to the world re. the events in corvallis

Corvallis has made national news for something other than having what may be the strangest mascot in college football. And Benny is darn weird.

Just a few days ago, a non-degree student from Corvallis tried to conduct an act of terrorism in Portland. He attempted to bomb a Christmas celebration. Thankfully our tight national security did pay off and he was subverted by some intricate work by Federal agents.

A few days later, in the wake of a huge electrical fire on campus, which damaged almost every building's systems, in some cases releasing asbestos and closing down facilities, a mosque in the town burned, and arson was suspected. Whether this be the case or not, undoubtedly it would be a show of "retribution" that I am sure many people feel. I'd say by now we all know someone who has been involved in the long-standing "war on terror" (whatever our perspectives of it are) and at least understand that there is some serious tension going on in the world, and that this tension follows us home in the form of individuals hurt (on either side) by the particular circumstances in the middle east.

So what happens when all of the sudden a peaceful, crime-free, little valley/mountain town full of vegetable-loving lumberjacks and hardcore bikers and snowshoe wearing professors is faced with national dilemma? Corvallis is one of the happiest and most educated towns in the United States. At just over 50,000 people, it's small enough to have a little downtown and town hall, but large enough to have many amenities (in other words, it's a college town!). There are people of many races, economic states, "styles", religions, and sexualities here, and everyone is accepted. In fact, I'd say it's part of the town appeal that there aren't boundaries separating hobos, hippies, engineers, coffee-drinkers, suburban moms, practicers of esoteric faiths, the GLBTQ community, etc. Everyone here not only tolerates but enjoys the differences we have. It is my favorite thing about this town-- that no one is an outcast-- not even me-- not even other people who may have felt more isolated than me. We each have to make it through the rain together.  In general, I would say it's the "most joyful" little town I've ever seen.

Now Corvallis hits national news for being the home of terror. It's kind of a shock, that this is how a little town gets its name. I feel kind of blown away by it-- my parents sending emails of warning about terror, reading all the police reports from the campus emails. I think it's important that we remember OSU's official response to the actions against Portland and against the mosque. While many places might tighten security, OSU elected to host a vigil for our Muslim community, to remember that they are an important part of the town just like everyone else. They are hurting too-- faced with discrimination and misunderstanding-- and the feeling of betrayal by a community member. To me this action on the part of the school and the town honors what we need to remember: not everyone who practices a certain faith is a terrorist, and people of every walk of life have the option to be good or evil. It is good to stop to remember this event, vigil or no vigil, and to remember the sufferings of the community when one of its members makes a bad choice.

I hope that other towns in the country can look to Corvallis in the wake of what has happened and think of it not as a little breedinig home for terror, but instead a community that fought terror with compassion. After all, our name does mean "heart" of the valley-- we might as well show some of it.

No good title for this

Today seagulls flew over the mountain. Three of them, white with grey wingtips, they looked like staples how they bent. The mountain is green this month, finally, and when they flew in front of it they cut v-shaped holes in it to the cloud behind the mountain.

I see patterns in everything. The way the clouds roll over the mountain and rise above it, a big plume, rounded, and then a smaller trail coming out, and then it repeats until it hits a little saddle and the whole thing comes plummeting down the side, and then it gets sucked back up the far side of the saddle into an explosion of cloud spiral that becomes nothing as it reaches the sky. I always have seen these patterns, and I can't shut down the part of my head that sees the world like a whirlwind of processes. Even in the east, these patterns are there, but they were muddled, and easier to try to ignore. The land is older, it has been used longer, it's more weathered. The trees forgot who they were, and are mixed with things that humans have added in. The natural pattern is gone, unless you remember the history-- in the south, savannah, longleaf, chestnut; in the north, deep bogs, residual organic matter, and slow leeching-- and then you start to see it, the patterns.

Here they are pristine. I can see them every day. I breathe deep air into my lungs. The rains fall, like they did last year, like they will next year. Patterns.

I learned when I studied English that there is a very small, select way of looking at the world through these bright events and patterns. It felt natural to me, more natural than learning about history and methods and culture, to look at words and their arrangement on a page, and to draw from that the meaning of it all. Some authors knew this, and their works were sharp and bright like conifer forests. I can't bear "hardwood writing" now because it's barren and decayed, filled with way too much florid language that ultimately falls off and leaves just a wet, cold stem. There's nothing active or exciting about a wet cold stem. There's nothing exciting about prose without pattern, pattern that acts as a machine to generate output, images, knowledge.

