9 ms·

Cost of ‘reformatting’ prompts a call for journals to change their requirements

145 points by headalgorithm 3y ago

JonChesterfield 3y ago
> For scientists submitting their papers to journals, there’s an all-too-familiar drill: spend hours formatting the paper to meet the journal’s guidelines; if the paper is rejected, sink more time into reformatting it for another journal; repeat. What? The journal provides (or at least should) a latex template, you write stuff in that, then you ship it. Last one I wrote in a browser through overleaf, spent zero time on formatting. edit: Nature's one appears to be https://www.overleaf.com/latex/templates/springer-nature-latex-template/myxmhdsbzkyd https://www.overleaf.com/latex/templates/springer-nature-lat...
- ftxbro 3y ago
  > "What? The journal provides (or at least should) a latex template, you write stuff in that" Millions of dollars in time wasted on learning other markup language
  - JonChesterfield 3y ago
    I definitely don't know how to write latex, can muddle through anyway. Total loss to trial and error / searching bits of syntax is probably below an hour so far this lifetime.
- light_hue_1 3y ago
  > What? The journal provides (or at least should) a latex template, you write stuff in that, then you ship it. Last one I wrote in a browser through overleaf, spent zero time on formatting. Then you don't have much experience writing papers. Formatting is very time consuming. Some want 8 pages, some are unlimited, others want you to use whatever makes sense. Every journal has a different page length. They expect to see results in different places. Some want a detailed appendix. Others are ok with a website. The latex template doesn't help at all with any of these. Reformatting is extremely painful and wasteful.
  - JonChesterfield 3y ago
    Three in the real world, some number in undergrad. Writing papers takes a fair amount of time - think how to express things, producing graphs and so forth - but reordering sections or adding things to a bibliography is yet to cause much grief. Maybe we mean different things by formatting.
  - IshKebab 3y ago
    The worst thing is references. They all have their own weird formats.
    - pbhjpbhj 3y ago
      Why isn't that handled by semantic markup? That said, recognising static academic reference format, then reformatting for the other 4 or 5 standard formats seems like a python project for first year students (to this non-programmer, I'd guess there are lots of edge cases to trip on making it a great learning experience!)?
      - cge 3y ago
        It often isn't so much the actual bibliography line item format, which are usually handled quite well be systems like bibtex or biblatex+biber, but overall citation formatting complexities. Sometimes journals want specific formats that become a challenge to implement. For example, on a recent submission, we needed our main text to have a numbered bibliography at the end, then needed our methods to have numbered bibliography at the end, but with numbers starting after the last number in the main text, and no repeats, but with references in the methods to items already in the main text bibliography referring to those numbers. This was surprisingly difficult to implement reliably in LaTeX and Biblatex. An additional annoyance is that to save space, journals often want formats that are compact but inefficient to use, for example, formats that are heavily abbreviated and don't include titles. These, however, are annoying to use, and annoying reviewers is generally unwise. So in our case, we actually intentionally submit PDFs for review that use the 'wrong' bibliography item format, of a similar form to the journal's but less abbreviated and including titles and hyperlink backreferences to citations in the text. Then for final submission we have to replace this with the journal's preferred format.
- cge 3y ago
  Nature accepts LaTeX+PDF submissions, and will send the PDF out for review, but for final submission after acceptance, they prefer mostly-unformatted Word files; if you submit a LaTeX+PDF final submission, they convert it to Word [1]. As they stress that authors should not bother working on the visual formatting of their final submissions, my expectation is that, internally, they then take the Word file and manually put it into their own typesetting system. Publishers like Dagstuhl Publishing that can require LaTeX submissions and use a completely LaTeX publishing workflow probably have significant efficiency advantages, but then rely on potential authors being sufficiently experienced with LaTeX that a LaTeX submission requirement doesn't drive people away. This can work well for computer science and some parts of physics, but for other fields it can be a significant burden. [1]: https://www.nature.com/nature/for-authors/final-submission https://www.nature.com/nature/for-authors/final-submission
LanceH 3y ago
Billions wasted pursuing publication over meaningful effort.
- ftxbro 3y ago
  how will they know you're good if you don't have good metrics in Science and Nature
  - Lk7Of3vfJS2n 3y ago
    By creating something they couldn't.
- seydor 3y ago
  Ultimately pursuing grants
- somat 3y ago
  Publication is the results. The effort is meaningless if no one knows about it. https://gwern.net/maze https://gwern.net/maze Yes but what about all this unnecessary gatekeeping? gatekeeping is necessary to maintain a certain level of quality. On this specific issue of formatting gatekeeping. There was no conspiracy. I imagine that the policy solidified over time. The paper wants to maintain a specific look. Authors are upset when changes get introduced while formatting. The paper then says "you can format it yourself if it meets our specification". Now you have to format it yourself. Thankfully in our web enabled era there a ways to publish without going through a traditional publisher. However you will note that the quality of these publishers is a mixed bag, real science right next to quackery. No one has done the gatekeeping needed to separate the wheat from the chaff.
  - akira2501 3y ago
    > Publication is the results. > The paper wants to maintain a specific look. Which does the paper want more? To be the first with the results or to appear a particular way? Do the appearances help with "the results?"
gammarator 3y ago
There’s rich irony in this article appearing in Nature, which has some of the most unusual and restrictive formatting requirements. Also, journal publication fees dwarf the implicit cost of reformatting and deliver arguably less value.
mixedmath 3y ago
There are a couple of journals in math that ask for the paper to be submitted using their particular latex template, and a typical latex template is incompatible with what I consider "standard" latex, i.e. either the `amsart` document class or `article` document class with certain AMS packages included. Sometimes it's small, like whether or not `\author{my name}` needs to be included in the preamble or in the main body. These are short but annoying. Sometimes it's very annoying. I'm glad that I've never tried to publish in a two-column journal (which might exist in math? I don't know) which would require more substantial superficial edits. I always assumed that this was a deliberate source of friction, slightly raising the bar of entry so as to discourage a certain sort of submission. I don't say I agree with this, but that's what I thought. This sounds like the sort of problem that latex would be great at solving: changing the look of an article just by using different document classes. And sometimes it is great --- but some templates are terrible, terrible, terrible. (And sometimes these terrible templates are for great journals! I see little to no correlation there).
- sh34r 3y ago
