Amino Acid properties

Because everyone is dying for one of these figures.
From Livingstone, C. D. and Barton, G. J. (1993),
"Protein Sequence Alignments: A Strategy for the Hierarchical Analysis of Residue Conservation", Comp. Appl. Bio. Sci., 9, 745-756.

Diamonds

Ahhh, here's that article I read a while ago about how the value of diamonds has been established.

Will they one day sell for $10 a carat?

The rats

My baby boy rats (Stanford and Harvey) got adopted and renamed Rudolph and Santa, which I must say aren't my favorite names.

My friends comment:

I thought the new names for your ex-rats were less elitist. You know, more like Joe the Rat than some Ivy League rat who pals around with left wing terrorist rats.

Joe the rat. Gotta remember that.

Book: Ahead of the Curve

My most recent book was by Philip Broughton about his two years in Harvard Business School. I was hoping I could learn about business like I usually do when I pick up a popular science book, but this book was more of a biography. However, it was a pretty compelling read so I finished it rather quickly.

One thing I found very interesting as I was reading it was that it was published just before the big market crash. The author talks about visits to the school by well-performing financial companies like AIG, Lehman Brothers and the Carlyle Group.

And one of my favorite quotes from the end:

The job statistics for our class showed that 42 percent went into financial services.. Ray Soifer, a graduate of the class of 1965 and a banking analyst, had been keeping track of the relationship between the condition of the American equity market and the percentage of Harvard MBA graduates choosing careers in financial services. Ten percent or less was a long-term buy signal. Thirty percent or more was a long-term sell. The choices of the class of 2006 told you the markets were soon to crash.

Anyway, the book was very interesting, especially as the author wrestled rather candidly about the choices between work and family and the impossible desire of having it all.

No bell? Seriously?

So this morning I was pulled over by the police. At 9:30am. In Kerrisdale (the retirement area). My crime, I was riding a bicycle and they were doing a community safety check. So I had to have a helmet (check), bike in working condition (check), white front light and red back light (check, even at 9:30am - but were they working? (check - we tested)). Problem - no bell. I was warned it was a $109 fine.

We looked up bicycles in the rule book, and found lights, helmet, how to ride on the road (both hands on the handlebars, seat in the saddle and no passenger (check)). Nothing about a bell. Well, ok then he said it was in the motor vehicles act. At this point I think both of us were tired of the exercise.

I didn't have to pay the fine but since they were randomly pulling over bicycles I was warned I could be stopped again. Since I was pulled over near the community policing centre and I cycle by it every weekend I just went out and bought a bell.

Since I'm now a completely legal vehicle on the road does this mean cars won't honk and gesture angrily at me for not being on the sidewalk (which BTW is illegal - we checked).

Great Intro

I thought the opening credits to Dexter was pretty good, but BoingBoing was right, the intro to True Blood is pretty fantastic. Be warned, NSFW.

Interesting, there's a whole webpage devoted to the art of the title.

Don't complain

Another reason I prefer to check out open source solutions first - EULA's. Those click through agreements full of legalese that you never get around to reading.

Stupid thesis

Sent to me by e-mail, if someone gives me the correct citations I can credit. I included as much of the credit as I could identify in the e-mail.

Lyrics to Little Mermaid, Part of your World
written by Ben Fortiscue (sp?)

Look at this work
Isn't it neat?
Wouldn't you think that my chapter's complete?
Wouldn't you think I was done?
I'd written up … everything?

Look at this draft
Isn't it slick?
Bound, single-sided and three inches thick
Wouldn't you think it would show
I know almost … everything?

For my tables and graphs are so pretty
I've got figures and footnotes galore
But I show it all to my committee
And they sigh
And they say
They want more

They want to see a new contour chart
They say I need more complete citations
Scanning the text for each typo, misstatement or goof

Seeking perfection in every part
Picking out flaws in my neat equations
Claiming right now they don't constitute - what's the word? - proof.

Chapters cut out
Chapters restored
What must I do for you to award
The PhD
I need to be
Part of your world?

A desk and a chair
I don't have to share
Quiet and cozy
My name on the door
A carpeted floor
Just like my peers

Who've spent the years
With real careers
Not stuck with massive bills on ROSI
Much more prudent
Than the student
Who perseveres

And fills up their brain with minutiae
Nonetheless needed to pass defences
What is a plasmon and why should I - what's the word - care?
Fight off despair
Save Chapter 3
Someday I'll print it, defend it and be
An overjoyed
And unemployed
Part of the world.

For my Australian friends

First China, then Saudi Arabia and now coming to Australia.... the great firewall!
As reported in Canada on the CBC radio show Search Engine , a podcast about Australia's new network filtering.

You can download it as an mp3 and take it with you, or listen to flash streamed content.

And another note, it took me a while to check it out but man I do love podcasts, I really recommend:
The Planet Money Podcast

Rat Boys

So the boy rats are named Stanford and Harvey. Here they are in their castle:



Here's Stanford


And here's Harvey. The boys like to crawl into my sweater and sit in my sleeve while I am writing.


