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05 Feb 01:46

The next potential horrorshow for our oceans

by Minnesotastan

I started monitoring the internet for articles about deep-sea mining in about 2012, when an article in The Guardian reported that a commercial firm was going to begin mining the seafloor near Papua New Guinea for precious metals.
A "new frontier" in mining is set to be opened up by the underwater extraction of resources from the seabed off the coast of Papua New Guinea, despite vehement objections from environmentalists and local activists.

Canadian firm Nautilus Minerals has been granted a 20-year licence by the PNG government to commence the Solwara 1 project, the world's first commercial deep sea mining operation.

Nautilus will mine an area 1.6km beneath the Bismarck Sea, 50km off the coast of the PNG island of New Britain. The ore extracted contains high-grade copper and gold.
The mining company dismissed fears of environmental damage:
"The material is very high grade so you have to mine less in order to get the same amount of metal," said Chris Yeats, a geologist at CSIRO, the Australian government's scientific arm. "At those depths there are bacteria, but there's a cut off at around 1,000m where most fish are, so it should have little impact."

"Unlike a terrestrial mine, you don't have to build infrastructure such as roads and you don't displace people. You chop off one of these venting chimneys and another one will grow back, so it's a little like the mining equivalent of cutting grass."
In 2016 a UK company joined the Canadian one, although that one was going to focus on extinct vents:
Prime minister David Cameron has said such exploits could be worth £40bn to the UK alone and in March, a UK company won a second licence from the International Seabed Authority to prospect in 75,000 sq km of the Pacific...

They will use robot submarines to be the first to drill into extinct vent deposits, using a specially hardened drill to probe 55 metres below the sea bed... A key question is how much the seawater has rusted away the metals deposited by the hot springs that stopped flowing up to 50,000 years ago.

The deposits can be extremely rich in valuable metals, including gold, cobalt, zinc, tellurium and so-called “rare earths”, which are used in many electrical technologies, including smartphones, wind turbines, solar panels and electric cars and in high-strength, lightweight alloys used in aircraft, for example...
There is absolutely no suggestion or enthusiasm from either scientists, or mining companies as far as I know, to go anywhere near the active hydrothermal systems,” said Murton. “They are extraordinarily rich areas of unique species and ecosystems and we wouldn’t do anything to disturb those.” 
The situation was informally summed up by a geology student
This is going to happen, people. The natural resources industry is becoming desperate to find new mineral deposits, as the replacement rate of new discoveries is lagging consumption by a significant margin. Never before has the industry been so desperate to find new projects, which is why multinational miners are more willing than ever to work in the worst of the third-world nations or in formerly frozen terrains that are only now being exposed by global warming...

Seafloor mining is NOT going to be particularly environmentally destructive. Nearly all of the black smokers in question that are going to be mined are geologically dead, having moved too far away from undersea volcanic activity. These deposits are MASSIVE. The potential profitability is astounding. Some of these deposits have been noted to contain nearly 20% copper in megaton quantities, versus the .4% that is typical of modern open-pit porphyry deposits, the immense pits in the earth that you've all seen pictures of.

Where you get to mining active black smokers, though, the situation gets interesting. In these cases, the smokers can physically grow by 3 feet or more per day, with god only knows what kinds of growth on the sulfide fields surrounding the smokers. Experts have been speculating that you could attach a pipe to the end of a black smoker and from there dry out and process the supercritical, black smoker water, which can be 50 weight percent or higher enriched in potentially economic metals. Here, we are for all intents and purposes talking about a renewable source of metals - an astounding proposition.

Success in black smoker mining will mean that land-based mining operations, which have immensely more potential for environmental harm, will begin to be phased out. The environmentalist movement will have thus scored a great victory. For this reason alone black smoker mining should be encouraged, though I'll be the first to march with the Sierra Club in insisting that 'oasis' black smokers that host unusual life-forms should not be mined. We geologists love the outdoors too!
And in addition to the hydrothermal vents, there are the manganese nodules that rest on the ocean floor.
Nodules lie on the seabed sediment, often partly or completely buried. They vary greatly in abundance, in some cases touching one another and covering more than 70% of the sea floor. The total amount of polymetallic nodules on the sea floor was estimated at 500 billion tons by Alan A. Archer of the London Geological Museum in 1981.

Polymetallic nodules are found in both shallow (e.g. the Baltic Sea) and deeper waters (e.g. the central Pacific), even in lakes, and are thought to have been a feature of the seas and oceans at least since the deep oceans oxidised in the Ediacaran period over 540 million years ago.
They represent totally different microecosystems from the vents.
Nodules lie loosely in the sand, but because they exist in places devoid of any other hard substrates—just muddy sediment—they end up acting like pseudo-reefs. Sponges and other sessile creatures can anchor themselves to the metallic rocks. They in turn provide habitat for a wide variety of other deep sea organisms...
And harvesting them requires a different process:
The machines mining companies are likely to use resemble giant potato harvesters. These giant 300-ton robot tractors trundle along the seafloor, ploughing through the sediment, scooping up manganese rocks. The resulting clouds of mud agitated by such a disturbance could be devastating to the fauna that live within it and in the water column.
In 2017, Hakai magazine showed a photo of a harvester (embedded at top of the post), and discussed regulatory challenges:
Officially, the nascent deep-sea-mining industry is governed by the International Seabed Authority (ISA), an intergovernmental organization established in 1996 by the United Nations Convention on the Law of the Sea (UNCLOS). The authority’s critical task is to coordinate its 168 member nations in establishing and enforcing regulations for the developing deep-sea-mining industry.

But the ISA’s teeth are just coming in, says Duncan Currie, a legal advisor to the Deep Sea Conservation Coalition, an advocacy organization. At the moment, the authority still hasn’t created an enforcement agency. In addition, “they won’t and they can’t force countries to comply with ISA regulations when drafting their own laws,” says Currie...

That the ISA has not yet landed on a set of rules puts countries such as Papua New Guinea—where Nautilus plans to open the first commercial deep-sea-mining operation—in an uncertain state. There’s no international template for Papua New Guinea to follow, says Conn Nugent, director of the Pew Charitable Trusts’ efforts to study and guide the development of seabed mining. Papua New Guinea’s Mining Act governs both onshore and offshore activities.

The ISA has also yet to determine how it will enforce regulations and respond to allegations of noncompliance. There are provisions within its mandate to create an inspection arm, says Lodge, but it has not been established because mining has yet to begin...

Besides, says Lodge, deep-sea mining is not a fly-by-night enterprise—a deep-sea-mining operation requires an investment of hundreds of millions of dollars. This means that companies will have to get money from banks, and banks want certainty. “The consequences of license denial are extremely high,” says Lodge. A company that opts to go rogue after failing to get ISA approval will quickly find itself without the financial backing it needs to operate.
The reason I'm writing this up now is because The Atlantic has just published a longread on the subject - History's Largest Mining Operation Is About to Begin.  The author is not sanguine about the future:
Today, many of the largest mineral corporations in the world have launched underwater mining programs. On the west coast of Africa, the De Beers Group is using a fleet of specialized ships to drag machinery across the seabed in search of diamonds. In 2018, those ships extracted 1.4 million carats from the coastal waters of Namibia; in 2019, De Beers commissioned a new ship that will scrape the bottom twice as quickly as any other vessel. Another company, Nautilus Minerals, is working in the territorial waters of Papua New Guinea to shatter a field of underwater hot springs lined with precious metals, while Japan and South Korea have embarked on national projects to exploit their own offshore deposits. But the biggest prize for mining companies will be access to international waters, which cover more than half of the global seafloor and contain more valuable minerals than all the continents combined...

Regulations for ocean mining have never been formally established. The United Nations has given that task to an obscure organization known as the International Seabed Authority, which is housed in a pair of drab gray office buildings at the edge of Kingston Harbour, in Jamaica. Unlike most UN bodies, the ISA receives little oversight. It is classified as “autonomous” and falls under the direction of its own secretary general, who convenes his own general assembly once a year, at the ISA headquarters. For about a week, delegates from 168 member states pour into Kingston from around the world, gathering at a broad semicircle of desks in the auditorium of the Jamaica Conference Centre. Their assignment is not to prevent mining on the seafloor but to mitigate its damage—selecting locations where extraction will be permitted, issuing licenses to mining companies, and drafting the technical and environmental standards of an underwater Mining Code...

The companies with permits to explore these regions have raised breathtaking sums of venture capital. They have designed and built experimental vehicles, lowered them to the bottom, and begun testing methods of dredging and extraction while they wait for the ISA to complete the Mining Code and open the floodgates to commercial extraction...

At full capacity, these companies expect to dredge thousands of square miles a year. Their collection vehicles will creep across the bottom in systematic rows, scraping through the top five inches of the ocean floor. Ships above will draw thousands of pounds of sediment through a hose to the surface, remove the metallic objects, known as polymetallic nodules, and then flush the rest back into the water. Some of that slurry will contain toxins such as mercury and lead, which could poison the surrounding ocean for hundreds of miles. The rest will drift in the current until it settles in nearby ecosystems...

The ISA has issued more mining licenses for nodules than for any other seabed deposit. Most of these licenses authorize contractors to exploit a single deepwater plain. Known as the Clarion-Clipperton Zone, or CCZ, it extends across 1.7 million square miles between Hawaii and Mexico—wider than the continental United States. When the Mining Code is approved, more than a dozen companies will accelerate their explorations in the CCZ to industrial-scale extraction. Their ships and robots will use vacuum hoses to suck nodules and sediment from the seafloor, extracting the metal and dumping the rest into the water.
Map of the CCZ below.  Black squares are no-mining zones; white ones are being explored for mining.
 
"We’re about to make one of the biggest transformations that humans have ever made to the surface of the planet. We’re going to strip-mine a massive habitat, and once it’s gone, it isn’t coming back.”
More at The Atlantic.  For reference: Economic minerals associated with black smokers (2006)
11 Jan 02:33

East, West, South and North Somewhat.

by noreply@blogger.com (Atrios)
At least Rumsfeld had a bit of a poet's soul.