  > I always assumed that this was a deliberate source of friction, slightly raising the bar of entry so as to discourage a certain sort of submission. There’s no doubt in my mind that it’s intentional gatekeeping. There’s a reason why many papers are being “published” on Arxiv and foregoing all this boxticking. The whole publishing process is fundamentally broken. Aaron Swartz (RIP) had the right idea all along. Get rid of the middlemen sucking up millions of dollars by paywalling government funded research. It’s been proven time and time again that a shocking number of studies can’t be reproduced and that the traditional peer review process just isn’t working. It’s a good old boys’ club putting a stamp of approval on their friends’ work and keeping the outsiders away. When it comes to Math though, I do have some sympathies. There are so many cranks that think they solved Collatz or a millennium problem and don’t even know what they don’t know. It must be exhausting to sift through all that noise in a volunteer, unpaid position. These shibboleths might be a necessary evil.
  - cratermoon 3y ago
    > It’s a good old boys’ club putting a stamp of approval on their friends’ work and keeping the outsiders away. > Math though, I do have some sympathies. There are so many cranks Lots of other fields have their cranks, quacks, fringe theorists, and whackjobs. Why give math special treatment?
axg11 3y ago
Go one level deeper and you'll find the problem with all of academia (source: I have a PhD). Most of academic science as we know it today is structured so that the output is "publishable" and/or helps future grant applications. Incremental improvements are very publishable, but that doesn't necessarily make good science. Grants are awarded to scientists who are consistently able to deliver results, in the form of published papers. I can only really speak for my little corner of science, but from my view, the entire incentive structure of science is broken.
- kenjackson 3y ago
  Incremental publication seems like a great idea. The only problem is that the publication process is so formal. But if we made publications as "blogs" or something, I think incremental units of forward progress are a reasonable way to do science. I suspect most science is done this way. I imagine there are few Wiles style FLT proofs around.
  - PeterisP 3y ago
    As the parent poster states, the key thing is that everything is structured about incentives conditional on delivering measurable results e.g. the quantity of published papers; but that implicitly includes a very important thing that "published" counts only if (and because) it has passed certain filters. There are no barriers to publish research outcomes as "blogs" or something, it is easy, so such "publication" doesn't imply that any reasonable research was done, and no incentives would reward such publishing, and that's why researchers often don't bother with it. Like, the existing system already has issues with publication being too easy to game, with predatory paid journals, lax standards for reviewing, etc; that's hard to fix, but it's considered a problem - and so any changes making the barrier to publication even lower than that won't be welcome. And from the perspective of researchers, we don't really want more publications - they're a pain to read, there's an overabundance of poor content that's salami-sliced, we do so many publications because the incentives push us toward this but we recognize that this is a bad thing and we'd be far better off if the same research would be published in fewer, better articles. But we can't, because anyone who does that will be effectively denied resources for future research.
seydor 3y ago
Ironic that this comes from nature. Do you remember which subscripts must be italicized?
Solvency 3y ago
[flagged]
d--b 3y ago
> the authors of the analysis, which was published in BBC Medicine on 10 May, propose that journals should allow free-format submissions so researchers can spend their time and money on research instead. Yeah right. This is YC though. Up-for-grabs: Untapped $260m market for reformatting scientific papers.
bluenose69 3y ago
Perhaps this is true in the field discussed in the essay, but in my field (a natural science) formatting is taken care of with latex stylesheets, so the effort of switching to another journal format usually amounts to changing a few lines. Of course there can be small details such as whether a given journal wants keywords, but dealing with such things doesn't take much time. The problem of switching to another journal is also overplayed in the essay, at least in my field. I don't know of many people who "shop" for journals to accept their work. Usually you know the right journal, and if the paper is rejected you just give up on it. Perhaps this is discipline-specific, though. (The essay is restricted to biomedical fields.) As a reviewer, I've never spent any time on journal rules. If the paper gets accepted, it's up to the technical editor to impose rules. Most authors employ the proper latex stylesheets from the first rough draft. They also use section headings that fit the journal's conventions, and so forth. I suppose it is possible that people in biomedical fields (are there any here on HN?) tend to submit to multiple journals before their work is accepted. But I sort of doubt that reviewers reject papers based on things like italics or citation formatting, so if folks are submitting to a lot of journals, maybe their work just isn't highly regarded by their peers. Basically there is no issue here, at least in my field. It's an unconvincing essay, and not one that encouraged me to waste time looking up the original work.
- physPop 3y ago
  It’s a huge issue in most fields. No one uses latex anymore outside of niches like math and physics.
  - pbasista 3y ago
    > No one uses latex anymore That is a very broad statement. Do you have any data to back it up? Do you suggest that it was used in the past but that has changed? If so, why?
  - PartiallyTyped 3y ago
    Well, we should go back to that, or something that is easier.
lower 3y ago
I've spent so much time for pointless reformatting. With Springer LNCS it's often that you have to work really hard to cram everything into the page limit. Then Springer does some editing in the bibliography, and the article then often overflows by one or two bibliography entries and is published like that, making the effort of meeting the page limit a complete waste time
- sacrosancty 3y ago
  [dead]
golergka 3y ago
...do these academics not know how to use latex and waste their time in Microsoft Word?
- yawnxyz 3y ago
  very few people use latex in biology
pornel 3y ago
You're all assuming it's about making papers pretty or fit a template, but the major time sink is length limits. The abstract has to have a specific number of chars or words (which varies by journal), and it's a critical part of the paper, so you never want to waste a single word. There's also limit for the total number of pages or words, which again needs text rewrites. Sometimes format of references is weird, and needs conversion macros or manual edits. Reviewers always want more information, more references, more tables, so publishing is an endless puzzle to fit all of that within limit that is always too short to fit everything you have to say. Having concise paper is of course great, but submitting to multiple places requires editing multiple variations, and that is busywork.
- gww 3y ago
  The length limits also forces authors to increase the complexity of their figures to cram as much data into the limited space as possible. I've seen papers with figures that have 10+ graphs all squished into a half page figure. EDIT: This usually limits proper explanations of the data in the text too because of very limited word counts.
  - patrick451 3y ago
