True Confessions of a Medical Scholar

Tagging In

2012-01-29T16:46:00.002-06:00

For the first time in quite a long time, I have been tagged and asked to participate in a "random stuff about you" post by Kennyo over at Lose The Shoes. As I believe there is some voodoo witchcraft effect that comes if you don't yourself participate, I suppose it is my duty to continue on with this tradition. Here we go.

1. Post these rules.
2. You must post 11 random things about yourself.
3. Answer the questions set for you in your tagger's post.
4. Create 11 new questions for the people you tag to answer.
5. Go to their blogs and tell them you’ve tagged them
6. No stuff in the tagging section about "you are tagged if you are reading this." You legitimately have to tag 11 people!

11 Random Facts about me:

1) I have run 6 marathons (planning my 7th in May)
2) I have two fake teeth, as my real teeth never grew in
3) I have been with my wife for 13 years, but only have been married for 5 (we met in high school)
4) My first CD, received for Christmas back in 1997, was Green Day's Dookie (I don't think my parents understood what it was at the time...)
5) I played trombone from 4th grade through college
6) I never pulled an all-nighter in high school, college, or grad school - I value sleep too much!
7) I had never been camping until my senior year of high school... and now I go every summer
8) I am finishing my PhD in chemistry this year
9) I wrote a blog for 5 years before I started this one (don't look online - it no longer exists!)
10) Despite being from Minnesota, I played basketball during the winter and not hockey
11) On the other hand, I'm married to a former hockey player!

The Questions:

1) What is your favorite color?

- Blue

2) Would you rather run up a hill or down a hill?

- First up the hill, then down the hill

3) Would you rather make millions doing something you disliked or struggle at something you love?

- I am currently struggling at something that I love and (often) dislike, so I'd rather make those millions

4) Would you rather workout with Jillian Michaels or Bob Harper?

- I work out on my own

5) If you could one place in the world, where would it be?

- Minnesota (home sweet home, where I haven't lived since 2006)

6) Would you rather downhill ski or water Ski?
     - Downhill... slowly.
7) If you could be drawn into one cartoon which one would it be?
     - Futurama
8) what child would you be off Willa Wonka and the Chocolate factory?
     - Hopefully Charlie Bucket, as he is the only one with values
9) Would you rather a dream truck or a Dream car?
     - Car
10) If you could stay in shape without working out would you enjoy that?
     - I'm not sure how that's possible
11) Would you rather be President of the biggest company in the world or start your own within its shadow?
   - I'm planning on being a physician, actually. :-)

I'm going to be a jerk and not tag people, but if you want you can always participate as well!

Happy Sunday!

I Had to Write SOMETHING

2012-01-21T13:24:00.000-06:00

It's Saturday, which has lately become a quite interesting day of the week for me. In the past (first year), it would have revolved around getting to the lab early in order to attend our "Donut Class", in which we were informed of all of the different areas of the department worth noting. While I didn't particularly get anything important out of the class (which, at one point, included a 20 minute build-up to how one works a Par Shaker that ended with "well, you can ask about it if you want" and no demonstration at all), it did get me to the lab early on that day. This habit continued through several years of graduate school, but has lately dwindled with the knowledge that I don't have anyone hanging over my head, ready to strike if I don't check in promptly at 9 am on Saturday, coupled more recently with my desire to get out and go running on the weekends. It is fairly nice out today, given the cold weather.

I had a conversation last night with my wife, whilst sipping on wine at our local wine/coffee shop (which I am in love with and would marry if I wasn't already happily married), about the state of affairs in the lab and my desire to push forward and finish up with my graduate work. I complained that I felt scatterbrained as of late, to which she replied "well, you are working really hard". When I countered by discussing our recent trend of turning on episodes of 30 Rock during the work day and the subsequent lack of focus on work because of said episodes, she replied that I didn't have that much time left before finishing my research, so therefore I must be working hard. I love how she has this ability to be incredibly straightforward, opposite of my inability to get to the point when discussing a subject (as evidenced by my full paragraph to get to this point). It's true, there really isn't an option to slack off anymore. Not that I've really been slacking off (I offered my point to hers that I certainly have collected a lot of data/failed experiments), but it has felt lately that I haven't been on the ball, and her frank description that "this is how is has to be" made me realize that, yes, she's correct. There isn't any room for slacking off anymore. Any time I'm awake, I must be thinking about what needs to be done and then doing it, not allowing myself to take my eyes off of the prize.

It's been kind of interesting to see how my stress levels have affected other areas of my life. In particular, I'm finding that my normal stress habit - eating excessively - has been complemented this go-round with excessive exercise. I've been running pretty much every day since May, interspersed with occasional breaks, mostly due to travel. Full days of driving, flights, and the occasional hangover (New Years Day had a combination of those activities), have been the only deterrents from increased mileage. Overall, I actually feel pretty good about this, although it has made the eating habits a little more acceptable, which I'm not entirely okay with. In any case, I'm in about as good of shape as I've been in graduate school, hovering below the 190 lbs mark since probably November and through the holidays. Regardless of the stress level, I'd call that a win.

As our travel plans for this spring/summer have been derailed by potential graduation dates, along with my wife having to stay in town because other nurses will be on maternity leave (hooray), I re-evaluated my running plan for the spring. I originally wanted to do the Illinois Marathon again, but I will be attending a conference over the same weekend, so instead I have homed in on the Green Bay Marathon. I had actually thought about this one before, but now that my folks are living there... makes it a lot easier, doesn't it? I will let you know how training goes.

That's about it for now. I have many, many things to do, and as the wife says, I don't have a choice.

I have to be working hard.

Wrap It Up

2012-01-12T21:19:00.003-06:00

Tonight at group meeting there were a number of instances in which folks in the group discussed wrapping up various parts of their research and asking what to do next from the boss. No more data to gather, just begin putting everything in correct order so it can be presented/published, with the end game in mind.

In fact, even the boss discussed "wrapping everything up" in the more literal sense - all of that equipment and glassware needs to be shipped out to California when we're done, so if there's anything that we're not using anymore we need to pack it up and get it shipped out.

I couldn't help but think to myself, as this was going on today (I wasn't presenting) - I'm not sure if I'm ready for that yet! Not because I don't want to be ready, but I feel like there are so many things that still need to be done. More assays, more coupling reactions, more analysis, more data, more data, more data... I don't know if I'm ever going to be ready to finish. I'm not sure when the boss is going to say "it's time to graduate", but hopefully it will be sometime soon. In an ideal world, I would be farther along than I am, but obviously life is not ideal.

All I can do is what I can do now.

In any case, it's time to push so I will continue to push!

On Making a Good Life

2012-01-05T08:55:00.004-06:00

“To make a good life for yourself and thosearound you; you must first love yourself and feel yourself to be a worthwhilehuman being. Then you can really loveothers. One must have a respect for the dignity of other human beings and beflexible in one’s ideas and judgments, because every individual is unique. One must have faith. To believe is to have hope and not to succumbto despair. Be happy without guilt, andenjoy all the wonderful gifts we have in our lives. And like a pebble thrown into a pond, ourhappiness touches the lives of those around us.”
- Eileen Margaret Cummings Ayers; May 1, 1920 - December 31, 2011

2012 Resolutions and Goals

2012-01-02T10:28:00.001-06:00

Folks, I was just looking over my list of resolutions from 2011, and let me tell you - pretty bad.

Well, not exactly. There were a number of goals that were easily achievable (most notably the transition to 28 years old) but many of them were strewn by the wayside of the year for various reasons, either because I completely forgot about them (i.e. reading a paper a day) and/or they just weren't possible (getting enough results to publish). Others were sidelined because of injury (running two marathons and an ultra) or because of poor planning (saving money/winning my race circuit). The good news is that I managed to hit some new highs (placing in the Clydesdale division at Allerton, presenting my research at the APSA conference) and maintain a healthy lifestyle, to the point where I am in about as good physical condition (was, anyway) as I've been since training for my first marathon back in 2005.

In reflecting on last year's goals and ambitious they were, I've got two possible options - tone it down to feel better about myself, or keep it up so that I can achieve more and feel better about myself. I was initially going to go with the former, but now that I think about it, why shouldn't I strive to achieve more? That's been the goal all along, hasn't it?

Rather than a discrete list, this is going to be a little more... free flowing. Here we go.

The main thing that I want to do is maintain the healthy, active lifestyle that I am trying to lead. This will help me in a number of ways, including the obligatory "make it to my next birthday", as well as the goal of running two marathons this year. With more careful attention to training, gear, and making sure I get rest when needed, I shouldn't have any problem running (and possibly racing) those marathons. While it would be nice to run an ultra, I think my most recent excursions with running shorter distances have taught me that it takes less time to run shorter distances, so I will not go beyond 26.2. Instead, let's see if I can't win a few more age group/division trophies.

As far as lab work goes, the main goal will be to be, well, in lab. More often. Past 5 pm. And putting in a full(ish) day on Saturday. The whole "time goal" thing has to be thrown out the window at this point, instead focusing on accomplishments - getting data, compiling data, analyzing data, etc. In the end, this will lead to two things - publications and a thesis defense, which by their very nature have to happen this year. There's really no other option available. I would like to take the time at the beginning and end of the day for reading and writing, both as an academic, and just for fun (writing here, reading Sense and Sensibility and Sea Monsters, among other things).

