Our research is based on the Neural Engineering Framework (NEF), created by Chris Eliasmith (my supervisor) and Charles Anderson. The principles of the NEF allow us to encode a signal using a group of neurons, do some transformation on it (say, double the signal) and then decode the result in another group of neurons.

So, maybe the signal is just a constant value of 0.4. We can encode that in a population of neurons, and then find a set of connection weights such that we can decode the value 0.8 in the next population of neurons.

Well wait, you may think. Are you saying that neurons in the brain represent numbers, and that the complexity of our behaviour is just some mathematical transformations of those numbers?

Yes and no.

Consider the physical world. Look at a metre stick. Obviously, you might tell me, a metre stick is 100 cm long. If you glued two metre-sticks together, end-to-end, you would end up with a piece of wood that's 200 cm long. You've doubled the length of that stick, and you can easily define that transformation: 100 to 200, you multiplied the first number by two. You doubled the length. Simple!

But why do you consider that metre stick to be 100 cm long? In another part of the world, it's 39.4 inches long. On another planet, that uses base 16 because they have 8 fingers per hand, it's 2C kerplorks long.

The way that we understand the length of the metre-stick is just a convenient way of understanding the world around us. We all (in the countries that use the metric system) agree on how long a centimetre is, so we can all agree that the metre-stick is 100 cm long.

But this is really just for convenience, because whether you say it's 100 cm or 39.4 inches, the transformation is the same -- you take the number and double it. Even if you use an entirely different system of math, that has no concept of doubling, there will be a way to take one number and get twice that number as a result. Or rather, there will be way of describing a length of material, and a method for describing a length of material that is twice the original length.

We think of doubling because it's the easiest way for us to understand it.

The same is true for the way that the NEF represents and transforms signals in a neural simulation. We have a group of neurons that fire at specific times. Those spikes induce current into another group of neurons, which spikes at specific times. We, to make it understandable, have defined a method to represent those firing patterns as numbers, and using that convenient way of looking at neurons, derived a method of finding connection weight matrices that will give us twice the value in the second group of neurons.

So, we have a profile of firing patterns for the first group that represents a number, and a way of eliciting a firing pattern for the second group that represents double that number.

Me, circa 2006. Yes, the doors in Japan are this tiny!
Note: normal Japanese doors not at all tiny in any way.

I spent a year in Tokyo, from September 2005 to August 2006, as part of Kokugakuin University's K-STEP program. A lot of fucked up things happened during that year, but if you were to ask me what was the most fucked up (which, amazingly, no one has asked) I would have to say it was the 8 day-long homestay that I did in Seto.

As tends to happen, memories fade over time, but I can assure you that these events happened. My translations are what I thought things meant at the time, but who knows how accurate they actually are.

The arrival

I arrived in Nagoya at around 4 a.m., having tried to save some money by taking the night bus.

I'm not entirely sure what prompted me to do the homestay, but part of it was to see a bit of Japan that was not Tokyo. Looking at the architectural excess that is the JR Towers did not give me the distinct impression that I was not in Tokyo any more.

But that meant Nagoya would probably also share another interesting feature of Tokyo: not far from this would be some old, forgotten buildings to serve as profound contrast.

Jackpot.

I always imagined that buildings like these housed old hermits that would refuse to sell their little plots of land. Incredible monuments to consumer excess -- like the JR Towers -- would rise around them, and they would look from their window and shake their heads. Real estate agents would visit constantly trying to get them to sell their choice plots, but they refused, and the entire community would avoid those roads with such an eyesore of a building, until eventually the old hermit would die and "progress" could commence.

I had another few hours until the trains started running to Seto, so I grabbed a beef bowl at the only place near the station that was open and not McDonald's. It was only me for a while, until a salaryman wearing the requisite all-black suit took a seat and bellowed an order that I did not at all understand. I wondered if he was on his way to work or just coming home from it.

I somehow made my way by train and foot to the Seto City International Center (featured also in a picture on Seto's Wikipedia page). I found the right office, and made small talk with the cute girl who was to introduce me to my host family. I was relieved that she spoke decent English, but reminded myself that the other part of this trip was to learn some goddamn Japanese. My host family, for better or worse, did not speak any English.

