Ragemaster

It's high time I started posting from something a little more professional-looking.  I'll keep my account active, for awhile at least, but I don't think I'll be maintaining this one much more.

I've got my own domain and web server running WordPress and managed to migrate all my LJ entries to it.  Some of the posts are a little weird and the layout isn't quite what I want, but I'll work on it.

Yesterday, as I went to the laundry room to put my clothes in the dryer, I went down a small staircase.  Since I still have issues going down stairs, I made a conscious effort to descend properly and use my left leg.  When I got to the bottom I continued towards the laundry room, I noticed something felt weird in my leg.  I looked down as I walked and noticed that with each step that it was bending the way it was supposed to.  Bam -- just like that I went from limping everywhere to walking normally.  It was completely involuntary.  Before the staircase I was still walking straight-legged and afterwards I was normal.

Since then I've been almost completely normal walking everywhere.  A few times when I start walking I notice that I'm goosestepping again, but now I know what it feels like to walk normally so I quickly change my gait.

I have a feeling that this process is similar to what Dilbert creator Scott Adams went through with his vocal disorder.  Though I would argue losing your voice in certain situations would be much worse than limping, the "remapping" of an area of your brain happened more or less involuntarily.  Adams figured out he could get his voice back by rhyming and once he knew what it felt like to talk normally, he could speak much more easily.  Now that I know what it feels like to bend my knee when walking, I can do it on a whim instead of trying to force it and look even weirder than with the limp.

Since upgrading my Ubuntu installation, I got plenty of compile warnings when compiling TinyOS applications.  To fix this, I just decided to reinstall TinyOS.  It can be a pain to install and each time I do it, I've got to look for resources on the internet and try a couple different things to get it working.  I'll try to keep this updated whenever I discover something new or have to upgrade or reinstall TinyOS again.  Here are the references I found to help me compile this:

All Platforms:
Installing TinyOS 2.0.2

Ubuntu:
5 Second Fuse - TinyOS Installation
Install TinyOS-2.x On Ubuntu << Udin Harun

I also got it running on my Leopard Macbook using this:
Installing TinyOS 2.x on Mac OS X (Tiger and Leopard)

This worked for me on Ubuntu 8.10 Intrepid Ibex.  I did have a previous install of TinyOS that I removed, but some stuff may have been left behind.

1.  Add the following line to /etc/apt/source.list:

deb http://tinyos.stanford.edu/tinyos/dists/ubuntu hardy main

Currently, there isn't any repository for Intrepid Ibex, but this seems to work fine.

2. Update the repository cache from a terminal window:

$sudo apt-get update

3.  Install TinyOS packages:

sudo apt-get install tinyos tinyos-avr tinyos-msp430 nesc tinyos-tools

In my case, "tinyos" caused a warning since it was an abstraction for several packages.  I installed "tinyos-2.0.2".

3a.  (Iris Support): Install TinyOS from CVS:

I also wished to have the latest TinyOS version from CVS since it seems those provided via the Stanford repository did not support the Iris mote.  To install from CVS, open a terminal window to the installation directory of your choice and run the following:

$cvs -d:pserver:anonymous@tinyos.cvs.sourceforge.net:/cvsroot/tinyos login
$cvs -z3 -d:pserver:anonymous@tinyos.cvs.sourceforge.net:/cvsroot/tinyos co tinyos-2.x
$cvs -z3 -d:pserver:anonymous@tinyos.cvs.sourceforge.net:/cvsroot/tinyos co tinyos-2.x-contrib

tinyos-2.x-contrib is a library of user-contributed code that can help in designing your own applications.  If you installed as su, you may want to change the permissions of your tinyos directory if you wish to compile anything in the apps directory or modify any TinyOS code:

$chown -R <uid> tinyos-2.x

4. Add the following environment variables to ~/.bashrc:
export TOSROOT=/opt/tinyos-2.x
export TOSDIR=$TOSROOT/tos
export CLASSPATH=$TOSROOT/support/sdk/java/tinyos.jar:.
export MAKERULES=$TOSROOT/support/make/Makerules
export PATH=/opt/msp430/bin:$PATH

Depending on the directory and version you have installed, you may need to change TOSROOT to reflect the correct directory.

5. Install TinyOS Java Toolset:
I had issues with this one: you may not have to do this step if you just use the tinyos package provided by the Stanford repository.  However, I installed via CVS and had to install the TinyOS Java toolset manually.  Ensure that you have performed Step 4 and modified your .bashrc file before proceeding.

First, from the terminal, run:
$sudo tos-install-jni

This will install the Java Toolset into your Java directory.  For some reason I had Java 1.5 (5.0), Java 1.6 (6.0), and OpenJDK installed on Ubuntu.  Oddly, javac pointed to Java 1.5 and the java command pointed to OpenJDK, which was causing errors when running TinyOS Java apps like TestSerial.  To fix this, I removed Java 1.6 and OpenJDK since these seemed to be causing nothing but problems and just about everything runs on 1.4 or 1.5 (including TinyOS Java libraries).  Now java and javac point to Java 1.5 (Hopefully doing this didn't toast some other application).

You can then compile the TinyOS Java libraries by running the following in the terminal:
$cd $TOSROOT/support/sdk/java
$make

6. Install Graphviz
This step seems to be optional, but you need it if you want to run the Oscilloscope application.  In a terminal, run:
$sudo apt-get install graphviz

TinyOS wants an old version of Graphviz, but Oscilloscope seems to run fine.

7. Check your TinyOS Installation:
From a terminal, run:
$ tos-check-env

Running this, I have received errors about the Graphviz version, but the Oscilloscope application runs fine with the newer version.

To test your installation with Telos-based motes, try:
$ cd /opt/tinyos-2.x/apps/Blink
$ make telosb install.0 bsl,/dev/ttyUSB0

To test with Iris motes, try:
$cd /opt/tinyos-2.x/apps/Blink
$make iris install.0 mib510,/dev/ttyUSB0

To test the serial connection with Telos-based motes, try:
$cd /opt/tinyos-2.x/apps/tests/TestSerial
$make telosb install.0 bsl,/dev/ttyUSB0
$java TestSerial -comm serial@/dev/ttyUSB0:telos

To test the serial connection with Iris-based motes, try:
$cd /opt/tinyos-2.x/apps/tests/TestSerial
$make iris install.0 bsl,/dev/ttyUSB0
$java TestSerial -comm serial@/dev/ttyUSB1:iris

It seems that with the Iris, applications must be installed via the mib510 board (ttyUSB0) and data can be retrieved by accessing the mote itself (ttyUSB1).