These guys are very cute and friendly. When I come home from the lab they get all excited and wait at the door for me to come and see them.

Yeah

My discussions about large... endowments has paid off. Gender Analyzer has determined I am male!

Rat names

From Chris, my new baby male rats shall be named Stanford and Harvard, because they have very large... endowments.

open open open

When I got my first digital camera about 10 years ago, it came with some pretty neat photo organizing programs. So I spent some time tagging and moving things around and it worked nicely. But where is all that hard work now? Well, time went on, I upgraded the camera, the software was no longer supported and I wasn't interested in spending all my time re-doing my work. I could see where this was going - all my effort was locking me into a camera and software and when the times changed, I would forced to pay more, or depend on the goodwill of the company to continue to support me.

My data, and specifically my data formats were holding me hostage. I see this happening with Microsoft Office. Right now Microsoft is the leader, everyone uses their proprietary formats and if some organization somewhere tries to break the mold, i.e. use an office suite that wasn't Microsoft office, they would be left out of the loop.

There are international efforts going on right now to create an open standard. You shouldn't have to be locked into using Microsoft Office. For example, I'm collaborating with my supervisor for writing papers and I run Open Office on my home computer because it's linux and on my laptop because it was small and free (smaller than Office2007 anyway). However, I am locked into writing in Microsoft Office because my supervisor uses it, and he is locked in because his collaborators use it. And everyone has to continue to purchase Microsoft Office because they really can't use anything else. So you can understand that Microsoft has no interest in participating or supporting international standards.

From a Slashdot post:

Duh. The reason they [Microsoft] want to control the standard is so they can force it to change, again and again.

The reason MS doesn't like open standards is not because they're crazy or evil (which actually they might be, but that's not the reason, here) but because file formats are the key to upgrades.

When you can change a file format so that older versions are incompatible, you can create a situation where 100 million people with word 2009 start getting new files from 1 million people with word 2010. The 100 million people cannot read them. They complain, they gripe, then THEY UPGRADE.

A file format which stays the same breaks this model, and that would reduce MS revenue by a colossal amount. They can't allow that. So they need to control ODF [Open Document Format]so that they can keep changing it.

Of course, Microsoft also doesn't want ODF because then why pay money for Microsoft Office when something like Open Office works fine.

What I find frustrating is that at this point, Universities and Government organizations are spending tons of money to buy Microsoft licenses for Office. Why aren't they considering alternatives? Because we've all locked ourselves into one companies solution.

This doesn't just end at Office products, the same question can be asked for home photo organization. Or home music collections, movie collections, audiobooks etc etc. Put in all the effort to organize it well, label it nicely and hope you can alway use the same program?

The same goes for learning software, especially big programs like Gimp or Blender. Gimp's commercial alternative is Photoshop, and unless you are a design house there's really no need to pay the ~$1000 license to use the software. Gimp probably does everything you want and for free. I initially learned how to use Photoshop (uhhh... a legal copy from a long time ago) and then had to put in the effort to relearn Gimp. I'll not make that mistake twice - for me its been Inkscape instead of Illustrator, Blender instead of Maya. Sure, our department has a site license for Illustrator, but will my next job? Why put in all the effort to learn Adobe products just to lock myself in to their upgrade cycle?

Being tied to their next upgrade cycle means being tied to whatever DRM they choose to implement to protect their IP. Will the next version of Photoshop need a dongle to run? Will you need to keep the CD-ROM in the drive? Does it need an internet connection and must call the Adobe servers every three days or it shuts itself down? (better hope your firewall and antivirus software permits the connection or you know how to fix it). What else is that program doing? Is Photoshop also scanning your computer to make sure the other Adobe products you have are legal? And if not does it call home to report it?

There's tons of great stuff out there that's free and open. The worst case scenario is that the software goes unsupported and if you are completely desperate, you can pay someone to look at the open file format and get your information out.
So check out (a very short list):

• Open Office
  
• Firefox
  
• Gimp
  
• Inkscape
  
• Blender, (Elephant's Dream, Big Buck Bunny, Yo Frankie)
  
• Audacity
  
• Ardour
  
• Songbird
  
• VLC
  
• RockBox
  
• TightVNC
  
• TrueCrypt
  

As media becomes even more integrated, what standards you have will become all the more important. Like those suckers who bought DRM'd music and then the authentication servers were going to be shut down.

If you want to find out more, google stuff like: Sourceforge, good open source free software.

Support for these programs is online in forums. If you have troubles you can usually search and find the answers. Even if you don't know the lingo - recently my search "how do I make boxes disappear when scrolling open office" gave me my answer.

update-- check out the wall street journal story where Microsoft offers financial ...incentives to have people in Africa run windows instead of linux.

update 2-- other cool openness Open Pandora

Dinners

Every time I think I my diners can't get any lamer I have evenings like this: raisins, olives, leftover beans and yogurt. At 10pm. And Bailey's, don't forget the Bailey's.

NAS with Linux

I bought a NAS to a) learn how to use and b) backup all my stuff and c) use when I eventually move (anyone want to buy my computer in the spring?).

