Category Archives: Favorites

ICCS: Time-Dependent Networks

Blogging on Peer-Reviewed ResearchYesterday, the International Conference on Complex Systems wrapped up with five talks on networks. For me, the most interesting was that by Dan Braha, who spoke about what happens when you analyze a system as a network which changes over time, instead of the aggregate network formed by lumping all the timesteps together. Imagine a system made out of a whole pile of parts. At time [tex]t[/tex], part number [tex]i[/tex] might or might not be interacting with part number [tex]j[/tex], which we could represent as a time-varying matrix [tex]C_{ij}(t)[/tex]. Many studies of network-related phenomena obscure the time-dependence part. For example, in a living cell, genes are switching on and off, concentrations of enzymes are going up and down, and all sorts of stuff is changing over time. You can mix proteins A, B and C in a test tube; perhaps A bonds both to B and to C. You’d then draw an interaction network with links connecting A to B and to C — but what if B and C are never present in the cell at the same time?

Braha and company looked at a collection of e-mails sent over 113 days, exchanged among 57,138 users. (The data comes from arXiv:cond-mat/0201476v2, published five years ago in Phys. Rev. E, and were gathered at Kiel University.) A node is an individual e-mail address, and a link is established when a message is sent from one address to another. They found, among other things, that whether or not a particular node is a “hub” changes over time: popular today, an outcast tomorrow. Moreover, a node which is in the top 1000 most connected on one day may or may not be in the top 1000 for the aggregate network. Furthermoreover, when the window of aggregation is gradually increased — from one day to two days, to a week, up to the entire time period — the similarity to the total aggregate network increases, as you’d expect, but without any threshold.

In the last few minutes of his talk, Braha did a brief overview of a related investigation, in which they studied a “social network” derived from Bluetooth devices. If my Bluetooth gizmo is within two meters of yours, we’ll call that a link. The network of Bluetooth devices will naturally change over time, so we can do the same comparison between the graphs observed at short timesteps to the graph formed by aggregating all connections. During the Q&A session afterwards — before I had to, ironically enough, run off to find my cell phone — I pointed out something which it appears Braha hadn’t fully grasped.
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All Hallows

To begin at the end:

This is Orson Welles, ladies and gentlemen, out of character to assure you that The War of The Worlds has no further significance than as the holiday offering it was intended to be. The Mercury Theatre’s own radio version of dressing up in a sheet and jumping out of a bush and saying Boo!

Starting now, we couldn’t soap all your windows and steal all your garden gates by tomorrow night… so we did the best next thing. We annihilated the world before your very ears, and utterly destroyed the C. B. S. You will be relieved, I hope, to learn that we didn’t mean it, and that both institutions are still open for business.

So goodbye everybody, and remember please, for the next day or so, the terrible lesson you learned tonight. That grinning, glowing, globular invader of your living room is an inhabitant of the pumpkin patch, and if your doorbell rings and nobody’s there, that was no Martian… it’s Halloween.

Tonight, if you aren’t spreading madness over the airwaves, as the Mercury Theatre did; if you’re not showing off comets as you hand out candy; if you’re not dressing up as an antiparticle seeking to annihilate with an attractive particle, as Jennifer Ouellette suggests; then you should at least have a song in your heart.
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Love Affairs of Neverwhere

Neil Gaiman says, apropos the Dumbledore fracas,

Neverwhere has two gay characters who are Out, as far as the book is concerned, and one major character who is gay but it isn’t mentioned, simply because that character was one of many people in that book who don’t have any sexual or romantic entanglements during the story. So it’s irrelevant.

He actually mentioned this a few years ago, saying that

I tend not to write characters with sexual orientation as a starting point, unless that’s how they define themselves. Most people don’t.

Just for fun, I wonder if we can guess which character in Neverwhere he’s talking about. My own copy of Neverwhere is I-don’t-know-where, at least a timezone away, so although I have the Carey/Fabry graphic novel adaptation with me, this will have to be from memory.
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Sunday Egan

Greg Egan writes,

I wish we had a good word in English that meant only “the shattering majesty of reality”, so atheists could make it abundantly clear that they’re aware of this majesty, but don’t imagine that it’s due to anything that resembles a person in any way. But what atheists absolutely should not do is say “Well, I’m going to use the word ‘God’ to mean ‘the awesomeness of the universe’”. This is helpful for selling lots of tenth-rate pop-science books with “God” in their titles, and for winning the Templeton prize, but even when it’s not plain venal and dishonest it’s linguistically sloppy.

This is why I describe quantum mechanics as Loki playing dice with the Universe. Come on, Loki may be subtle, but he’s not malicious, right?