7.  Issues
In addition to the Graphviz errors, for some reason the motelist command does not see the mib510 interface board or the Iris.  However, when I install to /dev/ttyUSB0 or listen to /dev/ttyUSB1, the installation works fine.  motelist does recognize the Iris on OS X, however.

I upgraded to Ubuntu Intrepid Ibex last night and now I can't connect to any WPA2 Enterprise networks.  Unencrypted works fine, but the school's WPA2 APs seem to be more pervasive.

This issue seems to be happening to a lot of people so I'm hoping someone is working on it.  That's the best thing about open source -- if something bothers you about the software you can change it yourself.  Unfortunately this problem isn't in my area of expertise and I have plenty of programming to do for a project of my own.

I should have waited at least a month after the release to upgrade instead of jumping right in.  New builds always have some serious problems that have to be worked out.  I hear on message boards that new vehicle models and redesigns of old ones are prone to all kinds of quirks during the first model year.  It's best to wait until the second year to buy one so all the issues can be worked out.  The same seems to go with electronics -- the first iPhone had no GPS and a terrible 2G data connection, while the second version fixed these issues.  And, of course, this quirkiness happens with software.  Windows XP was a mess when it first came out and Vista was worse when it came to drivers and stability.  XP is stable today (arguably), but Vista still has its problems.

Early adopters pay a high premium to get a product with limited functionality along with some unwanted side effects.  As I sometimes forget, it's best to wait until the problems have been worked out and the price comes down (if it's not free software).  Usually new and improved features get added in as the bugs get worked out.

So now I'm not even sure if I can drag my laptop around campus until this issue gets worked out.  Serves me right for just following the appeal of something new, but not necessarily better.

Tomorrow I get to try the regular stationary bike instead of the recumbent one.  Range of motion hasn't been an issue for awhile, but I still can't bend my leg all the way back without it getting really tight.  I can get to almost 150 degrees.

I notice that I'm starting to do things more normally, like bringing my leg up to tie my shoes instead of awkwardly leaning down to do it.  Going up stairs is fine, but I still have that initial worry when I go down them.  In Raleigh, just about everyone asked me about why I was limping, so I definitely have more progress to make in terms of walking normally.

At PT they are adding in more rigorous exercises for my hamstrings and quads and increasing the weight each time.  My leg looks like it is getting better, but it still is pretty small.  Every day I still do my normal free weight routine in the morning and do almost 30 minutes on the bike and elliptical later.  I've been adding a couple minutes a week to the elliptical/bike routine and it seems to be getting easier.  The bike doesn't hurt my quads as much but it still leaves me more sore after 15 minutes than I would have been before the surgery.  I figure about Thanksgiving I can move to the resistance trainer for my road bike and soon after I'll have enough stamina and leg strength to hit the roads for real.  The only problem with the road bike is my habit of crashing into the injured body part, making it worse.  I really don't want that.

It's interesting to watch the progress of everyone else at PT.  A lot of people have had knee replacements or surgery on their knees and appear to be going through a similar rehab process as me.  Today there was someone I hadn't seen before on crutches and was using the same passive range of motion machine that I had used for the first couple weeks.  It made me think how far I've come and how that guy will go through all the stuff that I've done and eventually be walking again.  A girl that's been in there a lot when I'm in there went from not doing anything to using the stair climber and elliptical, and is now doing the walk/jog on the treadmill.  A lot of the older patients with knee replacements I see gradually do more on the bike, but haven't done the elliptical or the stair climber.  The physical therapist probably tries to match their rehab with their ultimate recovery goals.  Running probably isn't something you can do on a knee replacement.

At this point I think I could just do most of the machines and exercises on my own in the rec center after biking or the elliptical.  However, I would need some guidance as to when to try the road bike and start running again.  From those that have made it back running successfully, they seem to start back at four months at the earliest and usually five months or more after the microfracture.  I could go off that.  I do know that I'll have to do the old walk/jog routine and probably wouldn't do it every day either.  I would also have to get some idea of how far I could work up to runningwise until it would be considered risky.  These are all things to keep in mind as I progress, but I still have a lot of time left before I get to them.

As with EmNets over the summer, the trip to SenSys this week was an experience.

The sessions went from Wednesday through Friday so my adviser, the other student in our group, and I left Tuesday afternoon and got back late last night.  The weather in Williamsburg sucked when I left and it sucked when I got back, but it was nice in Raleigh.  I also managed to get in my weight routine and the bike/elliptical every day while I was there, but I had to get up early to do it.  The whole thing really wore me out and I was asleep by ten every night.  Of course, I got up before seven to start my routine and kept awake with the terrible coffee they had.  Hard to believe I drink enough coffee now to have preferences (darker roasts are better).

Overall, the whole thing was kind of weird.  Nearly everyone there was foreign -- despite most schools being from the U.S., almost all the students and professors were not.  I guess this was to be expected -- it was like taking a 200 person sample of the world population and putting them in the same room.  A plurality were Chinese, a lot were Indian, and there were only a small number of Europeans and Americans.  Since my adviser and the other guy in the research group were Chinese, I found myself hanging out with everyone else speaking in Chinese.  The group meals we had and conversations during the break were kind of awkward since they would speak some in English and then just suddenly switch to Chinese.  For example, the first night we went out (to a Chinese restaurant of course), I was the only one of eight that used a fork and knife.  I should probably start learning Chinese so that I can at least pick up some of it.  My adviser encouraged me to talk to people during the session breaks, but it's tough when many aren't speaking a language you can understand.

