What If Papers Had APIs?

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What If Papers Had APIs?[modifier]

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!

Suresh says:[modifier]

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.

John Sidles says:[modifier]

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.

John Sidles says:[modifier]

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.

John Sidles says:[modifier]

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).

Noon Silk says:[modifier]

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.

John Sidles says:[modifier]

https://hottheory.files.wordpress.com/2014/04/ proposalpublic2.pdf}}, Month = {April29}, 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}}

John Sidles says:[modifier]

Noon Silk predicts “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’.”

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?) …

I like discussions, and when I am asked questions, I try to answer them. It’s true that I don’t like to get involved in polemics. […] I don’t belong to the world of people who do things that way. I insist on this difference as something essential: a whole morality is at stake, the one that concerns the search for truth and the relation to the other.

In the serious play of questions and answers, in the work of reciprocal elucidation, the rights of each person are in some sense immanent in the discussion. They depend only on the dialogue situation. The person asking the questions is merely exercising the right that has been given him: to remain unconvinced, to perceive a contradiction, to require more information, to emphasize different postulates, to point out faulty reasoning, and so on. As for the person answering the questions, he too exercises a right that does not go beyond the discussion itself; by the logic of his own discourse, he is tied to what he has said earlier, and by the acceptance of dialogue he is tied to the questioning of other. Questions and answers depend on a game ­ a game that is at once pleasant and difficult ­ in which each of the two partners takes pains to use only the rights given him by the other and by the accepted form of dialogue.

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}}

John Sidles says:[modifier]

N.B. One more amusing reflection is provided by (historian) Jonathan Israel …

Categories are terribly important, not just for philosophers, but for everyone.

Historians sometimes forget this and try to operate without categories, but I don’t think that’s a very good way of pursuing historical studies [because] one is always in danger of thinking about something, making up your mind about it, and then not being critical enough in your thinking on that topic subsequently.

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}}

John Sidles says:[modifier]

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:

Ultimately, we hope that it will be possible to formalize large amounts of modern mathematics in the univalent setting, and that doing so will give rise to both new theoretical insights and good numerical algorithms (extracted from code in a proof assistant like Coq) which can be applied to real-world problems by applied mathematicians.

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):

Another concern that I have [is] the language du jour problem. There have been many fads over the years in computer programming languages, CS folks seem to love inventing new ones*, and backwards compatibility with anything is generally not a central concern.

In mathematics, there has always been, for example, drift in notation and invention of new words, but it generally happens slowly enough that there isn’t much of a problem reading 50 year old papers.

Similarly, TeX, mathematic’s typesetting language, evolves slowly, generally has backward compatibility, and is the universally accepted standard.

In contrast, I suspect that we will see a proliferation of different “foundations,” proof checkers, and proof generators driven by CS folks*, and it will never settle down, mirroring the situation with programming languages. I see the chaos of a Tower of Babel. Tell me it ain’t so.

  • especially if research money starts to flow

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}}

John Sidles says:[modifier]

Here’s news of broad interest to readers of weblogs like The Quantum Pontiffs, Shtetl Optimized, Gödel’s Lost Letter, and Quantum Frontiers:

SYNOPSIS The Intelligence Advanced Research Projects Activity (IARPA) will host a Proposers’ Day on 19 May 2015 at the University of Maryland Stamp Student Union to provide information to potential proposers on the objectives of an anticipated Broad Agency Announcement (BAA) for the Logical Qubits (LogiQ) program.

PROGRAM OBJECTIVE AND DESCRIPTION The LogiQ program in IARPA’s Safe and Secure Operations (SSO) Office is seeking creative technical solutions to the challenge of encoding imperfect physical qubits into a logical qubit that protects against decoherence, gate errors, and deleterious environmental influences.

While quantum information processing has witnessed tremendous advances in high-fidelity qubit operations and an increase in the size and complexity of controlled quantum computing systems, it still suffers from physical-qubit gate and measurement fidelities that fall short of desired thresholds, multi-qubit systems whose overall performance is inferior to that of isolated qubits, and non-extensible architectures-all of which hinder their path toward fault-tolerance.

Underpinning the program’s strategy to build a logical qubit is a push for higher fidelity in multi-qubit operations, the pursuit of dynamically controlled experiments in multi-qubit systems to remove entropy from the system during computation, and characterization and mitigation of environmental noise and correlated errors.

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!

John Sidles says:[modifier]

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:

“Some day we may actually write our papers, not in LaTeX … but in language that some smart software could convert into a formal language, and every so often you get a compilation error: ‘THE COMPUTER DOES NOT UNDERSTAND HOW YOU DERIVE THIS STEP’.”

Note: Harris provides a link to an on-line video of this discussion.

Anderson says:[modifier]

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.

Pontifex Praeteritorum says:[modifier]

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”.

The Secret Order of the ArXiv[modifier]

Posted on June 10, 2009 by Pontifex Praeteritorum

The astro/physics blogosphere is all atwitter about papers the Nature embargo policy (See Julianne If a paper is submitted to nature does it still make a sound, the cat herder Hear a paper, see a paper, speak no paper, and he of less than certain principles Unhealthy obsessions of academia. He of uncertain principles loses the catchy title contest  )

In this discussion, the uncertain principal brings up an interesting effect for arXiv postings:

There’s an obsession in science with the order of publication that I don’t think is really healthy, and I think it’s only gotten worse. At the Science21 meeting last fall, Paul Ginsparg talked about how there’s a huge spike in arxiv submissions just after 4pm, because the daily update email puts papers in the order in which they were submitted, starting at 4pm. He said they can see scripts hitting the server to check the time, and then dumping papers in just as soon as the clock has ticked over. Apparently, the position of a paper in that email has a fairly significant effect on the number of views and citations that paper receives in the future.

Now I myself have been known to try to exploit this effect, but what I don’t understand is why, given that the arXiv crew knows about this effect, that they don’t fix it. I know it probably would be a bit of a hassle to rewrite the code, but really it shouldn’t be impossible to make the order of papers appearing in a day’s listing random.

Actually come to think of it is should be rather easy to fix this. Instead of ordering by date, one can just order by some hidden function of the, say, the title of the paper, the time submitted, and the author list. Of course that would just mean that we could spend some time cracking the arXiv’s hiding function 

On a related note, I just submitted a new version of arXiview to Apple (which means it will appear in a few days time) which has some new features, including….ordering the search and posting results by submitted time/date.

