API is an abbreviation that stands for “Application Program Interface.” Roughly speaking an API is a specification of a software component in terms of the operations one can perform with that component. For example, a common kind of an API is the set of methods supported by a encapsulated bit of code a.k.a. a library (for example, a library could have the purpose of “drawing pretty stuff on the screen”, the API is then the set of commands like “draw a rectangle”, and specify how you pass parameters to this method, how rectangles overlay on each other, etc.) Importantly the API is supposed to specify how the library functions, but does this in a way that is independent of the inner workings of the library (though this wall is often broken in practice). Another common API is found when a service exposes remote calls that can be made to manipulate and perform operations on that service. For example, Twitter supports an API for reading and writing twitter data. This later example, of a service exposing a set of calls that can manipulate the data stored on a remote server, is particularly powerful, because it allows one to gain access to data through simple access to a communication network. (As an interesting aside, see this rant for why APIs are likely key to some of Amazon’s success.)
As you might guess, (see for example my latest flop Should Papers Have Unit Tests?), I like smooshing together disparate concepts and seeing what comes out the other side. When thinking about APIs then led me to consider the question “What if Papers had APIs”?
In normal settings academic papers are considered to be relatively static objects. Sure papers on the arXiv, for example, have versions (some more than others!) And there are efforts like Living Reviews in Relativity, where review articles are updated by the authors. But in general papers exist, as fixed “complete” works. In programming terms we would say that are “immutable”. So if we consider the question of exposing an API for papers, one might think that this might just be a read only API. And indeed this form of API exists for many journals, and also for the arXiv. These forms of “paper APIs” allow one to read information, mostly metadata, about a paper.
But what about a paper API that allows mutation? At first glance this heresy is rather disturbing: allowing calls from outside of a paper to change the content of the paper seems dangerous. It also isn’t clear what benefit could come from this. With, I think, one exception. Citations are the currency of academia (last I checked they were still, however not fungible with bitcoins). But citations really only go in one direction (with exceptions for simultaneous works): you cite a paper whose work you build upon (or whose work you demonstrate is wrong, etc). What if a paper exposed a reverse citation index. That is, if I put my paper on the arXiv, and then, when you write your paper showing how my paper is horribly wrong, you can make a call to my paper’s api that mutates my paper and adds to it links to your paper. Of course, this seems crazy: what is to stop rampant back spamming of citations, especially by *ahem* cranks? Here it seems that one could implement a simple approval system for the receiving paper. If this were done on some common system, then you could expose the mutated paper either A) with approved mutations or B) with unapproved mutations (or one could go ‘social’ on this problem and allow voting on the changes).
What benefit would such a system confer? In some ways it would make more accessible something that we all use: the “cited by” index of services like Google Scholar. One difference is that it could be possible to be more precise in the reverse citation: for example while Scholar provides a list of relevant papers, if the API could expose the ability to add links to specific locations in a paper, one could arguably get better reverse citations (because, frankly, the weakness of the cited by indices is their lack of specificity).
What else might a paper API expose? I’m not convinced this isn’t an interesting question to ponder. Thanks for reading another wacko mashup episode of the Quantum Pontiff!
O brave new quantum world!
Some thoughts come to mind.
– micro-comments – I have the ability to tag a paragraph of your paper with a comment, much like what we can do now on certain blog posts (like with Medium)
– proof substitutions: fix bugs in a proof, or link to a simpler proof of a claim.
– code invocations: embedded code in my paper can be accessed via an API call, or even better, you could run my code with your data.
Notebook environments like iPython and iHaskell make it feasible to provide as “Supplemental Information” both a symbolic derivation of the main results (so less guesswork regarding “it can be shown”) and a replicable numerical computation of figures and tables (so less guesswork regarding “numerical computations indicate”).
It’s unfortunate (as it seems to me) that iPython and iHaskell are evolving rapidly … a great virtue of TeX is that it evolves not at all, and of LaTeX that it evolves with glacial slowness.
Also, thanks for sustaining The Quantum Pontiffs as a wonderful forum.
N.B. Some Quantum Pontiff readers may be interested too in the Knuth-style command-line “nuweb system for Literate Programming.”
Two attractive features of nuweb are: (1) enables literate programming in any text-file programming language, and (2) source-code sufficiently simple and well-documented that you can modify it yourself as-needed.
E.g., I’ve had pleasant experiences with nuweb/matlab literature programming. Needless to say, Knuth-style literate programming requires a *lot* of additional work in *any* API; neither nuweb nor any other literate programming api (that is known to me or anyone else) composes a magic bullet for eliminating this work.
Another reference Donald Knuth amusingly summarizes his present-day views on the virtues of API-stability in “The TEX tuneup of 2014“ (TUGboat, 35(1), 2014).