Asides from the demographics, the other thing that made it weird was the atmosphere.  These are some of the top people in sensor networks and the whole thing seemed so ... unprofessional.  The attitude of everyone and atmosphere seemed so relaxed and informal - at the end of a few presentations there were a few arguments between the presenters and a questioner.  Nearly everyone was in typical student-type clothes and the faculty were typically attired, and it seemed as much a chance to have a good time as it was to show off your work.  Some of the UVA guys came in one morning musing about how drunk they got the night before.  The closest thing I can compare this to is NCAAs for cross country.  With this conference and the NCAA meet, the idea is the same: the best schools come to show off their stuff, but the atmosphere at NCAAs was extremely professional and focused.  In both cases we had a banquet with everyone that was attending, but at NCAAs everyone was subdued, had their "game face" on, and kept conversation to those within their team.  In contrast, at SenSys, there was wine on the table and everyone was nearly out of control by the end.  Somehow, I expected something a little more formal, but I guess that's the appeal of academia -- you're given a fair amount of leeway as to what you can do in research and in your approach to your work.

I met up with the other people I had collaborated with over weekly Skype meetings since last winter.  It was interesting to meet them in person and I got some special hardware from the hardware guy we are working with for our current project.

In my opinion, about a third of the sessions were interesting, a third was okay, and another third wasn't of interest to me.  There was some cool stuff on measuring radio link connectivity burstiness, vehicle sensor networks, and integrating posture detection and geolocation data into social network sites.  There was stuff on distributed camera image recognition (detection people's gestures), ensuring privacy when sharing personal sensor data, and a environmental monitoring system using accelerometers to measure flow rate in water pipes.  I didn't care too much for the radio MAC protocol stuff and there were a few high-level programming frameworks that seemed uninteresting. 

According to my adviser, SenSys papers are focused on actual deployments and implementations while marginalizing theory in design.  Most of the papers had a giant deployment section with lots of pictures and evaluation statistics.  While deployments are practical, advancements are slow since so little new theory is developed.  One or two of the papers presented had simple data collection and evaluation schemes that were just tested extensively in the real world, such as a road pothole detection system using accelerometers and GPS/cell towers for localization.  I would like to work on stuff that can actually be deployed (I am now), but deployment and testing takes a lot of time and isn't really research.  Other conferences are more focused on theory and a simulation-based evaluation is acceptable.  The reviewers look more at algorithm design and novel theoretical ideas over real-world deployments and testing.  Additionally, the committees for each conference tend to have varying amounts of control over who gets accepted -- some are very tightly knit and seem to accept papers only from certain schools while others are more diverse and objective over their selections.

Listening to the paper presentations and going to the poster and demo sessions got me a few new ideas.  The poster and demo sessions were especially interesting because you could talk one-on-one with each person about what they had done or were working on.  A lot of people out there have a lot of good ideas.  Most of the presentations were done by students and a lot of them weren't much different than me in terms of age and experience.  It seems that students are typically listed as first authors and give the paper presentations while their advisers come to watch and ask all the hard questions.  That was also what was weird about it -- it wasn't much different than going to class and listening to student presentations, except that the work was exceptional.  I took a lot of notes and saw what made a good presentation: abstracting away details and making your main ideas clear.  It sounds like going to a conference (maybe not this one) and giving a talk on my paper is in my future.  I only have to get accepted first.

So now I come back motivated to get going on my current project.  The ideas are (hopefully) new and will actually work when we get the thing implemented.  I'll be able to do an actual test with sensors instead of just simulation.  The deadlines are looming and it's time to get moving.

A quick post between SenSys sessions on the last day.  It's actually really nice outside.

Looks like everyone I voted for lost except for one -- and he was the only Democrat I voted for (congressman).

I didn't sleep at all on Tuesday night since it seemed all of Raleigh was out in the streets burning couches or something.

Honestly, I can't see why people think that one person is going to suddenly solve all their problems.  There is one person who ultimately decides your fate -- you.  If you want change, make your own change.  Make your own life for the better if you've got problems.  More to the point, how many presidential policies have really affected you, and if they did, how much of an impact did they really make?

Government can be a guide to help everyone move towards their (and their country's) best interest, but it's the people themselves that really make things happen.

Regardless, it's still going to be interesting with Obama as president.

Halfway to running?  Another ten weeks and maybe I can try.

Today at the PT, one of the assistants put me on the treadmill and said I should go as fast as I can -- even run.  I guess he doesn't really understand what I've got, especially since the doctor was adamant about me not running.

The daily increase in weights and the addition of the stairmaster, leg curls, and leg extensions have started to help my strength.  As usual, though, my leg doesn't look any bigger.  I still have a limp when I'm walking since it seems that I've reprogrammed the walking part of my brain to compensate for the brace.  Now I've got to unlearn that.  Walking back from the office today, I made a conscious effort to bring my leg up bent, almost marching to try to get rid of the limp.  I felt better doing that but it still isn't anywhere near natural.

Stairs have gotten better and I have a hard time believing that I can go up and down them without pain.  When I see stairs, I see fear.  It takes a lot of courage for me to go down them using my left leg.  Up isn't so bad, but going down, before the surgery, was when I had all the problems.  It seems to be a huge improvement.

Over the weekend I was heading towards campus when I passed a group of law students.  One of them was talking about her knee and how she had been running on it for months with it bothering her.  It turned out it was a torn meniscus.  It sounded a lot like what happened to me, before the surgery, but tearing the meniscus has a two week recovery time from the surgery.  You can walk out of the surgery and go right back to running after a few weeks without any serious problems.  With knee injuries on the brain, I pick up all kinds of stuff about people getting hurt that I wouldn't have even thought of a year ago.  Tons of football players get into trouble every weekend and you hear about it on the commentary.  Like the girl I overheard a few days ago, I overhear all kinds of conversations about people and their knees hurting.  And, of course, at PT, there are plenty of people with knee problems, lots of them coming back from knee replacements.

Lately, I've really felt unable to get away from everything, that no matter where I go I've got to share my personal space with other people.  The smallest things are starting to bother me.  In the office, there's at least seven or eight other grad students around talking about stuff.  Outside there are mobs of tourists and other students -- I get asked for directions at least once every few days and someone always stares at me because of the brace or limp.  In my apartment, I've got to deal with my roommate and his fiancee.  Yesterday, I realized what was missing.  Running and biking somehow alleviated that "walls are closing in" feeling: it's hard to get mad when you're tired.  On the roads or trails there isn't anyone to bother me and everything just gets zoned out.  An hour of running or biking feels like three or four hours of doing work or reading or just messing around on the internet. Without it, days just whip by and I don't get the same sense of accomplishment.  Hopefully soon I will be able to bike more and I won't feel like I'm going insane.

