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04 May 22:50

Would you help this man get out of prison? - updated

by Minnesotastan

This petition is at Change.org:
Cornealious "Mike" Anderson is 36 years old, a married father of four, youth football coach, volunteer, homeowner and small business owner in St. Louis, Missouri.  In 1999, he was arrested and later convicted of participating in a robbery of a Burger King manager.  He was sentenced to 13 years in prison.  He was released on bail while his appeals were pending, and after he lost his appeals, the State of Missouri simply forgot about him.  They never told him to report to prison to serve his sentence.

When he was arrested, he was 22 years old, had no children, was not married, and did not own a home or a business.

From 1999 to 2013, he lived a law-abiding life, paid taxes, and worked to build a career as a carpenter. He never became a  fugitive, tried to change his identity, or flee from justice.  He had no further trouble with the law.  He stayed right in St. Louis.  He got married, had 4 children, built his own home in Missouri, and started several successful small businesses, including a contracting business.  He volunteered at his church and coached his son's youth football team.

In July, 2013, the State of Missouri suddenly realized, 13 years later, that Mike Anderson had never served the sentence, and that he was out on bail this entire time.  They raided his house with a SWAT team, and ripped him from his home without warning, hauled him off to prison, and told him he now had to serve 13 years in prison.

If he is required to serve the sentence, he will be 50 years old when he is released.  His kids will have grown up without a father, his wife will have had to raise 4 children alone, and they will lose their home and business - everything he had worked so hard to attain in the last 13 years of leading a normal life.

The victim of the robbery believes that Mike Anderson should not be forced to now serve a 13-year sentence, and believes the State of Missouri dropped the ball.  He has said that he believes it would serve no purpose in now incarcerating this man.
The full story, with extensive details, is at Riverfront Times.

I first heard the story as a podcast on This American Life.  It takes about 15 minutes, and I think is well worth a listen before you pass judgment.

I've signed the petition, as have 35,000 others.

Update:  He has been released.
Judge Terry Lynn Brown lauded Anderson's "exemplary" behavior during his 13 years of freedom before the arrest. "You've been a good father. You've been a good husband. You've been a good taxpaying citizen of the state of Missouri. "That leads me to believe that you are a good man and a changed man."

Anderson walked out of the courtroom with his wife and 3-year-old daughter on one arm and his mom on the other. Before being driven away to a freedom celebration at an undisclosed spot, Anderson told reporters he was "very happy. My faith has always been in God. I'm just so thankful. Thank God for everything."

The best place to follow the conclusion of the story is at the Riverfront Times (which was a favorite read of mine when I lived in St. Louis).

The podcast is still worth a listen; it's quite a story.
04 May 22:48

This is a living creature

by Minnesotastan

I find this photo to be endlessly fascinating.  The creature is a single-cell organism (Nassula).

And it has all that is needed for life.  What is it that converts this combination of membranes and complex molecules into a "living" organism capable of eating and reproducing.  It staggers my mind to think about it.

Photo credit: Mr. Riccardo Taiariol, La Spezia, Italy, using differential interference contrast at 25x, from an Olympus Bioscapes gallery.
04 May 22:27

Low dimensional topology of information

by dmoskovich

Is information geometric, or is it fundamentally topological?

Information theory is a big, amorphous, multidisciplinary field which brings together mathematics, engineering, and computer science. It studies information, which typically manifests itself mathematically via various flavours of entropy. Another side of information theory is algorithmic information theory, which centers around notions of complexity. The mathematics of information theory tends to be analytic. Differential geometry plays a major role. Fisher information treats information as a geometric quantity, studying it by studying the curvature of a statistical manifold. The subfield of information theory centred around this worldview is known as information geometry.

But Avishy Carmi and I believe that information geometry is fundamentally topological. Geometrization shows us that the essential geometry of a closed 3-manifold is captured by its topology; analogously we believe that fundamental aspects of information geometry ought to be captured topologically. Not by the topology of the statistical manifold, perhaps, but rather by the topology of tangle machines, which is quite similar to the topology of tangles or of virtual tangles.

We have recently uploaded two preprints to ArXiv in which we define tangle machines and some of their topological invariants:

Tangle machines I: Concept
Tangle machines II: Invariants

I’ve posted about an earlier phase of this work HERE and HERE.

Our terminology is classical computer-science inspired- the term “tangle machine” imitates “Turing machine”, our connected components are “processes”, our strands are “registers”, and our crossings are “interactions”. Tangle machines are envisioned as a diagrammatic calculus for information theory, in a big amorphous multidisciplinary sense, which capture an underlying topological nature to information manipulation and transfer.

In what sense is information topological?

Information manipulation should fundamentally be causal, by which I mean that one unit of information y causes another unit of information x to change (we’ll call it’s updated state x\triangleright y). By how much? That depends on your method of measurement. In what direction? That depends on your chosen (perhaps arbitrary) system of coordinates. But the plain fact of causation, that y causes x to change to x\triangleright y, doesn’t depend on any of that. I’d like to draw such an interaction as a crossing:

An interaction

Note: Statistics gives us the tools to detect such causal interactions inside real-world data, in which one piece of information triggers a transition between two pieces of information. This means we can actually detect tangle machines inside e.g. Google Trends search data! As a single-interaction example, given graphs of number of searches and nothing else, we can detect with statistical significance that iPhone 5 caused Samsung to update from S2 to S3. Some graphics for another detection example are given below.

interaction detected

Our information is in the form of colours on strands (i.e. in registers). For example, each strand might be coloured by a real number representing the entropy of a `typical sequence’ of zeros and ones. I’m imagining `information’ sitting as colours on each of the strands, with each crossing representing an information fusion or its converse.

Note also that information plays a dual role e.g. in the classical paradigms of computing, such as a universal Turing machine. On the one hand, information is something that is manipulated by a computer, such as the input or the output of a computation. Such information is called a patient. On the other hand, the computer programme that does the manipulation is itself information. Information in this capacity is called an agent. A computer programme can modify another computer programme, so that an agent in one context may be a patient in another context. A labeled digraph (such are the classical diagrammatic languages for such things) does not capture this dual nature of information. But a strand in a tangle diagram may be an overstrand mediating between an input understrand and an output understrand in one crossing, and it may be an understrand itself in another crossing.

We claim that interactions, i.e. crossings, satisfy the Reidemeister relations, and that these represent fundamental properties of information fusion. Indeed, Reidemeister 1 tells us that information cannot generate new information from itself and so, for example, that the entropy of a closed system cannot drop, and in fact can’t increase either, without outside intervention. This seems to contradict the second law of thermodynamics, but thanks to e.g. the Poincaré recurrence theorem I think it’s actually fine.

Reidemeister 2 is what information theorists call `causal invertibility’, telling us that we can recover the input x from the output x\triangleright y and the agent y, and that updating and then discounting by y- adding information and then taking it away- brings us back to where we started as though we had done nothing.

And Reidemeister 3, which comes from distributivity, tells us that if we find a common cause z for an interaction in which y causes x to change to x\triangleright y, then that doesn’t change our causal relationships: y\triangleright z still causes x\triangleright z to change to (x\triangleright y)\triangleright z. In information theory, this is equivalent to no double counting. If we update x\triangleright z by y\triangleright z then we obtain (x\triangleright y)\triangleright z, so z is counted towards the result `just once’.

One fun spinoff of this approach is that several classical information theoretical algorithms, such as Kalman filtering and covariance intersection, can be developed using Reidemeister move invariance for suitable choices of what we mean precisely when we say `information’. We can imagine a little Kalman filter fusing and discounting estimators, or a little covariance intersection, sitting at each crossing.

So what does this all give us? We now have a coordinate free `topological’ language with which to discuss fusion and discounting of information. Moreover, we can describe the same network in many different ways, which differ by finite sequences of Reidemeister moves. Different equivalent tangle machines may have different local performance- to fuse and then to discount may consume time and resources, although topologically we’ve done nothing. So tangle machines become a formalism for choosing between different ways to realize `the same’ network of information manipulation.

These ideas become quite concrete in the quantum physical context of adiabatic quantum computation (this is our Section 5.2). Here, the colours represent Hamiltonians, and the interaction is of the form x\triangleright y\stackrel{\textup{\tiny def}}{=} (1-s)x+sy, where s\in [0,1). As we move s from 0 to 1 (this is the computation), x\triangleright y evolves from x to y. Concatenate many such interactions, and the machine describes a controlled evolution (quantum annealing) of an initial groundstate of a Hamiltonian towards a final state, where we are forcing the Hamiltonian to pass through each state described by a groundstate of a Hamiltonian which overcrosses its strand. The effect may be to speed up adiabatic quantum computations! Farhi et.al. have a recent preprint in which they discuss such speedups by `inserting intermediate Hamiltonians’, and it seems to be known that you can speed up classical quantum algorithms such as the Grover algorithm in this way. Essentially, the idea is that the speed of the computation is inversely proportional to the minimum distance between the lowest two eigenvalues of the Hamiltonian along the evolution path. The `straight line annealing’ of `classical adiabatic quantum computing’ is like walking in a straight line between two points on hilly ground- you might have to climb over hills and down gullies, and, despite being a straight line, it may be a strenuous path. I wouldn’t necessarily want to hike between two peaks of a high mountains by going in a straight line! Tangle machines give a diagrammatic language to describe the process of choosing the traverse.

From another perspective, information manipulation might be just another word for computation. The word `computation’ is a charged word, which, like `information’, doesn’t have clear mathematical meaning. One way to ascribe the word `computation’ mathematical meaning would be to define computation as the operation of a Turing machine. Can a tangle machine simulate a Turing machine?

Let’s define the computation of a tangle machine to be `input colours into a set of registers S_{\text{in}}, and read off colours from another set of registers S_{\text{out}}‘. Assume that the colours of S_{\text{in}} uniquely determine the colours of S_{\text{out}}.

This notion of computation, unlike many others, makes no mention of the notion of `time’.

Let’s choose our set of colours to be 0, \frac{1}{2}, and 1, represented as red, green, and blue correspondingly. A colour acts trivially on itself, but switches any colour other than itself- this is a Fox 3-colouring.

We first simulate a NOT gate, exchanging 1 and 0. The arrow on the left is the input, and on the right is the output. The strand without the arrow is fixed at \frac{1}{2}, and is neither input nor output, but is merely part of the gate.

NOT gate

We next simulate a multiplexer, which copies a register labeled 0 of 1. This gate has one input and two outputs.

Multiplexer

To simulate an AND gate, we need one more piece (and its inverse). This is a trivalent vertex which accepts two colours as input, and outputs their minimum. This sends (0,0), (0,1), and (1,0), to zero, and it sends (1,1) to one.

AND gate

And that’s it! With an AND gate, a NOT gate, and a multiplexer, we can compute any recursively computable function, and tangle machines (in this new extended sense, which I haven’t properly defined) are Turing complete.

I haven’t explicitly written down the Reidemeister moves that such a machine satisfies in this blog post.

Tangle machines can further simulate a Turing machine, tape and all, and can further simulate neural networks. If we allow the overcrossing colour to also be updated, so our colour set is not a quandle but is instead a biquandle, we can also simulate machine learning.

Besides our approach, there are other quite different approaches which relate low dimensional topology with the theory of computation (although I don’t know other works relating low dimensional topology with information theory). One approach is to view the tangle itself as a unit of data, and to compute by applying rewrite rules. This approach originates with Kauffman, who is I think the father of applying low dimensional topology to computing. It is tremendously exciting, with possible applications in internet architecture and in biology. A recent preprint by Kauffman and Buliga outlines one such idea. Marius Buliga has a very nice research blog in which he explains his research programme. There is also another approach of Kauffman in which colours evolve along a braid. I think that this concept of computation is similar in spirit to ours (with knots instead of with tangle machines), in that his crossings are also performing computations. Meredith and Snyder have an approach in which they encode knot diagrams using Milner’s π calculus, with a view to using process calculi formalisms to find and compute knot invariants. In this approach also, crossings play the role of switches. Then there are the category theory approaches, outlined nicely in Baez and Stay’s survey.