    Yup. And then half the paper is fluff, citing similar work (and all the room those citations take up), trying to make an argument what they did is novel. It's interesting to note the difference between papers 30 (this might vary by field) years ago compared to now. The old papers are mostly substance, and spend very little space on the introduction and political "positioning". Partly this makes sense since things were younger and work tended to be more novel by default back then. But I also think it's a sign of a sort of petty dysfunction. Academics get graded on their "impact", and citations is part of that. So reviewers want you to cite their results, and your reviewers are likely to be folks with similar papers. So authors go citation crazy, trying to appease selfish reviewers, leaving themselves with less than three pages to describe what they actually did.
- boredemployee 3y ago
  And we are living in times where productivity, tight deadlines are more and more common, inevitably people will use generative AI to fulfill idiotic and antiquated bureaucracies.
albertzeyer 3y ago
As many people here write, with Latex, most of the technical issues are already resolved. A few other technical issues might arise due to Latex, but they are usually easy to deal with. However, what remains are rules on page limit, number of words or similar restrictions. And in most cases, you try to fit as much content as possible into the template. So when changing the template, you either have more or less space, so either you would want to add more content, or you need to remove content. Even with the same number of pages and other things being similar as well, due do small differences in the template, it will not match up. That is what takes effort. But for the aspect on space restrictions, I have heard actually the opposite argument: By having this limitation, you save the reading time of all your peers. Often, the work you did can actually be compressed into such short format. You might need to leave out some details (if you publish the source code and make it reproducible, people could anyway check for all details though, so not really a problem), but you can focus on the actual important part. So, by wasting some extra time and effort of the author, you save a lot of time and effort for all readers by having this restriction. If your work really does not fit the space limitations, maybe a different conference or journal would anyway be the better fit.
- Al-Khwarizmi 3y ago
  Papers are already structured in a way that makes reading them very efficient, by providing different layers: you read the title, if you're interested you read the abstract, if you're still interested you read the intro, conclusions and maybe charts/tables, if you're really interested you read the rest. I have the feeling that when my interest in a paper is enough to read everything, I might as well read a couple more pages if the paper is going to feel less crammed (often compression makes understanding harder). Although I might be underestimating the issue.
  - stevejpurves 3y ago
    +1 pdfs are a terrible format in which to store scientific knowledge, the reading experience as a whole is totally inefficient
- heisenbit 3y ago
jjk166 3y ago
It's not wasted - formatting things properly is incredibly useful as it allows for effective communication without researchers having to think of every possible ambiguity. The whole point of different journals existing is to allow people to publish to the ones that make sense for them, including the appropriate formatting. If you allow free-form submissions either you're going to need someone who is not familiar with the work to reformat it (and if it's more complicated than what a latex template can handle, it's probably not something you want a random editor doing either), or you publish things as they come in and wind up with a hodgepodge of poorly thought out formatting. Communicating is one of the most important parts of research, and researchers should be spending an appropriate amount of time on it.
- yawnxyz 3y ago
  the formatting requirements between journals are wholly arbitrary and sometimes counter to each other. This is beyond merely communicating
- patrick451 3y ago
  All these formatting requirements accomplish the opposite though. Every journal is different, so as a reader there is zero consistency. Even journals within the same publisher like IEEE don't have a consistent format. So functionally, there isn't much difference than authors just making up their own.
yawnxyz 3y ago
Our lab (phage therapy, plasmid therapy, AMR) spends a lot of time doing this kind of thing. So we're working on throwing the full weight of LLMs to help us fit things like length limits, format our citations properly, etc. Still a work in progress, since tiny context limit makes this so hard (I keep trying to get Claude access, including joining a Claude hackathon, but for some reason I never get access), but I'll be more than happy to share this thing for free so we can all go back to working on the science. As my PI says: "Science is not an exercise in creative writing"
- cratermoon 3y ago
  Howard S. Becker <https://press.uchicago.edu/ucp/books/book/chicago/W/bo47674306.html https://press.uchicago.edu/ucp/books/book/chicago/W/bo476743...> and Helen Sword <https://educational-innovation.sydney.edu.au/news/pdfs/Sword2009_Writing_HE_differently.pdf https://educational-innovation.sydney.edu.au/news/pdfs/Sword...> would both strongly disagree.
- wizzwizz4 3y ago
  Please don't. When I don't understand what a human's written, I can often reverse-engineer it by considering what sorts of thoughts would lead to that word choice. That's next-to-impossible when reading the output of a transformer-based predictive text system. Science is not an exercise in creative writing, so write straightforwardly.
- memefrog 3y ago
  In my opinion, science is an exercise in creative thinking, and thinking is an exercise in creative writing. Apply the >>= operator of the creative monad. QED. In all seriousness, I think that writing ideas down, condensing them, reading the result aloud and re-editing vigorously is where the real thinking takes place. That iterative process is thinking, for anything complex. It cannot be done by a computer. If you are completely confident in your ideas before you have written them down in concrete form, they are probably not novel enough to be worth publishing.
  - PeterisP 3y ago
politician 3y ago
I just want to be able to read PDFs on my phone without fighting the two-column journal layout.
- stevejpurves 3y ago
  attempts at fluid mode aside, the answer there is read a web based paper
Ekaros 3y ago
Should this be exactly where the journals have paid editors to do the busy work to match the output they want? Shouldn't there be some standard light format to slap the text and images and possibly references(hardest part) and then editors would take care of the rest?
- stevejpurves 3y ago
  more busy work leads to more justification for larger APCs... +1 on a light and accessible format, like submitting markdown and notebooks, which the tools around this markdown flavor is enabling https://myst-tools.org/ https://myst-tools.org/
londont 3y ago
That's literally one of the reasons I quit my PhD
bombcar 3y ago
If papers are basically write-only, then it makes sense to reduce the effort required by the authors. But if they're meant to be consumed by an actual audience, it makes sense to make that part easier. If one author spending 10 hours reduces the amount 10,000 people need to read the paper by 10 minutes, that's a savings overall that is worth it.
- yunohn 3y ago
  > reduces the amount 10,000 people need to read the paper Honestly, I’d wager most papers are read by a handful of people at best. Only the /most/ (top 1% or less) popular authors and papers get hundreds or thousands of real reads.
- stevejpurves 3y ago
  While changing and improving their content and the "form" of the article is probably time best spent -- probably we would do more to improve the experience for the audience by dumping the PDF and moving to web based articles entirely, structured data, html papers, linked content and customisable viewing experiences would all improve the reading experience massively.
thangalin 3y ago
