Photo: So we got a Chalkboard

I think the weather this summer has inspired Mélanie…

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Photos: Kayaking

What I’ve Been Up to Lately

Moving to Ottawa
In a little less than a month, Mélanie and I will be moving to Ottawa. We’ve found a small but comfortable apartment, and it will be our first time actually living together.

While doing research to prepare for the move, I found many cool things that I think will help make our lives better. They are:

• Dumping the phone company and going 100% voice-over-IP. I find Bell Canada’s prices for plain old voice phone outrageous in the Internet era, and felt it wouldn’t be right to support them out of inertia. The company I signed up with is Babytel.
• Switching to a new ISP (TekSavvy) that can do dry-loop DSL, so that I can connect to the internet from a phone line that isn’t active for voice calls. This ISP doesn’t throttle traffic (unlike most big ISPs in Canada) and offers premium routing for better pings.
• We bought a Mac Mini so we can use it as a media center (music, photos, films, TV series, etc). Plex is a free and open source app that allows you to do that and use a remote. This should replace a bunch of other electronics while also allowing me to do more scientific distributed computing.
• I read up on the best air-filtering plants; NASA had a study on this, and one of the authors of that study wrote a book that I’ll borrow from the library as soon as we move. I like having some plants around, and figure I might as we get those that will have the biggest impact on air quality.
• Mélanie has asthma and some allergies, so I did a bit of research on ways to help her breathe easier. Found some air vent filters that look like they could help some.
• The apartment is small, and I tend to go to bed later than Mélanie… So at first I looked into air purifiers, figuring the noise they make could help her sleep better and we’d have better air quality, but my research mostly told me that these devices didn’t do a very good job. So instead I looked into white noise machines. This one sounds good (literally). I figure that if it gives us both better sleep, it’s worth the money.
• I also want to get headphones in case one of us wants to read, and the other wants to listen to music or something like that. Not sure which model to get yet, but I’ve heard good things about Sennheisers.

Follow Up on “What You Can Measure…”
I recently wrote about some challenges I gave myself. I’m happy to say that it’s working well, possibly better than I expected.

On the fruits & vegetables side, I’ve kept to the “5 extra portions a day, what goes in regular meals doesn’t count” rule and since then (about 5 weeks ago) I’ve eaten 198 portions of fruits and vegetables (lots of carrots, bananas, apples, bell peppers, oranges) that I wouldn’t have eaten otherwise. That’s a big win for me, and I intend to keep doing it for as long as possible.

My other challenge was to read at least 4 pages a day from a molecular biology textbook (on top of the other things I read — yesterday I finished reading a biography of J. Robert Oppenheimer, for example). The reason was that while I loved reading it, it was more arduous than the other books I was reading, the textbook is big and heavy… I was always finding excuses to avoid it and wasn’t making good progress. At the rate I was reading it, it would have taken me years to go from cover to cover.

Well, in the past ±5 weeks I’ve read about 155 pages, and I’ve only missed two days (completely forgot about it). This means my real average is higher than 4 pages a day, and I should hit the back cover in about 6-7 months. I consider this another win, and plan to keep doing this – or something similar – with technical books (and maybe also with online video lectures). The goal is to avoid the “hay fire” trap, where I start with really high motivation and burn out quickly and kind of forget about the book (even if when I do actually pick it up I find it fascinating).

Trip to Cancun
In February, Mélanie and I went to Cancun, Mexico, to visit her grand-parents for a one-week vacation. It was my first time south of New York City, and I enjoyed it quite a lot. The first photo in this post was taken on the beach there, and the second one shows what I spent a lot of time doing (in this case, reading a compilation of letters by Richard P. Feynman).

What I’ve Learned from My First Big Trade Show

Everybody in this photo is a journalist.

I just finished covering the Detroit Auto Show as a journalist for Discovery. Here are a few things that I learned:

Care for a foot rub?

1) What works in a 5 seconds TV clip doesn’t always work as well in person. The pretty girls standing next to exotic supercars (Ferraris, Lamborghinis) that you usually only see briefly, well, they look a bit more awkward when you see them standing there all day. I almost felt like going up there and asking: “You want me to bring you a chair?”