03 Jan 20:28

The Real Butterfly Effect

by Sabine Hossenfelder
If a butterfly flaps its wings in China today, it may cause a tornado in America next week. Most of you will be familiar with this “Butterfly Effect” that is frequently used to illustrate a typical behavior of chaotic systems: Even smallest disturbances can grow and have big consequences. The name “Butterfly Effect” was popularized by James Gleick in his 1987 book “Chaos” and is usually
03 Jan 01:05

Quantum Dominance, Hegemony, and Superiority

by Scott

Yay! I’m now a Fellow of the ACM. Along with my fellow new inductee Peter Shor, who I hear is a real up-and-comer in the quantum computing field. I will seek to use this awesome responsibility to steer the ACM along the path of good rather than evil.

Also, last week, I attended the Q2B conference in San Jose, where a central theme was the outlook for practical quantum computing in the wake of the first clear demonstration of quantum computational supremacy. Thanks to the folks at QC Ware for organizing a fun conference (full disclosure: I’m QC Ware’s Chief Scientific Advisor). I’ll have more to say about the actual scientific things discussed at Q2B in future posts.

None of that is why you’re here, though. You’re here because of the battle over “quantum supremacy.”

A week ago, my good friend and collaborator Zach Weinersmith, of SMBC Comics, put out a cartoon with a dark-curly-haired scientist named “Dr. Aaronson,” who’s revealed on a hot mic to be an evil “quantum supremacist.” Apparently a rush job, this cartoon is far from Zach’s finest work. For one thing, if the character is supposed to be me, why not draw him as me, and if he isn’t, why call him “Dr. Aaronson”? In any case, I learned from talking to Zach that the cartoon’s timing was purely coincidental: Zach didn’t even realize what a hornet’s-nest he was poking with this.

Ever since John Preskill coined it in 2012, “quantum supremacy” has been an awkward term. Much as I admire John Preskill’s wisdom, brilliance, generosity, and good sense, in physics as in everything else—yeah, “quantum supremacy” is not a term I would’ve coined, and it’s certainly not a hill I’d choose to die on. Once it had gained common currency, though, I sort of took a liking to it, mostly because I realized that I could mine it for dark one-liners in my talks.

The thinking was: even as white supremacy was making its horrific resurgence in the US and around the world, here we were, physicists and computer scientists and mathematicians of varied skin tones and accents and genders, coming together to pursue a different and better kind of supremacy—a small reflection of the better world that we still believed was possible. You might say that we were reclaiming the word “supremacy”—which, after all, just means a state of being supreme—for something non-sexist and non-racist and inclusive and good.

In the world of 2019, alas, perhaps it was inevitable that people wouldn’t leave things there.

My first intimation came a month ago, when Leonie Mueck—someone who I’d gotten to know and like when she was an editor at Nature handling quantum information papers—emailed me about her view that our community should abandon the term “quantum supremacy,” because of its potential to make women and minorities uncomfortable in our field. She advocated using “quantum advantage” instead.

So I sent Leonie back a friendly reply, explaining that, as the father of a math-loving 6-year-old girl, I understood and shared her concerns—but also, that I didn’t know an alternative term that really worked.

See, it’s like this. Preskill meant “quantum supremacy” to refer to a momentous event that seemed likely to arrive in a matter of years: namely, the moment when programmable quantum computers would first outpace the ability of the fastest classical supercomputers on earth, running the fastest algorithms known by humans, to simulate what the quantum computers were doing (at least on special, contrived problems). And … “the historic milestone of quantum advantage”? It just doesn’t sound right. Plus, as many others pointed out, the term “quantum advantage” is already used to refer to … well, quantum advantages, which might fall well short of supremacy.

But one could go further. Suppose we did switch to “quantum advantage.” Couldn’t that term, too, remind vulnerable people about the unfair advantages that some groups have over others? Indeed, while “advantage” is certainly subtler than “supremacy,” couldn’t that make it all the more insidious, and therefore dangerous?

Oblivious though I sometimes am, I realized Leonie would be unhappy if I offered that, because of my wholehearted agreement, I would henceforth never again call it “quantum supremacy,” but only “quantum superiority,” “quantum dominance,” or “quantum hegemony.”

But maybe you now see the problem. What word does the English language provide to describe one thing decisively beating or being better than a different thing for some purpose, and which doesn’t have unsavory connotations?

I’ve heard “quantum ascendancy,” but that makes it sound like we’re a UFO cult—waiting to ascend, like ytterbium ions caught in a laser beam, to a vast quantum computer in the sky.

I’ve heard “quantum inimitability” (that is, inability to imitate using a classical computer), but who can pronounce that?

Yesterday, my brilliant former student Ewin Tang (yes, that one) relayed to me a suggestion by Kevin Tian: “quantum eclipse” (that is, the moment when quantum computers first eclipse classical ones for some task). But would one want to speak of a “quantum eclipse experiment”? And shouldn’t we expect that, the cuter and cleverer the term, the harder it will be to use unironically?

In summary, while someone might think of a term so inspired that it immediately supplants “quantum supremacy” (and while I welcome suggestions), I currently regard it as an open problem.

Anyway, evidently dissatisfied with my response, last week Leonie teamed up with 13 others to publish a letter in Nature, which was originally entitled “Supremacy is for racists—use ‘quantum advantage,'” but whose title I see has now been changed to the less inflammatory “Instead of ‘supremacy’ use ‘quantum advantage.'” Leonie’s co-signatories included four of my good friends and colleagues: Alan Aspuru-Guzik, Helmut Katzgraber, Anne Broadbent, and Chris Granade (the last of whom got started in the field by helping me edit Quantum Computing Since Democritus).

(Update: Leonie pointed me to a longer list of signatories here, at their website called “quantumresponsibility.org.” A few names that might be known to Shtetl-Optimized readers are Andrew White, David Yonge-Mallo, Debbie Leung, Matt Leifer, Matthias Troyer.)

Their letter says:

The community claims that quantum supremacy is a technical term with a specified meaning. However, any technical justification for this descriptor could get swamped as it enters the public arena after the intense media coverage of the past few months.

In our view, ‘supremacy’ has overtones of violence, neocolonialism and racism through its association with ‘white supremacy’. Inherently violent language has crept into other branches of science as well — in human and robotic spaceflight, for example, terms such as ‘conquest’, ‘colonization’ and ‘settlement’ evoke the terra nullius arguments of settler colonialism and must be contextualized against ongoing issues of neocolonialism.

Instead, quantum computing should be an open arena and an inspiration for a new generation of scientists.

When I did an “Ask Me Anything” session, as the closing event at Q2B, Sarah Kaiser asked me to comment on the Nature petition. So I repeated what I’d said in my emailed response to Leonie—running through the problems with each proposed alternative term, talking about the value of reclaiming the word “supremacy,” and mostly just trying to diffuse the tension by getting everyone laughing together. Sarah later tweeted that she was “really disappointed” in my response.

Then the Wall Street Journal got in on the action, with a brief editorial (warning: paywalled) mocking the Nature petition:

There it is, folks: Mankind has hit quantum wokeness. Our species, akin to Schrödinger’s cat, is simultaneously brilliant and brain-dead. We built a quantum computer and then argued about whether the write-up was linguistically racist.

Taken seriously, the renaming game will never end. First put a Sharpie to the Supremacy Clause of the U.S. Constitution, which says federal laws trump state laws. Cancel Matt Damon for his 2004 role in “The Bourne Supremacy.” Make the Air Force give up the term “air supremacy.” Tell lovers of supreme pizza to quit being so chauvinistic about their toppings. Please inform Motown legend Diana Ross that the Supremes are problematic.

The quirks of quantum mechanics, some people argue, are explained by the existence of many universes. How did we get stuck in this one?

Steven Pinker also weighed in, with a linguistically-informed tweetstorm:

This sounds like something from The Onion but actually appeared in Nature … It follows the wokified stigmatization of other innocent words, like “House Master” (now, at Harvard, Residential Dean) and “NIPS” (Neural Information Processing Society, now NeurIPS). It’s a familiar linguistic phenomenon, a lexical version of Gresham’s Law: bad meanings drive good ones out of circulation. Examples: the doomed “niggardly” (no relation to the n-word) and the original senses of “cock,” “ass,” “prick,” “pussy,” and “booty.” Still, the prissy banning of words by academics should be resisted. It dumbs down understanding of language: word meanings are conventions, not spells with magical powers, and all words have multiple senses, which are distinguished in context. Also, it makes academia a laughingstock, tars the innocent, and does nothing to combat actual racism & sexism.

Others had a stronger reaction. Curtis Yarvin, better known as Mencius Moldbug, is one of the founders of “neoreaction” (and a significant influence on Steve Bannon, Michael Anton, and other Trumpists). Regulars might remember that Yarvin argued with me in Shtetl-Optimized‘s comment section, under a post in which I denounced Trump’s travel ban and its effects on my Iranian PhD student. Since then, Yarvin has sent me many emails, which have ranged from long to extremely long, and whose message could be summarized as: “[labored breathing] Abandon your liberal Enlightenment pretensions, young Nerdwalker. Come over the Dark Side.”

After the “supremacy is for racists” letter came out in Nature, though, Yarvin sent me his shortest email ever. It was simply a link to the letter, along with the comment “I knew it would come to this.”

He meant: “What more proof do you need, young Nerdawan, that this performative wokeness is a cancer that will eventually infect everything you value—even totally apolitical research in quantum information? And by extension, that my whole worldview, which warned of this, is fundamentally correct, while your faith in liberal academia is naïve, and will be repaid only with backstabbing?”

In a subsequent email, Yarvin predicted that in two years, the whole community will be saying “quantum advantage” instead of “quantum supremacy,” and in five years I’ll be saying “quantum advantage” too. As Yarvin famously wrote: “Cthulhu may swim slowly. But he only swims left.”

So what do I really think about this epic battle for (and against) supremacy?

Truthfully, half of me just wants to switch to “quantum advantage” right now and be done with it. As I said, I know some of the signatories of the Nature letter to be smart and reasonable and kind. They don’t wish to rid the planet of everyone like me. They’re not Amanda Marcottes or Arthur Chus. Furthermore, there’s little I despise more than a meaty scientific debate devolving into a pointless semantic one, with brilliant friend after brilliant friend getting sucked into the vortex (“you too?”). I’m strongly in the Pinkerian camp, which holds that words are just arbitrary designators, devoid of the totemic power to dictate thoughts. So if friends and colleagues—even just a few of them—tell me that they find some word I use to be offensive, why not just be a mensch, apologize for any unintended hurt, switch words midsentence, and continue discussing the matter at hand?

