Wednesday, December 30, 2009

Amdahl's Law for speed-up from parallelization

Optimally, the speed-up from parallelization would be linear—doubling the number of processing elements should halve the runtime, and doubling it a second time should again halve the runtime. However, very few parallel algorithms achieve optimal speed-up. Most of them have a near-linear speed-up for small numbers of processing elements, which flattens out into a constant value for large numbers of processing elements.

The potential speed-up of an algorithm on a parallel computing platform is given by Amdahl's law, originally formulated by Gene Amdahl in the 1960s. It states that a small portion of the program which cannot be parallelized will limit the overall speed-up available from parallelization. Any large mathematical or engineering problem will typically consist of several parallelizable parts and several non-parallelizable (sequential) parts. This relationship is given by the equation S = 1/(1-P)

where S is the speed-up of the program (as a factor of its original sequential runtime), and P is the fraction that is parallelizable. If the sequential portion of a program is 10% of the runtime, we can get no more than a 10× speed-up, regardless of how many processors are added. This puts an upper limit on the usefulness of adding more parallel execution units. "When a task cannot be partitioned because of sequential constraints, the application of more effort has no effect on the schedule. The bearing of a child takes nine months, no matter how many women are assigned."

Saturday, December 26, 2009

Clock signals

Most integrated circuits (ICs) of sufficient complexity use a clock signal in order to synchronize different parts of the circuit and to account for propagation delays. As ICs become more complex, the problem of supplying accurate and synchronized clocks to all the circuits becomes increasingly difficult. The preeminent example of such complex chips is the microprocessor, the central component of modern computers, which relies on a clock from a crystal oscillator. The only exceptions are asynchronous circuits such as asynchronous CPUs.

Didn't know about this before. Another one of those points of difference which raises interesting questions about the nature of neural versus digital computation.

Thursday, December 24, 2009

Tuesday, December 22, 2009

Pitman Shorthand

Pitman shorthand is a system of shorthand for the English language developed by Englishman Sir Isaac Pitman (1813–1897), who first presented it in 1837. Like most systems of shorthand, it is a phonetic system; the symbols do not represent letters, but rather sounds, and words are, for the most part, written as they are spoken.

Thursday, December 17, 2009

Tuesday, December 15, 2009

Algorithm Design

In scientific computing, optimality of algorithms is not always something which receives full consideration by users-- if you want to run a sort or solve some combinatorial problem, you are more concerned with making the algorithm work than looking into how fast it runs. But in dealing with very large data sets, reducing the limiting behavior of your algorithm from N^2 to NlogN can reduce your runtime from something on the order of years to something on the order of seconds. So while there are many computational problems out there for which solutions are known to exist, the practical matter of implementing such solutions is so expensive that they are effectively useless-- but if a new algorithm could be found which would reduce their runtime, we might suddenly be able to use them.

This is the driving motivation behind much of the work that goes into quantum computing. Because bit state in a quantum computer is probabilistic rather than binary, the computer operates in a fundamentally different way, and we can design algorithms which take such differences into account. One vivid example is Grover's Algorithm for searching an unsorted array. Here's a good description from Google labs:
Assume I hide a ball in a cabinet with a million drawers. How many drawers do you have to open to find the ball? Sometimes you may get lucky and find the ball in the first few drawers but at other times you have to inspect almost all of them. So on average it will take you 500,000 peeks to find the ball. Now a quantum computer can perform such a search looking only into 1000 drawers.

So if you were opening one drawer a second, the traditional algorithm would take you an average of six days to run, while the quantum algorithm would take you a little under 17 minutes.

(Now, say each of those million drawers represented a different combination of letters and numbers, and you were trying to find the drawer/combination which corresponded to the password to someone's email account. Encryption standards which would be secure against attacks from a traditional computer are easily bypassed by quantum algorithms.)

While quantum computing still has a ways to go, parallel programming is already providing another alternative to traditional computer architecture. In parallel programming, you split your code up and send it to a number of computers running simultaneously (for our million-drawer problem: say you had 9 other people to help you, you could each search a different set of 100,000 drawers and it would only take 50,000 steps on average for the ball to be found.) So the trick in parallel programming is to figure out the right way to eliminate all the bottlenecks in your code and split up your task across processors as efficiently as possible.

