Archive for the ‘Nerd Interest’ Category

First they came for the Iranians

Wednesday, January 25th, 2017

Action Item: If you’re an American academic, please sign the petition against the Immigration Executive Order. (There are already more than eighteen thousand signatories, including Nobel Laureates, Fields Medalists, you name it, but it could use more!)

I don’t expect this petition to have the slightest effect on the regime, but at least we should demonstrate to the world and to history that American academia didn’t take this silently.

I’m sure there were weeks, in February or March 1933, when the educated, liberal Germans commiserated with each other over the latest outrages of their new Chancellor, but consoled themselves that at least none of it was going to affect them personally.

This time, it’s taken just five days, since the hostile takeover of the US by its worst elements, for edicts from above to have actually hurt my life and (much more directly) the lives of my students, friends, and colleagues.

Today, we learned that Trump is suspending the issuance of US visas to people from seven majority-Islamic countries, including Iran (but strangely not Saudi Arabia, the cradle of Wahhabist terrorism—not that that would be morally justified either).  This suspension might last just 30 days, but might also continue indefinitely—particularly if, as seems likely, the Iranian government thumbs its nose at whatever Trump demands that it do to get the suspension rescinded.

So the upshot is that, until further notice, science departments at American universities can no longer recruit PhD students from Iran—a country that, along with China, India, and a few others, has long been the source of some of our best talent.  This will directly affect this year’s recruiting season, which is just now getting underway.  (If Canada and Australia have any brains, they’ll snatch these students, and make the loss America’s.)

But what about the thousands of Iranian students who are already here?  So far, no one’s rounding them up and deporting them.  But their futures have suddenly been thrown into jeopardy.

Right now, I have an Iranian PhD student who came to MIT on a student visa in 2013.  He started working with me two years ago, on the power of a rudimentary quantum computing model inspired by (1+1)-dimensional integrable quantum field theory.  You can read our paper about it, with Adam Bouland and Greg Kuperberg, here.  It so happens that this week, my student is visiting us in Austin and staying at our home.  He’s spent the whole day pacing around, terrified about his future.  His original plan, to do a postdoc in the US after he finishes his PhD, now seems impossible (since it would require a visa renewal).

Look: in the 11-year history of this blog, there have been only a few occasions when I felt so strongly about something that I stood my ground, even in the face of widespread attacks from people who I otherwise respected.  One, of course, was when I spoke out for shy nerdy males, and for a vision of feminism broad enough to recognize their suffering as a problem.  A second was when I was more blunt about D-Wave, and about its and its supporters’ quantum speedup claims, than some of my colleagues were comfortable with.  But the remaining occasions almost all involved my defending the values of the United States, Israel, Zionism, or “the West,” or condemning Islamic fundamentalism, radical leftism, or the worldviews of such individuals as Noam Chomsky or my “good friend” Mahmoud Ahmadinejad.

Which is simply to say: I don’t think anyone on earth can accuse me of secret sympathies for the Iranian government.

But when it comes to student visas, I can’t see that my feelings about the mullahs have anything to do with the matter.  We’re talking about people who happen to have been born in Iran, who came to the US to do math and science.  Would we rather have these young scientists here, filled with gratitude for the opportunities we’ve given them, or back in Iran filled with justified anger over our having expelled them?

To the Trump regime, I make one request: if you ever decide that it’s the policy of the US government to deport my PhD students, then deport me first.  I’m practically begging you: come to my house, arrest me, revoke my citizenship, and tear up the awards I’ve accepted at the White House and the State Department.  I’d consider that to be the greatest honor of my career.

And to those who cheered Trump’s campaign in the comments of this blog: go ahead, let me hear you defend this.

Update (Jan. 27, 2017): To everyone who’s praised the “courage” that it took me to say this, thank you so much—but to be perfectly honest, it takes orders of magnitude less courage to say this, than to say something that any of your friends or colleagues might actually disagree with! The support has been totally overwhelming, and has reaffirmed my sense that the United States is now effectively two countries, an open and a closed one, locked in a cold Civil War.

Some people have expressed surprise that I’d come out so strongly for Iranian students and researchers, “given that they don’t always agree with my politics,” or given my unapologetic support for the founding principles (if not always the actions) of the United States and of Israel. For my part, I’m surprised that they’re surprised! So let me say something that might be clarifying.

I care about the happiness, freedom, and welfare of all the men and women who are actually working to understand the universe and build the technologies of the future, and of all the bright young people who want to join these quests, whatever their backgrounds and wherever they might be found—whether it’s in Iran or Israel, in India or China or right here in the US.  The system of science is far from perfect, and we often discuss ways to improve it on this blog.  But I have not the slightest interest in tearing down what we have now, or destroying the world’s current pool of scientific talent in some cleansing fire, in order to pursue someone’s mental model of what the scientific community used to look like in Periclean Athens—or for that matter, their fantasy of what it would look like in a post-gender post-racial communist utopia.  I’m interested in the actual human beings doing actual science who I actually meet, or hope to meet.

Understand that, and a large fraction of all the political views that I’ve ever expressed on this blog, even ones that might seem to be in tension with each other, fall out as immediate corollaries.

(Related to that, some readers might be interested in a further explanation of my views about Zionism. See also my thoughts about liberal democracy, in response to numerous comments here by Curtis Yarvin a.k.a. Mencius Moldbug a.k.a. “Boldmug.”)

Update (Jan. 29) Here’s a moving statement from my student Saeed himself, which he asked me to share here.

This is not of my best interest to talk about politics. Not because I am scared but because I know little politics. I am emotionally affected like many other fellow human beings on this planet. But I am still in the US and hopefully I can pursue my degree at MIT. But many other talented friends of mine can’t. Simply because they came back to their hometowns to visit their parents. On this matter, I must say that like many of my friends in Iran I did not have a chance to see my parents in four years, my basic human right, just because I am from a particular nationality; something that I didn’t have any decision on, and that I decided to study in my favorite school, something that I decided when I was 15. When, like many other talented friends of mine, I was teaching myself mathematics and physics hoping to make big impacts in positive ways in the future. And I must say I am proud of my nationality – home is home wherever it is. I came to America to do science in the first place. I still don’t have any other intention, I am a free man, I can do science even in desert, if I have to. If you read history you’ll see scientists even from old ages have always been traveling.

As I said I know little about many things, so I just phrase my own standpoint. You should also talk to the ones who are really affected. A good friend of mine, Ahmad, who studies Mechanical engineering in UC Berkeley, came back to visit his parents in August. He is one of the most talented students I have ever seen in my life. He has been waiting for his student visa since then and now he is ultimately depressed because he cannot finish his degree. The very least the academic society can do is to help students like Ahmad finish their degrees even if it is from abroad. I can’t emphasize enough I know little about many things. But, from a business standpoint, this is a terrible deal for America. Just think about it. All international students in this country have been getting free education untill 22, in the American point of reference, and now they are using their knowledge to build technology in the USA. Just do a simple calculation and see how much money this would amount to. In any case my fellow international students should rethink this deal, and don’t take it unless at the least they are treated with respect. Having said all of this I must say I love the people of America, I have had many great friends here, great advisors specially Scott Aaronson and Aram Harrow, with whom I have been talking about life, religion, freedom and my favorite topic the foundations of the universe. I am grateful for the education I received at MIT and I think I have something I didn’t have before. I don’t even hate Mr Trump. I think he would feel different if we have a cup of coffee sometime.

Update (Jan. 31): See also this post by Terry Tao.