Thanks to Lou Kauffman and to Marius Buliga, for useful feedback regarding tangle machines and computation.

As today there is information geometry, Avishy and I strongly believe that there will be information topology. The low dimensional topology of information.


01 May 14:56

'Classically Cannabis': Colorado Symphony Orchestra Goes to Pot

by Elizabeth Nolan Brown

Classical concerts just don't stir the kids like they used to. But the Colorado Symphony Orchestra has an idea it's hoping might help change that. This May, the symphony is introducing "Classically Cannabis: The High Note Series," a round of weed-friendly summer fundraising concerts. 

"It's an interesting way to connect ourselves to new audiences and new potential financial support," said Jerry Kern, Colorado Symphony CEO, in an NBC News clip (below).  

The concerts—each with a different theme—will take place in May, July, and August at a downtown Denver venue called the Space Gallery.

Edible Events Co., "Colorado’s premier producer of cannabis-friendly events," is curating, with all proceeds going to the Colorado Symphony. "I'd like to kind of start redefining what a cannabis user looks like," said Jane West, owner of Edible Events. 

Along with some sweet classical jams, the $75 ticket price will get concertgoers complimentary booze and food truck grub. But all shows are "BYOC"—bring your own cannabis.

The symphony is also hosting a series of "Beethoven and Brews" concerts, which wil have slightly cheaper tickets and take place in local breweries.

01 May 05:05

Perspective: Synthetic biology revives antibiotics

by Gerard Wright

Perspective: Synthetic biology revives antibiotics

Nature. doi:10.1038/509S13a

Author: Gerard Wright

Re-engineering natural products provides a new route to drug discovery, says Gerard Wright.

29 Apr 20:42

TGA: Grassmann Averages for Scalable Robust PCA - implementation -

by Igor
So it looks like we have a fast implementation of the Robust PCA

Grassmann Averages for Scalable Robust PCA by Søren Hauberg, Aasa Feragen, Michael J. Black

As the collection of large datasets becomes increasingly automated, the occurrence of outliers will increase“big data” implies “big outliers”. While principal component analysis (PCA) is often used to reduce the size of data, and scalable solutions exist, it is well-known that outliers can arbitrarily corrupt the results. Unfortunately, state- of-the-art approaches for robust PCA do not scale beyond small-to-medium medium sized datasets. To address this, we introduce the Grassmann Average (GA), which expresses dimensionality reduction as an average of the subspaces spanned by the data. Because averages can be efficiently computed, we immediately gain scalability. GA is inherently more robust than PCA, but we show that they coincide for Gaussian data. We exploit that averages can be made robust to formulate the Robust Grassmann Average (RGA) as a form of robust PCA. Robustness can be with respect to vectors (subspaces) or elements of vectors; we focus on the latter and use a trimmed average. The resulting Trimmed Grassmann Average (TGA) is particularly appropriate for computer vision because it is robust to pixel outliers. The algorithm has low computational complexity and minimal memory requirements, making it scalable to “big noisy data.” We demonstrate TGA for background modeling, video restoration, and shadow removal. We show scalability by performing robust PCA on the entire Star Wars IV movie.


from the text:

To further emphasize the scalability of TGA, we compute the 20 leading components of the entire Star Wars IV movie. This consist of 179,415 frames with a resolution of 352153. Computing these 20 components (see [15]) took 8.5 hours on an Intel Xeon E5-2650 with 128 GB memory.
my emphasis on the underlined word.

The project page is here and the attendant code is here. It will be added to the Advanced Matrix Factorization Jungle page shortly.



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29 Apr 20:10

(100 x 100)-dimensional entangled quantum system [Physics]

by Krenn, M., Huber, M., Fickler, R., Lapkiewicz, R., Ramelow, S., Zeilinger, A.
Entangled quantum systems have properties that have fundamentally overthrown the classical worldview. Increasing the complexity of entangled states by expanding their dimensionality allows the implementation of novel fundamental tests of nature, and moreover also enables genuinely new protocols for quantum information processing. Here we present the creation of a (100...
28 Apr 00:01

New Scientist Article

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

I’ve got a full-page opinion piece in this week’s New Scientist, on why mathematicians should refuse to cooperate with agencies of mass surveillance. If you’re in the US, UK or Australia, it’s the print edition that came out yesterday.

Thumbnail of New Scientist article

MathML-enabled post (click for more details).

The substance is much the same as my piece for the London Mathematical Society Newsletter, but it’s longer, and it’s adapted for a US readership too.

I don’t currently have much to add to the article or what I wrote about mathematicians and the secret services previously. But I do have some observations to make about the process of writing for New Scientist.

This was my first time writing for a magazine. The article received substantial edits from at least three editors; you can compare it with the version I originally submitted. I have mixed feelings about this process.

On the one hand, it’s great to have the input of experienced magazine journalists, and I can definitely see ways that they improved what I wrote. On the other hand — and despite the editors I dealt with being reasonable, helpful, and pleasant — I found the process pretty frustrating. I think that’s because of where the control lies.

What doesn’t happen is that you submit your piece, the editors read it and give you their critiques, and then you amend your article accordingly. What does happen is that you submit something, the editors change it how they like, and if you don’t like any of their changes, you have to argue for why it should be changed back. This process may be iterated several times, perhaps with different editors with different opinions. Rationally, I know that the article goes out not only under my name but also under the magazine’s, but by the end of the process, I did have the depressing feeling that the article wasn’t entirely mine.

(Small example: there were three words that I disliked and repeatedly removed from the editor’s edits: “moral”, “snoop” and “spook”. The editors I dealt with directly respected my wish to avoid them, after I’d made the case. But in the online version, the headline and the standfirst — which I neither wrote nor saw before publication — managed to use two out of those three words.)

Anyway, it was a new experience.

Comments are open. As ever, if you’re leaving comments on the political aspects, please keep them focused on the relationship between mathematicians and the secret services.


Update   Here’s a list of the various press articles that followed on from my original article:

MathML-enabled post (click for more details).MathML-enabled post (click for more details).
27 Apr 23:58

inkhorn

Merriam-Webster's Word of the Day for April 27, 2014 is:

inkhorn • \INK-horn\  • adjective
: ostentatiously learned : pedantic

Examples:
Richard's use of inkhorn terminology in his paper didn't impress his professor, whereas simple language demonstrating a clear understanding of the material would have done the trick.

"It was not until the 18th century that dictionary-makers began to include everyday words and weed out the weighty-sounding inkhorn terms." — From an article by Faye Carney in The Times Educational Supplement, September 23, 2005

Did you know?
Picture an ancient scribe, pen in hand, a small ink bottle made from an animal's horn strapped to his belt, ready to record the great events of history. In 14th-century England, such ink bottles were dubbed (not surprisingly) "inkhorns." During the Renaissance, learned writers often borrowed words from Latin and Greek, eschewing vulgar English alternatives. But in the 16th century, some scholars argued for the use of native terms over Latinate forms, and a lively intellectual debate over the merits of each began. Those who favored English branded what they considered ostentatious Latinisms "inkhorn terms" after the bottles carried by scholars, and since then we have used "inkhorn" as an adjective for Latinate or pretentious language.

26 Apr 17:19

The Poors Definitely Can't Have Nice Things

by noreply@blogger.com (Atrios)
It isn't the full story, but part of the acceptance of "only poor people get busted for drugs" is based on the idea that the poors don't deserve any "fun" at all. Obviously given addiction issues drug use is a bit more complicated than "fun," but people who have no problem shelling out $50 for a bottle of wine are horrified to see the poors with a six pack of cheap beer. Likewise, upper middle class people who for one reason or another rely on drugs, legal or not, think the poor, with their slightly more acute struggles, must have purity of essence.
25 Apr 17:27

Friday A/V Club: The Legend of Action Park

by Jesse Walker
Nosimpler

Watch this with someone you love.

I hate to imagine that form.Action Park was a legendarily unsafe amusement park in New Jersey, the sort of place that Blue Teamers imagine a libertarian society would be like. (There is a parallel universe, I'm sure, where Action Park occupies the place held by Somalia on our plane's compendium of comment-thread clichés.) "Action Park was less a water park and more a complete insult to the evolutionary concept of self-preservation," Matthew Callan wrote in a fun Freezerbox piece some years back. "And yet, despite all the danger, we kids kept going back, tempting fate like Russian-roulette-players."

You should read Callan's whole essay, with its detailed descriptions of the park's fate-tempting rides. Here's a sample:

The very first ride you saw when you entered Action Park involved a sled and a ramp of metal rollers. You slid down on your sled across the metal rollers, reaching speeds of roughly 300 miles an hour, and skipped thirty feet across the surface of a very shallow pool. The metal-roller ramps had no guardrails on them, so there was always a possibility that you would veer off to the side and fall very quickly into two feet of water. And since there were four metal-roller ramps emptying into this pool in tandem, snarls of sled collisions were constantly occurring, making it look like the Cross Bronx Expressway on a Friday night.

The Colorado River Ride was a water slide involving huge inner tubes that could fit seven people. It tried to approximate a mountain rapid, with lots of bumps and obstacles and so forth. But the most dangerous part of it was the fact that the borders that kept the tubes on the course were criminally short. And just off to the side of the Colorado River Ride was a steep tree-and-pricker-bush-lined hill. It was the perfect demonstration of the Action Park philosophy: Put seven people in a large inner tube, push them down a wet slide, and let the laws of physics handle the rest. People would gather around to watch folks scream their way down, cheering and hoping that a tube would hop the barrier and go careening down the side of the hill. When a large family would come close to flying away, the whole crowd would gasp and then sigh in disappointment, like the audience at the Indy 500 when the Tide car just narrowly misses hitting the Pepsi car and exploding in a beautiful orange ball of flame.

And then there was this thing:

A picture is worth a thousand depositions.

They called it the Cannonball Loop. "It was never open," Barry Petchesky recalls in Deadspin. "You wondered if it had ever been open." Turns out it had indeed been open, though apparently not for very long. Petchesky has located some footage of the slide in action, part of an alternately eerie and funny compilation of Action Park commercials and home movies:

If you want to watch people riding the slide, you can skip ahead to 8:17. But there's much more to see here, from the children-as-sewage-discharge footage at 5:12 to the breakdancing demonstration at 3:13. (The latter is recommended for hardcore '80s nostalgists only.) And at the very end of the video, there's the most frightening ad slogan I've ever heard: "where you and the rides become one."

Bonus link: "Anarchy, State, and Amusement Park."

(For past editions of the Friday A/V Club, go here.)

24 Apr 20:08

Why Two Artists Installed a Spy Lamp at McDonald's

by Elizabeth Nolan Brown

"Yeah right. Don't you know Loretta's an Aquarius?"

That's one snippet of conversation secretly recorded at an unspecified New York City McDonald's and broadcast on Twitter via @conversnitch, a project "bridging the gap between online and IRL" in the most terrifying way possible. It sharply highlights how easily we could all be surveilled without the slightest knowledge of it.

The conversations are being picked up by a device attached to an unassuming McDonald's table lamp by artists Brian House and Kyle McDonald. This "conversnitch" device cost under $100 to make and can plug into any ordinary light fixture. 

Using a microphone, a Raspberry Pi mini-computer, and the locale's own Wi-fi, conversnitch streams recordings to Amazon's Mechanical Turk, an online temp worker marketplace. Mechanical Turk freelancers then transcribe and tweet out bits and pieces of the digitally eavesdropped conversations. 

This has been going on for nearly seven months. 

"Conversations are fleeting in person, they last briefly and then disappear," McDonald, an adjunct professor at the New York University, told British magazine Dazed and Confused.