The first day

That hole in the paper curtain of the glass doors is approximately where my head would be when I slept.

The part of the homestay family that I got the most exposure to was the mother and one of the daughters, who was my age. It took the span of the car ride home to know that something was up: the mom worked most of the day, so it was going to be me and the daughter alone together for most of the eight days.

This wasn't necessarily unpleasant, as it meant I would get a ton of one-on-one conversation experience -- or at least, I would have, if either one of us were able to keep a conversation going for longer than two minutes.

We spent most of the first day in the car together -- me and the daughter -- running various errands. I really did try my best to keep a conversation going, but whether it be my weak Japanese or the fact that she was super boring, there was a lot of silence. I questioned what the fuck I was doing there, but that was not really that unusual for my year in Japan.

The dog

If there was a real relationship that I formed over the homestay, it was definitely with this adorable dog.

I've never had a dog, or any kind of animal that will do tricks on command, but I've always found it kind of awkward giving commands to dogs.

I say "Sit! Roll over!" and make some explanatory gesture with my hands.

They give me a funny look and wag their tails. Yet I'm the one that feels like an idiot.

That idiot-feeling multiplies by a bajillion when you're giving the commands in a language you're not fluent in. "Suwatte! Whatever-the-fuck-roll-over-is-in-Japanese!" *Awkward hand wave*

But that little dog actually did the things that I sort-of said. So we became friends.

The kid

It was probably the second day that the daughter realized that she was going to need some help wrangling me. Perhaps there was originally the thought that I would be a prospective mate for her and was judged unsuitable, or perhaps the homestay thing was all her mom's idea and she didn't really have any interest. In any case, she seemed to realize that she couldn't keep my entertained, so she brought in the big guns: this kid.

He was another daughter's son (I'll just call her daughter two (electric boogaloo) because I definitely don't remember any of their names). I'm not sure his actual age, but he was probably two or three -- able to speak, but not yet in school.

Now, I'm not really comfortable around kids. They're cute enough, but they don't really have a lot of music suggestions to share, and they don't think it's funny when I ironically call something "Kafka-esque."

Add in the fact that this kid knows Japanese better than I do, and you've got perhaps the most awkward exchanges ever known to humankind. People have claimed in the past that I'm awkward, and I stare them down, say "You don't know what awkward is" and then have a seizure as the memories of interacting with this kid come flooding back.

Most of those eight homestay days looked like this:

• Get up at around 9, try to stay in my room as long as possible.
• Inevitably get called for breakfast. Eat.
• Continue sitting at the table watching terrible Japanese chat shows while the kid jumps around and hits me with a little plastic samurai sword.
• Share desperate looks with the dog.
• Supper.
• Have an amazing bath (my god the baths were amazing).
• Shake myself to sleep.

There is an odd phenomenon that I've noticed in Japanese families: children are very rarely disciplined. The parents may be annoyed, embarrassed, and frequently depressed about their children's behaviour, but the smack isn't laid down. Instead, kids go on being rambunctious little bastards until the sixth grade, when entrance exams start, and they are told that they have to study all day and all night to get into a good junior high school, or else they won't get into a good high school, which means they won't get into a good college, which means they won't get a good job and they'll die penniless and alone.

After sixth grade, they behave. Or they're just depressed, whichever. The point is they stop bugging me.

The drinks

One of the highlights of each day was that supper would always involve the consumption of a beer or two; refreshing, of course, and conversation would be a bit freer as I imagined that my Japanese was better than it was, and the homestay family would find it hilarious.

One day we were joined for supper by the brother of the family. He was actually a really cool guy, a factory worker I think, or some other type of job involving manual labour. I had been watching the Baseball World Cup (which Japan actually ended up winning), because really what else was I going to watch, and we had what I thought was a decent conversation about it. I felt pretty good for probably the first time on the homestay.

We kept drinking even past supper, and he seemed to enjoy himself. Perhaps too much.

