Articles from arXiv.org as responsive HTML5 web pages - https://news.ycombinator.com/item?id=30835784 - March 2022 (8 comments)
They correctly point out a few of the limitations of arXiv (mostly: static LaTeX and PDFs). But I profoundly dislike the other things they propose:
1. "open comments and reviews". I have no problem with open reviews on a third-party website, but arXiv is literally a "distribution service". It has one job and does it pretty well. I don't want it to turn into Reddit or (worse?) ResearchGate.
2. "alternative metrics". Enough with the metrics already. We all know they're destructive, at least all that have been tried so far. I didn't even know that arXiv showed some bibliometrics (because they are thankfully hidden behind default-disabled switches). Their proposed alternatives? "How many times a paper has been downloaded, tweeted, or blogged." I am not joking, this is what they propose to include in addition to citations. Seriously???
PS: Just a heads-up to anyone who, like me, would be wondering about the ar5iv.labs.arxiv.org link. The article is a regular paper submitted to arXiv. The authors do not belong to the organization maintaining arXiv. The usual link is: https://arxiv.org/abs/1709.07020
The ar5iv.labs.arxiv.org thing is an experimental html5 paper viewer by the arXiv people.
Edit: typos.
I now see that Wikipedia says this.
Authorea was launched in February 2013 by co-founders Alberto Pepe and Nathan Jenkins and scientific adviser Matteo Cantiello, who met while working at CERN. They recognized common difficulties in the scholarly writing and publishing process. To address these problems, Pepe and Jenkins developed an online, web-based editor to support real-time collaborative writing, and sharing and execution of research data and code. Jenkins finished the first prototype site build in less than three weeks.
Bootstrapping for almost two years, Pepe and Jenkins grew Authorea by reaching out to friends and colleagues, speaking at events and conferences, and partnering with early adopter institutions.
In September 2014, Authorea announced the successful closure of a $610K round of seed funding with the New York Angels and ff Venture Capital groups. In January 2016, Authorea closed a $1.6M round of funding led by Lux Capital and including the Knight Foundation and Bloomberg Beta. It later acquired the VC-backed company The Winnower.
In 2018 Authorea was acquired for an undisclosed amount by Atypon (part of Wiley).
It is too far a stretch, murdering the poor subject:
PDFs are the best format available for long-term information, such as research papers. They have the advantages of digital data: Searchable, copy-able, transmittable, and data is extractable. They are also an open format, don't rely on a central service to be available, and they preserve presentation across platforms. They have metadata, and are annotatable and reviewable. And the PDF format is the best for long-term preservation, carefully designed to be readable in 50 years - partly because they preserve presentation across platforms - and that includes the metadata, annotations, and reviews.
PDFs are like paper in that they will look the same 50 years from now as they do today, unlike (almost?) any other digital format.
Yes, I wish they were a bit more dynamic in layout, and that the text was more cleanly extracted.
That's true for plain text (in the best case), but try extracting an equation, table or a diagram.
Stepping away from best case, PDFs in theory look the same everywhere, but turn into a mess on buggy implementations or differing rendering engines – due to the insistence on having a stable presentation, they assume positining and sizing always works, so when that fails, it fails worse than a buggy rendering of a presentation-agnostic document like an HTML page.
(In my experience, bugs either enter just before printing, or when displaying using JS-based renderers).
Good point. From what format are tables, diagrams, and formulas extractable (while retaining format)? I've had good luck moving tables between my web browser and email applications, though it always surprises me that the html is implemented similarly enough.
> PDFs in theory look the same everywhere, but turn into a mess on buggy implementations or differing rendering engines
I don't deal with PDFs programatically, and it sounds like you might, but from the user end, and from running networks of thousands of users, I've hardly ever seen problems in practice except for the browsers' JavaScript renderers.
Being sent a PDF of an academic paper to read (or do anything with other than send it to a printer) is about ten times lower on the user preference scale than having someone send a link to a blog post on the same subject. (The other reason for that being that when people are in the mode that involves writing an academic paper, they forget how to write anything that anyone would actually want to read. Most academic writing sucks.)