"It's exactly the opposite of everything the internet is. With everyone keeping more personal records every day, and various governments and corporations doing similarly, how much longer do we have until the idea of a fleeting moment, much less a private one, is a complete impossibility?"

 

As the video below shows, conversnitch is small and undetectable enough to be installed in restaurants, in libraries, on street corners, or just about anywhere. The code's available for free here. "Here were Brian and I trying to make something kind of scary, something that makes you wonder if someone’s watching you all the time," McDonald said in an interview with Wired. "And then Snowden says, 'They are.'"

24 Apr 19:32

How Nanoexplosives Could Help Solve One of the Biggest Mysteries of Astrophysics

Particles of dark matter should trigger nanoexplosions in certain materials, an idea that could lead to an entirely new generation of detectors, say physicists.


One of the great mysteries of modern astrophysics is the nature of dark matter. This is the mysterious stuff that astrophysicists say must exist to provide the gravitational forces necessary to hold galaxies together.

24 Apr 19:23

Juno is the egg Izumo receptor and is essential for mammalian fertilization

by Enrica Bianchi
Nosimpler

This is big.

Juno is the egg Izumo receptor and is essential for mammalian fertilization

Nature 508, 7497 (2014). doi:10.1038/nature13203

Authors: Enrica Bianchi, Brendan Doe, David Goulding & Gavin J. Wright

Fertilization occurs when sperm and egg recognize each other and fuse to form a new, genetically distinct organism. The molecular basis of sperm–egg recognition is unknown, but is likely to require interactions between receptor proteins displayed on their surface. Izumo1 is an essential sperm cell-surface

24 Apr 18:19

Reconstructing Nonlinear Biochemical Networks

by Igor
Nosimpler

"Since a cellular signalling system is in fact indivisible, this reductionistic approach may have an impact on the accuracy of the inference results." YAY




Inferring Cell-Scale Signalling Networks via Compressive Sensing by Lei Nie, Xian Yang, Ian Adcock, Zhiwei Xu, Yike Guo
Signalling network inference is a central problem in system biology. Previous studies investigate this problem by independently inferring local signalling networks and then linking them together via crosstalk. Since a cellular signalling system is in fact indivisible, this reductionistic approach may have an impact on the accuracy of the inference results. Preferably, a cell-scale signalling network should be inferred as a whole. However, the holistic approach suffers from three practical issues: scalability, measurement and overfitting. Here we make this approach feasible based on two key observations: 1) variations of concentrations are sparse due to separations of timescales; 2) several species can be measured together using cross-reactivity. We propose a method, CCELL, for cell-scale signalling network inference from time series generated by immunoprecipitation using Bayesian compressive sensing. A set of benchmark networks with varying numbers of time-variant species is used to demonstrate the effectiveness of our method. Instead of exhaustively measuring all individual species, high accuracy is achieved from relatively few measurements.

In this paper, we present a distributed algorithm for the reconstruction of large-scale nonlinear networks. In particular, we focus on the identification from time-series data of the nonlinear functional forms and associated parameters of large-scale nonlinear networks. Recently, a nonlinear network reconstruction problem was formulated as a nonconvex optimisation problem based on the combination of a marginal likelihood maximisation procedure with sparsity inducing priors. Using a convex-concave procedure (CCCP), an iterative reweighted lasso algorithm was derived to solve the initial nonconvex optimisation problem. By exploiting the structure of the objective function of this reweighted lasso algorithm, a distributed algorithm can be designed. To this end, we apply the alternating direction method of multipliers (ADMM) to decompose the original problem into several subproblems. To illustrate the effectiveness of the proposed methods, we use our approach to identify a network of interconnected Kuramoto oscillators with different network sizes (500~100,000 nodes).
22 Apr 12:37

Four Great Myths of the McCarthy Era

by Jesse Walker

Joseph McCarthy (artist's rendition).Sixty years ago today, the ABC and DuMont television networks began their live broadcasts of the Army-McCarthy hearings, a two-month Senate soap opera that marked the final stage of the Wisconsin Republican Joseph McCarthy's period of power. The hearings are most famous today for what happened when the senator tried to make hay of the fact that Army attorney Joseph Welch's law firm employed a man who had once been a member of an organization with links to the Communist Party. The guilt-by-loose-chain-of-association charge was a showcase for McCarthy's sleazy style, allowing Welch to let loose a line that is constantly quoted to this day: "Have you no sense of decency, sir, at long last? Have you left no sense of decency?"

The hearings would go on for another week, and McCarthy would remain in office until his death three years later. But it was that exchange—which wrapped up with McCarthy blustering, Welch cutting him off, and the gallery bursting into applause—that effectively ended the senator's career.

Today McCarthy has come to symbolize the entire postwar Red Scare, allowing the hearings to serve as a tidy end to a tidy story about a demagogue who attained outsized influence and then was cut down to size. But the crusade against Communist subversion that marked the late 1940s and the '50s began before McCarthy seized the issue; and if his downfall was a sign that those fears were fading, it did not bring them to an end. The biggest myth of the McCarthy era is that it was a McCarthy era, rather than an episode in which McCarthy was merely one of the most noisy and irresponsible figures.

World communism (artist's rendition).There are other myths of the period too. The great radical myth of the Red Scare is that it was nothing but a scare—that the Americans accused of being Russian agents were virtually all innocent. (It's hard to maintain that position now that the Venona files have been released and some of the left's biggest causes célèbres have come crumbling down—at this point even Julius Rosenberg's children have acknowledged that he was a spy—but some folks still hold onto the dream.) The great conservative myth of the period, meanwhile, is that the espionage justified the witch-hunts. People like Ann Coulter and M. Stanton Evans have taken to declaring that McCarthy was right without acknowledging that the bulk of his accusations were false, and that this was true of many other red-hunters too. And then there's the great liberal myth of the period: the idea that the libs of the day managed to plot a course between the Soviet apologists and the paranoid hysterics, striking a delicate balance between protecting the country's liberties and protecting its security. In fact, the Red Scare, like the Cold War itself, had liberal fingerprints all over it.

Some of those fingerprints were left before the Red Scare actually began, as Democrats eager to ferret out fascist subversives in the '30s and early '40s lent their support to tools that would later be turned against the left. The Smith Act, which made it illegal to advocate the overthrow of the U.S. government, was a potent weapon during the Red Scare. But it was passed with liberal backing in 1940 and then used against alleged fascists, most infamously in the great sedition trial of 1944. Similarly, when Congress rechartered the House Committee on Un-American Activities in 1938, many liberals voted with the ayes because they wanted to investigate the right.

TAKE THE RED PI—whoops, wrong movie.When the Cold War got underway and the threat of communism replaced the threat of fascism, liberals often found themselves in the red-hunters' crosshairs. But liberals also went on the hunt themselves. "It was the Truman administration," Richard Freeland notes in The Truman Doctrine & the Origins of McCarthyism, "that developed the association of dissent with disloyalty and communism, which became a central element of McCarthyism. It was the Truman administration that adopted the peacetime loyalty program, which provided a model for state and local governments and a wide variety of private institutions. It was the Truman administration, in the criteria for loyalty used in its loyalty program, that legitimized the concept of guilt by association." To his credit, Truman vetoed the McCarran Act of 1950, which went well beyond chasing spies to limit Communists' civil liberties. (Congress overrode the veto and the bill became law anyway, though the courts eventually struck down many of its provisions.) But the Democrats who broke with Truman and voted for the measure included both Lyndon Johnson and John F. Kennedy. Speaking of Kennedy: His brother Bobby, later a liberal heartthrob, was a counsel for the McCarthy committee, and McCarthy was godfather to Bobby's first child.

It may be tempting to put all the madness of the early Cold War on the shoulders of one Wisconsin senator, and then to cheer as Joseph Welch ritually exorcises him on the floor of the Senate and the TV screens of America. The truth, alas, is much messier and uglier than that. When it comes to the Red Scare, there's plenty of shame to go around.

22 Apr 00:56

The Airwaves Belong to the (Properly Licensed) People! Boston Radio Station Raided, Shut Down

by Brian Doherty

Reason contributor Garrett Quinn reports out of Boston on how the federal government keeps the fraying edges of civilization together: by raiding and shutting down a nice thing that made lots of people happy, Boston radio station Touch 106 FM:

An underground Boston radio station considered by some as the voice of Boston's African-American community while operating in Dorchester for last eight years was raided by federal agents on Thursday.

Touch 106.1 FM was shutdown after a raid by U.S. Marshals this morning, according to the station's owner and operator, former mayoral candidate Charles Clemons.

A defensive Clemons told reporters today that the station was shut down for operating without a license, something the station has been doing for years.

"We are unlicensed. It's point blank. We are unlicensed," said Clemons.

The station is a low power station with a range that does not extend very far beyond Dorchester, Mattapan, and Roxbury. Agents, according to Clemons, took anything related to transmitting from the Touch 106.1 FM studios....

Universal Hub is reporting that Clemons was fined $17,000 by the FCC for operating without a license in 2008.

Reason's Jesse Walker wrote a history of scrappy rebellious radio, Rebels on the Air. Hat tip: Jeff Patterson.

18 Apr 14:33

Gabriel Garcia Marquez (1927-2014)

by Minnesotastan

[from 2014] I just heard that Gabriel Garcia Marquez died today.  In his memory I would like to cite (part of) the most remarkable sentence I've ever read.   It was 25 years ago that I first read Love in the Time of Cholera, and a year or two later One Hundred Years of Solitude and The Autumn of the Patriarch.  The first two are in my view the better books, but Autumn of the Patriarch [fulltext at the link] has one truly awesome sentence.  It begins like this, at the start of the final chapter of the book...
THERE he was, then, as if it had been he even though it might not be, lying on the banquet table in the ballroom with the feminine splendor of a dead pope amidst the flowers in which he would not have recognized himself in the display ceremony of his first death, more fearsome dead than alive, the velvet glove stuffed with cotton on a chest armored with false medals of imaginary victories in chocolate wars invented by his persistent adulators, the thunderous full-dress uniform and the patent leather boots and the single gold spur that we found in the building and the ten sad pips of general of the universe to which he was promoted at the final moment to give him a rank higher than that of death, so immediate and visible in his new posthumous identity that for the first time it was possible to believe in his real existence without any doubt whatsoever, although in reality no one looked less like him, no one was so much the opposite of him as that showcase corpse which was still cooking in the middle of the night on the slow fire of the tiny space of the little room where he was laid out with candles while in the cabinet room next door we were discussing the final bulletin with the news that no one dared believe word by word when we were awakened by the noise of the trucks loaded with troops in battle gear whose stealthy patrols had been occupying public buildings since before dawn, they took up prone positions under the arcades of the main commercial street, they hid in doorways, I saw them setting up tripod machine guns on the roofs of the viceregal district when I opened the balcony of my house at dawn looking for a place to put the bouquet of wet carnations I had just cut in the courtyard, beneath the balcony I saw a patrol of soldiers under the command of a lieutenant going from door to door ordering people to close the doors of the few shops that were beginning to open on the commercial street, today is a national holiday they shouted, orders from higher up, I threw them a carnation from the balcony and I asked what was going on with so many soldiers and so much noise of weapons everywhere and the officer caught the carnation in midair and replied to me just imagine girl we don't know ourselves either, the dead man must have come back to life, he said, dying with laughter, because nobody dared think such an earthshaking event could have happened, rather, on the contrary, we thought that after so many years of negligence he had picked up the reins of his authority again and was more alive than ever, once more dragging his great feet of an illusory monarch through the house of power where the globes of light had gone on again...  [and ends thus]... he had arrived without surprise at the ignominious fiction of commanding without power, of being exalted without glory and of being obeyed without authority when he became convinced in the trail of yellow leaves of his autumn that he had never been master of all his power, that he was condemned not to know life except in reverse, condemned to decipher the seams and straighten the threads of the woof and the warp of the tapestry of illusions of reality without suspecting even too late that the only livable life was one of show, the one we saw from this side which wasn't his general sir, this poor people's side with the trail of yellow leaves of our uncountable years of misfortune and our ungraspable instants of happiness, where love was contaminated by the seeds of death but was all love general sir, where you yourself were only an uncertain vision of pitiful eyes through the dusty peepholes of the window of a train, only the tremor of some taciturn lips, the fugitive wave of a velvet glove on the no man's hand of an old man with no destiny with our never knowing who he was, or what he was like, or even if he was only a figment of the imagination, a comic tyrant who never knew where the reverse side was and where the right of this life which we loved with an insatiable passion that you never dared even to imagine out of the fear of knowing what we knew only too well that it was arduous and ephemeral but there wasn't any other, general, because we knew who we were while he was left never knowing it forever with the soft whistle of his rupture of a dead old man cut off at the roots by the slash of death, flying through the dark sound of the last frozen leaves of his autumn toward the homeland of shadows of the truth of oblivion, clinging to his fear of the rotting cloth of death's hooded cassock and alien to the clamor of the frantic crowds who took to the streets singing hymns of joy at the jubilant news of his death and alien forevermore to the music of liberation and the rockets of jubilation and the bells of glory that announced to the world the good news that the uncountable time of eternity had come to an end.
What is remarkable is not the content per se, but the fact that I used the ellilpsis in the center of the citation to pass over 53 pages of text - all of it one single sentence.  I once estimated that the sentence comprises about 17,500 words.  One might consider this creation to be a whimsy or a conceit by someone just playing with words, but in my view it is a sort of prose poem by a superbly skilled writer who loves the craft of language.  If you'd like to give it a try, go to this link.