Here the earth trembles and the trees cycle and the rain falls and the clouds roll. The place is alive. The weathered coast ranges are a repository for the history of the volcanic cycles that formed the Sierras and the Cascades a long time ago. My home is being ripped apart by a tectonic fault that in millions (or less) of years will tear western California and Mexico from the plate that the continent sits on. Every day that fault pulls just a little further. It is fascinating to me that this pattern has been occurring since the world began, slowly declining in strength as we cool off. How long do we have until we cool off? How much longer do we get to see the pattern?

It won't change in our lifetimes. The pattern world will keep on dancing, running, singing, and haunting me with stellar views of the sea and the bay and the coastal mountains. And so long as nature keeps on making strange music, I'll continue to try to find those harmonics, understand the song, and write it down for other people to see, hear, and learn to play.

The second day

I miss my wife.

This morning, it was pouring rain at the bus stop, dripping through the leaky shelter. Sea rain -- a spray of cold, tiny droplets. I pulled my collar up and watched the rain fall, thinking of her. I've found that the loneliness is most intense the second day after we part. On the first day, the memory is still so fresh it's almost as if we're together, and after the second day, it rounds out, dulling slowly as time passes. But the second day, I miss her ferociously, and the solitude is almost unbearable.

Today is the second day. She's planning to drive down the coast, but the road to the sea is covered with snow. Here, it is only raining; the rain quietly pelts the bus as it trundles its way up into the city. I am 600 miles to the south, on the Pacific coast, where it hasn't snowed in a hundred years. It's about a half mile to work from the bus stop at Potrero and 16th, and the rain has slowed to a drizzle by the time I start walking.

At noon, she calls to tell me she's bought snow chains for her car. It's the second day, and she's filled with the same terrible sense of loss. She'll drive through the night, slowly crawling her way down the hundreds of miles of coast. She says to expect her at about 4 AM. I will. I send all my luck her way.

Things will get better for us. One day, maybe just a couple years from now, my wife and I will live together. We won't be poor anymore or have to spend months apart. Someday not too long from now we'll both be finished with school, and we'll be working together, living together, in a beautiful place somewhere on the west coast. Just got to think about that, and keep focusing on it and working toward it, and I can make it real.

I'm walking in a winter wonderland

... unfortunately, right now it appears that I can't be driving in one!

Short Term Forecast


Central Willamette Valley (Oregon)

SHORT TERM FORECAST

NATIONAL WEATHER SERVICE PORTLAND OR

431 AM PST TUE NOV 23 2010

ORZ001>010-012-014-WAZ020>023-039-040-231615-

NORTH OREGON COAST-CENTRAL OREGON COAST-

COAST RANGE OF NORTHWEST OREGON-

CENTRAL COAST RANGE OF WESTERN OREGON-LOWER COLUMBIA-

GREATER PORTLAND METRO AREA-CENTRAL WILLAMETTE VALLEY-


SOUTH WILLAMETTE VALLEY-WESTERN COLUMBIA RIVER GORGE-

NORTHERN OREGON CASCADE FOOTHILLS-

CASCADE FOOTHILLS IN LANE COUNTY-UPPER HOOD RIVER VALLEY-

WILLAPA HILLS-SOUTH WASHINGTON COAST-I-

5 CORRIDOR IN COWLITZ COUNTY-GREATER VANCOUVER AREA-

SOUTH WASHINGTON CASCADE FOOTHILLS-

INCLUDING THE CITIES OF...ASTORIA...CANNON BEACH...TILLAMOOK...

LINCOLN CITY...NEWPORT...FLORENCE...VERNONIA...JEWELL...TRASK...

GRANDE RONDE...TIDEWATER...SWISSHOME...ST. HELENS...CLATSKANIE...

HILLSBORO...PORTLAND...OREGON CITY...GRESHAM...SALEM...

MCMINNVILLE...DALLAS...EUGENE...CORVALLIS...ALBANY...HOOD RIVER...

CASCADE LOCKS...MULTNOMAH FALLS...SANDY...

SILVER FALLS STATE PARK...SWEET HOME...VIDA...LOWELL...

COTTAGE GROVE...PARKDALE...ODELL...FRANCES...RYDERWOOD...

RAYMOND...LONG BEACH...CATHLAMET...LONGVIEW...KELSO...

CASTLE ROCK...STEVENSON...SKAMANIA...VANCOUVER...BATTLE GROUND...

