Fountain pens gone wild

Basically the title said it all about what happened to my fountain pen/ink collection this year.

It all started with a lovely Japanese movie that I watched on a trans-pacific flight back from Taiwan, Closed Note. I love the story and the pens that featured in the movie. Watching this movie re-ignited my craze about fountain pens.

Pretty soon I discovered the FPN. And with that, all hell breaks lose. New pens and ink keep coming in from all sources (including a "mile-stone" pen to celebrate my PhD, a Bexley Americana in Rio Grande Red). I even get a chance to attend my first pen show (in Atlanta).

My newest acquisition at the year's end, a Levenger True Writer Demonstrator (with a bottle of matching "Slightly Wild" Fireball ink), aptly concludes this wonderful year. Really look forward to a "bountiful" 2009. :)


The beginning of the end

This may sound strange, but the first item on my winter break to-do list is to potty train David. Hopefully we'll wrap this up before I return to work next year, then we can say goodbye to diapers.


Do not grass

The good thing about being bilingual.

Vivian: 弟弟不要吵!
David: 不要grass嗎? (一臉無辜狀)


First flat on the road

Well, technically this is not really the first. I have experienced tons of flats back in high school, but have not gotten one for more than 10 years.

It happened soon after I left office this afternoon. I was right next to a bus stop when it happened so I decided to take the easy way out (good thing that bike rack is standard on the city bus here).

Thinking back, I am really lucky that my commute route almost overlap completely with one of the bus routes. So in any event, I can always wait for <30 mins and take the bus home or to work. Kind of makes me wonder why I carry all the pump/spare tube/tire level/multi-tool with me anyway?


Bacteria genome and breast feeding

Unlike my earlier post, the two things in the title are actually quite tightly linked.

Read a paper about the genome sequence of Bifidobacterium longum infantis. Basically this is a bacterial species that dominates the gastrointestinal tract of breast-fed infants. By cracking the genome sequence, the scientists found that it has a whole battery of genes for utilizing human milk oligosaccharides that lack a nutritive value to human infants. In other words, this little critter is specialized in growing on breast milk (oh boy do the infants consume a lot of that, just ask my wife, a proud mother of 3 breast-fed babies) and thus out-compete other potentially harmful bacteria in infants' gut, all the while without taking up the nutrients that infants need.

Very cool science story about human-bacteria co-evolution indeed.


Where is everyone?

I only saw 1 other bike commuter this morning on my way to work, which definitely does not feel right in Tucson. With most of the the undergrads gone, riding around the UA campus is actually quite pleasant. Gotta enjoy this while I can.

Anyway, only 3 more days to go (yay) and some more eukaryote genomes to crack (yucks) before the winter break.


Why I decided to work on bacteria

After working exclusively on bacteria genomes for a couple of months, recently I went back to the world of eukaryotic genomics to compile some data sets for comparison with my findings in bacteria. Now that I am totally spoiled by the availability and quality of bacteria genome sequences, working on eukaryotes is excruciatingly frustrating and I just have to vent here.

1. The taxon sampling is so sparse (both within and across phylogenetic groups). Often the lineages are either too closely or too distantly related, which makes it really hard to do comparative genomics.

2. When I get lucky and find a group that has just the right level of divergence, some of the genome sequencing projects seemed to be "in progress" forever. Seeing that the last update was from several years ago, I really doubt if they intend to finish what they started.

3. Okay now, what about the published genomes? Everyone knows that you are supposed to deposit the sequences in GenBank/EMBL/DDBJ when you publish the genome paper, so people can get the sequences to do more analysis later. Well, as it turned out, this is quite tricky as well. While most groups followed this guideline, many of the deposited genome sequences do not contain annotation of any kind. To get the annotation, you have to hunt down the files from various sources, and needless to say, everyone uses whatever file format and convention that caught their fancy.

4. Just when I think I am done with all the painful data collection/file format conversion and ready to roll, my whole data analysis pipeline simply blows up in my face. As it turned out, some annotations are just plain horrible; there are annotated proteins with less than 60 amino acids and more than 3 in-frame stop codons, or worse yet, "genes" with one single amino acid. I mean, come on guys, even a first-pass-fully-automatic annotation can do better than that. While my pipeline worked well for what it was designed to do, there is very little that it can do about the classic garbage-in-garbage-out problem.

All these frustrations reminded me why I decided to switch from eukaryotes to bacteria last year, and I really glad that I did.

