Another perennial catch-up post

My goodness. I've managed to not speak up here for a while again. Here's some highlights of the past weeks.

Since I was already going to be in New Jersey for Thanksgiving, I dragged Jen into the boonies of Connecticut for my 15th high school reunion. This wasn't as much a train wreck as I expected. I chatted with a few folks that I remembered from marching band, ate alright food, and listened to the worst DJ in this sector of the Milky Way. His constant lite jazz muszaky torture is really the best story of the night, as a bunch of people that I would have liked to see (and with whom I could have maintained more conversation) were absent. Maybe I'll see them in another 15.

I joined a group tailgating all day in the Rose Bowl parking lot this past weekend for the UCLA/USC football game. Good times and good food. I think we kicked all 3 kegs, too. These are my kind of people, too, as the "worst" keg was Stella Artois.

Finally, my birthday today apparently coincides with the Annual Day of the Ninja. I'm not sure how my inner pirate feels about this.

When disco spreads like a bacteria

Jen, be careful when you bring up Europop in the future :)

I see your Alcazar (Swedish group, of course) and raise you Belgian trio Lasgo. At least Alcazar harmonize well, although they managed to top themselves with a very silly cover of "Don't You Want Me", apparently. Egads!

Happy New Year!

After an excellent month of relative (read: lots of) sloth following my oral exam, I am ready to jump into 2006:

- I am TAing an introductory class on bioinformatics, which should be a good challenge, but also good prep for the career I am setting up for myself.
- I am jumpstarting my research, too. More on that shortly.
- I am continuing the trend of going to the gym that allowed me to run marathons (only half-marathons this year, though).

Whee!

Jen! Stop this crazy thing!

Whew! I just need to catch my breath a little. A synopsis of the past few weeks (since May, really):

I saw a friend of mine from high school, who was visiting Vegas with another mutual aquaintance from high school. They decided to drive to LA for about 36 hours to say hello. The highlight for me was the Nature Attacks! quality to the short hike along the hills of Mulholland Drive. A large snake AND a swarm of bees.

I worked my tail off in a class directly related to my thesis work: an in-depth look at the computer science and algorithms behind the scenes in genomics/proteomics research. I plan to TA this class next year, and it's career-choice-affirming to have done well, but... an A+? Eep!

I am going to a parasite conference in September and it's in Alghero, Italy. It'll be great to visit Europe again, and this is luckily one of the little tiny parts that would be hard to think to go to from the US. Alghero in on Sardinia, an island north of Sicily. The conference center *is* a refurbished 13th century monastery. I managed to convince Jen that we should pretend to afford her airfare, too. I won't get to see her much during the days and early evenings full of science, but at least she will get to experience Mediterranean fish and wine, too.

Oh, and I borrowed clippers and cut all my hair off two weeks ago. The bleach and blue dye job for the LA marathon had faded to yellow and green patches that was beginning to bug me. So, I buzzed it all to one inch... first time my hair has been this short in about 14 years. I'll post a photo as soon as I can.

In summary: Booyah!

Moby rocked the house

Jen and I saw Moby perform at the Wiltern Theater on Saturday. It is always great when electronic-focused artists can produce an amazing live show. We saw him at a free Boston Hatchshell outdoor concert in (1999?) right before Play went bonkers on the airwaves. I keep forgetting how small he is, too.

He performed songs from all over his history, so you had new stuff off Hotel and songs from Play of course, but also old favorites like "Go" and other bits of his earlier driving techno. This time around, Moby has an incredible female backup singer (a quick search of the Internets say her name is Laura Dawn) who performed live renditions of most of the female vocal samples from his music, especially the blues stuff. This was by far the most amazing aspect of the show.

We were also treated to a great opening act, always a bonus. Buck 65 (more expensive than 50 cent?) is described as a rap artist from Nova Scotia, and I guess that's his pedigree. Jen and I decided he was more of Tom Waits with a turntable and David Byrne's stage presence/antics, producing a sound we can only assume Soul Coughing would be doing today if they hadn't imploded. He would describe his next song as, for example, "a mix of Charlie Parker, Kraftwerk, and ZZ Top", hit play on his system to get the beats going, and launch into a great beat poet rendition of new lyrics, and mix in some well done scratching. I couldn't tell if his songs are actually constructed from the samples he hinted at, but it was pretty funky and original. I declare this my first exposure to a new genre called electronic post-folk.

There was only one annoying story. We arrived semi-early, so we hung out against a dividing wall between sections of the general admission floor. When things filled up, this presented an opportunity for jerks to crowd us a bit, especially this one idiot. He was obviously wacked out on ecstacy or something, and is the type who can only dance by throwing elbows around. After getting knocked about, and becoming generally annoyed by his need to have full conversations with his companion, I finally poked his shoulder. Explaining how he was pushing me against the wall and too much in my face and would he please try to step forward a little bit must have harsed his mellow, because they moved to a different section. Score! Jen pointed out that this works two ways and I will probably be the asshole in his story about the show today, but feck 'um.