Tomorrow I'm off to Raleigh for a conference and I'll see how it goes in an environment other than school.  I'm hoping there are bikes or elliptcal machines in the hotel so I can continue to work on my range of motion, leg strength, and just get in some kind of workout.

This is my sentiment exactly. 

With most Americans unable to recite basic history and civics (even after college!), it's no surprise that I'm a tiny minority in a sea of foreign graduate students.  The average American just doesn't want to put in their best effort and try to be successful on a personal/community/national scale.

The article refers to IQ tests being cut in the 60s because nobody wants to be labeled as "below average".  Today, colleges are eliminating the SAT requirement and some are even refusing to be ranked in US News.  We can't compare people anymore, for it's "too unfair".  There are even the rumors about elementary schools banning tag because it's "too competitive".

You can see the result of this anti-competitiveness today.  Everyone gets in to college and they don't learn a thing when they leave.  There isn't any incentive to do well since the end result is the same no matter the effort.  Even the law student at the bottom of his class graduates and may go on to be a district court judge (that's a scary thought).

The issues aren't the reason I don't want Obama to win, it's the attitude.  The attitude of entitlement and laziness, the attitude that an Obama administration will magically take care of everyone without individuals having to lift a finger.  Even Michael Moore calls it the "Slacker Uprising".  Nobody wants to put in the effort to compete or accomplish anything and we are witnessing a huge shift as what little remaining cash, manpower, and brainpower flows out of this country and into others.  With tax policies that increase as income increases, there's no incentive to save or invest money -- just spend it.  With talk of legislation and funding to "rescue" those who default on their mortgages, there's no incentive to pay your bills.  When individuals get punished for being responsible, there isn't any reason for them to continue.

The rewards must end for those who do nothing.  Instead, help should go to those who do something.  Bring back the competitive drive.  Bring back the effort and creative thinking that brought us the moon landings, the Empire State Building, and the Eisenhower Interstate System.  Start learning stuff in college that will be useful for the good of yourself and everyone else so accomplishments like this will happen again.

Until then, we continue to flush ourselves down the toilet.

It used to be that I would sacrifice hours of sleep in high school to play computer games every night.  Many nights I would stay up past 11 playing Counter-Strike or the latest Command and Conquer.  I could stay on the computer forever and then be a zombie in class the next day, nodding off as early as 9 or 10 in the morning.  During the summers, it would be the same thing: suffer through a run in the late morning heat and then play games the rest of the day.  I don't think my mom cared for that, doing nothing most of the day, and was probably relieved when I started working after my junior year.

Those days are over and I don't think they are coming back.  Something happened when I started college that has really changed my interests in nearly everything.  I'm not sure what it was or exactly how it happened, but it seems to have been a slow, gradual process that probably completed its transformation by the time I finished undergrad.  I'm different now and I wish I knew why.

I want to play video games, but I just can't get into it.  I've started playing stuff occasionally, such as the latest episodes of Half-Life 2 and Portal.  Those I finished because of their brevity, but longer stuff, like Call of Duty 4 and some recent RTS games I just started on, got stuck in one place and then just said: "screw it".  None of them are nearly as exciting as they would have been eight or ten years ago.  The most recent stuff that's out there now would have been mind-blowing to me back then: the latest GTA, Fallout 3, and possibly Spore.  I would have spent most of my life playing them, but not anymore.

It appears as though I'm not the only one that this has happened to.  Some of the research says it's to do with social networking; that everyone would rather play games with people they know rather than against unknown opponents online or a computer in single player.  I do notice a correlation between the time I spend on sites like Digg and Facebook and the decrease in time I spent playing games.  However, I still notice tons of people about my age and older that still play a fair amount: the assistants at PT talk occasionally about meeting up after work to play Halo, the physical therapist (in his 40s) even says he plays Madden on the weekends, my roomate plays plenty of PC games, and even my dad finished Crysis when I just dropped it after the zero-grav part.

In some ways, programming replaced the satisfaction I got from playing video games.  It's better because I have complete control over the environment.  In video games, you are forced to live in the environment the developers create and play by their rules.  It's like the first Matrix movie: why play by the rules when you can bend them or even create your own?  Why should I be restricted to use a shotgun to solve the problem of a developer-imagined monster when I can solve much more interesting problems of my own creation with tools of my own creation?  Yesterday, I spent all day thinking about a job-scheduling type scenario for wireless sensor networks.  Last night, I finally figured out a solution.  While the problem wasn't entirely my doing, coming up with the solution was much more in-depth and satisfying than blasting the crap out of a few enemy soldiers with a C-130 in CoD 4.  And, my solution may not be the best.  My adviser or the other guys in our group may come back with some constructive criticism to help with a better answer.

Again, I would really like to get back into gaming.  Doing work can be satsifying, but it is also draining and it would be great to have some kind of release since I can't run.  Some of the stuff that's out there right now sounds like it could be fun, but I don't even know if my PC can handle it.  Possibly, I'd have to upgrade the video card at the least, and of course that's a slippery slope to just upgrade the whole desktop that's been rusting under my desk.  It's too loud when it's on and generates a ton of heat, so there's a massive incentive to figure out how to make the whole thing quieter.  Furthermore, I've only got one monitor that I use with my laptop, so I'd have to unplug it, the keyboard, and the headphones and put them all into the PC whenever I want to play anything.  There's also the cost issue: right now I've got to save since my surgery/rehab is expensive.

Maybe I'll try once again to get back into gaming, and maybe I won't.  Maybe there will be another sea change that will shift my attitude and fun factor when I play, but I'm not so sure.

Today it was back to the orthopedist to evaluate my recovery process.  The PT gave me a letter to take along and I voiced my concern that the brace I've had to wear is killing my gait.  I've been walking around the apartment without it, but it's really annoying being out and about with it on.  It's hard to bend my knee when the brace is on correctly and it's even harder when I've got long pants on and it sags down my leg.  Finally, they let me take it off.  The brace did give my leg a stronger and more protected feel and now with it off I can really tell the strength difference between my two legs.  Hopefully I should be walking without a limp within the next few weeks.  So many strangers have asked me what I've done to myself and I've got to tell them at least part of the story.  A lot of them think I've torn my ACL, but at least with that, they can reconstruct it in the worst case and you can go back to normal, but for me the damage is done and will never be completely repaired.