And then a few minutes later...

Awww

The movie

On one of the nights, we went to a video store with some of the daughter's friends to rent something to watch. I saw this, which made me giggle, but I realized that the humour would probably not translate to Japanese, so I didn't suggest it.

The title, "Basu otoko," translates to "Bus man," which I assume was an attempt to piggyback off the success of "Densha otoko," or "Train man," a very successful Japanese movie.

Instead, they picked up the Tim Burton / Johnny Depp version of Charlie and the Chocolate Factory. A fine choice.

Unfortunately, when we got back, we watched it in Japanese with no English subtitles. So much for my two hour reprieve from Moonspeak.

The misunderstandings

When you spend most of your day sitting around, watching television that you don't fully understand, and dodging toys wildly thrown from a surprisingly strong kid, you take pretty much any opportunity to do something to occupy your mind.

One day, the mom was heading to her mom's house (the grandma) and asked if me and the daughter wanted to come. I said "Sure."

She was a very nice old lady, but like a lot of the Japanese elderly, she was way too spry and active for her own good. As the three of us under-50s sat on the couch, the grandma was cooking us up a nice lunch and cleaning the kitchen simultaneously.

"Can I help?" I said. Or, that's what I thought I said. I think it probably came out more like "Am I able to help?" which is a weird thing to yell at someone as they're working in the kitchen.

"What?" she yelled back.

"Um... can I help?"

She walked into the living room. "What?" She turned her gaze from me to the mother, a move that anyone trying to get by in a foreign language knows is a huge diss.

"I think he's asking if he can help you," she translated from my broken Japanese.

"Oh. No, that's okay."

Another time, daughter two had come over to help watch the kid and do some chores around the house. When she was folding some laundry, we had the following exchange.

"Can I do something?" I said. Or, that's what I thought I said. Pronouns aren't really used in Japanese, so what daughter two thought I said was "Can you do something?"

"What do you mean?" she replied.

"You know, housework."

She brightened up, and with a huge smile replied "Oh yeah! I'm pretty good at cleaning up, though I'm not a really good cook."

"Oh, uh... I mean, can I help out by doing some housework?"

The smile left her face. "Oh. No, that's okay."

The family gathering

I'm not sure if this gathering was really in my honour or not, but on the second to last day, everyone in the family got together and had a huge meal. Everyone that I'd previously met, plus a few other random family members, crowded into the grandma's house.

One of the younger female cousins (who was pretty sassy) was playing a teach-yourself-English DS game. She was having some trouble with one part, so she asked me if I could do it.

Do it I could. Being a native English speaker with no significant hearing difficulties, writing the spoken English sentence in English was no problem. My captive audience of most of the people there seemed very impressed, and in a sick way, I was kind of happy to hear that praise. "Yeah, motherfuckers, when I'm not making a fool of myself in Japanese, I speak a language fluently! It's called English. Let me teach you of its ways."

Later on in the evening, probably about midway through dinner (and perhaps three or fours beers in) I had a bit of a moment with one of the uncles, the father of the cousin who I summarily crushed in the English-DS-game challenge.

"I should have taken you to the castle that's around here. You know, Oda Nobunaga occupied it for a time." He looked at his daughter. "You know why he's important?"

She shook her head. I said, "He was the first daimyo to use guns strategically in battle."

He smiled. "See, that's why I like you foreigners, you're keeping Japanese history alive. My stupid kids couldn't care less."

That translation makes him seem like kind of a dick, but he was an incredibly nice, warm guy and his kid clearly knew he was joking.

After the meal, everyone was loud and boisterous, and I was being bombarded with questions about what I thought about the meal, Japanese food in general, my time in Japan, what things are like back at home, and so on. I tried my best to answer, but even with my false alcohol-granted confidence, I couldn't come up with responses nearly as fast as questions were being asked.

It was at about this point that the following picture was taken.

The daughter is the girl in the top left, giving two peace signs. The uncle is to her right. The mom is to the left of me. The grandma is the farthest on the left. The cousin is the girl on the far right. I'm the white guy.