I think this is superseded by the idea of having papers essentially as code repositories (say as git repos on github, or similar). Then if there’s a horrible flaw, you just fix it, or open a bug report.
I think the “opt-in” form of citations will eventually die out anyway, to be replaced with programmatic style ones where my “paper” builds on yours because it literally *requires* it to “compile”, so I don’t see any point to try and make the “old” citation system marginally better.
@misc{Avigad:2014aa, Author = {Jeremy Avigad
and Steve Awodey and Robert Harper and Daniel
Licata and Michael Shulman and Vladimir
Voevodsky and Andrej Bauer and Thierry Coquand
and Nicola Gambino and David Spivak},
Howpublished = {{MURI} proposal: on-line
\url{https://hottheory.files.wordpress.com/
2014/04/ proposalpublic2.pdf}}, Month = {April
29}, Title = {Homotopy type theory: unified
foundations of mathematics and computation},
Year = {2014}}
@article{McLarty:1990aa, Author = {Colin
McLarty}, Journal = {British Journal of the
Philosophy of Science}, Pages = {351-375},
Title = {The uses and abuses of the history of
topos theory}, Volume = {41}, Year = {1990}}
@article{Lawvere:2014aa, Author = {F. William
Lawvere}, Journal = {Reprints in Theory and
Applications of Categories,}, Pages = {1-22},
Title = {Comments on the development of topos
theory}, Volume = {24}, Year = {2014}}
@article{cite-key, Author = {Richard Rorty},
Journal = {Wilson Quarterly}, Pages = {30},
Title = {Against Unity}, Volume = {(Winter)},
Year = {1998}}
@incollection{Foucault:2000aa, Author =
{Michel Foucault}, Booktitle = {Ethics:
Subjectivity and Truth}, Editor = {Michel
Foucault and Paul Rabinow}, Pages = {111–19},
Publisher = {Lane, The Penguin Press}, Title =
{Polemics, Politics and Problematizations},
Volume = {1}, Year = {2000}}
Works that consider (implicitly or explicitly) the features of a compiled STEM culture — features that are some regards positive, but mainly are negative — include the following:
(1) Homotopy Type Theory: Unified Foundations of Mathematics and Computation (Avigad et al., MURI Proposal, 2014) A STEM literature that ‘compiled’ in 20th century ZFC might not ‘compile’ in 21 century HoTT.
(2) The uses and abuses of the history of topos theory (Colin McLarty, 1990) It is adventageous for students to regard present-day ZFC dominance as a more-or-less accidental historical contingency.
(3) Comments on the development of topos theory (F. William Lawvere, 2014) “One should not get drunk on the idea that everything is general. Category theorists should get back to the original goal: applying general results to particularities and to making connections between different areas of mathematics.”
(4) Against Unity (Richard Rorty, 1998) Theorems natural in one language may be non-natural in another language.
(5) Polemics, Politics and Problematizations (Michel Foucault, 2000) summarizes broad cultural implications of discourse presented solely as logic grounded in postulates that are nominated as axioms (by whom?) …
Conclusion Each generation of researchers (including QIT researchers) has found ample reason to be glad that the previous generation of researchers did not insist upon rigid ‘compile-time’ axioms.
@misc{Avigad:2014aa, Author = {Jeremy Avigad
and Steve Awodey and Robert Harper and Daniel
Licata and Michael Shulman and Vladimir
Voevodsky and Andrej Bauer and Thierry Coquand
and Nicola Gambino and David Spivak},
Howpublished = {{MURI} proposal: on-line
\url{https://hottheory.files.wordpress.com/
2014/04/ proposalpublic2.pdf}}, Month = {April
29}, Title = {Homotopy type theory: unified
foundations of mathematics and computation},
Year = {2014}}
@article{McLarty:1990aa, Author = {Colin
McLarty}, Journal = {British Journal of the
Philosophy of Science}, Pages = {351-375},
Title = {The uses and abuses of the history of
topos theory}, Volume = {41}, Year = {1990}}
@article{Lawvere:2014aa, Author = {F. William
Lawvere}, Journal = {Reprints in Theory and
Applications of Categories,}, Pages = {1-22},
Title = {Comments on the development of topos
theory}, Volume = {24}, Year = {2014}}
@article{cite-key, Author = {Richard Rorty},
Journal = {Wilson Quarterly}, Pages = {30},
Title = {Against Unity}, Volume = {(Winter)},
Year = {1998}}
@incollection{Foucault:2000aa, Author =
{Michel Foucault}, Booktitle = {Ethics:
Subjectivity and Truth}, Editor = {Michel
Foucault and Paul Rabinow}, Pages = {111--19},
Publisher = {Lane, The Penguin Press}, Title =
{Polemics, Politics and Problematizations},
Volume = {1}, Year = {2000}}
N.B. One more amusing reflection is provided by (historian) Jonathan Israel …
Conclusion Israel’s categoric considerations read naturally (and amusingly) as applying broadly to STEM discourse, particularly to the Harrow/Kalai debate.