KeenWrite Themes[1] are instructions that tell ConTeXt how to typeset XHTML documents (content) into PDF files (presentation). I made a tutorial[2] that shows how my FOSS desktop text editor, KeenWrite[3], allows users to write in Markdown to typeset a document against a particular theme. Before it can be used for scientific papers, KeenWrite (by way of a flexmark-java extension) needs cross-references, which, unfortunately, aren't part of the CommonMark specification. I posit that the vast majority of LaTeX users don't grok how to separate content from presentation. When I asked a question on TeX.SE[4] about how to adjust the line spacing between enumerated items (spanning a couple dozen enumerated lists), the vast majority of people voted for the answer of using `\itemsep0em` to tweak each list individually. The correct answer, IMO, is to fix the problem globally, and not waste time tweaking individual lists. [1]: https://github.com/DaveJarvis/keenwrite-themes https://github.com/DaveJarvis/keenwrite-themes [2]: https://www.youtube.com/watch?v=3QpX70O5S30 https://www.youtube.com/watch?v=3QpX70O5S30 [3]: https://github.com/DaveJarvis/keenwrite https://github.com/DaveJarvis/keenwrite [4]: https://tex.stackexchange.com/questions/6081/reduce-space-between-enumerated-items https://tex.stackexchange.com/questions/6081/reduce-space-be...
- prennert 3y ago
  Even with LaTeX etc, content is not separate from presentation when you write papers. Once you have limits on pages, you have to adjust your content to the presentation to make it fit.
ineedasername 3y ago
It's unclear from the article if that's representative of either 1) Total time spent formatting or 2) The marginal increase in time spent formatting above what it would take to follow some other common format. #2 seems less likely, since, well, there isn't really a common format, as the article points out, so there's no default that researchers would use as a baseline. That leaves #1. But a paper has to be formatted somehow, and that's always going to take time. So the $230M cost the article cites is going to be at least a little smaller when you take out the time it takes to write up anything at all using a consistent style and format, whether it's your own or something imposed on you. And I can tell you based on my own profession & day to day work, format & presentation is extremely important in making it easier for your audience to consume information, and this is especially true with complex or novel information. Undoubtedly the industry can and should do better. There should be common standards. It would smooth readability and comprehension. But it's not going to completely eliminate the rough $/hour equivalent this article is citing. Also consider that different fields will be conveying different types of information, or have audiences with different skillsets, so there's not a one-size-fits-all approach here. Style & formatting guidelines, even made as common as possible, will still by necessity be different in different disciplines.
ckemere 3y ago
So many comments about fonts, subscripts, etc. No one cares about that at review time. I've never heard anyone complain about significant time on this. Major difference in paper _style_ between Nature Brief Communication (2 figures, one page of text) and J Neuroscience full (10 pages and 8 figures). That's a big reformating. Also, Nature has a very specific abstract, which is great for a general science audience (https://www.nature.com/documents/nature-summary-paragraph.pd https://www.nature.com/documents/nature-summary-paragraph.pd) but less so for specialists. Similarly, a clinical trial abstract has exact results so that it's easy to scrape. For the y-combinator audience, it seems obvious to me that a MobiCom and a ACM transactions will be very different papers. Fixing the format doesn't fix this.
- memefrog 3y ago
  Is it something that needs to be fixed? I surmise that Nature Brief Communication, by its name and the guidelines you gave, is about briefly communicating new results. People read it so that they can get brief summaries of new results in the natural sciences. It would do a disservice to the people that read it if they announced that they wouldn't require one page of text and two figures for new submissions, because it required too much work for authors. If you wrote a novella, and wanted to submit it to a magazine that published short stories, I don't think it would be reasonable to complain that they didn't want to publish your work unless it was edited down to meet their guidelines. Why is it different for scientific papers? It just seems natural to me that different publications would have different audiences and different goals with what they are publishing. They're read by different people for different reasons who want different things from the publication they're paying for. Naturally that means that if you want them to publish your work, it has to be right for their readers. Is there something I'm missing?
jacquesm 3y ago
Is there still no widely adopted standardized submission format across all of science? That seems like a complete no-brainer, some structured text format that would allow the journals to render the articles as they see fit. Finally an application for XML: https://www.xml.com/articles/2018/10/12/introduction-jats/ https://www.xml.com/articles/2018/10/12/introduction-jats/
- rowanc1 3y ago
  JATS is gaining adoption in publishing, but is difficult for scientists to actually _author_ in. This is one of the main reasons behind tools like MyST (https://myst-tools.org https://myst-tools.org) and Quarto (https://quarto.org/ https://quarto.org/) - both are semantic authoring tools that allow authors to export to JATS but author in Markdown (or in JupyterNotebooks). Having semantic authoring tools also means that you can easily change the template -- saving a ton of time for the author. For example, about 400 journal templates here: https://myst-tools.org/docs/mystjs/creating-pdf-documents https://myst-tools.org/docs/mystjs/creating-pdf-documents
hotBacteria 3y ago
I don't have much hope regarding this issue. Researchers work a lot on their own time, so the millions mentionned in the article don't directly impact the institutions employing them. They are alone in this fight. The petition (https://www.change.org/p/simplify-manuscript-submissions-in-academic-journals https://www.change.org/p/simplify-manuscript-submissions-in-...) linked in the article barely received 100 signatures in a month.
dbingham 3y ago
This is just one of many, many problems plaguing academic publishing. I've long thought a web platform with a recombination of features borrowed from Github and StackExchange could potentially solve many (maybe most) of those problems. Last summer I was able to take 6 months off of work to build a prototype and now I'm inching it forward as a side project. It's in early beta, and I'm looking for folks willing to use it to solicit review of their pre-prints and give me feedback and direction on where it take it. It's open source, open access, and intended to stay that way. If it gets traction I want to form a non-profit, multistakeholder cooperative (governed by its users and the team that builds it) to develop and maintain it. Though, that's a long way off. The beta is here: https://peer-review.io https://peer-review.io The source is here: https://github.com/danielbingham/peerreview https://github.com/danielbingham/peerreview A more in depth description of how it works is here: https://peer-review.io/about https://peer-review.io/about
dsr_ 3y ago
All these problems are non-technical. Therefore, they will not be solved by technology. They will be solved by people communicating with each other to reach a consensus, or not at all.
DanMa1 3y ago
[flagged]
aaron695 3y ago
[dead]
jononor 3y ago
From many of the comments here, it sounds like one of the main problems is varying content lengths. So an effort that would harmonize that across journals/conferences seems like it might have a very positive impact. Maybe have two standardized options, shorter/longer.