No Comment

Inspired by this T-shirt, here is what I usually say at work (arranged by how often I say it):

# No Comment

// No Comment

<comment>No Comment</comment>

See? Told you I'm a geek. :)


Lamy ABC comes to the US

Ever since I learned about the existence of Lamy ABC from Richard Binder's site, I have been wanting one (or two, it comes in 2 great colors) pretty badly. I can't really explain why I'd be so obsessed with a pen designed for children, may be I have never grown up or something.

Unfortunately this pen was not available in the US, and the trouble and cost involved in getting one is just too much so this pen has remained on my wish list for quite some time now. So, I am really happy to know that now
Fountain Pen Hospital started to carry this cute little pen.

With all that great news, I can only hope my play-money account will turn black soon...


The red bike combo

A combo that is not meant to be enjoyed together:

And an alternative use of the bottle cage:

And that makes seven

Alyssa got a used 20" 6-speed Raleigh Rowdy from Tucson BICAS to replace the 16" bike that is almost too small for her now. With this new addition, we have a total of 7 bikes in the house (Ann, David, and I have one each, the 2 girls share 4 bikes in the sizes of 12", 14", 16", and 20"). The sight of all the bikes lined up in the backyard is quite impressive.

I don't remember the my job description as a dad has "bike fleet maintenance and management" in it, but looks like this is going to take up a big chunk of time and effort.


Nice weather makes me a wimp

The temperature this morning was in low 40s and my thought was "Gosh, this is too cold to ride my bike to work."

Even though I have a mild cold and a 10 mph headwind weighing on my side, I still feel my argument was kind of weak. Then I thought to myself "Heck, if I can ride in Iowa's winter, where there was snow on the ground and the sky was depressingly gray, how come I can't ride on a beautiful sunny day in Tucson?"

And with that thought, I hopped on my bike heading to work. Fortunately the ride was not as painful as I've expected. Better yet, the work out helped to soothe my stuffy nose a bit when I got to my office.

*Sigh* Looks like I am completely spoiled by the nice weather in Tucson.


The cutest thing

I took David out for grocery shopping this evening. When the cashier saw David's bear jacket (completed with two little ears on the hood), he said to David "You are the cutest thing I have seen today."

The funny thing is that a muscular guy over at the next check out counter overheard this, and yelled "Hey, you just said that to me earlier!"

Everyone in the store had a good laugh.


Vulnerable cyclists

Read some quite scary stories about cyclists being attacked by crazy people and a classic case of hit-and-run. Surprisingly, the police seemed unable to do anything, even when the license number of the cars are available in both cases.

This is so sad.

Anyway, still waiting to see how the case of the El Tour de Tucson accident will pan out. Hopefully the injured cyclists (particularly Gary Stuebe) will make it out okay.

Because they are friends

Watching Alyssa and Vivian play chess can be a quite entertaining experience. Given the choice of

(1) take one of Alyssa's pieces, and
(2) group her own pieces together,

Vivian would go for option (2) most of the time. The reason? "Because they are friends."

Surprisingly, this seems to be an effective way for preserving most of her pieces to the end and sometimes even helps to secure a win.


Away it go

Got my first research paper from the new lab out of the door today. Hooray!

Lights at Reid Park Zoo

We took the kids to the zoo this evening to see the Zoo Lights event. It is the first time for us to be there after dark and we had some interesting experiences.

The zoo was totally packed with people, even more than the weekends. Everything looks so different with the lighting it feels like a new place for us.

While most of the animals were sleeping, the polar bear was extremely active while we were there. The kids enjoyed seeing the bear jumping in and out of the pool and swimming around having fun just like an super-sized otter.


It's riding time

After Alyssa got rid of her training wheels yesterday, David learned to ride his bike this morning.

He did quite well in pedaling and controlling his bike, he even handled some slopes without any problem.

And with that, we finally have everyone on the wheels and are ready to tackle some bike paths together! (sorry Nina, you have to stay at home until you learned to pedal..)


A busy Thanksgiving for Alyssa

Alyssa lost her 4th tooth after breakfast and then learned to ride her bike (without the training wheels) before lunch. A perfect example of one thing has nothing to do with the other. :)


Photo op at the Javalina Rock

In preparation of making the holiday postcards this year, we headed out to the Javalina Rock in Saguaro National Park this morning to take some pics of the kids.

And it's not just the kids, Alyssa also took some pics of Ann and I, which are pretty rare for us since we have the kids.

The kids are very excited about being able to do all the rock climbing. Ann and I are very surprised to find that Alyssa is so good at this, she just kept climbing higher and higher while we are looking after David. Eventually we had to call her down because it was too scary for us (but not for her, or Vivian for that matter).


The harassment food chain

Just ranting here.

When I ride my motorcycle, I was harassed by cars/trucks/SUVs. When I ride my bicycle, I was harassed by cars/trucks/SUVs AND motorcycles. Now what's with that? Do people just do something because they can (and/or stupid)?