WASHOUGAL...TOUTLE...ARIEL...COUGAR

431 AM PST TUE NOV 23 2010

.NOW...

VERY COLD AIR WILL REMAIN OVER SOUTHWEST WASHINGTON AND NORTHWEST

OREGON TODAY...WITH TEMPERATURES LIKELY REMAINING BELOW FREEZING

EXCEPT AT THE COAST. ISOLATED SNOW SHOWERS OR FLURRIES ARE ALSO

EXPECTED EARLY THIS MORNING...BUT THESE SHOULD END BY LATE IN THE

MORNING...WITH NO ADDITIONAL ACCUMULATIONS EXPECTED. HOWEVER...

ROADS AND SIDEWALKS WILL BE ICY THIS MORNING MAKING TRAVEL


DIFFICULT.


let us hope that as the day goes on it will get warmer. if i can get to the sea, it's just rain and wind (a.k.a. stuff that south carolinians drive in all the time)... i just have to get there!

I listened to a speaker the other day extol the virtue of transdiscplinary students. These students, he proclaimed, used tools from one field to impact signficant findings in another field. He was in an administrative position, and hoped to use that power to make all students transdisciplinary.

I don't agree with this approach.It is, of course, not my call, but I have found that this kind of overarching knowledge is not worth the effort it takes to gain it. Here is why:

There is only so much information a student can absorb in a day, week, month, year, Ph.D time period. You could, of course, get even less information, but there is a certain max capacity that exists. We work 100 hour weeks, sometimes staying up for 3-5 days in a row, hoping that we'll be able to absorb even 1/2 of what we're expected to know. Many graduate students take medications to help anxiety, stress, and depression. I for one can say that graduate students live on such low wages that they are sometimes homeless. We don't do this because it's always fun. We do it because we want to be able to have our work and our lives be gratifying. We want to push the boundary of what people know and what they can know. We do it because we have souls that seek deeper innovation and understanding.We accept that it will be hard and stressful because we don't really like living in a way that doesn't spurn us to learn something new every day. It's how we are made.  That being said: we are also human. We need to sleep, exercise, eat healthy foods, have shelter, spend time with those close to us, and sometimes just chill out. And actually, this rant does relate to what I will say:

Graduate degrees-- masters and to a greater sense, the Ph.D.-- are subject-specific. They are designed to make you an expert in a specific field. I don't deny that interdisciplinary skills are useful-- and that's why most committees put at least one "out of field" person on the committee-- but the very designation of having an "out of field" requisites that there is an "in field. Universities and colleges are sources of collarboration-- specific places where academics can get together with other academics with specific knowledge in other field, and work more productively.

So assume we have a limited quantity of knowledge that can be obtained, and 1 main field, and 9 tangential fields to which it can be allocated. A transdisciplinary student might give 40 percent of that knowledge to the main field, allocating ~6% to each of the tangential field. A regular student, on the other hand, might give something like 75-80 percent to the main field, and only ~3% to the tangential fields. Come exam and production time, it's clear to me that a specific approach is better. You get nearly twice as much knowledge about your main field, which is what you came to study. At a range of 3-6% your knowledge of tangential fields isn't really very significant anyway. Why press it?

This man cited a few specific examples of times when it would be good to be transdisciplinary. What if a technology were used in one field that could apply to another? What if a student attended another disciplines conferences and met new colleages?  But these things could be achieved through collaboration and networking as easily as through mandated transdisciplinary programs of study. If the Ph.D. is supposed to be a transdiscplinary degree, then we should never have to defend our work alone against committees of scholars with specific interests. Instead, there should be some kind of collaborative debate or application construction. If a defense is the way to go, then the Ph.D. should be specific, and specific to the student's interests and abilities. In terms of the world advancement, I can't say I would believe that the world would get better if a whole lot of people knew a little about everything. Not to mention negotiating would be nightmarish. Rather, having collaborations between specific knowledge benefits everyone.

So that's what I have to say of this. 

So...what now?

I passed my orals!

So...what now?

I guess the first order of business will be to actually carry out the research I proposed. However, I'm a fourth-year student, so my project is pretty far along. There's a substantial amount of work remaining, but my (naive?) expectation is that I'll publish my "main project" sometime this spring. I do have to do what I proposed, of course, but I have about two years left; I don't think that will be all I'll do for the remainder of my graduate work.