But then the other half of me wonders: once we’ve ceded an open-ended veto over technical terms that remind anyone of anything bad, where does it stop? How do we ever certify a word as kosher? At what point do we all get to stop arguing and laugh together?

To make this worry concrete, look back at Sarah Kaiser’s Twitter thread—the one where she expresses disappointment in me. Below her tweet, someone remarks that, besides “quantum supremacy,” the word “ancilla” (as in ancilla qubit, a qubit used for intermediate computation or other auxiliary purposes) is problematic as well. Here’s Sarah’s response:

I agree, but I wanted to start by focusing on the obvious one, Its harder for them to object to just one to start with, then once they admit the logic, we can expand the list

(What would Curtis Yarvin say about that?)

You’re probably now wondering: what’s wrong with “ancilla”? Apparently, in ancient Rome, an “ancilla” was a female slave, and indeed that’s the Latin root of the English adjective “ancillary” (as in “providing support to”). I confess that I hadn’t known that—had you? Admittedly, once you do know, you might never again look at a Controlled-NOT gate—pitilessly flipping an ancilla qubit, subject only to the whims of a nearby control qubit—in quite the same way.

(Ah, but the ancilla can fight back against her controller! And she does—in the Hadamard basis.)

The thing is, if we’re gonna play this game: what about annihilation operators? Won’t those need to be … annihilated from physics?

And what about unitary matrices? Doesn’t their very name negate the multiplicity of perspectives and cultures?

What about Dirac’s oddly-named bra/ket notation, with its limitless potential for puerile jokes, about the “bra” vectors displaying their contents horizontally and so forth? (Did you smile at that, you hateful pig?)

What about daggers? Don’t we need a less violent conjugate tranpose?

Not to beat a dead horse, but once you hunt for examples, you realize that the whole dictionary is shot through with domination and brutality—that you’d have to massacre the English language to take it out. There’s nothing special about math or physics in this respect.

The same half of me also thinks about my friends and colleagues who oppose claims of quantum supremacy, or even the quest for quantum supremacy, on various scientific grounds. I.e., either they don’t think that the Google team achieved what it said, or they think that the task wasn’t hard enough for classical computers, or they think that the entire goal is misguided or irrelevant or uninteresting.

Which is fine—these are precisely the arguments we should be having—except that I’ve personally seen some of my respected colleagues, while arguing for these positions, opportunistically tack on ideological objections to the term “quantum supremacy.” Just to goose up their case, I guess. And I confess that every time they did this, it made me want to keep saying “quantum supremacy” from now till the end of time—solely to deny these colleagues a cheap and unearned “victory,” one they apparently felt they couldn’t obtain on the merits alone. I realize that this is childish and irrational.

Most of all, though, the half of me that I’m talking about thinks about Curtis Yarvin and the Wall Street Journal editorial board, cackling with glee to see their worldview so dramatically confirmed—as theatrical wokeness, that self-parodying modern monstrosity, turns its gaze on (of all things) quantum computing research. More red meat to fire up the base—or at least that sliver of the base nerdy enough to care. And the left, as usual, walks right into the trap, sacrificing its credibility with the outside world to pursue a runaway virtue-signaling spiral.

The same half of me thinks: do we really want to fight racism and sexism? Then let’s work together to assemble a broad coalition that can defeat Trump. And Jair Bolsonaro, and Viktor Orbán, and all the other ghastly manifestations of humanity’s collective lizard-brain. Then, if we’re really fantasizing, we could liberalize the drug laws, and get contraception and loans and education to women in the Third World, and stop the systematic disenfranchisement of black voters, and open up the world’s richer, whiter, and higher-elevation countries to climate refugees, and protect the world’s remaining indigenous lands (those that didn’t burn to the ground this year).

In this context, the trouble with obsessing over terms like “quantum supremacy” is not merely that it diverts attention, while contributing nothing to fighting the world’s actual racism and sexism. The trouble is that the obsessions are actually harmful. For they make academics—along with progressive activists—look silly. They make people think that we must not have meant it when we talked about the existential urgency of climate change and the world’s other crises. They pump oxygen into right-wing echo chambers.

But it’s worse than ridiculous, because of the message that I fear is received by many outside the activists’ bubble. When you say stuff like “[quantum] supremacy is for racists,” what’s heard might be something more like:

“Watch your back, you disgusting supremacist. Yes, you. You claim that you mentor women and minorities, donate to good causes, try hard to confront the demons in your own character? Ha! None of that counts for anything with us. You’ll never be with-it enough to be our ally, so don’t bother trying. We’ll see to it that you’re never safe, not even in the most abstruse and apolitical fields. We’ll comb through your words—even words like ‘ancilla qubit’—looking for any that we can cast as offensive by our opaque and ever-shifting standards. And once we find some, we’ll have it within our power to end your career, and you’ll be reduced to groveling that we don’t. Remember those popular kids who bullied you in second grade, giving you nightmares of social ostracism that persist to this day? We plan to achieve what even those bullies couldn’t: to shame you with the full backing of the modern world’s moral code. See, we’re the good guys of this story. It’s goodness itself that’s branding you as racist scum.”

In short, I claim that the message—not the message intended, of course, by anyone other than a Chu or a Marcotte or a SneerClubber, but the message received—is basically a Trump campaign ad. I claim further that our civilization’s current self-inflicted catastrophe will end—i.e., the believers in science and reason and progress and rule of law will claw their way back to power—when, and only when, a generation of activists emerges that understands these dynamics as well as Barack Obama did.

Wouldn’t it be awesome if, five years from now, I could say to Curtis Yarvin: you were wrong? If I could say to him: my colleagues and I still use the term ‘quantum supremacy’ whenever we care to, and none of us have been cancelled or ostracized for it—so maybe you should revisit your paranoid theories about Cthulhu and the Cathedral and so forth? If I could say: quantum computing researchers now have bigger fish to fry than arguments over words—like moving beyond quantum supremacy to the first useful quantum simulations, as well as the race for scalability and fault-tolerance? And even: progressive activists now have bigger fish to fry too—like retaking actual power all over the world?

Anyway, as I said, that’s how half of me feels. The other half is ready to switch to “quantum advantage” or any other serviceable term and get back to doing science.

02 Jan 22:46

London Calling with Career Opportunities

by woit

At some point within the past couple years I noticed that one blog that had Not Even Wrong on its blogroll was the blog of Dominic Cummings, who was often getting credited with masterminding the political campaign that got the British to vote (narrowly) for Brexit in 2016. Cummings has had further success recently as Chief Special Adviser to British Prime Minister Boris Johnson, with a blow-out election victory three weeks ago putting him securely in control of the British state.

Today on his blog Cummings has, invoking Grothendieck, posted a job advertisement: ‘Two hands are a lot’ — we’re hiring data scientists, project managers, policy experts, assorted weirdos…. He’s looking for mathematicians, physicists and others to join him to change British society, working

in the intersection of:

  • the selection, education and training of people for high performance
  • the frontiers of the science of prediction
  • data science, AI and cognitive technologies (e.g Seeing Rooms, ‘authoring tools designed for arguing from evidence’, Tetlock/IARPA prediction tournaments that could easily be extended to consider ‘clusters’ of issues around themes like Brexit to improve policy and project management)
  • communication (e.g Cialdini)
  • decision-making institutions at the apex of government.

For some other descriptions of who Cummings would like to hire, on the economics side there’s:

The ideal candidate might, for example, have a degree in maths and economics, worked at the LHC in one summer, worked with a quant fund another summer, and written software for a YC startup in a third summer!

We’ve found one of these but want at least one more.

He also wants “Super-talented weirdos”, with examples given from William Gibson novels, such as “that Chinese-Cuban free runner from a crime family hired by the KGB.”

The remarkable things to me about this long document are what it doesn’t contain. In particular I see nothing at all about any specific policy goals. Usually a new government would recruit people by appealing to their desire to make the world a better place in some specific way, but there’s nothing about that here. The goal is to control the government and what the British population believes, but to what end?

In addition, a more conventional hiring process would be asking for candidates of high ethical values, with some devotion to telling the truth. Cummings seems to be asking for exactly the opposite: best if your background is “from a crime family hired by the KGB.”

Best of wishes to my British readers, now joining the US and other nations in a new dystopic post-truth era. It’s massively depressing to me to see how this has worked out here, I hope you do better. Maybe you should be sending in your applications to Cummings and hoping to sign up for a role in the new power structure. If so, tell him “Not Even Wrong” sent you…

Update: For more on Cummings, there’s a good Financial Times article.