The doctor advised me not to run, but at this point it's still obvious that I shouldn't.  Again, excluding the problem of damaging the microfracture area, my leg wouldn't last five steps of running before my quad would erupt into an inflamed mess.  I'm really starting to get sick of all these appointments and long periods at the physical therapist.  I understand that it's so I can get better, bike again, and maybe run, but it's really tiring.  I adapt to the increased weights and more bike/elliptical resistance, but the recovery process is mentally straining.  I remember being fed up with previous long lasting injuries where my coach wanted me in with the training room every morning doing the same kind of stuff.  This is like that but on a whole new level.

The PT still wants me to continue with them on strengthening and returning to nearly full range of motion with my leg.  Yesterday I got to 140 degrees, so I am getting there.  I know my teammate said he still doesn't have full range of motion in his bad leg.

There have been periodic arguments on LetsRun about the different articular cartilage repair methods, none of which are extremely robust.  It seems that most people on the message board and other boards that I've seen get microfracture for deep cartilage tears.  It's the go-to method for an attempt at repair since it's minimally invasive, has a moderate recovery time, and a good success rate compared to the other two techniques.  Autologous Chondrocyte Implantation is a new method where a small sample of your cartilage is taken out in an initial surgery, grown in a lab, and implanted over the defect in a second surgery.  They open up your whole knee to put the new cells back in and there is a ~2 year recovery time.  Apparently the cartilage is much stronger than fibrocartilage so it's better for long term results.  Most insurance companies don't cover it since it's considered an experimental procedure.  It seems that if this technique was improved/matured so that the recovery was shorter and became more mainstream so insurance would cover it that it would be a good option.  In the case where my microfracture doesn't hold up, maybe in ten years there will be a solid procedure to replace missing cartilage.  I've also heard of stem cell injections into the knee to help repair, but that seems almost completely unheard of and there aren't any proven results.

I finally got hold of my teammate who had microfracture on his knee a few years ago.  We talked for over an hour and I got an idea of what his take was on the whole injury->surgery->recovery process.  It was good to actually talk to someone that I knew that had this done to get an idea of where I stand.

I knew that he had some kind of knee issue that required surgery and a long recovery but I wasn't sure that it was microfracture.  It happened to him during the summer after my junior year of undergraduate while he was a freshman.  I remember talking to my coach over the summer about how everyone was doing and he mentioned my teammate as having some kind of major knee issue that had to do with the cartilage.  I remember returning to school and practice in the fall and seeing him do his therapy in the athletic training room.  Every time I went in there to get some ice or stretch, he was in there on the bike or doing some kind of exercises.  There were plenty of times I remember being in there and he wasn't having a good time or something was hurting and the trainers were telling him to take it easy; that there were good days and bad days.  Finally, I don't remember seeing my teammate doing workouts again until March of my senior year -- he started having issues in April or May of the previous year, so it was quite awhile before he was back to training normally again.

I didn't really think too much of it -- when I was healthy and running well I tended to forget about those on the team that were injured.  They went to the meetings at the beginning of practice and then I didn't see them until I was stretching or in the shower.  Usually I only really paid attention when someone I ran with regularly on maintenance runs or as part of a workout group suddenly disappeared one day.  I would be aware that they were injured for a few runs or workouts and then it would kind of slip my mind as I got used to them not being around.  Of course, when I was the one that was injured, which happened at least once per season, I always seemed aware of everyone else that was hurt.  We all spent plenty of time in the training room trying to get better.  Overall, I spent most of my worrying about trying to stave off or heal my own injuries. It seemed that some tendon or muscle was always about to take me out of the lineup, was in the process of keeping me from running, or trying to blow up again as I restarted training.  Of course, once one problem was on its way out, something else was desperately trying to start up.

Unlike me, my teammate said there wasn't anything that he remembered as the cause of his cartilage defect.  His doctor said he probably ran into something, but he didn't remember doing anything like that.  One day he remembered running a steeple race and being fine, and the next day on a long run the pain started.  It slowly got worse for awhile as our coach told him the problem was an IT band injury.  After a lot of stretching and no improvement he went in to see a doctor at home, which eventually led to his diagnosis.

His defect must have been more weight bearing than mine, as he said that it hurt when he walked, whereas mine didn't.  Like me, my teammate also had a lot of popping and locking in the joint with every leg extension.  Before the surgery, his doctor told him that the microfracture-induced fibrocartilage would most likely last about three or four years, enough to get him through his college career, but after that it might break down.  My doctor didn't really say this, but this short-term success seems to be the general assessment on the Internet.  He (and my PT) have said that the tissue will break down faster if I return to hard training, so I'm not really inclined to do that.

During the surgery, the doctor had to move my teammate's patella so that it wouldn't rub against the microfracture area.  The idea was so that bending the knee wouldn't scrape away the fibrocartilage-forming clot.  I was kept in a motion-limiting brace to prevent this from happening for the first couple weeks, but I didn't have my whole patella adjusted.  He said the defect area was about the size of a thumbnail, which seems to be smaller than the area I had that was more like two thumbnails.  My teammate said that he didn't have any pain in the microfracture area after the surgery but he could feel something in there sometimes.  Following the surgery, he was on crutches for about five weeks, biking at about two months, and then started running at about five months.  It was about seven months before running seemed more normal.  He also remarked that his leg strength didn't come back until nearly a year after the surgery and even today, four years after, the bad leg still seems smaller.  He still can't squat on his bad leg either.

My teammate remarked that I should really focus on abductor and adductor exercises which the PT really has me focus on.  It's one of the things I work on during my morning routine.  He remarked on this because he had a lot of tendinitis issues as he returned to running that would have been lessened with more leg strength.  Other than that, my teammate made it through the last two and a half years of his college career successfully and wasn't held back by his knee.  His mileage was high and he did all the workouts and raced well.  I remember running with him through some of the more treacherous trails around here last year, so I know his knee could definitely tolerate trail running.  He still ran 50 miles a week through the summer and is still doing well today.  It's great to hear that his microfracture procedure and recovery were a complete success and it's a good motivational tool.  Since I don't have to worry about burning eligibility or missing races, I can take it easy during my recovery and not force anything.  As I've mentioned before, just being able to run again to some degree will make my surgery a complete success.

