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.