home home in the bris

From Otis Redding's Sitting on the Dock of the Bay

Sittin' in the mornin' sun
I'll be sittin' when the evenin' come
Watching the ships roll in
And then I watch 'em roll away again, yeah

I'm sittin' on the dock of the bay
Watching the tide roll away
Ooo, I'm just sittin' on the dock of the bay
Wastin' time

I left my home in Georgia
Headed for the 'Frisco bay
'Cause I had nothing to live for
And looked like nothin's gonna come my way

So I'm just gonna sit on the dock of the bay
Watching the tide roll away
Ooo, I'm sittin' on the dock of the bay
Wastin' time

Perhaps the best article about fat I have ever read

Everything you wanted to know about fat

I'm serious, I'm not talking about "fat people" really as much as fat itself in different forms and the risks possible for CHD based on consumption.

Also is a good example of evidence chain statistics.

Let's talk about climate change models

Seriously. It frusterates me a bit to hear terms like "sequestration" and "global warming" used and abused with no pretense.

So to clear a few things up.

Sequestration is a gerund-- that is, it's a noun that comes from a verb, and that verb is "to sequester"-- that word means "to take up." The arguement is often made that grasslands sequester more carbon than trees, and therefore we should convert forestland to grass land. Yes, grasslands do sequester more carbon than trees-- they are more metabolically active, and they grow and die quicker. Which also means that the carbon they take up is-- you guessed it, being returned right back to the environment when they die. Trees on the other hand live for a very long time, and although they aren't as active, consider the size of a bole as compared to the amount of grass that would cover that same basal area. Now consider the timber industry-- harvest that bole on a regular basis (carbon removal) and plant new trees (more carbon storage) and you've got yourself a good natural atmosphere cleaning factory.
But no matter the opinions on what to do in this situation: remember-- sequestration is only half (or less) of the issue.Storage is also to be considered.

Global warming-- now obviously we don't "know" the future. And that means that we are using "climate models"-- essentially we are taking data from the past and interpolating it to future conditions. So statistically speaking, models are already on the fritz of the whole extent issue, which is that a model can't realistically describe something outside of its spatio-temporal extent. But there are things we know about climate patterns (summers are hotter than winters, ENSOs and SOs and PDOs have a certain pattern of spatiotemporal ossillation) that we can use to guide our extrapolations. Or even more generally, for as long as we have record of it (or understand the processes by geological reasoning),climate has oscillated. Which means that just because we have one cold winter or one warm winter doesn't mean that a global warming model is valid or crap. To be honest, the best way I could think to determine if there was warming would be exactly what Dr. Keeling did (filter the Mauna Kea temperature data set), and that did show that the filtered trend increased. Whether 55 years was long enough to show a trend, I don't know.
In short-- one years specific weather conditions in any one place is not enough to validate or invalidate a model.

In short, remember that words are words (sequestration is not "good!" and harvesting "bad!") and models are models.Neither may be accurate but both are quite precise.

/rant

PCA for optimization?

To do a multiobjective optimization over chi-square statistics of simulated data versus experimental data, I wonder if it would make sense to weight the individual objectives using the eigenvalues (standardized or not) of the covariance matrix of the different stats? That is, use PCA to assign weights in a non-arbitrary way. Hmm...

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!

On theoretical geology

"There is no nobler aspiration of the human intellect than the desire to compass the causes of things. The disposition to find explanations and to develop theories is laudable in itself. It is only in its ill placed use and abuse that it is reprehensible. The vitality of study quickly disappears when the object sought is a mere collocation of unmeaning facts"

- T. Chamberlain, 1897

its so beautiful

I believe yes, that is 45 and raining for the next 14 days!
WHY YES! I DO LIVE IN OREGON THANK YOU!

Ecohydrology ~ Synaptic Connections

This is an absolutely fascinating video about experimental mapping synaptic connections, using ecohydrology (trees, streams) as an analogy. It's great-- how connections are formed, how memories are created, how genes determine and don't determine a connectome. It is by  a professor of Neuroscience from Harvard.

One more reason to love Oregonians

http://www.urbanedibles.org/

Because really, where else would you find an online database of "plants in [name of city here] that you can pick for food."

It's SCIENCE really

All those years I spent teaching myself NOT to curse, and it turns out it just might help me.

Well, GOSH DARNIT.
*excerpted from the news article in which I read this*

They recruited 67 undergraduates, and asked to make two short lists of words - one containing five words they might use after hitting themselves on the thumb with a hammer, the other containing five words they might use to describe a table. The participants submerged one of their hands into room temperature water for three minutes, to provide a standardized starting point, then transferred it to a container of cold water and instructed to keep it submerged for as long as they could. In one condition, they were told to repeat the first swear word they had included in their list; in another, they repeated one of the words describing a table.

The researchers measured how long the participants kept their hands submerged in cold water, and asked them to rate the amount of pain they felt. Their heart rates were also recorded after they had submerged their hands in room temperature water as well as after the submersion in cold water. Contrary to their hypothesis, they found that swearing actually reduced the amount of pain felt. The participants kept their hands submerged in the cold water longer for longer, and also reported experiencing less pain, when they repeated a swear word than when they repeated a word describing a table. Swearing was also associated with increased heart rate. 

Swearing therefore enabled the participants to tolerate to the cold temperature for longer, and also caused a reduction in their perception of the pain felt. A difference between males and females was observed. Swearing led to a greater reduction in pain perception and a bigger increase in heart rate in females. Most interestingly though, the effect of swearing in females occurred regardless of their tendency to catastrophise their pain. On the other hand, in the males, catastrophising was found to diminish the effects of swearing on the felt pain. This is interesting in light of other findings which show that men generally catastrophise less, but swear more often, than women.