145 points by headalgorithm 3y ago

> For scientists submitting their papers to journals, there’s an all-too-familiar drill: spend hours formatting the paper to meet the journal’s guidelines; if the paper is rejected, sink more time into reformatting it for another journal; repeat. What? The journal provides (or at least should) a latex template, you write stuff in that, then you ship it. Last one I wrote in a browser through overleaf, spent zero time on formatting. edit: Nature's one appears to be https://www.overleaf.com/latex/templates/springer-nature-latex-template/myxmhdsbzkyd https://www.overleaf.com/latex/templates/springer-nature-lat...

ftxbro 3y ago
> "What? The journal provides (or at least should) a latex template, you write stuff in that" Millions of dollars in time wasted on learning other markup language
- JonChesterfield 3y ago
  I definitely don't know how to write latex, can muddle through anyway. Total loss to trial and error / searching bits of syntax is probably below an hour so far this lifetime.
light_hue_1 3y ago
> What? The journal provides (or at least should) a latex template, you write stuff in that, then you ship it. Last one I wrote in a browser through overleaf, spent zero time on formatting. Then you don't have much experience writing papers. Formatting is very time consuming. Some want 8 pages, some are unlimited, others want you to use whatever makes sense. Every journal has a different page length. They expect to see results in different places. Some want a detailed appendix. Others are ok with a website. The latex template doesn't help at all with any of these. Reformatting is extremely painful and wasteful.
- JonChesterfield 3y ago
  Three in the real world, some number in undergrad. Writing papers takes a fair amount of time - think how to express things, producing graphs and so forth - but reordering sections or adding things to a bibliography is yet to cause much grief. Maybe we mean different things by formatting.
- IshKebab 3y ago
  The worst thing is references. They all have their own weird formats.
  - pbhjpbhj 3y ago
    Why isn't that handled by semantic markup? That said, recognising static academic reference format, then reformatting for the other 4 or 5 standard formats seems like a python project for first year students (to this non-programmer, I'd guess there are lots of edge cases to trip on making it a great learning experience!)?
    - cge 3y ago
      It often isn't so much the actual bibliography line item format, which are usually handled quite well be systems like bibtex or biblatex+biber, but overall citation formatting complexities. Sometimes journals want specific formats that become a challenge to implement. For example, on a recent submission, we needed our main text to have a numbered bibliography at the end, then needed our methods to have numbered bibliography at the end, but with numbers starting after the last number in the main text, and no repeats, but with references in the methods to items already in the main text bibliography referring to those numbers. This was surprisingly difficult to implement reliably in LaTeX and Biblatex. An additional annoyance is that to save space, journals often want formats that are compact but inefficient to use, for example, formats that are heavily abbreviated and don't include titles. These, however, are annoying to use, and annoying reviewers is generally unwise. So in our case, we actually intentionally submit PDFs for review that use the 'wrong' bibliography item format, of a similar form to the journal's but less abbreviated and including titles and hyperlink backreferences to citations in the text. Then for final submission we have to replace this with the journal's preferred format.
cge 3y ago
Nature accepts LaTeX+PDF submissions, and will send the PDF out for review, but for final submission after acceptance, they prefer mostly-unformatted Word files; if you submit a LaTeX+PDF final submission, they convert it to Word [1]. As they stress that authors should not bother working on the visual formatting of their final submissions, my expectation is that, internally, they then take the Word file and manually put it into their own typesetting system. Publishers like Dagstuhl Publishing that can require LaTeX submissions and use a completely LaTeX publishing workflow probably have significant efficiency advantages, but then rely on potential authors being sufficiently experienced with LaTeX that a LaTeX submission requirement doesn't drive people away. This can work well for computer science and some parts of physics, but for other fields it can be a significant burden. [1]: https://www.nature.com/nature/for-authors/final-submission https://www.nature.com/nature/for-authors/final-submission

LanceH 3y ago

Billions wasted pursuing publication over meaningful effort.

ftxbro 3y ago
how will they know you're good if you don't have good metrics in Science and Nature
- Lk7Of3vfJS2n 3y ago
  By creating something they couldn't.
seydor 3y ago
Ultimately pursuing grants
somat 3y ago
Publication is the results. The effort is meaningless if no one knows about it. https://gwern.net/maze https://gwern.net/maze Yes but what about all this unnecessary gatekeeping? gatekeeping is necessary to maintain a certain level of quality. On this specific issue of formatting gatekeeping. There was no conspiracy. I imagine that the policy solidified over time. The paper wants to maintain a specific look. Authors are upset when changes get introduced while formatting. The paper then says "you can format it yourself if it meets our specification". Now you have to format it yourself. Thankfully in our web enabled era there a ways to publish without going through a traditional publisher. However you will note that the quality of these publishers is a mixed bag, real science right next to quackery. No one has done the gatekeeping needed to separate the wheat from the chaff.
- akira2501 3y ago
  > Publication is the results. > The paper wants to maintain a specific look. Which does the paper want more? To be the first with the results or to appear a particular way? Do the appearances help with "the results?"

gammarator 3y ago

There’s rich irony in this article appearing in Nature, which has some of the most unusual and restrictive formatting requirements. Also, journal publication fees dwarf the implicit cost of reformatting and deliver arguably less value.

mixedmath 3y ago

There are a couple of journals in math that ask for the paper to be submitted using their particular latex template, and a typical latex template is incompatible with what I consider "standard" latex, i.e. either the `amsart` document class or `article` document class with certain AMS packages included. Sometimes it's small, like whether or not `\author{my name}` needs to be included in the preamble or in the main body. These are short but annoying. Sometimes it's very annoying. I'm glad that I've never tried to publish in a two-column journal (which might exist in math? I don't know) which would require more substantial superficial edits. I always assumed that this was a deliberate source of friction, slightly raising the bar of entry so as to discourage a certain sort of submission. I don't say I agree with this, but that's what I thought. This sounds like the sort of problem that latex would be great at solving: changing the look of an article just by using different document classes. And sometimes it is great --- but some templates are terrible, terrible, terrible. (And sometimes these terrible templates are for great journals! I see little to no correlation there).