06 Dec 15:16

Same-Sex behavior in animals - a new view.

by mdbownds@wisc.edu (Deric Bownds)
Monk et al. offer a fresh perspective on the "problem" of how same-sex sexual behavior could have evolved. It is a problem only if different-sex sexual behavior is the baseline condition for animals, from which single-sex behavior has evolved. The authors suggest that same-sex behavior is bound up in the very origins of animal sex. It hasn’t had to continually re-evolve: It’s always been there. The arguments of Monk and collaborators are summarized in a review by Elbein:
Instead of wondering why same-sex behavior had independently evolved in so many species, Ms. Monk and her colleagues suggest that it may have been present in the oldest parts of the animal family tree. The earliest sexually reproducing animals may have mated with any other individual they came across, regardless of sex. Such reproductive strategies are still practiced today by hermaphroditic species, like snails, and species that don’t appear to differentiate, like sea urchins.
Over time, Ms. Monk said, sexual signals evolved — different sizes, colors, anatomical features and behaviors — allowing different sexes to more accurately target each other for reproduction. But same-sex behavior continued in some organisms, leading to diverse sexual behaviors and strategies across the animal kingdom. And while same-sex behavior may grant some evolutionary benefits, an ancient origin would mean those benefits weren’t required for it to exist.
But how has same-sex behavior stuck around? The answer may be that such behaviors aren’t as evolutionarily costly as assumed. Traditionally, Ms. Monk said, any mating behavior that doesn’t produce young is seen as a waste. But animal behavior often doesn’t fit neatly into an economic accounting of costs and benefits.
Here is the abstract of Monk et al.:
Same-sex sexual behaviour (SSB) has been recorded in over 1,500 animal species with a widespread distribution across most major clades. Evolutionary biologists have long sought to uncover the adaptive origins of ‘homosexual behaviour’ in an attempt to resolve this apparent Darwinian paradox: how has SSB repeatedly evolved and persisted despite its presumed fitness costs? This question implicitly assumes that ‘heterosexual’ or exclusive different-sex sexual behaviour (DSB) is the baseline condition for animals, from which SSB has evolved. We question the idea that SSB necessarily presents an evolutionary conundrum, and suggest that the literature includes unchecked assumptions regarding the costs, benefits and origins of SSB. Instead, we offer an alternative null hypothesis for the evolutionary origin of SSB that, through a subtle shift in perspective, moves away from the expectation that the origin and maintenance of SSB is a problem in need of a solution. We argue that the frequently implicit assumption of DSB as ancestral has not been rigorously examined, and instead hypothesize an ancestral condition of indiscriminate sexual behaviours directed towards all sexes. By shifting the lens through which we study animal sexual behaviour, we can more fruitfully examine the evolutionary history of diverse sexual strategies.
26 Nov 16:42

The Functional Role of Thalamocortical Coupling in the Human Motor Network

by Opri, E., Cernera, S., Okun, M. S., Foote, K. D., Gunduz, A.

The amplitude of high broadband activity in human cortical field potentials indicates local processing and has repeatedly been shown to reflect motor control in the primary motor cortex. In a group of male and female subjects affected by essential tremor and undergoing deep brain stimulation surgery, ventral intermediate nucleus low-frequency oscillations (<30 Hz) entrain the corticomotor high broadband activity (>40 Hz) during rest, relinquishing that role during movement execution. This finding suggests that there is significant cross-rhythm communication between thalamocortical regions, and motor behavior corresponds to changes in thalamocortical phase-amplitude coupling profiles. Herein, we demonstrate that thalamocortical coupling is a crucial mechanism for gating motor behavior.

SIGNIFICANCE STATEMENT We demonstrate, for the first time, how thalamocortical coupling is mediating movement execution in humans. We show how the low-frequency oscillation from the ventral intermediate nucleus, known as the motor nucleus of the thalamus, entrains the excitability of the primary motor cortex, as reflected by the phase-amplitude coupling between the two regions. We show that thalamocortical phase-amplitude coupling is a manifestation of a gating mechanism for movement execution mediated by the thalamus. These findings highlight the importance of incorporating cross-frequency relationship in models of motor behavior; and given the spatial specificity of this mechanism, this work could be used to improve functional targeting during surgical implantations in subcortical regions.

26 Nov 16:16

The Golomb--Dickman Constant

by john
MathML-enabled post (click for more details).

I’m falling in love with random permutations. There’s something both simple and fairly deep about them. I like to visualize a random permutation as a “gas of cycles”, governed by the laws of statistical mechanics. I haven’t gotten very with this analogy yet.

MathML-enabled post (click for more details).

Here’s one of the many cute facts about random permutations. Let a na_n be the average length of the longest cycle in a permutation, averaged over all permutations of an nn-element set. Then a na_n is asymptotically equal to λn\lambda n where

λ≈0.6243299885… \lambda \approx 0.6243299885 \dots

is called the Golomb–Dickman constant. There’s a cool formula for this constant: λ=∫ 0 1e Li(x)dxwhereLi(x)=∫ 0 xdtlnt \lambda = \int_0^1 e^{\mathrm{Li}(x)} dx \; \; where \; \; Li(x) = \int_0^x \frac{dt}{\ln t} But nobody has been able to prove that it’s irrational!

The Golomb–Dickman constant also shows up in number theory… in a very similar way! If you randomly choose a huge nn-digit integer, the average number of digits of its largest prime factor is asymptotic to λn\lambda n.

So, there’s a connection between prime factorizations and random permutations! And this fact is both simpler and more interesting to me than the Golomb–Dickman constant. You can read more about this in Sections 3.10-3.12 here:

The Golomb–Dickman constant is a kind of relative of Euler’s constant, though there’s no known formula expressing one in terms of the other.

Here’s another appearance of this constant. Say you randomly choose a function from a huge nn-element set to itself. Then the average length of its longest periodic orbit is asymptotic to

λπn2 \lambda \; \sqrt{\frac{\pi n}{2}}

26 Nov 16:07

Random Permutations (Part 1)

by john
MathML-enabled post (click for more details).

I’m going to solve some problems on random permutations in my combinatorics class, to illustrate some of the ideas on species and generating functions, but also to bring in some ideas from complex analysis.

In all these problems we choose permutations randomly from S nS_n, with each permutation having probability 1/n!1/n! of being chosen.

I’ll start with one that’s easy, given the stuff I’ve already explained in class.

MathML-enabled post (click for more details).

Puzzle 1. What is the probability that a randomly chosen permutation of an nn-element set has exactly kk fixed points? What does this probability converge to as n→∞n \to \infty?

In homework the students already computed the probability that a randomly chosen permutation of an nn-element set has no fixed points. A permutation with no fixed points is called a derangement, and the number of derangements of an nn-element set is called the subfactorial !n!\!n.

Using the inclusion-exclusion principle, the number of derangements of {1,…,n}\{1,\dots, n\} is the number of permutations of this set, minus the number of permutations that fix the point 11, minus the number that fix the point 22,… minus the number that fix the point nn, plus the number that fix the points 11 and 22, plus the number that fix the points 11 and 33,… minus the number that fix the points 1,21, 2 and 33,… and so on.

In short:

!n=n!−(n1)(n−1)!+(n2)(n−2)!−⋯+(−1) n(nn)(n−n)! !n = n! \; -\; \binom{n}{1} (n-1)! + \binom{n}{2} (n-2)! - \cdots + (-1)^n \binom{n}{n} (n-n)!

We can simplify this to

!n=n!(10!−11!+12!−⋯+(−1) nn!) !\!n = n! \, \left(\frac{1}{0!} - \frac{1}{1!} + \frac{1}{2!} - \cdots + \frac{(-1)^n}{n!} \right)

Thus, the probability that a permutation of an nn-element set has no fixed points is

!nn!=10!−11!+12!−⋯+(−1) nn! \frac{!\!n}{n!} = \frac{1}{0!} - \frac{1}{1!} + \frac{1}{2!} - \cdots + \frac{(-1)^n}{n!}

and this approaches 1/e1/e as n→∞n \to \infty. So cool.

Now, what about kk fixed points? To choose a permutation of an nn-element set with kk fixed points, we need to choose kk points and then choose a derangement of the remaining (n−k)(n-k)-element set. There are

(nk)!(n−k) \binom{n}{k} \, !(n-k)

ways to do this. Thus, the probability that a permutation of an nn-element set has kk fixed points is

(nk)!(n−k)n! \binom{n}{k} \; \frac{!\!(n-k)}{n!}

which can be written more charmingly as

1k!!(n−k)(n−k)! \frac{1}{k!} \; \frac{!\!(n-k)}{(n-k)!}

We have seen that as n→∞n \to \infty we have

!(n−k)(n−k)!→1e \frac{!\!(n-k)}{(n-k)!} \to \frac{1}{e}

Thus, as n→∞n \to \infty, the probability that a permutation of an nn-element set has kk fixed points approaches

1ek! \frac{1}{e \, k!}

Note that these probabilities sum to 11, as they must.

Puzzle 2. In the n→∞n \to \infty limit, what is the expected number of fixed points of a permutation of an nn-element set?

You might naively think it would be infinite, but remember as we increase the size of our set we decrease the probability that any point gets mapped to itself.

We know that in the n→∞n \to \infty limit the probability of there being kk fixed points is

1ek! \frac{1}{e \, k!}

so in this limit, the expected number of fixed points is

∑ k≥0k1k!e=1e∑ k≥11(k−1)!=1 \sum_{k \ge 0} k \frac{1}{k! e} = \frac{1}{e} \sum_{k \ge 1} \frac{1}{(k-1)!} = 1

Exactly one!

You might also wonder what’s the expected number of fixed points for an arbitrary finite nn, but I’ll leave that to you.

22 Nov 21:41

College Athletes

Their signature play is the three-point combinator, a recursive offense which is guaranteed not to halt and continues accumulating points until the buzzer.
22 Nov 21:33

Discovery Of The First Human Retro-Giant Virus: Description of its morphology, retroviral kinase and ability to induce tumours in mice

by Lusi, E. A., Caicci, F.
Background: The study of retroviruses dates back to the early 1900s during investigations on neoplastic diseases in chickens. Subsequently, Robert Gallo reported the first human retrovirus HLTV in 1980. What we report here is not an archetypal retrovirus, but the discovery of an oncogenic giant microbial agent with a mega-genome, where the transforming retroviral nature co-exists with multiple archaeal oncogenes. Methods: After their isolation from human T cells Leukaemia, these organisms were examined at electron microscopy, tested for reverse transcriptase activity, fully sequenced, used for transformation tests on NIH-3T3 cells in vitro and tumours formation in mice. Same type of particles were also isolated from Canine Transmissible Venereal Tumour (CTVT), the oldest contagious cancer in nature. Results: EM showed the presence of giant viral particles displaying retroviral antigens. These microbial entities harbour in their mega-genome a transforming retroviral kinase, cell-based oncogenes and have reverse transcriptase activity. The purified viral particles transformed NIH-3T3 cells and induced metastatic tumours in nude mice, three weeks post infection. Ruling out the possible presence of filterable retroviruses, a filtered supernatant did not display RT activity and did not transforms. Conclusions: We discovered an ancestral microbial agent, acutely transforming. For its giant dimensions, the ability to retain the Gram stain, the presence of a mega-genome and its retroviral nature, we tentatively named the agent Retro-Giant-Virus (RGV). However, distinct from amoeba giant Mimiviruses, this transforming human agent has a different nature and does not require for its isolation amoeba co-culture, since amoeba is not its natural host. The morphology, biology and genetic features allocate this mammalian giant microbe halfway in between a classic oncogenic virus and an infectious cancer cell. Its transforming nature goes with its constant ability to induce tumours formation in mice.
22 Nov 17:14

Spiders detect electrical fields and use them for ballooning

by Minnesotastan
Everyone knows that spiders fly through the air on strands of their silk.  But it's not just a matter of chance and favorable winds.  The relevance of a surprising factor (earth's electrical field) is explained in a recent issue of Cell:Current Biology:
... the involvement of electrostatic forces in ballooning has never been tested. Several issues have emerged when models using aerodynamic drag alone are employed to explain ballooning dispersal. For example, many spiders balloon using multiple strands of silk that splay out in a fan-like shape. Instead of tangling and meandering in light air currents, each silk strand is kept separate, pointing to the action of a repelling electrostatic force. Questions also arise as to how spiders are able to rapidly emit ballooning silk into the air with the low wind speeds observed in ballooning; the mechanics of silk production requires sufficient external forces to pull silk from spinnerets during spinning...