In short, the main goal this year is to finish my PhD, get going in med school, and be happy and healthy while doing it.

And maybe an Alaska trip in there would be nice.

Hope this year brings you great things!

End of the Year and What's Next

2011-12-28T11:25:00.001-06:00

As I sit here in my home office, splitting my time between reading papers, watching the dog try to get into a comfortable position, and choosing which music I wish to listen to next, I can't help but think about the future and what it will hold for me.

Not that any of those different things correlate to the future... I'm thinking that it's really just a mechanism for me to avoid doing actual work.

Not that I'm not getting things done here!

Anyway, as I mentioned, it's the time of year where I reflect on what's gone by this past 360-some-odd days and look forward to what will happen in the coming year. It hasn't exactly been the best year overall - there are many things that I would have been thrilled to not have had happened, both to myself, my family, and my friends - but there have been many happy occurrences that have lightened the mood, so to speak. Throughout the year, good things have happened the have softened the blow of the not-so-good things, and like anything in life we just have to sit back, say "well, that sucked", and focus on what was good.

I don't want to focus too much on what went poorly this year, so I will focus on what went well. For example, this spring I had the opportunity to present my research and attend my first "national" conference, the American Physician Scientist Association meeting in Chicago. It was quite interesting to hear from other physician-scientists at various stages of their careers, and how their projected career paths changed (often frequently) as they discovered the path that they eventually chose to follow. It certainly helped me justify still being a graduate student at this point in my career! In the same vein, as a research group we attended the Corn Belt RNA conference, a fantastic opportunity to discuss our research and learn from other RNA scientists, many of whom are located in our own backyard (relatively speaking). Missouri wasn't half bad, either!

Athletically, I began and sustained a running streak that lasted over 4 months, helping me to cope with the stress of my adviser moving away as well as to shed a few pounds. I'm feeling quite good about myself physically these days, and I'm looking forward to giving the marathon another go in 2012. Perhaps. I also did well in a few races this year, placing in the Clydesdale division at the Allerton Trail Race, a goal of mine since first running it back in 2006.

Travel was a big theme this year as well, and we had opportunities to get to locations such as North Carolina, New York, Florida, and (quite often) Minnesota. Despite not being in the lab (and the associated stress therein) it was quite nice to visit the people living in these locations, spend time exploring areas where I had not been ever (or, in some cases, had not been in over 20 years), and release some of the stress associated with other things at home and on the job.

As far as what the future holds, there are a number of themes that will be associated with the upcoming year. These include:
- Taking back Chicago (best not to ask, but suffice it to say that we need to take it back)
- Fixing all of the things (mostly around the house)
- Writing consistently (both on lab-related stuff and in the blog)
- Finishing what I've started (with regard to research work)

I have a plan for the blog, the gist of which is to refocus my energies on reviewing papers and research that I come across as I work on my thesis (both the actual thesis and the research associated with it). A quick review of the ASAP alters from ACS and the like can provide a lot of material suitable discussion, so I hope that I can make it a consistent topic of conversation on the ol' blogger. I also intend to continue discussing my running here, hopefully in the context of research as well, because there is a pretty good body of research being conducted on exercise ("exercise science" I believe is the term) right now.

So, if I don't get to it before then, I hope you have an amazing holiday, a Happy New Year, and I hope that 2012 brings you all of the good things 2011 brought and much, much more!

Holding Steady

2011-12-07T12:30:00.001-06:00

No great news to report over here - I've been doing a lot of stuff around the lab and at home, both in preparation for the holidays and for what I am going to term my post-holiday "Writing Week", in which I will spend a majority of the time writing out procedures, crunching old data, organizing papers, and trying my hardest to get something tangible on the computer for the upcoming semester.

While I'm not exactly certain that everything is working, things have been looking pretty good from a number of perspectives, and I'm glad that I'm feeling motivated and willing to put in the work to get things accomplished. Let's just hope that this can continue.

Switching It Up

2011-11-30T19:03:00.001-06:00

Alternate title: Switching Loyalties

This afternoon we had our new cable service installed. In the end, it will probably be about the same as the previous service, but it will be nicer as it will cost less (for at least a little while). It was a somewhat momentous occasion, as we ended up switching service providers (and had to spend a while on the phone explaining why we did that with the previous service provider). In a bigger sense, it was a way to make a change and switch from the status quo that we had been following for the past few years, trying something new and different. As someone who is committed to the same program for many, many years (having already devoted many, many years to it already), something like this is beneficial if only because it's something different.

In a larger context, it's a pretty good thing to change it up every once in a while and do something different. While it's nice to have stability, I'm finding more and more how important it is to get outside the comfort zone and try something new. There are a number of ways this has happened to me...

- In purchasing equipment, I had an opportunity to speak to a number of companies about possibly picking up a new PCR machine. After discussing different prices with both companies, I ended up going with the new one that I had not interacted with as often before, because it was a better deal. I felt bad switching up loyalties and going with a newer company, but in the end it was a better decision financially and the benefits were better than with the first company. Even if I had to cut ties, I made a good decision about it.

- In the lab, switching to a new technique or reaction scheme when the previous one isn't working so well can save time overall, even with the requisite learning curve associated with developing that new technique. I myself have gone through several iterations of a particular molecule type (a dendrimer) in order to make it both easier to synthesize and more modular for additional synthetic derivatives. Had I not stepped out of the comfort zone of a known pathway, I would not have gotten the molecules I currently use.

- In running, there are many ways to step out of the comfort zone - trying a new workout, a new piece of equipment, a new route, and - most recently - new pairs of shoes. While it may not always work out (see my recent attempt to use Puma Faas 500 shoes), it's much better to try something different when you're in a rut.

While it's difficult to step outside of the comfort zone, it ends up being better for everyone if you do!

Being Thankful

2011-11-23T10:06:00.001-06:00

As we make the final preparations for our annual trip to Minnesota for Thanksgiving (as opposed to all of our other trips to Minnesota for other reasons - birthdays, holidays, desire for good State Fair food, etc.), I want to take a brief moment and let the internet know what kinds of things I am thankful for. We often don't take the time to truly appreciate what we have, and despite the other factors that tend to take a higher priority nowadays - the meal, the football, the shopping - at its core this is a holiday where we celebrate the things that make us happy and fulfilled. In no particular order...

My lovely wife. For 13+ years we have continued to learn of each others' likes, dislikes, little quirks, personal values, and what our favorite rides were at Disney World as kids, among other things. Despite the stresses associated with our lives, we continue to find joy in one another, and I can think of no one else I would want to see when I come home after a long day than her.

My family, both immediate and extended. I have a very, very large family (12 aunts and uncles, ~40 first cousins... and that doesn't include my wife's family!) and am lucky that I have the opportunity to spend time with many of them at various points throughout the year. We have made it a priority to get to family events, despite living so far away, because we care so much about being connected. I am happy to have their support in what I'm doing and to support them in theirs. My parents did a great job instilling me with good core values, and I continue to try to make them proud. My brother continues to amaze me with his drive to follow his dreams and put himself out there for all to see, and I admire his willingness to step well outside of his comfort zone to push himself forward. Also he's a pretty snappy dresser.

My friends from all over the country, and the world (it's true!). I have made many good friends in my life, and try my best to keep in contact with them. I realize that I've created a somewhat skewed view of what most people do for a living, because most of my friends are pursuing advanced degrees and exciting, compelling career paths. I am continually impressed (and somewhat jealous!) of their successes, and I'm quite happy to know that I can say "I knew that person before they did X", whether that's "became a physician" or "won the Nobel prize" or "opened a restaurant". Although many of them live far away or are moving away from here, I appreciate the time I've had with them, and hope to continue to stay in contact.

My running career. Yes, I talk about running a lot, and I'm thankful that I get to do it. The main reason I'm thankful here is that, despite it sometimes being a chore or causing problems through injury, my attitude about running has remained very, very positive and I can't imagine myself without a pair (or 3) of running shoes near the front door. That I have been able to continue running and really enjoying it for 15+ years really says something, don't you think? Getting a trophy every once in a while doesn't hurt...
My science career. Despite how much I complain about grad school, I really do think that this is the best possible use of my talents and what I want to do with myself as a career. Every time I have a setback, I look at the literature and read about the great possibilities that these therapies hold, and how they could have a real impact on a terrible disease with few treatments, and that keeps me going. How many people have this opportunity? I always need to step back and appreciate that.
Walter. He's a dog. He's quite adorable. While I don't know how long he will be staying with us, he's a continual source of entertainment and makes sure I get my butt out of bed in the morning. What else could you ask for?
Ur-Paign. Again, despite complaining sometimes about this town, I really do like it here. It's easy to get around, there are many places I enjoy to eat, there's a strong church community, and we have a good set of friends. I'll be happy to leave so we can be closer to family, but for now it's not a bad place to live.
Social media. It's difficult to be away from your friends, but fairly easy to connect!

Alright, I think that's a fairly exhaustive list. I'm thankful that you, dear reader, find the time to read what I have to say occasionally. I hope you have a wonderful and safe holiday (especially if you are traveling) and that you have the opportunity to be thankful for the good things in your lives as well.

What, Again?