sh34r 3y ago
> I always assumed that this was a deliberate source of friction, slightly raising the bar of entry so as to discourage a certain sort of submission. There’s no doubt in my mind that it’s intentional gatekeeping. There’s a reason why many papers are being “published” on Arxiv and foregoing all this boxticking. The whole publishing process is fundamentally broken. Aaron Swartz (RIP) had the right idea all along. Get rid of the middlemen sucking up millions of dollars by paywalling government funded research. It’s been proven time and time again that a shocking number of studies can’t be reproduced and that the traditional peer review process just isn’t working. It’s a good old boys’ club putting a stamp of approval on their friends’ work and keeping the outsiders away. When it comes to Math though, I do have some sympathies. There are so many cranks that think they solved Collatz or a millennium problem and don’t even know what they don’t know. It must be exhausting to sift through all that noise in a volunteer, unpaid position. These shibboleths might be a necessary evil.
- cratermoon 3y ago
  > It’s a good old boys’ club putting a stamp of approval on their friends’ work and keeping the outsiders away. > Math though, I do have some sympathies. There are so many cranks Lots of other fields have their cranks, quacks, fringe theorists, and whackjobs. Why give math special treatment?

axg11 3y ago

Go one level deeper and you'll find the problem with all of academia (source: I have a PhD). Most of academic science as we know it today is structured so that the output is "publishable" and/or helps future grant applications. Incremental improvements are very publishable, but that doesn't necessarily make good science. Grants are awarded to scientists who are consistently able to deliver results, in the form of published papers. I can only really speak for my little corner of science, but from my view, the entire incentive structure of science is broken.

kenjackson 3y ago
Incremental publication seems like a great idea. The only problem is that the publication process is so formal. But if we made publications as "blogs" or something, I think incremental units of forward progress are a reasonable way to do science. I suspect most science is done this way. I imagine there are few Wiles style FLT proofs around.
- PeterisP 3y ago
  As the parent poster states, the key thing is that everything is structured about incentives conditional on delivering measurable results e.g. the quantity of published papers; but that implicitly includes a very important thing that "published" counts only if (and because) it has passed certain filters. There are no barriers to publish research outcomes as "blogs" or something, it is easy, so such "publication" doesn't imply that any reasonable research was done, and no incentives would reward such publishing, and that's why researchers often don't bother with it. Like, the existing system already has issues with publication being too easy to game, with predatory paid journals, lax standards for reviewing, etc; that's hard to fix, but it's considered a problem - and so any changes making the barrier to publication even lower than that won't be welcome. And from the perspective of researchers, we don't really want more publications - they're a pain to read, there's an overabundance of poor content that's salami-sliced, we do so many publications because the incentives push us toward this but we recognize that this is a bad thing and we'd be far better off if the same research would be published in fewer, better articles. But we can't, because anyone who does that will be effectively denied resources for future research.

seydor 3y ago

Ironic that this comes from nature. Do you remember which subscripts must be italicized?

Solvency 3y ago

[flagged]

d--b 3y ago

> the authors of the analysis, which was published in BBC Medicine on 10 May, propose that journals should allow free-format submissions so researchers can spend their time and money on research instead. Yeah right. This is YC though. Up-for-grabs: Untapped $260m market for reformatting scientific papers.

bluenose69 3y ago

Perhaps this is true in the field discussed in the essay, but in my field (a natural science) formatting is taken care of with latex stylesheets, so the effort of switching to another journal format usually amounts to changing a few lines. Of course there can be small details such as whether a given journal wants keywords, but dealing with such things doesn't take much time. The problem of switching to another journal is also overplayed in the essay, at least in my field. I don't know of many people who "shop" for journals to accept their work. Usually you know the right journal, and if the paper is rejected you just give up on it. Perhaps this is discipline-specific, though. (The essay is restricted to biomedical fields.) As a reviewer, I've never spent any time on journal rules. If the paper gets accepted, it's up to the technical editor to impose rules. Most authors employ the proper latex stylesheets from the first rough draft. They also use section headings that fit the journal's conventions, and so forth. I suppose it is possible that people in biomedical fields (are there any here on HN?) tend to submit to multiple journals before their work is accepted. But I sort of doubt that reviewers reject papers based on things like italics or citation formatting, so if folks are submitting to a lot of journals, maybe their work just isn't highly regarded by their peers. Basically there is no issue here, at least in my field. It's an unconvincing essay, and not one that encouraged me to waste time looking up the original work.

physPop 3y ago
It’s a huge issue in most fields. No one uses latex anymore outside of niches like math and physics.
- pbasista 3y ago
  > No one uses latex anymore That is a very broad statement. Do you have any data to back it up? Do you suggest that it was used in the past but that has changed? If so, why?
- PartiallyTyped 3y ago
  Well, we should go back to that, or something that is easier.

lower 3y ago

I've spent so much time for pointless reformatting. With Springer LNCS it's often that you have to work really hard to cram everything into the page limit. Then Springer does some editing in the bibliography, and the article then often overflows by one or two bibliography entries and is published like that, making the effort of meeting the page limit a complete waste time

sacrosancty 3y ago
[dead]

golergka 3y ago

...do these academics not know how to use latex and waste their time in Microsoft Word?

yawnxyz 3y ago
very few people use latex in biology

pornel 3y ago

You're all assuming it's about making papers pretty or fit a template, but the major time sink is length limits. The abstract has to have a specific number of chars or words (which varies by journal), and it's a critical part of the paper, so you never want to waste a single word. There's also limit for the total number of pages or words, which again needs text rewrites. Sometimes format of references is weird, and needs conversion macros or manual edits. Reviewers always want more information, more references, more tables, so publishing is an endless puzzle to fit all of that within limit that is always too short to fit everything you have to say. Having concise paper is of course great, but submitting to multiple places requires editing multiple variations, and that is busywork.

gww 3y ago
The length limits also forces authors to increase the complexity of their figures to cram as much data into the limited space as possible. I've seen papers with figures that have 10+ graphs all squished into a half page figure. EDIT: This usually limits proper explanations of the data in the text too because of very limited word counts.
- patrick451 3y ago
  Yup. And then half the paper is fluff, citing similar work (and all the room those citations take up), trying to make an argument what they did is novel. It's interesting to note the difference between papers 30 (this might vary by field) years ago compared to now. The old papers are mostly substance, and spend very little space on the introduction and political "positioning". Partly this makes sense since things were younger and work tended to be more novel by default back then. But I also think it's a sign of a sort of petty dysfunction. Academics get graded on their "impact", and citations is part of that. So reviewers want you to cite their results, and your reviewers are likely to be folks with similar papers. So authors go citation crazy, trying to appease selfish reviewers, leaving themselves with less than three pages to describe what they actually did.
boredemployee 3y ago
And we are living in times where productivity, tight deadlines are more and more common, inevitably people will use generative AI to fulfill idiotic and antiquated bureaucracies.

