Category Archives: food

Terrible beauty

“The Patrician took a sip of his beer. ‘I have told this to few people, gentlemen, and I suspect I never will again, but one day when I was a young boy on holiday in Uberwald I was walking along the banks of a stream when I saw a mother otter with her cubs. A very endearing sight, I’m sure you will agree, and even as I watched, the mother otter dived into the water and came up with a plump salmon, which she subdued and dragged onto a half-submerged log. As she ate it, while of course it was still alive, the body split and I remember to this day the sweet pinkness of its roes as they spilled out, much to the delight of the baby otters who scrambled over themselves to feed on the delicacy. One of nature’s wonders, gentlemen: mother and children dining on mother and children. And that’s when I first learned about evil. It is built into the nature of the universe. Every world spins in pain. If there is any kind of supreme being, I told myself, it is up to all of us to become his moral superior.’”

Terry Pratchett, Unseen Academicals

Corn muffin coefficient

From a recent Quotation of the Day Mailing List email comes this gem from a collection of letters written in response to the US Department of Agriculture‘s redesign of the Food Pyramid:

“The cleansing properties of urine are not even addressed in the food pyramid. This must be corrected. We cannot allow small minds and prejudice to bury this useful health information from our brothers and sisters in light.

“Write back IMMEDIATELY and tell me where to report with my diagrams. I am including corn muffins prominently in my calculations. That alone should tell you that I know what I am doing!”

– Mark Martin, Foodician, from his submission to the U.S. Department of Agriculture on the redesign of the “food pyramid”.

Here’s a snapshot of the original letter from the collection of letters the USDA received:

I think it’s an artist’s prank. He claims he received a response from the USDA but it was just a generic form letter. Nevertheless, the prominence of corn muffins in his calculations is hard to ignore.

Scientists discover breakfast on Mars

“This image from NASA’s Phoenix Mars Lander’s Optical Microscope shows a strongly magnetic surface which has scavenged particles from within the microscope enclosure before a sample delivery from the lander’s Robotic Arm. The particles correspond to the larger grains seen in fine orange material that makes up most of the soil at the Phoenix site. They vary in color, but are of similar size, about one-tenth of a millimeter.”

“This image from my breakfast table shows a rounded surface containing scavenged puffs of breakfast product known as Trix. These particles correspond to part of this nutritious and delicious breakfast.”

I am always happy when science and food are brought together for the common good.

Fun with crystals

Very sugary water + skewers + time + iStopMotion = Time lapse video of rock candy formation:

Homemade rock candy – timelapse from David Oranchak on Vimeo.

(vimeo link)

This is about four days of crystal growth. Not massive, but cut us some slack – this was our first attempt! :)

Atlanta GECCO trip report

Article sections: Atlanta | GECCO 2008 | Contests | Research


The Atlanta trip was a lot of fun. We stayed in a really nice rental house not far from Turner Field. The McCubbins managed to put up with me for a week and even went so far as to make dinner for me on several occasions. You haven’t had a good meal until you’ve tried their cooking. Mmm, tuna bites, fruit and goat cheese salad, steak, and black bottomed cupcakes. Our friends Jon and Kate are also accomplished cooks – we should host a cookoff between both couples so we can reap the delicious benefits.

Gecco Trip, Atlanta, Day 6 - Our rental house

Our rental house

Between home-cooked meals we sampled a variety of Atlanta dining options. Chris and I ate at Gladys and Rons Chicken and Waffles, a restaurant chain started by Gladys Knight that serves the most delicious fried chicken and waffles I’ve ever had. The waffles are warm and soft on the inside and nice and crispy on the outside. Perfect. And eating there has only amplified my weakness for fried chicken. I also managed to meet up with the Atlanta-based contingent of my LegalEdge coworkers at the Vortex Bar and Grill. While I did not sample the infamous bypass burgers, I did partake of the big-ass mushroom swiss burger, and my brain’s burger receptors were alight with glee. This celebration of manliness was a mere coverup for the earlier, emasculating experience of eating at the American Girl Boutique and Bistro to celebrate Eris’ fifth birthday. Despite the pink/pastel surroundings, bad service, and proliferation of little girls tending to their creepy shark-eyed dolls, we had a great time and the food was really good.