Good thing I don't have to walk to work.


My favoriate tree in Tucson

I pass by this Palo Verde tree on Glenn St. everyday on my commute route. The way it waves with winds reminds me of cotton candy.

Seeing a beautiful tree like this always gives me a boost and makes my bike ride much more pleasant.

My new job description

"Mad scientist by day, bike mechanic by night" seems to be pretty accurate.

The mad scientist part hasn't changed for quite some years now, but the bike mechanic part is somewhat much more demanding than I expected. Currently there are more bikes than people in my house: Ann, David, and I each has one (the relatively trouble-free trio), while Alyssa and Vivian share three bikes of different sizes between them (the source of all my trouble).

Every day I get home, I'd be greeted with:

"Daddy, I have a flat tire."
"Daddy, I need to take my training wheels off."
"Daddy, I need to put my training wheels back on."
"Daddy, my saddle is too high."
"Daddy, my saddle is too low."
"Daddy, daddy, daddy, daddy, AAAAARRRRGGGGGHHHHH".

I am not complaining, I do enjoy riding and working on bikes. It's just that I've never dreamed of running a bike shop when I grow up, let alone managing a team. Now if I can get a dollar for every job, I'll be rich really soon.

Don't mess with my pens

Thanks to a generous donation from my boss, now there is a guardian dragon watching over my pens in the office.


The wonderful morning adrenaline rush

Now that I got a new bike, I am back to the saddle for my commute.

Oh boy was the new bike a sweet ride. Before I was always wondering how those crazy people pass me with such amazing speed, now I know that the bike really makes a huge difference. Even though my muscle is not any stronger compare to a couple weeks ago, I can go much faster with ease. And I have to say, the feeling of racing to work is really fun. Despite going easy on the bike and myself for our first ride, I made a record time on my bike commute.

More importantly, I confirmed my suspicion about what was wrong with me in the last couple weeks. All my drowsiness and headache was gone after a nice adrenaline rush from the ride and I had a wonderful day at work. With that, I guess this is what I have to do:

"Hi, my name is CH and I am an adrenaline junkie."


A brand new start

I finally got a new bike to replace my stolen Trek 7300. The replacement is an aptly named Fuji Newest 1.0.

Originally I was looking at a Newest 3.0 and contemplating about getting a Newest 2.0 (for the better frame). When we got to the shop this evening, I tried to explain to Ann what the differences are and thought I'd know what I want better after discussing with her. Much to my surprise, she said that there's no way I'm getting a 2.0! Instead, she insisted on buying a 1.0 for me.

I am not used to buying something that is the top of the line (I'm more of a getting-the-most-bang-for-the-buck guy). So while I was thrilled about what she said, I was a bit hesitate to accept the generous offer. However, after test riding the bike, I was completely hooked by the better shifters on the 1.0 (2.0 comes with Shimano Sora, which is difficult to use when you are tucked in. 1.0 comes with Shimano Tiagra, which is much easier to use).

So that's the story about getting my first road bike. With a wife like this, I really don't know what to say (secret note to myself: always bring Ann along for toy shopping).

The only person who was more excited than I do is David. Ann prepared some snacks for the kids after we got home from the shop. While Alyssa and Vivian enjoyed the feast, David refused all his favorite foods and just stood beside my new bike and smiled the whole time. It looks like the little guy has some potentials.


Anger and hatred

Several weeks have passed since my bike was stolen and I have finally gave up the hope of ever getting it back. Now I am really mad about the whole situation as the reality is kicking in. The amount of time, effort, and money involved in getting a replacement is way more than what I have expected.

One thing I learned is that the regular inflation index certainly does not apply to bikes. I was so shocked when I see the same model is selling for about 50% more than when I got the bike a few years ago. What's the deal with that? I mean, yes, the spec is somewhat better now, but the huge price spike certainly is in no way justified.

What's even worse is that the shopping process made me realize how much I missed my old bike. I thought shopping for a new bike will make me happy (just like all my previous experiences of getting big new toys). Unfortunately, I can't help but to think about my old bike when I stare at those shiny new bikes in the store. Before losing the bike, I thought I wasn't very attached to it. The way I think about this is to ask myself an hypothetical question: if someone offers me to trade a new one of the same make and model for one of my toys, will I take up the offer?

I thought about this question some time ago and my answers are:
fountain pens? no way!
motorcycle? maybe.
bicycle? sure! why not?

Sadly, I learned it the hard way that I am way more attached to my bike than I thought. And whenever I think about it, I have this outrageous anger and hatred toward the thief who stole my bike. The whole thing is really scary because I'd never have guessed that a quite insignificant event like having a bike stolen can get to me like this.