Now, what about a task like image recognition? If you had a couple thousand processors at your disposal and a single image to feed them, what is the most efficient way for your processors to break up that image so that between them they can reconstruct an understanding of what it depicts? You might decide to give each computer a different small piece of the image, and tell it to describe what it sees there-- maybe by indicating the presence or absence of certain shapes within that piece. Then have another round of computers look at the output of this first batch and draw more abstract conclusions-- say computers 3, 19, and 24 all detected their target shape, so that means there's a curve shaped like such-and-such. And continue upwards with more and more tiers representing higher and higher levels of abstraction in analysis, until you reach some level which effectively "knows" what is in the picture. This is how our current understanding of the visual cortex goes-- you have cells with different receptive fields, tuned to different stimulus orientations and movements, which all process the incoming scene in parallel, and in communication with higher-level regions of the brain.

It would be interesting, then, to see what sensory-processing neuroscience and parallel programming could lend one another. Could the architecture of the visual cortex be used to guide design of a parallel architecture for image recognition? Assuming regions like the visual cortex have been evolutionarily optimized, an examination of the parallel architecture of the visual processing system could tell us a lot about how to best organize information flow in parallel computers, and how to format the information which passes between them. Or in the other direction, could design of image-recognition algorithms for massively parallel computers guide experimental analysis of the visual cortex? If we tried to solve for the optimal massively-parallel system for image processing, what computational tasks would the subunits perform, and what would their hierarchy look like-- and could we then look for these computational tasks and overarching structure in the less-understood higher regions of the visual processing stream? It's a bit of a mess because the problem of image processing isn't solved from either end, but that just means each field could benefit from and help guide the efforts of the other.

So! Brains are awesome, and Google should hire neuroscientists. Further reading:

NIPS: Neural Information Processing Systems Foundation
Cosyne: Computational and Systems Neuroscience conference
Introduction to High-Performance Scientific Computing (textbook download)
Message-Passing Interface Standards for Parallel Machines
Google on Machine Learning with Quantum Algorithms
Quantum Adiabatic Algorithms employed by Google
Optimal Coding of Sound

Wednesday, December 9, 2009

Saturday, December 5, 2009


From the video description: "Ryan" is based on the life of Ryan Larkin, a Canadian animator who, 30 years ago, produced some of the most influential animated films of his time. In the film, we hear the voices of prominent animators and artists discussing Ryan's work, and from waitresses, mission-house caretakers and homeless people who make up Ryan's life. These voices speak through strange, twisted, and disembodied computer-generated characters--which combine to reflect the film's creator, Chris Landreth. In the words of Anais Nin, "We don't see things as they are. We see things as we are."

First saw this at the end of my senior year in high school, the year it won the Oscar for best short animated film. Ryan Larkin himself received renewed attention following this film's success, and gave up some of his bad habits to briefly resume his career in animation before dying of lung cancer in early 2007.

Sunday, November 22, 2009

Delia Derbyshire, Alchemist of Sound

The amazing Delia Derbyshire, pioneer of British electronic music, demonstrating tape loops. A clip from the documentary "Alchemists of Sound" on the history of the BBC Radiophonics Workshop, where Derbyshire worked from 1962-1973.

Derbyshire is best known for her realization of the original Doctor Who theme-- from Wikipedia: Derbyshire's interpretation of Grainer's theme used electronic oscillators and magnetic audio tape editing (including tape loops and reverse tape effects) to create an eerie and unearthly sound that was quite unlike anything that had been heard before. Derbyshire's original Doctor Who theme is one of the first television themes to be created and produced by entirely electronic means. Much of the Doctor Who theme was constructed by recording the individual notes from electronic sources one by one onto magnetic tape, cutting the tape with a razor blade to get individual notes on little pieces of tape a few centimetres long and sticking all the pieces of tape back together one by one to make up the tune. This was a laborious process which took weeks.

From her web site: A recent Guardian article called her 'the unsung heroine of British electronic music', probably because of the way her infectious enthusiasm subtly cross-pollinated the minds of many creative people. She had exploratory encounters with Paul McCartney, Karlheinz Stockhausen, George Martin, Pink Floyd, Brian Jones, Anthony Newley, Ringo Starr and Harry Nilsson.

Friday, November 20, 2009

High Speed Sequencing

This video dedicated to my undergraduate degree in biology, in which it was never deemed necessary to introduce the fact that sequencing technology more sophisticated than the Sanger method exists. This is an animation explaining the process behind Helicos's new single-molecule sequencing technology. Like all other modern sequencing methods, this technique is based on short-read sequences-- DNA is replicated and then broken into millions of tiny fragments (25-50 base pairs at the low end), all of which are sequenced simultaneously. Given about 30-fold coverage of your genome, you can align these fragments to confidently reconstruct it as a single sequence.