In the early 20th century, atmospheric electricity was intensively studied, establishing the ubiquity of the atmospheric potential gradient (APG); from fair to stormy weather, an APG is always present, varying in strength and polarity with local meteorological conditions. Over a flat field on a day with clear skies, the APG is approximately 120 Vm−1... Closer to the tree, around sharp leaf, needle, and branch tips, e-fields easily reach tens of kilovolts per meter... the spider’s unlearned response to e-fields is to engage in ballooning, and, on becoming airborne, switching the e-field on and off results in the spider moving upward (on) or downward (off) [video at the link].
Ed Yong discusses this research in his Atlantic column.
Plants, being earthed, have the same negative charge as the ground that they grow upon, but they protrude into the positively charged air. This creates substantial electric fields between the air around them and the tips of their leaves and branches—and the spiders ballooning from those tips.

Many of the spiders actually managed to take off, despite being in closed boxes with no airflow within them.
22 Nov 17:12

Russian cursive looks like scribbles

by Minnesotastan

Image cropped for clarity from the original, where there is a little bit of relevant commentary about why this happens and how someone can use context to read it.  Readers here may be able to offer additional insights.

Addendum:   Several good comments from readers, and a hat tip to Aleksejs for providing this dissection of the cursive "chinchilla":

22 Nov 17:05

The "technical debt" of America's infrastructure

by Minnesotastan
Excerpts from a very sobering article in The Atlantic:
A kind of toxic debt is embedded in much of the infrastructure that America built during the 20th century. For decades, corporate executives, as well as city, county, state, and federal officials, not to mention voters, have decided against doing the routine maintenance and deeper upgrades to ensure that electrical systems, roads, bridges, dams, and other infrastructure can function properly under a range of conditions. Kicking the can down the road like this is often seen as the profit-maximizing or politically expedient option. But it’s really borrowing against the future, without putting that debt on the books.

In software development, engineers have long noted that taking the easy way out of coding problems builds up what they call “technical debt,” as the tech journalist Quinn Norton has written...

Almost everywhere you look in the built environment, toxic technical-debt bubbles are growing and growing and growing. This is true of privately maintained systems such as PG&E’s and publicly maintained systems such as that of Chicago’s Department of Water Management. It’s extremely true of roads: Soon, perhaps 50 percent of Bay Area roads will be in some state of disrepair, not to mention the deeper work that must occur to secure the roadbeds, not just the asphalt on top.

Then there are the sewers and the wastewater plants. Stormwater drains. Levees. And just regular old drinking water. Per capita federal funding for water infrastructure has fallen precipitously since the 1970s. Cities are forced to make impossible decisions between funding different services. And even when they do have the money they need, officials make bad or corrupt decisions. So, water systems in the United States have built up a $1 trillion technical debt, which must be paid over the next 25 years. The problem is particularly acute in the Great Lakes states. One investigation, by American Public Media, found that from 2007 to 2018 Chicago residents’ water bills tripled, and Cleveland residents’ doubled. In Detroit, a city with a median income of less than $27,000, the average family paid $1,151 for water. At these rates, poor residents are far more likely to have their water shut off, and the systems still aren’t keeping up with the maintenance they need. Runaway technical debt makes it nearly impossible to pay the “interest,” which is just keeping the system running, let alone to start paying down the principal or start new capital projects.

All told, the American Society of Civil Engineers estimates that it will cost $3.6 trillion to get Americans back to an acceptable level of technical debt in our infrastructure.
The linked article by Quinn Norton is also sobering.
What Californians, as well as many other Americans, and hundreds of millions of people around the world need to give up on is living where they think they ought to be able to live. Californians are busy building new neighborhoods into the rightful territory of giant fast moving infernos; post-Hurricane Texans think they have the right to build in low-elevation Houston, and poverty-stricken Bangladeshis and Indonesians think they should hold on to the shores they’ve always lived on.
Houston is technical debt. New Orleans is technical debt. Puerto Rico is plagued by intertwined monetary and technical debt.
22 Nov 16:46

An introduction to "Dolly Parton's America"

by Minnesotastan


I long ago gave up radio in favor of podcasts.  The most interesting and enjoyable one I've heard this year is embedded above.
Radiolab creator and host Jad Abumrad spent the last two years following around music legend Dolly Parton, and we're here to say you should tune in! In this episode of Radiolab, we showcase the first of Jad's special series, Dolly Parton's America. In this intensely divided moment, one of the few things everyone still seems to agree on is Dolly Parton—but why? That simple question leads to a deeply personal, historical, and musical rethinking of one of America’s great icons.

We begin with a simple question: How did the queen of the boob joke become a feminist icon? Helen Morales, author of “Pilgrimage to Dollywood,” gave us a stern directive – look at the lyrics! So we dive into Dolly’s discography, starting with the early period of what Dolly calls “sad ass songs” to find remarkably prescient words of female pain, slut-shaming, domestic violence, and women being locked away in asylums by cheating husbands. We explore how Dolly took the centuries-old tradition of the Appalachian “murder ballad”—an oral tradition of men singing songs about brutally killing women—and flipped the script, singing from the woman’s point of view. And as her career progresses, the songs expand beyond the pain to tell tales of leaving abuse behind.
It's probably fair to say that "nobody doesn't like Dolly Parton."
JAD: Like, she tore right through all of that noise. Through the general election and beyond. And I kept bumping into people who would describe the experience of being at a Dolly show as, like, standing in an alternate vision of America than what was unfolding on the TV.

JESSIE WILKERSON: I remember just standing out in the lobby and just people watching, because it was the most diverse place I’ve ever been. I was seeing a multi-racial audience. People wearing cowboy hats and boots. I was seeing people in drag. Church ladies. Lesbians holding hands. Little girls who were there with their families.

WAYNE BLEDSOE: You had a whole audience of people who absolutely their philosophies were in opposition to each other co-mingling, and everybody is polite to each other.

JAD: So that was one thing that caught my attention. That in this very divided moment, Dolly seems to maybe be a kind of unifier. And after doing a little poking around, the data does kind of bear this out. If you look at her global Q Score, this is a measure of how well people think about your brand, globally. What they do is they assemble a very diverse sample of people, they ask them a bunch of questions, and out of all of these different brands that are out there, all these different performers, she is in the top 10 globally in terms of everybody's favorites. But she's almost number one when it comes to lack of negatives, if that makes any sense.
The embed above is from a Radiolab presentation.  The series is available here.
22 Nov 16:41

To detect a hidden "nannycam"

by Minnesotastan

Hidden cameras are everywhere nowadays.  Travelers especially need to be wary in rented rooms.  A WikiHow article shows how to find one using your smartphone.

Note the red dot in the blackness above (from a hidden camera) is not visible light - you could see that with your naked eye.  This is infrared light from the spy camera, detected by the front-facing camera on your phone.


More procedural details at the link.
21 Nov 20:19

Socially dominant, aggressive males are poor influencers of group-consensus in a social fish

by Rodriguez-Santiago, M., Nuehrenberg, P., Derry, J., Deussen, O., Garrison, L. K., Garza, S. F., Francisco, F., Hofmann, H., Jordan, A. L.
In many species, cultures, and contexts, social dominance reflects the ability to exert influence over the behavior of others. Yet the behavioral attributes of those in dominant positions, and the behaviors of actually influential individuals may not be the same, and the behavioral attributes that generate influence in one social context may reduce influence in others. The question of what makes an effective leader is therefore not straightforward, and has many answers depending on the context in which leadership and influence is to be manifested. Most importantly, social dominance cannot always be assumed to be equivalent with social influence. Here we examine whether socially dominant males in the cichlid fish Astatotilapia burtoni are more effective in exerting social influence than socially subordinate males. Using machine-vision based automated tracking of behavior, we find that dominant males in this species display behavioral traits that typify leadership across taxonomic systems - they are aggressive, occupy central social network positions, and lead group movements, whereas subordinate males are passive, socially peripheral, and have little influence over typical group movement. However, in a more complex group-consensus task the influence of dominant males breaks down, and subordinate males become more effective agents of social change. In a more sophisticated group consensus task involving a visual association task, the behavioral attributes that define male dominance - aggression, rapid movement, and increased physical distance to others - interfere with the ability of dominant males to generate group to consensus. Dominant males occupy more spatially distant positions, and had lower signal-to-noise ratio of informative behavior in the association task, while subordinate males are typically is close physical association with their group members, have high signal-to-noise behaviors in the association task, and equal visual connectivity to other group members as dominant males. The attributes that define effective social influence are therefore highly context-specific in this species. These results demonstrate that in this and many other species including humans, behavioral traits that are typical of socially dominant individuals may be the same that reduce their social influence in other contexts.
21 Nov 19:50

The Statistical Foundations of Colour Space

by Wilkins, L.
The idea of a colour space where distance corresponds to discriminability has been fundamental to colour vision research since the 19th century. Despite their long-standing success there is a contradiction between the geometric framework that is typically used in these spaces (a particular application of Riemannian geometry) and a view of the transduction of sensory information as the result of a stochastic process. When this is made explicit, a subtly different approach is suggested which turns out to provide a general, and more complete framework for colour space. It is argued further that not only is a contradiction avoided, but that this framework is both intuitive and of real practical value, in particular for researchers interested in the visual behaviour and ecology of animals.
15 Nov 18:57

