bekolay.org

Bromine, which plays a role in a new project's chemical computer.

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.

Information lies not only in how this new chemical computer is like a brain, it is also in how it is not like a brain. In neglecting this piece of the puzzle, this article does a disservice to the reader and to the public's scientific consciousness.

Giving money advice is tricky business. Everyone's financial situation is different, so in general, there is no universally good advice. This post does not aim to give any advice. I aim only to look deeper into an issue I encountered recently.

The question I was faced with was, essentially, should I open an RRSP if I'm saving for a house?

I am in a fairly stable financial situation; I have no debts, and while my income is not worth bragging about on the internet, I have enough that I can put a chunk away into savings. A book that I half-read at one point espoused the idea that putting 10% of your income in savings is basically all you need to do to solve most of your financial problems.

While I'm not one to say if this is a good or a bad idea, I've always been annoyed by how that simple advice quickly becomes more complex once you realize that "saving" is not a passive process: saving is something you have to do. The amount of effort ranges from opening up a savings account to spending most of your day watching the stock ticker (and your life) roll by.

I've always heard the advice that you should start an RRSP as soon as you can, so when I went to open up a savings account it seemed natural to also open up an RRSP. The person at PC Financial asked me a question that I had honestly never really thought about.

She said that opening the RRSP would be a good idea as, later on, I could use the money in the RRSP as a down payment through the Federal Home Buyers' Plan. Well, she didn't really say that, she said something like that, and then later I googled it (see a verbose explanation or a bureaucratic one).

When I talked to grandfather (a certified accountant who has always graciously done my taxes) about it, he noted that I don't pay enough taxes to make an RRSP worthwhile, and that it would be more beneficial to me to keep my savings more liquid.

Some websites also say that, even if I did open an RRSP, I shouldn't use the Home Buyers' Plan.

So should I open an RRSP? I did, but I haven't contributed to it. And I don't plan to for the time being. Most of my money is in a savings account, so as long as it's making some amount of interest, that's good enough for me.

If there's one thing I've learned in the little time I've taken to research the subject and write up this entry, it's that there are so many programs and rules and stipulations that there is no such thing as an objectively optimal financial decision. In that sort of environment, I'm much happier spending my free time reading webcomics and playing dumb (but brilliant) games. That's what I'd suggest you to do as well.

Unless you're in debt.

School's back in session, I'm afraid, and all reports indicate that it will be a busy semester. That's fine; after this semester I will be done the classes I need for my masters and can just focus on research and writing, and I'm liking my classes at the moment (in both content and schedule).

Last semester, in my statistics class, we kept a collaborative set of notes that everyone contributed to, and it was an interesting experience. Consolidating my notes online has always been one of the goals of bekolay.org, though the original plan was to have them in of the protected areas of the site, not accessible to the public.

But, then I figured what the hell. I doubt they will be of any use to anyone not in these courses, or really to those in the courses, but you can find my notes here.

Update: In case anyone was worried, my notes won't show up on my RSS feed, as that would be super annoying.

In what is a more traditional (read: uninteresting) blog post, today I will let you know what I've been up to, then rant.

Cracked.com's Michael Swaim. He's pretty funny, I guess.

With a project deadline quickly approaching, I've been more productive than ever. Soon, I will even start working on my project.

If you've watched The Hangover, there's about an 80% chance that you liked it. I really didn't, so I spent entirely too long making fun of it over on Cracked.com.

Pictured: The Computational Neuroscience Research Group.
Not pictured: Any girls, cripes.

Back when I was a journalist, I would spend far too much time researching each article, only to hurriedly write up what I'd learned minutes before (or perhaps after) my deadline. As a researcher, I find that as I wait for my experiments to finish running, I feel the need to write (and Photoshop (see above)).

A lot of researchers find publishing to be a hassle -- an unwelcome interruption of their research. Personally, I think it's more of a perfection thing: they want to publish the best results ever, and become god-like in their field. I can definitely understand that, and perhaps I will feel the same when the time comes to submit abstracts to academic journals, but in my opinion there is still merit (academic merit even) in writing as much as you can.