This study shows that swearing appears to have an analgesic effect under certain conditions. Exactly how is unclear, but the authors suggest that it is because swearing induces negative emotions. It is well known that pain has a strong emotional aspect to it. Fear of pain, for example, is known to enhance pain perception, possibily by activating pathways which descend from the brain and modulate noxious stimuli entering the spinal cord. Swearing, too, is known to induce negative emotions (according to Steven Pinker, it taps into the "deep and ancient parts of the emotional brain"). It may therefore trigger a physiological alarm reaction known as the fight or flight response, which accelerates the heart rate and reduces sensitivity to pain. 

http://scienceblogs.com/neurophilosophy/2009/07/swearing_increases_pain_tolerance.php

my secret dream finally coming true

I don't know if this worked. If not, try here:

http://www.ted.com/talks/stefano_mancuso_the_roots_of_plant_intelligence.html

Also! he mentions networks!

I lol at this

Weather At-a-Glance:

On Average:

Marietta, GA is warmer than Corvallis, OR by 6°F.   Marietta, GA is wetter than Corvallis, OR by 8.2 in.

Records:

Corvallis, OR recorded the highest temperature of 108°F in 1981.   Marietta, GA recorded the lowest temperature of -10°F in 1985.

"Marietta, GA is wetter than Corvallis...."

Weather At-a-Glance:

On Average:

The average temperatures are the same for San Francisco, CA and Marietta, GA.   Marietta, GA is wetter than San Francisco, CA by 29.5 in.

Records:

San Francisco, CA recorded the highest temperature of 103°F in 2000.   Marietta, GA recorded the lowest temperature of -10°F in 1985.

"Marietta, GA is wetter than San Francisco..."

Strange, I think. I would not have expected this. I suppose its looking at total precip, not precip frequency??

Weather At-a-Glance:

On Average:

San Francisco, CA is warmer than Corvallis, OR by 6°F.   Corvallis, OR is wetter than San Francisco, CA by 21.4 in.

Again, how interesting when you think of these charts. Corvallis is sort of a skewed bell curve with a really hot july and august and the rest about the same. San Francisco is a flat line above all the rest of the months. But that skew pulls our entire mean above the SFO mean. 

I have  learned today that statistics and real life don't really seem to agree. 

On a side note, regarding a particular issue with multivariate weighting statistics. I was thinking of this the other day, how to weight the clustering coefficient, boundary parameter and the other stuff. It occurred to me this: PCA is really a weighting based idea, right? The eigenvectors are the weights, and the eigenvalues are the associated variances. So the weight that should be assigned to each one should be the proportion of the variation that it explains.

I think the original PCA was called "multivariate scaling" actually and.... looks it up... some guy named W.S. Torgerson came up with it. I have also read here that there is a special set of algorithms for "multiscale multivariate analysis for given measurements of dissimilarity measures and variables in mulitvariate data" and that this is found in Meuman J and Verboon P, 1989. 

Articles and I have a little misunderstanding

The following fun comes from Steven M. Chambers' Spatial Structure, Genetic Variation, and the Neighborhood Adjustment to Population Size. Conservation Biology 9(5): 1312-1315. No harm is meant to Mr. Chambers' original article, he just used lots of lines to play with--->

While flipping through 110 years of journal articles about "spatial structure" of "forest populations" I have inevitably found many articles that use the term "subdivision." Of course, this isn't referring to West Hills or something, it's an ecological term.  but now just imagine, what if you were reading an article about something like this, and you interpreted the words "subdivision" "neighborhood" and "neighbor" to mean exactly what they mean in the non-science world, people living in a community. Behold! Humor!

example: making fun of people living in a red-neck place "Fragmentation can reduce local population size to an extent that demographic instability and dangerous levels of inbreeding may occur."

example:why there's always very interesting people in your neighborhood, even if your township seems mostly the same: "Effective subdivisions may retard the rate of loss of overall variation, but there are limits and exceptional conditions determined by among population migration and extinction rates." 

example: why you should marry your neighbor: "The size of a neighborhood... was intended to approximate the effective size of the local random-mating unit within a continously distributed population." 

:) WIN.

mmmmm

Today I received a beautiful thing in the mail, which came in a brown box... FILLED WITH CHILI BAMBOO SHOOTS!!

Oh HOORAY! I AM VERY HAPPY! THE BEST MAIL EVER.

My stir-frys will be EPIC from now on... Chili Bamboo Shoots + Broccoli + Soy Sauce + Brussels Sprouts + Bean Sprouts + Pumpkin + Zucchini

I think I get about every major vegetable with that!

On a side note I also have mostly finished my carbon paper for my geophysics class. It was pretty hard working in a group with that many people. The discipline barrier can be quite large; for example, at one point we are looking at a south facing slope. A forester, hearing south facing slope, would think "this aspect means more radiation, leading to dry climate, low vegetation." A geophysicist thinks, "perpendicular intersection of cap rock with the underlying bedrock, slippage of soil, low vegetation"---- we get the same end, but have two different means. So then you go along wondering, why are they talking about this perpendicular rock, and they're thinking, why are you talking about radiation and in the end everyone's kind of confused about everything. I ended up just doing a model for decompostion of stream wood, standing dead wood, and (with a lot of help) wood lying on the ground. The distributions turned out to match the ideal distributions for the stand types and I think that my carbon balance is within the acceptable range for our (bad) sample size, so I'm going to go with that for now.