The Great Firewall of Collaboration[modifier]

Posted on July 16, 2009 by Pontifex Praeteritorum

A fellow quantum computing researcher of mine recently joined FriendFeed. Along with another researcher we got involved in a discussion about a paper concerning a certain recent claimed “disproof of Bell’s theorem.” (arXiv:0904.4259. What it means to “disprove a theorem” like Bell’s theorem is, however a subject for another comment section on a different blog.) But, and here is the interesting thing, this colleague then made a trip to China. And FriendFeed, apparently, is blocked by the great firewall of China, so he had to email us his comments to continue the conversation. Which got me thinking.

China is a country that has been, historically, a great power. It is, by all accounts, returning to that status with the a wave of lifting of its people out of poverty (numbers I’ve seen are from like over 60 percent below poverty a few decades ago to 10 percent recently, though it’s not clear to me that the poverty level (a few dollars per day) used is the really relevant number.) It has, even more interestingly, achieved an amazing increase in the production of people with a large amount of education. From under 10,000/year PhDs a decade ago to nearly 50,000/year recently, there has been a huge increase in PhDs in a very short span of time. In some minds, the rise of China is the dominant story of the coming decades. This is equally true in academic circles where the productivity of science in China has been rising rapidly.

But my colleague’s experience made me wonder a bit. Suppose that you take at face value the idea that online tools are going to change how we do science (through any of the numerous forms that such tools can now take.) If the Chinese government is banning tools that allow for collaboration (in our case, just a mere discussion) then, despite all they do, I wonder if this might cause a severe lack of bang for their Ph.D buck. Do we really believe that the kind of large scale data sharing or online collaborating, for example, that characterize Science 2.0 will be easy to carry out under the probing eye of the Chinese government? Of course, I’m as far from an expert in China and Science 2.0, so I can’t even begin to approach this question. But it did strike me that there are some fairly strong preconditions assumed by those pushing online tools for science that don’t seem to hold for numerous countries around the world, including China.

Or, in other words (executive summary), those of you doing Science 2.0 can now think about yourselves as modern freedom fighters. Hazzah!

Janne says:[modifier]

More probably, Chinese scientists join and collaborate in Chinese-language collaboration tools within the country. Just like most Japanese use Japanese language-based tools to communicate and collaborate in Japanese rather than trying to do so badly in English on some foreign web site.

You haven’t reflected on the fact that most of the people you interact with are Americans or situated in the US could be not because most researchers are stationed there, but because the sites and tools you use are self-selecting for a particular demographic?

Dave Bacon says:[modifier]

Hi Janne,

More probably, Chinese scientists join and collaborate in Chinese-language collaboration tools within the country. Just like most Japanese use Japanese language-based tools to communicate and collaborate in Japanese rather than trying to do so badly in English on some foreign web site. Agreed, but I’m not sure why China won’t touch these sites.

The point I was at least trying to make was that a lot of the ideas floating around the world of Science 2.0 share a large overlap with ideas that would make any country whose power rests on suppressing information. I don’t see where I made a claim about these tools being US centric, except that currently my colleague can’t use a tool from behind the firewall.

Matt,

Anyway, I think that most people with a science Ph.D. can probably figure out how to use a proxy server.

I’m sure they can (though you know, those biologists j/k!) but barriers to entry cut down fractions. Especially if you are, in some way, risking being thrown in jail. It’s an extreme example, but Iran demonstrates what can happen to internet infrastructure when the people at the top are bent on keeping the lid on.

Matt Leifer says:[modifier]

Thanks for pointing out the comment thread on Scott’s blog. I somehow missed that, but it was very entertaining.

Anyway, I think that most people with a science Ph.D. can probably figure out how to use a proxy server.

Eric Lund says:[modifier]

Janne: What you say is probably true, but it doesn’t address the points that (1) the Chinese government is known to be censoring internet content and (2) sometimes Chinese people, or foreign visitors to China, collaborate with scientists outside China who do not necessarily read Chinese. So, far, most cutting edge research in China has been in collaboration with non-Chinese institutes. That may not always be true, and when it ceases to be true the Great Firewall will no longer be a major problem. Until scientists have to start learning Chinese in order to avoid missing important papers, the Great Firewall remains a problem.

Janne says:[modifier]

Eric, you’re absolutely right, and I deplore the Chinese firewall myself.

But, actual research collaboration always happens on a personal level. Email or personal visits kind of thing. A general censorship policy doesn’t touch that, just as the general language barrier between Japanese (or German, or French or whatever) scientists doesn’t impede the high-level research collaboration between them very much.

But here you highlight something I naively thought everybody already knew to be a serious problem:

“Until scientists have to start learning Chinese in order to avoid missing important papers, the Great Firewall remains a problem.”

Unless you read (and follow) academic English, German, Japanese, Chinese, French and Spanish you are already missing important papers. “Important”, as in “our next step is a Science/Nature publication” kind of important. Each of those languages have large and thriving scientific communities in their own right, with journals and conferences publishing significant results. And those publications count. If you’re not aware of the stuff being published in other major languages you’re at a definite disadvantage.

But of course very few people are. The scientific community is already long split by language and cultural barriers. We manage to muddle through.

Janne says:[modifier]

Dave, as I said I am firmly against everything the Chinese firewall stands for – and the same goes for the Australian and other government attempts at censorship.

My point is that your concept of “Science 2.0” is parochial in nature; some incidental censorship firewall doesn’t affect it. Nobody is censoring communication with German or Japanese or Spanish scientists, and yet your “science 2.0” idea doesn’t even acknowledge the idea of participants communicating in other languages.

Wim van Dam says:[modifier]

> Unless you read (and follow) academic English, German, Japanese, Chinese, French and Spanish you are already missing important papers.

To which fields of science does this apply? Only once a year do I need to read an (old) math article in French, otherwise everything else is done in English. Seriously, which research journal or conference in Spanish am I missing out on?

not quite chinese says:[modifier]

Well, Tibetans and Uyghurs, among others, are repressed, Falun Gong practitioners are being made to “disappear” and being tortured in jails. China and the Chinese people have bigger problems than whether to hold scientific conversations on friendfeed or over email.