We checked out the Georgia Aquarium and World of Coca Cola during our stay. The aquarium is fantastic; definitely a must-see. The whale shark tank there is a massive, imposing, wondrous display. The Coca Cola museum is fun but they really hammer you with Coca Cola propaganda while you are there. YOU MUST DRINK IT. The tasting room is awesome, though. In it you can try unlimited samples of around 70 different Coca-Cola products sold around the world. We shuffled among dispensers over the sticky floors and tasted all sorts of delicious sugary carbonated water, and occasionally experienced horrid drinks such as Beverly. The tasting room gets you nice and high on sugar and caffeine before you go to the gift shop, which is the only way to exit the museum. A brilliant scheme to coax dollars from your wallet.

Georgia Aquarium / Coca Cola Museum (youtube link)

My trip photos | Chris and Angel’s trip photos

GECCO 2008

According to Nic McPhee’s twitters, GECCO 2008 had 471 attendees from 46 countries. This universal appeal of scientific research is one of things I liked about last year’s GECCO conference, too. This year’s conference, though, was almost as bad as last year’s when it came to feeding the attendees. Food was given out during the two hour poster session where I was presenting my poster, but all the food was gone in less than 20 minutes, and it was not replenished. Boo!


Nevertheless, there were plenty of fascinating presentations and workshops. The keynotes were again from experts in the field of biology, source of many of the great ideas in evolutionary computing. Dr. Martin I. Meltzer, senior health economist at the Centers for Disease Control, gave an interesting keynote talk about developing scientific models to study public health policy and how well we’d react to sudden outbreaks of disease. In particular, he used the example of pandemic influenza. Overall it was a fascinating but extremely depressing talk, since much of it dwelled on how unprepared we are for situations such as the 1918 flu pandemic. Well-known biology professor, popular science blogger, fierce skeptic, and “expelled from Expelled” victim PZ Meyers gave the second keynote talk. He spoke about the importance of development during evolutionary processes (aka “evo-devo”). For example, many animals share the same exact genes but the organisms themselves have vast differences. The differences are due to other important developmental processes outside of the animals’ genes. He talked about some interesting specific examples, such as development of bats and mice. Cretekos et al (2008) recently chopped out a regulatory sequence from bats and stuck them into mice. The mice then developed longer forelimbs, corresponding to the lengthened forelimbs of bats needed for flight. PZ’s blog post explains this in more detail (and with cool pictures!) This example showed that there are many elements at play that create variety in organisms, and many of these elements are strongly influenced by their environment. We are only barely beginning to understand how these things all work together to form life.

PZ’s other interesting example of environmental factors in evolutionary development was Suzuki and Nijhout’s 2006 paper “Evolution of a Polyphenism by Genetic Accommodation”. The researchers were able to evolve environmentally-driven traits in a type of caterpillar. In cooler temperatures, the evolved caterpillars remain black in color. But some of the ones exposed to hotter temperatures turn green in color; all the rest remain black. So the experimenters selected the greenest caterpillars and let them breed with each other. They also selected the black, unchanging caterpillars and bred them with each other. Over a small number of generations, descendants of the green-changing caterpillars more reliably changed colors, while the unchanging caterpillars reliably resisted changing colors in hotter temperatures. Read PZ’s post for more interesting info on how this all works. It reminds me of Ryan Somma’s post about Daisyworld, a thought experiment world in which black and white daisies affect the temperature of their planet as well as their own survival.

Gecco Trip, Atlanta, Day 4 - PZ Meyers keynote

PZ Meyers giving his evo-devo keynote

Here are some other links recounting PZ’s Atlanta visit: PZ blogging about a meet up with his blog readers. Detailed description of the keynote. PZ’s post about his GECCO keynote (including a PDF of his slides).