Go back to sleep Max

For some unknown reasons, one of the car dealers in town put up a giant inflatable gorilla in their lot.

The kids love seeing it and even have a silly song made up for it. Whenever we drive by, they sing something about "Go back to sleep Max or we'll tickle you".

Exponential regression in Excel

As it turned out, Excel calculates the R-squared values of exponential regression based on transformed data. For example, for a exponential curve y=ae^bx, Excel computes R^2 using ln(y) = ln(a) + bx.

I know I shouldn't rely on Excel to do my stats but occasionally I do use it to do some quick analyses before pulling out R. What happened today was I did the regression in Excel first to see the plot and then calculate the P-value in R. Luckily, I caught the discrepancy in the R-squared value and decided to find out what the problem was. It took me quite some time to figure it out, and needless to say, I am not happy about it.

Lack of capability is one thing; Pretending being able to do something and then screw it up is totally another.

[Edit to add on 03/16/2010]
I am a bit surprised to find that this appears to be one of the most read entries of my blog. Lots of people landed here through googling some combination of "excel", "regression", and other words.
Anyway, I have a slightly more detailed explanation of the problem with performing exponential regression in Excel, plus some simple tutorials of doing regression analysis in R on my wiki at:


Feel free to take a look there if you are interested, hope this helps.


Animal control agents

Not sure how they get the idea (maybe from Annie). This afternoon Alyssa and Vivian came up with the game of "Animal Control" and had a lot of fun chasing after Nina in the yard (cowgirl style, complete with the lariat).

Anyway, the girls and the dog are all worn out afterward. For this reason, I think it's a GREAT game.

See the agents in action:

M+O Lab retreat

When you spend lots of time staring at strings of ATCG in the lab, it makes you want to scream AAAAAAAAAAHHH!!! (wait, I see a homonucleotide run here)

To prevent us from going mad in the lab, the bosses took us out to the Santa Rita Experimental Range to have a lab retreat over the weekend. I took this opportunity to have my first long ride in AZ.

Getting ready to go:

The ride down on I-19 was uneventful, although seeing all the km signs in the US for the first time got me a bit confused. However, after getting off the main road, I was surprised to find that there are a couple miles of unpaved road ahead:

It was definitely not fun to play motocross on a Ninja. Nonetheless, my bike handled the road okay and I got to the station without any incident.

After having a light lunch, we went out for a hike along the trail up to Mt. Wrightson:

We only spent about 3 hrs on the trail and did not make it all the way up, but we did enjoyed some really nice views along the way:

After the hike, we sat down and chatted about our ongoing and future research projects. I talked about my gene fossil hunt in bacterial genomes and the frustration with some bad gene annotations on some sequences that was done using 454 (homonucleotide runs are indeed a headache).

The dinner was incredible and I can't remember when was the last time I ate so much. Zakee's steaks are the best that I had in recent years and Gaelen's chocolate cake is simply delicious.

I am pleasantly surprised to find that Gaelen and Kevin are fellow boardgames nuts (we are a rare breed). We enjoyed a couple rounds of games (including For Sale and Bohnanza) well late into the night and had a lot of fun.

On Sunday morning, we all put on the lab T-shirt to have a group picture before we go.

Instead of going for another hike, I decided to go home early. On my way back I stopped by the San Xavier Mission:

When I get home the bike was really dirty after all the riding on unpaved road.

I don't mind riding a dirty bike and usually wouldn't spend time on washing my bike. However, the chain and brake looks really bad this time and I decided to give them a good cleaning. Fortunately that didn't take too long.

Vivian's barnyard

Moments before it was destroyed by the Davilla.


Running a desert resort

It looks like our home is becoming a popular resort among our old friends from college; three weeks after Ho-Yi's visit, Yung-Yao came from Cambridge, UK for a short visit.

We are very happy to see another old friend here; there are just so many things we can talk about, from our old days in college to our current life as a postdoc in biology.

The weekend was extremely busy and fun. Together, we went to:

Saguaro National Park

Rillito River Path

Halloween trick-or-trick at Tucson Electric Park

Artist's market at Plaza Palomino

Kartchner Caverns State Park

Sabino Canyon

Biosphere 2

And of course, we ended the wonderful weekend with our long-running tradition since college, a dumpling feast:

Also because YY received the great news that one of his papers got accepted while he was here (you lucky bastard, how come I never had such good luck when I was taking a vacation), we had a good excuse to enjoy a bottle of nice wine.

So that's pretty much what we have done over the weekend. Now, who's the next? :)