IMHO China is in pretty awful shape, and it doesn’t have one bit to do with scientific collaboration. The reason is that the stronger China gets, the less the world can tell it to stop oppressing minorities and freedoms. It seems that the Chinese government will not stop the oppression and censorship, and that Chinese people are generally Okay with it, as long as it doesn’t happen to their family (the common approach as far as I can tell is “if someone is in jail, they must have done something wrong, and besides, everyone is getting richer!”).

If I extrapolate, then in 50 years China will rule the world, take away everyone’s freedoms, and have some Westerners do scientific research because an overwhelming majority of Chinese people cannot think freely anyway (which is why they’re willing to live with censorship in the first place).

China’s problem is not censorship. Censorship is the symptom to a society that has been degraded and broken down to the point of considering itself to be a mindless flock and embracing that view of itself. It’s a Fascist state of mind if I ever saw one. The country and its unity is above all, and the default behavior is to obey authority.

Remark: there are exceptions, of course. There were also exceptions in Fascist Italy. Of the exceptional people, some stayed quiet, and those who had spoken up went to jail or were killed. The general public would assume that they must have done something wrong. After all, the country and its unity is above all.

By the way, read the story of the lawyer Gao Zhisheng http://en.wikipedia.org/wiki/Gao_Zhisheng[modifier]

who was first selected as one of the top ten lawyers in China by China’s Ministry of Justice, in 2001, for his work protecting human rights in Xinjiang, but when he started speaking against the torture of Falun Gong practitioners, he was put in jail and tortured himself, and his family suffered many ordeals. His family fled (in quite an escape) to the US, and he has “disappeared” shortly thereafter. He’s quite a remarkable man. Read his letters to the Chairman. Parts of them are quoted in the wikiepdia entry. The Wikipedia entry is blocked in China, naturally.

Falun Gong practitioners, by the way, are tortured in all manners of terrible ways. Read about it here: http://en.wikipedia.org/wiki/Persecution_of_Falun_Gong . The numbers are unbelievable: more than 50,000 tortured, more than 100,000 sent to reeducation camps. From my experience, Chinese people know about this (although maybe not the complete details, which they never bothered finding out) and support this, giving as a reason that “Falun Gong is a cult”. It’s amazing to see how Chinese people who more often than not are mad about the government for not allowing freedom of speech, putting the great firewall, etc, are almost uniformly supportive of oppression of Tibetans, Uyghurs, Falun Gong, and others.

By the way, Falun Gong might be a cult for all I know. It’s unclear what they’re really about, but I wouldn’t be surprised if they are a cult. No one in their right mind would keep resisting the government given such violence and risk. This is exactly why the government is afraid of them. However, I hardly see being a cult as a reason that justifies torture or incarceration.

John Sidles says:[modifier]

Janne says: Unless you read (and follow) academic English, German, Japanese, Chinese, French and Spanish you are already missing important papers.

That is true not only in mathematics and science, but in engineering too … especially in engineering.

A key word in Janne’s statement (IMHO) is the word “important”. What quality(s) distinguish a paper as important? If we take that quality to encompass the launching of new enterprises, then the Chinese literature­particularly in simulation science and engineering­is already hugely important.

This is good. Because our planet needs all the new enterprises it can create.

Paul Murray says:[modifier]

Surely you could just as fairly reach the opposite conclusion? That web 2.0 for scientific collaboration is all hoohey, because the chinese manage to do great research without it?

Paul A. Helgeson says:[modifier]

China is in a very delicate situation. Very nearly 1.5 billion people with a 6,000 year history of oppression and revolution. The powers-that-be KNOW which side their bread is buttered on.

Democracy and capitalism IS going to come to China regardless of an one person’s or group of peoples desires and they KNOW this.

However, consider the process of transitioning 1.5 billion people from effectively a state run poverty system to a system that will be as powerfully successful and progressive as China with the throttle wide open and the limits removed without implosion or explosion.

No, this process can not be done wide open and with everyone doing as they wish or as they want. There MUST be controls and limits to what everyone does and what everyone has access to.

No, I do NOT appreciate many of the sanctions and limitations that the Chinese government has elected to impose – Tibet should be free, people should be free from fear, etc. I had a Chinese language professor whose family was deeply affected by the politics of China (imprisonments, etc.) so have some idea of what can and does happen.

But, to imagine pulling out all the stops on 1.5 billion people overnight…that would be the cruelest thing the Chinese government could do to their own people. The chaos and deception and fraud not to mention how many people would be taken advantage of…

The China of today is so incredibly different from the China of 20 years ago and the China of 10 years from now will be so incredibly different from today as to make our complaints today seem laughable.

Give them a chance to grow. Support them as best you can. Help when and where you can. Stand for what you stand for. But never ever tell them what them must or should do. They’ve been doing it much longer then we have. Much, much longer.

And they are not particularly interested in the opinions of some wet behind the ears westerner who thinks that 500 years of civilization under their belt qualifies them for a learned opinion of how things ought to be.

The one other thing to recognize is the China has always had and probably always will have the ability to conquer most if not all of the peoples of the Earth. They have stood ready to do so on a couple of occasions in history and returned home. The reason has been the same as the reason they pose no real threat to national security today…they are interested in one thing and one thing only. China, The Middle Kingdom. If if isn’t China, to them, it is not particularly important.

Why I Left Academia[modifier]

Posted on September 22, 2013 by Pontifex Praeteritorum

TLDR: scroll here for the pretty interactive picture.

Over two years ago I abandoned my post at the University of Washington as a assistant research professor studying quantum computing and started a new career as a software developer for Google. Back when I was a denizen of the ivory tower I used to daydream that when I left academia I would write a long “Jerry Maguire”-esque piece about the sordid state of the academic world, of my lot in that world, and how unfair and f:*ked up it all is. But maybe with less Tom Cruise. You know the text, the standard rebellious view of all young rebels stuck in the machine (without any mirror.) The song “Mad World” has a lyric that I always thought summed up what I thought it would feel like to leave and write such a blog post: “The dreams in which I’m dying are the best I’ve ever had.”

But I never wrote that post. Partially this was because every time I thought about it, the content of that post seemed so run-of-the-mill boring that I feared my friends who read it would never ever come visit me again after they read it. The story of why I left really is not that exciting. Partially because writing a post about why “you left” is about as “you”-centric as you can get, and yes I realize I have a problem with ego-centric ramblings. Partially because I have been busy learning a new career and writing a lot (omg a lot) of code. Partially also because the notion of “why” is one I­as a card carrying ex-Physicist­cherish and I knew that I could not possibly do justice to giving a decent “why” explanation.