I remember reading a quote at some point that the further you go in academics, the more important it is to be a good communicator, both in print and in presentations.

Then today I read a this fantastic article about Grigory Perelman, the man who proved the Poincaré conjecture. It is a super badass story, worth a read if you have time.

One of the things that struck me about the article is that he really could give a shit about communicating -- in fact, he has not communicated with anyone other than his mother in quite some time. A geometer (dude that is all about geometry), when talking about Perelman, says, "the ideal scientist does science and cares about nothing else. He wants to live this ideal."

For better or worse, I can't be that kind of scientist.

One thing I definitely agree with him about is academic honesty issues. Perelman has now essentially quit mathematics, saying, "It is not people who break ethical standards who are regarded as aliens. It is people like me who are isolated."

I obviously don't have the experience that Perelman has, but something that has been bugging me lately is how so few of the papers that I'm reading publish their source code.

I do recognize that one more clearly understands a problem if they are forced to implement the solution themselves, but this is hardly a justification for the majority of code written in academia to be kept secret within each lab.

I think that publishing source code should be the norm, especially in mathematics and computer science. It should be seen as suspect when source code is not provided. And that source code should be made available to other researchers to build on. Software packages like ACT-R and OpenCV have become standard in their field not because they are the best, but because they are the best available.

Whatever scares people away from publishing source code, these projects -- as well as decades of open source software development -- should be strong evidence that sharing is good.

When I talked about this with a post-doc in my lab, Terry Stewart, he shared my concerns and even recounted a number of studies that have tried and failed to replicate the results of published results in a number of fields. Further details can be found in his PhD thesis (skip to chapter 5).

He showed me a website he helped create, which aimed to be a central repository for computational models associated with scientific papers. Unfortunately, it is nearly barren of content, the last contribution being from over a year ago.

The idea is sound, but I really think that the key to having a system like this work is to get the cooperation of big journals; if it becomes standard practice to submit your source code when submitting to ACM or IEEE, then smaller journals are sure to follow (especially if the software to link articles with code is well developed).

Unfortunately, due to the inherent fuddy-duddiness of old, well established journals, I am not confident that this will happen. Perhaps someone needs to start a site like arXiv.org and start a revolution that way. I think with a lot of young researchers raised on open source software just starting to start making academic contributions, it could work.

Perelman, by the way, published his Poincaré proof on arXiv.org, meaning it was immediately available to everyone for free.

Since I'm on an academic rant, I figure now's as good a time as any to show this video produced by the lab I'm a part of. It was just shown at NIPS, and demos a few simulations in our neural modelling software nengo. To really understand what it's doing would take some time to explain (I don't quite understand it all myself yet) but it's still worth giving up five minutes to check out. Plus you get to see where I work.

Rest assured, as I find out more about what nengo's doing, I'll post details (time permitting).

Oh, also, I found a super kickass fixed-width font today called Inconsolata. It's free, so do yourself a favour and start using it today for all your fixed-width needs!

Sometimes you come across things on the internet that are pretty badass. Usually, you are the millionth person to discover it, and no matter how great it is, the experience is tainted by the shadows of laughter passed -- the knowledge that you are playing catch-up and not breaking new ground.

Not today, my friends.

I want to introduce you to Kintaro (Kris to foreigners with terrible pronunciation).

Kintaro on the right, someone about to get punk'd on the left.

You know, I'm screwing this up. I'll just let him introduce himself.

Yeah, Kintaro has some pretty hilarious Engrish, but underneath that, it is clear that he is a genuinely hilarious person. Let's see how he spends his typical days:

I always hoped -- dreamed -- that all of the salarymen on the trains in Japan, despite the matching suits, similar behaviour, and samey sameness, all had interesting and unique worlds in their heads. Really, I like to think that about most people, but I'm generally disappointed. Kintaro has shown me that there is at least one salaryman out there that still has a soul.

I'll close with my favourite of his blog posts, about Basu Otoko / Napoleon Dynamite, which I mentioned in my homestay post. Make sure to check out more of his hilarity on his Myspace page.