Human Olfaction without Apparent Olfactory Bulbs

by Tali Weiss, Timna Soroka, Lior Gorodisky, Sagit Shushan, Kobi Snitz, Reut Weissgross, Edna Furman-Haran, Thijs Dhollander, Noam Sobel
The olfactory bulbs are the sole known relay station of odor information from nose to brain. Using MRI, Weiss et al. discover that ∼4% of left-handed women have normal olfaction without apparent olfactory bulbs. How these women can smell remains unknown.
13 Nov 01:50

Thermodynamic uncertainty relations constrain non-equilibrium fluctuations

by Jordan M. Horowitz

Nature Physics, Published online: 11 November 2019; doi:10.1038/s41567-019-0702-6

A new class of inequalities known as thermodynamic uncertainty relations provides quantitative tools for the description of physical systems out of equilibrium. A perspective is offered on these results and their future developments.
12 Nov 22:58

Einstein's E = mc^2 derivable from Heisenberg's Uncertainty Relations. (arXiv:1911.03818v1 [quant-ph])

by Sibel Baskal, Young S. Kim, Marilyn E. Noz

Heisenberg's uncertainty relation can be written in terms of the step-up and step-down operators in the harmonic oscillator representation. It is noted that the single-variable Heisenberg commutation relation contains the symmetry of the Sp(2) group which is isomorphic to the Lorentz group applicable to one time-like dimension and two space-like dimensions, known as the O(2,1) group. This group has three independent generators. The one-dimensional step-up and step-down operators can be combined into one two-by-two Hermitian matrix which contains three independent operators. If we use a two-variable Heisenberg commutation relation, the two pairs of independent step-up, step-down operators can be combined into a four-by-four block-diagonal Hermitian matrix with six independent parameters. It is then possible to add one off-diagonal two-by-two matrix and its Hermitian conjugate to complete the four-by-four Hermitian matrix. This off-diagonal matrix has four independent generators. There are thus ten independent generators. It is then shown that these ten generators can be linearly combined to the ten generators for the Dirac's two oscillator system leadingto the group isomorphic to the de Sitter group O(3,2), which can the be contracted to the inhomogeneous Lorentz group with four translation generators corresponding to the four-momentum in the Lorentz-covariant world. This Lorentz-covariant four-momentum is known as Einstein's E = mc^2.

31 Oct 13:38

Structure of the space of taboo-free sequences

by Manuel, C., von Haeseler, A.
Models of sequence evolution typically assume that all sequences are possible. However, restriction enzymes that cut DNA at specific recognition sites provide an example where carrying a recognition sequence can be lethal. Motivated by this observation, we studied the set of strings over a finite alphabet with taboos, that is, with prohibited substrings. The taboo-set is referred to as T and any allowed string as a taboo-free string. We consider the graph {Gamma}n(T) whose vertices are taboo-free strings of length n and whose edges connect two taboo-free strings if their Hamming distance equals 1. Any (random) walk on this graph describes the evolution of a DNA sequence that avoids deleterious taboos. We describe the construction of the vertex set of {Gamma}n(T). Then we state conditions under which {Gamma}n(T) and its suffix subgraphs are connected. Moreover, we provide a simple algorithm that can determine, for an arbitrary T, if all these graphs are connected. We concluded that bacterial taboo-free Hamming graphs are nearly always connected, although 4 properly chosen taboos are enough to disconnect one of its suffix subgraphs.
31 Oct 13:37

BlackSheep: A Bioconductor and Bioconda package for differential extreme value analysis

by Blumenberg, L., Kawaler, E., Cornwell, M., Smith, S., Ruggles, K., Fenyo, D.
Nosimpler

EXTREEEEME

Unbiased assays such as shotgun proteomics and RNA-seq provide high-resolution molecular characterization of tumors. These assays measure molecules with highly varied distributions, making interpretation and hypothesis testing challenging. Samples with the most extreme measurements for a molecule can reveal the most interesting biological insights, yet are often excluded from analysis. Furthermore, rare disease subtypes are, by definition, underrepresented in cancer cohorts. To provide a strategy for identifying molecules aberrantly enriched in small sample cohorts, we present BlackSheep--a package for non-parametric description and differential analysis of genome-wide data, available at https://github.com/ruggleslab/blackSheep. BlackSheep is a complementary tool to other differential expression analysis methods that may be underpowered when analyzing small subgroups in a larger cohort.
25 Oct 20:33

How do we segment text? Two-stage chunking operation in reading

by Yang, J., Cai, Q., Tian, X.
Chunking in language comprehension is a process that segments continuous linguistic input into smaller chunks that are in the mental lexicon of reader. Effective chunking during reading facilitates disambiguation and enhances efficiency for comprehension. However, the mechanisms of chunking remain elusive, especially in reading given that information arrives simultaneously yet the written systems may not have explicit cues for labeling boundaries such as Chinese. What are the mechanisms of chunking operation that mediates the reading of the text that normally contains hierarchical information? We investigated this question by manipulating the lexical status of the chunks at distinct levels of grain-size in four-character Chinese strings, including the two-character local chunk and four-character global chunk. Participants were asked to make lexical decision on these strings in a behavioral experiment, followed by a passive reading task when their electroencephalography (EEG) were recorded. The behavioral results showed that the lexical decision time of lexicalized two-character local chunks was influenced by the lexical status of four-character global chunk, but not vice versa, which indicated that the processing of global chunks possessed priority over the local chunks. The EEG results revealed that familiar lexical chunks were detected simultaneously at both levels and further processed in a different temporal order -- the onset of lexical access for the global chunks was earlier than that of local chunks. These consistent behavioral and EEG results suggest that chunking in reading occurs at multiple levels via a two-stage operation -- simultaneous detection and global-first recognition.
25 Sep 06:00

Scott’s Supreme Quantum Supremacy FAQ!

by Scott

You’ve seen the stories—in the Financial Times, Technology Review, CNET, Facebook, Reddit, Twitter, or elsewhere—saying that a group at Google has now achieved quantum computational supremacy with a 53-qubit superconducting device. While these stories are easy to find, I’m not going to link to them here, for the simple reason that none of them were supposed to exist yet.

As the world now knows, Google is indeed preparing a big announcement about quantum supremacy, to coincide with the publication of its research paper in a high-profile journal (which journal? you can probably narrow it down to two). This will hopefully happen within a month.

Meanwhile, though, NASA, which has some contributors to the work, inadvertently posted an outdated version of the Google paper on a public website. It was there only briefly, but long enough to make it to the Financial Times, my inbox, and millions of other places. Fact-free pontificating about what it means has predictably proliferated.

The world, it seems, is going to be denied its clean “moon landing” moment, wherein the Extended Church-Turing Thesis gets experimentally obliterated within the space of a press conference. This is going to be more like the Wright Brothers’ flight—about which rumors and half-truths leaked out in dribs and drabs between 1903 and 1908, the year Will and Orville finally agreed to do public demonstration flights. (This time around, though, it thankfully won’t take that long to clear everything up!)

I’ve known about what was in the works for a couple months now; it was excruciating not being able to blog about it. Though sworn to secrecy, I couldn’t resist dropping some hints here and there (did you catch any?)—for example, in my recent Bernays Lectures in Zürich, a lecture series whose entire structure built up to the brink of this moment.

This post is not an official announcement or confirmation of anything. Though the lightning may already be visible, the thunder belongs to the group at Google, at a time and place of its choosing.

Rather, because so much misinformation is swirling around, what I thought I’d do here, in my role as blogger and “public intellectual,” is offer Scott’s Supreme Quantum Supremacy FAQ. You know, just in case you were randomly curious about the topic of quantum supremacy, or wanted to know what the implications would be if some search engine company based in Mountain View or wherever were hypothetically to claim to have achieved quantum supremacy.

Without further ado, then:

Q1. What is quantum computational supremacy?

Often abbreviated to just “quantum supremacy,” the term refers to the use of a quantum computer to solve some well-defined set of problems that would take orders of magnitude longer to solve with any currently known algorithms running on existing classical computers—and not for incidental reasons, but for reasons of asymptotic quantum complexity. The emphasis here is on being as sure as possible that the problem really was solved quantumly and really is classically intractable, and ideally achieving the speedup soon (with the noisy, non-universal QCs of the present or very near future). If the problem is also useful for something, then so much the better, but that’s not at all necessary. The Wright Flyer and the Fermi pile weren’t useful in themselves.

Q2. If Google has indeed achieved quantum supremacy, does that mean that now “no code is uncrackable”, as Democratic presidential candidate Andrew Yang recently tweeted?

No, it doesn’t. (But I still like Yang’s candidacy.)

There are two issues here. First, the devices currently being built by Google, IBM, and others have 50-100 qubits and no error-correction. Running Shor’s algorithm to break the RSA cryptosystem would require several thousand logical qubits. With known error-correction methods, that could easily translate into millions of physical qubits, and those probably of a higher quality than any that exist today. I don’t think anyone is close to that, and we have no idea how long it will take.

But the second issue is that, even in a hypothetical future with scalable, error-corrected QCs, on our current understanding they’ll only be able to crack some codes, not all of them. By an unfortunate coincidence, the public-key codes that they can crack include most of what we currently use to secure the Internet: RSA, Diffie-Hellman, elliptic curve crypto, etc. But symmetric-key crypto should only be minimally affected. And there are even candidates for public-key cryptosystems (for example, based on lattices) that no one knows how to break quantumly after 20+ years of trying, and some efforts underway now to start migrating to those systems. For more, see for example my letter to Rebecca Goldstein.

Q3. What calculation is Google planning to do, or has it already done, that’s believed to be classically hard?

So, I can tell you, but I’ll feel slightly sheepish doing so. The calculation is: a “challenger” generates a random quantum circuit C (i.e., a random sequence of 1-qubit and nearest-neighbor 2-qubit gates, of depth perhaps 20, acting on a 2D grid of n = 50 to 60 qubits). The challenger then sends C to the quantum computer, and asks it apply C to the all-0 initial state, measure the result in the {0,1} basis, send back whatever n-bit string was observed, and repeat some thousands or millions of times. Finally, using its knowledge of C, the classical challenger applies a statistical test to check whether the outputs are consistent with the QC having done this.

