain points would it have saved to write the scientific paper in org-mode? For me, latex is the pain point. I don't want to have to read through pages of inscrutable error messages about overfull mboxes and then read dozens of contradictory stack overflow answers for outdated versions that only half-address the problem I'm having.

why-el 6y ago

I think you are correct. I do everything personal in org-mode, but I switch to manual if the doc ends up being shared. Heck, I even elect to use google doc if I have at least one collaborator.

eigenhombre 6y ago
This for me is the biggest pain-point about Org Mode -- most of my colleagues won't touch it, so it's off to Google Docs we go....

dan-robertson 6y ago

I think that’s probably reasonable. Fortunately, AUCTEX mode works well for latex so the main loss is org’s document structure management and maybe syntax. I don’t know if there’s a way to get that in AUCTEX

eigenhombre 6y ago

I've written a few hundred Org mode docs, and a doctoral thesis in LaTeX. I would not write a complex technical paper in Org Mode, other than just to get my thoughts together initially to eventually copy/paste into LaTeX. But, Org Mode is good enough for most of my writing over the last several years. It is more readable as plain text, and exports to HTML or PDF trivially (the latter via the LaTeX export hook). I like it enough that I use it as the basis of my blog, exporting each article to HTML and then massaging the HTML programmatically to generate static files styled and cross-linked the way I want. This approach gives me math formulas via MathJax, still images, tables, code snippets... basically everything I want for a somewhat tech-y blog. But, yeah, if you're going to just write a full-on technical paper for publication, I'd go right to LaTeX.

_emacsomancer_ 6y ago
I agree with this. I often write up notes in Org mode, but, after trying for a while to have all of my 'sources' in Org, I also came to the conclusion that for actual papers, it's far better just to write them directly in LaTeX (other than initial notes).

alxlaz 6y ago

IMHO (15+ years of Emacs and counting) you are not wrong. First, Emacs already has excellent LaTeX support. Unless org-mode brings you any major advantage over plain LaTeX (which I doubt it is when you're writing a paper, that's not exactly 400 pages of loosely-coupled ideas) the extra headaches of dealing with one more intermediary language and set of packages isn't useful. If hacking on org-mode is your hobby, then yes, it's an enjoyable experience. But if you're just using it, then it's one of those cases where knowing you can is not enough, and you should maybe stop for a second and think if you should. Second, I don't think anyone ever intended for org-mode to be used (as a wrapper) for authoring scientific papers. It's great that you can export your notes to LaTeX because it allows you to easily integrate them with existing manuscripts, it allows you have formulae embedded in them and so on. It just so happens that it's so good, and so flexible, that you can do it -- but there's no world in which a simple (no matter how flexible!) export engine for/wrapper around a language will ever be able to deal with complex matters that even said language can barely deal with. It's one thing to use it for authoring simple documents (like blog posts), that works great. But when it takes hours of fiddling just to get the editor-supplied template to play nice with your text and figures, the last thing you need is one more moving piece.

bachmeier 6y ago

I'd never author a paper directly in latex. That would suck. I'd author in Pandoc markdown, convert to latex, and then add tables and whatever using latex around it. It's pretty painful IMO to write documents in latex vs markdown.

ArneBab 6y ago
In that case you have a perfect example of starting with org-mode instead: Then you can already add tables and images and all the stuff and have much less finetuning to do: - create draft in org - export to LaTeX - polish for publication

Myrmornis 6y ago

Plug: I've been working on a new LaTeX-editing minor mode to use in conjunction with auctex: https://github.com/dandavison/xenops https://github.com/dandavison/xenops It's basically a replacement for preview-latex: it renders math/TikZ/table fragments automatically and asynchronously. If any emacs-lisp programmers who are interested in LaTeX editing would like to help out please get in touch!

ArneBab 6y ago

I authored my PhD in org-mode, where the planning and re-structuring provided huge benefits. But for the shorter paper I just used LaTeX.

kindahero 6y ago

Oh I know the pain, I did the same back in 2015. That was my first scientific paper ever. Then "never again" said to myself. Now I use pure latex. org-mode is only good for quick exports should not think it as an alternative to latex.