2011-11-10T16:49:00.001-06:00

This morning I woke up feeling some pain in my legs... nothing unusual, mind you, but it was more than just the normal aches and pains associated with being a runner. Side note before I begin - since we've gotten the dog, I've had to put extra time into stretching out my IT bands, because he squishes up next to me when we sleep at night and I end up sleeping right on the band, causing me pain. Good thing he's so cute...

Anyway, I did wake up with some pain that began to increase during our morning walk. I then went for a run... and the pain got significantly worse. Unfortunately, the pain was in my shin. The same shin that was giving me grief back in March, and again in May. The same shin that put me out of action for a few months, until I decided that enough was enough and started a 4+ month running streak. It hadn't given me guff for the last few months (really since I went to the doctor back in May), but recently it's been more of a problem. It's likely because of my new running shoes (the Asics Speedstar 5), which could be because they are too structured (i.e. none of the cushioning or stability elements have broken down) or too light (i.e. not as much cushioning or support as a heavier, more durable pair of shoes). Either way, I have the pain today, so I need to change my strategy for a little while. Luckily for me, I am currently in some "down time" athletically (my goal race was Allerton, in which I kicked some butt), so I have the flexibility to try some different things and work on areas other than running. So, here's the plan:

Cardiovascular - as running hurts, slow down/stop the running and do other things. I've been lamenting the fact that I haven't felt I have the time to do things like rowing, stair climbing, and elliptical. So, when I go to the gym, that's what I'm going to do. I'm doing to dust off the trainer downstairs as well so I can do some stuff at home. I think I'll still do some running, probably focusing on off-road running (dirt road near my house) or on the track. It may eliminate my commuting or running to the store, but I'd rather have the pain down first before I do that.

Strength - I've been trying to incorporate more strength work into my routine, including core work and weights. I do both once per week, and I think this is the best opportunity to include more days in the schedule. I should at least be able to throw in some push-ups and sit-ups on a daily basis. So, 2-3 days weights, 2-4 days core work (I remember reading once that some elite runners do core work 6 days a week, which is pretty ambitious, I think).

Diet - as always, try to keep diet under control so I don't gain back the weight I lost over the summer.

Form - this is one area that I never felt I had time for, but now that I'm a little injured it's as good as time as any to look into it. I'm curious about the "100-up" method posited by Chris McDougall (see the article here), and although I know it's likely not scientifically sound, it looks interesting and, well, hey, I've got to do something, right? It will be interesting to see how well it works (if it works at all), and how it affects my running form. Worst-case scenario (as is always the case) I will go back to wearing shoes and following a running plan that I know works.

My goal is to be healthy and ready to go for marathon training starting in January, giving me about 2 months to get myself together. We'll see how it goes!

In the meantime, the dog won't walk himself!

Corn Belt RNA Conference 2011

2011-11-06T21:04:00.001-06:00

This year the RNA Society held its annual meeting in Japan - a little far for the average graduate student to travel. Not that I even knew about this meeting before it happened, but even so. It's quite a long distance for many of us to travel to hear about the latest research in RNA, so unfortunately we had to miss it this year.

The good news is that a number of RNA researchers felt the same way, and decided to organize an alternative, RNA Society-sponsored, more local conference, appropriately titled the Corn Belt RNA Conference. Held at the University of Missouri Columbia (or Mizzou, as the kids call it), the 2-day conference provided the opportunity to researchers from around the Midwest to travel to a central location and discuss the research ongoing in their labs. Topics ranging from RNA aptamers to single-molecule spectroscopy to control of RNA-protein interactions were presented by grad students from local universities. The conference also featured a poster session that gave more students the opportunity to discuss research in an informal setting, and a number of different socializing opportunities during coffee breaks and dinner on Friday night. The conference also featured keynote speaker John Abelson, whose work includes, among other things, being one of the first researchers to elucidate the mechanism of alternative splicing. Oh, and he discovered and named the spliceosome. You know, no big deal.

My overall impression of the conference, held for the first time this year, was extremely positive! The conference was held at the Bond Life Sciences Center, an extremely nice building that holds many of the biological science labs at Mizzou. Not only that, but it has a cafe called the Catalyst Cafe (with sandwiches like the Double Helix Hoagie - check out the sign... anyone know what that is?) and a number of great artistic flairs, such as a sidewalk shaped like a DNA double helix.

The auditorium had a nice set-up, allowing for presenters to clearly show their work. The poster session and set-up for coffee, snacks, and dinner were not too crowded (although they could have spread out a little bit more - they could have taken out a few tables and given the posters a little more space). As it was the first conference, it was much smaller than your bigger, more established conferences, with probably between 50 and 100 people total (on the lower end for sure). And, because it was smaller, and the organizers received money from the University and the RNA Society, there was no registration fee! The only payment we needed to make was for the hotel, and with the discount for attending the conference and splitting the room between multiple people, the cost ended up being fairly small (about $30 per person). Only the cost of gas and occasional food not provided by the hotel or the conference (during travel, at the local bars after the poster session) added to our expenses.

Probably the best thing about this conference, something that I haven't experienced in other conferences and events I've attended, was that everything was so relevant. Unlike other conferences, which are much more general and cover a wide range of topics, all of the topics revolved around RNA and the techniques associated with studying RNA, which we could understand even if we hadn't used them before. Every talk had questions afterward from a number of different people, who likely hadn't heard of the research before the talks, showing how easily we could talk about different aspects of RNA. In my case, I had a good conversation with someone working on research that was very relevant to my own work, and he even suggested that I email his boss for advice. I wouldn't have gotten that suggestion, nor the good advice about my project, had I not attended!

If you are in RNA work and have the opportunity in the future (assuming they continue to hold the conference), you should attend next year!

Oh, and on the way to and from the conference from Illinois you can stop at crazy places and pick up cheesy gifts, as we did during our stop at Ozarkland.

Allerton Trail Run Race Report

2011-10-30T22:07:00.001-05:00

This morning I ran the Allerton Trail Run in Allerton Park, located down in Monticello, IL. It's a 5ish mile trail race that takes place in late October each year. I've actually run it several times over the past six years, and luckily the weather has always been good - sunny, cool, and the trails are usually relatively dry. This year was no different - the temps were in the 40's, there was a good amount of sun, and only one muddy patch on the trail. Great conditions for a great run!

I went into today's race feeling confident and having a big goal - wanting to place in the Clydesdale division. For those of you who don't know, the Clydesdale division is for those individuals who are a little bigger than the rest - in my case, it's for men who are above 190 lbs. Although I've been well into the Clydesdale division in the past (about a year and a half ago I was about 220 lbs), I entered this race sitting right around the lower end of the scale (pun intended). I've been running a lot lately, and posting some pretty good times over on Dailymile, so I thought that I had a pretty good shot at doing well today.

The race starts off heading through a sculpture garden before hitting the trail. I started off behind a group of folks that kept me slower than I wanted to go... within about 100 yards I managed to get around them and get up to speed. We traveled along the Sangamon River through dirt trails covered with leaves and a small scattering of roots (which, I may add, were well marked and easily visible). I felt good, controlling my breathing and pace, and hit the first mile at 8:22. Good, but not quite as fast as I was hoping for... so I tried to speed it up a little. Moving along the trail, I increased my pace and hit the second mile around 16 minutes, putting my second mile around 7:40. I was still feeling good, but could feel that I had taken that mile a little fast. I settled down into a comfortable pace for mile 3 and 4, still breathing relatively easily and feeling strong in the legs. As we rounded the Sun Singer statue, I continued passing folks, but I was starting to struggle to hold on to my pace. It was clear that I would be trying to hold on to the pace as I approached the finish line.

During the race, I had made it a point to try to pass anyone who looked big enough to be a Clydesdale. There was one guy who I passed early on (since he dropped something), who then passed me, who I then caught and passed again for good around mile 5. Aside from him, though, everyone I passed during the race never caught up with me again. I struggled through the last 0.7 miles (apparently it was a 5.7 mile race this year), which consisted of the three largest uphills (including an uphill sprint at the finish), and managed to get to the finish line at 44:37. I tried to work out the pace, and it ended up being a 7:50/mile pace! It was a really good result!

After the race, I hung around to see how the results would pan out - I was pretty sure that I had placed, but I didn't know how it would come out. An hour and a half later, they announced the results... 3rd place was someone else, but they said the time was 45 and change, and I knew I was in!

They called my name for 2nd place! I didn't hear the winner at the time, but it turns out I was beaten by over a minute, so there's no way I would have caught him. Regardless, I was extremely happy with how I did!

Overall, I had a great race this year! The race itself was well organized as always, there was a good spread at the end, and all of the volunteers did a great job! I would definitely recommend it to anyone looking for a fall trail race.

As far as my race plans go... perhaps I'll be able to pull off first place some day. Until then, I'm pretty happy with the result!

(Race photos by Erin D. Photography http://erindphotography.zenfolio.com/allerton)

Happiest Place on Earth

2011-10-26T09:04:00.002-05:00

This last week we went out to Disney World with the wife's family, an annual trip that spearheaded by her father and funded by her grandmother. This is the first time that we've attended, and I have to say that it was a lot of fun! Also, a lot of work - we were up at 6 am each day of the trip, going non-stop for a majority of the day, covering a lot of distance and a lot of rides. I hadn't been there in over 20 years, so it was nice to see that some things were added and a lot of stuff had remained the same. In fact, there were a number of rides and attractions that were exactly the same as they were the last time I was there. Kind of cool, in a way.