albertzeyer 3y ago

As many people here write, with Latex, most of the technical issues are already resolved. A few other technical issues might arise due to Latex, but they are usually easy to deal with. However, what remains are rules on page limit, number of words or similar restrictions. And in most cases, you try to fit as much content as possible into the template. So when changing the template, you either have more or less space, so either you would want to add more content, or you need to remove content. Even with the same number of pages and other things being similar as well, due do small differences in the template, it will not match up. That is what takes effort. But for the aspect on space restrictions, I have heard actually the opposite argument: By having this limitation, you save the reading time of all your peers. Often, the work you did can actually be compressed into such short format. You might need to leave out some details (if you publish the source code and make it reproducible, people could anyway check for all details though, so not really a problem), but you can focus on the actual important part. So, by wasting some extra time and effort of the author, you save a lot of time and effort for all readers by having this restriction. If your work really does not fit the space limitations, maybe a different conference or journal would anyway be the better fit.

Al-Khwarizmi 3y ago
Papers are already structured in a way that makes reading them very efficient, by providing different layers: you read the title, if you're interested you read the abstract, if you're still interested you read the intro, conclusions and maybe charts/tables, if you're really interested you read the rest. I have the feeling that when my interest in a paper is enough to read everything, I might as well read a couple more pages if the paper is going to feel less crammed (often compression makes understanding harder). Although I might be underestimating the issue.
- stevejpurves 3y ago
  +1 pdfs are a terrible format in which to store scientific knowledge, the reading experience as a whole is totally inefficient
heisenbit 3y ago

jjk166 3y ago

It's not wasted - formatting things properly is incredibly useful as it allows for effective communication without researchers having to think of every possible ambiguity. The whole point of different journals existing is to allow people to publish to the ones that make sense for them, including the appropriate formatting. If you allow free-form submissions either you're going to need someone who is not familiar with the work to reformat it (and if it's more complicated than what a latex template can handle, it's probably not something you want a random editor doing either), or you publish things as they come in and wind up with a hodgepodge of poorly thought out formatting. Communicating is one of the most important parts of research, and researchers should be spending an appropriate amount of time on it.

yawnxyz 3y ago
the formatting requirements between journals are wholly arbitrary and sometimes counter to each other. This is beyond merely communicating
patrick451 3y ago
All these formatting requirements accomplish the opposite though. Every journal is different, so as a reader there is zero consistency. Even journals within the same publisher like IEEE don't have a consistent format. So functionally, there isn't much difference than authors just making up their own.

yawnxyz 3y ago

Our lab (phage therapy, plasmid therapy, AMR) spends a lot of time doing this kind of thing. So we're working on throwing the full weight of LLMs to help us fit things like length limits, format our citations properly, etc. Still a work in progress, since tiny context limit makes this so hard (I keep trying to get Claude access, including joining a Claude hackathon, but for some reason I never get access), but I'll be more than happy to share this thing for free so we can all go back to working on the science. As my PI says: "Science is not an exercise in creative writing"

cratermoon 3y ago
Howard S. Becker <https://press.uchicago.edu/ucp/books/book/chicago/W/bo47674306.html https://press.uchicago.edu/ucp/books/book/chicago/W/bo476743...> and Helen Sword <https://educational-innovation.sydney.edu.au/news/pdfs/Sword2009_Writing_HE_differently.pdf https://educational-innovation.sydney.edu.au/news/pdfs/Sword...> would both strongly disagree.
wizzwizz4 3y ago
Please don't. When I don't understand what a human's written, I can often reverse-engineer it by considering what sorts of thoughts would lead to that word choice. That's next-to-impossible when reading the output of a transformer-based predictive text system. Science is not an exercise in creative writing, so write straightforwardly.
memefrog 3y ago
In my opinion, science is an exercise in creative thinking, and thinking is an exercise in creative writing. Apply the >>= operator of the creative monad. QED. In all seriousness, I think that writing ideas down, condensing them, reading the result aloud and re-editing vigorously is where the real thinking takes place. That iterative process is thinking, for anything complex. It cannot be done by a computer. If you are completely confident in your ideas before you have written them down in concrete form, they are probably not novel enough to be worth publishing.
- PeterisP 3y ago

politician 3y ago

I just want to be able to read PDFs on my phone without fighting the two-column journal layout.

stevejpurves 3y ago
attempts at fluid mode aside, the answer there is read a web based paper

Ekaros 3y ago

Should this be exactly where the journals have paid editors to do the busy work to match the output they want? Shouldn't there be some standard light format to slap the text and images and possibly references(hardest part) and then editors would take care of the rest?

stevejpurves 3y ago
more busy work leads to more justification for larger APCs... +1 on a light and accessible format, like submitting markdown and notebooks, which the tools around this markdown flavor is enabling https://myst-tools.org/ https://myst-tools.org/

londont 3y ago

That's literally one of the reasons I quit my PhD

bombcar 3y ago

If papers are basically write-only, then it makes sense to reduce the effort required by the authors. But if they're meant to be consumed by an actual audience, it makes sense to make that part easier. If one author spending 10 hours reduces the amount 10,000 people need to read the paper by 10 minutes, that's a savings overall that is worth it.

yunohn 3y ago
> reduces the amount 10,000 people need to read the paper Honestly, I’d wager most papers are read by a handful of people at best. Only the /most/ (top 1% or less) popular authors and papers get hundreds or thousands of real reads.
stevejpurves 3y ago
While changing and improving their content and the "form" of the article is probably time best spent -- probably we would do more to improve the experience for the audience by dumping the PDF and moving to web based articles entirely, structured data, html papers, linked content and customisable viewing experiences would all improve the reading experience massively.