Update (Feb. 2): If you haven’t been checking the comments on this post, come have a look if you’d like to watch me and others doing our best to defend the foundations of Enlightenment and liberal democracy against a regiment of monarchists and neoreactionaries, including the notorious Mencius Moldbug, as well as a guy named Jim who explicitly advocates abolishing democracy and appointing Trump as “God-Emperor” with his sons to succeed him. (Incidentally, which son? Is Ivanka out of contention?)

I find these people to be simply articulating, more clearly and logically than most, the worldview that put Trump into office and where it inevitably leads. And any of us who are horrified by it had better get over our incredulity, fast, and pick up the case for modernity and Enlightenment where Spinoza and Paine and Mill and all the others left it off—because that’s what’s actually at stake here, and if we don’t understand that then we’ll continue to be blindsided.


Sunday, January 1st, 2017

Happy New Year, everyone!  I tripped over a well-concealed hole and sprained my ankle while carrying my daughter across the grass at Austin’s New Years festival, so am now ringing in 2017 lying in bed immobilized, which somehow seems appropriate.  At least Lily is fine, and at least being bedridden gives me ample opportunity to blog.

Another year, another annual Edge question, with its opportunity for hundreds of scientists and intellectuals (including yours truly) to pontificate, often about why their own field of study is the source of the most important insights and challenges facing humanity.  This year’s question was:

What scientific term or concept ought to be more widely known?

With the example given of Richard Dawkins’s “meme,” which jumped into the general vernacular, becoming a meme itself.

My entry, about the notion of “state” (yeah, I tried to focus on the basics), is here.

This year’s question presented a particular challenge, which scientists writing for a broad audience might not have faced for generations.  Namely: to what extent, if any, should your writing acknowledge the dark shadow of recent events?  Does the Putinization of the United States render your little pet debates and hobbyhorses irrelevant?  Or is the most defiant thing you can do to ignore the unfolding catastrophe, to continue building your intellectual sandcastle even as the tidal wave of populist hatred nears?

In any case, the instructions from Edge were clear: ignore politics.  Focus on the eternal.  But people interpreted that injunction differently.

One of my first ideas was to write about the Second Law of Thermodynamics, and to muse about how one of humanity’s tragic flaws is to take for granted the gargantuan effort needed to create and maintain even little temporary pockets of order.  Again and again, people imagine that, if their local pocket of order isn’t working how they want, then they should smash it to pieces, since while admittedly that might make things even worse, there’s also at least 50/50 odds that they’ll magically improve.  In reasoning thus, people fail to appreciate just how exponentially more numerous are the paths downhill, into barbarism and chaos, than are the few paths further up.  So thrashing about randomly, with no knowledge or understanding, is statistically certain to make things worse: on this point thermodynamics, common sense, and human history are all in total agreement.  The implications of these musings for the present would be left as exercises for the reader.

Anyway, I was then pleased when, in a case of convergent evolution, my friend and hero Steven Pinker wrote exactly that essay, so I didn’t need to.

There are many other essays that are worth a read, some of which allude to recent events but the majority of which don’t.  Let me mention a few.

Let me now discuss some disagreements I had with a few of the essays.

  • Donald Hoffman on the holographic principle.  For the point he wanted to make, about the mismatch between our intuitions and the physical world, it seems to me that Hoffman could’ve picked pretty much anything in physics, from Galileo and Newton onward.  What’s new about holography?
  • Jerry Coyne on determinism.  Coyne, who’s written many things I admire, here offers his version of an old argument that I tear my hair out every time I read.  There’s no free will, Coyne says, and therefore we should treat criminals more lightly, e.g. by eschewing harsh punishments in favor of rehabilitation.  Following tradition, Coyne never engages the obvious reply, which is: “sorry, to whom were you addressing that argument?  To me, the jailer?  To the judge?  The jury?  Voters?  Were you addressing us as moral agents, for whom the concept of ‘should’ is relevant?  Then why shouldn’t we address the criminals the same way?”
  • Michael Gazzaniga on “The Schnitt.”  Yes, it’s possible that things like the hard problem of consciousness, or the measurement problem in quantum mechanics, will never have a satisfactory resolution.  But even if so, building a complicated verbal edifice whose sole purpose is to tell people not even to look for a solution, to be satisfied with two “non-overlapping magisteria” and a lack of any explanation for how to reconcile them, never struck me as a substantive contribution to knowledge.  It wasn’t when Niels Bohr did it, and it’s not when someone today does it either.
  • I had a related quibble with Amanda Gefter’s piece on “enactivism”: the view she takes as her starting point, that “physics proves there’s no third-person view of the world,” is controversial to put it mildly among those who know the relevant physics.  (And even if we granted that view, surely a third-person perspective exists for the quasi-Newtonian world in which we evolved, and that’s relevant for the cognitive science questions Gefter then discusses.)
  • Thomas Bass on information pathology.  Bass obliquely discusses the propaganda, conspiracy theories, social-media echo chambers, and unchallenged lies that helped fuel Trump’s rise.  He then locates the source of the problem in Shannon’s information theory (!), which told us how to quantify information, but failed to address questions about the information’s meaning or relevance.  To me, this is almost exactly like blaming arithmetic because it only tells you how to add numbers, without caring whether they’re numbers of rescued orphans or numbers of bombs.  Arithmetic is fine; the problem is with us.
  • In his piece on “number sense,” Keith Devlin argues that the teaching of “rigid, rule-based” math has been rendered obsolete by computers, leaving only the need to teach high-level conceptual understanding.  I partly agree and partly disagree, with the disagreement coming from firsthand knowledge of just how badly that lofty idea gets beaten to mush once it filters down to the grade-school level.  I would say that the basic function of math education is to teach clarity of thought: does this statement hold for all positive integers, or not?  Not how do you feel about it, but does it hold?  If it holds, can you prove it?  What other statements would it follow from?  If it doesn’t hold, can you give a counterexample?  (Incidentally, there are plenty of questions of this type for which humans still outperform the best available software!)  Admittedly, pencil-and-paper arithmetic is both boring and useless—but if you never mastered anything like it, then you certainly wouldn’t be ready for the concept of an algorithm, or for asking higher-level questions about algorithms.
  • Daniel Hook on PT-symmetric quantum mechanics.  As far as I understand, PT-symmetric Hamiltonians are equivalent to ordinary Hermitian ones under similarity transformations.  So this is a mathematical trick, perhaps a useful one—but it’s extremely misleading to talk about it as if it were a new physical theory that differed from quantum mechanics.
  • Jared Diamond extols the virtues of common sense, of which there are indeed many—but alas, his example is that if a mathematical proof leads to a conclusion that your common sense tells you is wrong, then you shouldn’t waste time looking for the exact mistake.  Sometimes that’s good advice, but it’s pretty terrible applied to Goodstein’s Theorem, the muddy children puzzle, the strategy-stealing argument for Go, or anything else that genuinely is shocking until your common sense expands to accommodate it.  Math, like science in general, is a constant dialogue between formal methods and common sense, where sometimes it’s one that needs to get with the program and sometimes it’s the other.
  • Hans Halvorson on matter.  I take issue with Halvorson’s claim that quantum mechanics had to be discarded in favor of quantum field theory, because QM was inconsistent with special relativity.  It seems much better to say: the thing that conflicts with special relativity, and that quantum field theory superseded, was a particular application of quantum mechanics, involving wavefunctions of N particles moving around in a non-relativistic space.  The general principles of QM—unit vectors in complex Hilbert space, unitary evolution, the Born rule, etc.—survived the transition to QFT without the slightest change.


“THE TALK”: My quantum computing cartoon with Zach Weinersmith

Wednesday, December 14th, 2016

OK, here’s the big entrée that I promised you yesterday:

“THE TALK”: My joint cartoon about quantum comgputing with Zach Weinersmith of SMBC Comics.