@misc{Israel:2014ab, Author =
{Jonathan Israel}, Howpublished =
{\emph{Five Books} on-line interviews
(\url{http://fivebooks.com/interviews
/jonathan-israel-on-enlightenment})},
Month = {Nov 28}, Title = {An
interview with.{J}onathan {I}srael on
the {E}nlightenment}, Year = {2014}}
Another API-related reference Per recent API-related discussion on Gödel’s Lost Letter, the attention of Quantum Pontiff readers is directed to the recent Bulletin of the AMS article by Pelayo and Warren “Homotopy type theory and Voevodsky’s univalent foundations” (2014). The concluding paragraph of Pelayo and Warren’s article is an explicit roadmap for an API that encompasses both mathematical, scientific, and engineering publications:
Needless to say, plenty of mathematicians are expressing concern. On Michael Harris’ weblog Mathematics without apolofies (which is a *very* fun weblog), a comment by Richard Séguin speaks for many folks (including me):
Conclusion At present the STEAM community suffers not from too-few too-old research APIs, but rather too many research APIs that are too new.
@article{Pelayo:2014aa, Author = {{\'A}lvaro
Pelayo and Michael A. Warren}, Journal = {Bull.
Amer. Math. Soc.}, Pages = {597-648}, Title =
{Homotopy type theory and Voevodsky's univalent
foundations}, Volume = {5}, Year = {2014}}
Here’s news of broad interest to readers of weblogs like The Quantum Pontiffs, Shtetl Optimized, Gödel’s Lost Letter, and Quantum Frontiers:
There’s plenty more material on the LogiQ Program Proposer’s Day announcement page.
Readers of Michael Harris’ book and/or weblog Mathematics Without Apologies (as they are both titled) will appreciate that IARPA is designating stable logical qubits as an avatar (in Harris’ phrase) for catalyzing advances in our general understanding of noise, decoherence, and entropy.
Conclusion The physical process of removing von Neumann entropy from systems of qubits/qudits can be appreciated as a mathematical avatar — in Michael Harris’ phrase — for the computational algorithms that (heuristically) are so marvelously effective in removing Boltzmann entropy from atoms/molecules in large-scale quantum simulation software … sufficient to compose (F)foundations for the $120M/5yr investment by the Swiss-based pharmaceutical corporation Sanofi in the Portland-based quantum simulation corporation Schrödinger.
Hopefully at least some East Coast quantum cognoscenti will attempt/report on this fine workshop!
Further high-value discussion of mathematical API’s — by luminaries like Lurie, Tao, Donaldson, etc — is summarized by Michael Harris in this week’s Mathematics Without Apologies “Univalent Foundations: “No Comment.”“ (May 13, 2015).
Terry Tao’s view:
Note: Harris provides a link to an on-line video of this discussion.
Assuming I understand what you’re suggesting…
Having just recently read about controversial papers, this came to mind. Suppose someone publishes research that is considered “politically incorrect” or “politically sensitive”, whatever field it may be. Allowing for revisions of papers allows for effectively “changing the past”, which, in my opinion, is the kiss of death for the preservation of truth. Yes, some fields might benefit from it, such as computer science, which, at the moment, has no serious political or social issues I’m aware of that would be negatively affected from this… at least until super AI is invented. That too may change when culture decides that AI should have a prominent role in society – for better or for worse – and like-minded new generations of scientists decide to go back and “change the books” to fit cultural trends.
The fact that scientific papers are set-in-stone, so to speak, allows us to go back and reference things of the past without worry that they will be modified to fit current views. For example, challenges have been made about the traditional Copenhagen interpretation on quantum mechanics. Notably, those views were stomped on for a long time but are coming back in recent years. The papers about them dating back to the 70s haven’t changed. No one went back to “change the books” because that’s not what we do in science.
Wrong or right, the paper needs to stay the same.
Furthermore, consider all of those papers that reference papers that are wrong. Such papers may explicitly call attention to the wrongs. But if those wrongs are corrected, readers of the new papers won’t know the problem (in the old papers) that the new papers are referring to. The new papers may say “Previously, we thoughtPQR [1][2][3], but recent studies show XYZ [4][5][6]”, and such.
Unchanging scientific papers show us where we’ve been and give us a standard to compare our current work against. Let’s leave them alone please.
N Anderson I think this is easily addressed by having the system keep a history of changes. Very similar to how arxiv.org keeps a history of all papers that have been submitted (so if you find a withdrawn one you can find the previous version). Exposing this history I think would be an problem, but by preserving it you won’t be able to “rewrite the past”.