thangalin 3y ago

KeenWrite Themes[1] are instructions that tell ConTeXt how to typeset XHTML documents (content) into PDF files (presentation). I made a tutorial[2] that shows how my FOSS desktop text editor, KeenWrite[3], allows users to write in Markdown to typeset a document against a particular theme. Before it can be used for scientific papers, KeenWrite (by way of a flexmark-java extension) needs cross-references, which, unfortunately, aren't part of the CommonMark specification. I posit that the vast majority of LaTeX users don't grok how to separate content from presentation. When I asked a question on TeX.SE[4] about how to adjust the line spacing between enumerated items (spanning a couple dozen enumerated lists), the vast majority of people voted for the answer of using `\itemsep0em` to tweak each list individually. The correct answer, IMO, is to fix the problem globally, and not waste time tweaking individual lists. [1]: https://github.com/DaveJarvis/keenwrite-themes https://github.com/DaveJarvis/keenwrite-themes [2]: https://www.youtube.com/watch?v=3QpX70O5S30 https://www.youtube.com/watch?v=3QpX70O5S30 [3]: https://github.com/DaveJarvis/keenwrite https://github.com/DaveJarvis/keenwrite [4]: https://tex.stackexchange.com/questions/6081/reduce-space-between-enumerated-items https://tex.stackexchange.com/questions/6081/reduce-space-be...

prennert 3y ago
Even with LaTeX etc, content is not separate from presentation when you write papers. Once you have limits on pages, you have to adjust your content to the presentation to make it fit.

ineedasername 3y ago

It's unclear from the article if that's representative of either 1) Total time spent formatting or 2) The marginal increase in time spent formatting above what it would take to follow some other common format. #2 seems less likely, since, well, there isn't really a common format, as the article points out, so there's no default that researchers would use as a baseline. That leaves #1. But a paper has to be formatted somehow, and that's always going to take time. So the $230M cost the article cites is going to be at least a little smaller when you take out the time it takes to write up anything at all using a consistent style and format, whether it's your own or something imposed on you. And I can tell you based on my own profession & day to day work, format & presentation is extremely important in making it easier for your audience to consume information, and this is especially true with complex or novel information. Undoubtedly the industry can and should do better. There should be common standards. It would smooth readability and comprehension. But it's not going to completely eliminate the rough $/hour equivalent this article is citing. Also consider that different fields will be conveying different types of information, or have audiences with different skillsets, so there's not a one-size-fits-all approach here. Style & formatting guidelines, even made as common as possible, will still by necessity be different in different disciplines.

ckemere 3y ago

So many comments about fonts, subscripts, etc. No one cares about that at review time. I've never heard anyone complain about significant time on this. Major difference in paper _style_ between Nature Brief Communication (2 figures, one page of text) and J Neuroscience full (10 pages and 8 figures). That's a big reformating. Also, Nature has a very specific abstract, which is great for a general science audience (https://www.nature.com/documents/nature-summary-paragraph.pd https://www.nature.com/documents/nature-summary-paragraph.pd) but less so for specialists. Similarly, a clinical trial abstract has exact results so that it's easy to scrape. For the y-combinator audience, it seems obvious to me that a MobiCom and a ACM transactions will be very different papers. Fixing the format doesn't fix this.

memefrog 3y ago
Is it something that needs to be fixed? I surmise that Nature Brief Communication, by its name and the guidelines you gave, is about briefly communicating new results. People read it so that they can get brief summaries of new results in the natural sciences. It would do a disservice to the people that read it if they announced that they wouldn't require one page of text and two figures for new submissions, because it required too much work for authors. If you wrote a novella, and wanted to submit it to a magazine that published short stories, I don't think it would be reasonable to complain that they didn't want to publish your work unless it was edited down to meet their guidelines. Why is it different for scientific papers? It just seems natural to me that different publications would have different audiences and different goals with what they are publishing. They're read by different people for different reasons who want different things from the publication they're paying for. Naturally that means that if you want them to publish your work, it has to be right for their readers. Is there something I'm missing?

jacquesm 3y ago

Is there still no widely adopted standardized submission format across all of science? That seems like a complete no-brainer, some structured text format that would allow the journals to render the articles as they see fit. Finally an application for XML: https://www.xml.com/articles/2018/10/12/introduction-jats/ https://www.xml.com/articles/2018/10/12/introduction-jats/

rowanc1 3y ago
JATS is gaining adoption in publishing, but is difficult for scientists to actually _author_ in. This is one of the main reasons behind tools like MyST (https://myst-tools.org https://myst-tools.org) and Quarto (https://quarto.org/ https://quarto.org/) - both are semantic authoring tools that allow authors to export to JATS but author in Markdown (or in JupyterNotebooks). Having semantic authoring tools also means that you can easily change the template -- saving a ton of time for the author. For example, about 400 journal templates here: https://myst-tools.org/docs/mystjs/creating-pdf-documents https://myst-tools.org/docs/mystjs/creating-pdf-documents

hotBacteria 3y ago

I don't have much hope regarding this issue. Researchers work a lot on their own time, so the millions mentionned in the article don't directly impact the institutions employing them. They are alone in this fight. The petition (https://www.change.org/p/simplify-manuscript-submissions-in-academic-journals https://www.change.org/p/simplify-manuscript-submissions-in-...) linked in the article barely received 100 signatures in a month.

dbingham 3y ago

This is just one of many, many problems plaguing academic publishing. I've long thought a web platform with a recombination of features borrowed from Github and StackExchange could potentially solve many (maybe most) of those problems. Last summer I was able to take 6 months off of work to build a prototype and now I'm inching it forward as a side project. It's in early beta, and I'm looking for folks willing to use it to solicit review of their pre-prints and give me feedback and direction on where it take it. It's open source, open access, and intended to stay that way. If it gets traction I want to form a non-profit, multistakeholder cooperative (governed by its users and the team that builds it) to develop and maintain it. Though, that's a long way off. The beta is here: https://peer-review.io https://peer-review.io The source is here: https://github.com/danielbingham/peerreview https://github.com/danielbingham/peerreview A more in depth description of how it works is here: https://peer-review.io/about https://peer-review.io/about

dsr_ 3y ago

All these problems are non-technical. Therefore, they will not be solved by technology. They will be solved by people communicating with each other to reach a consensus, or not at all.

DanMa1 3y ago

[flagged]

aaron695 3y ago

[dead]

jononor 3y ago

From many of the comments here, it sounds like one of the main problems is varying content lengths. So an effort that would harmonize that across journals/conferences seems like it might have a very positive impact. Maybe have two standardized options, shorter/longer.