Frustration, frustration, frustration

My brother said "... My little brother has a bright career in science, making a shitload of money is not his top priority in life. It's just like I am in business and you can't judge my success by counting how many research papers I have published...."

My mom heard "blah blah blah. Your second-born is a loser. blah blah blah. Your first-born is a failure. blah blah blah"

Seriously, WTF?

The ridiculous health insurance bill

Just been hit by the new health insurance bill: a 42.4% increase over the previous year. Honestly, I didn't get the memo about some hyperinflation going on in the US.

So, here is my plead to the guy who just won the Nobel Peace prize: Could you please do something about this ridiculous situation? *Sigh*

It's not fair

The girls had their last day of school today. We are all very happy that the school year is finally over and almost everyone can enjoy the summer vacation. But, here is what the girls have to say: "It's not fair! Why daddy has to go to work and not staying at home with us?"

Yeah, right. Why? Hmmm... may be I should throw a tantrum at work tomorrow?

Serious backlog

The stress of writing at work is a bit of overwhelming now, which makes me unable to bring myself to spend time on blogging in my precious evening time (hey, it's supposed to be fun). At the last count, there are 93 half-baked blog entires on my list. How depressing. I need a vacation, seriously.

Idiotic racers in a truck

Two guys in a truck yelled at me on my way home today, first time when they passed me on the road and second time when I passed them after they parked on their driveway. It was fast and loud so I can't quite understand what they were trying to say, but it sounds like something along the line of "We are awesome and you suck because we can drive faster in a truck than you can go on a bike". Pure idiots.

On a side note, the new tires I put on yesterday held up well to some unplanned tests. They are quite rigid compared to the stock tires so the ride wasn't as comfortable. The funny thing is that just seconds after I had this thought, I was forced to ride through two piles of broken glasses that spread across the entire bike lane. Maybe I am being superstitious, but it seemed like the tires want to convince me that puncture resistance is far more important than supple rides. You won, I am sold.

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.

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.

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.

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.

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:

http://wiki.chkuo.name/

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

The lonely rack

When I went downstairs after work this afternoon, I was quite shock to find that my bike was stolen. Rationally I know this shouldn't be so surprising, given it is a nice bike and I park it at the same spot everyday on a university campus. However, somehow I just can't get over the shock and kept staring at the rack as if my bike will appear again out of the thin air.

STOP means... bump?

Somehow I kept being rear-ended by college kids when I was stopping at stop signs. Fortunately they are riding a bike too and not driving a car so no one has been hurt in these incidences, but it is still quite annoying.

Life is not fair

I got upset this evening when I heard Alyssa complained that "I am sad because daddy and mommy get to watch a lot of TV after we go to bed and we don't". I was so mad that I can't even tuck her into bed like what I do every day. Is this what we get for spending all our time and attention on our kids? Should I just do whatever I want whenever I want (and let them do the same) so my first-born would think that life is fair?

Of course life isn't fair, it never was and will never be.

The guy who does not have enough balls

Two months into my bike commute, I met the first d-head in Tucson on the road. Probably provoked by my passing at the intersection, this guy took half of the bike lane and revved his engine like crazy when he caught up with me. What's funny about this incidence is that this guy has a pair of fake balls installed on his truck, and I can see them shaking violently as he drives away. The disgusting view is quite pathetic when you think about it.

Normally I don't really care what people do to their cars. But if someone is willing to go out of their way to harass me, I guess I am entitled to ridicule them in my diary.

Bad weathers bring out the worst of drivers

This doesn't happen very often, but when it rains people in Tucson drive like they are ready to become serial killers. Similarly, when it snows in Athens people drive like they are ready to commit a suicide (in Hollywood style with a big bang).

Honestly, these people should have been shipped to Taipei, where the crazy taxi drivers can give them a lesson or two.

Rude neighbor

For the first time in my life, I got yelled at by a stranger at the roadside in our neighborhood. Apparently she thinks that she is entitled to a superior right of way because she is driving a big bad SUV with a little child in the back (and I am a guy on a motorcycle). Not wanting to argue with a stranger (particularly an arrogant one), I just let it go at that time.

Now that I think about it, I am kind of regretted. Maybe I should have yelled back. Or I should trade in my bike and get a 18-wheeler so I can harass other stupid cagers.

We are not sharing anymore

The road crew in town are working on replacing road signs recently. So far they have only put in the new signs but haven't remove the old ones yet, so there are double signs everywhere and is kind of an interesting view. Curiously there are some signs that didn't get replaced, and those are all "Share the road" signs that are used to remind drivers about cyclists have their right of way too. What's even worse is that there are some graffiti on one of the signs that covered the bicycle on the sign.

This seems to be consistent with my experience that Athens is not really as bike friendly as the city officials like to say, and there are some weird people here who do go out of their way to harass cyclists on road.

To be fair, most people here are pretty nice to cyclists. But encountering one of the bastards when you are on a bike is enough to ruin a nice day (assuming that you can survive the encounter).

Annoying commercials

"This holiday season, what do you give to people who have everything?"

How about NOTHING? You idiots!

Those stupid radio commercials really get to me, particularly when I am struggling with my physical therapy.

A bad day

Today is a bad day for us.

First we went to the dentist's office and found out all our appointments were canceled by mistake and we'll have to reschedule again. Being so busy recently, I don't remember what my schedule will be and have to call them when I get back to my computer. Who knows when we can find a time to squeeze in again?

Then Ann went to pick up David's prescription and couldn't get it. The pharmacy has the prescription ready for us, just as they promised. However, because the insurance company's computer was down, they can't give it to us unless we are willing to pay it in full by ourself. I almost choked when I hear that some skin cream for rash would cost $37, which is totally ridiculous. So Ann came home empty-handed and we will need to make a trip tomorrow after the insurance company fixes their computer.

After we all got home, we received the new passport for Alyssa. Originally we were happy that something finally went right today. We paid an arm and a leg to have the passport expedited, worrying that we might not get it in time for our trip back to Taiwan. The passport came earlier than they promised, but the date of birth on it was WRONG! I ended up have to call the passport service, figure out that we have to fill out another form, send it back again, and pray it will come back in time.

The day was so bad that we decided to stay home after dinner and skip our evening walk. Then we hear from Ann's mom that one of the construction workers fell down from the second floor of their new home. Oh what a day!

Absurd fund-raising call

I've never said something bad about the schools which I graduate from before (or at least haven't done so in public), but I guess everything has its first time.

Ann got a really absurd fund-raising call from the College of Design at Iowa State University today. To begin with, I don't think it is appropriate to set a "minimum donation" of $500. I thought the way donation works is you go out and ask people how much they are WILLING to give you, NOT to ask people for a minimum amount of money they HAVE to give you. When Ann told them that we cannot afford to give out that much money (considering that our parents are stilling paying for a part of our living expenses), they said we can do this in "five easy payments". This is way too ridiculous, what do they think they are doing? Some TV shopping network selling vacuum cleaners? Why not ask for $499.99 (plus $4.99 for shipping and handling of the acknowledge card)?

Ann was too polite to just hang up the phone or say something that's not so nice and the phone call lasted a good while. They said that they will call back again soon to see if Ann will change her mind. I look forward to getting that call. Usually I try to be nice to everyone but sometime I do want to take it out with someone who deserves it.