Now, I've been in a lot of pictures in my day, and a lot of those pictures are pretty fucked up. Look through the pictures that I'm tagged in on Facebook and you're probably going to ask yourself "What the fuck" at least once.

Well forget all that stuff, this is by far the most fucked up picture I've ever been in. In fact, this post was inspired by me stumbling upon this picture recently; I don't think I've ever actually shown it to anyone before, and I thought to myself "How can I ever explain how fucked up this picture is?"

The departure

I really wish I still had those shoes.

The eighth day was my last. I had booked the night bus again, so I had to be back in Nagoya by 10 p.m. or so. My homestay family didn't need to know that. I had them drive me to Nagoya once I got up.

It wasn't that they were unbearable to be around or anything, but when I compared another day as described in bullet points above with a day of walking around Nagoya, which I hadn't really explored much on the way out, I had to opt for Nagoya. Also, they were kind of unbearable to be around.

I locked my suitcase in a locker at the station, and walked around for a good eight hours, listening to music. Nagoya has an area analogous to the Akihabara district of Tokyo, which I checked out, but left unimpressed.

Texting and Youtube commenting (two of the lowest forms of communication) have made waves in the English language, though mostly in the form of embarrassing news articles and ironically poorly written blog posts.

I've noticed that it's also seeped into my writing; specifically, I find myself omitting the period in some sentences.

It's a special case. It must be a sentence that makes up the entirety of a piece of communication (be it a comment, email, tweet, or whatever). Having a normally period-ed sentence followed by one with no period is obviously dumb, but I find that when all I have to say is one sentence, sometimes the period just makes it feel too... serious? Finite?

A Wired article referencing a short article in the recently published volume of Current Biology makes the claim that "spontaneous brain rhythms" predict how heavy or light a sleeper you are.

Quick summary: if you take an EEG recording of a sleeping person, they will have little bursts of 11-15 hz oscillations called "sleep spindles" (pictured above). There is evidence that the number of sleep spindles positively correlates with learning potential -- that is, the more sleep spindles that are produced when you're sleeping, the higher your IQ. This new research adds that there is also a positive correlation between sleep spindle production and resistance to sleep disturbances -- that is, the more sleep spindles that are produced when you're sleeping, the harder you are to wake up.

It's an interesting article, and the research is sound, but there are some disconnects between the way I look at brains and how these researchers (and perhaps many biologists) do.

First, these studies are trying to decipher brain functions using EEG. EEG is a measurement of electrical activity on the scalp -- it gives you an idea of the average electrical activity of a large group of neurons (on the order of thousands or millions). This doesn't give us enough granularity to investigate function, just like looking at the NASDAQ doesn't tell you very much about a company's or a group of companies' financials. You can find thousands of phenomena that a particular pattern of EEG activity is correlated with, but no amount will tell you how the brain performs a certain function.

Second, the title of the original article calls sleep spindles "spontaneous brain activity". Perhaps this is just a case of different jargon, but in the way I see the brain, there is no such thing as spontaneous activity. There is some base firing rate for each neuron, but once you connect them together the activity of each neuron is just a function of the inputs it receives from other neurons. Even if we take the definition of spontaneous as something that happens without an identifiable stimulus, everyone is constantly being bombarded with stimuli, whether it be visual or tactile and so on. When you're asleep, you're responding to the accumulation of stimuli throughout the day, picking through which are important, replaying them, and consolidating those memories in cortex. Classifying brain activity as spontaneous or not spontaneous tells us absolutely no information, unless you think the brain is acausal or magic.

Even in interpreting the results, the investigators think differently than I. In the Wired article, one of the researchers writes, "During sleep, our neurons are busy doing very complicated processing, including, this study shows, generating sleep spindles to protect us from being awoken from noises in the environment."

Wouldn't an evolutionary biologist suggest the exact opposite? Evolutionarily, it's more advantageous to wake up when you are being attacked, or are otherwise in peril -- sleeping through it is a death sentence!