Addendum (2020):


It would be presumptuous of me to offer a review/critique of a novel that is a modern classic, written by a Nobel Laureate in literature, but after giving it a final good-bye reread, I wanted to jot down some notes about it.

Although I'm filing this post in my recommended books category, I have to admit that this is not a book that everyone will enjoy.   To be honest, not much happens in the novel.  A young man falls in love with a young woman who tentatively agrees to marry him ("Very well, I will marry you if you promise not to make me eat eggplant"), but they are separated by circumstances including her marriage, and he waits for her ("... convinced in the solitude of his soul that he had loved in silence for a much longer time than anyone else in this world ever had...") until her husband's death.  "Florentino Ariza never had another opportunity to see or talk to Fermina Daza alone in the many chance encounters of their very long lives until fifty-one years and nine months and four days later, when he repeated his vow of eternal fidelity and everlasting love on her first night as a widow." In the devotion of her mourning she rejects him, so he continues to wait, as their lives go from the late nineteenth century to the first decades of the twentieth.

As he follows the two protagonists separately, Marquez uses their lives as a platform for discussing the passage of time ("... contemplating with regret the banana plants in the mire of the patio, the stripped mango, the flying ants that came after the rain, the ephemeral splendor of another afternoon that would never return") and the process of aging:
    "... only then did he realize that his life was passing.  He was shaken by a visceral shudder that left his mind blank, and he had to drop the garden tools and lean against the cemetery wall so that the first blow of old age would not knock him down." 
    "She had barely turned the corner into maturity, free at last of illusions, when she began to detect the disillusionment of never having been what she had dreamed of being when she was young..." 
    "... they marked the passage of his life, for he experienced the cruelty of time not so much in his own flesh as in the imperceptible changes he discerned in Fermina Daza each time he saw her."
And finally a reunion:
"By the time she had emptied the teapot and he the coffeepot, they had both attempted and then broken off several topics of conversation, not so much because they were really interested in them but in order to avoid others that neither dared to broach."

"It was the first time in half a century that they had been so close and had enough time to look at each other with some serenity, and they had seen each other for what they were: two old people, ambushed by death, who had nothing in common except the memory of an ephemeral past that was no longer theirs but belonged to two young people who had vanished and who could have been their grandchildren."

"Then he reached out with two icy fingers in the darkness, felt for the other hand in the darkness, and found it waiting for him.  Both were lucid enough to realize, at the same fleeting instant, that the hands made of old bones were not the hands they had imagined before touching.  In the next moment, however, they were."
Herewith various excerpts, curiosities, and interesting words:

"On Friday, June 8, 1708, at four o'clock in the afternoon, the galleon San Jose set sail for Cadiz with a cargo of precious stones and metals valued at five hundred billion pesos in the currency of the day; it was sunk by an English squadron at the entrance to the port, and two long centuries later it had not yet been salvaged."  I love treasure stories, and the wealth carried by the Spanish galleons was fabulous; I was in awe watching reports of the recoveries from the Atocha.  Apparently the San Jose was located by staff from Woods Hole in 2015, and recovery and conservation efforts are currently underway.

"He was a fine parrot, lighter than he seemed, with a yellow head and a black tongue, the only way to distinguish him from mangrove parrots who did not learn to speak even with turpentine suppositories."  ???

"They brought in live chickens from Cienaga de Oro, famous all along the coast not only for their size and flavor but because in colonial times they had scratched for food in alluvial deposits and little nuggets of pure gold were found in their gizzards."  ??true - or an old wives' tale?

The death of Dr. Urbino: "But he released [the parrot] immediately because the ladder slipped from under his feet and for an instant he was suspended in air and then he realized that he had died without Communion, without time to repent of anything or to say goodbye to anyone, at seven minutes after four on Pentecost Sunday."

"The use of the mullein plant to put the fish to sleep had been prohibited by law since colonial times, but it continued to be a common practice among the fishermen of the Caribbean until it was replaced by dynamite."  No time to look this up - anybody know?

"... the black doll that was sent to her without any letter... it had been bought in Martinique, according to the original tag, and it was dressed in an exquisite gown... it seemed so charming to Fermina Daza that she overcame her scruples and laid it on her pillow during the day and grew accustomed to sleeping with it at night.  After a time, however, she discovered when she awoke from an exhausting dream that the doll was growing: the original exquisite dress she had arrived in was up above her thighs, and her shoes had burst from the pressure of her feet.  Fermina Daza had heard of African spells, but none as frightening as this.."  ??? constructed with dehydrated material that swells with time/humidity, or ?? new larger dolls being surreptitiously switched in place??

"She learned to smoke backward, with the lit end in her mouth, the way men smoked at night during the wars so that the glow of their cigarettes would not betray them."  I've heard of this before, during wartime.  I wonder if this technique also enhances nicotine absorption by preventing external loss.

"... he allowed himself to be swayed by his conviction that human beings are not born once and for all on the day their mothers give birth to them, but that life obliges them over and over again to give birth to themselves."

"She had written versions of the deportment and civics texts in hendecasyllabic couplets, like those used for spelling..."  From the Latin, having eleven syllables.

"... the sibylline fragrance of gardenias on hot nights..."  Literally 'having the characteristics of an oracle' but perhaps metaphorically 'mysterious.'

"... Florentino Ariza learned what he had already experienced many times without realizing it: that one can be in love with several people at the same time, feel the same sorrow with each, and not betray any of them."

Re her husband's death: "Once he had told her something that she could not imagine: that amputees suffer pains, cramps, itches, in the leg that is no longer there.  That is how she felt without him, feeling his presence where he no longer was."

"... at last he put on his chamois mustache cover and lay down without removing his trousers and shirt..."  ??why useful?

Next year perhaps I can add some notes about One Hundred Years of Solitude.
18 Apr 04:05

The Problem of Now

by Sabine Hossenfelder
[Image Source]

Einstein’s greatest blunder wasn’t the cosmological constant, and neither was it his conviction that god doesn’t throw dice. No, his greatest blunder was to speak to a philosopher named Carnap about the Now, with a capital.

“The problem of Now”, Carnap wrote in 1963, “worried Einstein seriously. He explained that the experience of the Now means something special for men, something different from the past and the future, but that this important difference does not and cannot occur within physics”

I call it Einstein’s greatest blunder because, unlike the cosmological constant and indeterminism, philosophers, and some physicists too, are still confused about this alleged “Problem of Now”.

The problem is often presented like this. Most of us experience a present moment, which is a special moment in time, unlike the past and unlike the future. If you write down the equations governing the motion of some particle through space, then this particle is described, mathematically, by a function. In the simplest case this is a curve in space-time, meaning the function is a map from the real numbers to a four-dimensional manifold. The particle changes its location with time. But regardless of whether you use an external definition of time (some coordinate system) or an internal definition (such as the length of the curve), every single instant on that curve is just some point in space-time. Which one, then, is “now”?

You could argue rightfully that as long as there’s just one particle moving on a straight line, nothing is happening, and so it’s not very surprising that no notion of change appears in the mathematical description. If the particle would scatter on some other particle, or take a sudden turn, then these instances can be identified as events in space-time. Alas, that still doesn’t tell you whether they happen to the particle “now” or at some other time.

Now what?

The cause for this problem is often assigned to the timeless-ness of mathematics itself. Mathematics deals in its core with truth values and the very point of using math to describe nature is that these truths do not change. Lee Smolin has written a whole book about the problem with the timeless math, you can read my review here.

It may or may not be that mathematics is able to describe all of our reality, but to solve the problem of now, excuse the heresy, you do not need to abandon a mathematical description of physical law. All you have to do is realize that the human experience of now is subjective. It can perfectly well be described by math, it’s just that humans are not elementary particles.

The decisive ability that allows us to experience the present moment as being unlike other moments is that we have a memory. We have a memory of events in the past, an imperfect one, and we do not have memory of events in the future. Memory is not in and by itself tied to consciousness, it is tied to the increase of entropy, or the arrow of time if you wish. Many materials show memory; every system with a path dependence like eg hysteresis does. If you get a perm the molecule chains in your hair remember the bonds, not your brain.

Memory has nothing to do with consciousness in particular which is good because it makes it much easier to find the flaw in the argument leading to the problem of now.

If we want to describe systems with memory we need at the very least two time parameters: t to parameterize the location of the particle and τ to parameterize the strength of memory of other times depending on its present location. This means there is a function f(t,τ) that encodes how strong is the memory of time τ at moment t. You need, in other words, at the very least a two-point function, a plain particle trajectory will not do.

That we experience a “now” means that the strength of memory peaks when both time parameters are identical, ie t-τ = 0. That we do not have any memory of the future means that the function vanishes when τ > t. For the past it must decay somehow, but the details don’t matter. This construction is already sufficient to explain why we have the subjective experience of the present moment being special. And it wasn’t that difficult, was it?

The origin of the problem is not in the mathematics, but in the failure to distinguish subjective experience of physical existence from objective truth. Einstein spoke about “the experience of the Now [that] means something special for men”. Yes, it means something special for men. This does not mean however, and does not necessitate, that there is a present moment which is objectively special in the mathematical description. In the above construction all moments are special in the same way, but in every moment that very moment is perceived as special. This is perfectly compatible with both our experience and the block universe of general relativity. So Einstein should not have worried.

I have a more detailed explanation of this argument – including a cartoon! – in a post from 2008. I was reminded of this now because Mermin had a comment in the recent issue of Nature magazine about the problem of now.

In his piece, Mermin elaborates on qbism, a subjective interpretation of quantum mechanics. I was destined to dislike this just because it’s a waste of time and paper to write about non-existent problems. Amazingly however, Mermin uses the subjectiveness of qbism to arrive at the right conclusion, namely that the problem of the now does not exist because our experiences are by its very nature subjective. However, he fails to point out that you don’t need to buy into fancy interpretations of quantum mechanics for this. All you have to do is watch your hair recall sulphur bonds.

The summary, please forgive me, is that Einstein was wrong and Mermin is right, but for the wrong reaons. It is possible to describe the human experience of the present moment with the “timeless” mathematics that we presently use for physical laws, it isn’t even difficult and you don’t have to give up the standard interpretation of quantum mechanics for this. There is no problem of Now and there is no problem with Tegmark’s mathematical universe either.