Just to whet your appetite:

In case you’re wondering how this came about: after our mutual friend Sean Carroll introduced me and Zach for a different reason, the idea of a joint quantum computing comic just seemed too good to pass up.  The basic premise—“The Talk”—was all Zach.  I dutifully drafted some dialogue for him, which he then improved and illustrated.  I.e., he did almost all the work (despite having a newborn competing for his attention!).  Still, it was an honor for me to collaborate with one of the great visual artists of our time, and I hope you like the result.  Beyond that, I’ll let the work speak for itself.

The teaser

Tuesday, December 13th, 2016

Tomorrow, I’ll have something big to announce here.  So, just to whet your appetites, and to get myself back into the habit of blogging, I figured I’d offer you an appetizer course: some more miscellaneous non-Trump-related news.

(1) My former student Leonid Grinberg points me to an astonishing art form, which I somehow hadn’t known about: namely, music videos generated by executable files that fit in only 4K of memory.  Some of these videos have to be seen to be believed.  (See also this one.)  Much like, let’s say, a small Turing machine whose behavior is independent of set theory, these videos represent exercises in applied (or, OK, recreational) Kolmogorov complexity: how far out do you need to go in the space of all computer programs before you find beauty and humor and adaptability and surprise?

Admittedly, Leonid explains to me that the rules allow these programs to call DirectX and Visual Studio libraries to handle things like the 3D rendering (with the libraries not counted toward the 4K program size).  This makes the programs’ existence merely extremely impressive, rather than a sign of alien superintelligence.

In some sense, all the programming enthusiasts over the decades who’ve burned their free time and processor cycles on Conway’s Game of Life and the Mandelbrot set and so forth were captivated by the same eerie beauty showcased by the videos: that of data compression, of the vast unfolding of a simple deterministic rule.  But I also feel like the videos add a bit extra: the 3D rendering, the music, the panning across natural or manmade-looking dreamscapes.  What we have here is a wonderful resource for either an acid trip or an undergrad computability and complexity course.

(2) A week ago Igor Oliveira, together with my longtime friend Rahul Santhanam, released a striking paper entitled Pseudodeterministic Constructions in Subexponential Time.  To understand what this paper does, let’s start with Terry Tao’s 2009 polymath challenge: namely, to find a fast, deterministic method that provably generates large prime numbers.  Tao’s challenge still stands today: one of the most basic, simplest-to-state unsolved problems in algorithms and number theory.

To be clear, we already have a fast deterministic method to decide whether a given number is prime: that was the 2002 breakthrough by Agrawal, Kayal, and Saxena.  We also have a fast probabilistic method to generate large primes: namely, just keep picking n-digit numbers at random, test each one, and stop when you find one that’s prime!  And those methods can be made deterministic assuming far-reaching conjectures in number theory, such as Cramer’s Conjecture (though note that even the Riemann Hypothesis wouldn’t lead to a polynomial-time algorithm, but “merely” a faster exponential-time one).

But, OK, what if you want a 5000-digit prime number, and you want it now: provably, deterministically, and fast?  That was Tao’s challenge.  The new paper by Oliveira and Santhanam doesn’t quite solve it, but it makes some exciting progress.  Specifically, it gives a deterministic algorithm to generate n-digit prime numbers, with merely the following four caveats:

  • The algorithm isn’t polynomial time, but subexponential (2n^o(1)) time.
  • The algorithm isn’t deterministic, but pseudodeterministic (a concept introduced by Gat and Goldwasser).  That is, the algorithm uses randomness, but it almost always succeeds, and it outputs the same n-digit prime number in every case where it succeeds.
  • The algorithm might not work for all input lengths n, but merely for infinitely many of them.
  • Finally, the authors can’t quite say what the algorithm is—they merely prove that it exists!  If there’s a huge complexity collapse, such as ZPP=PSPACE, then the algorithm is one thing, while if not then the algorithm is something else.

Strikingly, Oliveira and Santhanam’s advance on the polymath problem is pure complexity theory: hitting sets and pseudorandom generators and win-win arguments and stuff like that.  Their paper uses absolutely nothing specific to the prime numbers, except the facts that (a) there are lots of them (the Prime Number Theorem), and (b) we can efficiently decide whether a given number is prime (the AKS algorithm).  It seems almost certain that one could do better by exploiting more about primes.

(3) I’m in Lyon, France right now, to give three quantum computing and complexity theory talks.  I arrived here today from London, where I gave another two lectures.  So far, the trip has been phenomenal, my hosts gracious, the audiences bristling with interesting questions.

But getting from London to Lyon also taught me an important life lesson that I wanted to share: never fly EasyJet.  Or at least, if you fly one of the European “discount” airlines, realize that you get what you pay for (I’m told that Ryanair is even worse).  These airlines have a fundamentally dishonest business model, based on selling impossibly cheap tickets, but then forcing passengers to check even tiny bags and charging exorbitant fees for it, counting on snagging enough travelers who just naïvely clicked “yes” to whatever would get them from point A to point B at a certain time, assuming that all airlines followed more-or-less similar rules.  Which might not be so bad—it’s only money—if the minuscule, overworked staff of these quasi-airlines didn’t also treat the passengers like beef cattle, barking orders and berating people for failing to obey rules that one could log hundreds of thousands of miles on normal airlines without ever once encountering.  Anyway, if the airlines won’t warn you, then Shtetl-Optimized will.

May reason trump the Trump in all of us

Wednesday, October 19th, 2016

Two years ago, when I was the target of an online shaming campaign, what helped me through it were hundreds of messages of support from friends, slight acquaintances, and strangers of every background.  I vowed then to return the favor, by standing up when I saw decent people unfairly shamed.  Today I have an opportunity to make good.

Some time ago I had the privilege of interacting a bit with Sam Altman, president of the famed startup incubator Y Combinator (and a guy who’s thanked in pretty much everything Paul Graham writes).  By way of our mutual friend, the renowned former quantum computing researcher Michael Nielsen, Sam got in touch with me to solicit suggestions for “outside-the-box” scientists and writers, for a new grant program that Y Combinator was starting. I found Sam eager to delve into the merits of any suggestion, however outlandish, and was delighted to be able to make a difference for a few talented people who needed support.

Sam has also been one of the Silicon Valley leaders who’s written most clearly and openly about the threat to America posed by Donald Trump and the need to stop him, and he’s donated tens of thousands of dollars to anti-Trump causes.  Needless to say, I supported Sam on that as well.

Now Sam is under attack on social media, and there are even calls for him to resign as the president of Y Combinator.  Like me two years ago, Sam has instantly become the corporeal embodiment of the “nerd privilege” that keeps the marginalized out of Silicon Valley.

Why? Because, despite his own emphatic anti-Trump views, Sam rejected demands to fire Peter Thiel (who has an advisory role at Y Combinator) because of Thiel’s support for Trump.  Sam explained his reasoning at some length:

[A]s repugnant as Trump is to many of us, we are not going to fire someone over his or her support of a political candidate.  As far as we know, that would be unprecedented for supporting a major party nominee, and a dangerous path to start down (of course, if Peter said some of the things Trump says himself, he would no longer be part of Y Combinator) … The way we got into a situation with Trump as a major party nominee in the first place was by not talking to people who are very different than we are … I don’t understand how 43% of the country supports Trump.  But I’d like to find out, because we have to include everyone in our path forward.  If our best ideas are to stop talking to or fire anyone who disagrees with us, we’ll be facing this whole situation again in 2020.