What's that? Timmy fell in the well again?

...dogs' barks have evolved into a relatively sophisticated way of communicating with humans. Adam Miklósi, an ethology professor, set out in a recent experiment to see if humans can interpret what dogs mean when they bark. He recruited 90 human volunteers and played them 21 recordings of barking Hungarian mudis, a herding breed.

The recordings captured dogs in seven situations, such as playing with other dogs, anticipating food, and encountering an intruder. The people showed strong agreement about the emotional meaning of the various barks, regardless of whether they owned a mudi or another breed of dog, or had never owned a dog. Owners and nonowners were also equally successful at deducing the situation that had elicited the barks, guessing correctly in a third of the situations, or about double the rate of chance.

File USA Income Taxes Online For Free

For those who have been procrastinating about doing the dreaded income tax crap for this year, apparently a lot of providers have an unpublicized deal with the IRS to offer their online filing service for free (with certain qualifications necessary in a few cases). This likely will apply to only Federal and not state filing, but now I know where to start when I finally get around to this over the weekend...

IRS.gov - File Free Home

(via Lifehacker)

Guess which one is me

Why journalism and science don't work together as well as they should

As /. points out, here is a prime example of how the current state of journalism is "hurting America" (thank you, Jon Stewart): acting a little too balanced in scientific coverage.

From the November/December 2004 Columbia Journalism Review, Blinded by Science
How ‘Balanced’ Coverage Lets the Scientific Fringe Hijack Reality
By Chris Mooney

In part,

The basic notion that journalists should go beyond mere “balance” in search of the actual truth hardly represents a novel insight. This magazine, along with its political Web site, Campaign Desk, has been part of a rising chorus against a prevalent but lazy form of journalism that makes no attempt to dig beneath competing claims. But for journalists raised on objectivity and tempered by accusations of bias, knowing that phony balance can create distortion is one thing and taking steps to fix the reporting is another.

...

Yet in each case, the basic journalistic remedy would probably be the same. As a general rule, journalists should treat fringe scientific claims with considerable skepticism, and find out what major peer-reviewed papers or assessments have to say about them. Moreover, they should adhere to the principle that the more outlandish or dramatic the claim, the more skepticism it warrants. The Los Angeles Times’s Carroll observes that “every good journalist has a bit of a contrarian in his soul,” but it is precisely this impulse that can lead reporters astray. The fact is, nonscientist journalists can all too easily fall for scientific-sounding claims that they can’t adequately evaluate on their own.

That doesn’t mean that scientific consensus is right in every instance. There are famous examples, in fact, of when it was proved wrong: Galileo comes to mind, as does a lowly patent clerk named Einstein. In the vast majority of modern cases, however, scientific consensus can be expected to hold up under scrutiny precisely because it was reached through a lengthy and rigorous process of professional skepticism and criticism. At the very least, journalists covering science-based policy debates should familiarize themselves with this professional proving ground, learn what it says about the relative merits of competing claims, and “balance” their reports accordingly.

Voting the Vote Vote

I had to be on campus at 9am, and I'm in class until 7pm. Since it was likely that I would miss the pesky deadline of 8pm if I tried to end the day by voting, given the reliability of my bus sometimes, I opted for attempted voting early in the morning.

At 7:25am, there was a line of at least 50 people. I was inside after close to an hour wait. When I left, the line was much longer than when I initially joined it. Thankfully, I had 5 minutes to spare and catch a bus and made it to school on time.

There was no turmoil or calamity at my polling station, unless you count little children running around outside as they arrived at school (I vote at Palms Elementary around the corner from my apartment). One 8ish-year old boy called out "Vote for Kerry!" at least twice, in clear violation of electioneering law.

If you haven't voted yet, get the heck over to your polling station and do it now, my friends. The registered voter has been coming out of the woodwork this morning, and news coverage makes it sound like I should expect riots as polls begin to close.

Fly On, Superman

CNN.com - Christopher Reeve dies at 52 - Oct 11, 2004

A telling quote from the article, given the re-emergence of stem cell research as a campaign issue:

The actor went through months of therapy to train himself to breathe without the continuous aid of a respirator. He then became an advocate for the disabled, lobbying Congress, appearing at the Academy Awards and returning to acting and directing. His name was mentioned by Sen. John Kerry during Friday's presidential debate when the talk turned to stem cell research.

Reeve himself was vocal on the subject. In 2001, while President Bush considered a decision on stem cell research -- he eventually allowed federal funding of research using existing stem cell lines -- Reeve spoke to CNN's John King about the impact of delaying study.

"That would be a big mistake because you could spend the next five years doing research on the adult stem cells and find that they are not capable of doing what we know that embryonic cells can do now," he said. "And five years of unnecessary research to try to create something that we already have would cause -- well, a lot of people are going to die while we wait."