The nice thing about my overall project -- not just the part that comprised my orals proposal, which I zeroed in on because it was (1) biological and (2) easily defensible -- is that it's broad enough to take me in almost any direction I want. "Stochastic power laws" are everywhere. Biological networks, solar flares, earthquakes, scientific citations, electrical blackouts, stock price fluctuations, the growth of cities, links to websites, and a wide variety of other things. I've also been digging into graph theory and statistical physics, two subjects with a great many applications.

I've been considering taking some physics classes over at Berkeley or Stanford. UCSF has an arrangement with both schools that allows our students to take classes at either school for free. Mostly from necessity, my approach to my research has been to look at each task as sort of an engineering problem, and learn whatever I needed for the task at hand. However, coming from a physics background, I find this piecemeal approach to be unsatisfying. I spent a fair amount of time thinking about this, during the buildup to my orals, and I think what it comes down to is that I'd really like to complete the standard physics PhD curriculum. I originally thought of biophysics as one of many physics specializations -- like particle physics, astrophysics, nuclear physics, etc. -- but in reality, it's something else altogether. More to the point, it isn't exactly physics, and I think that I would like to salvage my physics education, to whatever extent that's possible. My strategy may be to simply drive down to Stanford and ask if they have some kind of certification program; I can't be the only interdisciplinary student who's thought this way.

Now that I'm not frantically studying for orals, one thing I've resolved to do is resume learning Chinese. Realistically, what I'll need to do is brush up my Chinese just by studying, then, with everything fresh in mind, immerse myself in the language for at least a few months. That will be the tricky part. But, if I study it slowly but consistently over the next two years, right after I finish my PhD might be a good opportunity to go abroad! So the timing might actually work.

One thing I'm seriously considering is (at least, temporarily) transitioning away from biological networks, and into a more physical system -- solar flares. This is appealing for a few reasons. First and foremost, it's a natural way for me to segue into a field that's always fascinated me, astrophysics. Biology is interesting, too, but it's more of a practical interest (for me, at least). I'm not sure if I'd want to jump over to astrophysics entirely, but getting some experience in the area so that the option is there strikes me as something I'd be very foolish to turn down. This is one of the great appeals of studying networks -- it's one of the very few academic fields that allows you to avoid hyperspecialization. It's not unrealistic that my research actually could cover both biology and astrophysics, linked through the study of networks. A side benefit of pursuing this is that I'd be forced to learn some new physics.

I guess the real quandary for me is how heavily I want to emphasize the theoretical, foundational aspects of my work, versus modeling specific systems. To some extent they're related, and I can do them simultaneously. But given the choice -- and apparently I really do have this choice -- to (1) study a fascinating physical system (solar flares) in detail or (2) really dig into the theory of variational principles and their application to network dynamics...well, it's a tough choice. But, I guess I've got at least a few months before I have to make a decision...

Six ways to increase your stress level

At UCSF, the widely-agreed-upon worst experience of a graduate student's academic life is the oral qualifying exam. The most succinct explanation for how orals work is that you stand in a room with 4 professors, who are experts in your field, and you have to defend a research proposal from three hours of grilling from them. Here are several reasons why this is an awful experience, in no particular order:

1. Evaluating a research proposal is subjective. The research hasn't been done yet. Deciding whether or not a proposal is likely to work is (in my view, at least) a much harder task than evaluating a finished project. So you might think your proposal is airtight, but in the end, the outcome of your exam rests on getting your committee to agree with you.

2. The committee isn't required to limit the scope of questions to your proposed research. The exam is very open-ended: the committee can ask you whatever they feel like asking you. This makes it impossible to ever feel like you've studied enough for the exam.

3. You have to get 4 busy professors to sit down in a room with you for 3 hours. Not surprisingly, this is a scheduling nightmare.

4. You're expected to have "preliminary results." This extremely unfortunate feature of the exam was (I think) set up with the best of intentions: it's supposed to be a demonstration that what you're proposing to do is basically plausible, and provide a framework for discussion. However, in most cases, it's not at all clear what constitutes "plausibility," and how detailed these results need to be for the proposal to pass the laugh test. This leads to proposals that are (1) unnecessarily tentative and incremental, and (2) impossible to defend until they're just short of completion.

5. You take the exam alone. This sounds obvious, but if you're in an interdisciplinary program, often there's a big emphasis on collaboration -- as a not-so-hypothetical example, if your project requires some expertise in graph theory, bioinformatics, statistical physics, structural biology, and genetics, then as a practical matter, typically the way you'd handle that is to collaborate with people with deep expertise in those areas. Interdisciplinary programs are set up to encourage this collaboration, it being recognized as the most efficient way to handle projects of this nature. However, as you write your orals proposal, the horrifying fact begins to dawn on you that you can't take your collaborators into the exam with you. You're going to be interrogated on all of those subjects, and be expected to answer detailed questions and objections.