I was remarking to the wife as we came back from our trip (a full 10 hours of traveling) that I wouldn't be taking a day off until Thanksgiving, and her response was "shouldn't that always be how it is?". It's a good point - at this point of my career I should be putting in the time 7 days a week, spending at least a few hours a day in the lab even on the weekends. I've gotten into the routine of coming home in the evenings and trying to do things around the house, which is fine, but it doesn't help me make progress toward my research goals. Better time management has always been a goal of mine, and I think I'm finally realizing (for the 10th or 11th time) that I need to hone in on what needs to be done rather than just floundering around.

It's interesting how much of my research experience has been like the Tower of Terror. If you haven't been on the ride, it's sort of elevator that goes up and down and up and down and will suspend you in the air before dropping you without warning. As with any job, you experience highs and lows associated with your performance - sometimes experiments work incredibly well, while other times you can't explain why a condensation reaction can produce so many side products. It takes a great deal of effort to stabilize yourself and find the solutions to problems as they arise. In fact, I would argue that the whole gamut of PhD training is an exercise in problem solving - developing methods, experiments, and ultimately solutions to problems that you choose to evaluate, as well as those that develop along the way. In the end, you are hopefully left with a better understanding of science in general, if not your specific area of interest.

Anyway, back at it for the next month.

Inhale... Exhale... Repeat

2011-10-17T16:20:00.002-05:00

I'm not exactly sure where this is going to go, so bear with me.

This week I've declared it to be "Reading and Writing Week". This is primarily because I'm spending a majority of the week traveling. Thus, I don't have a lot of time to sit down and run reactions like a normal graduate student. I'm actually finding that I'm out and about a lot lately, making it much more difficult to get into a normal routine for more than about a week. Every time I settle down, I have to get up and go somewhere else again. It's annoying, not only because I can't really get into a rhythm, but because I have to let go of any thoughts of work while I'm away because I'm usually off doing something fun. Hence, the reading part of the week, which should hopefully help me get back on track with figuring out why the heck I'm doing this in the first place.

A friend of ours (my wife and me) recently asked "are you buying wine?" while we were over at her house with our dog visiting. I had to think for a second, primarily because yes, we do buy wine from time to time. In fact, I had made it a point a few months ago of regularly stocking up the wine rack so we had something to imbibe whilst watching the sunset at our country villa... no, wait, I should say, so we have something to drink while watching Buffy The Vampire Slayer on Netflix. We actually did do a good amount of wine tasting in the late spring and early fall, a combination of going to the vast wine country of northern Wisconsin and doing our best to be supportive at our favorite wine shop, Wines at the Pines. Lately, however, we really haven't been doing that much wine drinking, making it a lot more difficult to justify buying more wine. The other reason for this is because we simply don't have the space for new bottles. I was saying to my wife that we should get some sort of wine rack or cabinet for the house other than the one on our fridge, but was informed that a) that costs money, and b) that would take up space that we don't currently have. My interest in the idea resurfaced recently after hearing about Laura's bar, when I realized I could also use a wine/liquor cabinet as a piece of furniture. The quest is ongoing...

Science news... did you read about the Nobel prizes for this year? Some of them were quite interesting, with the Physics prize about the expansion of the universe and the Chemistry prize going to quasicrystals (which I understand are pretty fascinating, but, as an organic chemist/chemical biologist/physician-in-training, don't find particularly exciting). I myself was happy about the Physiology/Medicine prize, which went to 3 scientists who made important discoveries about the innate and adaptive immune systems. We often take for granted that our immune systems work quite well to keep us from getting sick, but from their work one can see how complex a dance it really is to keep us going. Having spent last year learning about immunology (and the microbes that the immune system is constantly fighting off) I can really appreciate that this prize awarded to these folks. And, of course, RIP to Ralph Steinman, who passed away before receiving the prize. The Nobel Foundation did the classy thing in still awarding it to him, despite the fact that they normally wouldn't award it posthumously.

Random question having to do with reading and writing week - do you find yourself falling asleep while reading papers? It feels like my body is trying to stop me from learning by making me start to doze whenever I work on getting through a scientific paper. Perhaps I need to begin napping on a regular basis?

On the shoe front, the latest news is that my next attempt at purchasing a shoe without trying it on should be arriving by Wednesday. If you haven't heard, I spent some time trying out the Puma Faas 500 shoes a few weeks ago, after reading through a number of positive reviews and finding that I could get them at a good discount at Running Warehouse. Unfortunately, they were too narrow and actually made my legs and feet sore while just standing and walking, so they had to go back to the store. I did some more searching/analysis/narrowing down by price, and decided to pay an extra $9 to get the Asics Gel Speedstar 5, another lightweight trainer that looks pretty interesting. I'm somewhat worried about the fact that I read on several different places that it may run narrow, which was the problem with the other shoe, but I know now to just try it on and if it doesn't fit well, just send it back. Thank goodness for free return shipping. I will let you know how it goes.

I think that's all I've got for now. Thank you for indulging me.

I'm Adam L.
Thanks for listening. :/-

Purchasing Your Running Shoe: A Lifetime Case Study

2011-10-10T16:26:00.000-05:00

Let me first preface this with my running resume, so I can (hopefully) prove to you that I know a thing or two about this and that my advice can be (hopefully) trusted. I will also say that a very good resource for running shoe knowledge is Runblogger, so feel free to go there as well.

I've been running since I was 12 (1995 - I'm currently 28), beginning by running with my mom while she trained for her first half and full marathons. My first organized race was a 5K when I was 13, which I ran on several occasions in the years leading up to high school. In high school, I ran cross country in the fall before playing basketball in the winter, picking up recreational running as an activity in the spring. Following high school, I was a recreational runner, staying in shape while dealing with the stresses (and well-stocked cafeteria) of a college lifestyle. I ran my first marathon during my senior year, and have since run 5 more marathons, several half marathons, and shorter distances from 5K to 10 mile. My running shoe style is neutral cushioned, and I've tried a number of shoes from different brands over the years, with the most prominent being the Gel Nimbus line from Asics. I believe I went through 4 or 5 iterations of that shoe before switching to a different brand.

With that in mind, let's discuss my running shoe journey.

When I began running, I had no clue the intricacies associated with choosing a shoe (and it's highly likely that fewer of them existed back then). As I had been a basketball player for many years at that point, the strategy that made the most sense was to wear basketball shoes while running. I'm fairly certain that my shoe choices were based on two things at that point - style and price (the latter being something that my father made sure was an important factor). I worried little about form and function of my shoes, and did the miles when appropriate.

The first big change came back before freshman year of high school, when I was beginning to become a "runner". I still had little knowledge of the subject, but had the distinct advantage of knowing several marathoners, including both my parents (9 marathons between the two of them) and my uncle (27 marathons total, including a number of qualified Boston marathons). I also knew (and this was pretty obvious back then) that I have a very similar foot shape to my mom. This meant that whatever shoe she was wearing would probably work just as well for me in the appropriate size. I believe my first real running shoes were a pair of Nikes, some sort of Air Max Triax deal that was discontinued not long afterward. As I said, I capitalized on her experience and was able to run essentially injury free for my first few years in high school.

Looking to purchase my second pair of shoes, I then had the opportunity to go to the running store myself to try on the shoes. This was my first opportunity to get the analysis and thoughts of fellow runners trained in identifying what types of shoes would work with certain runners. As I had been somewhat experienced at that point, I had a reference point to work from, and after a few tries we settled in on a different Nike shoe that looked an awful lot like a basketball shoe (no idea what kind). Again, it was a neutral cushion model similar to my previous shoe, and it seemed to work pretty well... until I managed to leave them in Mexico at the end of my senior year of high school. Yikes.

I returned to the running store to get further feedback for my next few pairs of shoes. I should point out how useful it is to go to a running shoe store (versus a department or big box type store), as the people working there are often runners themselves and usually have plenty of experience when it comes to picking out shoes. If anything, you can give them a starting point (i.e. whatever shoe I was wearing before that), your thoughts on different features, and together can find a shoe that should work. I went to two lightweight, neutral trainers (Nike Skylon, I think), which did well overall but had some durability issues. I'm a big guy (6'1", 190 lbs), and the shoes had the correct pronation control features but not a lot of cushioning, so they wore out a lot faster than different pairs of shoes would.

And then... the Nimbus. Like my early shoes, my mom was again the impetus for this purchase. She had gone to the shoe store and been pointed to them, and suggested that I give them a try as well. They are, as many have stated, probably one of the most cushioned shoes available, and they were great for long miles on the road. Throughout college and my first few years of grad school, I went through multiple iterations, wearing out the previous shoe with marathon training and long runs, exploring the new features which really didn't change the performance of the shoe. I was quite happy and brand loyal, not very willing to make a change.

But then minimalist running shoes happened.

Well, sort of. As the costs of purchasing the thickly cushioned, top of the line running shoes have increased (I think there's a shoe that costs $200 now? Seriously?), and the promises of potential increases in running performance and injury prevention with minimal shoes have become clearer, I've been changing my tune about what kind of shoe I want to have. I actually used to take pride in the fact that I was quite the heel striker, something that I don't find so appealing now (the jury is out about whether I still do it, but at least now I don't say that it's one of my strong points). After years of purchasing the same shoe (and, I might add, suffering from a chronic hamstring problem... probably the result of no stretching and overtraining, but still), I went back to the running store and asked to see what kind of minimal shoes they had available. Unfortunately the list was small (mostly confined to racing flats), but there were some less expensive choices available, and I switched from the cushy Nimbus to the middle of the road Saucony Progrid Ride. Less shoe, less expensive, and it seemed to fit and work as well as the Nimbus.