Also of note, the Velvet algorithm is one cool sequence assembly program which, instead of aligning DNA fragments by simply looking for overlapping regions between them, plots all the fragment sequences generated onto a De Bruijn graph, and then uses principles of graph theory to condense them into a single sequence. Yay math!

Monday, November 9, 2009

Solomon Burke-- None of Us Are Free

Jazz organ: great instrument, or the greatest instrument?

Wednesday, October 28, 2009


breve is a free/open-source 3d environment for multi-agent simulations and artificial life, which can be used to simulate things like BZ reactions, evolution by natural selection, and the flocking patterns of birds (which by the way is a good example of how realistic behavior can be produced using a drastically simplified model).

Also on the site is the breveCreatures screensaver, a simple simulation of evolution by selective pressure which you can download on its own. Creatures are initiated as random configurations of moving blocks, and selected through successive generations for the most effective walking behavior. The video below shows the products of some other evolution processes in breve:

Wednesday, October 14, 2009

Kadykchan, Russia -- the Phantom City

Kadykchan is a Russian city located way the hell up in the Siberian peninsula, where the winter air temperature could drop below -40 degrees Celsius. In spite of these conditions, the city had a population of around 10,000 in 1986, when it was a tin-mining town for the Soviet Union. But when a pipe burst in the city's central boiler house, the whole city lost heat and everyone quickly evacuated-- and between this and the decline of its tin mines after the fall of the USSR, Kadykchan never recovered. As of 2008 the population was estimated to be less than 300 people; the city is still full of the abandoned possessions of those who fled.

For more photos, see this post on the impressive Russian blog Brusnichka, which seems to be dedicated largely to exploring and photographing abandoned bits of Russia (and there's even more up on English Russia). I linked Brusnichka's photos from an abandoned Russian army neuroscience lab here almost a year ago (my second post here, in fact) but never thought to explore the site in more depth. Like most of Russia, the site now seems to be abandoned-- but what remains of the content is beautiful. I like this this and this for starters.

Monday, October 12, 2009

Vladislav Delay -- Lumi

Good stuff. The video reminds me a bit of David ORielly's work, I like how the old mechanical quirks of early CG (flickering landscapes, stark textures, rigid movement, low polygon counts) are now being used aesthetically-- like impressionist painters intentionally using visible brush strokes, turning a flaw of their medium into a feature of their work.

Sunday, October 11, 2009

Belousov-Zhabotinsky Reaction

And speaking of oscillations, here's a nice video of the Belousov-Zhabotinsky reaction in a petri dish:

(The video info for the above also has a nice description of waveforms in the brain which is worth reading.) You can see someone setting up the reaction (ie pouring some chemicals together and stirring, really) here.

The BZ reaction is an example of a chemical oscillator, a system which instead of arriving at a steady state transitions between two different chemical states (which two states have two different colors, whence the waves above). Boris Belousov discovered it in the 1950's when he happened to mix together potassium bromate, cerium(IV) sulfate, propanedioic acid and citric acid in dilute sulfuric acid (hell, why not?); he made two attempts to publish his findings, but was rejected from peer-reviewed journals because he couldn't explain why the oscillations occurred.

Steven Strogatz's Sync

Steven Strogatz's wonderful book Sync discusses how synchrony in biological networks is not only common, but neigh-inevitable. His opening discussion of fireflies is particularly vivid: along some riverbanks in Southeast Asia, populations of fireflies stretching for miles will all flash in synchrony, a phenomenon which baffled western explorers for decades. It turns out the effect is easy to replicate in a model-- say you have a collection of periodic oscillators which fire a burst of light at their peak and then reset, you can achieve synchrony if you make it so that each oscillator, when it fires, bumps its neighbors forward a bit in their cycles. Because firing induces a forced reset of the cycle, oscillators will be pushed forward in their cycles until they fall into sync, and then stay locked there; this effect takes off in small groups and quickly grows until the entire network is firing together.

The important points here being that a) neurons do this too (in fact it can be hard to get spiking neural networks to stop doing this) and it's really probably important to coding somehow, and b) you guys, fireflies are totally attempting to form some sort of massive insect-based consciousness here.

You can read more on the subject in the preview of the first chapter and a half, posted on Google Books.

