Episode CXXXV: Home for the Holidays

We celebrated the holidays (Thanksgiving, Christmas and New Year's Eve) with family this year. We went to see Meg's parents in Maine for Thanksgiving (where it snowed around half a foot). We then finished up Thanksgiving weekend with a short road-trip to Rhode Island, where, among other things, we brunched in America's oldest tavern (established in 1673!)

 

For Christmas we visited both sets of families. While in Maine, Meg got her hair cut. While in California, I got my hair cut. Below is the before & after picture:

Some other things we did in California-

We celebrated Brian's birthday:

Ate sushi off giant conveyor belts:

Compared and contrasted new in-laws:

And spent a few hours celebrating the New Year with church friends and family. Right before boarding a plane to return to Boston.

Episode CXXXIV: 9-Piano Tune

Last year at about this time the city of Boston teamed up with the Play Me, I'm Yours organization to distribute dozens of pianos throughout the public spaces of Boston and Cambridge. I traveled to a good handful of them and brought my video camera along. The result was this little piece: a nine-piano cover version of my own song "Oh All The Beauty," inspired by Calvin Coolidge, and available wherever fine music is sold (like here!)


Did you miss any of the other videos? See them here.

Did you miss the album? Get it here.

Episode CXXXIII: A Wedding Trip

My cousin Amanda, who is currently going to school in Blacksburg Virginia, got married last weekend! Meg and I had some work flexibility, so we decided to make a road trip out of it. And we also met up with my parents there at the wedding.

The ceremony was lovely, being held outdoors on Virginia Tech's campus, surrounded by autumnal foliage and the stately stone university buildings.

Meanwhile, we had been road-tripping our way to the wedding, stopping at some places Meg wanted to see, such as Philadelphia:

And the District of Columbia:

And a place I wanted to see: Shenandoah National Park, with its beautiful 3-hour Skyline Drive road, weaving through mountain and forest.

 [Appalachian Trail!]

We also spent an extra couple of days after the wedding with my parents, doing things like touring Jefferson's Monticello:

 Visiting the Jefferson-designed University of Virginia:

[Just about the loveliest campus you'll ever see]

And dining on fried chicken in a centuries-old tavern:

[Chicken! Biscuits! Gravy! All-you-can-eat!]

All in all it was a lovely trip to a lovely wedding.

Episode CXXXII: September Adventures With the Wife

Here are some September Adventures my wife and I have been on this year:

Departmental Retreat in Cape Cod

This year Harvard's Molecular Biology department graciously allowed me to attend its annual retreat on The Cape (though I'm not technically a member of Molecular Biology), so I got to join my wife for a weekend with lots of science, seafood and lovely scenery/weather in Woods Hole, MA.

 

[Nice location for 'work,' eh?] 

Camping in Acadia 

As a (belated) celebration of our anniversary, Meg and I took a camping trip to Acadia National Park in Maine. It's a lovely little park. A nice place to just soak it all in- the sea and the forest and the salt and the changing leaves.

While on the beach, I came across two of the biggest clams I've ever seen. I took them back to camp and cooked them over the campfire. Best shellfish ever!

Harvesting Acorns

We have this little white oak tree in front of our house, and this year it is having a bumper crop of acorns. I happen to know that white oak acorns, being more palatable than those of its siblings, were used by many ancient peoples (including Native Americans) to make a sort of flour. And so, I engaged in a little cultural/historical/culinary experiment!

Step 1: Forage for acorns (we live on a busy enough street that squirrels tend to stay away, thus I had little competition in my foraging).

Step 2: Crack acorns. I do not own a nutcracker, but I own a lobster cracker.

Step 3: Chop the seeds into flour.

Step 4: Leech out water-soluble tannins (bitter [and bad for the kidneys]) by soaking in water.

Step 5: Dry out in the oven

Step 6: Bake! I mixed in a bit of wheat flour and made some surprisingly delicious honey-acorn pancakes:

Would I do it again? Despite the degree of difficulty (mostly in the cracking of the nuts), I think I would! Those pancakes were most delicious.