Tidbits

I'm teaching this quarter (TA for what is essentially an intro genetics course), so I'm already over-extended and sleep-deprived six days into the quarter. Here's some stuff I've been meaning to post about.

• GOOD STUFF CATEGORY: SpaceShipOne captures X Prize
• BAD STUFF CATEGORY: Rhino hunting approved by wildlife delegates

Francis Crick RIP

Francis Crick, co-discoverer of the structure of DNA, is reported to have died today. Much respect, yo.

(found what should be a stable link to an obit at Salk Institute for Biological Studies)

The Peaches of Despair

I finally read The Grapes of Wrath, to atone for going the Cliff Notes path in high school, and also because Steinbeck is cool. I agree with Jen that this is a better book for adults anyway, since you need to know the joys and sorrows of working to buy your own food before this novel can hit home.

Extra poignancy points for paralleling the modern employment age 70 years later, too.

My favorite bits offering advice to try and live by each day:

Our people are good people; our people are kind people. Pray God some day kind people won't all be poor. Pray God some day a kid can eat.

and

"Jus' live the day," Ma said. "Don' worry yaself."

Watching Paint Dry

Watching Paint Dry

The British tire of reality TV. Go Eggshell Red!

(via The Register)

Al Gore makes the baby Jesus cry

I caught the speech that Al Gore made today calling for Rumsfeld, Rice, and Tenet resignations on the MoveOn website (via political blog Eschaton). I like it when Democrats remember that they can speak their minds.

The GOP response is a great example of faulty logic, naturally.

"That shock at the mansion had done something to my brain"

I just spent about 15 minutes or so, passing time while super geek math software compiles on my laptop, cleaning SPAM from this blog's comments sections. I am utterly confused. This is not a high traffic site. Does it even have traffic?

Most of the posts looked like a computer-generated bad novel, with words replaced here and there with drug names, and links to this obviously illegal online drug store. Yet, they also linked occasionally to real FDA or manufacturer information. And all this in early April, when this site hadn't been updated in several months.

I've preserved the text below for posterity. The mind boggles...

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Catching Up

End of the summer and fall school preparations have kept me away from this site for too long. Here's a snap shot of the last week or so.

End of the summer and fall school preparations have kept me away from this site for too long. Here's a snap shot of the last week or so.

Beer in the Closet!

Jen and I have started our first batch of beer. It's a porter, and I predict a good amount of hoppiness. We boiled all the good stuff on our stovetop, though with some trouble keeping the boil going as strong as I wanted. It's all sitting in a five-gallon plastic tub in the living room closet, where the yeast are doing their primary fermentation magic.

Beer geek note

The starting specific gravity was only 1.030, where we should have expected more like 1.045. But we're beginners, and this should be tasty, if not that alcoholic in the end. (Higher SG at the start of fermentation is more sugar to convert to alcohol and carbon dioxide.) Potential culprits in this newbie brewing experience are too much boil down during the hopping (we had to add over 3 gallons of water in the end, rather than the 2.5 we expected, so perhaps we diluted too much), not enough mixing before taking the SG reading, or sloppiness in the reading itself, since I haven't used a hydrometer since high school chemistry.

Jen will probably say that I'm harping on the negatives too much here. I guess I'm being the analytical scientist brewer at the moment. This was a lot of fun, and we'll be doing it again and again, I think.

School update

Orientation for my program at UCLA is Thursday. I'm a little nervous, but not too much, as I've been on campus already for three months, and know some people and know my way around already.

My first research rotation in the Chemistry and Biochemistry department (proteomics, mass spectrometry, and data visualization) finished up yesterday. I have a tentative arrangement to work with a professor in the Human Genetics department in the fall. This will involve microarrays, another hot topic and excellent skillset to get my feet wet in. I'm happy to take advantage of the opportunity to try out different departments through this program, as Ph. D. students usually are locked into rotating in one department.

I'm spending the next two days chilling out before the crazy schedule begins, and reviewing calculus. I decided to start fulfilling pre-requisites in math and computer science that are missing from my previous attempt at academics, so I'm taking linear algebra in the Fall quarter (UCLA does 3 quarters a year instead of 2 semesters). Expect me to grumble about this schedule a few times, though, as this class is at 8am four days a week, to free up my afternoons for research seminars. Bleh. It's only for three months, but at least I'm motivated for this whole school thing!

Gotta Start Somewhere

Dear Diary,

Well, not quite. But I could resist the temptation to publish myself no longer. See, in case someone who doesn't know me personally is actually reading this, my wife Jen and I moved from Boston, MA to Los Angeles, CA in June 2003. As if that situation wasn't a great source for blogging material already, I am also enrolled full-time in a Ph.D. program at UCLA.

Consider this a test post, so I have some content on the screen to better fiddle with the web interface design, but it's a start. More meaningful (?) posts to follow...