It should be noted that this notion is not present in the original article, perhaps because of the peer review process. Well, like Wired, bekolay.org goes through no peer review, so I'm going to make some claims of my own.

During sleep, our day's experiences -- temporarily held in the hippocampus -- get selectively replayed and consolidated into cortex. The better you are at this process, the better you are at efficiently forming memories. The better you are at forming memories, the more activity will occur during sleep -- producing more "sleep spindles," an artifact of the memory consolidation process. Since your brain is attending to memory consolidation, it takes a higher threshold of disturbance to disrupt sleep -- just like someone concentrating while conscious can ignore distractions (to a point).

The evolutionary significance of this suggests some kind of plateau to the overall intelligence of a group of animals living in a dangerous environment. The animals with the best memory will the last to wake up when the group is attacked.

I'm not sure if it's because I'm back in Winnipeg and consequently thinking about the past, but I've been reading some old things I wrote and one entry in particular caught my attention. I guess it's something that's been on my mind passively for a while, so it's interesting to read how I thought about the subject two years ago.

Originally posted as a Facebook note, edited for boooring:

It's been a few weeks since my last update -- I've been busy okay? But it's reading week so I have enough time to blatantly self-promote.

I got a gig writing guides for the How-To Geek. I'll be writing a fair bit about Linux, which I realize has already excluded many of you from caring, but I'll do Windows articles as well.

So far I've had four articles published, so please do visit them. They're great, I swear.

• How To Hide Kernel Updates in Ubuntu
• Getting Started with SMPlayer on Windows (to Play Movies Better)
• How To Fix Sound Issues in Ubuntu 9.10
• Fix Windows Update Errors by Letting ActiveX Traffic Through

Another project of mine has been putting up all of the old Manitoban articles I wrote; really, I'm fine with just linking to the Manitoban website, but the articles from the 2008-2009 publishing year aren't online, so I must preserve them, lest someone wish to read "The 'meatatarian' saga: douche vs. bully" and not be able to.

They're going up gradually; you can see them as they're uploaded here.

Finally, another tasty morsel that I added to this here website recently is the transcript of an interview I did with a master's of social work student for her thesis on student exchange experiences. Basically, it was an excuse for me to wax nostalgic about my year in Tokyo, and I think I produced some decent sound bites. The full transcript is here, but I'll end this post with a few choice passages.

In a previous post I voiced my concern that scientific researchers do not have to provide the source code that produces their results. Now, Darrel Ince, Professor of Computing at The Open University, has written an article for the Guardian also calling for scientists to release their source code. Slashdot covered the story this morning.

Ince argues this as part of the fallout of "climategate," the incident in which it was shown that climate researchers had been fudging scientific data to produce desired results. It is a compelling example, but Ince goes on to say that "the situation is by no means bad across academia." He cites the example of the four colour theorem from graph theory, which was proved partly by a computer program. The program was published and highly scrutinized, and eventually found to be correct.

However, not all results are that nice in mathematics and computer science. In his PhD thesis, Terry Stewart notes one result that, to this day, has not been recreated.

SHRDLU

SHRDLU was a natural language understanding system developed from 1968-1970 by Terry Winograd at MIT. This 40-year old system produces some very interesting interaction, and was one of the first great results in artificial intelligence research. The following are two snippets from a demo found at Winograd's website:

That is crazy impressive. The question is: why haven't we seen systems like it in common use today? A page maintained by Semaphore Corp. that provides source code for an implementation of SHRDLU gives some insight:

40 years of natural language research and infinitely more powerful computers are still not able to reproduce SHRDLU's 1970 results. How is this possible?

One of Winograd's students, Dave McDonald, notes, "In the rush to get [SHRDLU] ready for his thesis defense [Winograd] made some direct patches to the Lisp assembly code and never back propagated them to his Lisp source... We kept around the very program image that [Winograd] constructed and used it whenever we could."

Back in those days, most computers ran different operating systems, so as changes were made to the operating system of the computer Winograd and his students were using, the program became less robust (a phenomenon known as software rot).