Anyway, I got it working with both my linux boxes! Yeah! Well, halfway there anyway. I'm going to write this post so I can use it for future reference and also to solidify the ideas in my head.

The NAS device is running a file serving program that will serve files to windows and linux (Samba). Since I have no windows machines, it would be best if I could use nfs instead but my NAS doesn't have that file server installed.

I connected to the server using the linux program smbmount, though I think the newer way to connect is with mount.cifs.

To connect to my NAS I used (from eeePC forums):

smbmount //192.168.0.XXX/Volume_1 /home/user/MyShare -n -o -username=username, -password=password, uid=user, umask=000

the -n flag is needed because it disables writing to the /etc/mtab file, which is read only. and we have the uid=user so it makes the user your logged in as the owner of that mounted folder.

If you don't supply a password you will be prompted.
This assumes you have created user accounts on the NAS (which I did).

And from another webpage:

umask 000 (or 0)

   rwxrwxrwx
mask   ---------
what comes through rwxrwxrwx (directories)
   rw-rw-rw- (files)

Which means it gives the user who is mounted to the device full control of the directory that was mounted for them.

To unmount: smbumount /home/user/MyShare

Of course, this means that each time I open my computers, I need to manually mount the NAS. I can do this automagically with fstab, and mount my drive permanently (which I haven't done yet).

To complete the info in this post, to get the IP of the NAS I had to log into my router and see which IP it had been assigned. In the future I can make this easier by reserving a permanent IP to be assigned to the NAS.

Yeah, looks difficult. Well, they provided the for dummies does it automatically software but it only installs on windows. I guess they figure if you run linux you can figure it out.

Evolutionary timeline for kids

I liked dinosaurs when I was kid, but to be honest I was curious about the older weirder things. I would have thought this was very cool, a kid friendly timeline showing not just the dinosaurs but all the way back to the beginning.

Evolution

As a biologist, I have great interest in evolutionary theory. I'm really keen on how life evolves on a biochemical level and how these are manifested on a whole organism scale. It's also the reason that the echidna is my favorite animal (egg laying mammal how cool!!). As part of this interest I pay attention to how evolution is taught in the schools and how it conflicts with creationism. I found an excellent review of a creationist text book called Explore Evolution and I thought it was a very informative article.

Ars book reviews typically focus on works for the general public that we consider significant and insightful. But today we're making an exception: the work in question is meant for school children, and it's an atrociously bad book. So why review it? Because, unfortunately, it may well turn out to be very significant. The leading lights of the Intelligent Design Movement, the Discovery Institute, have written this textbook on evolution, and they are doing everything they can to make sure it gets into schools.

Bloggers be tracked

Of course, its no surprise that the personal opinions offered on blogs will be eventually mined by marketers to figure out how to make a profit. One such company is Umbria which is a case study in the book "The Numerati" by Stephen Baker.

This company monitors blogs and based on posts sorts people into groups or tribes and then looks for correlations between these groups and products. One specific example from this is as follows:

Sometimes this tribal knowledge helps marketers draw distinctions between consumers. One cell phone company, Kaushanksy tells me, started charging extra for Bluetooth data connections - radio signals that replace wires. The people who wear the blinking phone clip on their ear use Bluetooth to relay their conversation to their handset. News of the extra charge on the phone bill sent bloggers into a fury. But Umbria, Kaushansky says, studied the blogs and discovered that almost all of the anger came from one tribe: the "power users." [ed aside, oh so that's where the period goes with quotes]. Those are the folks who spend lots of time and money hunched over their handsets, sending e-mails and photos and fooling around with spreadsheets. The other tribes - the fashionistas, the music lovers, the cheapskates - shrugged off the Bluetooth charge. Many of them probably didn't know what it was. With this intelligence, the phone company conceivably, could raise the price a few bucks on the handsets favored by power users, and then offer them "free" Bluetooth. Meanwhile, they could continue charging everyone else.

So the power of the bloggers that was supposed to give strength in numbers to the little people has instead turned into a free research tool for marketers.

And with that, let me state how as a male I strongly support ... Ax body spray and ... puppies.

Take that stupid new window openers...

I am always frustrated at those stupid webpages that insist on opening new content in a new window or tab each time, I'm looking at you Pubmed. So I found the tweak in firefox (about:config), to change Browser.link.open_newwindow. I changed the value to 1 and problems are more or less solved. Not that I expect this will interest many people, I just want to make a note of it so I don't forget and can change my other computers with this setting.

That is all.

Post-Buffy

After Buffy, what's a girl to watch? I picked up the two seasons of Dark Angel pretty cheap because I'm always a fan of dystopia's. It was created by James Cameron and I like his work and for years I've been wanting to check it out. I didn't realize it starred Jessica Alba. She is a bit grating in the pilot but it gets better. The show is no Buffy but not bad.

I volunteer for a rat rescue and I thought the rats thrown in the dumpster in their cage that I talked about in a previous post was pretty low. But apparently people can always do better.... some lady in Kits found two domestic rats sealed in a ziplock bag. One died a few minutes after being rescued and the second one hung on for a few more hours. How sick is that!!!