6. The point of the exam is, as I understand it, to see at what point your knowledge fails. That is, have you thought deeply and critically enough about your project, and the underlying subjects, to be able to competently carry out the proposed research? (Another, more cynical, way to say this is, Will you be an embarrassment to our school's good name if we give you a PhD with "UCSF" stamped on it?) The reason this is extremely stressful is that you know going into the exam the committee is going to keep pushing you until you break -- and then decide if what it took to break you was high-level enough that you deserve to continue on towards your doctorate.

Anyway, preparing for and taking orals is a pretty harrowing experience. I'm happy to report that I passed my orals this past week. As one of my labmates observed to me afterwards: "It's nice to know that you'll only have to do this once, ever, in your entire life." That, in fact, is one of the things that helped me keep my nose to the grindstone -- the knowledge that, if I failed the exam, I'd have to re-take it in a few months (and get kicked out of school if I failed again). The thought of going through this again was more than sufficient motivation to keep me hitting the books, night after night.

Now I'm done, and I'm taking a week or two off, during which I have to decide what to do next. It's the first time in a long time that I have something like an open, unknown road in front of me, and I intend to make the most of it.

on his way to doctordom!

SOMEONE WHO POSTS ON HERE IS REALLY GOOD AT PHYSICS, I HEAR!!!!!


CONGRATULATIONS!!!

That's him....

He's BRILLIANT

A PHYSICIST!

I breathe a sigh of relief

Nervousness has been high in Benton county because of the possible winning of Republican Governor Dudley.
Thankfully it was just announced that Multinomah Co. (Portland) had a 90% voting compliance rate and that in fact Kitzhaber, the Democratic Governor, won the election.
http://www.oregonlive.com/politics/index.ssf/2010/11/kitzhaber_savors_win_emphasize.html
I like Kitzhaber because he runs on a green platform. Which is especially important when you live in a state with more trees in it than population of the entire world.
I feel proud today to be an Oregonian.

I'm not normal

Long story short, I had a prof back at CU who I am not sure the nature of my relationship. On one hand, I could rant with this prof in a friendly way for hours, mostly about pet peeves such as "abuse of linear regression" (argh) and also about "why do people eat so much sausage and cheese when they are on the Atkins diet?" You see this professor was trying to lose some weight by eating healthy and meanwhile so was the department head, who was on the Atkins plan.  

Now, the Atkin's plan in its original, scientific context, based on the work of Kekwick and Padwan (1953) is a good idea for people with Type 2 diabetes. Essentially the doctors noticed that extremely obese people in a very controlled study (water intake monitored, food intake monitored, exercise monitored, etc.) who were put on a diet of > 80% carbohydrates would gain weight, even when eating less than 900 calories per day. This of course violates the laws of thermodynamics, so the scientists were confused. They also had some subjects on a 2000 calorie per day diet (normal male or active female intake) that was approximately equal proportions carbohydrate, protein and fat, and found that these people lost weight steadily. When they took their subjects on the high carbohydrate diet and increased their diet by 1000 calories of solely protein and fat (some all protein, some all fat, some mixed) they found that these subjects lost weight, and it was concluded that substances in proteins and fats were needed to metabolize carbohydrate. It was then recommended that a diet should have a significant amount of protein and fat for weight loss, and in a calorie controlled diet, that meant that carbohydrate was often reduced. To make a long story short people get carried away with ideas and so the whole Atkins thing spun out of this with the thought of carbs are evil.

Anyway, he often observed the department head eating entire plates of sausage, which seems very excessive. Somehow we got into a joke about weird things you could do with bacon, and it ended up becoming sort of an email thing over a while of bacon related webpages and recipes, and even some bacon chocolate was included at one point.

So i've not heard from this prof in nearly a year, and today I received:
http://www.aolnews.com/weird-news/article/bacon-flavored-soda-sizzles-onto-shelves/19697827?test=latestnews
That is right. Bacon flavored soda.

ICK.

I think like a dog, I think!

I saw this on LoLcats and thought, well, that's funny, when I am thinking I pretty much sound just like that dog. 

My favorite thing! Posting on blogger! My favorite thing! ARCGIS! My favorite thing! Going running!