To those who are studying for Oral Exams...

those of us who are still trying to figure out what "nearest neighbor interactions" means...
those of us who think, "eigenvalue" means "that thing you calculate with PCA"
those of us who find matlab most useful as a quick way to organize massive amounts of data
        and yet can't program even a "hello world!" into matlab
those of us whose job involves running through the woods looking for where the red cable intertwines with the green cable because that means we're within 1/2 mile of where we need to be
those of us who still google "inches to centimeters!" or worse, "meters to kilometers"
those of us who think we are researching hard but really have "xkcd" "dinosaur comics" and "wow armory" on their top 8 pages (also the internet company and gas company and wachovia and email... where is web of science? nowhere to be found)

those of us who really aren't working hard yet but just can't seem to think efficiently

salute you. because you are really smart.

Not to judge a book by its first chapter but...

It's pretty rare that I come across a piece of academic literature that I find interesting yet understandable. I mean, so rare that it almost never happens. It's either, well, that abstract looks cool, but what is going on in that paper? Or, well, I can understand this, but it's actually written for middle school science education (I kid you not, that's how I learned about declination, watching flash files that were intended for middle school kids created by NOAA). 

But this spatial-temporal stats class I am in so far has a really cool book. I don't want to judge a book by its first chapter, but it's pretty cool. There's a few formulas, but a lot of it is "well, if you see these key words in a study, you know that they are probably using this kind of technique, and this is how it applies to this one really accessible example." I'll be eager to see how chapter 6, fourier transforms, is made easy. The class seems pretty alright: essentially it's how to model spatial temporal patterns without relying on regression or ordination. Some of the stuff I heard said today was fourier transforms, alternate steady states, and modulated response. I have no idea what those are. But it will be a new look for me. 

How to convince southerners to protect the environment

Promote eradication of wetland pests as food!

http://www.nutria.com/site14.php

Fueling my mulitasking need one online video at a time

After my introduction to "six ways that fungi can save the world" I discovered the enjoyment of TED videos. I guess I would call this "random professors giving progressive slide shows on natural resource management"

I think this one is pretty cool.
http://www.ted.com/talks/lisa_margonelli_the_political_chemistry_of_oil.html

And hey, there's 700 of them. That will distract me for days. The image of the "green gas station" is pretty strange.

Also I recommend the seed bank one. It's cool actually. Makes me want to visit SVALBARD even more!

Fine-Scale Gravity

http://gsc.nrcan.gc.ca/gravity/index_e.php

Clearly, I are NOT physicist, and I never even thought of this before. How cool! I had no idea that this even existed! I'm reading a study now where they are using paleogravity to discuss the formation of the cascade boundaries. WHOA. DEEP.

Can't sleep

Darn it, I can't sleep, so I watched "Avatar" again. :D

Made me think of something-- I remember when I first saw that film I said to my family, oh, it's awesome, you've got to see it. They responded, oh, but we don't like that fantasy kind of stuff.  Started to think as I watched it today-- doesn't everyone like, in one way or another, watching a fantasy of epic proportions-- whether that be a space fantasy, a heroic fantasy, or a romantic fantasy? I mean, so much literature that people have been into over time, like Beowulf, Tristan and Isolde, Knights Tales, Pride and Prejudice... all distort reality in a beautiful way.. and people like it, some like one story more than others, but everyone likes to forget the limits from time to time. As far as entertainment goes, I say that it is good to spend a few hours being immersed in a world where good things happen to people who act well to others. Is reality like that? No. But sometimes letting ourselves dream outside of the bounds of our physical and moral capacities is okay, too.

It's not that far away

Recently, I noticed something very great!

Oregon is kind of near Alaska!

I really thought it was far away, but as it turns out, the "Panhandle" of Alaska is very close...Okay, so you have to take a ferry to get there, which adds on about 18 hours drive time (I don't know about fly time)... but still...

Fresh figs

There is really nothing quite so tasty as fresh figs. I suggest you eat some when you return to California. I bet if Washington figs are good (even though kind of temperate in much of WA so a lot of wet soils), California figs are even better.

Did you know that the Ficus genus has the fastest growing trees in the world? (Ficus = figs).  I believe it is Ficus lutea that is the fastest, although I could be wrong.

Add figs to "plants I will cultivate some day when I have a garden"

As a side note, my "compost experiment" on the limited space on my patio is failing miserably.  I discovered there is concrete beneath the few inches of soil I have, so I have no primary consumers like worms to eat up the nitrogenous scraps I have been putting on it. I am hoping to increase bacterial decomposition by tarping the area and raising the heat level.  I originally thought I could do minor planting in the site, but it looks like I'm stuck with flowers and herbs, possibly I could put up vines, I guess.

I was thinking today of my idea "vegetable patch" were I to make one. I have learned that it is good to stick to only a few crops at first and add more as your original ones get established.  I will assume that I will get a Pacific climate, which means that I would start with blueberries and summer squash for summer crop and wintersquash. and pumpkin for winter crop.  Later additions of tomatoes, peppers, califlower, small and large brocolli, strawberries, and grapes would be added. Figs and citrus can be grown inside.

Also some kind of indoor sprouting would be cool. I have tried a few seeds here with varying success but I think my lighting is not correct for the little leaflets. Aerogardens = party time.

Well, that was a worthless post. But I do love some plants.

The end!