Indeed: what would a “why” explanation for a life decision such as the one I faced look like? For many years when I would think about this I would simply think “well it’s complicated and how can I ever?” There are, of course, the many different components that you think about when considering such decisions. But then what do you do with them? Does it make sense to think about them as probabilities? “I chose to go to Caltech, 50 percent because I liked physics, and 50 percent because it produced a lot Nobel prize winners.” That does not seem very satisfying.

Maybe the way to do it is to phrase the decisions in terms of probabilities that I was assigning before making the decision. “The probability that I’ll be able to contribute something to physics will be 20 percent if I go to Caltech versus 10 percent if I go to MIT.” But despite what some economists would like to believe there ain’t no way I ever made most decisions via explicit calculation of my subjective odds. Thinking about decisions in terms of what an actor feels each decision would do to increase his/her chances of success feels better than just blindly associating probabilities to components in a decision, but it also seems like a lie, attributing math where something else is at play.

So what would a good description of the model be? After pondering this for a while I realized I was an idiot (for about the eighth time that day. It was a good day.) The best way to describe how my brain was working is, of course, nothing short than my brain itself. So here, for your amusement, is my brain (sorry, only tested using Chrome). Yes, it is interactive.

Florin Moldoveanu says:[modifier]

Why I want to come back to academia.

There seem to be a natural relationship between physicists and software development. I started my career in physics in prolific group oversees which produced a publication a month in serous journals like Phys Rev and then I came to US to do a PhD here. When I graduated, I faced the uncertainty of funding because the cold war ended. Not wanting to take risks with my green card, I took a job as a software developer for my adviser’s company utilizing my math skills very well. I was thinking that if I will have something really important to say in physics I’ll come back.

Fast forward through 3 software developer companies, I learned the inside and out of every aspect of software development and management. I was responsible for development software worth tens of millions of dollars in recurring revenue, I managed 3 development groups in 3 countries at the same time, I managed millions of lines of code. Now with this came an unexpected side effect. I earn a sizable salary. Also it happens that now I have very important things to say in quantum mechanics.

First when I tried to came back to physics, nobody took me seriously but this is gradually changing. The big problem however is that I cannot get a salary to match the software career salary right away. Increasing salary is like increasing entropy: irreversible process. Given my long term financial commitments (mortgages, college expenses for my kids) I cannot take a pay cut and start as a post doc someplace.

I do want to come back to academia because I am working on very hard problems and they started producing amazing results. They sure beat any job satisfaction in the software world by orders of magnitude. But I am trapped in software development by my current high standard of living.

So my advice for you is DON’T DO IT.

A says:[modifier]

I think the advice here is more like getting a wife with more money than you do.

angry says:[modifier]

Hmm, I was hoping for more about your departure from academia. I have fantasies about leaving, but the prospect of having a 9-5 schedule, having to wear clothes other than jeans, and not being completely free during the summer just seems too much. More disposable income and different challenges though… “Mad World” is great, as is the whole of “The Hurting.”

Dave Bacon says:[modifier]

angry: at Google the dress code is “wear something” 

Michael Nielsen says:[modifier]

Loved the interactive graph!

Regarding the rant: if you’re worried that it’d be “run-of-the-mill boring”, why not just focus on the less run-of-the-mill bits? (I.e., publish the diffs.)

Alice says:[modifier]

As one of your former advisees, this is actually really interesting to poke at. Personally I think I’m well out of academia – I was probably never going to be happy as faculty (at least not in quantum computing/CS theory), but I could have easily spent another 3-4 years in grad school figuring that out if I hadn’t hit a decision point when I did.

I’d also be interested to read the bigger “leaving academia” story. While CS/physics grad school isn’t overall the same kind of trap as, say, a PhD in English (which is probably only something you should do if you’re very, very good, and if someone will pay you to do it), it’s still a major commitment that’s not a good fit for a lot of people. Few, if any, of the students I started with in 2007 have graduated, and even fewer have academic jobs. Many have left academia entirely. So when I talk to people who are in grad school or considering it, it’s hard to really know what to say. Success rates can be high or low depending on how you define “success”. I currently work on a software team that’s full of PhDs (in CS), most of whom are quite vocal about the fact that they probably could have skipped the whole dissertation thing and pretty much gotten the same benefit from the experience.

John says:[modifier]

Did graph isomorphism burn you out? I think you were doing good work, for what it’s worth. I’m sure you still are. I ask because you left out the other obvious option, of working at an industrial or government research lab. There are quite a few out there, including Microsoft outside Seattle and even now Google.

Dave Bacon says[modifier]

Thanks for the kind words John. Part of burning out was certainly the frustration of spending a lot of time working on problems I considered important (graph isomorphism among them, I’d also include self-correcting quantum memories as another) and not making significant progress. I think when you work on these problems and you meet lots of very smart people you start to question whether you stand a chance. Plus it is particularly heart wrenching to work on these problems and think you’ve found a path forward only to realize that you don’t. These are part of my character weakness, no doubt. Burnout doesn’t mean you don’t care about what your working on, at least for me, it meant that I needed a break from the emotional roller coaster. Also, at least for the first year after I left, I also still spend a portion of my free time thinking about the problems I care about.

You’re right that I didn’t seriously consider research labs. This was partially a conscious decision: if I was going to try something new, it seemed that a research position at one of these institutes, or a large company, would have not been healthy (if you’re burned out, continuing to do the same thing seems like a bad choice). I never even applied at Microsoft ; (I once got rejected for a postdoc there, and when you look at the people they hire, well…. I don’t have a fields medal )

Matthias Gallé says[modifier]

Thanks for this extremely sincere picture from your brain. This is better than any page-long post. What did you use to do the network?

Dave Bacon says:[modifier]

D3.js

It’s a neat little framework. I’m trying to find some time to build more fun graphics with it.

Kingsley Jones says:[modifier]

As one who left Academia close to two decades ago I would say this… It is good to move around and do different things. I left Academia because I got frustrated. I had, at a very young age, already discovered plenty, published some, found some good enemies, and built a huge stock of unpublished results. It was time to leave or I would just get grumpy. I did a simple demographic calculation. I looked around the department and asked myself this question: “What is the Bell Curve for Expected Retirement Age?”.