2) Old experienced journalists, especially those with white hair and pirate mustaches, are experts at cutting in front of you during a one-on-one, and they’ll ask 3-4 questions and then say: “One more question”.

And then they’ll ask 10 more. As soon as the interviewee is done answering, they say something like “Now…” or “Ok, but…” and then take a few seconds to think of a follow up question. These words are just placeholders so that nobody cuts in.

Elon Musk.

3) Even if you meet the people you really want to meet, you might not actually be able to have a conversation with them. I was looking forward to meeting Elon Musk of SpaceX, Tesla Motors, SolarCity, etc.

I actually got to talk to him a bit, but it was only while photographers were asking him to pose in front of various things (the electric Roadster, the car frame and powertrain, etc).

He was laughing at the situation a bit, and I said: “Maybe you should’ve brought a piece of Falcon 9.” He said: “Yeah, but it wouldn’t fit in here. It’s 180 feet tall,” and I said: “I hear it’s all assembled now,” and he said that it was, and something about testing next summer, but then the press conference had to start rolling.

Compared to most other CEOs who gave speeches at press conferences, Elon wasn’t very smooth, but I’m kind of glad he’s not some smooth-talking manager-type. He rose to the top because of his brains, not his silver tongue. Not that you can’t have both, but if I had to choose…

After the announcements were done, he was surrounded by a horde of TV cameras and I never could get close to him again.

All photos by Michael Graham Richard.

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Photos: Making Cookies

Melanie wants to give some homemade cookies to her friends for xmas. Here are the results of our teamwork (pajamas and all).

Photos: A Bunch of Ducks & A Lady Squirrel

Went to see some ducks today and took the new camera along (Nikon D60 with 18-200mm Nikkor lens). Don’t miss the exhibitionist squirrel at the end.

Photo: Chili Overload

Here’s another fascinating update about my Chili plant. I first wrote about it last Autumn, then gave you an update about my hand-pollinated winter Chili crop.

I thought that 7 peppers at once was a pretty good harvest. Boy, was I wrong. Above is a photo I just took of the very same plant. It now lives in my parents’ garden and it looks like it’s about to collapse from the sheer weight of all those chili peppers. Incredible.

Fold It: The Protein Folding Game

Fold It is a game developed by the Rosetta@Home team (learn more about distributed computing) under the direction of Dr. David Baker at the University of Washington.

It features a new approach to protein prediction. Instead of using a more or less brute-force approach, with a CPU trying lots and lots of possibilities and calculating which ones give the best results, the game uses the human brain’s pattern recognition abilities (with help from a few automated tools) to try to find the lowest-energy folded state of a protein.

It has the potential to be on the cutting edge of a new generation of scientific games that are fun to play, teach you things, and can actually help researchers.

Words are inadequate to describe it, so please watch the two videos below to get an idea.

Is There a DNA Puzzle in Alberts’ Molecular Biology of the Cell?

Last November, I bought Molecular Biology of the Cell by Alberts (5th edition). I’m a few chapters in, and so far it’s an excellent textbook, I recommend it.

But there’s something that has been intriguing me for months: Once every few pages, seemingly at random, there are groups of 4 red letters inside pointy brackets. At first, I thought it was probably formatting meta-data, some kind of printing accident. But the second time the red letter popped up in a weird place, I noticed that the letters were all DNA letters (T,A,G,C).

Could this be a puzzle? Is this some kind of clever biological joke by the authors?

If it is, what do these code for? Some well-known protein?

It’s a mystery so far.

Update: Unless this is a well-known joke among biologists (it’s a common textbook, after all) and someone tells me about it in the comments or via email, I’ll probably compile a sequence of nucleotide letters long enough for it to be unique and then Google it. I had my “duh” moment and realized there’s no need to go through the whole 1000-page book and compile all of red letters…

Big Cruncher

I love distributed computing. It’s a great way to help science even if you don’t work in a lab or don’t have lots of money to donate.