And Lee Smolin, well, he is neither wrong nor right, he just has a shaky motivation for his cosmological philosophy. It is correct, as he argues, that mathematics doesn’t objectively describe a present moment. However, it’s a non sequitur that the current approach to physics has reached its limits because this timeless math doesn’t constitute a conflict with our experience. observation.

Most people get a general feeling of uneasiness when they first realize that the block universe implies all the past and all the future is equally real as the present moment, that even though we experience the present moment as special, it is only subjectively so. But if you can combat your uneasiness for long enough, you might come to see the beauty in eternal mathematical truths that transcend the passage of time. We always have been, and always will be, children of the universe.
17 Apr 18:53

Synopsis: Bird Flocks Shatter on Impact

Nosimpler

what

Simulations show that flocks hitting a wall disintegrate like brittle solids rather than splash like fluid drops.

Published Tue Apr 15, 2014
16 Apr 23:55

No Perisaccadic Mislocalization with Abruptly Cancelled Saccades

by Atsma, J., Maij, F., Corneil, B. D., Medendorp, W. P.
Nosimpler

Not 100% sure of the implications, but seems interesting.

Every saccadic eye movement that we make changes the image of the world on our retina. Yet, despite these retinal shifts, we still perceive our visual world to be stable. Efference copy from the oculomotor system to the visual system has been suggested to contribute to this stable percept, enabling the brain to anticipate the retinal image shifts by remapping the neural image. A psychophysical phenomenon that has been linked to this predictive remapping is the mislocalization of a stimulus flashed around the time of a saccade. If this mislocalization is initiated by saccade preparation, one should also observe localization errors when a saccade is planned, but abruptly aborted just before its execution. We tested this hypothesis in human subjects using a novel paradigm that combines a flash localization task with a countermanding component that occasionally requires saccade cancellation. Surprisingly, we found no trace of mislocalization, even for saccades cancelled close to the point of no return. This strongly suggests that the actual execution of the saccade is a prerequisite for the typical localization errors, which rejects various models and constrains neural substrates. We conclude that perisaccadic mislocalization is not a direct consequence of saccade preparation, but arises after saccade execution when the flash location is constructed from memory.

15 Apr 21:41

Edward Snowden’s NSA Leaks Lead to Pulitzer Prize; Pension Crisis Also Noticed

by Scott Shackford

We won't hold our breath for a White House responseThe Pulitzer Prize has rendered its vote on what it thinks of Edward Snowden’s revelation of the National Security Agency’s (NSA) domestic surveillance techniques today by giving a gold medal in public service to The Guardian US and The Washington Post for breaking the stories. The Pulitzer committee credits the Post for helping "the public understand how the disclosures fit into the larger framework of national security," while The Guardian is recognized for "helping through aggressive reporting to spark a debate about the relationship between the government and the public over issues of security and privacy."

Snowden has already put out a statement:

"Today's decision is a vindication for everyone who believes that the public has a role in government. We owe it to the efforts of the brave reporters and their colleagues who kept working in the face of extraordinary intimidation, including the forced destruction of journalistic materials, the inappropriate use of terrorism laws, and so many other means of pressure to get them to stop what the world now recognizes was work of vital public importance."

Rosie Gray of BuzzFeed tracked down NSA hard-core surveillance-defender and Snowden-hater Rep. Pete King (R-IRA). He told her "Anybody who got a Pulitzer in the past should give it back. The Pulitzer Prize doesn’t mean anything now."

The NSA responded by hacking the Twitter feed of US Airways and distracting the world by putting up a picture of a naked woman with a model plane in her nethers. I am kidding about the hacking, but the tweet actually happened and quickly became all everybody was talking about online. It’s still not as horrifying as last year, when the Boston Marathon bombing happened right as the winners were being announced. (The Boston Globe got a Pulitzer for breaking news for their coverage.)

Getting much less attention, partly because of the Snowden debate but also because the subject just gets less attention, The Oregonian’s editorial board won a Pulitzer Prize in the category of editorial writing for its coverage of the state’s pension crisis. The Pulitzer Prize committee praised "its lucid editorials that explain the urgent but complex issue of rising pension costs, notably engaging readers and driving home the link between necessary solutions and their impact on everyday lives." The Oregonian ’s package of editorials can be read here.

The full list of Pulitzer winners can be found here.

There’s also some interesting topics tackled by the runners-up. The NSA coverage beat out a report by Newsday of concealed police abuse and misconduct by the Long Island police. And The Oregonian beat out editorials at the Des Moines Register challenging Iowa’s restrictive licensing laws.

11 Apr 15:03

Heartbleed Explanation

Are you still there, server? It's me, Margaret.
11 Apr 03:01

Compressive Direct Measurement of the Quantum Wave Function. (arXiv:1404.2680v3 [quant-ph] UPDATED)

by Mohammad Mirhosseini, Omar S. Magaña-Loaiza, Seyed Mohammad Hashemi Rafsanjani, Robert W. Boyd

The direct measurement of a complex wavefunction has been recently realized by using weak-values. In this paper, we introduce a method that exploits sparsity for compressive measurement of the transverse spatial wavefunction of photons. The procedure involves a weak measurement in random projection operators in the spatial domain followed by a post-selection in the momentum basis. Using this method, we experimentally measure a 192-dimensional state with a fidelity of $90\%$ using only $25$ percent of the total required measurements. Furthermore, we demonstrate measurement of a 19200 dimensional state; a task that would require an unfeasibly large acquiring time with the conventional direct measurement technique.

08 Apr 02:55

The Modular Flow on the Space of Lattices

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

Guest post by Bruce Bartlett

The following is the greatest math talk I’ve ever watched!

  • Etienne Ghys (with pictures and videos by Jos Leys), Knots and Dynamics, ICM Madrid 2006. [See below the fold for some links.]

Etienne GhysA modular knot

I wasn’t actually at the ICM; I watched the online version a few years ago, and the story has haunted me ever since. Simon and I have been playing around with some of this stuff, so let me share some of my enthusiasm for it!

The story I want to tell here is how, via modular flow of lattices in the plane, certain matrices in SL(2,ℤ)\SL(2,\mathbb{Z}) give rise to knots in the 3-sphere less a trefoil knot. Despite possibly sounding quite scary, this can be easily explained in an elementary yet elegant fashion.

MathML-enabled post (click for more details).

As promised above, here are some links related to Ghys’ ICM talk.

I’m going to focus on the last third of the talk — the modular flow on the space of lattices. That’s what produced the beautiful picture above (credit for this and other similar pics below goes to Jos Leys; the animation is Simon’s.)

Lattices in the plane

For us, a lattice is a discrete subgroup of ℂ\mathbb{C}. There are three types: the zero lattice, the degenerate lattices, and the nondegenerate lattices:

Lattices

Given a lattice LL and an integer n≥4n \geq 4 we can calculate a number — the Eisenstein series of the lattice: Gn(L)=∑ω∈L,ω≠01ωn. G_{n}(L) = \sum _{\omega \in L, \omega \neq 0} \frac{1}{\omega ^{n}}. We need n≥3n \geq 3 for this sum to converge. For, roughly speaking, we can rearrange it as a sum over rr of the lattice points on the boundary of a square of radius rr. The number of lattice points on this boundary scales with rr, so we end up computing something like ∑r≥0rrn\sum _{r \geq 0} \frac{r}{r^{n}} and so we need n≥3n \geq 3 to make the sum converge.

Note that Gn(L)G_{n}(L) = 0 for nn odd since every term ω\omega is cancelled by the opposite term −ω-\omega . So, the first two nontrivial Eisenstein series are G4G_{4} and G6G_{6}. We can use them to put `Eisenstein coordinates’ on the space of lattices.

Theorem: The map {lattices}→ℂ2L↦(G4(L),G6(L)) \begin{aligned} \{ \text{lattices} \} &\rightarrow \mathbb{C}^{2} \\ L & \mapsto (G_{4} (L), \, G_{6}(L)) \end{aligned} is a bijection.

The nicest proof is in Serre’s A Course in Arithmetic, p. 89. It is a beautiful application of the Cauchy residue theorem, using the fact that G4G_{4} and G6G_{6} define modular forms on the upper half plane HH. (Usually, number theorists set up their lattices so that they have basis vectors 11 and τ\tau where τ∈H\tau \in H. But I want to avoid this ‘upper half plane’ picture as far as possible, since it breaks symmetry and mystifies the geometry. The whole point of the Ghys picture is that not breaking the symmetry reveals a beautiful hidden geometry! Of course, sometimes you need the ‘upper half plane’ picture, like in the proof of the above result.)

Lemma: The degenerate lattices are the ones satisfying 20G43−49G62=020 G_{4}^{3} - 49G_{6}^{2} = 0.

Let’s prove one direction of this lemma — that the degenerate lattices do indeed satisfy this equation. To see this, we need to perform a computation. Let’s calculate G4G_{4} and G6G_{6} of the lattice ℤ⊂ℂ\mathbb{Z} \subset \mathbb{C}. Well, G4(ℤ)=∑n≠01n4=2ζ(4)=2π490 G_{4}(\mathbb{Z}) = \sum _{n \neq 0} \frac{1}{n^{4}} = 2 \zeta (4) = 2 \frac{\pi ^{4}}{90} where we have cheated and looked up the answer on Wikipedia! Similarly, G6(ℤ)=2π6945G_{6}(\mathbb{Z}) = 2 \frac{\pi ^{6}}{945}.

So we see that 20G4(ℤ)3−49G6(ℤ)2=020 G_{4}(\mathbb{Z})^{3} - 49 G_{6}(\mathbb{Z})^{2} = 0. Now, every degenerate lattice is of the form tℤt \mathbb{Z} where t∈ℂt \in \mathbb{C}. Also, if we transform the lattice via L↦tLL \mapsto t L, then G4↦t−4G4G_{4} \mapsto t^{-4} G_{4} and G6↦t−6G6G_{6} \mapsto t^{-6} G_{6}. So the equation remains true for all the degenerate lattices, and we are done.

Corollary: The space of nondegenerate lattices in the plane of unit area is homeomorphic to the complement of the trefoil in S3S^{3}.

The point is that given a lattice LL of unit area, we can scale it L↦λLL \mapsto \lambda L, λ∈ℝ+\lambda \in \mathbb{R}^{+} until (G4(L),G6(L))(G_{4}(L), G_{6}(L)) lies on the 3-sphere S3={(z,w):|z|2+|w|2=1}⊂ℂ2S^{3} = \{ (z,w) : |z|^{2} + |w|^{2} = 1\} \subset \mathbb{C}^{2}. And the equation 20z3−49w2=020 z^{3} - 49 w^{2} = 0 intersected with S3S^{3} cuts out a trefoil knot… because it is “something cubed plus something squared equals zero”. And the lemma above says that the nondegenerate lattices are precisely the ones which do not satisfy this equation, i.e. they represent the complement of this trefoil.

Since we have not divided out by rotations, but only by scaling, we have arrived at a 3-dimensional picture which is very different to the 2-dimensional moduli space (upper half-plane divided by SL(2,ℤ)\SL(2,\mathbb{Z})) picture familiar to a number theorist.

The modular flow

There is an intriguing flow on the space of lattices of unit area, called the modular flow. Think of LL as sitting in ℝ2\mathbb{R}^{2}, and then act on ℝ2\mathbb{R}^{2} via the transformation (et00e−t), \left ( \begin{array}{cc} e^{t} & 0 \\ 0 & e^{-t} \end{array} \right ), dragging the lattice LL along for the ride. (This isn’t just some formula we pulled out the blue — geometrically this is the ‘geodesic flow on the unit tangent bundle of the modular orbifold’.)

We are looking for periodic orbits of this flow.