Of the properties you listed that PDF does share with self-contained HTML, on the other hand, there isn't one that PDF isn't worse at—not even "transmittable". (Initially I would have put them on the same level there, but of course that's wrong. When you're in an environment where for whatever reason a file copy is not an option, PDF's binary format makes it harder to transmit the bytestream than HTML.)
Who cares if a PDF looks the same everywhere if that means everyone who encounters it bounces away rather than having to slog through any attempt to actually read it?
That would be fantastic, but there are no available solutions that meet the specs I listed, including long-term preservation and annotation (what annotation subsystems are there for HTML?). ePub is 'responsibly wielded HTML', but it lacks annotation and long-term preservation is iffy.
I much prefer PDFs to blog posts, personally - they are mine, I can annotate them, etc. Also, I find much more thought is put into a PDF than a blog post (which both beat Twitter!).
By separating the meaning from the visual representation there is no incentive to keep the invisible data workable.
PDF might as well be replaced with SVG, in terms of rendering consistency and metadata extraction capabilities. Because for a plain vector image format it's not that impressive.
>> Searchable, copy-able, transmittable, and data is extractable. They are also an open format, don't rely on a central service to be available, and they preserve presentation across platforms. They have metadata, and are annotatable and reviewable. And the PDF format is the best for long-term preservation, carefully designed to be readable in 50 years - partly because they preserve presentation across platforms - and that includes the metadata, annotations, and reviews.
> None of those virtues hold in practice.
> You always OCR the PDF visuals to get the text, because that's the only thing reliable about PDF. Everything else is often wrong, broken, or non-existent.
Which don't hold in practice? Are they not searchable? Is presentation not preserved? I use a lot of PDFs and they hold for me. PDFs are very popular, so they must work pretty well.
> SVG
Is there a standard way to do review and annotation, and is presentation preserved, for example when printing? Also, PDFs contain various image formats; do they contain SVG?
> What is the single most important factor that has prevented the arXiv to quickly innovate? We believe it is LaTeX. The same technological advancement that has allowed the arXiv to flourish, is also, incredibly, its most important shortcoming. Indeed, the reliance of the arXiv on LaTeX is the source of all the weaknesses listed below.
> The research products hosted by the arXiv are PDFs. A title, abstract, and author list are provided by the authors upon submission as metadata, which is posted alongside the PDF, and is rendered in HTML to aid article discoverability.
It's interesting to me that the authors ignore that it is possible to read the source tex for most papers on the arxiv. The arxiv prefers to be given tex and source files, and then to compile and serve the pdf --- when this is done, you can read the source. In this way the arxiv is a repository of both the plain text source of the document and a formatted output.
In some of my papers, I deliberately include comments or extra data in the source for others. I'm not alone here; I've used the code embedded in this paper [1], for example.
While I think there would be some advantages if the arxiv required all papers to be compilable tex source files, I understand that the arxiv also accepts other formats to not exclude potential writers who do not know tex. [The other formats are pdfs (e.g. converted from Word) or HTML with jpg/png/gif images (which I have never seen in practice)].
Maybe instead of using the obsolete toolset arxiv provides, they could host their groundbreaking research on their own platform? The combination of ground breaking features and insightful commentary would draw users?
Actually, many of the negatives they list are positives in my book. The latex barrier screens out a ton of garbage in my view - I'm on some social science / word based research lists, and the quality of stuff is mind bogglingly bad.
Getting stuff it fit into a PDF (instead of the NY times new scrollable story stuff) makes grabbing or print off or even reading easy - less dynamic is good in my book.
"PDFs are prohibited, especially shared in private. All data, hypotheses, references, tables, code, must be presented in formats that are conducive to steali ^H^H^H^H replication and fostering a global science ethos of sharing."
"Authors who obey will have a beautiful platinum star printed next to their author nameplate. Extra star opportunities will exist for authors who announce their papers on Twitter with required levels of irony, hipness and verve!"
I think ArXiv (edit: Actually this is not by ArXiv, but some other group) is drastically over-estimating the desire to submit papers to their service. They are popular because they host the documents you were going to produce, in the format that the journals expect. The production of a Arxiv appropriate document is a side effect of the actual job, which is writing a paper to submit to a journal (hey, I'm as unhappy as you are that this is the actual job, but everyone hates publish-or-perish, if it could be overthrown it would have been).