Motorcycle for sale!

So I am trying to sell my motorcycle, now that the season is almost over and it is running well. Isn't it pretty? I cleaned it up at Ivan's place, it took several hours. It was really nice to use Ivan's home and equipment, with an apartment you just can't find places to store lots of tools and greasy wash containers etc.


I also have a new rat - just for the month. Its a single male again and his name is Hemmingway. I didn't name him. He's pretty shy but very very friendly.

I also fixed my computer. When I merely upgraded Ubuntu it broke sound (again) but after I did a clean install it works fantastic. So if you want to try it out, I highly recommend Ubuntu as a free operating system.

Quote

From Reading Lolita in Tehran, quoting an book only identified by the name Mr. Bellow.

...first these people murdered you, then they forced you to brood over their crimes.

Oh yes, and bloody hell do I hate writing my thesis.

Youtube Snob

If you ever want to lose at least a dozen IQ points, check out the comments on any youtube video. This was pointed out in XKCD.

And now there is a program, apptly called the comment snob which sorts through and tries to clean it up.

The end of Summer

(picture from Indexed. Too funny).

Well, it's getting to the end finally, the end of the PhD. A month left of experiments. I have about half the thesis written. Doing experiments and writing at the same time is hard. I'm so tired. Two weeks ago it was headaches in the lab and unable to focus on my writing, last week it was decent work but not much writing. This week I'm fantasizing about a broken rib and punctured lung. You know, something I could heal from but would require some time in bed. It would be a bit like on a cruise vacation, I'd just have to sit around, watch tv, get fed. Hot damn that would be nice. I'm so tired.

Nothing much has happened during the rest of my month after my grand adventure up Baker (closes eyes, remembers sitting in a t-shirt in the sun on the glacier eating chocolate and no one asking me where to find the BL21(DE3) competent cells). My motorcycle is in the shop - I think the carb jets just needed cleaning. I haven't ridden a horse all month because my riding stable is no longer offering lessons and I haven't changed stables yet. Money goes from one ride (single horsepower) to the other (mutiple horse power).

I read the first two books of the Twilight series (coming to movie screens this Christmas). It's a teen fic beach read and covers the fantasy of a powerful, strong, rich, handsome boyfriend who's also a little bit dangerous (vampire) combined with the ideal romantic love of a 13 year old. The idea is pretty standard - I mean, Pride and Prejudice had the same rich, handsome, strong, powerful man with the happy ending that continues to inspire today's chick lit, but at least Lizzie had some personality. Bella of Twilight is as plain and boring as they come. It would be easier to ignore if they weren't calling the author the J.K. Rowling of America. That's shameful, sure HP is YA-Fic but at least there was some depth to the characters. And they grew up. Anything that Bella is, is because of the man.

My knee was hurting after Baker so no hiking plans for the long weekend. My bike comes out of the shop tomorrow so there will be some motorcycling. And filling my freezer up with food again because I anticipate a lot of dinners in the lab....

Climbing Mount Baker

On the long weekend I climbed Mount Baker in Vancouver. This is a mountain in Washington state that on a clear day is visible from Vancouver and dominates the horizon. Its part of the volcano chain that includes Mount St. Helen's and Mount Ranier. These mountains rise up above everything around them. Mount Baker is just under 11 000 feet which puts it just in the zone where you might feel altitude sickness. Our trip had significant amount of faff below the glacier before our final Monday ascent so no one was feeling sick.

The first day we camped beside the Coleman glacier, if you look carefully you can see tiny people doing a glacier school just where the glacier starts to flatten out.

The next day we hiked over to the climbers ridge where you would start your ascent of Baker. We ran into a Marmot who made faces at us as he (she?) defended the path because there were babies off to the side.

We climbed up the first part of the glacier and camped on a rocky section surrounded by the snow. Here's a great photo looking at the horizon. Already we are fairly high up.


And here's a picture of the peak of Baker in sunset. At the very far right of the picture just behind the peak is a flat snow section which is called the Roman Wall. That's the final part of the climb up Baker so we spent our afternoons watching parties slowly make their descent. We did not go up the front which you can see here but around to the left and eventually up to the Roman Wall.

Monday started at 6 am with breakfast and then we started out onto the glacier. We had to be roped in because there were lots of crevasses. The day previously we had practiced our ice ax arrests (yes, we had ice axes) on the snow slope and we also carried some crevasse rescue equipment. Roland Burton (66? and MEC member number 2) led the charge (he also led the charge on the Neve).

This is a photo of our route, hugging below the black buttes and then up around to the Roman Wall.


Here I am almost at the base of the Roman Wall, the Black Buttes (now yellow) are behind me. It took us only 2.5 hours to get here but then another 2 hours up the wall. You can see that even though we are well below the peak we are well above anything else around.