The answer I came up with (in 1994) was: 2012!

That gave plenty of time for me to get on with life and learn new things. The simple truth about Physics (and Science in general) is that there is so very much to fix that none of it will get fixed until we get a change of the guard.

That is happening now, so things will improve. However, the entire Academic research model is broken so it will not happen in Academia. It will certainly happen, and will be driven by Academically trained persons, but it will not be in the Ivory Tower.

Don’t worry, be happy about that… the age of the MooC, the blog, the self-published and self-organized research community is the way of the future.

The Academy is properly a state of mind, not a job, a place, or a title.

If you like researching new things, being paid well, respecting the manifold areas of life you can never fully master then be happy in commerce and industry.

It is not a bad place and you could well make several fortunes.

Also, you should rest assured that much of the Academic orthodoxy will be swept aside in five years time by a new generation. Discovering new things has never been easier!

Almost nobody in the orthodox Academic sphere is even trying 

YS says:[modifier]

Seeing clearly what is going on in the head of my 6-year-old often makes me realize we adults behave the same, just with more cover-ups. For example, she is pretty good at justifying her actions, like “I ate the candy because I didn’t want Di-Di (her brother) to get cavity”. One such episode gave me the inspiration that perhaps many of the paper reviews I’ve seen, looking so professional and well reasoned, were merely justifications of emotions. That may very well apply to reviews I wrote (but I never say “not of general interest”) …

Thus perhaps the “why” question isn’t as meaningful as one would think. What you say now tells more about what you are now, not the subject of the question. To use the language of our field, you were “measured” in making that decision and once it was made, you were permanently changed so what you said about the past you isn’t as much about the past you than about the current you…. So, why not just move on; you are enjoying what you are doing and that’s the only thing matters, isn’t it?

There are clearly pros and cons for academia and most of us have options now and then. Life is a N=1 experiment but we have to roll dices along the way. It’d be too hash to ourselves (but clearly hard to resist) to base our mental states on the outcome of the dices. I’d be happy if I roll them gracefully. Analogy: If we only have CHSH to play, no reason to blame ourselves if we fail. The important thing is to play that cos^2 pi/8 strategy, in which case even if we fail, the output bit is still golden (perfectly random).

Even if we don’t play optimally, we still get high smooth min-entropy that can be made into pure golden bits. So to the young and the hopeful, roll your dices and find happiness either way.

The Secret Order of the ArXiv[modifier]

Posted on June 10, 2009 by Pontifex Praeteritorum

The astro/physics blogosphere is all atwitter about papers the Nature embargo policy (See Julianne If a paper is submitted to nature does it still make a sound, the cat herder Hear a paper, see a paper, speak no paper, and he of less than certain principles Unhealthy obsessions of academia. He of uncertain principles loses the catchy title contest  )

In this discussion, the uncertain principal brings up an interesting effect for arXiv postings:

There’s an obsession in science with the order of publication that I don’t think is really healthy, and I think it’s only gotten worse. At the Science21 meeting last fall, Paul Ginsparg talked about how there’s a huge spike in arxiv submissions just after 4pm, because the daily update email puts papers in the order in which they were submitted, starting at 4pm. He said they can see scripts hitting the server to check the time, and then dumping papers in just as soon as the clock has ticked over. Apparently, the position of a paper in that email has a fairly significant effect on the number of views and citations that paper receives in the future.

Now I myself have been known to try to exploit this effect, but what I don’t understand is why, given that the arXiv crew knows about this effect, that they don’t fix it. I know it probably would be a bit of a hassle to rewrite the code, but really it shouldn’t be impossible to make the order of papers appearing in a day’s listing random.

Actually come to think of it is should be rather easy to fix this. Instead of ordering by date, one can just order by some hidden function of the, say, the title of the paper, the time submitted, and the author list. Of course that would just mean that we could spend some time cracking the arXiv’s hiding function 

On a related note, I just submitted a new version of arXiview to Apple (which means it will appear in a few days time) which has some new features, including….ordering the search and posting results by submitted time/date.

The Great Firewall of Collaboration[modifier]

Posted on July 16, 2009 by Pontifex Praeteritorum

A fellow quantum computing researcher of mine recently joined FriendFeed. Along with another researcher we got involved in a discussion about a paper concerning a certain recent claimed “disproof of Bell’s theorem.” (arXiv:0904.4259. What it means to “disprove a theorem” like Bell’s theorem is, however a subject for another comment section on a different blog.) But, and here is the interesting thing, this colleague then made a trip to China. And FriendFeed, apparently, is blocked by the great firewall of China, so he had to email us his comments to continue the conversation. Which got me thinking.

China is a country that has been, historically, a great power. It is, by all accounts, returning to that status with the a wave of lifting of its people out of poverty (numbers I’ve seen are from like over 60 percent below poverty a few decades ago to 10 percent recently, though it’s not clear to me that the poverty level (a few dollars per day) used is the really relevant number.) It has, even more interestingly, achieved an amazing increase in the production of people with a large amount of education. From under 10,000/year PhDs a decade ago to nearly 50,000/year recently, there has been a huge increase in PhDs in a very short span of time. In some minds, the rise of China is the dominant story of the coming decades. This is equally true in academic circles where the productivity of science in China has been rising rapidly.

But my colleague’s experience made me wonder a bit. Suppose that you take at face value the idea that online tools are going to change how we do science (through any of the numerous forms that such tools can now take.) If the Chinese government is banning tools that allow for collaboration (in our case, just a mere discussion) then, despite all they do, I wonder if this might cause a severe lack of bang for their Ph.D buck. Do we really believe that the kind of large scale data sharing or online collaborating, for example, that characterize Science 2.0 will be easy to carry out under the probing eye of the Chinese government? Of course, I’m as far from an expert in China and Science 2.0, so I can’t even begin to approach this question. But it did strike me that there are some fairly strong preconditions assumed by those pushing online tools for science that don’t seem to hold for numerous countries around the world, including China.

Or, in other words (executive summary), those of you doing Science 2.0 can now think about yourselves as modern freedom fighters. Hazzah!

  • Janne says:

More probably, Chinese scientists join and collaborate in Chinese-language collaboration tools within the country. Just like most Japanese use Japanese language-based tools to communicate and collaborate in Japanese rather than trying to do so badly in English on some foreign web site.