We can take this one step further. There is a model of the early Universe called string gas cosmology, in which the reason why the Cosmos has three dimensions is essentially the same as the reason why knots can exist in three dimensions but not more or less. (In 2D, there’s not enough “room” for a string to overlap itself, and in 4D or higher, there’s too much room, and a knotted loop can always “slip free”, returning to a simple circle.) I wonder if the Templeton Foundation will pay me for declaring that the Cosmos is the way it is because Aphrodite likes to get tied up in knots?

(Hah! And you thought I was going to quote a passage from Quarantine, didn’t you?)


Ah, some light Friday fare!

By now, everybody has probably heard about the forthcoming crackpot “documentary” from David de Hilster, Einstein Wrong – The Miracle Year. Currently looking for financial backing, de Hilster hopes to release this flick in 2008, doing for relativity what What the Bleep Do We Know (2004) did for quantum physics: namely, let the fractured ceramics have free play.

As it turns out, David de Hilster is one of the Network’s classic relativity cranks. He’s been pushing his pet theory, “Autodynamics,” since at least the early 1990s (on the sci.physics Usenet group). As it also turns out, Autodynamics has plenty of problems. For example, it chucks out the Lorentz transformations, thereby making itself inconsistent with the Maxwell equations, which form our basic understanding of electricity and magnetism, without which the technological support system of modern society couldn’t exist.

What’s more, they don’t like that nasty ol’ equation

[tex]E = mc^2.[/tex]

The Autodynamicist revulsion at this horrible formula has led them to propose — no, I’m not making this up — that [tex]E[/tex] should equal [tex]mc^3[/tex] instead.
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Nine Minutes of Science

OK, this is too good to pass up. Jim Blinn, the computer-graphics expert responsible for the Mechanical Universe animations — and therefore, responsible for filling my childhood with arrows — summarizes The Mechanical Universe in nine minutes. Watch all of first-year physics packed in a single morsel:

Blinn also worked on Caltech’s Project MATHEMATICS! series. I’m a little surprised that so few of the Project MATHEMATICS! videos have found their way onto the Intertubes yet. Here’s a “teaser trailer” of sorts, made from clips of “The Story of π”:
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Document Typesetting Fantasy

“This is TeXnical support. How may I be of assistance?”

“Yes, I’m trying to typeset the conference book for an upcoming conference — you know, the thing we give everybody which has the abstracts of all the presentations, and so forth — and LaTeX isn’t working.”

“What seems to be the problem, sir?”

“Well, the alphabetical list of speakers, the index at the very end, isn’t displaying.”

“It doesn’t appear in the DVI output?”

“That’s right.”

“This is an alphabetical list of speakers which tells where in the conference book their abstracts will be found?”

“Yes, each abstract is given a number with the \label command, and the list refers to them with the \pageref command. The LaTeX source is actually the output of a Perl script which reads the conference data from a MySQL database, so all of this is automatically generated.”
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The Mathematics of Love

Or, at least, of nostalgia — who else here remembers Square One?

And no, the Phoenicians did not use Arabic numerals. Those were cooked up a couple hundred years after Rome fell, in India, and spread to Europe via the Arabs. The forms of the written digits changed over time, and the idea of “0” seems to have come around later than the use of numerals for 1 through 9.

It suddenly occurs to me that people who watched too much Square One grow up to sing about the Finite Simple Group of Order Two.

More on New Scientist

I felt sort of bad saying all that stuff about Wired when the guy who wrote the piece I did like showed up to say “Thanks for the link.” But hey, I’m not going to stop criticizing bad science reporting, nor can I imagine shutting myself up about the practices which I think cause bad science journalism. (Nor do I have the vanity to think that by myself, I’ll make any difference.) I’d feel considerably more uncomfortable if Greg Egan didn’t go and provide a whole new plateful of reasons to be upset with pop science.

Egan has been masochistically plowing through New Scientist ever since the EmDrive incident, when he had found himself “gobsmacked by the level of scientific illiteracy” the magazine had put on display. Now, commenting at The n-Category Café, he gives two additional recent “absurdities.”
Continue reading More on New Scientist

Math in the Movies

I’ve been running around this weekend doing important things like appearing in a musical comedy — 22, in which the terrorist threat involves an Infinite Improbability Drive — so thanks for not breaking the Internet whilst I was away! I notice that Mollishka has raised the topic of science and math in the movies, which sounds like a nice way to ease everybody back into the work-week.

Several years ago, I was visiting a friend in a mental institution. (See? Your first story of the week is shaping up just great!) In fact, she was a resident of McLean Hospital, whose wards have housed such notables as John Nash, James Taylor and Sylvia Plath (and oddly enough, I’ve seen the first two of those notables, live). My friends and I had driven out to Belmont to visit our colleague, and while we were chatting in the dining area, another resident of that hall poked into the conversation. He was of average height, but wiry, and spoke as if drawing upon deep reservoirs of energy; he had been placed in McLean by his family, he said, and he let loose a shrill cascade of invective upon the orderlies who eventually took him away.