I got 2/10 suckers

The sad thing is that, well, it's true. I have worked at both a museum and in an entry level retail job where I was assaulted by superiors. 

http://www.holytaco.com/2008/06/03/the-10-most-worthless-college-majors

And since  the website is named holy taco you know it must be teh science.

A lesson for the living

I read the post below, and I think about it. It seems remarkable to me that many folks don't realize the limitations on their actions when their health is gone. I've always felt more limited by my health than anything-- it's almost an OCD thing for me, trying to figure out what the hell is wrong with me and why I can't have that same freedom as everyone else. Here's what I reflect:

The drive from Athens to Atlanta seemed long at the time, and longer when I considered that I was completely immobile once I got out of the car. It was stupid, really. One day I'm running along, shivering in the February morning, and the next I've got searing pain in my ass anytime I try to move. I'd tried everything-- hot baths, massage, e-stim, no exercises, running through the pain, swimming, everything.  On the road, a billboard, and on it, a picture of an old man in a wheelchair with a grandson tenderly poking him in the face. Big white letters proclaimed "You don't have to live in pain."

You don't HAVE to live in pain. But what about when life and pain go hand in hand? I was a runner then, fit and active, which is completely different than being happy and healthy. I could run for two hours per day on one meal in the evenings.  The world was regimented. When my body ached, I pressed through it, until I was too sick to run, then I took to bed hard until I got better. There was no middle ground, and so it was always a flux of sickness and activity, one or the other. It was 100% on or 100% off, and at no time did I ever feel like I was in good health as I was in high school, when I could wake up every day and blaze through the streets, and fight men 2 or 3 times my size. Quite often I would think walking through the downtown of Athens, if a car was coming at me right now, I couldn't possibly run away from it. But put a timer in a coaches hand and my scholarship papers in the other and I was on fire.

When I dislocated my SI joint I was lost. I literally could not run. My ass would burn from my shoulders to my feet. It had crushed my sciatic nerve and any motion hurt. They shot me in the ass with corticoids, powerful steroids to make me numb. When I was numb, I could run. They wore off at about seven PM and I was immobile until the next morning at 5 when we practiced first. We were greyhounds, expendable dogs. What mattered was "could I run a 17:00 5k?" not that getting into the car caused me to scream with pain. I bit my lips not to wake up my neighbors. I drove 200 feet so that I wouldn't have to walk, because I couldn't make it.  I laid down in elevators. They shot me every day, a direct needle between the joints of my back and butt. It hurt like hell. It was a like a spinal tap every morning and afternoon. It didn't get better. I saw that old man sign, and I was mad, who was that man to say I didn't have to live in pain. I was doing everything right, and the pain got worse and worse.


With time, and lack of patience, the pain subsided, only to be replaced by some other pain. If it wasn't my ass, it was my knees, and if not knees, feet, or shins. As I got older, and sicker, and out of school, it became more serious. My intestines didn't work. My pancreas doesn't work. My kidneys don't work. Everything I chose to do lead me to pain, and was it all my fault? Yes.

It isn't cool, or fair, to be 25 years old and sometimes your eyelids are so swollen you can't open them in the morning. Some days you feel fine and the next days your legs are filled with so much water that when you press them it makes dents. You think to yourself, I'm supposed to be young and healthy, but I've abused my body so much, now I've got chronic pain. It just plain sucks. Your mind burns with questions at simple choices-- every decision is an ultimatum. Wouldn't it be great to be able to make normal choices without painful consequences? Let me exemplify:  for me, the decision of "should I eat this bit of blackberries?" is not "do I want blackberries?" but "am I willing to sacrifice feeling stable for having a huge blood sugar rush, a stomachache, and swelling in my hands so much that my rings cut into my fingers for blackberries?" I mean, for god's sake, it's just a piece of fruit. Or to exercise, the question "do I want to go for a run, get in a bit of better shape and tone myself, and enjoy the dark morning" becomes "am I willing to trudge along, dragging my legs that always feel like anvils across creaking joints all over my body, just for the sake of trying to have 1/5 of what a normal person's metabolism might be like?" And then the worst part, you realize that 4 years of stubborness and a free ride to college with a few thousand dollars to spare that you chose is the reason for all this pain. I would ask, was it worth it, but it wasn't. It was a complete waste of time, for the sake of fitting into what others wanted me to be, and what I could afford.

I think that the caged bird is more cognizant of the vast openness of the sky than the free falcon. You dream, everyday, that you can fly. You seek out cures, remedies, anything, a new way of life, studies showing that it works, something to get to that blueness. Sometimes you take a risk, and always it fails. Time brings relief, but anxiety that something more will happen.

I read that people don't realize the limitations on their health until it's gone, and I think, hell, I learned that lesson when I was eighteen years old, when mine left. There's a giant life ahead of me yet. I am your subject, old wise ones. Imagine that you have that knowledge young, what do you do? Where do you go when  you view realizing and honoring your dreams in light of the fact that you have lost a powerful tool for that end?

You reflect, conditionally. What if I hadn't listened? I was told to wear certain clothes and feel happy in certain situations; my brain literally cannot do this. It doesn't behave correctly to do this-- when I see my skin exposed it agonizes me. I look in the mirror, and it agonizes me. People tell me to just make the choices anyway. I struggle against myself and I do it, just like I ran through pain to chase a scholarship, and I find it only makes the situation worse. The mind is ill and not tending to the illness makes it sicker. I am not everyone else. People say, become a great athlete, and the training I was given caused me to not only fail at that dream, but to become significantly less atheltic than I was before. Again, some people may train themselves fit, but I am not everyone else. All it should have taken from me is a "no! that's not for me, it doesn't work like that for me, this makes me ill"-- but for some reason getting turned around and following what most think is true is easier than forging a path.