You haven’t reflected on the fact that most of the people you interact with are Americans or situated in the US could be not because most researchers are stationed there, but because the sites and tools you use are self-selecting for a particular demographic?

  • Dave Bacon says:

Hi Janne,

More probably, Chinese scientists join and collaborate in Chinese-language collaboration tools within the country. Just like most Japanese use Japanese language-based tools to communicate and collaborate in Japanese rather than trying to do so badly in English on some foreign web site. Agreed, but I’m not sure why China won’t touch these sites.

The point I was at least trying to make was that a lot of the ideas floating around the world of Science 2.0 share a large overlap with ideas that would make any country whose power rests on suppressing information. I don’t see where I made a claim about these tools being US centric, except that currently my colleague can’t use a tool from behind the firewall.

Matt,

Anyway, I think that most people with a science Ph.D. can probably figure out how to use a proxy server.

I’m sure they can (though you know, those biologists j/k!) but barriers to entry cut down fractions. Especially if you are, in some way, risking being thrown in jail. It’s an extreme example, but Iran demonstrates what can happen to internet infrastructure when the people at the top are bent on keeping the lid on.

  • Matt Leifer says:

Thanks for pointing out the comment thread on Scott’s blog. I somehow missed that, but it was very entertaining.

Anyway, I think that most people with a science Ph.D. can probably figure out how to use a proxy server.

  • Eric Lund says:

Janne: What you say is probably true, but it doesn’t address the points that (1) the Chinese government is known to be censoring internet content and (2) sometimes Chinese people, or foreign visitors to China, collaborate with scientists outside China who do not necessarily read Chinese. So, far, most cutting edge research in China has been in collaboration with non-Chinese institutes. That may not always be true, and when it ceases to be true the Great Firewall will no longer be a major problem. Until scientists have to start learning Chinese in order to avoid missing important papers, the Great Firewall remains a problem.

  • Janne says:

Eric, you’re absolutely right, and I deplore the Chinese firewall myself.

But, actual research collaboration always happens on a personal level. Email or personal visits kind of thing. A general censorship policy doesn’t touch that, just as the general language barrier between Japanese (or German, or French or whatever) scientists doesn’t impede the high-level research collaboration between them very much.

But here you highlight something I naively thought everybody already knew to be a serious problem:

“Until scientists have to start learning Chinese in order to avoid missing important papers, the Great Firewall remains a problem.”

Unless you read (and follow) academic English, German, Japanese, Chinese, French and Spanish you are already missing important papers. “Important”, as in “our next step is a Science/Nature publication” kind of important. Each of those languages have large and thriving scientific communities in their own right, with journals and conferences publishing significant results. And those publications count. If you’re not aware of the stuff being published in other major languages you’re at a definite disadvantage.

But of course very few people are. The scientific community is already long split by language and cultural barriers. We manage to muddle through.

  • Janne says:

Dave, as I said I am firmly against everything the Chinese firewall stands for – and the same goes for the Australian and other government attempts at censorship.

My point is that your concept of “Science 2.0” is parochial in nature; some incidental censorship firewall doesn’t affect it. Nobody is censoring communication with German or Japanese or Spanish scientists, and yet your “science 2.0” idea doesn’t even acknowledge the idea of participants communicating in other languages.

  • Wim van Dam says:

> Unless you read (and follow) academic English, German, Japanese, Chinese, French and Spanish you are already missing important papers.

To which fields of science does this apply? Only once a year do I need to read an (old) math article in French, otherwise everything else is done in English. Seriously, which research journal or conference in Spanish am I missing out on?

  • not quite chinese says:

Well, Tibetans and Uyghurs, among others, are repressed, Falun Gong practitioners are being made to “disappear” and being tortured in jails. China and the Chinese people have bigger problems than whether to hold scientific conversations on friendfeed or over email.

IMHO China is in pretty awful shape, and it doesn’t have one bit to do with scientific collaboration. The reason is that the stronger China gets, the less the world can tell it to stop oppressing minorities and freedoms. It seems that the Chinese government will not stop the oppression and censorship, and that Chinese people are generally Okay with it, as long as it doesn’t happen to their family (the common approach as far as I can tell is “if someone is in jail, they must have done something wrong, and besides, everyone is getting richer!”).

If I extrapolate, then in 50 years China will rule the world, take away everyone’s freedoms, and have some Westerners do scientific research because an overwhelming majority of Chinese people cannot think freely anyway (which is why they’re willing to live with censorship in the first place).

China’s problem is not censorship. Censorship is the symptom to a society that has been degraded and broken down to the point of considering itself to be a mindless flock and embracing that view of itself. It’s a Fascist state of mind if I ever saw one. The country and its unity is above all, and the default behavior is to obey authority.

Remark: there are exceptions, of course. There were also exceptions in Fascist Italy. Of the exceptional people, some stayed quiet, and those who had spoken up went to jail or were killed. The general public would assume that they must have done something wrong. After all, the country and its unity is above all.

    • By the way, read the story of the lawyer Gao Zhisheng http://en.wikipedia.org/wiki/Gao_Zhisheng who was first selected as one of the top ten lawyers in China by China’s Ministry of Justice, in 2001, for his work protecting human rights in Xinjiang, but when he started speaking against the torture of Falun Gong practitioners, he was put in jail and tortured himself, and his family suffered many ordeals. His family fled (in quite an escape) to the US, and he has “disappeared” shortly thereafter. He’s quite a remarkable man. Read his letters to the Chairman. Parts of them are quoted in the wikiepdia entry. The Wikipedia entry is blocked in China, naturally.

Falun Gong practitioners, by the way, are tortured in all manners of terrible ways. Read about it here: http://en.wikipedia.org/wiki/Persecution_of_Falun_Gong . The numbers are unbelievable: more than 50,000 tortured, more than 100,000 sent to reeducation camps. From my experience, Chinese people know about this (although maybe not the complete details, which they never bothered finding out) and support this, giving as a reason that “Falun Gong is a cult”. It’s amazing to see how Chinese people who more often than not are mad about the government for not allowing freedom of speech, putting the great firewall, etc, are almost uniformly supportive of oppression of Tibetans, Uyghurs, Falun Gong, and others.