Episode CXXXI: Cool and Unusual Things About Japan

I recently returned from a two-week trip to Japan. I had so many unique experiences there that I will have to present my trip in the form of a top-10 list, ranked in no particular order- Top Ten Cool and Unusual Things About Japan:

1) Toilets

Japanese toilets make Western toilets look severely outdated. Nearly every toilet in Japan has (at minimum) heated seats and a contraption for rinsing one's nether-parts after one has relieved oneself (saves on toilet paper!) Other toilets get fancier. For instance, this one:

[Plays music for greater discreteness, sensitive control of the water temperature and pressure, and a bunch of buttons in Japanese that I couldn't decipher]

Also, for toilets located in small spaces (a common occurrence), here's a two-in-one toilet/sink. The sink starts automatically when you flush the toilet.

2) Kyoto

This is such a nice city! A great mix of old and new. A lovely river full of waterfowl. A world-class shopping district where Japanese women still walk around in kimonos. A series of ancient shrines and temples, built at the foot of the eastern mountains, connected by a winding Philosopher's Path.

 

 

3) Amenities present and absent 

A) Unlike  most cities, I found Japanese cities to have a TON of free public restrooms.

B) However, these restrooms almost never have drinking fountains. Nor do hotels have drinking fountains. Nor do universities, nor conference centers. In fact, I encountered a total of 3 water fountains in my entire trip.

C) Even more rare are public trash cans. People actually bring bags around with them to carry their trash home in. I walked many dozens of miles during my trip, and encountered only ONE location with a public trash can.

4) Tokyo

This city is great. All the excitement and electricity of New York City without all the incessant horn honking. Literally, NO ONE honks in Tokyo. What can you do in Tokyo? Just about anything:

Looking for an arcade dedicated to claw crane games? Check. An arcade dedicated to music-themed games? Check. A hundred stores dedicated to anime? A three-story McDonalds? A lake full of giant lily pads? An imitation Eiffel Tower? The world's largest fresh fish market? A whole store of vending machines? Check, check, check, check, check and check!

[Vending machines serving ice cream, beer, fresh-popped popcorn, canned goods, etc. etc. etc.]

 5) The Deer of Nara Park

My conference was held in the moderately-sized town of Nara, where for centuries deer have been considered "sacred," and it has been illegal to harm them. Thus in modern Nara, the deer are extremely friendly to humans (when they have food). Look how well they've integrated into the culture:

[Deer patiently letting me pet it]

 [Deer patiently letting me touch its antlers]

 

[Deer patiently waiting for the bus]

 

[Deer 'patiently waiting' for man to feed them deer cookies]

 

 [Deer patiently waiting to be served at a restaurant]

6) Bike lanes
There are no bike lanes, but there are a lot of bikes. They all ride on the sidewalks, where there are a lot of pedestrians. You would think this would cause a lot of chaos and collisions. But I did not see a single collision, or a single person getting cut off, or a single angry or agitated pedestrian or cyclist.(Besides myself.)

7) Old wooden buildings

Japan is a very old country,  but most of its ancient buildings were constructed entirely of wood. Therefore, many ancient buildings have been lost to fire. But those that remain are pretty spectacular.

 [The largest ancient all-wooden structure in the world]

 [Inside it houses this ginormous Buddha statue. Note the size of the person (bottom right), then note the size of the Buddha, then note that it was built in the year 751 (!)]

8) Food

I was not at all disappointed by the food. Excellent ramen, sushi, fish of all sorts, exotic snacks (cuttlefish jerky anyone?) and the like. Most of the meals I ate were of the traditional variety, where you are served a very large number of very small portions. My guidebook says that traditional Japanese meals strive to include five tastes, five colors (white, black, red, green and yellow) and  five "ways" (simmered, fried, steamed, grilled and raw) into every meal. Makes for a fun meal!

Only problem is, all the meals are pretty similar in theme. Even breakfast tastes just like dinner. (Apparently the translation of "breakfast" from Japanese is "The Morning Rice.")

 [Yes, this is breakfast. Note the whole grilled fish to the right of the grapefruit. Also, NO COFFEE. OR JUICE.]

9) Bullet train

These things are fast. They go up to 200 mph. The craziest part is not riding the train, but sitting at a station and watching a bullet train speed by (one that's not stopping at your station). The train appears at the station, and in about two seconds the whole ~20 cars have zoomed by and disappeared out of sight.

 [Doesn't this just look like the future??]