Yesterday marked over two months since the surgery.  I've come a long way, but there's a long way to go too.  I'm now allowed to bike and elliptical on my own, so I took advantage of that today and went to the school rec center: 15 minutes on the bike, and ten on the elliptical.  This I did in addition to my usual morning weight routine which takes nearly 45 minutes.  It would be great to bike outside, especially since the weather is nice today, but I don't think I'm ready for that and won't be for awhile.  My leg still shakes with weakness after 15 minutes.  Also, it seems that my good knee has been hurting and popping some, which must be some kind of compensation problem.  I'm hoping it's nothing serious and just a mild consequence of putting most of my weight on the good knee, since the pain started when I was on the crutches.

Last night one of my old teammates who goes to dental school in Richmond came down to see the team massage therapist.  I dropped by while he was there since I hadn't seen him since the summer.  The massage guy, who punished and tortured me for so many years, had an interesting comment about leg strength that I hadn't heard before: your quads should be 20 percent stronger than your hamstrings.  That is, if you are on a leg press that works your quads, you should use 100 pounds if you are using 80 pounds on a leg curl machine for your hamstrings.  No wonder runners have so much trouble with knees: quads get very little action compared to hamstrings and calves.  Biking can change that, though.

My teammate's got knee issues like I do and has been out ever since dominating the Boston marathon last spring.  He really hasn't been able to run since then and an MRI indicated grade 1 or 2 damage to the articular cartilage.  That's where the cartilage is bruised or has a small divot in it, but not like my grade 4 where it's chipped out all the way to the bone.  He seems so motivated to run again and get back into regular training, but with permanent damage like that, it may not be possible.  Since his damage wasn't as severe as mine, the docs say surgery wouldn't accomplish anything, which leaves him out in the cold if the pain persists.  Hopefully most of the pain is caused by some inflammation from whatever he did and once that subsides he'll be able to run again, but if I were him I would change my mindset.  Right now, I would consider my recovery a success if I am able to run 20 -30 miles a week.  It's so bad because he was running so well and even got some sponsorship offers.  Maybe it's not as bad and he'll be out there kicking butt again soon.

It begs an interesting philosophical question: would you like to run the race of your life knowing that you would never be able to run again?  You would sacrifice everything to blow the field out of the water.  Your time and place would be so much better than you ever hoped it would be, but when you finished, you would never be able to start again.  Would that be worth it instead of having a lifetime career of running but only making modest personal gains?  I don't know for sure, but I do like running just to be outside and to feel like I accomplished something.

I'm finally making some headway on the latest school project.  It should be an interesting experiment since we will get to wear some sensors for awhile to test our model.  Since we are going to use human test subjects, my advisor blindly checked off some box about it when sending in the research proposal to the school.  Now they are making us fill out all this liability stuff and explain our exact test procedure when we aren't really finalized on everything.  And, we, the researchers working on the project, are the only ones who are going to be the subjects, so I think we are completely aware of any "dangers" that go along with wearing some sensors.

Lastly, I got home to vote absentee at the city municipal center when I was on fall break.  I got that taken care of since I'll be at SenSys on election day.  Really, I don't think either presidential candidate matches my choices.  Obama's tax plan raises marginal tax rates for those who make under $45k per year (poor grad student). McCain plans to freeze all research spending for a year after he enters office.  Obama hasn't even finished a full term in the Senate; McCain is going to be 80 if he gets elected for two terms.

Both have the wrong idea on the economy.  The problem goes beyond government regulation or lack of it.  It starts with individuals.  A lot of people today are lazy and want everything for nothing. They want the car and house they can't afford, so they go into credit card debt and default on their mortgage.  They want the college that puts them $40k in the hole only to graduate and bus tables.  They want health care and retirement benefits without lifting a finger.  These people purchase what they can't afford and then expect everyone else to pay for it when the repo man comes knocking.  It's a sense of entitlement and it drives me mad.  Here's a hint to fix this mess: stop buying stuff that you can't afford or shouldn't be, get off your ass, and start contributing to society.  The same mindset of the CEOs with enormous golden parachutes and corrupt politicians taking enormous sums from lobbyists is present in everyone.  If this persists, we'll be in a barter economy real soon.  The problem is that the candidates and government can't blame the constituents without taking heat for it and risking their own jobs and re-election.  The solution starts from the bottom up, with you and me, not from the top down (government).

The physical therapist suddenly increased my activity level.  Until this week, everything was pretty easy, but this week was different.  I do the bike with hard resistance -- it feels like going up a steep hill for 15 minutes.  Since my legs are so weak, it probably isn't that much resistance, but it sure seems like it.  Then, they had me get on the elliptical.  That was about the highest my heart rate has been since before the surgery.  If that wasn't enough, there were tons of step and stair routines that they started me on.  Until now, I avoided stairs as much as possible and always put my weight on the good leg.  Not anymore.  Plus they increase the weight each time I come in for all the weight machines and free weights.  This, combined with my free weight routine in the morning really wears me out.  It's probably because I'm not used to it. 

The PT thinks the pain I'm having is coming from where my IT band attaches to the tibia, which is good because it's not in the joint.  He said a lot of pressure was offloaded onto my IT band after the cartilage tear as a "protective" measure.  It seems to explain the shockwave of pain I had that went up from below my knee when I had the tear and when I had occasional pain during the two or so years leading up to it.   Now, it kind of makes sense since I haven't bent my leg much and everything has tightened up.  Stretching more should help this and I've already noticed it feeling better towards the end of the week.  Overall, my leg strength is getting better but I still have trouble walking correctly and it's still going to be awhile before I can bike for a prolonged period of time.

In the movies, every researcher, scientist, and professor has some kind of cryptic notebook that contains all their life's work and secrets.  Usually this entails some younger relative trying to decipher/recover the notebook after the professor dies/goes missing.  Lots of advice websites for research-oriented grad students suggest to keep a log of everything you do.  Maybe I should, too.