I ran on 2 pairs of the Ride 2 (the second of which brought me through a marathon), and stayed with online purchasing to get the Ride 3, which (at the time) had about the same cost as the Ride 2. As before, I figured that I could stay with the same style and, even with the upgrades going from 2 to 3, have no problems. Whatever the cause, I ended up getting shinsplints, and had to stop running for a little while.

In thinking about my running career and what I wanted to do with it, I again considered the possibility that cushy shoes may not be as helpful as they seem, so I began to explore other options. Through the internet and Runblogger, among other places, I settled in on the New Balance MT101 shoes, minimalist trail shoes that I could use for running on the grass (where I had been running because of the shin problems). I think I got lucky in that I ordered these shoes online, without having tried them previously, and found that they fit pretty well. Thus, a new paradigm was born - find inexpensive shoes on the internet which should fit, and give them a try.

I recently tested this method again by purchasing a different pair of shoes, the Puma Faas 500, which were again inexpensive and matched the neutral cushioning type of shoe that I normally wear. I found, however, that they were a bit narrow for my feet, and despite giving them a chance for a few runs I ended up returning them because they just didn't work for me, causing my hamstring injury to flare up. Unfortunately this means that the new strategy has been met with its caveat - since you can't try out the shoe before purchasing it, you're stuck having to wait until you've actually purchased the shoe to find out if it will work for you. For the record, I'm currently 1 for 2 in that department, and will be waiting for the exchange to be made to see if I will be successful on the next purchase (Asics Speedstar 5, which I decided on in a similar fashion to the one I returned).

I should point out here that I purchased the most recent two pairs of shoes at Running Warehouse, a company that not only has free shipping for both purchases and returns (thank goodness) but also very helpful customer service. I wrote them an email on a Sunday morning thinking that I wouldn't hear back for at least a day, and they promptly responded and were very flexible with their return policy for me. I'd highly recommend them if you're looking to find a pair of shoes online!

In the end, there are a number of bullet points I want to bring up with purchasing your first, second, or (in my case, probably) 20th pair of shoes.

If you haven't had a pair of running shoes before, get to a running specialty store and talk to someone about what you're hoping to get out of your running. They'll be able to watch you run and, based on your input and physical mechanics, offer some suggestions to what types of shoes you should try. Other methods like the wet foot test can also be helpful, but I believe that there's research indicating that this doesn't always tell you the type of shoe that works the best.
Try your shoes out by both wearing them around the store and by running in them (something that most running stores will encourage). You should feel comfortable in them from the get-go, and not have any screaming pain when running in them. If you choose a pair, try to get to a treadmill or jog around your house for a little bit to decide if you want to stick with them. I had one pair of shoes that were different from my normal shoe type, and after running on a treadmill for 5 miles I more than realized that I shouldn't have been running in them.
If you go to a running store to look at shoes, and you try out a bunch of shoes and pick one you like, buy the shoes from them. I've gotten yelled at for suggesting otherwise. :/-
Once you've established what kind of shoes you want, feel free to look online for subsequent models, keeping in mind that certain shoes may change from year to year, meaning you may have to go back to the running store to see how different they feel before purchasing.
If you want to take the risk and try something new without going to the running store, use some sort of shoe-fitting analysis program first (Running Warehouse uses one) to see if you should wear a different size than you normally would wear (i.e. if the shoe you want is more snug than the one you have, you may have to size up a little)
Be sure to learn about the return policy for where ever you purchase your shoes, to make sure that they are not too damaged before you decide you want to send them back. Most running shoe stores will be pretty flexible, but online retailers probably won't be as nice to you (Running Warehouse being an exception, in my case).
Don't be afraid to step outside of your comfort zone when it comes to shoe purchasing, but be sure to do the research before you do it to make sure you don't get injured/have to deal with returning shoes.

Anyway, I hope that my personal experiences will be helpful to you when getting your shoes. Running is something that I really enjoy, and having good equipment is always a helpful thing!

I'm Adam L.
Thanks for listening. :/-

Gear Review: REI Flash 18 Pack

2011-10-07T10:34:00.002-05:00

One of the challenges I had during my running streak over the summer was trying to find time to do the runs while at the same time staying in lab as much as possible, getting up to walk the dog in the morning, maintaining a relationship with my wife, etc. To put it another way, it's hard to find time to do runs. One solution I had for this was to make my runs part of my commute - whether taking the bus or getting a ride to work, it usually took the same amount of time to run to or from the lab, so it wouldn't result in a hit in my time during the day, with the added bonus that my run would then be done. The challenge I had was that, if I did decide to commute to or from work, I would have to plan well ahead with clothing, towels, and food for the week so I wouldn't have to worry about arriving at work and incubating in my sweaty clothes all day.

The alternative to this was to get some sort of bag I could use to transport my stuff with me while running. In fact, I had seen on numerous occasions another gentleman running by me in the morning, pack strapped on his back, and thought that I should be doing that as well. I had, on occasion, used drawstring bags that I had gotten for running and volunteering at the Illinois Marathon, but I found that the bag moved wildly while I was running, and any attempt to restrain the straps resulted in them digging into my neck from either side. Suffice to say, I wasn't happy with the performance, and needed something different.

My criteria - relatively small and lightweight; able to hold clothes, a towel, and other random necessities; adjustable so I could strap it tightly to my back; and, most importantly, inexpensive. Through several rounds of research at local stores and online, I decided upon the REI Flash 18 pack.

This pack fit the bill - about the size of a stuff sack (and those, if you don't know, are small bags that can be used to hold sleeping bags and other junk), lightweight, rugged, and much less expensive than other packs that were available (about 30 bucks). It was pretty light on the features (not many pockets, for example), but for the price I was thinking it would be a good choice. Plus, it was pretty well reviewed, so at least I knew that other folks had liked it.

It's been a few months, so I think I have a pretty clear idea of my thoughts on this pack. In short, it works pretty well! I am able to pack in what I need - for example, yesterday, I had my outfit (jeans, underwear, socks, long sleeved shirt), towel, accessories, toiletries, and lunch, with some room to spare. The pack had adjustable shoulder and waist straps, so I'm able to position it tightly to my upper back with minimal movement. The straps can be tightened while running, so if they do get loose (and they will reach an equilibrium where they're not incredibly tight, leading to some movement) they can be adjusted accordingly. There are additional features I haven't taken advantage of yet - the daisy chains could be used to attach additional gear, and there's a pocket for a water bladder so it could be used as a hydration pack, which may be helpful for hiking later down the line.

The biggest issue with the bag has been the position of the straps - if you want the bag to sit high and tight on your back, the waist strap comes down about mid-stomach. This has actually been a bit of a problem for breathing deeply, as tightening the straps can constrict your breathing a little. I've adjusted it to place the bag lower on my back, so the waist strap actually goes around my waist, but I've found the bag moves around too much for my liking if it's placed there. I've dealt with having the straps up high just fine, however, as the lack of movement makes up for the somewhat constricting placement of the bag.

Overall, I've been quite happy with the bag, and I would highly recommend it as a running or hiking pack. It has enough room for the important stuff, can be easily compacted for transport, and seems to be durable enough to use for a long time. Go out and get one! (I think REI is having a sale, in fact, so now's a good time to get it!)

I'm Adam L.
Thanks for listening. :/-

Congratulations to the Beer Runner

2011-10-03T09:11:00.003-05:00

A special congratulations to The Beer Runner (@TheBeerRunner), who today completed 365 consecutive days of running and beer drinking. That's quite an accomplishment, and he's been an inspiration to me and others throughout this year.

Following his model, I started a streak that lasted 4+ months, enjoyed many new craft beers that I never would have tried otherwise, and ended up losing a fair amount of weight in the process (I've been hovering around 190 lbs for the past few months - it's as light as I've been since training for my first marathon back in college).

So anyway, congrats to the Beer Runner! May you enjoy another year of beer and running!

Movie Review: Contagion

2011-10-01T12:58:00.000-05:00

With an almost documentary-like quality, the film Contagion documents the spread of a novel viral disease and the efforts made by individuals and organizations to isolate, identify, and find a possible treatment for it. An all-star cast, containing all of the heavy hitters, deliver a well-acted and startlingly realistic account of the spread of this virus, to the point that you may end up wondering how many times you touch your face per day and if you should go back and wash your hands one more time, just in case.

I won't get too much into the plot details (you can look at the link above), but I've essentially covered the essentials (disease spreads, disease identified, disease treated). Instead, I want to give my overall impressions, some specifics that I liked, and some stuff that I think could have been done better.