"Getting academics to act in a way that is not directly in their self-interest because they just love sharing information" is a usually a pretty safe bet, but I think this would be a bit too far. Unless ArXiv can somehow get journals to expect their format (good luck!) I think this is going to be hard.
The authors are from Authorea.com, a for-profit that wants to replace arXiv.
Edit: Aside from that, fully agree with you. Good luck to them.
> Designed to replace journals and papers as the place to establish priority and record your work in full detail, Octopus is free to use and publishes all kinds of scientific work, whether it is a hypothesis, a method, data, an analysis or a peer review.
> Publication is instant. Peer review happens openly. All work can be reviewed and rated.
> Your personal page records everything you do and how it is rated by your peers.
> Octopus encourages meritocracy, collaboration and a fast and effective scientific process.
> Created in partnership with the UK Reproducibility Network.
This article about ArXiv is clearly in the "Democracy and Transparency school" as categorized article, but it doesn't yet address the other three camps. The arxiv article proposes machine-readable semantics, easier sharing and discoverability, papers + supplementary materials + reviews all open; this floods the world with even more publications with varying quality, so it's even harder to identify good quality work; and when things can be more easily aggregated by machines and measured with the alternative metrics proposed, it often leads to a more powerful winner-takes-all system that can be gamed (there's now a subtle game of increasing citations that appear on Google Scholar); finally, with an increase in submissions and materials that go along with submissions, it puts an even greater strain on the review system. These problems are not unsolvable, but almost every idea I've seen proposed so far has only been in a single camp, and there's side effects that harm the goals of the other three camps. So I'd love to see more ideas that balance the interests of all four camps that want to reform peer review and publishing.
[1]: https://blogs.lse.ac.uk/impactofsocialsciences/2022/03/24/th...
http://worrydream.com/ExplorableExplanations/
http://worrydream.com/MediaForThinkingTheUnthinkable/
http://worrydream.com/ScientificCommunicationAsSequentialArt...
etc.
Arxiv needs to go HTML.
I imagine all scientific publications available on a distrusted block store, including raw emails, data and notes on a voluntary basis.
Stuff that could be published would include reviews, corrections in version control fashion, and enough metadata to model scientific progress.
What this article is describing sounds reasonable but not game changing.
Didn't this use to be Latex's tagline? Separate format from content. Which the authors of the article don't find separate enough.
How does the proper separation of format from content even work? Don't you need to markup your content in order for it to become formatted?
But LaTeX is largely an extension of TeX, and these markup languages seem not very amenable to re-implementing parsing / automated processing (given numerous attempts that have resulted in stalemates).
That's what the future will probably look like. With the SQLite decentralized on IPFS or torrent, where only queries get stored on each computer, making more popular queries faster to load (more peers).
*(or maybe an archive of a tons of zstd parquets for each table? - Not sure what the best way to organize several tables in parquet is yet)
Why? The output pdf is typically smaller than the input that produces it. Using rendered pdfs seems simple and very natural, and at worst can use twice the total amount of space.
Although, I had no idea PDFs were smaller than the input. I thought that they were substantially larger actually. But regardless, storing things twice is wasteful.
And if it solves some problems for someone else but not the authors, then how would a comprehensive majority of papers enter the system? Papers are even less interchangeable than movies; if you want to have a particular movie and it isn't available on PopcornTime, you might watch something else, for papers you just have to go elsewhere that actually does have everything.
Can you imagine some of the minds on academic Twitter holding a poll on article popularity? <SHUDDER> Leave science to the foul-tempered misanthropes, I say! j/k
> [Submitted on 20 Sep 2017]
Shouldn't this be "(2017)" - original article was submitted in 2017.
> Web-native and web-first
Absolutely not. It should be "physical paper first". Any long-term archiving cannot rely on electrical devices for viewing archived material. Electrical grids fail. Technology changes. Even if ArXiv is not a print archive, the material in it must be, first and foremost, printable in a consistent manner, and with the authors targeting the physical printed form. Of course, one would need to actually print ArXiv items to physically archive them, but still.
Now, of course archiving data is useful and important; and large amounts of data are less appropriate for print archiving. But that should always be secondary to the archiving on knowledge.