Saturday, October 10, 2009

Urban Speculation Links

Been reading a bit lately on urban architecture and design, which turns out to be a much more active field than I'd have expected. The work I've read comes from an interesting perspective-- there's the creative mindset of art and design students (which also lends itself to an unfortunate affinity for lovely but impractical concept art), mixed with a love of new technology, and an interest in complex city infrastructure and human culture, particularly the way cultural boundaries develop and shift over time and the way behavior is controlled by environment.

While there are certainly some fun ideas floating around, the focus is more on these concepts than their realization, and as such things can get pie-in-the-sky fairly quickly. But if you keep this in mind it can be interesting reading, and it will at the very least introduce to you a new way of thinking about the way we shape and are shaped by our surroundings.

Some introductory links:
May have to post in more detail on some of these in the future. Fun times!

Friday, October 9, 2009

Population dynamics in Yemen

From the beginning of T.E. Lawrence's Seven Pillars of Wisdom comes an account of how population and cultural forces drove human geography in early 20th-century Yemen. I have no idea how realistic this account is, but as an engineer I think it's kind of inspiring to see this kind of systems-minded analysis used to describe complex human behavior-- and so poetically, at that.

In Yemen the solution was different. There was no foreign trade, and no massed industries to accumulate population in unhealthy places. The towns were just market towns, as clean and simple as ordinary villages. Therefore the population slowly increased; the scale of living was brought down very low; and a congestion of numbers was generally felt. They could not emigrate overseas; for the Sudan was even worse country than Arabia, and the few tribes which did venture across were compelled to modify their manner of life and their Semitic culture profoundly, in order to exist. They could not move northward along the hills; for these were barred by the holy town of Mecca and its port Jidda: an alien belt, continually reinforced by strangers from India and Java and Bokhara and Africa, very strong in vitality, violently hostile to the Semitic consciousness, and maintained despite economics and geography and climate by the artificial factor of a world-religion. The congestion of Yemen, therefore, becoming extreme, found its only relief in the east, by forcing the weaker aggregations of its border down and down the slopes of the hills along the Widian, the half-waste district of the great water-bearing valleys of Bisha, Dawasir, Ranya and Taraba which ran out towards the deserts of Nejd. These weaker clans had continually to exchange good springs and fertile palms for poorer springs and scantier palms, till at last they reached an area where a proper agricultural life became impossible. They then began to eke out their precarious husbandry by breeding sheep and camels, and in time came to depend more and more on these herds for their living.
Finally, under a last impulse from the straining population behind them, the border people (now almost wholly pastoral) were flung out of the furthest crazy oasis into the untrodden wilderness as nomads. This process, to be watched to-day with individual families and tribes to whose marches an exact name and date might be put, must have been going on since the first day of full settlement of Yemen. The Widian below Mecca and Taif are crowded with the memories and place-names of half a hundred tribes which have gone from there, and may be found to-day in Nejd, in Jebel Shammar, in the Hamad, even on the frontiers of Syria and Mesopotamia. There was the source of migration, the factory of nomads, the springing of the gulf-stream of desert wanderers.

Sunday, October 4, 2009

Rite of Spring

On a bit of a modernism kick; really such interesting stuff. Quoth Peter Childs (from wikipedia), "There were paradoxical if not opposed trends towards revolutionary and reactionary positions, fear of the new and delight at the disappearance of the old, nihilism and fanatical enthusiasm, creativity and despair." Or as Fitzgerald put it (at 23, goddamn I feel like an underachiever now), a generation "grown up to find all Gods dead, all wars fought, all faiths in man shaken."

So anyway, here's the Rite of Spring:

And here's a snip of a documentary on the music.

Saturday, September 26, 2009

The Squeeze

And now it is time for the Holding Tide horrifying underwater exploration vocabulary word of the day: the squeeze (on page 55) (yum).

Wednesday, September 23, 2009

Cargo Cult Science

Richard Feynman's address on Cargo Cult Science. Starts off in deceptively simple language talking about general pseudoscience silliness (and also girls; this is Feynman after all), but then later goes into more serious discussion of some troubling shortcomings seen in big university research programs. The rat maze example in particular stuck with me the first time I read this-- it's a real reminder to think critically about the assumptions you make in designing experiments.

Monday, September 21, 2009

Swine Flu Aftermath in Egypt

Hmm, and Egypt is now dealing with the repercussions of their decision during last May's swine flu panic to cull over 300,000 pigs in the country: before the cull, the zabaleen were Christian pig-farmers living on the outskirts of Cairo and other cities who went door to door collecting trash, which they either sold to recycling facilities or fed to their pigs. Now that they've been driven out, the streets of Cairo are filling with excess garbage which the city lacks the infrastructure to handle properly, creating a health hazard far worse than the flu itself.