You speak from experience. I think it's true that we all have our own dreams and methods of achieving them. To young people everywhere I encourage that you explore the world and yourself without fear of social conviction. Become comfortable with yourself and with being with yourself. Learn to say "no" and realize that people who love you won't hate you for doing it. Don't accept a lot of responsibility. Spend your afternoon outside and sometimes, eat ice cream for dinner. Don't go to a church that makes you dress up. Or dress up, if you like doing so, for a soccer game. Most importantly, do things that make you feel good. When you have to make a hard choice and money is a driving factor, remember that money isn't happiness.It certainly can buy nice toys, but in the end it's better to feel good and take out a loan so that you can live in the mountains and buy your food at WINCO than to be completely sick and miserable, but be able to afford premium cable and sushi dinner.

Here it is. To the living, I say, learn to be brave, and be yourself. Learn to be brave about being yourself. Remember that people are each different, and that everyone is struggling with something. Everyone around you is hurting in some way, and it's not the same way that you hurt. Be compassionate. Don't argue or blame people for wanting attention-- of course they want attention-- so give it to them in the form of love and sympathy. To the dying, you are right.  Reflect and know you are special and significant not for what you think now, but how you lived and loved, and mostly, how you took care of yourself during your life. May all have the grace (rather than the misfortune) to realize and embrace their own frailty.

Regrets of the dying

From Inspiration and Chai:

I wish I'd had the courage to live a life true to myself, not the life others expected of me.

This was the most common regret of all. When people realise that their life is almost over and look back clearly on it, it is easy to see how many dreams have gone unfulfilled. Most people had not honoured even a half of their dreams and had to die knowing that it was due to choices they had made, or not made.

It is very important to try and honour at least some of your dreams along the way. From the moment that you lose your health, it is too late. Health brings a freedom very few realise, until they no longer have it.

Powerful stuff. Read the whole thing. On a (somewhat?) related note, I stumbled across a peculiar finding with regards to solar flares. Sure is an interesting topic, and I have always loved space... Oh, if only there were some way to connect what I'm doing to this fascinating topic!

Heh.

For the morbidly curious...

My first first-author paper came out today, in PNAS's early edition:

G.J. Peterson, S. Presse, and K.A. Dill. 2010. Nonuniversal power law scaling in the probability distribution of scientific citations. Proc. Natl. Acad. Sci. USA. 10.1073/pnas.1010757107.

I'm pretty excited about this! This was my first real experience with publishing a scientific paper. The main thing that was a surprise to me is how much journal-specific formatting is required from the authors. I had expected the journal itself would take care of most of the typesetting and aesthetic details, but (at least at PNAS) this is not the case. This isn't a bad thing, just a bit unexpected. (My only previous paper, from my undergraduate work, had me as third-author, and I wasn't involved with the publication process at all. For the very morbidly curious, that paper can be found here.)

EXTREME COMEDY VIDEOS

http://www.youtube.com/watch?v=wdc344K_rPM

T Rex's CompSci Advice

I have no idea if that actually works, but... I would definitely LOL if I heard someone say that phrase about a language.

With a pocket tree...

...the sky's the limit!

O great one who knows of many computational things...

I hereby summon ye, knower of all that is having to do with making computers do menial tasks I don't want to do by hand, to give thy best advice regarding a data situation:

Suppose that I have 3000 text files (saved as whatever format you want, right now in .txt) which each represent one day (for example, 01.01.2005) with a format like this inside of each:

PLOT ID     X     Y    CARBON   WATER
101              100  200  0.009           3.00
102              106  201  0.003           5.00

And each has say, 11000 lines in it.  So each text file is showing me data for 11000 locations on a specific day.

This is not what I am interested in, though. What I want to know is, how does the CARBON on a specific locaiton, like PLOT ID 102, change over the course of the 3000 days (each of which are in a different file). Notice that each file has these two things that uniquely identify the PLOT-- the first is the PLOT ID and the second is the X and Y (together) coordinates.  The X and Y are more descriptive, of course, than the PLOT ID, but also in two different columns.

I am not sure where to start on this. Any ideas? This is what I have thought of so far-- but I think I am still in the mindset of "think like an accountant" and not "think like a ph.d. student who needs to learn to think in complex ways." this is summarized as: "lulz i r n00b." here's my n00bish thoughts:

1. put all data from one year into a single spreadsheet. use the sort function in excel to sort that year by plot ID....  then do something (??) to separate each of those plot ID's into separate files-- maybe a command in MatLab can do this?
2. do this for all years (let's say we are using 10 of them)
3. when trying to use matlab, just find all of those files using the command similar to the one about data1.txt, data2.txt that is in the worlds most awesome tutorial for MATLAB use that you made for me (also known as "reference manual of the gods").

I like this idea, but I know i will be updating the file information a lot over the next however many years-- is there a way to develop an automated "process" that the computer can run to do this for me? it sounds to me like a task for python but I'm still on the "Hello WORLD" level with that one.

Neat R trick

Neat R-trick of the day.  Transform pixelated coordinates and elevation data into a 3D scatterplot-- it's a really cool way to see if the pixels are accurately depicting the landscape!!

You can also make MOVIES, but I can't figure out how to upload them onto here yet. 

I mean, look! It's a valley-- how cool is THAT? I'm excited. 

did I mention that I have a cool job? why.... yes!

Beautiful Places

To brighten your day.