My current system is basically using printer paper to write down or sketch out stuff I'm working on, which I then carry around in a folder.  I usually carry the paper around until the stuff on it makes its way into latex or code or the stuff on the paper isn't worthy of any more effort.  Then I throw it away.  It usually takes from a few days to a week or two for me to get a new sheet, fill it up, and do something with what I put on it.  Sometimes I have several sheets going at once, which all go in the folder.  There isn't really any order to it either, just a bunch of bullet points on some idea or a sketch of something.

This isn't really working out and I need a better way to organize everything, or at least keep it around in case I want to go back and look at it. A white board would be great, but you can't carry it with you and there is also the issue of erasing stuff when you run out of space.  So white boards are out.  Plenty of computerized note taking/sketch programs are available, but writing stuff out can be faster and I like to make drawings and diagrams of stuff.  I don't have a wacom tablet or tablet PC to make sketches with, so that's out too.

So, research notebooks sound like the answer.  Except that I'm picky.  I want a notebook with:

• Hardcover, so I can bear down on it without the need of a desk
• Spiral binding, so I can flip one side of it underneath the other to save space
• Grid rules, so I can lay out writing and sketches neatly
• Heavyweight paper, since I'm a heavy-handed writer and my writing pushes through thin paper
• 75-100 pages, so I don't have to get a new one every month

It seems difficult to find such a notebook, even if it exists.  I've been looking at BookFactory, which seems to have a lot of options, but I haven't really found one yet that meets my specs.  The closest I found was a sketchbook at the school bookstore that had everything but the grid rules, but the paper was also really coarse and not really good for handwriting.

Maybe I'll find something.  For now, I got a regular spiral notebook with grid rules and will see how that goes.  At least I'll try to keep everything I write down.

No more crutches.  I gave them up last weekend and it's been great ever since.  I have a great deal of trouble bending my knee properly when I walk which is going to take awhile to work out.  The therapist shortened the brace which helps, but everything will come in time.  My range of motion is better too, at about 120 degrees, but at that point it feels like my leg is going to break off.  Until that improves, I won't be able to use the regular stationary bike, much less the road bike.

I think my leg strength has improved significantly in the week that I've been walking and I no longer feel like I'm about to topple over.  At PT they have me using the leg press and this hamstring machine with actual weights instead of the spring machines I was using before.  Hopefully that will help me get back to normal more quickly.  My leg still looks like a stick and it takes an incredible amount of effort to stand on my right leg and lift the bad one.  15 minutes on the recumbent bike is getting easier and my leg isn't shaking when I finish.  I can't imagine what would happen if I tried to bike with real resistance or even run at this point.  I wouldn't last two steps.  Again, it will take a few more months to really get everything back.

The physical therapist thinks that the popping and pain that I get occasionally is scar tissue.  "Scar tissue" seems to be the catch-all explanation for pain that I've received from my past coaches, multiple massage therapists, and athletic trainers while on the team.  What is scar tissue, anyway?  Why does it cause pain?  Is it really "scar tissue", or is it the kneecap digging out the formation of fibrocartilage?  I couldn't really find a definitive answer on the internet, so I'm not really sure.  I know you get scars from really bad cuts, maybe the scar is swollen and gets in the way of other stuff that moves around, which is what causes the pain.

I've continued to do leg strengthening and upper body exercises in the morning and going out for walks in the afternoons.  It's better than nothing, but now that I'm walking again I suddenly have the urge to go out and run and bike.  Nobody had better ever again bother me about being obsessive about running every day.  I went every day because I could, because I enjoyed it, and I knew that I might as well "get while the gettin's good."  Because on a day like today, I might not be able to run and I don't have to regret any days that I was too lazy to go.  Lots of guys on the team would give me grief about running every day during the active rest phase of our training.  I knew that I was healthy and in shape and I wanted to make the most of it.  It's a waste if you don't, because there will be days when you are injured and can't go.  So, I say to those with good knees: make the most of every day and don't waste your talent or effort: get out there and run.  Enjoy it.

Today while doing one of the leg exercises at the therapist and then again when I moved my knee at my desk, I felt the unmistakable pain I had before the surgery.  It was just as sharp and pronounced as ever.  I wonder if there is any new tissue at all where the microfracture was, or if there was, I've destroyed it.

It's the pain I always felt for the first minute or two on the bike, but it would go away.  When I ran the pain seemed different, almost duller and deeper in the joint but just as uncomfortable.  Before the surgery, I don't really remember having that kind of pain when not running or biking.

I know what I do that causes it: extending my leg when it's off the ground.  I have to try to avoid doing that.  I didn't think much of it when it happened the first time today, but the second time really got to me.  I'll say something to the PT about it on Friday.  Until now, I didn't have much pain at all in the knee, especially where the microfracture was.

It could be a sign that I've been a bit too aggressive coming back since I did do a few minutes of biking and I'm almost off using one crutch.  The doctor wanted me off the crutches soon and the PT seemed to think my progress was fine.  Maybe if I go a bit easier on things I will have spared my knee.  I know almost everyone has pain following microfracture, but I wonder if the pain they get is the pain they had before the surgery.

Hopefully it's okay, but I've got a feeling otherwise.  I'm really afraid of being a cripple for the rest of my life.

Yeah, that's progress.

This week at the physical therapist was good from a flexibility standpoint.  I can now sit on the edge of a table and let my leg hang down without any tightness.  I couldn't do that at the start of this week.  Because I can now bend my knee to 90 degrees -- and move the brace that much, I can now get my left shoe on without using a giant shoehorn.

I've progressed to using one crutch for a lot of my getting around, but when I go longer distances, I still stick to two.  My knee feels a lot more stable than it did and it seems to tolerate the weight bearing more without getting sore.  Slowly, I will try to walk farther with only one crutch and I am already going short distances without anything at all, but I feel kind of like I'm on stilts.

Yesterday, the weather started taking a crap and it's been terrible outside.  While I was headed to and from the office in the miserable mess, at least five people asked me if I needed a ride or help getting around.  I did have to go farther than normal to get to my parking space since it seemed everyone drove.  Nobody ever said anything to me before.  Maybe that says something good about human nature when stuff gets tough. 