The usual criticism of nerds is that we might have narrow technical abilities, but we lack wisdom about human affairs.  It’s ironic, then, that it appears to have fallen to Silicon Valley nerds to guard some of the most important human wisdom our sorry species ever came across—namely, the liberal ideals of the Enlightenment.  Like Sam, I despise pretty much everything Trump stands for, and I’ve been far from silent about it: I’ve blogged, donated money, advocated vote swapping, endured anonymous comments like “kill yourself kike”—whatever seemed like it might help even infinitesimally to ensure the richly-deserved electoral thrashing that Trump mercifully seems to be headed for in a few weeks.

But I also, I confess, oppose the forces that apparently see Trump less as a global calamity to be averted, than as a golden opportunity to take down anything they don’t like that’s ever been spotted within a thousand-mile radius of Trump Tower.  (Where does this Kevin Bacon game end, anyway?  Do “six degrees of Trump” suffice to contaminate you?)

And not only do I not feel a shadow of a hint of a moral conflict here, but it seems to me that precisely the same liberal Enlightenment principles are behind both of these stances.

But I’d go yet further.  It sort of flabbergasts me when social-justice activists don’t understand that, if we condemn not only Trump, not only his supporters, but even vociferous Trump opponents who associate with Trump supporters (!), all we’ll do is feed the narrative that got Trumpism as far as it has—namely, that of a smug, bubble-encased, virtue-signalling leftist elite subject to runaway political correctness spirals.  Like, a hundred million Americans’ worldviews revolve around the fear of liberal persecution, and we’re going to change their minds by firing anyone who refuses to fire them?  As a recent Washington Post story illustrates, the opposite approach is harder but can bear spectacular results.

Now, as for Peter Thiel: three years ago, he funded a small interdisciplinary workshop on the coast of France that I attended.  With me there were a bunch of honest-to-goodness conservative Christians, a Freudian psychoanalyst, a novelist, a right-wing radio host, some scientists and Silicon Valley executives, and of course Thiel himself.  Each, I found, offered tons to disagree about but also some morsels to learn.

Thiel’s worldview, focused on the technological and organizational greatness that (in his view) Western civilization used to have and has subsequently lost, was a bit too dark and pessimistic for me, and I’m a pretty dark and pessimistic person.  Thiel gave a complicated, meandering lecture that involved comparing modern narratives about Silicon Valley entrepreneurs against myths of gods, heroes, and martyrs throughout history, such as Romulus and Remus (the legendary founders of Rome).  The talk might have made more sense to Thiel than to his listeners.

At the same time, Thiel’s range of knowledge and curiosity was pretty awesome.  He avidly followed all the talks (including mine, on P vs. NP and quantum complexity theory) and asked pertinent questions. When the conversation turned to D-Wave, and Thiel’s own decision not to invest in it, he laid out the conclusions he’d come to from an extremely quick look at the question, then quizzed me as to whether he’d gotten anything wrong.  He hadn’t.

From that conversation among others, I formed the impression that Thiel’s success as an investor is, at least in part, down neither to luck nor to connections, but to a module in his brain that most people lack, which makes blazingly fast and accurate judgments about tech startups.  No wonder Y Combinator would want to keep him as an adviser.

But, OK, I’m so used to the same person being spectacularly right on some things and spectacularly wrong on others, that it no longer causes even slight cognitive dissonance.  You just take the issues one by one.

I was happy, on balance, when it came out that Thiel had financed the lawsuit that brought down Gawker Media.  Gawker really had used its power to bully the innocent, and it had broken the law to do it.  And if it’s an unaccountable, anti-egalitarian, billionaire Godzilla against a vicious, privacy-violating, nerd-baiting King Kong—well then, I guess I’m with Godzilla.

More recently, I was appalled when Thiel spoke at the Republican convention, pandering to the crowd with Fox-News-style attack lines that were unworthy of a mind of his caliber.  I lost a lot of respect for Thiel that day.  But that’s the thing: unlike with literally every other speaker at the GOP convention, my respect for Thiel had started from a point that made a decrease possible.

I reject huge parts of Thiel’s worldview.  I also reject any worldview that would threaten me with ostracism for talking to Thiel, attending a workshop he sponsors, or saying anything good about him.  This is not actually a difficult balance.

Today, when it sometimes seems like much of the world has united in salivating for a cataclysmic showdown between whites and non-whites, Christians and Muslims, “dudebros” and feminists, etc., and that the salivators differ mostly just in who they want to see victorious in the coming battle and who humiliated, it can feel lonely to stick up for naïve, outdated values like the free exchange of ideas, friendly disagreement, the presumption of innocence, and the primacy of the individual over the tribe.  But those are the values that took us all the way from a bronze spear through the enemy’s heart to a snarky rebuttal on the arXiv, and they’ll continue to build anything worth building.

And now to watch the third debate (I’ll check the comments afterward)…

Update (Oct. 20): See also this post from a blog called TheMoneyIllusion. My favorite excerpt:

So let’s see. Not only should Trump be shunned for his appalling political views, an otherwise highly respected Silicon Valley entrepreneur who just happens to support Trump (along with 80 million other Americans) should also be shunned. And a person who despises Trump and works against him but who defends Thiel’s right to his own political views should also resign. Does that mean I should be shunned too? After all, I’m a guy who hates Trump, writing a post that defends a guy who hates Trump, who wrote a post defending a guy’s freedom to support Trump, who in turn supports Trump. And suppose my mother sticks up for me? Should she also be shunned?

It’s almost enough to make me vote . . . no, just kidding.

Question … Which people on the left are beyond the pale? Suppose Thiel had supported Hugo Chavez? How about Castro? Mao? Pol Pot? Perhaps the degrees of separation could be calibrated to the awfulness of the left-winger:

Chavez: One degree of separation. (Corbyn, Sean Penn, etc.)

Castro: Two degrees of separation is still toxic.

Lenin: Three degrees of separation.

Mao: Four degrees of separation.

Pol Pot: Five degrees of separation.

The Ninth Circuit ruled that vote-swapping is legal. Let’s use it to stop Trump.

Saturday, September 10th, 2016

Updates: Commenter JT informs me that there’s already a vote-swapping site available:  (I particularly like their motto: “Everybody wins.  Except Trump.”)  I still think there’s a need for more sites, particularly ones that would interface with Facebook, but this is a great beginning.  I’ve signed up for it myself.

Also, Toby Ord, a philosopher I know at Oxford, points me to a neat academic paper he wrote that analyzes vote-swapping as an example of “moral trade,” and that mentions the Porter v. Bowen decision holding vote-swapping to be legal in the US.

Also, if we find two Gary Johnson supporters in swing states willing to trade, I’ve been contacted by a fellow Austinite who’d be happy to accept the second trade.

As regular readers might know, my first appearance in the public eye (for a loose definition of “public eye”) had nothing to do with D-Wave, Gödel’s Theorem, the computational complexity of quantum gravity, Australian printer ads, or—god forbid—social justice shaming campaigns.  Instead it centered on NaderTrading: the valiant but doomed effort, in the weeks leading up to the 2000 US Presidential election, to stop George W. Bush’s rise to power by encouraging Ralph Nader supporters in swing states (such as Florida) to vote for Al Gore, while pairing themselves off over the Internet with Gore supporters in safe states (such as Texas or California) who would vote for Nader on their behalf.  That way, Nader’s vote share (and his chance of reaching 5% of the popular vote, which would’ve qualified him for federal funds in 2004) wouldn’t be jeopardized, but neither would Gore’s chance of winning the election.

Here’s what I thought at the time:

  1. The election would be razor-close (though I never could’ve guessed how close).
  2. Bush was a malignant doofus who would be a disaster for the US and the world (though I certainly didn’t know how—recall that, at the time, Bush was running as an isolationist).
  3. Many Nader supporters, including the ones who I met at Berkeley, prioritized personal virtue so completely over real-world consequences that they might actually throw the election to Bush.