Computational Neuroscience Links

Computational Neuroscience on the World Wide Web-- a pretty comprehensive resource on comp neuro labs, tools, and conferences.

Friday, September 18, 2009

Ferrofluid Friday

An old video, but still fun. Dynamic sculpture using electromagnets + sound waves + magnetic fluid.

Monday, September 7, 2009

The New Settlers of Detroit

The economic recession has taken a particularly heavy toll on the American auto industry, and cities like Detroit which were once central to the industry have been gutted by job losses and home foreclosures in the past year. This effect has been so extreme that property in Detroit must practically be given away: Yahoo Real Estate shows dozens of homes around the city selling for mere hundreds of dollars. And still the population of Detroit, a city designed to support roughly 2 million people, has dwindled to less than a million, while the shutdown of many supermarket chains has created a food desert in the city.

Detroit's plight has been well covered in the news, and organizations are already forming to take advantage of the area's collapsed economy. Artists, sustainability enthusiasts, survivalists, and hippie-types in general are coordinating the mass purchase and transformation of land in and around the city. And since this recession coincides with a period of increased interest in locally-grown produce and sustainability, many efforts have a heavy focus on urban farming-- a fact which has received attention from Canada's Office of Urban Agriculture, the Beeb, and NPR among others.

Naturally there's a lot of hype surrounding the whole thing, and it will be interesting to see how this new influx impacts the culture of the city in coming years. For further reading, here are a few people and organizations currently involved in settling the area and documenting their impact:
  • Andrew Kemp is a resident of East Detroit who has bought up five lots in his neighborhood and is now farming four of them

  • Urban Farming is an NPO which farms vacant lots in Detroit and gives collected produce to the needy

  • Detroit UnReal Estate Agency is a group which tracks cultural development in Detroit and inventories cheap property in the area

  • the Yes Farm is a collective of artists and urban farmers living and creating in Detroit

  • the Power House Project is a social art project attempting to develop an efficient, sustainable home in the city for under $99,000

Wednesday, September 2, 2009

Lau Nau: Painovoimaa, valoa

I've got a couple posts brewing on augmented reality and architecture and modeling, but the days have been just packed lately. So here's this instead:

Sunday, August 30, 2009


(available here)

Saturday, August 29, 2009

Basin Street Blues

Kid Koala's cover of Basin Street Blues, by way of Constant Siege. Really love the underwater feel of the animations, it goes well with the song.

Friday, August 28, 2009


TinEye is a reverse image search engine-- ie you upload a picture from your computer and it'll look for sites that use that picture. Seems to work pretty well, though sadly it was unable to tell me where the above picture came from-- it's been sitting orphaned on my PC for ages. Their Cool Searches page shows some examples of what the site is capable of in terms of image recognition-- impressive stuff. Similar to this, Google has a Similar Images search function, which seems to work pretty well but doesn't seem to support searching uploaded images so far.

Hmm, I wonder what it'd take to make a content search for music-- I'm not sure how input to the search would work, but it'd be an interesting project just to study feature/melody extraction from mp3s. Most music has some sort of regular structure: could you automatically find the hook or the chorus of a pop song? Maybe make a filter that converts complex orchestral sound to pure tones, or even generates sheet music from sound files? Time to do some digging.

Imaging a molecule

Researchers at IBM announce that the detailed chemical structure of a single molecule has been imaged for the first time.

Thursday, August 20, 2009

Google News timelines

So I've just discovered Google News has an Archive Search feature, which lets you search historical news articles for a given phrase and return a histogram of hits. It makes an interesting way to map the rise and fall of concepts, events, and phrases in the public mind. Here are some queries I've come across that have interesting patterns:

First, some normalization: a search for the, and, a, etc gives us an estimate of the number of articles on record-- gradual uphill increases like those seen here should be attributed to the nature of the data set and not the data itself. (Science!)

There's lots of modern words and phrases we can watch grow into popularity, like outer space and DNA. More subtly, we see the emergence of the adjective global starting in the 1940's, and a sudden rise in popularity of the word deadly in the 1980's (wut?). Robot grows gradually in use over the 20th century, though there is a funny spike in the summer of 1944, which correlates to German use of "robotic" planes to bomb Britain during WW2. And atom shows a boom midway through 1945, of course, though it's curious to note that its appearance in the news is deminished prior to that, during the war-- this could be a result of wartime news censorship, but then if you search science itself, you see that science reporting in general tends to drop during wartime, which could also be a factor.