1. Milford Sound, NZ
2. Qinghai-Tibetan Railway
3. Ngorongoro Crater, Tanzania
4. Aberysthwyth, Wales
5. Santorini, Greece
6. Mt. Ossa, Tasmania
7. Grossglockner High Alpine Road (Hochalpenstrasse), Austria
8. Ankara, Madagascar
9. Tierra del Fuego, Argentina
10. Adam's Peak, Sri Lanka
11. Venezuela Falls, Venezuela
12. Iguazu Falls, Argentina
13. Dead Sea, Israel
14. Carpathian Railway, Romania
15. Iceland
16. Svalsbard, Norway
17. Paranal Observatory, Chile

Nothing like the beautiful starkness of nature.

A resource that needs to exist for us n00bs

Someone needs to write a document on "how to open files" for every data management application. It's really nice and all to have tons of analysis toolpaks, but if you can't get your data into there, how the heck do you analyze it?

I say this because I wasted 45 minutes trying to figure out "how do I open an .shp file in ArcGIS?" before I realized that: 1) the real ArcGIS is not ArcView (what CU had) but actually a very large set of files, about seven of which are executable programs named other things that start with "Arc"-- ArcMap, ArcInfo, ArcGlobe, ArcCatalog, ArcTools, 2) You can't actually open a file directly in any of those applications and 3) Using ArcCatalog to set a working directory in a drive that can be opened in ArcMap is pretty darn confusing.

Okay, so I'm sure there are a lot of people out there who wouldn't find that confusing. But I did. Just like I found "set wd()", "importdata," and even using Excel for the first time really confusing. It's like, okay, I have all this stuff, but how the hell do I get to it...

There needs to be a middle ground in computer help manuals-- one for people who are capable of using the advanced features on a program (because they have used them on other similar programs) but need to learn the fundamentals of "where do I click for what?" You know, for example, in Excel, it would be great to have a book that wasn't just "and THIS IS A CELL!!" but also not one that was like "and if you want to program your own macro to do such and such thing you will never use this is similar to insert the name of some other programming language here you have never heard of." What I want is something that is like: do you need to use v-lookup tables? First click here. Then type this. BAM. Look up table good to go.

If only my idea wasn't so fail, I'd make "the big book of doing easy stuff on computers for those who want to pretend to be saavy" also known as "someone else has already written a program to do that: what to click to make yourself look smart." And then I'd be super rich. Right.

Where do I sign up?

For the Oregon that existed in April, May, and June... you know, the 45 and rainy one?

It was 61 yesterday! What's with this (see below):

Special K

Depressed? Not any more!

The effect described on depressed patients is pretty jaw-dropping. Ordinarily I'd worry that this wouldn't fare well with regulators, due to its potential for abuse as a "recreational drug," but given its astonishing effectiveness, surely this will get approved.

Mathematical innuendo

searching "natural log LaTeX" gets me some VERY INTERESTING results.

note to academic publishers: you are smart! what is with the names?

Good:
MatLab
ArcGIS

Bad:
Maple
SAS

Ugly:
R
LaTeX

But what does it mean

I was sitting on the wax-paper table at Dr. Julian's office because my shin wasn't broken.

They told me that an x-ray had shown a seven-inch vertical fracture down my shin and that if they caught me not using crutches within the next three months I would be promptly removed from the team and my scholarship taken away.  But three days later my shin didn't hurt and I wanted to walk again.We know, they said, that you just want to go to California for the meet. This is not your time. Maybe it's never your time. Maybe this isn't for you. How often do you get hurt and we come telling you that you need to take time off, and you don't do it.

How many times do I heal faster on my own than your ridiculous nonsense, I wanted to ask. I have always been too prideful for my own good. Always. I've also always been a tremendous pushover. But instead I said, okay, I'm headed to the elliptical machine.  They said, see you in three hours. The sign on the wall said, be polite to others, do not sweat. Dr. Julian came into the office to tell me what I knew all along-- my shin was not broken.  I had another problem that was causing microtears in my muscles that he could see on the MRI-- a condition called hypotonia, common in people with defunct mental states-- it meant that my body couldn't communicate dualing signals with my muscles.  When it told one muscle to relax, it automatically told another one to tense. He pulled some strings for me and got me into therapy for free. I have not had any serious sports "injuries" since. The university was very hush-0hush about the whole thing. There was talk of a scheme underlying, as I was certainly not a great team member, and it took me a long time to become brainwashed to the mindset of making sacrifices for the team hierarchical hold. Eventually they cracked my brain, but my shin was nonetheless intact.

It was at that time that I said to myself, sitting on the table, and talking to Dr. Julian, that I said to myself, I need to be an orthopaedist. After all, I had been "saved" by one.  I had paper and images to prove that I in fact had a problem that was not a broken shin. This must be the most rewarding work, "saving" athletes so that they can pursue their passions. Dr. Julian was for a while my hero.

I typed before and I should reiterate here that I have always wanted to be a "hero." I realized the implications of this sentence about two days after I wrote it. I am by training a symbolist. Language is fascinating in that it takes so much breadth of idea and theme and compresses it into a single word. Hero. Love. Life. When we use that term through a standard  syntactical construction we bridge together word and idea and inherently create a set of analytical tools to use for it. We are very metonymical.  I say hero, and suddenly things that I never first imagined: superman, Einstein, ancient Greek lore, these are all part of the sentence. What is a hero? A standard protagonist of sorts, having epic adventures filled with meaningful failures and a barely make it climax and then a life is great and easy conclusion? Or some kind of lone spectre summiting mountains and passing distant judgement on the world, to cunning and smart for her own good? Maybe a hero is some Jane Austen woman who manages to convince both herself and Mr. Darcy to change? Tools we use to assess these protagonists are now fair game for assessing ourselves: is it a question of what Lucy DID to save Narnia or who she was? Or both? How are heroes made and analyzed?