Before he was hauled back to his room, he got to talking about Darren Aronofsky movies. At the time, those were Pi (1998) and Requiem for a Dream (2000). I’m grateful to him for providing a calibration mark by which I can judge those movies, for in the interval before the orderlies carried him away, he told us that Aronofsky was going to be making more movies, and — children, cover your eyes —
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Stuart Pivar Sues PZ Myers


Remember that Stuart Pivar fellow who wrote a book called LifeCode (2004), a book which purported to advance a new theory of developmental biology — a theory which would, naturally, overturn everything biologists have figured out so far? Well, here’s a quick refresher:

  • On 7 November 2005, PZ Myers reviewed LifeCode on his old blog. The upshot is that pretty pictures do not a body of evidence make.
  • This past July, on the twelfth to be specific, Myers reposts his review on, because Pivar started promoting his book again.
  • Down in the comments, my Pharynguloid pals and I started noticing that the laudatory quotes Pivar had stuck on LifeCode couldn’t be traced back to their purported sources. In particular, an endorsement from Neil deGrasse Tyson turned out to be a chimera: the first part from an unrelated NOVA interview, and the second completely fabricated.
  • On the seventeenth, Myers posts his review of Pivar’s new edition. In Pivar’s illustration, a spider has ten legs. The money quote from Myers: “This book is a description of the development and evolution of balloon animals.” Later, Mark Chu-Carroll will agree that, in the end, Pivar’s claim “just doesn’t hold up to the least bit of scrutiny.”
  • The next day, PZ makes note of the puzzling endorsement situation. He says that he’s written several of the people whose names Pivar invoked, and Neil deGrasse Tyson had written back: “Tyson replied, and has said that part of the quote is an out of context reference to a completely different subject, and that another part is a fabrication. He has asked that Pivar remove his name from his website, which he has not done. Tyson’s name is also prominently used on the back cover of his book — I don’t see that going away, either.”
  • Stuart Pivar sends an e-mail to my place of employment, using our generic departmental e-mail address; an administrative assistant eventually notices the message and forwards it to me. The text follows.

    Dear Dr Stacey,

    Thank you for your interest in Lifecode. It presents a solution to the ultimate systems problem, living taxonomy. The model is considered very serious now by many. But it freaks out biologists into cognitive dyfunction.

    Robert Hazen is a prominent NASA scientist in this field . His review recommending publication is appended.

    The review of PZ Myers may be also seen today. Please note that he not an embryologist.

    May I send you a copy of the book?.

    Stuart Pivar

    Note: there were no actual appended items.

OK — followed all that? Now, you better be sitting down for this. Via ERV, I just learned that Stuart Pivar is suing PZ Myers and the Seed Media Group.
Continue reading Stuart Pivar Sues PZ Myers

Behe on The Colbert Report

Last night, Michael Behe was Stephen Colbert’s guest on The Colbert Report. It was, shall we say, educational.

BEHE: Nobody was searching for the limits of Newton’s theory when Newton first proposed it. He thought that he had solved all of physics. But then when —

COLBERT: You mean about how — how apples fall?

BEHE: Apples fall, cannonballs go. But then —

COLBERT: Mm-hmmm.

BEHE: But then when —

COLBERT: He invented the cannonball? He invented the dive — the cannonball?

[audience laughs]

BEHE: Cannonballs fly.

Oh, yes. It’s nice to know that nobody checked to see if Newton was right, or if “universal gravitation” was really universal.

Wait. You say that it was Edmund Halley who used Newton’s laws to predict that comets travel in elliptical orbits, and that the comet seen in 1456, 1531, 1607 and 1682 would return in 1758? How could Halley say such a thing, after Newton had made his view clear that all comets travel in parabolic paths? It’s in the Principia, for Heaven’s sake! And you say that Halley was the one who realized that the stars are not fixed to a “celestial firmament” but instead move through space? How dare you imply that the views of one person are not the entirety of science! Sir, how dare you have the temerity to insist that people did not take Newton at his word but instead used his theories to make predictions about the world which they could then compare to observations to — I can hardly even articulate such a heretical notion — see if Newton was wrong.

What! Are you telling me it was the French, those wine-swilling, toad-munching surrender monkeys, who had the audacity to test Newton’s prediction that the Earth is an oblate spheroid? Sir, you could tell me all you want about the 1735 expeditions to Peru and Lapland under Charles-Marie de La Condamine and Pierre-Louis Moreau de Maupertuis respectively — the former of which incidentally brought back the first rubber and curare Europe had ever seen — but the mere suggestion that Newton’s word was not good enough is so repugnant I refuse to consider the matter further.

It gets better:
Continue reading Behe on The Colbert Report