 
10) Madame Fuji

The Grandmother of all mountains (the Japanese call it "Mr. Fuji," but the "Mr." is gender-neutral, and my Japanese companions tell me it's mythologized as a lady). Climbing a volcano is utterly unlike any hiking I've done before. It's like hiking on Mars.

 

[Fuji or Mars? You tell me!]

 

[Fuji or Mars? You tell me!]

To climb Mount Fuji: There are no "trails" with switchbacks. You hike straight up the mountain. At never-ceasing ~45-degree angle. There is no dirt. You climb from one lava rock to the next. There is no shade. You are above tree-line for 90% of the hike. There are no streams or rivers. There is no wildlife. If you wish to be at the summit for sunrise, you camp out halfway up the mountain in a hut, where you sleep shoulder-to-shoulder with 100 other people. Then you awake at 1 a.m. to finish the last 3-4 hours of the hike.

Is it all worth it? Yeah, it is.

 [Sunrise over the caldera's edge]

 [Just hanging out, above the sky]

Episode CXXX: A Publication

I am happy to announce that my first research article as a postdoctoral fellow is now fully published, available online and anywhere highly-specialized molecular biology journals are sold. If you happen to be at a library or a university, you may be able to access the paper in all its online glory by clicking here. Otherwise, check out the PDF, and/or read on!

This paper was a bit of a family affair. As you can see above, I am the "first author" of this paper, but my wife also appears as a "middle author" (i.e. she had substantial scientific contributions to the paper- this was while she was working in my lab the year before entering graduate school).

[In case you missed it the first time]

Moreover, while he is not acknowledged in the paper, my brother Brian gave a helping hand as well. I needed to run a program in Linux, but the program was no longer being updated/supported, and thus the OS needed substantial modifications to run the program. Who better to ask than Brian Norris??

 

[The experiments marked in red- made possible in part by Brian Norris (from pages 950 and 957)]

And remember this picture, from when Mom came to visit and insisted on helping me with my experiment?

Well that happened to be a last-minute experiment for this paper (required by the reviewers). I was harvesting worms to measure their RNA levels by "RT-PCR," and she was helping me harvest them. Here are the results:

 

 [Made possible in part my Sandra (Mom) Norris (from "supplemental data")]

So there you have it. Norris et al. 2014. With contributions by no less than four Norrises.

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Appendix: 

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If, per chance, you would be interested in my attempted explanation of the research contained in this paper tailored to a lay audience, read on:

(1) Most genes in animals are modular, in that individual modules (called exons) are spliced together to form "mature RNAs" from which proteins are made. Think of it like a film- there's a ton of raw footage, from which a handful of modules (scenes) are spliced together to make a coherent film.

(2) Many of these genes can be spliced together in a multitude of ways, in a process called "alternative splicing". Individual exons can be included in some RNAs, whilst being excluded from otherwise identical RNAs from the same gene. Think of it like alternate cuts of a movie- director's cut, final cut, extended-special-edition cut, etc. They're all the same movie, but each is partially unique.

 [Wikipedia image- a gene before splicing on the left, after splicing on the right. The bottom example would be analogous to the theatrical cut, and the upper analogous to the director's cut (because it has an extra "scene" included!)]

(3) Points (1) and (2) were already known before my paper. I endeavored to observe: how prevalent is alternative splicing between different types of neurons? In the analogy, the question would be- for most genes, do all neurons possess the same version of the film, or is there substantial use of alternative editions from one neuron to the next? The answer turned out to be the latter- alternative splicing within the nervous system is widespread and diverse.

(4) One particularly interesting case of alternative splicing was in a gene that was spliced in one way in excitatory motor neurons (the neurons that allow you to flex your muscles) and spliced differently in inhibitory motor neurons (those that allow you to relax your muscles). The rest of the paper seeks out the mechanism and identifies the "director" responsible for this alternative splicing event (it turns out to be two different directors! [i.e. two different proteins]).

(5) Why is this important? We think alternative splicing is critical for increasing the complexity of cells and complex organs like the brain. It may well be that complex organisms and/or nervous systems would be impossible without robust alternative splicing. Indeed, many neuromuscular diseases (as well as cancers) are associated with failures in proper splicing and/or alternative splicing. Therefore understanding its proper regulation is of high importance.