NaderTrading, as proposed by law professor Jamin Raskin and others, seemed like one of the clearest ways for nerds who knew these points, but who lacked political skills, to throw themselves onto the gears of history and do something good for the world.

So, as a 19-year-old grad student, I created a website called “In Defense of NaderTrading” (archived version), which didn’t arrange vote swaps themselves—other sites did that—but which explored some of the game theory behind the concept and answered some common objections to it.  (See also here.)  Within days of creating the site, I’d somehow become an “expert” on the topic, and was fielding hundreds of emails as well as requests for print, radio, and TV interviews.

Alas, the one question everyone wanted to ask me was the one that I, as a CS nerd, was the least qualified to answer: is NaderTrading legal? isn’t it kind of like … buying and selling votes?

I could only reply that, to my mind, NaderTrading obviously ought to be legal, because:

  1. Members of Congress and state legislatures trade votes all the time.
  2. A private agreement between two friends to each vote for the other’s preferred candidate seems self-evidently legal, so why should it be any different if a website is involved?
  3. The whole point of NaderTrading is to exercise your voting power more fully—pretty much the opposite of bartering it away for private gain.
  4. While the election laws vary by state, the ones I read very specifically banned trading votes for tangible goods—they never even mentioned trading votes for other votes, even though they easily could’ve done so had legislators intended to ban that.

But—and here was the fatal problem—I could only address principles and arguments, rather than politics and power.  I couldn’t honestly assure the people who wanted to vote-swap, or to set up vote-swapping sites, that they wouldn’t be prosecuted for it.

As it happened, the main vote-swapping site,, was shut down by California’s Republican attorney general, Bill Jones, only four days after it opened.  A second vote-swapping site,, was never directly threatened but also ceased operations because of what happened to voteswap2000.  Many legal scholars felt confident that these shutdowns wouldn’t hold up in court, but with just a few weeks until the election, there was no time to fight it.

Before it was shut down, voteswap2000 had brokered 5,041 vote-swaps, including hundreds in Florida.  Had that and similar sites been allowed to continue operating, it’s entirely plausible that they would’ve changed the outcome of the election.  No Iraq war, no 2008 financial meltdown: we would’ve been living in a different world.  Note that, of the 100,000 Floridians who ultimately voted for Nader, we would’ve needed to convince fewer than 1% of them.

Today, we face something I didn’t expect to face in my lifetime: namely, a serious prospect of a takeover of the United States by a nativist demagogue with open contempt for democratic norms and legendarily poor impulse control. Meanwhile, there are two third-party candidates—Gary Johnson and Jill Stein—who together command 10% of the vote.  A couple months ago, I’d expressed hopes that Johnson might help Hillary, by splitting the Republican vote. But it now looks clear that, on balance, not only Stein but also Johnson are helping Trump, by splitting up that part of the American vote that’s not driven by racial resentment.

So recently a friend—the philanthropist and rationalist Holden Karnofsky—posed a question to me: should we revive the vote-swapping idea from 2000? And presumably this time around, enhance the idea with 21st-century bells and whistles like mobile apps and Facebook, to make it all the easier for Johnson/Stein supporters in swing states and Hillary supporters in safe states to find each other and trade votes?

Just like so many well-meaning people back in 2000, Holden was worried about one thing: is vote-swapping against the law? If someone created a mobile vote-swapping app, could that person be thrown in jail?

At first, I had no idea: I assumed that vote-swapping simply remained in the legal Twilight Zone where it was last spotted in 2000.  But then I did something radical: I looked it up.  And when I did, I discovered a decade-old piece of news that changes everything.

On August 6, 2007, the Ninth Circuit Court of Appeals finally ruled on a case, Porter v. Bowen, stemming from the California attorney general’s shutdown of  Their ruling, which is worth reading in full, was unequivocal.

Vote-swapping, it said, is protected by the First Amendment, which state election laws can’t supersede.  It is fundamentally different from buying or selling votes.

Yes, the decision also granted the California attorney general immunity from prosecution, on the ground that vote-swapping’s legality hadn’t yet been established in 2000—indeed it wouldn’t be, until the Ninth Circuit’s decision itself!  Nevertheless, the ruling made clear that the appellants (the creators of voteswap2000 and some others) were granted the relief they sought: namely, an assurance that vote-swapping websites would be protected from state interference in the future.

Admittedly, if vote-swapping takes off again, it’s possible that the question will be re-litigated and will end up in the Supreme Court, where the Ninth Circuit’s ruling could be reversed.  For now, though, let the message be shouted from the rooftops: a court has ruled. You cannot be punished for cooperating with your fellow citizens to vote strategically, or for helping others do the same.

For those of you who oppose Donald Trump and who are good at web and app development: with just two months until the election, I think the time to set up some serious vote-swapping infrastructure is right now.  Let your name be etched in history, alongside those who stood up to all the vicious demagogues of the past.  And let that happen without your even needing to get up from your computer chair.

I’m not, I confess, a huge fan of either Gary Johnson or Jill Stein (especially not Stein).  Nevertheless, here’s my promise: on November 8, I will cast my vote in the State of Texas for Gary Johnson, if I can find at least one Johnson supporter who lives in a swing state, who I feel I can trust, and who agrees to vote for Hillary Clinton on my behalf.

If you think you’ve got what it takes to be my vote-mate, send me an email, tell me about yourself, and let’s talk!  I’m not averse to some electoral polyamory—i.e., lots of Johnson supporters in swing states casting their votes for Clinton, in exchange for the world’s most famous quantum complexity blogger voting for Johnson—but I’m willing to settle for a monogamous relationship if need be.

And as for Stein? I’d probably rather subsist on tofu than vote for her, because of her support for seemingly every pseudoscience she comes across, and especially because of her endorsement of the vile campaign to boycott Israel.  Even so: if Stein supporters in swing states whose sincerity I trusted offered to trade votes with me, and Johnson supporters didn’t, I would bury my scruples and vote for Stein.  Right now, the need to stop the madman takes precedence over everything else.

One last thing to get out of the way.  When they learn of my history with NaderTrading, people keep pointing me a website called, and exclaiming “look! isn’t this exactly that vote-trading thing you were talking about?”

On examination, Balanced Rebellion turns out to be the following proposal:

  1. A Trump supporter in a swing state pairs off with a Hillary supporter in a swing state.
  2. Both of them vote for Gary Johnson, thereby helping Johnson without giving an advantage to either Hillary or Trump.

So, exercise for the reader: see if you can spot the difference between this idea and the kind of vote-swapping I’m talking about.  (Here’s a hint: my version helps prevent a racist lunatic from taking command of the most powerful military on earth, rather than being neutral about that outcome.)

Not surprisingly, the “balanced rebellion” is advocated by Johnson fans.

Shtetl-Optimized Open Thread

Friday, September 2nd, 2016

Sorry for a post-free month.  I was completely preoccupied with the logistics of the move to Texas.  But now that I’m finally more-or-less settled on my 1000-acre cattle ranch, with my supply of shotguns and whiskey, I’ve decided to ease myself gently back into blogging, via Shtetl-Optimized‘s first-ever SlateStarCodex-style “Open Thread.”  This is not an Ask Me Anything thread.  Rather, it’s a thread for you, the readers, to ask each other whatever you want or bring up any topic on your mind.  I’ll chime in occasionally, and will moderate if needed.  No personal attacks or local hidden variable theories, please.

My biology paper in Science (really)

Friday, July 22nd, 2016

Think I’m pranking you, right?