Chris and I entered the 2D packing problem contest, where you have to evolve a grid of numbers that yield the highest scores for adjacent pairs of numbers. We didn’t win but we did well enough to give a presentation about our approach. We developed an “embryonic” growth technique to evolve the 2D grid, using block-based growth, and something that ended up looking like mold.

Animation of the “mold” evolution technique. Brighter red spots indicate formation of high-scoring areas of the grid. Click to see the supersized version.

Other contests included evolving Rubik’s cube solvers on a massively parallel grid computing platform (the winner gets $1000), evolving L-systems to match pre-existing images, and evolving intelligent agents to search a virtual landscape for food as efficiently as possible. Nobody qualified for the Rubik’s cube contest, and nobody entered the L-system contest. Which is too bad, since they are very interesting problems. And the $1000 bounty for the Rubik’s cube problem remains unclaimed; Parabon is keeping the competition open and is upping the ante to $2000 for GECCO 2009.

There was also the so-called “HUMIES” awards, which is a competition to showcase evolutionary methods that match or outperform human efforts to solve problems. The winning paper used genetic programming to evolve ways to find special algebraic terms that no human has been able to accomplish.

Interesting research

Below is a list of some of the other presentations and papers that interested me:

  • Games: Moshe Sipper spoke about evolving artificial players for Robocode, backgammon, and chess. The evolved Robocode player was able to beat all of its competitors, which were all written by humans. The evolved backgammon player beat “pubeval”, a strong hand-written backgammon algorithm, 62% of the time. Sipper claims the evolved player will beat human players “most of the time”. The evolved chess-playing AI was able to win or draw against Crafty, a hand-written chess-playing program that is a top competitor at the World Computer Chess Championships.
  • Kenneth Stanley discussed “generative and developmental systems”. He explored the question, “how is it possible that 100 trillion connections in the human brain can arise from a mere 30,000 genes in the human genome?” The belief is that biological processes such as embryonic development cause complex things to emerge. If we stole some of these ideas from nature and used them in evolutionary computing, maybe we could solve some really interesting and difficult problems. Dr. Stanley cited the work of Gregory Hornby, who evolved robots and other objects using an L-system grammar. The advantage of using an L-system is you can get complex behaviors out of very compact, simplistic rules instead of describing or defining each part individually.

    Animations of Hornby’s evolved L-system robots. Click the images if they don’t animate for you.

    Dr. Stanley went on to describe a technique to evolve abstract representations for development, based on how evolutionary artwork is made. This was a big surprise to me; I’ve done a little bit of evolutionary art research, so I was happy to discover that there are real uses for the techniques other than just making pretty pictures. Along the way, the technique Dr. Stanley described turned into a side project called Picbreeder where computer-generated art is evolved via an online community. I’ve been wanting to see something like this!

    Sample high-ranked pictures from

  • In the defense applications track, we saw a talk about evolving swarm behaviors for unmanned aerial vehicles (UAVs). Some of the swarming, self-organizing, and attacking behaviors are inspired by behaviors of insects such as bees and wasps. Several interesting micro-UAV technologies were mentioned, such as the Black Widow, UAVs with flapping wings (including bat wings), and parasitic (!!!) UAVs such as SilentEyes (it is launched from larger UAVs). Don’t do anything suspicious, or a swarm of these damned things will form a stinging cloud around you.

    Black Widow micro-UAV. Watch out for its poisonous bite.

    In another talk, an Australian researcher described their technique of evolving collective intelligence for UAVs to detect and report bush fires (that’s Australian for “wildfires”). Their challenge was to evolve swarm behaviors so the UAVs have the best possible coverage of the surveyed area, and also so the UAVs can adapt if there are malfunctions in members of the swarm.