Then some words are tied to a certain time period-- like fallout shelter and elixir. Others fall from popularity: for some odd reason, the word obituary became wildly unpopular in 1986, while the civil rights movement (I assume) soundly quashed use of the word negro after the late 60's. And lipstick, after rising in popularity starting in the roaring 20's (a phrase which didn't actually take off 'til the 60's-- does that mean 20's culture was to the 60's what baby boomer culture is to the 90's/today?), lipstick suffered a temporary blow in the 1970's, either from the growth of the feminist movement or simply from the fashion of the time.

What other trends are out there?

Tuesday, August 4, 2009

More Weapon Salves

Also, the book I got the previous quote from has the most fantastic extended metaphor title thing going on, which merits a post of its own. The top bit reads:
Doctor Fludd's Answer unto M. Foster
The Squeezing of Parson Foster's Sponge, ordained by him for the wiping away of the Weapon Salve.

Wherein the Sponge-bearer's immodest carriage and behavior towards his brethren is detected; the bitter flames of his slanderous reports are by the sharp vinegar of Truth corrected and quite extinguished; and lastly, the virtuous validity of his Sponge, in wiping away of the Weapon-Salve, is crushed out and clean abolished.


On Weapon Salves

My new hobby: using my lovely institution access to EEBO to look up random subjects from a course I took on History of Science. Here's a mention of usnea, which is moss taken from the skull of a hanged man, from a text published in 1631:

Scull-mosse, or Bones, (saith Doctor Fludd,) Mummy, and the Fat of Man (the especiall ingredience) comprehend the corpor all perfection of man, and so are apt to heale, by reason of a naturall Balsam resting in them, sympathizing with the hypostaticall Balsam residing in the living Man.

"Mummy" here being dried out human flesh, it appears; Doctor Fludd made a balm out of these things to treat injured people, a la weapon salves.

The premise of weapon salves is that when a person is injured by a weapon, there forms a Sympathetic link between that weapon and the person. Now, when someone gets their arm hacked open with a sword, one's first instinct would be to treat the arm-- but because of this sympathetic link, one other option would be to apply your treatment to the sword instead. There was a lot of argument back and forth about this theory, but the weapon salve people held their ground for a while, in part because their method was rather successful. This is, of course, because medical balms at the time were made from bear fat and chunks of rotting corpses: weapon salves worked better because they put the rotting fat salve on the sword instead of the person's arm, which in the weapon salve treatment was simply cleaned and wrapped in fresh bandages each day.

One wonders what seemingly reasonable (and in fact genuinely successful) methods of today will look equally bats to future generations.

Saturday, July 4, 2009

Spectrogram to Sound

I'm still vaguely searching for a good free spectrogram-to-sound program, but this Sound to Graph to Sound Java applet is a good start.

The default resolution is pretty low, but if you're not interested in any of their demo sounds and just feel like doodling, you can hit the reset button to adjust some of the parameters. You can increase the resolution to MxN = 448x448, and to get the frequency bounds closer to vocal range I'd set FL to 10, keeping FH at 4000 (or possibly changing to 8000). You can also increase the value of NFRAME, which lets you store multiple sounds which you can navigate through with the arrow keys, or check the animate box to play them in sequence.

Mostly so far I have succeeded in making lots of drawings that all sound like frogs. Curious.

Friday, July 3, 2009

Protein Vaults

Vaults are the Protein Data Bank's molecule of the month. Nerdy, yes, but these sound kind of cool:
Vaults are composed of many copies of the major vault protein, which assembles to form a hollow football-shaped shell. The one shown here is from rat liver cells (PDB entries 2zuo, 2zv4, and 2zv5) and contains 78 copies of the protein. Inside cells, the vault also encloses a few other molecules, which were not seen in the crystal structure because they don't have a symmetrical structure inside the vault. These molecules include several small RNA molecules, a protein that binds to RNA, and an enzyme that adds nucleotides to proteins.

23 Questions

Darpa's 23 mathematical challenges in modern scientific efforts, with a distinct emphasis on computational biology.

Larry Abbott's 23 questions in computational neuroscience.

23 is a reference to the father of all such lists, Hilbert's 23 problems posed to the International Congress of Mathematicians in 1900; these problems shaped much of 20th century mathematics, and some remain unresolved to this day.