I tile this "But what does it mean" because the question of venerating a Narnian warrior girl has something to do with how I view a job or career prospect. But what does it mean to be a hero in career fields? At the risk of being myopic, I even say, what does it mean to be a hero in the sciences? I don't know the answer to this question. Is it great achievement, like winning the Nobel Prize? Would that make me a scientific hero? Or is it better to be less prolific but more productive, maybe doing something small that changes the way that people look at a certain problem. Who invented the ANOVA? How many statisticians use ANOVA every day? Try to name all the Nobel Prize winners-- these are the top folks in science, the number ones, the "heros"-- I can't do it.  I can't even get five. And realistically, the honor of being even in contention for the prize would be pretty big. How many Nobel finalists can I name? None. Not a single one. These are the top dogs-- they should be the heros.  So it makes me wonder. Dimensional analysis shows that my goal and my progress are using two different units. Conversion is needed for understanding results.

I I have to give a presentation in December to a field that is entirely not mine. I will be batting in the big leagues when all I have ever encountered was a bowling ball.  Spheres carry different weights, to say the least. So it is safe to say that none will ask me questions about trees or something I know and am prepared for-- nor am I scared to say "well, I don't know" to questions that are out of my grasp. Questions that I should be able to answer will be the broader, structural kind. My past experiences with this sort of thing have shown me that for the most part professors and government bigwigs aren't interested in my methods, whether or not I've used a certain statistical test or whatever, but to use a terribly inappropriate aphorism, the "forest for the trees." I impressed my way to eight job interviews in my last year at Clemson dropping only one resume by talking to people about big pictures. Look at a forest fire and tell me who is concerned about needle length-- its not the leaf but the landscape. What is the goal of this project? How will you get there? And why the hell is it important? Why do we care about trees growing on mountains? The fact that it interests me is irrelevant. Cutting my toenails also interests me and that's not getting me anywhere in life. I can't say, well, I just want to know everything there is to know about how mountains work and how they affect forests.  Means are not ends. Unless you are a statistician, I guess.

In the 1960's, a bunch of forest rangers in the southwest were walking through a forest ravaged by fire.  In the charred woods they found a tiny bear cub, clinging to a burned tree.  They took him back to the station and nursed him to health.  At one point, a ranger, joking around, put his hat on the bear cub and took a photo. Smokey the bear is now a commonly recognized symbol of wild fire prevention.  What did Smokey do to become a hero? He was an icon of life in a dead wood. Maybe that's the key-- the hero isn't what is accomplished by the attitude with which it is presented. A scientific hero is new, fresh, and simple.  She describes the mountain forests with a passionate directness and creates applicable models for all people.  She isn't concerned with making a name for herself, but her system speaks louder than her words. Snow falls on a porch and no one hears it, but everyone knows its there and they feel different. The world is quiet and sublime.

These are ways to think of it, I suppose-- quiet and sublime-- secretly grand-- the lone spectre on the mountaintop knows that she in fact created the whole landscape in her view. Grandeur belongs to the creation; to its creator, satisfaction.

Zotero

Maybe I spent too much time with Apple, but I think I like this little crispy bibliographical software better than BibTex.  Especially if writing the .bib file seems sort of "follow this template and it's all okay" straightforward.

http://www.zotero.org/

Check this thing out-- it integrates with your firefox, so you can just ISI or JSTOR up the results, and then do all sorts of crap like take notes.

I know that one thing that sucks for me on reading papers is that I don't really keep notes I might take on them, or if I do keep them, I never reference them. Having these linked to the articles is salvation for me!

T-Rex's great insight

I didn't know T-rex lived in South Carolina!

A Life Story of Sorts (also known as, no! I don't want to write in LaTeX right now).

Once upon a time there was a girl who lived in a big house in a big neighborhood in a big city. The house was on a street called Red Spruce Lane and there were tricycles in the cul-de-sac.  Business was good for businessmen in the city in those days, and the plan to build a great radio station company was well underway for three young book binders from Decatur. They decided to buy a nice office on the north side of town and the girl and her family moved to another standard-grade house in another standard-grade neighborhood.

This time was before the time of computers, gameboys, and ipod.  It was when the Sony Walkman was just coming out and wow, you could take your cassette with you? Amazing. It was too expensive for her family. They were traditionalists from South Carolina mixed with half-hearted coal-miner kids from Pennsylvania.  They were very much to structure and social pecking orders. Every day when the girl went to school her mom made her wear a dress.  She hated the dress because it meant she couldn't run on the playground with the boys.  Instead she had to sit on the slide and in the dirt with the girls. The playground didn't have a "floor" then like it did now.  It was just some monkey bars, bars, and dirt. When she came home she put on Michael Jordan high tops and biking shorts and t-shirts that she got free from the world wildlife foundation.  She inherited her male cousin's mountain bike and she would ride it from school end until nearly six PM, when she would come inside to enjoy Kid Cuisine and the Carmen Sandiego show.