“Impossible!” you say. “The points of the lattice go off to infinity!” Indeed they do… but disregard the individual points. The lattice itself can ‘click’ back into its original position:

animation

How are we to find such periodic orbits? Start with an integer matrix A=(abcd)∈SL(2,ℤ) A = \left ( \begin{array}{cc} a & b \\ c & d \end{array}\right ) \in \SL(2, \mathbb{Z}) and assume AA is hyperbolic, which simply means |a+d|≥2|a + d| \geq 2. Under these conditions, we can diagonalize AA over the reals, so we can find a real matrix PP such that PAP−1=±(et00e−t) P A P^{-1} = \pm \left ( \begin{array}{cc} e^{t} & 0 \\ 0 & e^{-t} \end{array} \right ) for some t∈ℝt \in \mathbb{R}. Now set L≔P(ℤ2)L \coloneqq P(\mathbb{Z}^{2}). We claim that LL is a periodic orbit of period tt. Indeed: Lt=(et00e−t)P(ℤ2)=±PA(ℤ2)=±P(ℤ2)=L. \begin{aligned} L_{t} &= \left ( \begin{array}{cc} e^{t} & 0 \\ 0 & e^{-t} \end{array} \right ) P (\mathbb{Z}^{2}) \\ &= \pm PA (\mathbb{Z}^{2}) \\ &= \pm P (\mathbb{Z}^{2}) \\ &= L. \end{aligned} We have just proved one direction of the following.

Theorem: The periodic orbits of the modular flow are in bijection with the conjugacy classes of hyperbolic elements in SL(2,ℤ)\SL(2, \mathbb{Z}).

These periodic orbits produce fascinating knots in the complement of the trefoil! In fact, they link with the trefoil (the locus of degenerate lattices) in fascinating ways. Here are two examples, starting with different matrices A∈SL(2,ℤ)A \in \SL(2, \mathbb{Z}).

animation

The trefoil is the fixed orange curve, while the periodic orbits are the red and green curves respectively.

Ghys proved the following two remarkable facts about these modular knots.

  • The linking number of a modular knot with the trefoil of degenerate lattices equals the Rademacher function of the corresponding matrix in SL(2,ℤ)\SL(2, \mathbb{Z}) (the change in phase of the Dedekind eta function).
  • The knots occuring in the modular flow are the same as those occuring in the Lorenz equations!

Who would have thought that lattices in the plane could tell the weather!!

I must say I have thought about many aspects of these closed geodesics, but it had never crossed my mind to ask which knots are produced. – Peter Sarnak

MathML-enabled post (click for more details).MathML-enabled post (click for more details).
07 Apr 18:25

Will the social sciences ever become hard sciences?

by Sabine Hossenfelder
Nosimpler

See Point 3. It seems like the argument is incomplete, but I am lazy and waking up still.

The term “hard science” as opposed to “soft science” has no clear definition. But roughly speaking, the less the predictive power and the smaller the statistical significance, the softer the science. Physics, without doubt, is the hard core of the sciences, followed by the other natural sciences and the life sciences. The higher the complexity of the systems a research area is dealing with, the softer it tends to be. The social sciences are at the soft end of the spectrum.

To me the very purpose of research is making science increasingly harder. If you don’t want to improve on predictive power, what’s the point of science to begin with? The social sciences are soft mainly because data that quantifies the behavior of social, political, and economic systems is hard to come by: it’s huge amounts, difficult to obtain and even more difficult to handle. Historically, these research areas therefore worked with narratives relating plausible causal relations. Needless to say, as computing power skyrockets, increasingly larger data sets can be handled. So the social sciences are finally on the track to become useful. Or so you’d think if you’re a physicist.

But interestingly, there is a large opposition to this trend of hardening the social sciences, and this opposition is particularly pronounced towards physicists who take their knowledge to work on data about social systems. You can see this opposition in the comment section to every popular science article on the topic. “Social engineering!” they will yell accusingly.

It isn’t so surprising that social scientists themselves are unhappy because the boat of inadequate skills is sinking in the data sea and physics envy won’t keep it afloat. More interesting than the paddling social scientists is the public opposition to the idea that the behavior of social systems can be modeled, understood, and predicted. This opposition is an echo of the desperate belief in free will that ignores all evidence to the contrary. The desperation in both cases is based on unfounded fears, but unfortunately it results in a forward defense.

And so the world is full with people who argue that they must have free will because they believe they have free will, the ultimate confirmation bias. And when it comes to social systems they’ll snort at the physicists “People are not elementary particles”. That worries me, worries me more than their clinging to the belief in free will, because the only way we can solve the problems that mankind faces today – the global problems in highly connected and multi-layered political, social, economic and ecological networks – is to better understand and learn how to improve the systems that govern our lives.

That people are not elementary particles is not a particularly deep insight, but it collects several valid points of criticism:

  1. People are too difficult. You can’t predict them.

    Humans are made of a many elementary particles and even though you don’t have to know the exact motion of every single one of these particles, a person still has an awful lot of degrees of freedom and needs to be described by a lot of parameters. That’s a complicated way of saying people can do more things than electrons, and it isn’t always clear exactly why they do what they do.

    That is correct of course, but this objection fails to take into account that not all possible courses of action are always relevant. If it was true that people have too many possible ways to act to gather any useful knowledge about their behavior our world would be entirely dysfunctional. Our societies work only because people are to a large degree predictable.

    If you go shopping you expect certain behaviors of other people. You expect them to be dressed, you expect them to walk forwards, you expect them to read labels and put things into a cart. There, I’ve made a prediction about human behavior! Yawn, you say, I could have told you that. Sure you could, because making predictions about other people’s behavior is pretty much what we do all day. Modeling social systems is just a scientific version of this.

    This objection that people are just too complicated is also weak because, as a matter of fact, humans can and have been modeled with quite simple systems. This is particularly effective in situations when intuitive reaction trumps conscious deliberation. Existing examples are traffic flows or the density of crowds when they have to pass through narrow passages.

    So, yes, people are difficult and they can do strange things, more things than any model can presently capture. But modeling a system is always an oversimplification. The only way to find out whether that simplification works is to actually test it with data.

  2. People have free will. You cannot predict what they will do.

    To begin with it is highly questionable that people have free will. But leaving this aside for a moment, this objection confuses the predictability of individual behavior with the statistical trend of large numbers of people. Maybe you don’t feel like going to work tomorrow, but most people will go. Maybe you like to take walks in the pouring rain, but most people don’t. The existence of free will is in no conflict with discovering correlations between certain types of behavior or preferences in groups. It’s the same difference that doesn’t allow you to tell when your children will speak the first word or make the first step, but that almost certainly by the age of three they’ll have mastered it.

  3. People can understand the models and this knowledge makes predictions useless.

    This objection always stuns me. If that was true, why then isn’t obesity cured by telling people it will remain a problem? Why are the highways still clogged at 5pm if I predict they will be clogged? Why will people drink more beer if it’s free even though they know it’s free to make them drink more? Because the fact that a prediction exists in most cases doesn’t constitute any good reason to change behavior. I can predict that you will almost certainly still be alive when you finish reading this blogpost because I know this prediction is exceedingly unlikely to make you want to prove it wrong.

    Yes, there are cases when people’s knowledge of a prediction changes their behavior – self-fulfilling prophecies are the best-known examples of this. But this is the exception rather than the rule. In an earlier blogpost, I referred to this as societal fixed points. These are configurations in which the backreaction of the model into the system does not change the prediction. The simplest example is a model whose predictions few people know or care about.

  4. Effects don’t scale and don’t transfer.

    This objection is the most subtle one. It posits that the social sciences aren’t really sciences until you can do and reproduce the outcome of “experiments”, which may be designed or naturally occurring. The typical social experiment that lends itself to analysis will be in relatively small and well-controlled communities (say, testing the implementation of a new policy). But then you have to extrapolate from this how the results will be in larger and potentially very different communities. Increasing the size of the system might bring in entirely new effects that you didn’t even know of (doesn’t scale), and there are a lot of cultural variables that your experimental outcome might have depended on that you didn’t know of and thus cannot adjust for (doesn’t transfer). As a consequence, repeating the experiment elsewhere will not reproduce the outcome.

    Indeed, this is likely to happen and I think it is the major challenge in this type of research. For complex relations it will take a long time to identify the relevant environmental parameters and to learn how to account for their variation. The more parameters there are and the more relevant they are, the less the predictive value of a model will be. If there are too many parameters that have to be accounted for it basically means doing experiments is the only thing we can ever do. It seems plausible to me, even likely, that there are types of social behavior that fall into this category, and that will leave us with questions that we just cannot answer.

    However, whether or not a certain trend can or cannot be modeled we will only know by trying. We know that there are cases where it can be done. Geoffry West’s city theory I find a beautiful example where quite simple laws can be found in the midst of all these cultural and contextual differences.
In summary.

The social sciences will never be as “hard” as the natural sciences because there is much more variation among people than among particles and among cities than among molecules. But the social sciences have become harder already and there is no reason why this trend shouldn’t continue. I certainly hope it will continue because we need this knowledge to collectively solve the problems we have collectively created.
07 Apr 18:08

The Poetic Torture-House of Language by Slavoj Žižek

Annotations:
  • The military dictatorship in Argentina from 1976 to 1983 brought about a grammatical peculiarity, a new passive use of active verbs: when thousands of Leftist political activists and intellectuals disappeared and were never seen again, tortured and killed by the military 
who denied any knowledge about their fate, they were referred to as “disappeared,” where the verb was not used in the simple sense that they disappeared, but in an active transitive sense: they “were disappeared” (by the military secret services). In the Stalinist regime, a similar irregular inflection affected the verb “to step down”: when it was publicly announced that a high nomenklatura member stepped down from his post (for health reasons, as a rule), and everyone knew it was really because he lost in the struggle between different cliques within the nomenklatura, people said he “was stepped down.” Again, an act normally attributed to the affected person (he stepped down, he disappeared) is reinterpreted as the result of the nontransparent activity of another agent (secret police disappeared him, the majority in the nomenklatura stepped him down).
  • This is also why, in order to get the truth to speak, it is not enough to suspend the subject’s active intervention and let language itself speak — as Elfriede Jelinek put it with extraordinary clarity: “Language should be tortured to tell the truth.” It should be twisted, 
denaturalized, extended, condensed, cut, and reunited, made to work against itself.
03 Apr 17:35

Crowdsourced Amateurs Outperform CIA at Predicting World Events

by Zenon Evans

Elaine Rich is a pharmacist in her 60s. She and a team of 3,000 other amateur forecasters in the Good Judgment Project (GJP) use Google to keep current on the news. The Central Intelligence Agency (CIA) employs over 20,000 professionals, operates with an annual budget north of $14 billion, and has access to oodles of classified information.

Which of these groups is better at predicting world affairs?

When it comes to “everything from Venezuelan gas subsidies to North Korean politics,” reports National Public Radio (NPR), amateurs outperform the pros. Rich, in particular, has “been put on a special team with other superforecasters whose predictions are reportedly 30 percent better than intelligence officers.” NPR explains how this is possible:

"Everyone has been surprised by these outcomes," said Philip Tetlock, one of the three psychologists who came up with the idea for the Good Judgment Project. The other two are Barbara Mellers and Don Moore....

But also, if you take a large crowd of different people with access to different information and pool their predictions, you will be in much better shape than if you rely on a single very smart person, or even a small group of very smart people....

"There's a lot of noise, a lot of statistical random variation," Tetlock said. "But it's random variation around a signal, a true signal, and when you add all of the random variation on each side of the true signal together, you get closer to the true signal."

The GJP has been operating for about three years. Tetlock's team provides people like Rich with some basic training in probability estimation, and then they're good to go.

This network of folk forecasters isn't likely to supplant the CIA, but it is looking to make changes in the way the intelligence community operates. The GJP blogged this week that “for many geopolitical forecasting questions, we see promise in a human-machine hybrid approach that combines the best strengths of human judgments and statistical models.”