So, even though the source code exists in some form, the original results he produced cannot be replicated because they don't include Winograd's direct patches, and because the platform that the code was created for longer exists.

The lesson

What should be taken from this example is that mathematics and computer science do still suffer the same problem of irreproducible results. Ever-changing platforms are less of a problem now -- a Matlab program produced on one computer should run the same on any other computer -- but source code is rarely shared as part of the publication process.

I think it should be. But for that to happen we need a central repository to store code and meaningfully link it to the papers that use it.

This repository should have the same amount of peer review and, therefore, authority that scientific journals have now. Maybe that can happen by existing journals adding the ability to link code to a paper (and enforce that any code used to generate results is included), or maybe a new organization has to rise up to the challenge (I would love to see code.arxiv.org).

Slashdot just posted a BBC story about a new chemical computing project that, in some ways, mimic neurons.

The article is a bit light on details -- understandably -- but essentially their approach is to build networks of connected chemical computing cells.

The cell bodies are a mixture of liquids that undergo Belousov-Zhabotinsky chemical reactions when the concentration of bromine in the cell reaches some threshold value.

The outside of the cells is a material that the article calls a "lipid." When one layer of this lipid material comes into contact with another layer, a protein forms a passage that can transport signaling molecules between them.

I don't know much about chemical computers, but a cursory look at Wikipedia tells me that the BZ-reaction is a common element of chemical computers; the new contribution appears to be this lipid material. And it does appear to be a very interesting contribution.

While it's not explicitly stated, the tone of the BBC article is pretty clearly "hey look, we might be able to make or simulate human brains." I completely understand this urge; certainly, it's the reason it got picked up by Slashdot, and will likely find its way to other big websites. Unfortunately, it's just not true.

The BBC article touches on some of the similarities between this project's chemical computer and the human brain:

• It's made up of a network of cells.
• It shares information through chemical signals sent from one cell to another.
• The cell body processes input, and after producing an output, has a "refractory period" -- some short period of time in which input is not processed.

These similarities are minor in comparison to the sweeping differences:

• The connections between neurons are one-way: a neuron receives a number of inputs (on average about 10,000), and produces one output (though that output may be connect to many other neurons). The article does not mention whether the chemical computer's connection are one way, but it seems unlikely, for a number of reasons that I won't get into.
• A neuron communicates with other neurons by sending an action potential (a short burst of electricity), also called a "spike" due to its appearance on a graph of neuron voltage.
  
  After spiking, the neuron goes into a rest period during which it will not respond to input, called the refractory period.
  The BZ-reaction does not appear to exhibit a similar voltage graph, even though, according to the article, it does exhibit a refractory period in which input is ignored.
  
  It is possible that the particular reaction used by these researchers is more neuron-like, though I am not aware of such a chemical reaction.
• Chemical computing (as described by Wikipedia, anyway) aims to use chemicals to perform computations as we know them in computers; so, we're talking about bits and logic gates (specifically NAND gates in chemical computers). Brains, as far as we can tell, do not compute things in this way. The notion of the "bit" (binary digit, essentially a one or zero) does not even make sense in the brain, as it is a noisy system.

Of course, these differences in no way mean that the chemical computing project is not interesting and exciting. This lipid material that is able to make spontaneous connections between simple computing devices is fascinating, and while I am, again, not well versed in how chemical computers work, a huge network of these cells (perhaps 100 billion -- the number of neurons in human cerebral cortex) might have incredibly computing power.

And indeed, the quotes from one of the researchers, Klaus-Peter Zauner, tell me that it is not the goal of the project to make a human brain or human brain analogue.

The article has to go to a different chemical computing researcher, Frantisek Stepanek, to get the juicy brain quote.

And even then he only talks about "computers of similar power and complexity."

The thing that bugs me about this article is that it's not about imparting information, it's about trying to fulfill a science fiction fantasy.

The idea that this chemical computer would bring us closer to being able to make or simulate brains is a natural thing to think, but rather than futilely trying to show that it may be possible, the article should use the idea as a platform to entice the reader and then tell them something interesting about chemical computers and about how the brain works.