By the way, Falun Gong might be a cult for all I know. It’s unclear what they’re really about, but I wouldn’t be surprised if they are a cult. No one in their right mind would keep resisting the government given such violence and risk. This is exactly why the government is afraid of them. However, I hardly see being a cult as a reason that justifies torture or incarceration.

  • John Sidles says:

Janne says: Unless you read (and follow) academic English, German, Japanese, Chinese, French and Spanish you are already missing important papers.

That is true not only in mathematics and science, but in engineering too … especially in engineering.

A key word in Janne’s statement (IMHO) is the word “important”. What quality(s) distinguish a paper as important? If we take that quality to encompass the launching of new enterprises, then the Chinese literature­particularly in simulation science and engineering­is already hugely important.

This is good. Because our planet needs all the new enterprises it can create.

  • Paul Murray says:

Surely you could just as fairly reach the opposite conclusion? That web 2.0 for scientific collaboration is all hoohey, because the chinese manage to do great research without it?

  • Paul A. Helgeson says:

China is in a very delicate situation. Very nearly 1.5 billion people with a 6,000 year history of oppression and revolution. The powers-that-be KNOW which side their bread is buttered on.

Democracy and capitalism IS going to come to China regardless of an one person’s or group of peoples desires and they KNOW this.

However, consider the process of transitioning 1.5 billion people from effectively a state run poverty system to a system that will be as powerfully successful and progressive as China with the throttle wide open and the limits removed without implosion or explosion.

No, this process can not be done wide open and with everyone doing as they wish or as they want. There MUST be controls and limits to what everyone does and what everyone has access to.

No, I do NOT appreciate many of the sanctions and limitations that the Chinese government has elected to impose – Tibet should be free, people should be free from fear, etc. I had a Chinese language professor whose family was deeply affected by the politics of China (imprisonments, etc.) so have some idea of what can and does happen.

But, to imagine pulling out all the stops on 1.5 billion people overnight…that would be the cruelest thing the Chinese government could do to their own people. The chaos and deception and fraud not to mention how many people would be taken advantage of…

The China of today is so incredibly different from the China of 20 years ago and the China of 10 years from now will be so incredibly different from today as to make our complaints today seem laughable.

Give them a chance to grow. Support them as best you can. Help when and where you can. Stand for what you stand for. But never ever tell them what them must or should do. They’ve been doing it much longer then we have. Much, much longer.

And they are not particularly interested in the opinions of some wet behind the ears westerner who thinks that 500 years of civilization under their belt qualifies them for a learned opinion of how things ought to be.

The one other thing to recognize is the China has always had and probably always will have the ability to conquer most if not all of the peoples of the Earth. They have stood ready to do so on a couple of occasions in history and returned home. The reason has been the same as the reason they pose no real threat to national security today…they are interested in one thing and one thing only. China, The Middle Kingdom. If if isn’t China, to them, it is not particularly important.

Why I Left Academia[modifier]

Posted on September 22, 2013 by Pontifex Praeteritorum

TLDR: scroll here for the pretty interactive picture.

Over two years ago I abandoned my post at the University of Washington as a assistant research professor studying quantum computing and started a new career as a software developer for Google. Back when I was a denizen of the ivory tower I used to daydream that when I left academia I would write a long “Jerry Maguire”-esque piece about the sordid state of the academic world, of my lot in that world, and how unfair and f**ked up it all is. But maybe with less Tom Cruise. You know the text, the standard rebellious view of all young rebels stuck in the machine (without any mirror.) The song “Mad World” has a lyric that I always thought summed up what I thought it would feel like to leave and write such a blog post: “The dreams in which I’m dying are the best I’ve ever had.”

But I never wrote that post. Partially this was because every time I thought about it, the content of that post seemed so run-of-the-mill boring that I feared my friends who read it would never ever come visit me again after they read it. The story of why I left really is not that exciting. Partially because writing a post about why “you left” is about as “you”-centric as you can get, and yes I realize I have a problem with ego-centric ramblings. Partially because I have been busy learning a new career and writing a lot (omg a lot) of code. Partially also because the notion of “why” is one I­as a card carrying ex-Physicist­cherish and I knew that I could not possibly do justice to giving a decent “why” explanation.

Indeed: what would a “why” explanation for a life decision such as the one I faced look like? For many years when I would think about this I would simply think “well it’s complicated and how can I ever?” There are, of course, the many different components that you think about when considering such decisions. But then what do you do with them? Does it make sense to think about them as probabilities? “I chose to go to Caltech, 50 percent because I liked physics, and 50 percent because it produced a lot Nobel prize winners.” That does not seem very satisfying.

Maybe the way to do it is to phrase the decisions in terms of probabilities that I was assigning before making the decision. “The probability that I’ll be able to contribute something to physics will be 20 percent if I go to Caltech versus 10 percent if I go to MIT.” But despite what some economists would like to believe there ain’t no way I ever made most decisions via explicit calculation of my subjective odds. Thinking about decisions in terms of what an actor feels each decision would do to increase his/her chances of success feels better than just blindly associating probabilities to components in a decision, but it also seems like a lie, attributing math where something else is at play.

So what would a good description of the model be? After pondering this for a while I realized I was an idiot (for about the eighth time that day. It was a good day.) The best way to describe how my brain was working is, of course, nothing short than my brain itself. So here, for your amusement, is my brain (sorry, only tested using Chrome). Yes, it is interactive.

  • Florin Moldoveanu says:

Why I want to come back to academia.

There seem to be a natural relationship between physicists and software development. I started my career in physics in prolific group oversees which produced a publication a month in serous journals like Phys Rev and then I came to US to do a PhD here. When I graduated, I faced the uncertainty of funding because the cold war ended. Not wanting to take risks with my green card, I took a job as a software developer for my adviser’s company utilizing my math skills very well. I was thinking that if I will have something really important to say in physics I’ll come back.

Fast forward through 3 software developer companies, I learned the inside and out of every aspect of software development and management. I was responsible for development software worth tens of millions of dollars in recurring revenue, I managed 3 development groups in 3 countries at the same time, I managed millions of lines of code. Now with this came an unexpected side effect. I earn a sizable salary. Also it happens that now I have very important things to say in quantum mechanics.