Overall - this was a very well done movie. From beginning to end, it was compelling without requiring a lot of overacting, melodrama, or heavy plot points found in other movies. There was no big love story, no dramatic cure, just a lot of folks doing the best they can to isolate the virus and discover a cure. The responses from different people, individuals and larger groups, were about what you would have expected - mass hysteria from a panicked public, serious thought and consideration from scientists attempting to learn about disease and how to treat it. The level of science presented in the movie is thorough without being overwhelming, so the standard movie-goer can understand and the scientifically inclined can really appreciate the level of detail. Again, the acting was spot-on, with nothing crazy on the lines of something like Outbreak (a movie that I also enjoy). Finally, both the wife and I agreed that the end of the movie could have had a message from the CDC - get vaccinated! (the folks at Science-Based Medicine should get a kick out of the movie, I think)

What I liked - My wife, an oncology nurse, often is miffed at the large inaccuracies in medical terminology and practice in film and on TV, to which I often reply "it's a movie". This movie had none of that - we were both quite impressed with the accuracy and detail to which they portrayed the quest to identify the disease. Terms like fomite were correctly used and applied when appropriate, differences between killed and live attenuated viruses were discussed (including the use of adjuvants!), and genomic overlays and PDB structures were shown and explained so they could be understood. Never during the movie did I roll my eyes about the inaccuracy of the science - in fact, I did a lot of nodding in agreement for what they were doing. Who knew they would be able to make using a centrifuge look cool? Maybe it's because Dimitri Martin was doing it...

Aside from the science, I again was again impressed with the acting and the convincing accuracy with which they portrayed how people would react to such an outbreak. From scientists to epidemiologists to the general public, everyone reacted like they should have. It was even to the point that the conspiracy loving folks got their nod in the form of one character acting as a "professional blogger" who "seeks the truth", pushing the use of his homeopathic remedy and suggesting people not get vaccinated. In a world where vaccine scares are still in our minds (hello autism), this movie shows what can happen when misappropriate and scientifically lacking ideas and treatments are pushed on the general public. It ended up acting as almost a message against folks promoting CAM and homeopathic remedies, again instead backing the message that you should trust scientifically backed treatments.

Most importantly - a lot of the movie takes place in Minnesota. They even had KARE 11 news on there! Made me miss home...

What could have been better - my only real problem with the movie was a limitation of it being a movie - a lot of stuff ends up getting dropped at one time or another. It's impossible to tie up every loose end, but to a certain extent I wish they could have spent a little more time on different points - what happens to the WHO officer after she realizes a bunch of villagers received a placebo treatment, or just what made one of the characters immune (and why wasn't it utilized? Probably because it was unrealistic, but still). The wife suggested it's because the folks played their role and then "bowed out" when their time was done (as is often the case with scientific progress, I suppose), but I would have loved more and more detail!

One other plot point I'm curious about was how the disease spread. I can understand that it wasn't airborne and required contact with surfaces or diseased folks, but given it's relatively limited starting point, how could it have hit every major city in the world? It seemed like they chose all of the major cities and just assumed it would get there, even when it doesn't seem like it could have spread that quickly. Perhaps that's the only somewhat unrealistic part of it, but it's likely a result of (again) just not having enough time to tell the story.

Bottom line - if you are a fan of science, critical thinking, and a compelling movie, go see this movie.

I'm Adam L.
Thanks for listening. :/-

Doing it in a Group

2011-09-30T09:12:00.000-05:00

How are your meetings? Are they productive? Do you get the chance to voice your opinions, make suggestions, increase synergy, or do you just whittle away at some random sketch while the others argue about platitudes and the proper way to graph data?

I only ask this because, as someone who has (relatively) recently been thrown a paradigm shift with the boss leaving, we have had to make some changes to the way we do meetings. For the past 5 years, it's been a pretty standard format - 1/2 research presentation, 1/2 literature presentation, a little literature abstracts thrown in, and a singular focus on the person who's speaking at the time. There are many ways to do group meeting, and this was it for us.

With the boss leaving, we had to think about what we wanted out of group meetings, and what we felt would be the best format to get our thoughts across to other group members. On a day-to-day basis there is a varying degree of communication between folks in the lab, depending on what projects people are working on and whether or not someone is trying to learn something new that another person in the lab has mastered (be it a technique, a computation, etc.). This constant communication is very important, and made justifying the "one person gives a big talk" easier because one could argue that everyone was getting help on a consistent basis. That being said, it didn't happen for everyone, so some folks who are working on their own projects (i.e. me) did not get the same level of feedback on a regular basis.

Fast forward to recently, and we've had the opportunity to try several different formats with our meetings, seeing what works and what doesn't work. What definitely doesn't work is having everyone present, because it just takes way too long and doesn't allow for a good amount of discussion for each person (especially if some folks are taking longer than others). Last night we followed a similar format, but had only half the people present, and it ended up being a very fruitful discussion for everyone involved, I think! What seemed to be the most helpful was getting that more casual discussion happening with everyone in the lab, so one could get input from other lab members who aren't normally involved in the day-to-day conversation.

It's clear that there's value to this format - who doesn't like input? At the same time, however, we appear to be moving away from the "one person does a more formal presentation" format, which may detract from opportunities to, well, present. An interesting twist to this has been attending the group meetings from other groups, which was something we chose to do to help us stay "in the loop" and "visible" within the department. The group that I currently attend actually does both formats - weekly group meetings in which one or two people present, as well as subgroup meetings in which folks do more of an informal presentation with discussion. While this is similar to the way we've done it in the past, I think the benefit is that the subgroups are more broad - synthesis-based one week, assay-based the other week, rather than having a particular project meet separately, leading ultimately to me being by myself for meetings. I like the format better because it does what it sets out to do - gives folks in the lab who are not working on your project the chance to bring an outside perspective and insight into what you're trying to accomplish.

Feedback time - how do you group meeting? Informal discussions, formal presentations, or a combination of the two? Do you have to present for an hour once every few weeks/months, or 15 minutes on a more frequent basis? As someone who is now a refugee and seeing the world for the first time, I'd be interested to hear how you do it in a group.

I'm Adam L.
Thanks for listening. :/-

Facebook is not a verb

2011-09-28T10:00:00.002-05:00

There's been some uproar about the changes in the design of the Facebook recently. Is this surprising? I suppose not, given the tendency for us to hold on vehemently to what we have before embracing the changes the occur.

And they occur pretty frequently these days.

I've been at hard at work in the lab, evaluating things and trying to make the changes necessary to get my work done, while at the same time struggling to let go of those beliefs that I hold to vehemently myself.

Luckily for me, none of them have to do with any social media redesigns.

Anyway, the point that I'm going to make now is this: as far as it goes here, I've been missing putting down my thoughts on the occasions in which they occur. Other outlets are simply too constricting or too annoying for me to most accurately describe the things going on inside my head, and I've come to the conclusion that this is going to be the place to do it. That means that I'm no longer going to worry about sticking to a format - as it was originally stated, this is a place for me to chronicle my journey to being who I am destined to be, and it doesn't always necessary fit within the realm of a "science blog" (despite my designation as such on one Carbon-Based Curiosities). Will I continue to incorporate science into the blog? Of course, seeing as how I live it every day. It just means that if I deem it necessary to discuss something other than science (or running, for that matter) then I'll write it down.

Maybe I'll make up a new logo, too. We'll see what Powerpoint and MS Paint have to offer. Unless someone wants to make one for me?

Leading on to my final point - I'm realizing that many of my relationships with folks have become entirely virtual, including people with whom I have actually had conversations in person. I realize that it can be much more difficult to have that face-to-face conversation with someone when it can be easily accomplished via email, text, etc., but more and more I am depressed by the fact that these people are starting to exist only on the virtual level.

Therefore, if you have any interest (especially if you are someone who lives nearby) then I would rather communicate in person. Let me know if you are interested and I will buy the coffee.

The internet is a fun place to connect, but I'd rather give you a handshake and a how you doin' than Facebook you. Srsly.

Keep on keepin' on, everyone. :/-

All Things Must Pass

2011-08-17T10:06:00.000-05:00

Folks, there comes a time in a man's life when important decisions need to be made...

Okay, a little melodramatic, but here's the point: I'm off for a while. Not sure how long. I'm not finding inspiration in writing about anything lately, I'm feeling stressed out in the lab, and I need to reduce the number of distractions I have.

Thank you for stopping by and saying hello on occasion for the past 2+ years. I've had fun writing, and look forward to trying something new (and perhaps even coming back here) after I've finished my PhD. When that happens... who knows?

Soon, I hope.

Take care, my friends!

Changes

2011-08-09T15:47:00.000-05:00

Boss is gone, back from vacation, thinking about changes in research, in life, in the blog.

Stay tuned.

Running Update

2011-07-26T14:16:00.000-05:00

15 years.

I realized today that I have been running and racing consistently since the summer I turned 13, during June of which I ran the William Irvin 5K in Duluth. Yesterday I turned 28, so it's abundantly clear that I've been running for longer than 15 years - all of my teenage years and all of my adult life. I've done a good amount - 6 marathons, several halves, and distances from 2 miles to the 10K in between.

I'm currently on day 65 of my running streak, having completed a nice and hot five-miler an hour ago or so. I'm finding that the streak is having positive and negative impacts - on the positive side, I feel really confident in my running, with few problems with injury (aside from my IT band, which I'll get to in a second), and I'm getting relatively fast, averaging in the low 8 min/mile pace. Unfortunately, the frequency of running means that I'm not doing as much distance (I've not run longer than 45 minutes at a time during the streak), and - coupled with the heat and humidity - I'm finding it difficult to make extra time to run longer than that. I have my occasional moments (such as the 5-miler today) but otherwise it's a lot of 2, 3, and 4-mile runs. I'm also fairly tired, but that's more of a general thing (especially from having the dog).