You can see the paper right here (“Synthetic recombinase-based state machines in living cells,” by Nathaniel Roquet, Ava P. Soleimany, Alyssa C. Ferris, Scott Aaronson, and Timothy K. Lu).  [Update (Aug. 3): The previous link takes you to a paywall, but you can now access the full text of our paper here.  See also the Supplementary Material here.]  You can also read the MIT News article (“Scientists program cells to remember and respond to series of stimuli”).  In any case, my little part of the paper will be fully explained in this post.

A little over a year ago, two MIT synthetic biologists—Timothy Lu and his PhD student Nate Roquet—came to my office saying they had a problem they wanted help with.  Why me? I wondered.  Didn’t they realize I was a quantum complexity theorist, who so hated picking apart owl pellets and memorizing the names of cell parts in junior-high Life Science, that he avoided taking a single biology course since that time?  (Not counting computational biology, taught in a CS department by Richard Karp.)

Nevertheless, I listened to my biologist guests—which turned out to be an excellent decision.

Tim and Nate told me about a DNA system with surprisingly clear rules, which led them to a strange but elegant combinatorial problem.  In this post, first I need to spend some time to tell you the rules; then I can tell you the problem, and lastly its solution.  There are no mathematical prerequisites for this post, and certainly no biology prerequisites: everything will be completely elementary, like learning a card game.  Pen and paper might be helpful, though.

As we all learn in kindergarten, DNA is a finite string over the 4-symbol alphabet {A,C,G,T}.  We’ll find it more useful, though, to think in terms of entire chunks of DNA bases, which we’ll label arbitrarily with letters like X, Y, and Z.  For example, we might have X=ACT, Y=TAG, and Z=GATTACA.

We can also invert one of these chunks, which means writing it backwards while also swapping the A’s with T’s and the G’s with C’s.  We’ll denote this operation by * (the technical name in biology is “reverse-complement”).  For example:


Note that (X*)*=X.

We can then combine our chunks and their inverses into a longer DNA string, like so:


From now on, we’ll work exclusively with the chunks, and forget completely about the underlying A’s, C’s, G’s, and T’s.

Now, there are also certain special chunks of DNA bases, called recognition sites, which tell the little machines that read the DNA when they should start doing something and when they should stop.  Recognition sites come in pairs, so we’ll label them using various parenthesis symbols like ( ), [ ], { }.  To convert a parenthesis into its partner, you invert it: thus ( = )*, [ = ]*, { = }*, etc.  Crucially, the parentheses in a DNA string don’t need to “face the right ways” relative to each other, and they also don’t need to nest properly.  Thus, both of the following are valid DNA strings:

X ( Y [ Z [ U ) V

X { Y ] Z { U [ V

Let’s refer to X, Y, Z, etc.—the chunks that aren’t recognition sites—as letter-chunks.  Then it will be convenient to make the following simplifying assumptions:

  1. Our DNA string consists of an alternating sequence of recognition sites and letter-chunks, beginning and ending with letter-chunks.  (If this weren’t true, then we could just glom together adjacent recognition sites and adjacent letter-chunks, and/or add new dummy chunks, until it was true.)
  2. Every letter-chunk that appears in the DNA string appears exactly once (either inverted or not), while every recognition site that appears, appears exactly twice.  Thus, if there are n distinct recognition sites, there are 2n+1 distinct letter-chunks.
  3. Our DNA string can be decomposed into its constituent chunks uniquely—i.e., it’s always possible to tell which chunk we’re dealing with, and when one chunk stops and the next one starts.  In particular, the chunks and their reverse-complements are all distinct strings.

The little machines that read the DNA string are called recombinases.  There’s one kind of recombinase for each kind of recognition site: a (-recombinase, a [-recombinase, and so on.  When, let’s say, we let a (-recombinase loose on our DNA string, it searches for (‘s and )’s and ignores everything else.  Here’s what it does:

  • If there are no (‘s or )’s in the string, or only one of them, it does nothing.
  • If there are two (‘s facing the same way—like ( ( or ) )—it deletes everything in between them, including the (‘s themselves.
  • If there are two (‘s facing opposite ways—like ( ) or ) (—it deletes the (‘s, and inverts everything in between them.

Let’s see some examples.  When we apply [-recombinase to the string

A ( B [ C [ D ) E,

we get

A ( B D ) E.

When we apply (-recombinase to the same string, we get

A D* ] C* ] B* E.

When we apply both recombinases (in either order), we get

A D* B* E.

Another example: when we apply {-recombinase to

A { B ] C { D [ E,

we get

A D [ E.

When we apply [-recombinase to the same string, we get

A { B D* } C* E.

When we apply both recombinases—ah, but here the order matters!  If we apply { first and then [, we get

A D [ E,

since the [-recombinase now encounters only a single [, and has nothing to do.  On the other hand, if we apply [ first and then {, we get

A D B* C* E.

Notice that inverting a substring can change the relative orientation of two recognition sites—e.g., it can change { { into { } or vice versa.  It can thereby change what happens (inversion or deletion) when some future recombinase is applied.

One final rule: after we’re done applying recombinases, we remove the remaining recognition sites like so much scaffolding, leaving only the letter-chunks.  Thus, the final output

A D [ E

becomes simply A D E, and so on.  Notice also that, if we happen to delete one recognition site of a given type while leaving its partner, the remaining site will necessarily just bounce around inertly before getting deleted at the end—so we might as well “put it out of its misery,” and delete it right away.

My coauthors have actually implemented all of this in a wet lab, which is what most of the Science paper is about (my part is mostly in a technical appendix).  They think of what they’re doing as building a “biological state machine,” which could have applications (for example) to programming cells for medical purposes.

But without further ado, let me tell you the math question they gave me.  For reasons that they can explain better than I can, my coauthors were interested in the information storage capacity of their biological state machine.  That is, they wanted to know the answer to the following:

Suppose we have a fixed initial DNA string, with n pairs of recognition sites and 2n+1 letter-chunks; and we also have a recombinase for each type of recognition site.  Then by choosing which recombinases to apply, as well as which order to apply them in, how many different DNA strings can we generate as output?

It’s easy to construct an example where the answer is as large as 2n.  Thus, if we consider a starting string like

A ( B ) C [ D ] E { F } G < H > I,

we can clearly make 24=16 different output strings by choosing which subset of recombinases to apply and which not.  For example, applying [, {, and < (in any order) yields

A B C D* E F* G H* I.

There are also cases where the number of distinct outputs is less than 2n.  For example,

A ( B [ C [ D ( E

can produce only 3 outputs—A B C D E, A B D E, and A E—rather than 4.

What Tim and Nate wanted to know was: can the number of distinct outputs ever be greater than 2n?

Intuitively, it seems like the answer “has to be” yes.  After all, we already saw that the order in which recombinases are applied can matter enormously.  And given n recombinases, the number of possible permutations of them is n!, not 2n.  (Furthermore, if we remember that any subset of the recombinases can be applied in any order, the number of possibilities is even a bit greater—about e·n!.)

Despite this, when my coauthors played around with examples, they found that the number of distinct output strings never exceeded 2n. In other words, the number of output strings behaved as if the order didn’t matter, even though it does.  The problem they gave me was either to explain this pattern or to find a counterexample.

I found that the pattern holds:

Theorem: Given an initial DNA string with n pairs of recognition sites, we can generate at most 2n distinct output strings by choosing which recombinases to apply and in which order.

Let a recombinase sequence be an ordered list of recombinases, each occurring at most once: for example, ([{ means to apply (-recombinase, then [-recombinase, then {-recombinase.