The only project I’m crunching for right now is Rosetta@home (I’m waiting for Orbit@home).

I’m excited about it because computational protein/enzyme/RNA design has the potential to move biotech forward a great deal and cure many terrible diseases, help with bioremediation and clean fuel production, and increase our understanding of biology in general.

So I was surprised when I looked at Rosetta@home’s Top Computers list and saw that my new Mac Pro ranks #4. That probably won’t last forever since the project has almost 200,000 users and is still growing at a good pace, so I took a screenshot for posterity (above).

Technology Review recently published a piece about Dr. Baker’s work (the head of Rosetta@home and of the Baker Lab at Washington University) and what they call “a major step forward for computational protein design”. Check it out, and if you aren’t already crunching, I strongly encourage you to join a project.

Idle CPUs are sad little unproductive things, wasting their potential. Give yours something interesting to work on.

Made me Smile

From the preface of Roger Penrose’s The Road to Reality: A Complete Guide to the Laws of the Universe:

Considering the current state of my math skills, I expect to look like the third drawing most of the time.

Photo: Winter Chili

Last November, I posted some pictures of chili peppers I was growing. Here’s a whole new batch: I pollinated the flowers by hand and 7 of them turned into peppers. Some are still green, so they’re harder to see.

Ode to my CPU

This is a picture of the CPU that has been in my desktop computer for the past 4 years. It is an AMD Athlon 64 3000+. One “Windsor” 90nm core running at 1.8 GHz, fitting on socket 939 with dual channel memory.

There’s no problem with it. It’s still working, and has always been dependable, running cooly even when I pushed it to 100% usage with distributed computing projects. But I’ve replaced it with an Athlon 64 X2 3600+ (2 cores running at 2 GHz). These are so cheap now, and I figured it would be a good way to do more data crunching inexpensively. I know that my computer will keep being used for a few years – if not by me, but my parents or someone else – so more than doubling the amount of scientific work it can do makes a difference.

I don’t get sentimental about objects. I don’t collect stuff. But holding that CPU in my hand made me realize how fantastic our technology is, and how many great things it allows us to do. Had I been born in a non-networked world without inexpensive computers, there is so much things I wouldn’t know, so many people I never would have connected with, so many books unread, so much music unheard. I wouldn’t have the job I have now, and you wouldn’t be reading this.

I certainly wouldn’t be the same person…

So this is my homage to my CPU.

In the Mail: A.I. & Neuroscience Books

Beyond AI: Creating the Conscience of the Machine, by J. Storrs Halls.

Synaptic Self: How Our Brains Become Who We Are, by Joseph LeDoux

The Emotion Machine: Commonsense Thinking, Artificial Intelligence, and the Future of the Human Mind, by Marvin Minsky

Photos: Trip to New York City

I went to NYC for business between December 11th and 14th. Here are some photos. More on my Flickr account here.

Me looking out the window.

Here’s what I was looking at. They were removing snow from the plane.

Now it’s our turn. First orange stuff…

…then green stuff.

Mark Bittman’s Pasta Sauce

After watching this video of New York Times food columnist Mark Bittman, I decided to try his pasta sauce myself. The video isn’t really about the sauce, rather it’s about the concept of changing the pasta/sauce ratio, something that I think makes lots of sense. But the sauce looked really good and easy to do…

Here are the results (high resolution pics here):

It was delicious!

In the Mail: Macbook

For someone that spends his days and many of his evenings on a computer, I’ve had relatively few computers. I tend to keep my PCs for a very long time, all the while obsessing about potential upgrades (and never actually pulling the trigger — there’s always something better coming soon).

Well, I finally did it. I’ve wanted a Mac for 4-5 years, and now it’s here:

In the Mail: Molecular Biology of the Cell

By Alberts & al. 5th edition. According to Amazon, it’s supposed to come out on December 31st, but here it is in all its glory:

Related:

• In the Mail: Lehninger Principles of Biochemistry
• Teaching Myself Molecular Biology