In doing the streak, several important aspects of maintaining the streak have come to light.

Stretching. I had some trouble sleeping in the days after getting the dog because my IT bands were so tight that I could not sleep on my side. I've been doing the foam roller thing, and they feel much better. I'm not sure if I would have had to worry about it without the streak, but now that I'm firmly entrenched in running every day it's become a necessity.
Nutrition is also important, as I need high-quality foods to achieve my running goals... not that I'm always getting them, but I'm trying!
Rest. I need to get more sleep, getting to bed earlier, because no matter what I do 5:45 am will be coming and my dog will be calling.
Prioritization. Finding the time to run and do it for more than 10 minutes at a time has been relatively difficult, so I've had to make some changes to my schedule. More short runs in the morning, more trips to the gym during the day, so that I don't have to worry about fitting in the run at the last minute.

As far as goals go these days, I've been focused mainly on continuing the streak. My thoughts about running a fall marathon go back and forth, with money and time being the hottest commodities that I don't seem to be willing to live without. Thinking about it some more (and on the suggestion of one of my friends) I'm thinking of doing a few 5K's this fall to test out my speed. I had a good race earlier this year, but I think I can do better, and the recent performances I've been having on the track are convincing me that this is true. I also think I can turn out a half marathon without much training, so hey, you never know.

Overall, it's going well! I'm not doing a lot of long running, and (unfortunately) not a lot of trail running, but I'll have the opportunity to do both next week on vacation in Northern Minnesota. Should be a fun time!

As a side note, for my birthday the wife bought me many, many pairs of socks, a pair of gaiters (which are geared more for winter hiking and comically tall, but I'm still going to use them on the trails), and a new, professional messenger bag! I'm pretty happy right now!

Business Computer

2011-07-22T10:13:00.000-05:00

For the first time in my 5 years (or so) here I have an official University computer at my desk. Having brought my laptop with me for the most part (or relying on other lab computers) I have not had a desktop in a long time. Given our lab contraction and the fact that there was a computer lying around, along with the fact that my laptop has a tendency to, well, let's say, overheat to the point I think it's going to explode, I was happy for the change.

It will mean a lot less goofing around (I hope) and more work, but we'll see how it goes.

Glad I finally got on the bandwagon 5+ years into the job. As my wife says, your employer should provide you with the appropriate tools to complete your work, and this is that finally happening for real.

Proof You're Getting Older

2011-07-19T20:55:00.000-05:00

This morning I went off to the ID Center to renew my student ID. A right of passage reserved for those who spend more than 5 years at the U of I, it was an interesting experience to go in and tell them that my ID had expired and that I had to renew it. It meant that I was still here and still had a ways to go in my career.

I look at the picture on the card now, comparing to my previous photo, and notice more than a few differences between the two (luckily, although they took my previous ID, I still have a copy on my Res Life ID from when I was a tutor). The haircut is similar, a little bit shorter and a little less styled. I'm now sporting a goatee, hiding the changes in body size (although at this point I probably weigh less than I did then, a result of 58 consecutive days of running).

Most tellingly, though, is the overall appearance of age. I look older, a few more lines on my face and much deeper bags under my eyes. A spry 23-year-old in the old picture, I was not aware of how much age and experience I would obtain in the 5 years between these two pictures. Next week I'll be 28, and while that's not an advanced age, I've gotten a lot of experience in the intervening time that has made me both wiser and much more sleepy a lot of the time. I've learned a lot of different things, from chemical reactions to ways to interact in a professional context with others, to how to change a light-switch, to caring for a dog. I've worked hard, played hard, gotten more than a few scars along the way, and I think my picture reflects that experience.

I'm looking forward to finishing the PhD and moving on to the MD, but I'm glad to know that the experience I've had will continue to drive me forward, and that this experience is reflected in my appearance. I want people to know that I'm older and wiser than the college students I'm constantly surrounded by, so that people will come to me for advice and knowledge as I continue forward in my career.

We all like to stay young, but sometimes it's nice to be a little older.

Connectitude (or: Linkativity)

2011-07-14T08:52:00.000-05:00

So I've officially signed up for the Google+. Come and find me.

I did it because we are looking to find ways to communicate with the boss once she moves off to her new job. There's apparently a feature where you can "hang out" and video chat with more than one person at a time, which will probably be useful somehow in having multiple people chatting at the same time. The only problem I see with it so far is that my computer just isn't that great, so it crashed the last time I tried it. I think I can solve that with a cooling pad and turning up the performance settings on my computer, but that's neither here nor there right now.

The point I'm getting to is the fact that I now have all of the important social medias, meaning that I'm highly connected to the internet world. I'm not sure how I feel about it. It's equal parts good and bad - you have a strong connection to a number of folks and can communicate ideas and cat videos across great distances, discuss running form and chemical synthesis, etc., but there's a great incentive to then make interpersonal interactions less important.

One of my friends in Minnesota was telling me about how the people he interviews for jobs are terrible at interviewing because they never have the need to interact with people in a professional capacity face-to-face. They just don't know how to talk to people anymore! In a world where you don't need to present yourself in person, it appears to be more difficult to develop those necessary skills for being a dynamic speaker who can actually talk to the person in front of them. I myself have that problem anyway, and I'm sure the increased usage of social medias and electronic communication have chipped away on any interpersonal skills I managed to develop in the past.

Despite my connectitude, I'm going to try to avoid using it too frequently, especially with regard to personal interactions that I could be having with people who are nearby. I can understand how important it is to be clear and straightforward with people on internet, but I'd rather do it in person.

When Science Goes Bad, and Finding Encouragement

2011-07-09T18:21:00.000-05:00

There are a number of interesting things happening in the world of science (understatement of the year) that pertain particularly to poor results being altered, modified, or just misinterpreted as positive and useful. I won't spend a lot of time talking about them, as there are a number of very good summaries available, but I do want to point out to people who read my blog several other blogs and news outlets that have some useful information on the topic.

Well, both stories are discussed and reviewed by In The Pipeline, one of my favorite blogs relating to science and industry news. There is a good summary of the news items in each of his last two posts, along with the requisite links to the stories. I'll give you the links, plus my view on the matter.

The first story revolves around a PhD student who apparently falsified nearly all of her research over the course of her PhD and only relatively recently was caught for the amount of false data she fabricated. While the story is older (she "got" her PhD in 2005) there are a number of new documents that have surfaced in the public further damning her for her efforts. It's a very interesting story about how someone can so easily deceive her labmates and PI, despite the problems that came with others trying to reproduce her work. As someone who has been trying to generate a lot of data, I find it somewhat hard to believe just how much effort one could put into falsifying results, especially considering it probably took more work than just, well, getting the results, but some people are just crazy enough to do it. It seems that they're finally catching her and bringing her to "justice" (in whatever sense of the word that means... I guess retracting papers and taking away her doctorate, not allowing her to do research, etc.), so hopefully this can serve as a lesson to all of us not to cheat our way out of doing the work and suffering the foibles of obtaining a PhD.

The second story is a lot more troublesome, as it not only affects the people of a laboratory but also a whole slew of folks. It appears that a lot of research being done looking into biomarkers for medicine, stretching from the lab to the clinic, was - while not fraudulent like the first story - poorly done and analyzed, causing many folks to be treated rather poorly for cancer. It's been interesting to read more into the story because it highlights just how little we know about the genetics of cancer and ways to detect exactly what kind of cancer (and other disease, for that matter) any given patient is dealing with. In reading about epigenetics, it's clear that there's a lot more going on than just the genetic sequence, making it much more difficult to truly tell, without a shadow of a doubt, what exactly each individual is dealing with. There's also a good discussion of "personalized medicine", something I believe is a possibility as a medical treatment but requiring a lot more work to become plausible. While the Duke study has gone awry, hopefully future work will produce better, more meaningful results that don't lead to the same kinds of problems that were encountered here.

On a positive note, I've actually been finding some encouragement at work recently. I was writing about being in a funk on the research front, and recently some fruitful discussions with the boss have produced some interesting things to think about and examine. I'm hoping to continue pushing for positive results here as the summer progresses, and then by the fall into the winter have a good amount of material for publications and thesis writing. It's about as positive as I've felt about lab work lately, so hooray for that!

Finally, the dog has settled into our lives and we're doing fine with him! I'm getting more walks in that I would have under other circumstances (and he is as well!) and I'm learning what it's like to be up at the crack of dawn every day. So far - not bad!

Summer Vacation Continues...

2011-07-05T12:51:00.000-05:00

You're welcome.

Long and exciting weekend over the 4th... got a lot of sun, not much sleep, and now we have a dog who is probably hating me for leaving him at home today. I envision many walks and explanations that, yes, we will be back later.

Science continues to be a chore, but I'm working through this period and will, by the end of it, be much better off and will hopefully have some interesting data to share. I've read a handful of interesting articles about regulation of telomeres and how study of this can give insight into the expansion of triplet repeats in diseases like mytonic dystrophy... perhaps I'll do a write-up about it at some point. I've also got some reading to do about epigenetics and regulation of epigenetic markers with small molecules, which I will try to turn into a post as well.

I've also managed to continue the running streak - 44 days and counting!

Just gotta keep going, and hope the dog didn't eat anything/make a mess in the living room. The joys of parenthood, am I right?