The proof of the theorem hinges on one main definition.  Given a recombinase sequence that acts on a given DNA string, let’s call the sequence irreducible if every recombinase in the sequence actually finds two recognition sites (and hence, inverts or deletes a nonempty substring) when it’s applied.  Let’s call the sequence reducible otherwise.  For example, given

A { B ] C { D [ E,

the sequence [{ is irreducible, but {[ is reducible, since the [-recombinase does nothing.

Clearly, for every reducible sequence, there’s a shorter sequence that produces the same output string: just omit the recombinases that don’t do anything!  (On the other hand, I leave it as an exercise to show that the converse is false.  That is, even if a sequence is irreducible, there might be a shorter sequence that produces the same output string.)

Key Lemma: Given an initial DNA string, and given a subset of k recombinases, every irreducible sequence composed of all k of those recombinases produces the same output string.

Assuming the Key Lemma, let’s see why the theorem follows.  Given an initial DNA string, suppose you want to specify one of its possible output strings.  I claim you can do this using only n bits of information.  For you just need to specify which subset of the n recombinases you want to apply, in some irreducible order.  Since every irreducible sequence of those recombinases leads to the same output, you don’t need to specify an order on the subset.  Furthermore, for each possible output string S, there must be some irreducible sequence that leads to S—given a reducible sequence for S, just keep deleting irrelevant recombinases until no more are left—and therefore some subset of recombinases you could pick that uniquely determines S.  OK, but if you can specify each S uniquely using n bits, then there are at most 2n possible S’s.

Proof of Key Lemma.  Given an initial DNA string, let’s assume for simplicity that we’re going to apply all n of the recombinases, in some irreducible order.  We claim that the final output string doesn’t depend at all on which irreducible order we pick.

If we can prove this claim, then the lemma follows, since given a proper subset of the recombinases, say of size k<n, we can simply glom together everything between one relevant recognition site and the next one, treating them as 2k+1 giant letter-chunks, and then repeat the argument.

Now to prove the claim.  Given two letter-chunks—say A and B—let’s call them soulmates if either A and B or A* and B* will necessarily end up next to each other, whenever all n recombinases are applied in some irreducible order, and whenever A or B appears at all in the output string.  Also, let’s call them anti-soulmates if either A and B* or A* and B will necessarily end up next to each other if either appears at all.

To illustrate, given the initial DNA sequence,

A [ B ( C ] D ( E,

you can check that A and C are anti-soulmates.  Why?  Because if we apply all the recombinases in an irreducible sequence, then at some point, the [-recombinase needs to get applied, and it needs to find both [ recognition sites.  And one of these recognition sites will still be next to A, and the other will still be next to C (for what could have pried them apart?  nothing).  And when that happens, no matter where C has traveled in the interim, C* must get brought next to A.  If the [-recombinase does an inversion, the transformation will look like

A [ … C ] → A C* …,

while if it does a deletion, the transformation will look like

A [ … [ C* → A C*

Note that C’s [ recognition site will be to its left, if and only if C has been flipped to C*.  In this particular example, A never moves, but if it did, we could repeat the analysis for A and its [ recognition site.  The conclusion would be the same: no matter what inversions or deletions we do first, we’ll maintain the invariant that A and C* (or A* and C) will immediately jump next to each other, as soon as the [ recombinase is applied.  And once they’re next to each other, nothing will ever separate them.

Similarly, you can check that C and D are soulmates, connected by the ( recognition sites; D and B are anti-soulmates, connected by the [ sites; and B and E are soulmates, connected by the ( sites.

More generally, let’s consider an arbitrary DNA sequence, with n pairs of recognition sites.  Then we can define a graph, called the soulmate graph, where the 2n+1 letter-chunks are the vertices, and where X and Y are connected by (say) a blue edge if they’re soulmates, and by a red edge if they’re anti-soulmates.

When we construct this graph, we find that every vertex has exactly 2 neighbors, one for each recognition site that borders it—save the first and last vertices, which border only one recognition site each and so have only one neighbor each.  But these facts immediately determine the structure of the graph.  Namely, it must consist of a simple path, starting at the first letter-chunk and ending at the last one, together with possibly a disjoint union of cycles.

But we know that the first and last letter-chunks can never move anywhere.  For that reason, a path of soulmates and anti-soulmates, starting at the first letter-chunk and ending at the last one, uniquely determines the final output string, when the n recombinases are applied in any irreducible order.  We just follow it along, switching between inverted and non-inverted letter-chunks whenever we encounter a red edge.  The cycles contain the letter-chunks that necessarily get deleted along the way to that unique output string.  This completes the proof of the lemma, and hence the theorem.


There are other results in the paper, like a generalization to the case where there can be k pairs of recognition sites of each type, rather than only one. In that case, we can prove that the number of distinct output strings is at most 2kn, and that it can be as large as ~(2k/3e)n. We don’t know the truth between those two bounds.

Why is this interesting?  As I said, my coauthors had their own reasons to care, involving the number of bits one can store using a certain kind of DNA state machine.  I got interested for a different reason: because this is a case where biology threw up a bunch of rules that look like a random mess—the parentheses don’t even need to nest correctly?  inversion can also change the semantics of the recognition sites?  evolution never thought about what happens if you delete one recognition site while leaving the other one?—and yet, on analysis, all the rules work in perfect harmony to produce a certain outcome.  Change a single one of them, and the “at most 2n distinct DNA sequences” theorem would be false.  Mind you, I’m still not sure what biological purpose it serves for the rules to work in harmony this way, but they do.

But the point goes further.  While working on this problem, I’d repeatedly encounter an aspect of the mathematical model that seemed weird and inexplicable—only to have Tim and Nate explain that the aspect made sense once you brought in additional facts from biology, facts not in the model they gave me.  As an example, we saw that in the soulmate graph, the deleted substrings appear as cycles.  But surely excised DNA fragments don’t literally form loops?  Why yes, apparently, they do.  As a second example, consider the DNA string

A ( B [ C ( D [ E.

When we construct the soulmate graph for this string, we get the path


Yet there’s no actual recombinase sequence that leads to A D C B E as an output string!  Thus, we see that it’s possible to have a “phantom output,” which the soulmate graph suggests should be reachable but that isn’t actually reachable.  According to my coauthors, that’s because the “phantom outputs” are reachable, once you know that in real biology (as opposed to the mathematical model), excised DNA fragments can also reintegrate back into the long DNA string.

Many of my favorite open problems about this model concern algorithms and complexity. For example: given as input an initial DNA string, does there exist an irreducible order in which the recombinases can be applied? Is the “utopian string”—the string suggested by the soulmate graph—actually reachable? If it is reachable, then what’s the shortest sequence of recombinases that reaches it? Are these problems solvable in polynomial time? Are they NP-hard? More broadly, if we consider all the subsets of recombinases that can be applied in an irreducible order, or all the irreducible orders themselves, what combinatorial conditions do they satisfy?  I don’t know—if you’d like to take a stab, feel free to share what you find in the comments!

What I do know is this: I’m fortunate that, before they publish your first biology paper, the editors at Science don’t call up your 7th-grade Life Science teacher to ask how you did in the owl pellet unit.

More in the comments:

  • Some notes on the generalization to k pairs of recognition sites of each type
  • My coauthor Nathaniel Roquet’s comments on the biology

Unrelated Announcement from My Friend Julia Wise (July 24): Do you like science and care about humanity’s positive trajectory? July 25 is the final day to apply for Effective Altruism Global 2016. From August 5-7 at UC Berkeley, a network of founders, academics, policy-makers, and more will gather to apply economic and scientific thinking to the world’s most important problems. Last year featured Elon Musk and the head of This year will be headlined by Cass Sunstein, the co-author of Nudge. If you apply with this link, the organizers will give you a free copy of Doing Good Better by Will MacAskill. Scholarships are available for those who can’t afford the cost.  Read more here.  Apply here.