I don't have any photos as we ascended the Roman Wall (we took off the rope because if someone fell they would drag us all down). The Roman Wall was like a steep snow covered roof that took at least an hour to climb. I don't have any photos because I didn't want to lose my balance. It was a long slide down to end up dead at the bottom of a crevasse. For us the wall was mostly crusty soft snow but it could be quite technical when it turns icy. While climbing the Roman Wall we were blasted by sulphur fumes. Baker is an active volcano and we could see steam rising from the crater which was down a little ways from the true peak.

Here's a picture looking down into the crater, you can see some of the steam.

And here I am at the peak.

And another shot looking in the opposite direction. Behind me is the giant snow dome that's visible from Vancouver.

So after a great lunch on the summit we hiked back. I almost went down the wrong glacier! This one is the Eastman glacier and not only does it take me to the opposite side of the mountain but it is considerably more crevassed than our ascent was. The top however, was easier than the Roman Wall.

At the base of the Roman Wall we ran into another party that we had seen at the summit. Everyone who summited that day wore crampons except us, Roland is not a fan unless you are on ice or wear them all the time because they can be dangerous. We saw just how dangerous because a guy had broken his ankle close to the peak when he had glissaded down (purposfully slide down on his ass for a faster descent) a slope wearing crampons and his foot caught and snap. Ouch. That's why they say never wear crampons and glissade. Anyway, his party had stabilized the leg with an ice ax and tied his legs together and they were in the process of sliding him down the glacier. They had their glacier rope tied to his harness but he kept rolling around. Our group joined in and some clipped in and we dragged him almost the entire way down. He was in pretty good spirits but by the time he reached our camp he was ready to throw up.

Here you can see them tying in. You can also see my glacier travel rope that I'm tied in to.

So all in all it was a fantastic trip. The route and weather that we had made Baker the 'baby mountaineer' trip but I had tons of fun. My knee was a bit sore by the end but it was worth it. We had perfect weather and no accidents and I didn't kill myself getting to the top (considerably less work than crossing the Neve). Although I did sunburn the inside of my nose from all the reflections.

Not hiking too much on the weekend

So this weekend it was a hiking attempt. We wanted to go up Golden Ears and hiked in to Alder flats (5.5km in). Man did we get there early. Noon. With nothing else to do. I can't remember the last time I had hours to fill and nothing to fill it with. We filled it with faff. Roland and I hike up the trail to the helicopter landing and I saw a pika. That was really amazing, they are really cute. In fact, all I could think about when I saw it was that it looked like a teddy bear walking on four legs.

After a few hours of walking, it was nap time. And then a diner which we stretched out for a few hours and then finally bed at 9pm.

The next day we started the hike up, a long haul. We got about an hour into it when the rain started. So we faffed under the trees. Then decided to head home rather than put in all the effort to sumit in clouds and rain.

Back at the campsite was more rain and another nap. Hike out. Wendy's. Clean up. That was the weekend. A good warmup for the long weekend because I'm hoping to do the same Neve traverse I did in the winter but well, in the summer. We will circumnavigate the lake rather than the directd route. Unless its raining and then it might be more faffing.

Mambo the Rat

The baby girl rats have been adopted and my next foster is Mambo. This is a very friendly boy who is used to getting lots of attention. He's very cuddly and I was sitting on my bed giving him scritches while I was reading when I checked out the reaction I was getting. Check out the tail (yes, the gross rat tail). Sorry the video is on its side, it will take me a while to figure out video editing. And as a sidenote check out the awesome duckies... Anyway, after quarantine period Mambo will be getting a spayed girl to keep him company.



On the motorcycle front my little bike is still running fine and I take it out for a ride almost every weekend. The thesis (or thes-ass as Rhonda lovingly described hers) is finally looking like its going to finish and then I'll be selling the bike, handing off Mambo and going... who knows where!

I was also going to suggest watching the next Joss Whedon experiment (also featuring the still dashing Nathion Fillion) Dr. Horrible but it has been taken off-line (free) and soon to be on sale.

On the Weekend

So I have new baby rats that I am fostering since Salt and Pepper were adopted while I was away. They are so cute! They play chase with your hand, pounce and then flee back to safety only to emerge again hopping with excitement to take on the fingers of doom again.

I got to name these two little girls, they are Pippa and Peanut.
Peanut fishing for peas on a hot day.




Tongue shot of Pippa




To hold hammocks that I hang in the cage I went to the dollar store and bought some cheap shower curtain hangers. They cost me a dollar. This evening as I was walking past the swanky Restoration Hardware (no customer is too yuppie) I saw the exact same shower curtains, repackaged, for $15. Wow, that's some markup. I guess as always its buyer beware.

I also had my fantastic riding lesson today. I rode a different horse and he takes a lot less leg to direct around the ring so I was able to do a whole mini course of jumps complete with the flying lead changes.

Watched the original Die Hard, the movie message seemed to be that no matter how well she climbs the corporate ladder, she still wants a sweaty, bloody manimal.

And finally, its been two weeks already and I still really love this eeePC. I love wireless and sitting on the balcony, man this thing is fantastic!

Canada Day

Canada Day this year including a little bit of swing dancing at the Jazz Festival and then some Sushi the beach. While we were eating we saw a BBQ fire and the fire department was called.