There were many more interesting papers, too numerous to describe, showcasing the widespread and diverse applications of evolutionary computing. Some examples include evolving circuits with high testability, automatic defect classification in electronic wafer manufacturing, quantifying quality degradation on voice-over-IP networks, detection of malware (including zero-day virus attacks) using techniques inspired by biological immune systems, evolving color schemes for people with color blindness, investment portfolio optimization, modeling the Milky Way galaxy using BOINC volunteer computing, developing no-loss strategies for tic-tac-toe, finding deadlocks in large concurrent java programs, radar jamming, evolving functions that can detect computer program code plagiarism by students (beware, cheaters!), automatic route planning that takes traffic into consideration, automatic composition of rock music using genetic algorithms (seriously?), interactive evolution of facial composites of suspects in criminal investigations, detection of moving objects in videos, using a bacterial foraging algorithm to detect circles on images (wait, what?), evolving a World Computer Chess Champion-beating chess program by mimicking the behavior of a mentor, and prediction of whether a company will have financial losses.

The list goes on. But I’ve punished you long enough with this mercilessly long post. Long story short: Trip good. Science good. Computers fun.

Update on the triops invasion

Their horrific cannibalism continued; now only four big triops remain out of the three dozen or so that hatched almost two weeks ago. How’s that for a survival tactic? I’ve been reading The Road by Cormac McCarthy; the novel describes apocalypse survivors who resort to cannibalism due to a severe lack of food. Hopefully we will never have to experience such gruesome necessity employed by the resourceful little triops.

Video of them on days 5 and 12: (cannibalism at 0:38!)

(youtube link)


day 6

Triops, day 6Triops, day 6

day 10

Triops, day 10Triops, day 10

day 12

Triops, day 12Triops, day 12Triops, day 12

day 13

Triops, day 13Triops, day 13Triops, day 13Triops, day 13Triops, day 13

Atlanta suicide

These burgers are offered by The Vortex Bar & Grill in Atlanta:

I should try them when I go to Atlanta in July. That way, I won’t have to buy the return ticket to fly back to Roanoke.

I wish more businesses shared The Vortex’s policies:

The Vortex Bar & Grill is not politically correct. If you are easily offended, there is a good possibility that you will be offended here. We offer our customers delicious grilled animal products, a great selection of booze, and the option to smoke cigarettes. Consider yourself warned.

At The Vortex Bar & Grill the customer is NOT always right. We reserve the right to refuse service to anyone, especially if we think that you’re a great big jerk. We strive to keep The Vortex an official “Idiot-Free Zone” at all times, so if you’re acting like an idiot, we’ll be sure to let you know, right before we throw your stupid ass out.

(Thanks, Eric (resident DBA at LegalEdge), for this restaurant tip)

London report: Vacation and GECCO conference

It was sad to have to come back from our London trip. We had a lot of fun experiencing the city with Chris, Angel, and Eris. London is such a fascinating city and there is just so much to see. We are always struck by London’s diversity of cultures; walking down a busy street, you’ll overhear dozens of different languages being spoken. Our rental apartment was very nice. It was situated on the relatively quiet Pembroke Street near the busy streets of Kensington High Street and Earl’s Court.

Quite comfortable-looking, innit?

Our spacious and comfortable apartment was home to a vast array of hard-to-use and barely-working appliances with extremely confusing user interfaces packed with incomprehensible hieroglyphics. The combination of bizarre buttons, confusing instructions, and malfunctioning appliances generated a nine-day-long comedy of errors that added some frustration and entertainment value to our vacation.

Exhibit A – Why is step 4 of the dryer instructions in a completely different language??

We can’t go to London without sampling a pub, so Kathryn and I picked one at random on Kensington High Street. She tried to order an amaretto sour, and the bartender had no idea what we were talking about, even after we explained how to make it. OK, how about a cosmopolitan then? Nope, that also stumped the bartender. So Kathryn finally settled a gin and tonic. I looked at the draught taps and fancied a pint of bitter. The bartender then told me the bad news that all the draughts were empty. What kind of pub is this? Do you in fact have anything whatsoever to drink?? Somehow I ended up with an amaretto mixed with Pepsi. Luckily, there were thousands of other pubs to choose from and I was able to sample some British ale.