ITCS’2017: Special Guest Post by Christos Papadimitriou

Wednesday, July 6th, 2016

The wait is over.

Yes, that’s correct: the Call for Papers for the 2017 Innovations in Theoretical Computer Science (ITCS) conference, to be held in Berkeley this coming January 9-11, is finally up.  I attended ITCS’2015 in Rehovot, Israel and had a blast, and will attend ITCS’2017 if logistics permit.

But that’s not all: in a Shtetl-Optimized exclusive, the legendary Christos Papadimitriou, coauthor of the acclaimed Logicomix and ITCS’2017 program chair, has written us a guest post about what makes ITCS special and why you should come.  Enjoy!  –SA

ITCS:  A hidden treasure of TCS

by Christos Papadimitriou

Conferences, for me, are a bit like demonstrations: they were fun in the 1970s.  There was the Hershey STOC, of course, and that great FOCS in Providence, plus a memorable database theory gathering in Calabria.  Ah, children, you should have been there…

So, even though I was a loyal supporter of the ITCS idea from the beginning – the “I”, you recall, stands for innovation –, I managed to miss essentially all of them – except for those that left me no excuse.  For example, this year the program committee was unreasonably kind to my submissions, and so this January I was in Boston to attend.

I want to tell you about ITCS 2016, because it was a gas.

First, I saw all the talks.  I cannot recall this ever happening to me before.  I reconnected with fields of old, learned a ton, and got a few cool new ideas.

In fact, I believe that there was no talk with fewer than 60 people in the audience – and that’s about 70% of the attendees.  In most talks it was closer to 90%.  When was the last conference where you saw that?

And what is the secret of this enhanced audience attention?  One explanation is that smaller conference means small auditorium.  Listening to the talk no longer feels like watching a concert in a stadium, or an event on TV, it’s more like a story related by a friend.  Another gimmick that works well is that, at ITCS, session chairs start the session with a 10-minute “rant,” providing context and their own view of the papers in the session.

Our field got a fresh breath of cohesion at ITCS 2016: cryptographers listened to game theorists in the presence of folks who do data structures for a living, or circuit complexity – for a moment there, the seventies were back.

Ah, those papers, their cleverness and diversity and freshness!  Here is a sample of a few with a brief comment for each (take a look at the conference website for the papers and the presentations).

  • What is keeping quantum computers from conquering all of NP? It is the problem with destructive measurements, right?  Think again, say Aaronson, Bouland and Fitzsimons.  In their paper (pdf, slides) they consider several deviations from current restrictions, including non-destructive measurements, and the space ‘just above’ BQP turns out to be a fascinating and complex place.
  • Roei Tell (pdf, slides) asks another unexpected question: when is an object far from being far from having a property? On the way to an answer he discovers a rich and productive duality theory of property testing, as well as a very precise and sophisticated framework in which to explore it.
  • If you want to represent the permanent of a matrix as the determinant of another matrix of linear forms in the entries, how large must this second matrix be? – an old question by Les Valiant. The innovation by Landsberg and Ressayre (pdf, slides) is that they make fantastic progress in this important problem through geometric complexity: If certain natural symmetries are to be satisfied, the answer is exponential!

(A parenthesis:  The last two papers make the following important point clear: Innovation in ITCS is not meant to be the antithesis of mathematical sophistication.  Deep math and methodological innovation are key ingredients of the ITCS culture.)

  • When shall we find an explicit function requiring more than 3n gates? In their brave exploration of new territory for circuit complexity, Golovnev and Kulikov (pdf, slides) find one possible answer: “as soon as we have explicit dispersers for quadratic varieties.”
  • The student paper award went to Aviad Rubinstein for his work (pdf) on auctioning multiple items – the hardest nut in algorithmic mechanism design. He gives a PTAS for optimizing over a large – and widely used – class of “partitioning” heuristics.

Even though there were no lively discussions at the lobby during the sessions – too many folks attending, see? – the interaction was intense and enjoyable during the extra long breaks and the social events.

Plus we had the Graduating Bits night, when the youngest among us get 5 minutes to tell.  I would have traveled to Cambridge just for that!

All said, ITCS 2016 was a gem of a meeting.  If you skipped it, you really missed a good one.

But there is no reason to miss ITCS 2017, let me tell you a few things about it:

  • It will be in Berkeley, January 9 -11 2017, the week before the Barcelona SODA.
  • It will take place at the Simons Institute just a few days before the boot camps on Pseudorandomness and Learning.
  • I volunteered to be program chair, and the steering committee has decided to try a few innovations in the submission process:
  • Submission deadline is mid-September, so you have a few more weeks to collect your most innovative thoughts. Notification before the STOC deadline.
  • Authors will post a copy of their paper, and will submit to the committee a statement about it, say 1000 words max. Think of it as your chance to write a favorable referee report for your own paper!  Telling the committee why you think it is interesting and innovative.  If you feel this is self-evident, just tell us that.
  • The committee members will be the judges of the overall worth and innovative nature of the paper. Sub-reviewers are optional, and their opinion is not communicated to the rest of the committee.
  • The committee may invite speakers to present specific recent interesting work. Submitted papers especially liked by the committee may be elevated to “invited.”
  • Plus Graduating Bits, chair rants, social program, not to mention the Simons Institute auditorium and Berkeley in January.

You should come!

Leonard Susskind’s Open Letter on “The Lunatic”

Wednesday, June 22nd, 2016

In my own anti-Trump post two weeks ago, I started out by mentioning that Terry Tao and Stephen Hawking had recently denounced Trump, and jokingly wondered when we’d hear from Ed Witten.  Well, will Leonard Susskind of Stanford University—a creator of string theory, and one of the most legendarily original physicists and physics expositors of our time—do instead?

Over the last decade, it’s been a privilege for me to get to know Lenny, to learn from him, and recently, to collaborate with him on quantum circuit complexity and AdS/CFT.  Today, Lenny wrote to ask whether I’d share his open letter about the US election on this blog.  Of course I said yes.  Better yet, Lenny has agreed to my request to be available here to answer questions and comments.  Lenny’s views, even when close to mine (as they certainly are in this case), are still his, and I’d never want to speak on his behalf.  Better that you should hear it straight from the horse’s mouth—as you now will, without further ado.  –Scott A.

Letter to My Friends, by Leonard Susskind

I’m watching this thing that’s happening with disbelief, dismay, and disgust. There is a lunatic loose—I’m sure we all agree about that—but I keep hearing people say that they can’t vote for Hillary. I heard it at my daughter’s birthday party Sunday. Boy oh boy, will these people be sorry if the lunatic gets his way. Personally I do not find it an excuse that “I live in California, which will go Democrat whatever I do.”

I strongly believe in all things Bernie, but Hillary is not the Anti-Bernie. There is much less difference between Clinton and Sanders than the distortions of the nominating process might lead people to think. She’s for health care, he’s for health care; he’s for increased minimum wage, she’s for increased minimum wage; she’s for immigrant rights, he’s for immigrant rights; and on and on it goes.

The lunatic may be just that—a lunatic—but he is also a master of smear and innuendo.  He is a gigantic liar, and he knows that if you keep saying something over and over, it sticks in people’s minds. It’s called the Big Lie, and it works. Say it enough and it sows confusion and distrust, not only among the know-nothings, but even among those who know better.

The lunatic and his supporters are exceedingly dangerous. Tell your friends: don’t be fooled. The only thing between us and the lunatic is Hillary. Get off your ass and vote in Nov.

Leonard Susskind

Director, Stanford Institute for Theoretical Physics,

Stanford University