First when I tried to came back to physics, nobody took me seriously but this is gradually changing. The big problem however is that I cannot get a salary to match the software career salary right away. Increasing salary is like increasing entropy: irreversible process. Given my long term financial commitments (mortgages, college expenses for my kids) I cannot take a pay cut and start as a post doc someplace.

I do want to come back to academia because I am working on very hard problems and they started producing amazing results. They sure beat any job satisfaction in the software world by orders of magnitude. But I am trapped in software development by my current high standard of living.

So my advice for you is DON’T DO IT.

    • A says:

I think the advice here is more like getting a wife with more money than you do.

  • angry says:

Hmm, I was hoping for more about your departure from academia. I have fantasies about leaving, but the prospect of having a 9-5 schedule, having to wear clothes other than jeans, and not being completely free during the summer just seems too much. More disposable income and different challenges though… “Mad World” is great, as is the whole of “The Hurting.”

  • Dave Bacon says:

angry: at Google the dress code is “wear something” 

  • Michael Nielsen says:

Loved the interactive graph!

Regarding the rant: if you’re worried that it’d be “run-of-the-mill boring”, why not just focus on the less run-of-the-mill bits? (I.e., publish the diffs.)

  • Alice says:

As one of your former advisees, this is actually really interesting to poke at. Personally I think I’m well out of academia – I was probably never going to be happy as faculty (at least not in quantum computing/CS theory), but I could have easily spent another 3-4 years in grad school figuring that out if I hadn’t hit a decision point when I did.

I’d also be interested to read the bigger “leaving academia” story. While CS/physics grad school isn’t overall the same kind of trap as, say, a PhD in English (which is probably only something you should do if you’re very, very good, and if someone will pay you to do it), it’s still a major commitment that’s not a good fit for a lot of people. Few, if any, of the students I started with in 2007 have graduated, and even fewer have academic jobs. Many have left academia entirely. So when I talk to people who are in grad school or considering it, it’s hard to really know what to say. Success rates can be high or low depending on how you define “success”. I currently work on a software team that’s full of PhDs (in CS), most of whom are quite vocal about the fact that they probably could have skipped the whole dissertation thing and pretty much gotten the same benefit from the experience.

  • John says:

Did graph isomorphism burn you out? I think you were doing good work, for what it’s worth. I’m sure you still are. I ask because you left out the other obvious option, of working at an industrial or government research lab. There are quite a few out there, including Microsoft outside Seattle and even now Google.

  • Dave Bacon says:

Thanks for the kind words John. Part of burning out was certainly the frustration of spending a lot of time working on problems I considered important (graph isomorphism among them, I’d also include self-correcting quantum memories as another) and not making significant progress. I think when you work on these problems and you meet lots of very smart people you start to question whether you stand a chance. Plus it is particularly heart wrenching to work on these problems and think you’ve found a path forward only to realize that you don’t. These are part of my character weakness, no doubt. Burnout doesn’t mean you don’t care about what your working on, at least for me, it meant that I needed a break from the emotional roller coaster. Also, at least for the first year after I left, I also still spend a portion of my free time thinking about the problems I care about.

You’re right that I didn’t seriously consider research labs. This was partially a conscious decision: if I was going to try something new, it seemed that a research position at one of these institutes, or a large company, would have not been healthy (if you’re burned out, continuing to do the same thing seems like a bad choice). I never even applied at Microsoft  (I once got rejected for a postdoc there, and when you look at the people they hire, well…. I don’t have a fields medal  )

  • Matthias Gallé says:

Thanks for this extremely sincere picture from your brain. This is better than any page-long post. What did you use to do the network?

    • Dave Bacon says:

D3.js

It’s a neat little framework. I’m trying to find some time to build more fun graphics with it.

  • Kingsley Jones says:

As one who left Academia close to two decades ago I would say this… It is good to move around and do different things. I left Academia because I got frustrated. I had, at a very young age, already discovered plenty, published some, found some good enemies, and built a huge stock of unpublished results. It was time to leave or I would just get grumpy. I did a simple demographic calculation. I looked around the department and asked myself this question: “What is the Bell Curve for Expected Retirement Age?”.

The answer I came up with (in 1994) was: 2012!

That gave plenty of time for me to get on with life and learn new things. The simple truth about Physics (and Science in general) is that there is so very much to fix that none of it will get fixed until we get a change of the guard.

That is happening now, so things will improve. However, the entire Academic research model is broken so it will not happen in Academia. It will certainly happen, and will be driven by Academically trained persons, but it will not be in the Ivory Tower.

Don’t worry, be happy about that… the age of the MooC, the blog, the self-published and self-organized research community is the way of the future.

The Academy is properly a state of mind, not a job, a place, or a title.

If you like researching new things, being paid well, respecting the manifold areas of life you can never fully master then be happy in commerce and industry.

It is not a bad place and you could well make several fortunes.

Also, you should rest assured that much of the Academic orthodoxy will be swept aside in five years time by a new generation. Discovering new things has never been easier!

Almost nobody in the orthodox Academic sphere is even trying 

  • YS says:

Seeing clearly what is going on in the head of my 6-year-old often makes me realize we adults behave the same, just with more cover-ups. For example, she is pretty good at justifying her actions, like “I ate the candy because I didn’t want Di-Di (her brother) to get cavity”. One such episode gave me the inspiration that perhaps many of the paper reviews I’ve seen, looking so professional and well reasoned, were merely justifications of emotions. That may very well apply to reviews I wrote (but I never say “not of general interest”) …

Thus perhaps the “why” question isn’t as meaningful as one would think. What you say now tells more about what you are now, not the subject of the question. To use the language of our field, you were “measured” in making that decision and once it was made, you were permanently changed so what you said about the past you isn’t as much about the past you than about the current you…. So, why not just move on; you are enjoying what you are doing and that’s the only thing matters, isn’t it?

There are clearly pros and cons for academia and most of us have options now and then. Life is a N=1 experiment but we have to roll dices along the way. It’d be too hash to ourselves (but clearly hard to resist) to base our mental states on the outcome of the dices. I’d be happy if I roll them gracefully. Analogy: If we only have CHSH to play, no reason to blame ourselves if we fail. The important thing is to play that cos^2 pi/8 strategy, in which case even if we fail, the output bit is still golden (perfectly random). Even if we don’t play optimally, we still get high smooth min-entropy that can be made into pure golden bits. So to the young and the hopeful, roll your dices and find happiness either way.