So, this is not a problem like factoring with a single right answer. The circuit C gives rise to some probability distribution, call it DC, over n-bit strings, and the problem is to output samples from that distribution. In fact, there will typically be 2n strings in the support of DC—so many that, if the QC is working as expected, the same output will never be observed twice. A crucial point, though, is that the distribution DC is not uniform. Some strings enjoy constructive interference of amplitudes and therefore have larger probabilities, while others suffer destructive interference and have smaller probabilities. And even though we’ll only see a number of samples that’s tiny compared to 2n, we can check whether the samples preferentially cluster among the strings that are predicted to be likelier, and thereby build up our confidence that something classically intractable is being done.

So, tl;dr, the quantum computer is simply asked to apply a random (but known) sequence of quantum operations—not because we intrinsically care about the result, but because we’re trying to prove that it can beat a classical computer at some well-defined task.

Q4. But if the quantum computer is just executing some random garbage circuit, whose only purpose is to be hard to simulate classically, then who cares? Isn’t this a big overhyped nothingburger?

No. As I put it the other day, it’s not an everythingburger, but it’s certainly at least a somethingburger!

It’s like, have a little respect for the immensity of what we’re talking about here, and for the terrifying engineering that’s needed to make it reality. Before quantum supremacy, by definition, the QC skeptics can all laugh to each other that, for all the billions of dollars spent over 20+ years, still no quantum computer has even once been used to solve any problem faster than your laptop could solve it, or at least not in any way that depended on its being a quantum computer. In a post-quantum-supremacy world, that’s no longer the case. A superposition involving 250 or 260 complex numbers has been computationally harnessed, using time and space resources that are minuscule compared to 250 or 260.

I keep bringing up the Wright Flyer only because the chasm between what we’re talking about, and the dismissiveness I’m seeing in some corners of the Internet, is kind of breathtaking to me. It’s like, if you believed that useful air travel was fundamentally impossible, then seeing a dinky wooden propeller plane keep itself aloft wouldn’t refute your belief … but it sure as hell shouldn’t reassure you either.

Was I right to worry, years ago, that the constant drumbeat of hype about much less significant QC milestones would wear out people’s patience, so that they’d no longer care when something newsworthy finally did happen?

Q5. Years ago, you scolded the masses for being super-excited about D-Wave, and its claims to get huge quantum speedups for optimization problems via quantum annealing. Today you scold the masses for not being super-excited about quantum supremacy. Why can’t you stay consistent?

Because my goal is not to move the “excitement level” in some uniformly preferred direction, it’s to be right! With hindsight, would you say that I was mostly right about D-Wave, even when raining on that particular parade made me unpopular in some circles? Well, I’m trying to be right about quantum supremacy too.

Q6. If quantum supremacy calculations just involve sampling from probability distributions, how do you check that they were done correctly?

Glad you asked! This is the subject of a fair amount of theory that I and others developed over the last decade. I already gave you the short version in my answer to Q3: you check by doing statistics on the samples that the QC returned, to verify that they’re preferentially clustered in the “peaks” of the chaotic probability distribution DC. One convenient way of doing this, which Google calls the “linear cross-entropy test,” is simply to sum up Pr[C outputs si] over all the samples s1,…,sk that the QC returned, and then to declare the test a “success” if and only if the sum exceeds some threshold—say, bk/2n, for some constant b strictly between 1 and 2.

Admittedly, in order to apply this test, you need to calculate the probabilities Pr[C outputs si] on your classical computer—and the only known ways to calculate them require brute force and take ~2n time. Is that a showstopper? No, not if n is 50, and you’re Google and are able to handle numbers like 250 (although not 21000, which exceeds a googol, har har). By running a huge cluster of classical cores for (say) a month, you can eventually verify the outputs that your QC produced in a few seconds—while also seeing that the QC was many orders of magnitude faster. However, this does mean that sampling-based quantum supremacy experiments are almost specifically designed for ~50-qubit devices like the ones being built right now. Even with 100 qubits, we wouldn’t know how to verify the results using all the classical computing power available on earth.

(Let me stress that this issue is specific to sampling experiments like the ones that are currently being done. If Shor’s algorithm factored a 2000-digit number, it would be easy to check the result by simply multiplying the claimed factors and running a primality test on them. Likewise, if a QC were used to simulate some complicated biomolecule, you could check its results by comparing them to experiment.)

Q7. Wait. If classical computers can only check the results of a quantum supremacy experiment, in a regime where the classical computers can still simulate the experiment (albeit extremely slowly), then how do you get to claim “quantum supremacy”?

Come on. With a 53-qubit chip, it’s perfectly feasible to see a speedup by a factor of many millions, in a regime where you can still directly verify the outputs, and also to see that the speedup is growing exponentially with the number of qubits, exactly as asymptotic analysis would predict. This isn’t marginal.

Q8. Is there a mathematical proof that no fast classical algorithm could possibly spoof the results of a sampling-based quantum supremacy experiment?

Not at present. But that’s not quantum supremacy researchers’ fault! As long as theoretical computer scientists can’t even prove basic conjectures like P≠NP or P≠PSPACE, there’s no hope of ruling out a fast classical simulation unconditionally. The best we can hope for are conditional hardness results. And we have indeed managed to prove some such results—see for example the BosonSampling paper, or the Bouland et al. paper on average-case #P-hardness of calculating amplitudes in random circuits, or my paper with Lijie Chen (“Complexity-Theoretic Foundations of Quantum Supremacy Experiments”). The biggest theoretical open problem in this area, in my opinion, is to prove better conditional hardness results.

Q9. Does sampling-based quantum supremacy have any applications in itself?

When people were first thinking about this subject, it seemed pretty obvious that the answer was “no”! (I know because I was one of the people.) Recently, however, the situation has changed—for example, because of my certified randomness protocol, which shows how a sampling-based quantum supremacy experiment could almost immediately be repurposed to generate bits that can be proven to be random to a skeptical third party (under computational assumptions). This, in turn, has possible applications to proof-of-stake cryptocurrencies and other cryptographic protocols. I’m hopeful that more such applications will be discovered in the near future.

Q10. If the quantum supremacy experiments are just generating random bits, isn’t that uninteresting? Isn’t it trivial to convert qubits into random bits, just by measuring them?

The key is that a quantum supremacy experiment doesn’t generate uniform random bits. Instead, it samples from some complicated, correlated probability distribution over 50- or 60-bit strings. In my certified randomness protocol, the deviations from uniformity play a central role in how the QC convinces a classical skeptic that it really was sampling the bits randomly, rather than in some secretly deterministic way (e.g., using a pseudorandom generator).

Q11. Haven’t decades of quantum-mechanical experiments–for example, the ones that violated the Bell inequality–already demonstrated quantum supremacy?

This is purely a confusion over words. Those other experiments demonstrated other forms of “quantum supremacy”: for example, in the case of Bell inequality violations, what you could call “quantum correlational supremacy.” They did not demonstrate quantum computational supremacy, meaning doing something that’s infeasible to simulate using a classical computer (where the classical simulation has no restrictions of spatial locality or anything else of that kind). Today, when people use the phrase “quantum supremacy,” it’s generally short for quantum computational supremacy.

Q12. Even so, there are countless examples of materials and chemical reactions that are hard to classically simulate, as well as special-purpose quantum simulators (like those of Lukin’s group at Harvard). Why don’t these already count as quantum computational supremacy?

Under some people’s definitions of “quantum computational supremacy,” they do! The key difference with Google’s effort is that they have a fully programmable device—one that you can program with an arbitrary sequence of nearest-neighbor 2-qubit gates, just by sending the appropriate signals from your classical computer.

In other words, it’s no longer open to the QC skeptics to sneer that, sure, there are quantum systems that are hard to simulate classically, but that’s just because nature is hard to simulate, and you don’t get to arbitrarily redefine whatever random chemical you find in the wild to be a “computer for simulating itself.” Under any sane definition, the superconducting devices that Google, IBM, and others are now building are indeed “computers.”

Q13. Did you (Scott Aaronson) invent the concept of quantum supremacy?

No. I did play some role in developing it, which led to Sabine Hossenfelder among others generously overcrediting me for the whole idea. The term “quantum supremacy” was coined by John Preskill in 2012, though in some sense the core concept goes back to the beginnings of quantum computing itself in the early 1980s. In 1993, Bernstein and Vazirani explicitly pointed out the severe apparent tension between quantum mechanics and the Extended Church-Turing Thesis of classical computer science. Then, in 1994, the use of Shor’s algorithm to factor a huge number became the quantum supremacy experiment par excellence—albeit, one that’s still (in 2019) much too hard to perform.

The key idea of instead demonstrating quantum supremacy using a sampling problem was, as far as I know, first suggested by Barbara Terhal and David DiVincenzo, in a farsighted paper from 2002. The “modern” push for sampling-based supremacy experiments started around 2011, when Alex Arkhipov and I published our paper on BosonSampling, and (independently of us) Bremner, Jozsa, and Shepherd published their paper on the commuting Hamiltonians model. These papers showed, not only that “simple,” non-universal quantum systems can solve apparently-hard sampling problems, but also that an efficient classical algorithm for the same sampling problems would imply a collapse of the polynomial hierarchy. Arkhipov and I also made a start toward arguing that even the approximate versions of quantum sampling problems can be classically hard.

As far as I know, the idea of “Random Circuit Sampling”—that is, generating your hard sampling problem by just picking a random sequence of 2-qubit gates in (say) a superconducting architecture—originated in an email thread that I started in December 2015, which also included John Martinis, Hartmut Neven, Sergio Boixo, Ashley Montanaro, Michael Bremner, Richard Jozsa, Aram Harrow, Greg Kuperberg, and others. The thread was entitled “Hard sampling problems with 40 qubits,” and my email began “Sorry for the spam.” I then discussed some advantages and disadvantages of three options for demonstrating sampling-based quantum supremacy: (1) random circuits, (2) commuting Hamiltonians, and (3) BosonSampling. After Greg Kuperberg chimed in to support option (1), a consensus quickly formed among the participants that (1) was indeed the best option from an engineering standpoint—and that, if the theoretical analysis wasn’t yet satisfactory for (1), then that was something we could remedy.