As she got older, doors, literal and figurative, closed.  The family bought their first computer, an MS DOS machine that didn't even have windows.  It had a few black and green programs for learning arithmetic and typing.  On Saturday mornings before she went to Tae Kwon Do practice, the girl's mom would sit her down in front of the machine and make her practice typing.  She had to do it, because somehow the machine could tell her mom if she practiced or not. On Saturday afternoons, she'd get back on her bike and ride as far as she could, sometimes all the way to Cherokee County, crossing roads with reckless abandon.  She only got stopped for jaywalking once, about 10 years later. In the evenings, she would go to her friend's house for dinner. The friend was Jewish and her parents always made fresh hallah bread.  She would stay sometimes for a few days, and her friends mom never nagged. This was just her other home that was sometimes a better home. She learned how to say a few words in Hebrew and how to bless various parts of the meal.  She often thought about the fact that she loved Judaism-- the sounds of the chants and the somber feeling of the rituals.  And also the foods. Moreover, it was a happy place where ancient rituals superceded social systems.

The times at home were sad. Her father lost his job right after her sister was born. Broadcasting business was bad and it was hard to get rehired in the age headed towards digital media. Ted Turner was entirely to blame. Didn't he own enough stuff in Montana?  The family had hard times for many years.  Money was tight. Everyone was half-alive, and many time removed relatives were constantly passing away. When she got in trouble she was sent outside, shut out from the inside.  It was sometimes cold-- very cold-- so she would huddle by the dog door near the basement and sometimes weasel her way through onto the cement floor. Other times, she'd walk down the street and climb into the big magnolia tree, waiting for her friend's mom to get home. They had fescue lawn that never went brown in the winter.  She learned that green grass was really a key to happiness. The friend's mom put a key for her in the big planter on their deck.  She'd go there sometimes in the afternoons while the mom was work and the friend at Jewish school. Then they would all eat hallah.

Throughout this time she dreamed and wrote stories. Sometimes she'd curl up with a spiral book her friend's mom bought her and just write adventure tales about girl warriors who lived in hollowed out trees on tall mountains. They were friends with the birds and had wolf lovers. There were passionate exchanges of single kisses and glorious sacrifices for good things. They wore shirts made of falcon feathers and leather pants skinned from dragons. They fought glimmering city men who tried to tame them. She thought C.S. Lewis would love her stories, like her friends loved her stories. Her parents never read them, didn't know they existed, didn't ask. What was the most important was passing algebra, not creating things. Why was the minus different than the subtract? Or were they? Doesn't minus mean negative and parentheses mean subtract? An accountants daughter couldn't get it through her head that basic algebra didn't work in terms of loans and equity. And why bother with scientific notation when you could just write out 100,000?  When she was in seventh grade, she started a story exchange with another girl in the school. They had a notebook that told an epic tale about a class of students fighting great enemies in a fantasy world. The notebook circulated to the extent that teachers tried to pursue it from the class front.  It was never found, and the girl found herself achieving detention by other means, none of which were serious. She learned a lot when she wasn't supposed to learn anything, and found that passing school was sort of a side job to learning how to build tree forts and dig deep holes.  One day she built an irrigation system for the blackberries in her yard, but wasn't allowed to power it because they were "weeds."  Also, putting nails in a hose was a bad idea.

There came a day that she realized that something was wrong.  She was driving around at night in a silver volvo, looking for meaning. It was two am and she had incidentally fallen asleep at a friends house. It wasn't her fault that the movies were boring. The town was more brick and cement than trees and grasses, and everything looked silver at night, even the sky, because city-glow was stuck in it. She was listening to angry rock music, wanting to be able to jump and run across fields and fight great enemies.  Instead she lived in the city of plastics.  Doors were shut now.  Televisions that worked had been invented and computers made interesting games. Gaming consoles drove afterschool wanderers to a digital world. It wasn't cool to have a hand-me-down bike or an old silver-volvo.  At best, in her circle, it was okay to be a bit of a somber social slider, slipping in and out of groups without making attachments.  At worst, all the other groups filled their guts and brains with poisons that were unallowed.  She wondered to herself if they had ever seen a close friend be killed by a drunk motorist? She had been at her coach's funeral and she knew that an innocent choice taken too far could take the life of a friend and the lives of his family. The whole place had an aura of soft repulsion to it, like a bubble or a pile of half-molded wax.  You could either fit in and be absorbed, or you were destined to street drive at night, planning your escape. She drove and drove, coming home and going to bed in silence. Something was wrong, and always was. She lay in her bed on the side, waiting for whatever should be coming with greatness. She got the feeling that it wouldn't come.

She wanted to become a hero. A scientist? An athlete? A doctor? Someone who made discoveries and explored the world.  She cared less about what she did than how she got to do it-- if it took her to somewhere beautiful and happy, rugged and glorious, that was the goal. Yet she made choices against that goal-- choices that reflected on financial obligations and the social frenzy that one should stay close to home for familial respect.  It was duty to remain in the soft place and take care of your relationships.  Duty is also rolling sisiphys's wheel in hell though. There was something great in the rugged places.  On the final saturdays in that town she took her bike to Cherokee county, looking for adventure.  She ended up on creek shores or climbing on mill ruins. Some people grow out of the need to be wandering around in the woods, but she didn't.

There are soft places that people get stuck in.  They stay there forever, sometimes because they like soft places, and other times because there's nothing to pull up on to get out. I have lived in a soft place. There are some beautiful old rituals in the soft places to remind us what is real. Seizing those can help us to pretend that the place is not all bad. Or perhaps good luck can rescue us. Or tenacity to wander.  Eventually wandering far enough will probably take you to the edge of the cotton ball. Today everything is crisp. I feel air on my face and see clouds on mountain tops. My coffee tastes vindictive this morning, and I now feel motivated to get back to work.