Visit to Ontario

I recently went back home for a quick visit and wedding attendance. Man I've been to a lot of weddings. There were two this weekend. So I got to visit with both sides of the family for a wedding and a birthday. Here's a photo from the birthday party with my first cousin once removed.


I also got to go to Toronto for another wedding. We hung out at the CN tower the day after the wedding, its been a long time since I've been up there and now I don't feel tempted to go up for a long time. Neat views though, it would be fantastic to live on Toronto island.

On my flight to Ontario I set my alarm for the wrong time, I woke up at 5:15 am and my flight was leaving at 6 am. Holy crap. I made it from bed to the airport in under 20 minutes and just managed to catch the flight. My luggage, however, did not. But at least this time it showed up at home two days later unlike the last time when it was scheduled to show up after I had flown back to Vancouver.

The flight back had the fancy air canada entertainment system so I watched two movies. Jumper - with a neat premise but the guy was such a twit I had no connection and kept waiting for the movie to build but suddenly it was over. The other movie was Cloverfield, it also had an interesting idea but featured these vapid 20-somethings who just could not make good decisions. I mean, come on, the lights are flickering out, you're in an electronic store why the hell don't you pick up a flashlight! And if something was hunting me in the dark I'd keep my hands on the rebar that was so successful fighting them off the last time. As Erwin likes to plan for a world of zombies, I like to think about surviving post apocalypse (i.e. the book Last Canadian). So perhaps my reading has better prepared me... So my recommendation- skip Jumper and Cloverfield was worth the rental.

New PC

Yeah, I got my new eeePC! I swore I was never going to get another laptop until I found a computer I was actually willing to carry around and now the cheap ultraportables are coming out.

So its a nice small portable reasonably priced computer. They keyboard is rather small but not unexpected. I won't be writing my thesis on this guy but its great for surfing and checking e-mail. And the big point is, it actually is a portable computer. There's a huge glut of them coming out, especially since the new atom processor for good battery life is being released. My eeePC doesn't have that but the new 901's starting to come out in July will.

update: to continue my rant about my crappy vaio, I just reformatted it in preparation of donating it and what's really annoying is when you do the factory install, they don't just give you the OS disk, no, you have to install all the crap. Sony has sold space on your computer to advertiser's etc and every time you reset your computer their crap comes back.

The eeePC is decidedly short on bloat. Not that it doesn't have its shortcomings, I haven't seen a way to add software in the easy mode yet. But at least the system is open enough and people have created a huge number of resources for tweaking. Starting fresh on the stupid Vaio always meant at least half an hour of deleting the crap and of course you could never be sure you were getting rid of all of it.

Pet rats

So tonight I handed over the pet rats that I'm looking after to another couple from Little Mischief Rescue who I am fostering them for. I haven't had them for very long but I'm going to miss them! When I come back from all my travels I'll get them back and see how much they've changed.

They have great personalities, very different and obvious. Anyway, here are two pictures right after they had a bath.

Their names are Salt and Pepper. I read this morning on the newsgroup for the rescue that someone in Victoria is dumping rats. These are domesticated animals and will probably die quickly out on their own. Its just the owners way of killing them without actually having to think they are responsible and its disgusting. Someone even dumped the rats, in their cage, into the dumpster! How can you do that! You aren't even pretending to yourself that the rats are going to run free and live off the land.

Anyway, my experiences with the rescue makes me aware of how beneficial it would be to adopt an animal from them (or others). You'll get an animal who's personality has been assessed and the rescue wants to suggest a good match to people who are adopting. The animals are well socialized, Salt and Pepper are litter trained already and used to handling. All in all, you get animals that have had a lot of attention and care unlike a pet shop, especially one of those big generic ones.

So I will miss the stinky boys (they are rats after all) in the evenings, when I sit at the computer and Salt or Pepper will run up my arm to sit on my shoulder and just hang out. So cute!

Ratz

So I am fostering rats. I volunteered for a rat rescue that takes in animals that have been abandoned. Yes, there exist organizations that do this, they foster the animals they get in people's homes rather than a shelter till they get adopted. I thought since I was curious this would be a good way for me to see what pet rats are like, help out and get support like the cage provided.

So I have two very very cute males. They're interesting and I always go for interesting. They also sleep a lot. And they vocalize in an ultrasonic register but you can hear some of the lower chirping notes.

Thanks Erik for the picture, my experiments are ongoing...

The thesis

Hmmm, I think probably the only thing worse than going through your really old lab books from 5 years ago trying to figure out details of experiments, is going through someone else's old lab book trying to figure out experimental details. Holy crap I'll be doing this for a while.

Also, while I never considered the daily '24' a bastion of journalistic competence, I can't believe they referred to Owin Wilson as the 'butterscotch stallion'. Unless of course that's some tabloid standard that I'm unaware of... probably a good thing.

Long time no blog

In the end of April I got to watch one of my scientific heros in real life, Dr. Richard Dawkins gave a talk at the Chan centre and I was lucky enough to have scored some tickets. His talk was mainly about what had been covered in the God Delusion. He was a very good speaker and a very generous question answerer.