03 Apr 05:22

Other People's Pathologies - Ta-Nehisi Coates - The Atlantic

03 Apr 05:21

Boundaries and Subtleties: the Mysterious Power of Naming in Human Cognition

by Yohan John

by Yohan J. John

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“Little does my lady dream / Rumpelstiltskin is my name!" Rumplestiltskin, by Anne Anderson. Image from Wikimedia Commons

Of all the strange and wonderful fairy tales I encountered as a child, Rumpelstiltskin always struck me as the most peculiar. The story revolves around a girl who must spin straw into gold or face death at the hands of the king. A dwarf appears out of nowhere, and spins the straw into gold — for a price. On the first night he takes a necklace, and on the second a ring. On the third night the girl has nothing left to pay him with, and so the dwarf makes her promise to give him her firstborn child. The king's greed is sated after three days of gold-spinning, and he marries the girl. In due time the new queen gives birth to a child, and sure enough, the dwarf returns to receive his pounds of flesh. But the queen refuses, and tries to offer him some of her newly acquired riches instead. The dwarf agrees to give up his claim on the child, but only if the queen can guess his name within three days. Her guesses on the first two days fail. But then one of her spies returns with a strange tale. He came across a little cottage in the woods, in from of which he saw a dwarf prancing around a fire, singing a song that ended "Little does my lady dream / Rumpelstiltskin is my name!" On the third day the queen initially pretends not to know the dwarf's name. Finally she says, "Could your name be Rumpelstiltskin?" At this the dwarf flies into a rage, and stomps his foot on the ground so hard that a chasm opens up in the ground, swallowing the dwarf, who was never seen again.

As a child I found the dwarf's plunge into the subterranean void the most eerie element in the story, but in recent years I've been pondering another, perhaps deeper mystery. Why did Rumpelstiltskin's name have so much power?

Fairy tales notwithstanding, by the time I got to college I had come to think that names were mere conventions that had no intrinsic meaning or value. For all practical purposes, surely one label was as good as any other? Dismissing a debate on what to call something as "mere semantics" seemed to be an act of hard-nosed skepticism and realism.

But as I came to discover, naming involves much more than simply assigning a label to something that has already been identified. The act of naming is one of the central mysteries of human cognition — it is the visible tip of an iceberg whose depth below the surface of conscious thought we have only just begun to plumb. I cannot claim to have solved this mystery, but I'd like to present what I have cobbled together so far: a handful of puzzle pieces which I hope will entice the reader to join in the investigation. (Perhaps more puzzle pieces will turn up in future columns.) I've divided up the essay into four parts. Here's the plan:

  1. We'll introduce two key motifs — the named and the nameless — with a little help from the Tao Te Ching.
  2. We'll examine a research problem that crops up in cognitive psychology, neuroscience and artificial intelligence, and link it with more Taoist motifs.
  3. We'll look at how naming might give us power over animals, other people, and even mathematical objects.
  4. We'll explore the power of names in computer science, which will facilitate some wild cosmic speculation.

1. The name that can be named

My change of attitude towards naming started with a book on Chinese philosophy that I found in a second-hand book store. I discovered to my initial bafflement that most ancient Chinese philosophical schools had a theory of "names and actualities". In Confucianism the correspondence between names and things took on special ethical importance — ranks, duties and functions needed to be clearly delineated in order for society to be harmonious. I initially put this sort of thing down to the inscrutableness of ancient modes of thought — the same ancient alienness that caused people to impute divinity and power into the names of their deities. Perhaps this just came down to a confusion about words and the things they refer to? Surely it is the things — the objects, forces, people, and processes — that are important, and not what we choose to call them?

But not all ancient thinkers thought names and things were the same. Lao Tzu, the founder of Taoism, seemed to go against the Confucian ideal, and denied the equation of names with actualities. The very first chapter of Lao Tzu's Tao Te Ching sets the stage for a more ambivalent attitude towards names.

The Tao that can be expressed Is not the Tao of the Absolute.
The name that can be named
Is not the name of the Absolute.
The nameless originated Heaven and Earth.
The named is the Mother of All Things.

One way to read this is to say that the Tao, or the way of nature, goes beyond our expressive capabilities. Whatever we can name, delineate, and define is not enough to encapsulate the way nature works, or the way we should work with nature. This is the usual mystical interpretation. Taoist metaphysics has at least two parallels — one from the West, and one from India. Apophatic theology developed in Europe, and centers on the belief that because God is ineffable, no positive attributes can be assigned to Him. One can only list all the things that God is not. This often amounts to listing everything that one can think of, and then asserting God is not any of them. A similar approach is taken in the Jnana Yoga and Advaita Vedanta schools of Hindu thought. The supreme reality, Brahman, is "neti neti", or "not this, not this". It is the essence of "suchness" for which no other definition applies.

If unnameable forces are so powerful, why then does Lao Tzu bestow upon the named the honor of being the "Mother of All Things"? Why give naming any credit at all? Perhaps there is a clue in the saying "the namer of names is the father of things" (a maxim whose origins I am unable to trace). The mystery of names seems to lead us to the mystery of creation.

2. Manifest boundaries

The act of naming requires at least two components: the name, and the thing to be named. So in order to understand the process of naming, we have to think about things. The "namer of names" needs raw material for his task. So what are things? How do we decide that a thing is a thing? The question seems so absurd that I suspect most people never think of it. Perhaps more people have pondered the following question: before you are introduced to the name of an emotion, have you really experienced it?  When I was a child I didn't really know what "ennui" meant, so maybe I never truly experienced it. But once I was given the definition, I could discern the outlines of this emotion in my own life. How does this sort of thing happen?

This is where the cognitive and neural sciences come in. Unlike philosophers, cognitive scientists, neural network modelers and artificial intelligence researchers are trying to emulate human cognition, rather than just come up with verbal theories about it. Complex emotions are among the most difficult topics for scientists to address. (Plus, for the time being robots that display signs of ennui are not high on our priority list.) We have a hard enough time grappling with things! For researchers trying to imitate human intelligence, the nature of objects is a matter of practical concern. Brains and artificial systems are not directly presented with objects — what we receive are patterns of energy: photons on our retinas and vibrations on our ear drums. Artificial intelligence researchers learned the hard way that getting separate objects to "pop out" of these undifferentiated sensory fields is an unexpectedly complex ability that most humans take for granted. Objects aren't completely "out there" in the world — they're also products of our minds and brains, and therefore of our cultures. So naming an object can be a creative act. (Also, deciding which naming system to adopt can be a political act.) Philosophers have often acknowledged the subjective and creative aspects of naming, but the sheer mechanistic complexity of naming is best appreciated through the attempts to get machines to do what humans find trivially simple.

When presented with a rich visual scene — like a cluttered desk, for instance — how can we pick out separate things: coins, keys, wallet, pen, phone? This is a problem that humans are extraordinarily good at. The process is called visual object segmentation, and it is thought to be a key first step in pattern recognition. Even after decades of research, most advanced algorithms cannot perform object segmentation better than little children. The artificial approaches are improving and will soon overtake humans, partly as a result of taking inspiration from the human brain. Still, the way in which Google and Facebook's artificial neural networks pick out the faces in our photographs is only a loose approximation of how we seem to do it. There exists the distinct possibility that we will come up with devices that imitate human intelligence without shedding light on how natural, biological intelligence works. Only time will tell, but in the meantime the scientists and engineers will keep probing, coding, and tinkering. Perhaps they'll need to engage with the philosophers and their verbal theories.

Many artificial object segmentation systems start by trying to discover the boundaries in an image. You can use these boundaries — lines, contours, edges, discontinuities of lighting and texture — to discover the outlines of objects present in the image. This itself is a challenging task for machines. The trick is to find the important boundaries, because there are many contours that don't mark the outlines of things. Neural networks and other techniques such as Bayesian modeling often require considerable training in order to approach the performance that comes naturally to a toddler. The result of this training is a form of expectation. These models learn to sort images into different categories, and then use the categorization system as a guide for what to expect in a new image. In the case of neural networks, this expectation takes the form of connection weights between artificial neurons. In a Bayesian model, the expectation takes the form of probability distributions called priors, which help the model determine how likely it is for a particular object to be found given other information present in the image. If the image has been categorized as an photograph taken in a forest, the probability that the model picks out the outlines of trees should be much higher than the probability that it picks out the shape of a sofa. The model, like a human, should expect to see trees in the image, not sofas. For both humans and machines, prior expectations seem necessary in order to perceive useful boundaries. Without these prior expectations, the sensory world might appear poorly defined — like an impressionistic painting in continuously varying shades of grey, lacking distinct nameable objects.

Characterizing pattern recognition in terms of boundaries and expectation evokes these lines from chapter 1 of the Tao Te Ching, which immediately follow the lines I quoted earlier:

Thus, without expectation,

One will always perceive the subtlety;

And, with expectation,

One will always perceive the boundary.

With the Tao Te Ching, every translation captures subtly different shades of meaning. Consider this version of the four lines I just quoted:

Ever desireless,

One can see the mystery.

Ever desiring,

One can see the manifestations.

Subtlety and mystery are easy to link. A mystery, after all, is the absence of a clear dividing line between truth and falsehood, an absence that renders everything subtle, shadowy and indistinct. How about desire and expectation? A desire for food, for instance, is closely linked to the expectation that the reassuring outlines of edible objects will soon appear, perhaps with a little effort. When someone sitting at a restaurant table says they expect prompt service, you can be pretty sure they desire the rapid manifestation of a waiter.

More problematic for me initially was the link between "boundary" and manifestation". The connection became apparent only after I was exposed to visual object recognition research. If you are unable to see boundaries in the world, you will be unable to perceive objects. In a very real sense boundaries are required for things to become manifest to you.

What do expectation and desire have to do with objects? The typical mystical approach is to downplay them in order to gain a heightened awareness of subtlety and mystery. But I like to think that that Lao Tzu was telling us that the two ways of seeing both have their roles to play. He probably didn't know about expectation values in Bayesian decision theory, but he may have intuited that when you look at the world with desire, or with the expectation of getting something from it, you tend to assess your perceptions in starkly delineated terms: good and bad, useful and useless, dangerous and safe, edible and poisonous. A starving person is not usually interested in subtleties. Acknowledging the importance of both desire and desirelessness is consistent with the dialectical style that characterizes Taoism, a philosophy that often emphasizes the interplay of opposing forces: yin and yang. Lao Tzu ends the chapter like this:

The source of these two is identical,

Yet their names are different.

Together they are called profound.

Profound and mysterious, the gateway to the Collective Subtlety.

Floating in a sensory world without boundaries, lacking expectation or desire, nothing would ever become manifest. Being set adrift in a grey sea of subtlety sounds rather depressing. In fact depression has been described as a "flaw in love", a disease that attacks the very basis of desire and other strong motivations. Antonio Damasio, in his book Descartes' Error, documents neurological disorders that lead to reductions in emotional expression. The surprising result of such disorders is that they sometimes render the patient incapable of making decisions. Such patients' cognitive abilities seem untouched — they can solve problems when asked to do so. But when asked to make decisions for themselves, they cannot pick one alternative over any other. All the alternatives seem equally good — shades of grey everywhere, and no way to draw a line between them. There is some preliminary neuroscientific data that suggest that some clinically depressed people have a weakened ability to tell apart different patterns. In other words, their "desireless" condition is correlated with an inability to draw boundaries between perceptual objects, memories, and situations. [1]

There is no doubt that the act of naming requires that objects and patterns become manifest to us. In order for things to become manifest, their boundaries must be delineated. But the mystery of naming seems to go deeper. Where does the power of names come from?

3. Naming and Taming the Infinite

When your dog has learned its name, you can exercise a small but useful amount of control over its behavior. When you call it by name, it comes. Perhaps it has been trained to expect a treat when its name is called. Most cats on the other hand are unable or unwilling to react strongly to their own names. Evolutionary biologists inform us that dogs may have been the first animals to be domesticated — perhaps 12000 years ago. Perhaps names were crucial to the transformation from wild wolves into tame dogs.   Cats may have joined the party much later, around 5000 years ago. Maybe we haven't fully domesticated them yet! Or maybe to gain power over something by naming it requires a degree of consent on the part of the named.