Sunday, June 7, 2009

Photos of Decay in Detroit and Chernobyl

Like the title says. Here's:

A flikr photoset of the Detroit Public Schools Book Depository (read the backstory in the blog post here)

and, photos taken from a motorcycle trip through the dead zone of Chernobyl. (Looks like there's some argument over whether it's real, but it is an interesting site nonetheless.)

Tuesday, May 26, 2009


Tuesday, May 19, 2009


Code2HTML converts a program source code to syntax-highlighted HTML. Helpful if you, um, write a lot of programming tutorials or post code to forums and want it to look pretty?

Also Perl is so good at strings, oh my goodness. Of course, next to Matlab anything looks good at strings.

Wednesday, May 6, 2009

Visualizing Music and Looking for Patterns

Found this and many other impressive videos on one Stephen Malinowski's YouTube channel. I really like the way the colored bar visualization separates out the different voices in a piece, especially the fugues.

The opening to Gödel, Escher, Bach has a fun discussion on the structure of the fugue-- the gist of it is that the composer develops the piece out of one short theme (a few measures of some simple melody), carried by a fixed number of voices. Starting with one voice expressing the theme, each additional voice chimes in repeating the theme until all are present. The theme is further explored and varied throughout the piece via transformations of the original melody: inverting, reversing, transposing, compressing. Soooo the video above is really cool, because the visualizations make it that much easier to pick out all the transformations that are taking place. Yay!

I wonder if you could make other visualization methods which help you pick out recurring themes in a piece, and are robust to transformations from the original theme (or measure distance from the original). It seems like a problem that crops up a lot, in problems from network analysis to predicting structural motifs in proteins. For instance, all integral membrane proteins will have a hydrophobic region which crosses the lipid bilayer-- this requires an extended sequence of hydrophobic amino acids, which will be reflected in the genetic code. There would be variation in sequence (not all membrane proteins would have the same arrangement of hydrophobic amino acids), but there might still be trends which might be picked up. Fourier/Laplace transforms can break a signal down into its periodic components; is there some way to transform a signal to visualize it in the space of its recurrent themes and their variations?

Saturday, April 25, 2009

Machine with Wishbone

"Caught in a symbiotic relationship, both the wishbone and the machine are unable to manifest fully without the other. We drag our pasts with us and move according to unseen forces. More and more, we interface with the world through our mental and technological creations."

View more of Arthur Ganson's kinetic sculptures on his YouTube channel.

Thursday, April 23, 2009

Kurzweil Reading Machine

Huh, I never knew this: according to a profile of Ray Kurzweil in Wired, the LexisNexis database-- now an enormous resource with extensive corporate, legal, and academic use-- grew out of a late 70's venture using Kurzweil's recently-developed character-recognition algorithms to scan legal documents and news articles.

Said character-recognition algorithms are a part of a text-to-speech tool Kurzweil continues to refine; its current incarnation is a software package for Nokia phones which will read aloud to you when held above a page.

Tuesday, April 21, 2009

The Wason Selection Task

The Wason Selection Task, a fun little test of logical reasoning commonly used in experimental psychology.

Sunday, April 19, 2009

The Amen Break

Okay okay, I couldn't resist grabbing this as well-- again via the Worldwide Cultural Gonzo Squad, an oddly captivating video on the Amen Break, a six-second-long drum loop from the b-side of a 1969 single which was taken up by early sample-based music and is now the basis for entire musical subgenres, as well as every advertisement soundtrack ever. Also interesting for its discussion of copyright law, and the fact that it's narrated by a surprisingly realistic electronic voice.

Saturday, April 18, 2009

Sound to Pixels

Found a nifty article about a piece of digital music software called Photosounder, posted on a blog called Create Digital Music. Photosounder is an image-sound editing program-- that is, music creation is done visually, by drawing and editing the sound's spectrogram. The videos in the CDM article show some of the ways in which this software is being used; it's pretty impressive stuff. I also found this plugin for winamp which produces a simple spectrogram of your music as a visualization, if you're just curious to see what the music you're listening to would look like.

The spectrogram is actually a good representation of how sound is coded in the brain-- the cochlea in your ear breaks down sound input into narrow frequency bands, just as we see on the X axis of the spectrogram, and cells in each frequency band fire in proportion with the intensity of sound at that frequency (so, you have a physical structure in your ear which performs a Fourier transform-- how cool is that?) As seen in this video, a single sound object usually consists of several harmonics, and a full spectrogram can be quite complex-- and yet our brain can easily segment that spectrogram to identify different instruments, even when there's a lot of frequency overlap. We are even able to focus our attention on one specific instrument, which means selectively responding to one particular batch of signals as they move up and down across frequency channels/cell populations. Brains are pretty awesome, guys.