One thing I observed at this talk were the militant vegetarians. I'd only heard of them but in real life they were like a dog with a bone (picture the growling and the shaking and the not letting go). During question period there were three questioners challenging Dawkins to give up meat because he was popular and they claimed not eating meat was a natural outcome of his species-ism philosophy. The idea is that we are not obviously related to any other living organism only because the 'missing links' are all dead. If the missing links were still alive (say between chimp and human) we couldn't tell when humans stop and chimps begin and therefore we shouldn't eat 'anyone'. Dawkins agrees that the species divide is completely arbitrary and therefore not a good way to decide who can be hurt and who can't, Jane Goodall is also involved in this movement and one focus is to eliminate experimentation on primates. Anyway, Dawkins said we could choose to draw the line (eatable vrs non-eatable) anywhere in all life and that he wanted to draw the line based on capacity for pain and the animal's understanding of its fate (i.e. humans would be horrified about living in a field knowing they were only being fattened up for the kill but we have no indication that cows have the same dread). But the vegetarians wouldn't take anything other than a complete capitulation to their ideal. I wondered how they decided their line was the correct one. Of course, there's always a Simpson's quote "I'm a fifth level vegan, I don't eat anything that casts a shadow".

After Dawkins I was sick for a week and completely behind in life. I told one of my labmates that I really wanted a secretary and a personal assistant and she pointed out that what I really wanted was a housewife. Then everyone in the lab was agreed that what we really needed was a housewife - dinner on the table, house clean, groceries and laundry done plus free child care.

So after another week of trying to get by without a housewife I had the most perfect weekend ever. It included:
Friday:

• tequila shots and board games.

Saturday:

• great riding lesson


• dress shopping (normally a horror but I went to Plum, had some great assistance and was out in no time with three great looking dresses.)


• more board games


• Memphis Blues - I'm not much of a meat eater but damn that BBQ is tasty


• second showing of Ironman (great summer blockbuster, I highly recommend).

Sunday:

• got the motorcycle on the road with minimal fuss


• hanging out on a nice porch in the sun. Maybe doesn't sound so exciting but I don't have much access to those nice backyards/porches since you pretty much need to spend a million dollars to get a place like that in Vancouver.

So after a nice break, its back to the lab on Monday but significantly less stressed out. I even am starting to think I can handle it without the housewife...

Big birthday

My birthday was a Friday this year so it started with a cake I baked for the lab.


Then I cleaned up my apartment and had guests over for drinks. I made these apple martini's based on a recipe from Bryan:

1 oz Sour Apple Liqueur
1/2 oz Butter Ripple Schnapps (yum!)
1/2 oz Vodka
splash fireball whiskey
splash cranberry juice

These went over very well. I also put out all kinds of fresh veggies and dip but of course it was the chips that were finished... I'm going to be eating a lot of veggies this week...

My apartment is pretty tiny but we all fit in. I also had some work done that I'd been waiting to do. Shawn and Frank cleaned the heat sink on my computer so it can now run with the case on. I didn't get around to cleaning things up and the computer would overheat unless I had the electronics exposed.


We also found the stud in my wall and after 8 months of living in this apartment I finally hung up all the art work.

After drinks we walked down to Thai House for dinner, about a 20 minute walk away.


There we were met by more guests who couldn't make it for drinks. Dinner was really good (though I was pretty full from all the chips.... I mean veggies!) and I didn't really sit and eat because I wanted to go around and talk with everyone.



Erwin bought me a motorcycle for my birthday. It can go next to the Horse my housemates bought me for my birthday a few years ago (the My Little Pony).


Finally, the night ended with snow. Yes, snow, in April, in Vancouver. It was giant puffy flakes and it is still on the ground the next morning. I am going out for dinner with labmates tonight so this time I should be able to concentrate on the food more.


All in all, a pretty good birthday. Geneva took all the photos which I really appreciated since then I could talk to people. We also drank only half the booze, so if you come over to visit me you are getting martini's and veggies. And that's it!

Birthday

Also celebrating on this day is the release of the movie Expelled, a disingenuous movie about intelligent design. I wonder if mainstream will pick it up at all, like that other piece of garbage - What the Bleep do we Know.

How could I forget to mention April 4th

April 4th was walk like a T-rex day! I'll try and remember it for next year, this day needs some momentum!

Stuff in April

So I haven't been posting all that much... here's a recap:

Manning Park, over the Easter long weekend I camped in Manning Park with friends. We were in the snow in a tent and as usual I was freakin cold. The Manning Park downhill ski area was small but we had a fantastic day skiing. Either I need to tent with someone warm and cuddly or figure out how to be exothermic.

Red Heather, just another fun day ski. I really suck at skiing in fresh powder and spent most of the day on my feet but with very little style. The ski out was on this narrow little track with banked turns so it was kinda like a video game. Tons of fun.