We visited many popular tourist spots: The London Eye (awesome views of the city from the top of an enormous, slow-moving ferris wheel), Big Ben / Parliament, Kensington Gardens, Trafalgar Square (the opening ceremonies of this year’s Tour de France happened here during our trip), St. James’ Palace (obligatory tourist vs guard photo op), “Theatreland” in London’s West End, National History Museum (site of the fascinating GECCO “Complexity and Evolution” keynote by Richard Dawkins, Lewis Wolpert and Steve Jones, SoHo, Chinatown (many awesome types of Asian food – ALL IN ONE PLACE!), Shakespeare’s Globe Theatre, Science Museum, Amora sex museum (the world’s first “sex theme park”), London Trocadero (cool entertainment complex with a huge arcade and casino), Picadilly Circus (I got a free tart here), the Tower of London (so many stories about famous executions, so little time), St. Paul’s Cathedral (incomprehensibly huge and beautiful), Tate Modern (the building is as stark as some of the modern art it houses), Millennium Bridge (Angel made it across despite her fear!), the Bramah Museum of Tea & Coffee (the McCubbins enjoyed high tea there), and the Carnaby Street shops (there is a very cool toy store there called Playlounge).

The food. Oh, the food. London is a glorious cornucopia of dishes for every palate. While there we sampled stuff like Iranian food at Yas Persian restaurant (bad service, incredible food), pan-Asian food (Japanese, Chinese dim sum, Thai curry) at Ikkyusan restaurant, fresh baguettes, pub food, fish and chips, Greek cuisine, gourmet hamburgers (so big and juicy you gotta eat em with fork and knife), and halal kebabs. Chris and Angel are great cooks so they made coq au vin at the apartment – YUMM!! Seriously, we need to get Jon and Kate AND Chris and Angel together on our next trip somewhere, so we can really benefit from their combined cooking knowledge. We’ll eat like kings!!!

Chris and Angel had the hankering for dim sum, so we all went to a dim sum place in Chinatown. The dim sum was awesome. Except for the chicken feet.

Yes, chicken feet. It tastes like it looks.

Iris and Eris had a lot of fun as well. I think we wore them out a lot with all the walking through the city. Plus, they wore each other out because they are such good friends and play very well together. Exhausting for the parents as well! Iris and Eris both say that their favorite thing about visiting London was riding the trains. Mind the gap!!

Iris doesn’t look all that excited here about the train.

GECCO Conference

A highlight of the trip for me was attending the GECCO evolutionary computing conference and presenting my poster, the culmination of a toy project I started last year in a graduate course in Genetic Algorithms. Chris also went to GECCO. He’s a legitimate computer science researcher (he does R&D for a living for APL), so he got to go as part of his job to present his paper (Using Genetic Algorithms for Naval Subsystem Damage Assessment and Design Improvements). I went to GECCO mainly as a newbie bystander, since I don’t yet have as much research experience. Which made me quite starry-eyed when I saw all the cool research going on.

We saw many tutorials and presentations – the speakers represented many countries: Spain, England, America, Italy, Germany, Romania, Poland, Iran, Czech Republic, Portugal, Netherlands, and Australia. It was a good feeling to be part of something so globally-reaching. The first tutorial we attended was John Koza‘s introduction to genetic programming. He gave us a fascinating tour of solving problems with genetic programming by essentially making computers program themselves using evolution-inspired techniques. The automated inventions arising from the techniques are fascinating – some have even infringed on existing patents for inventions previously designed by humans (example).

John Koza getting excited about genetic programming

(an odd side note: John Koza also invented the scratch-off lottery ticket).