(And on another note: as you can see in the aforelinked video, one of the easiest ways to pick out one instrument from a spectrogram is to look for elements which "move together" in time/across the spectrum-- this notion drives a lot of work in both auditory processing and the corresponding problem of object recognition in computer vision.)

Wednesday, April 15, 2009

Mayang's Free Texture Library

Mayang's Free Texture Library is a great source of high-res textures and some object stock. A lot of the images in the man-made, metal, and nature sections make nice texture overlays to add some depth and, um, texture to digital artwork.

See this page for one method for applying these images as texture overlays in photoshop.

Tuesday, April 14, 2009

Please Say Something

Please Say Something - Full Length from David OReilly on Vimeo.

A troubled relationship between a Cat and Mouse set in the distant Future. Winner of the Golden Bear for best short film at the 2009 Berlinale. (Click the link for full view.) His other stuff is pretty cool too, like When You're Smiling and the video he did for Venetian Snares.

Monday, April 13, 2009

Supernumerary Phantom Limbs

People with amputated limbs sometimes experience the presence of a phantom limb which continues to exist where their old limb was-- they can perceive pain or temperature changes in the missing limb, and have a sense of its orientation. It seems like this is probably caused by lingering activity in the parts of the brain which previously processed such sensory data coming from the limb.

Well, it turns out that it's also possible to experience a supernumerary phantom limb: for instance, one Swiss woman reported feeling the presence of a pale, translucent third arm following a stroke. Researchers have found that this woman's brain treats the arm just as it would a real one-- when she uses it to perform a task like scratching an itch, an MRI of her brain shows activity in regions corresponding to her sense of touch, as well as activity in the visual cortex from where she perceives the arm's presence. And it relieves the itch where she'd scratched it, too.

Friday, April 10, 2009

Color Palettes

Two beautiful color resources for artists:

Color Scheme Designer lets you play around with a color wheel to generate color palettes based around single colors or sets of complimentary colors, and includes a tool to preview websites designed with your generated color schemes. is a site where users can post and rank color swatches, palettes, and patterns.

Wednesday, April 1, 2009


Investigators with Infowar Monitor have recently exposed a vast spy system dubbed GhostNet which has been gathering intelligence information from over 1200 government, military, and NGO computers across 103 countries, mostly in South and Southeast Asia. The system is based almost entirely in China, but it is yet unclear whether it is the work of the Chinese government, independent Chinese citizens, or some outside organization.

A recent New York Times article on the system is full of spooky facts, such as evidence of the system's use against the Dalai Lama and the Tibetan rights movement, and descriptions of its capacities including the ability to activate infected computers' audio and visual recording equipment to covertly eavesdrop on their surroundings.

View the 53-page report detailing the GhostNet investigation here.

Wednesday, March 25, 2009

Kowloon Walled City

Found a fantastic blog post on Coilhouse (go read for more details and nifty video), on Kowloon Walled City-- a dystopian monolith of overgrown urbanization which existed in anarchic limbo in the middle of Hong Kong between 1945 and 1993.

Kowloon's bizarre state of lawlessness attracted thousands of people-- drug dealers, unlicensed dentists, entrepreneurs, refugees-- and the city's population boomed to a high of 50,000, making it one of the most densely populated areas on the planet. Thousands of makeshift expansions were built to cope with the growing population, and the city developed into 14-story monolith, a place where sunlight rarely reached street level and denizens drilled down to tap into water pipes from surrounding regions of Hong Kong. The city was evacuated in the early 90's and demolished in 1993, but its legacy now lives on in popular culture-- it is the basis of dozens of dystopian cities created in movies, books, and video games. Quality of life and sanitation were poor, but the reported crime rate was low, and many small shop owners found it a city of unique opportunity.

Wednesday, March 18, 2009

Tom Gauld on Flickr

Tom Gauld has recently started a flickr stream, mostly for the ballpoint pen cartoons he draws for the Guardian; also check out more art on his website. Some of my favorites include this, this, this, and this.

Monday, January 12, 2009

Café Le Sélect

Rick Tulka on Flickr: lovely drawings of patrons at a French cafe. Some of my favorites so far are here, here, here, and here. I swear that first one is one of my professors.