Curling with the department. For the first time in my life I went curling, I've never even watched it on TV and I must say I feel like I've been missing out as a Canadian. It was tons of fun but I fell half of the times when I released the rock. My knee is black and blue. Needless to say, I won't be on the olympic team any time soon.

So I have to recommend curling to anyone. The rink was great, we played a laid back game and then went for cheap beer upstairs. Not that I drink beer, but I guess I was happy with cheap popcorn.

eeePC and civilization

First a paraphrase from a Neil Gaiman book I'm reading (Good Omens, very funny): The world is 24 hours and 2 meals away from loss of civilization.

Second, have you heard about the eeePC? Yes, I'm a geek for mentioning it but you knew that already. Here is the unofficial site since the official one sucks. Anyway, they are upgrading to a larger screen and some other upgrades for the second quarter so I was waiting for that before deciding to purchase.

I like the fact that it runs linux out of the box (but you can stick on WindowsXP, until they stop selling it that is...)

Speaking of more geeky free software, there was just an upgrade of Open Office.

I was thinking about putting up a last link that was slightly more hip and cool but I got nothing. So I'll just end with Disapproving Rabbits.

XKCD

From the webcomic XKCD:



And while we're at it, PhD also feels what I feel.

Type 2 fun

Tears are nature's way of saying you are having Type 2 fun.
- Roland Burton.

So the tears were shed in the middle of the Garibaldi Neve, and they weren't because I was scared, or tired but when I looked down at the damage to the flesh of my heel I became actually rather concerned. I seriously wondered if you could wear away a heel to the bone since I had another 25km to go and another glacier to climb. But first the beginning...

The hike started out as epic with the 2 hour car ride that actually took 8 hours. We left Vancouver Friday evening in hopes of missing Whistler traffic Saturday morning but we made the wrong choice of bridge leaving town which had an accident. After we had cleared that traffic we still had to hang out in Squamish for several hours because of a severe fatal accident on the highway to Whistler. Finally we got going and reached the parking lot at the bottom of Rubble Creek. It was 1:30 am by the time we got the tents set up so we didn't do the car exchange.

The next morning Roland got everyone up at 6:30 am for an early morning start. He did this by starting the truck and shining the headlights on the tents and starting the camp stove. At that point no one could sleep anymore so we had breakfast. The drivers drove the cars to the end point and we were on our way.

We started at Rubble Creek and hiked up the Barrier. This was actually my first hiking trip but I had done it in the summer.

Here I am while I can still take my boots off without gasps of pain.

This was one of the lower lakes on the way to Garibaldi lake. You can see the very lovely skin tracks that the more experienced members in our group had made while they broke trail.

This is a great view of Garibaldi Mountain. Our trail is essentially up to the saddle on the left of the peak and hugging the mountain, down the other side to the Neve and then out the creek trail to Elfin Lakes.


Here we are crossing Garbaldi Lake heading towards Sphinx Hut. The first time I hiked up to the lake and was told about Sphinx hut I couldn't imagine hiking those extra kilometers. Well, with the skin tracks it was pretty nice actually, you just couldn't pay too close attention to the hut in the distance that never seemed to get closer.

Here we are at the hut, if you aren't one of the keen ones you don't have to be digging it out... The hut has a top floor and the bottom floor has a big bench that people slept on. The hut could comfortably fit 12 but we put 18 in it. Well, at least it wasn't near as cold as the tent the night before.

Roland, true to form had everyone up the next morning when he turned on the lamp and started the stove. Then we continued along the lake towards Sentinel glacier (and the second hut located there).

After climbing the glacier we could look down on a snow field? Glacier bed? There were about 3 or 4 glaciers that came down off this patch. You can see the small spots of people far ahead. The sharp peak centre right is the Shark's fin and our trail skirts it to the left. The weather was glorious, it was warm and sunny. This was also where I had a look at my blister and realized it had gotten a lot worse. Zach was on the trip and was with me at the time. He handled the knife and did the cutting and bandaging because at that point I just wasn't mentally on top of things.

So once my foot was taped up we continued skiing up towards the Shark's fin. Here is a photo looking back towards the saddle that we had climbed.


Here is a photo of someone from our party that I can't identify skirting Mount Garibaldi. What a fantastic view! At this point the wind had picked up. The Neve is down to the left. We skied down (I fell down) onto the neve and then across to....

... Ring creek. This was our exit point out of the Neve and it was still another 5 km plus some climbing to get to the hut. This was the worst part for avalanches. As I was skiing in this section a metre-long section sloughed off just 2 m in front of me. The best I could do was do my best to get out of there.

We skied out to Elfin Hut, a massive hut that can sleep about 60 people (officially?). We got there before sunset which was excellent timing, had some dinner and went to bed.

The next day was a fantastic ski out. Here we are stopping for a break along the ridge. It was another day of fantastic weather and pretty decent snow conditions.

If you are interested in seeing the heel damage, its a gross photo but you have been warned.

Finally, I had a great time. If I was stopped it was type 1 fun, if I was grinding up a glacier and my heel was hurting like hell it was more like type 2 fun. However, it was all fun when it was over and I could look back on what I had done.