Other interesting tutorials and presentations we attended:

  • solving computationally difficult problems (such as knapsack, traveling salesman, diameter-constrained minimum spanning tree, and intersecting spanning trees from multiple geometric graphs) using multiobjective evolutionary computing
  • using peer-to-peer networks to distribute evolutionary computation tasks (my main interest in this is using the DREAM distributed evolutionary package with ECJ, my favorite evolutionary computing framework. incidentally, Chris and I got to meet Sean Luke, the creator of ECJ.)
  • taking advantage of the multiple processors in graphics cards for distributed evolutionary computing
  • simulated robots that produce offspring
  • optimizing the flow of experiments that are run by a robot scientist
  • using genetic programming to evolve lace knitting stitch patterns
  • incorporating characteristics of human creativity into an evolutionary art algorithm (similar to my project but much more sophisticated)

    From the evolutionary art paper: Source Darwin picture plus evolved portraits
  • artificial ecosystems for creative discovery (check out eden, “an interactive, self-generating, artificial ecosystem.”)
  • evolving artificial brains developmentally to play Wumpus World
  • generating XUL user interfaces using genetic algorithms
  • automatic music transcription from a source by evolving polyphonic synthesized waveforms and comparing them to the source
  • evolving musical expressiveness performance models to produce rules that can be applied automatically to musical sequences to make them sound “better”
  • evolution of computerized surface reconstruction techniques to model physical objects for manufacturing
  • designing microstructures in optical fibers using artificial “embryogeny” (a form of artificial development, inspired by the idea of an embryo developing from rudimentary elements) (sample microstructures)
  • evolution of solutions to very dynamic missile targeting problems
  • taking noisy signals from a big metal detector and using linear genetic programming to accurately identify signals related to buried unexploded 37mm and 75mm ordinance
  • evolving image compression filters that can retain the same image file size while increasing the amount of detail in the image

The keynote event was very interesting. Richard Dawkins, Lewis Wolpert, and Steve Jones, well-known in biology circles, answered questions about complexity in evolution. The fascinating discussion was punctuated by some hilarious anecdotes. For example, Wolpert described how he got into biology in the first place, and was once asked why he was so fascinated with evolutionary development. His answer: “My nose is too big, and some of my genitals are a bit small, and I want to understand this.” Steve Jones joked about how many sociological things, from acne to zoophilia (from A to Z), can be mistakenly explained using evolutionary language. For example, acne can be a way to make sexually maturing but financially bereft young males undesirable to females. And zoophilia can be a way for shepherds (and sheep) to gain a survival advantage, since “the sheep like it”, and will congregate with shepherds that will give them this extra love. Another Steve Jones quote: “I am a geneticist. And my job is to make sex boring.”

After the keynote, the attendees poured into the poster session held in an overly narrow hallway in the natural history museum. “Nibbles” of food were provided, which is an overstatement of how little food was actually provided: a few handfuls of nuts in small shared dishes. I had fun meeting people while explaining my poster; there were a lot of interesting people at GECCO. Many of the people I talked to about my poster had good ideas on different ways to apply the art-generation color-matching technique to other areas.

The crowded, narrow hall of the poster session. Photo credit: JJ.

There’s me in the blue shirt explaining my poster. It was kind of like being in grade school again, standing with a science fair project poster. Photo credit: Kumara Sastry.

Ah yes, turns out I’ve done this before… but it’s been 17 years! (photo is from my junior high school yearbook)

Fractals! I just can’t get away from computer graphics and fractals. This is a picture of an old math fair project from my junior high school yearbook.

Hmm, I’ve regressed to my childhood. This level of self-indulgence can only mean that the ending to this blog post is overdue!

Baby Jesus has returned…

…as a pork product?

See for yourself!

The money quote:

The Baby must dry several weeks before it is ready to be sold.

I’m off to buy some Baby Jesus and Lil Chub.

(thanks to Galen for the discovery.)

p.s., why is there a Buddha on the banner for

p.p.s., there is a band called Jesus Sausage. because you needed to know that.

Gluten-free time capsule

I have always suspected that there is something peculiar about the construction of the foul-tasting energy bars Kathryn is fond of buying:


Lasting for one thousand years is an admirable feat. But I don’t think that will improve the flavor.

(My guess is it’s supposed to mean “May 30, 2007″.)