The behavioral control we wield over (some!) named animals even shows up in when we use a human's name. If you hear your name being spoken you will most likely direct your attention to the source of the sound. In conversation with someone, judiciously slipping in their name can cause them to lower their guard. Salespeople, confidence tricksters and politicians routinely use this to their advantage. Dale Carnegie, in his legendary self-help book How to Win Friends and Influence People, tells us to "Remember that a person's name is to that person the sweetest and most important sound in any language." Perhaps the act of naming allowed humans to domesticate each other, completing our transition from wild apes to cultured individuals.

Stories like Rumpelstiltskin might be cultural relics from a time when language was new and strange, and just beginning to reveal its powers. The belief in the power of names may have roots in the prehistoric infancy of our species, but it lives on in many of the world's religions. Perhaps the sacred place given to particular names reflects an appreciation of the civilizing, domesticating role of naming itself. In the Hindu Namakarana ceremony, a child is given two names: one ordinary name, and one secret name that is derived from astrology and known only to the father. The Hebrew scriptures seem to link God's creative power with the act of naming. In Genesis, "God said, ‘Let there be Light', and there was light." The Jewish people came to believe that the name of God — the Tetragrammaton - was too holy to be uttered. Some Christians inverted this belief, and held that the name of God, or of Jesus, was so holy that it ought to be uttered repeatedly. A particular version of this belief, known as name-worshiping, emerged in Tsarist Russia, and persists to this day despite condemnation from the Russian Orthodox Church. The name-worshipers believe that "The name of God is God Himself and can produce miracles." In a twist that brings us closer to the idea that names have power, this strange, heretical belief system may have had an impact on the world of pure mathematics.

Mathematics, it should be pointed out, is distinct from science in that it deals with what appear to be pure forms of thought — entities that seem to have no necessary connection with the natural world, other than the fact that they are produced by human minds. For this reason mathematics departments may be the last bastions of platonism — the belief that there exist objects that are neither material nor mental, but are in essence abstract. Only a subset of mathematics is of relevance to science (though one never knows which arcane branch with prove useful in the future). Mathematicians are often given to wonder about the ontological status of the concepts and patterns they work with. What are mathematical "objects"? Do mathematical objects exist? Are the names of mathematical objects important? The celebrated 20th Century Russian-French mathematician Alexander Grothendieck was said to have "a flair for choosing striking evocative names for new concepts; indeed, he saw the act of naming mathematical objects as an integral part of their discovery, as a way to grasp them even before they have been entirely understood.'' [2]

In the late 1800s Georg Cantor initiated a seminal phase in the discussion of whether mathematical objects are "real" through his study of infinity. Cantor might as well be called the Father of Infinity; though he didn't invent the word, he created a set of concepts that he assigned the name "infinity" to, forever changing how mathematicians think about it. Before Cantor, most mathematicians followed Aristotle's approach, holding that infinity was a potentiality rather than an actuality. Cantor broke with this tradition by asserting that infinity was real, not a potentiality, and that there were several different sorts of infinity, each with rigorously provable properties. To cut a long and complex story short, Cantor created a formal system called set theory, which was used to study collections of mathematical objects, such as numbers. He used set theory to show that there were different sorts of infinite sets. So the set of all natural numbers (1,2,3,4, and so on) was infinite yet countable, and the set of real numbers — the collection of all points on a real line — was infinite but uncountable. He then showed in very convincing ways that the set of points on the real line was in a sense "bigger" than the set of natural numbers, despite the fact that both sets are infinite. He also showed that the rational numbers, the numbers that can each be written as a ratio of two integers, were also countable. So the uncountable real numbers vastly outnumber the countable rational numbers. The real numbers that aren't rational are called, unsurprisingly, irrational numbers, and a tiny handful of them do have names, such as the square root of two, pi, and Euler's number e.  As if the notion of two sort of infinity were not mind-boggling enough, Cantor went on to reveal an infinite number of such infinite sets, each "bigger" than the last.

By naming the properties of new, unheard-of objects, Cantor seemed to be drawing them out of the shadows and into the light of day, where they were forced to obey the rules of pen-and-paper mathematics. The ontological question is this: did Cantor create these dizzying infinities, or simply bestow names on mathematical objects that already existed in some sense? Does something need to exist before you can name it? Or can a concept arise at the very moment it is named? Influential French mathematicians followed Cantor into this strange domain where naming and creation resemble each other, but according to one version of the story, they lost their nerve, and climbed down from the vertiginous precipice of infinity. Perhaps that was the safe thing to do, because some people think Cantor's attempt to tame infinity drove him to depression and madness.

A handful of Russian mathematicians lead by Dmitri Egorov and Nikolai Luzin had no such failure of nerve. Egorov and Luzin were both name-worshipers. They believed that "if they named God, they assured his existence, and similarly they thought that by naming the new sets they could make them real. God could not be defined, but he could be named." The concepts that Egorov and Luzin picked up in Paris were hard to visualize, but they could be named, as Cantor had demonstrated. Luzin's personal papers contain a suggestive account of his attitude to definitions:

Each definition is a piece of secret ripped from Nature by the human spirit. I insist on this: any complicated thing, being illumined by definitions, being laid out in them, being broken up into pieces, will be separated into pieces completely transparent even to a child, excluding foggy and dark parts that our intuition whispers to us while acting; only by separating into logical pieces can we move further, towards new successes due to definition.

This belief may have contributed to Egorov and Luzin's role in starting up the influential ‘Moscow School of Mathematics'.  A modern Taoist might say that in desiring to understand Nature, Luzin and his colleagues perceived new mathematical manifestations. But Luzin may also have been aware that this came at a price: perhaps the "foggy and dark parts that our intuition whispers to us" are the subtle mysteries that can only be seen without expectation. [2]

4. The Algorithm helps those who help themselves

There is another modern domain that makes use of "name magic", and it may be the most unexpected of all. Where do you suppose the following quote comes from?

One of the things that every sorcerer will tell you is if you have the name of a spirit you have power over it.

It's not from a medieval grimoire or a fantasy novel. It's from an MIT lecture on computer science from 1986 (and no, it is not a Dungeons & Dragons reference either). As the textbook that accompanied this course explains,

A computational process is indeed much like a sorcerer's idea of a spirit. It cannot be seen or touched. It is not composed of matter at all. However, it is very real. It can perform intellectual work. It can answer questions. It can affect the world by disbursing money at a bank or by controlling a robot arm in a factory. The programs we use to conjure processes are like a sorcerer's spells.

Despite the fact that computers programs can only work their magic in the decidedly material world of electronic circuits, there is a sense in which computer programs are like mathematical objects — they seem to reside in a platonic realm of pure forms. After all, a program can move from device to device, but it is still the same program. But why do names crop up in computer science? What is the source of their power? Another line might give us a clue. "To call up a demon, you must learn its name".  (This time it is from a novel: William Gibson's Neuromancer.)

In computer science, a "daemon" is a program running as a background process that quietly performs system "chores". It was named after Maxwell's demon, a creature from a physics thought experiment who works tirelessly to sort molecules into two piles. Maxwell's demon can trace its roots to the demons of Greek mythology — nature spirits who were believed to be constantly working behind the scenes. So we can draw a genealogical line from the mythical demons of the past to the real daemons operating on your computer or smartphone. The program daemons are working behind the scenes without your explicit permission, so to gain control of them, you need to know what they're called.

In recent years, some physicists have speculated that the whole universe could be a simulation — a labyrinthine algorithm running on some vast alien supercomputer. One can never tell how seriously physicists take concepts like this. But some claim that there are ways to establish this experimentally, implausible as this sounds [3]. If this idea takes hold, perhaps history will come full circle, and we will discover our commonality with ancient seers and medieval alchemists, invoking the hidden daemons that keep the Universal Algorithm running smoothly. Like cosmic hackers, some of us might seek to learn the names of these code-spirits in order to gain power over them. The tendency to see our minds and our genetic material as computational codes might turn the daemon quest inwards as well.

Every generation features people who think that they have arrived at a comprehensive rational understanding of how the Universe works. They think they already know the names of all the daemons that keep the Universal Algorithm from crashing. Perhaps these new daemons, instead of being called Abraxas or Gorgon or Pantalaimon (or Rumpelstiltskin?), have names like "Higgs Boson" or "Quark" or "Superstring" or "Selfish Gene". Let's call the set of all known concepts the "nameable concepts". Are the nameable concepts all there is to the universe? An analogy with mathematics is in order. The nameable numbers are infinite, but like the rational numbers, they are countably infinite. We can say the same about the nameable concepts. We can always list them one by one, as entries in a limitless encyclopedia like Wikipedia. But just as there are unnameable numbers, there could be unnameable concepts — a far larger infinite set whose elements we may never fully list, or count, or compute, or even point to. [4]

When we take our nameable concepts too seriously and forget about the possibility that there are things we haven't named, we are confusing the map with the territory. We mistake the finger pointing at the moon with the moon itself, and we forget that there might be other heavenly bodies out there — some that astronomers might one day discern, and some that are so far away that their light will never reach us. But even this analogy doesn't capture the possibilities outside the reach of our named concepts — things that we can only talk about negatively, apophatically. Perhaps there are things out there that are not galaxies, not stars, not planets, not dark matter, not living, not dead…

Maybe the story of Rumpelstiltskin, in its cryptic way, is trying to tell us two intertwined tales. On the one hand it is telling us that unnamed powers lurk in the shadows: capricious spirits that can both help and harm us. Like stories themselves, these powers may be infinite. Perhaps our rational concepts can never fully account for them. But on the other hand, it seems to be telling us that when malevolent or irrational forces manifest themselves, we can — if we're lucky — name them and tame them.

But maybe I'm wrong about this. After all,

The Tao that can be expressed

Is not the Tao of the Absolute.

The name that can be named

Is not the name of the Absolute.

 

_____

Notes & References

[1] A recent study indicated that people suffering from depression has a weakened pattern separation ability — compared to healthy people, the boundaries between their memories were more blurred. This may have something to do with the loss of the ability to produce new neurons in the hippocampus, as Siddhartha Mukherjee explains is his masterful New York Times article, "Post-Prozac Nation: The Science and History of Treating Depression".

[2] The mathematical section of the article was inspired by the paper "The Power of Names" by Loren Graham which appeared in the journal Theology and Science. The quotes in this section also come from this paper. Graham and co-author Jean-Michel Kantor expand on the theme of name-worshiping and mathematics in their book Naming Infinity: A True Story of Religious Mysticism and Mathematical Creativity.

[3] See, for example, recent news items in the New York Times ("Is the Universe a Simulation?") and Discover Magazine ( "Do We Live in the Matrix?").

[4] In the arcane psychoanalytic theories of Jacques Lacan  — which I confess I have only encountered via Slavoj Žižek and Wikipedia — experience is divided into three orders: the Imaginary, the Symbolic and the Real. I don't know whether Lacan or Žižek studied higher mathematics, but the concept of the Real might have something in common with the concept of real numbers, or perhaps with Georg Cantor's concept of the Absolute Infinite, which he equated with God. The real numbers are uncountably infinite, and therefore always "exceed" the rational numbers. As Cantor demonstrated using his surprisingly intuitive and nontechnical diagonal argument, the rational just can't keep pace with the real. As far as I can discern, the psychoanalytic Real involves the unnameable, unanticipated aspects of experience that break through our cozy certainties, exposing the inadequacy of our named concepts. Perhaps the Real is the experience — sometimes exciting, sometimes traumatic — of discovering that Nature always has a trick up her sleeve. Perhaps the Real is where black swans come from. The Real eludes our attempts to draw neat boundaries to pick out perceptual and conceptual objects, forever lurking unmanifest in the "foggy and dark parts" of the universe, and of the mind.