I need to go to the grocery store but I don't feel confident enough to go by myself since I can't really carry much with only one crutch.  When I do, it throws off my balance.  The Trader Joe's is open that rose out of one of the new vast swaths of clearcut woods.  I thought about going in there after my appointment today, but it was a complete mob scene, since today was the first day it was open.  I figured it would be bad when everyone at the physical therapist was talking about it.  People were almost parking along the highway to get in there.  I'll go back after some of the hype dies down and when I'll be able to get around better on my own.

They finally gave me my diploma today and for the longest time I thought I hadn't done something that I was supposed to in order to graduate.  I was supposed to get it in August.  Finally, this morning I got an email and I went over to the registrar and picked it up.  No real ceremony this time.  It looks just like my other one except that the president has changed and it reads "Scientae Magistrum".  They didn't give me a cover for it either, so I've got to get something to protect it.

Next week I'll get to ride the bike.  Of course, the therapist's idea of riding the bike is probably a lot different than mine at this point.  It will still be good to start back, though, even if it's just ten minutes of slowly turning my legs around.

Today was my first day with the physical therapist.  It went really slowly -- I was there from 2:30 until after 5.  Apparently someone that worked there wasn't in which caused the holdup, but I can't just carve out 3 hours of my day to just mostly waiting.  Even the receptionist remarked that I had spent seemingly most of the day there.  I spent probably 30 minutes total actually doing stuff.  They said it should be much faster next time -- I hope so because I have to go three times a week.

It really wasn't anything that I hadn't seen or done before in the training room, but at least I made some forward progress for the first time.  It was mostly leg exercises, but I was put on a range of motion machine and got up to 50 degrees with the brace off.  It felt really weird with it bent that much but it didn't really hurt except a little each time the machine increased the range of motion.  They set the brace at 50 degrees so I can now move it more.  I also have the go ahead to walk more on one crutch.  Like the doctor said, the goal is to try to be off the crutches in two weeks.  That will be great. 

When the brace was off, I remarked that my left knee seemed swollen compared to the right.  Instead, the PT said that it wasn't, only it just looked that way because I had lost so much muscle in my quad.  My left leg above the knee has a circumference 3 cm smaller than my right, and now that he said that, it's really noticeable.  Mostly, the brace is on so I can't see it except for when I shower.

Like the orthopedist, the PT said he was optimistic about me returning to running, only that I probably would not be able to do any serious training or races.  He had several microfracture patients in the past and said that I've got to really be careful since one guy had to have several surgeries after running too far and really screwing things up.  Again, he remarked that recovery is different from individual to individual.

At least now I have some kind of progression to look forward to, even if I'm only taking small steps towards a target that's hundreds of miles away.

With injuries in the past, and with this one, the actual 'getting hurt' part is extremely frustrating but there isn't really anything I can do about it.  Once whatever it is that is bothering me crosses a threshold, there's no going back and no decrease in training or extra stretching or icing will allow me to keep running.  Usually that threshold comes really fast after the onset and by the time I realize anything is going on, it's too late.  That was especially the case with my knee.  One step I was fine and the next, pow!  I did have a lot of soreness in my leg just beneath it for quite awhile leading up to the meltdown, but no way I would have predicted that it would erupt into torn cartilage one morning.

The actual rest period kind of goes the same way -- it's frustrating, but again, it's out of my control.  The damage has been done so I just have to sit tight and wait for whatever it is to heal.  In previous cases, however, I just couldn't run, but I could do just about anything else.  This time, I can't even walk.  But, that's coming to an end.

It's not until I start to come back that things really get tough.  Then, things start to come back under control.  The choices I make and the things I do start to have an effect on how quickly I can return to normal.  Try to do stuff too fast and the injury will come back and I'll be out for even longer, perhaps permanently in this case.  Don't do anything at all or not enough and recovery becomes agonizing and difficult.  There is some optimal level of increasing activity, but it's hard to figure out what that is.  Even when I was on the team and with the help of my coach and the trainers, nothing ever worked out perfectly and I found myself suffering a lot of setbacks when trying to come back from an injury.

It isn't just the difficulty of figuring out what and how much to do when that makes recovery hard, but the entire transition itself that can be a real pain.  The amount of time and effort required is just so much more than during the most difficult weeks of normal training when I was running track and cross country.  Going out for a run or workout every day is pretty easy because it's pretty much the same kind of thing every day and I've done it a zillion times before so I know exactly what to do.  Even alternative exercise isn't all that bad since I get into a routine with biking or whatever it is that I'm doing instead of running.  Unfortunately, in this case, I really can't do much of anything.  However, when I start to come back, there is this transitional phase where I'm forced to do things differently almost every day -- all kinds of weird strengthening stuff and the gradual addition of more activity (which isn't always running).  It takes a lot more time and effort than I'm used to, but in most cases it's the only way I'll ever get back to normal.

It's now time to start coming back.  Yesterday, I went to the doctor and now I can start walking again, slowly.  Within two weeks or so, I am supposed to try to get off the crutches completely.  I've slowly moved around the apartment with one crutch and it's hard.  My left leg just isn't used to it, but it doesn't really hurt.  I'm also supposed to take off the brace and gradually try to increase my range of motion in the leg.  I've also got to set up PT appointments which will probably also help with my return to walking normally as well as range of motion.  That will involve all the weird exercises and will probably be at some strange time of day so that I feel like I have a lot less time than I used to.  I'm sure eventually they'll help me figure out when I can start biking again and hopefully even run.

At this point, I can see I still have a very long way to go.  The past four and a half weeks has seemed like forever, though each day individually seems to go by pretty quickly.  The weather suddenly changed and it's no longer the typical jungle summer weather but cooler and like fall.  I know that it probably won't even be until the end of the year or even into next year when I'll be able to run again.  The long, drawn-out recovery process is what makes things especially hard.  My teammate who went through this same process was back to full strength in over six months after the surgery, but it's different for everyone, and I don't even know if I'll be able to make it back.  If the microfracture didn't work, I'll be back to feeling that awful grinding pain again when I run.  I have to hope for the best, and at the least, I'll be better off than I am now.