[Update: Sergio Boixo tells me that, internally, the Google group had been considering the idea of random circuit sampling since February 2015, even before my email thread. This doesn’t surprise me: while there are lots of details that had to be worked out, the idea itself is an extremely natural one.]

After that, the Google group did a huge amount of analysis of random circuit sampling, both theoretical and numerical, while Lijie Chen and I and Bouland et al. supplied different forms of complexity-theoretic evidence for the problem’s classical hardness.

Q14. If quantum supremacy was achieved, what would it mean for the QC skeptics?

I wouldn’t want to be them right now! They could retreat to the position that of course quantum supremacy is possible (who ever claimed that it wasn’t? surely not them!), that the real issue has always been quantum error-correction. And indeed, some of them have consistently maintained that position all along. But others, including my good friend Gil Kalai, are on record, right here on this blog predicting that even quantum supremacy can never be achieved for fundamental reasons. I won’t let them wiggle out of it now.

[Update: As many of you will have seen, Gil Kalai has taken the position that the Google result won’t stand and will need to be retracted. He asked for more data: specifically, a complete histogram of the output probabilities for a smaller number of qubits. This turns out to be already available, in a Science paper from 2018.]

Q15. What’s next?

If it’s achieved quantum supremacy, then I think the Google group already has the requisite hardware to demonstrate my protocol for generating certified random bits. And that’s indeed one of the very next things they’re planning to do.

[Addendum: Also, of course, the evidence for quantum supremacy itself can be made stronger and various loopholes closed—for example, by improving the fidelity so that fewer samples need to be taken (something that Umesh Vazirani tells me he’d like to see), by having the circuit C be generated and the outputs verified by a skeptic external to Google. and simply by letting more time pass, so outsiders can have a crack at simulating the results classically. My personal guess is that the basic picture is going to stand, but just like with the first experiments that claimed to violate the Bell inequality, there’s still plenty of room to force the skeptics into a tinier corner.]

Beyond that, one obvious next milestone would be to use a programmable QC, with (say) 50-100 qubits, to do some useful quantum simulation (say, of a condensed-matter system) much faster than any known classical method could do it. A second obvious milestone would be to demonstrate the use of quantum error-correction, to keep an encoded qubit alive for longer than the underlying physical qubits remain alive. There’s no doubt that Google, IBM, and the other players will now be racing toward both of these milestones.

[Update: Steve Girvin reminds me that the Yale group has already achieved quantum error-correction “beyond the break-even point,” albeit in a bosonic system rather than superconducting qubits. So perhaps a better way to phrase the next milestone would be: achieve quantum computational supremacy and useful quantum error-correction in the same system.]

Another update: I thought this IEEE Spectrum piece gave a really nice overview of the issues.

Last update: John Preskill’s Quanta column about quantum supremacy is predictably excellent (and possibly a bit more accessible than this FAQ).

25 Sep 05:37

Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface

by Trautmann, E. M., O'Shea, D. J., Sun, X., Marshel, J. H., Crow, A., Hsueh, B., Vesuna, S., Cofer, L., Bohner, G., Allen, W., Kauver, I., Quirin, S., Macdougall, M., Chen, Y., Whitmire, M., Ramakrishnan, C., Sahani, M., Seidemann, E., Ryu, S., Deisseroth, K., Shenoy, K.
Calcium imaging has rapidly developed into a powerful tool for recording from large populations of neurons in vivo. Imaging in rhesus macaque motor cortex can enable the discovery of new principles of motor cortical function and can inform the design of next generation brain-computer interfaces (BCIs). Surface two-photon (2P) imaging, however, cannot presently access somatic calcium signals of neurons from all layers of macaque motor cortex due to photon scattering. Here, we demonstrate an implant and imaging system capable of chronic, motion-stabilized two-photon (2P) imaging of calcium signals from in macaques engaged in a motor task. By imaging apical dendrites, some of which originated from deep layer 5 neurons, as as well as superficial cell bodies, we achieved optical access to large populations of deep and superficial cortical neurons across dorsal premotor (PMd) and gyral primary motor (M1) cortices. Dendritic signals from individual neurons displayed tuning for different directions of arm movement, which was stable across many weeks. Combining several technical advances, we developed an optical BCI (oBCI) driven by these dendritic signals and successfully decoded movement direction online. By fusing 2P functional imaging with CLARITY volumetric imaging, we verify that an imaged dendrite, which contributed to oBCI decoding, originated from a putative Betz cell in motor cortical layer 5. This approach establishes new opportunities for studying motor control and designing BCIs.
20 Sep 09:30

Polyunsaturated fatty acid analogues differentially affect cardiac Nav, Cav, and Kv channels through unique mechanisms

by Bohannon, B., Wu, X., Perez, M., Liin, S. I., Larsson, H. P.
The cardiac ventricular action potential depends on several voltage-gated ion channels, including Nav, Cav, and Kv channels. Mutations in these channels can cause Long QT Syndrome (LQTS) which increases the risk for ventricular fibrillation and sudden cardiac death. Polyunsaturated fatty acids (PUFAs) have emerged as potential therapeutics for LQTS because they are modulators of voltage-gated ion channels. Here we demonstrate that PUFA analogues vary in their selectivity for human voltage-gated ion channels involved in the ventricular action potential. The effects of specific PUFA analogues range from selective for a specific ion channel to broadly modulating all three cardiac ion channels (NaV, CaL, and IKs). In addition, PUFA analogues do not modulate these channels through a shared mechanism. Our data suggest that different PUFA analogues could be tailored towards specific forms of LQTS, which are caused by mutations in distinct cardiac ion channels, and thus restore a normal ventricular action potential.
20 Sep 08:38

Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain

by Johan Winnubst, Erhan Bas, Tiago A. Ferreira, Zhuhao Wu, Michael N. Economo, Patrick Edson, Ben J. Arthur, Christopher Bruns, Konrad Rokicki, David Schauder, Donald J. Olbris, Sean D. Murphy, David G. Ackerman, Cameron Arshadi, Perry Baldwin, Regina Blake, Ahmad Elsayed, Mashtura Hasan, Daniel Ramirez, Bruno Dos Santos, Monet Weldon, Amina Zafar, Joshua T. Dudman, Charles R. Gerfen, Adam W. Hantman, Wyatt Korff, Scott M. Sternson, Nelson Spruston, Karel Svoboda, Jayaram Chandrashekar
An efficient pipeline for brain-wide imaging and morphological reconstruction of individual neurons, including long-range projection neurons, is presented along with a searchable database containing more than 1,000 fully reconstructed neurons in the mouse neocortex, hippocampus, thalamus, and hypothalamus.
20 Sep 08:31

Detecting social (in)stability in primates from their temporal co-presence network. (arXiv:1909.09090v1 [physics.soc-ph])

by Valeria Gelardi, Joël Fagot, Alain Barrat, Nicolas Claidière

The stability of social relationships is important to animals living in groups, and social network analysis provides a powerful tool to help characterize and understand their (in)stability and the consequences at the group level. However, the use of dynamic social networks is still limited in this context as it requires long-term social data and new analytical tools. Here, we study the dynamic evolution of a group of 29 Guinea baboons using a dataset of automatically collected cognitive tests comprising more than 16M records collected over 3 years. We first built a monthly aggregated temporal network describing the baboon's co-presence in the cognitive testing booths. We then used a null model, considering the heterogeneity in the baboons' activity, to define both positive (association) and negative (avoidance) monthly networks. We tested social balance theory by combining these positive and negative social networks. The results showed that the networks were structurally balanced and that newly created edges also tended to preserve social balance. We investigated several network metrics to gain insights into the individual level and group level social networks long-term temporal evolution. A measure of similarity between successive monthly networks was able to pinpoint periods of stability and instability and to show how some baboons' ego-networks remained stable while others changed radically. Our study confirms the prediction of social balance theory but also shows that large fluctuations in the numbers of triads may limit its applicability to study the dynamic evolution of animal social networks. In contrast, the use of the similarity measure proved to be very versatile and sensitive in detecting relationships' (in)stabilities at different levels. The changes we identified can be linked, at least in some cases, to females changing primary male, as observed in the wild.

29 Aug 16:27

Americans continue to drink bleach

by Minnesotastan
As reported by Ars Technica:
The US Food and Drug Administration this week released an important health warning that everyone should heed: drinking bleach is dangerous—potentially life-threatening—and you should not do it. The warning may seem unnecessary, but guzzling bleach is an unfortunately persistent problem.

Unscrupulous sellers have sold “miracle” bleach elixirs for decades, claiming that they can cure everything from cancer to HIV/AIDS, hepatitis, flu, hair loss, and more. Some have promoted it to parents as a way to cure autism in children—prompting many allegations of child abuse.

Of course, the health claims are false, not to mention abhorrent. When users prepare the solution as instructed, it turns into the potent bleaching agent chlorine dioxide, which is an industrial cleaner. It’s toxic to drink and can cause severe diarrhea, vomiting, life-threatening low blood pressure, acute liver failure, and damage to the digestive tract and kidneys.

In this week’s warning, the FDA noted that some sellers will warn consumers that vomiting and diarrhea are common but say that those unpleasant effects indicate the solution is “working.”

“That claim is false,” the FDA wrote succinctly.
What kind of society have we evolved that it becomes necessary to warn the public - repeatedly - not to drink bleach because someone has suggested they do so??
The FDA says that the products have been hard to scrub out because of claims on social media, where the drinks are promoted along with false health information. Most of the claims can be traced back to Jim Humble, founder and “archbishop” of the Genesis II Church of Health and Healing, aka “The Church of Bleach.”

Humble has been touting the solution for nearly two decades, referring to it as MMS—Miracle or Master Mineral Solution. (It’s also known as the Miracle Mineral Supplement, the Chlorine Dioxide (CD) Protocol, and Water Purification Solution (WPS).) Humble is a former Scientologist who reportedly claims to be a billion-year-old god from the Andromeda galaxy.