Yarrr, Science Be a Fickle Mistress

2011-06-28T13:44:00.000-05:00

The seas of chemistry be rolling and tumbling mightily these days...

No, really, it's one of those times when the unexplainable occurs and you have to spend a lot of time figuring out why the heck things aren't going as planned. I've spent a good time of the past several months having thought I worked out the kinks and was getting everything to work great, and lately I'm not finding any success in anything. I'm not sure what the cause is - the hot weather, the lack of an additional stress in the form of a class, the running streak I'm focusing on, etc. - but lately I'm not able to get into a good rhythm and get everything done.

I'm actually quite surprised at a number of things not working well lately. For all conceivable reasons there shouldn't be any of these shenanigans going on when it comes to the science - not a month ago all of the reactions seemed to be working fine and I could reliably make and attach molecules to my peptides and dendrons without much hassle. Lately, though, it appears that whatever I've done to offend the gods has caused me nothing but trouble - I can't get reliable mass spec results, my molecules don't want to be synthesized, and I can't muster up the courage to run another splicing assay for fear of wasting materials. I'm at a cross roads and all I can do is wander back and forth without making a decision.

This is, of course, compacted by many additional factors, such as an increased travel frequency, an overwhelming number of distractions (this included), and an overall "summer apathy" that tends to overwhelm at this time of the year. As I do see a separation between the academic year and the summer, I'm more inclined to "take the night off" because of the fact that I couldn't during the year. Makes it a lot harder to make progress on many fronts, even the simplest area of reading papers and planning experiments.

At this point, I'm not entirely sure what to do. I'll be introducing some additional stresses into my life (specifically, we are taking care of my parents' dog for a while starting next week), which may have the intended effect of making me a little more efficient with time-management and sleep (we'll see) so we can take care of the guy. I'm also hoping that I can make a better effort at not goofing around online, but I'm not sure if that will happen.

Especially because I need to figure out why those reactions are not showing up by mass spec, when there is clearly something there in a high mass.

Sorry for complaining, but I need to vent somehow, and I'm thinking they'd frown upon me smashing glassware. Maybe I'll go for a run for the 37th day in a row. That should help. :-)

5 Years and Counting...

2011-06-24T10:35:00.000-05:00

Rethinking Things

2011-06-22T09:31:00.001-05:00

A recent post over on my favorite science blog, Science-Based Medicine, has gotten me to thinking about my position on a certain area of medicine - health as it relates to exercise and nutrition. I complain sometimes about folks who seem to have no care about their health, whether that be via unwillingness to exercise (it's so easy) or eat healthy or take medications, etc.

The post in question is a response to a response, responding to an email about a previous post discussing the effects of nutrition on human health. There are those who believe that we have control over whether we have disease, and that there are "magic bullet" methods for curing and preventing disease, such as diet and exercise. The response to the previous post is taken down point by point, mostly identifying the errors in logic by the commenter as they relate to his knowledge of the information being discussed. Fine, it's probably a good thing to point out that this guy's arguments, no matter how logical he may make them, don't make sense because they aren't supported by factual evidence.

The thing the got me was the argument that nutrition and exercise are not the be-all, end-all cure for disease, which I agree with. What I have been coming to realize is that my views on the importance of exercise and nutrition, however logical they may be, are starting to get extreme. I've been making it a point, for whatever reason, of being hyper aware of the health problems of others. In other words, I've been spending a lot of time judging others lately for being unhealthy, eating poorly, not exercising, etc. And I'm beginning (and continuing) to regret that. No matter how easy I think it is, it's not that easy to get yourself into an exercise program and make the time for exercise and better nutrition if it's not something that's a priority.

My points: 1) Are exercise and better nutrition the cure to all disease? Of course not. 2) Are exercise and nutrition helpful in producing a better quality of life? Of course they are. 3) While I think all folks should be able to take control of their health and find the time to exercise, it can be a difficult thing to start and commit to, so I'm going to lay off judging others for not doing it.

I am, however, going to encourage others to partake in a healthier lifestyle. You will have no idea how good it feels until you try it, and there are a lot of people just like you who have made the transition and are happier and more well-off for doing it!

Running Streak

2011-06-16T13:58:00.000-05:00

If you at all pay attention to any of the stuff over on the side bar, you'll see that I have a little widget for dailymile, an online training log. Every once in a while, you will see an update where I write down how far I ran, how long it took, and how I felt about it. It's a neat tool and a good substitute for a written log, which I have had at home the last few years.

Also you can occasionally get some good feedback from others about training questions, techniques, gear, etc.

Anyway, if you've been watching it you may notice a tag that I've been adding to my posts: #Runstreak (I put in the hash because it's also posting to Twitter). Another runner on Twitter and dailymile, aptly titled The Beer Runner, made a request recently on those social media outlets: start a running streak. He's currently on a streak where he runs every day and tries a different beer every day, and I think he just passed 250 days in a row. The challenge was to start something and maintain it, with the incentive that if at least 30 people ran 5 days in a row, he'd do a beer mile (still waiting for that to happen...).

That was almost(?) a month ago. After having gone through my shin splints and the requisite therapy and rest associated with that, I decided to take on the challenge and do at least one short run per day. I'm currently 24 days into the streak, with no signs of slowing down. Despite often having to make time for the run, I've managed to find a time, even going so far as to running in the middle of the night to find a Walmart before they stopped selling beer at 1:00 am (true story). While my shin feels sore sometimes, it's actually doing pretty well, and I'm feeling confident that continued short runs can help me better control (and lose) weight and have a good aerobic base for any training I decide to do later in the year.

Having started and continued to do this, I got to thinking about how the streak is analogous to other areas of my life. Making the commitment to run every day should transfer to my commitment to my research, reading papers, learning new techniques, etc. If I have the wherewithal to put forth that effort on a daily basis, shouldn't I be able to do that with everything else?

The answer, of course, is that it's still kind of difficult.

Running has become such an integral part of my existence that I can't imagine going without it. Research doesn't fall into that category, but I feel like it's getting there. Perhaps making myself a good example of being consistent and working hard in one part of my life will translate me into getting inspired in other areas. Sometimes I get super excited about research, and other times I get extremely frustrated... a more consistent approach to research may be better!

Hopefully my running streak will translate into better research!

Barefoot Running is Good For You. Or It Isn't.

2011-06-08T15:06:00.000-05:00

I've been reading a lot of good stuff lately from a variety of sources on the continuing debate about both running in barefoot or minimalist shoes, as well as whether or not changes in running form can have beneficial effects and reduce injuries. Articles in Runner's World and blog posts such as those written over on Runblogger (probably the most complete takedown of comments against barefoot running I've read) have continued fueling the debate on this series of issues, resulting in a fairly straightforward divide between those for and those against examining form and what kind of footwear we should be wearing. Reading a recent article (and accompanying comments) on the NY Times blog solidified the arguments of the different camps for me.

Those who are for barefoot running make an argument that is something along the lines of this:
1) Humans evolved to run, but not to run in shoes
2) I made change x (x = switched to minimalist/barefoot running, changed to forefoot strike) and had effect y (y = reduced injury, increased joy in running, etc.)

While those who are against barefoot running often make arguments that contain these points:
1) Humans may have evolved to run, but not to run on hard surfaces like concrete
1a) Evolving humans also had problem x (x = died at the age of 40 or younger, etc... which, by the way, is pretty much completely irrelevant... people still die young now)
2) If barefoot running is so good why aren't we all doing it already
3) I tried to switch to barefoot/minimalist running and I hurt myself, either temporarily (discomfort) or extensively (muscle tears)

The basic gist of the argument is that true believers are completely and 100% behind the cause, while skeptics of this trend are quick to point out possible flaws and rationalize reasons not to make a change (be it running surfaces, lack of necessary time/effort to make changes, the argument that changes in form can be made in traditional shoes, etc.).

*Before I go on, don't get me wrong here - I'm perfectly happy with everyone who is a runner. And who is not a runner. And everyone in between. In the rest of the post, what I'm frustrated with is the arguments made and the unwillingness to let go of certain beliefs that are not allowing people to see potential benefits of change. Just FYI.*

There are several things about this debate that I find particularly interesting, especially with regard to those who are in the camp of "this is a fad so we should just ignore it".
- Those who present the points of the argument from both sides but are not believers in it are very quick to point out that "this is not for everyone" and "you should exercise extreme caution" and "you probably won't need to make a change". They bias their presentation of the evidence (highly anecdotal but containing an increasing amount of rigorous scientific investigation) by putting in an asterisk at the end. I really think it's something to present the evidence, but then almost immediate rescind on the evidence by saying you probably shouldn't try it. It's a similar thing to the shoes - these shoes are interesting and may be useful tools, but you probably shouldn't use them. (It's been a common theme in Runner's World as this debate has gone on... perhaps they're appealing to the masses?).
- In a similar vein to the debate on vaccines (linking to Science-Based Medicine here if you are interested in reading about it), there's a small sub-population people who demand evidence that form and running shoes matter, but when they are presented with evidence (see the Runblogger post for direct citation and addressing of this issue) they aren't willing to accept it. Based on the literature I'm willing to accept that a) shoes with big heels promote heel striking, b) physiologically speaking it makes more sense to land on the forefoot where it is more likely to absorb impact, and c) landing on the forefoot produces a smaller amount of impact force. Some people seem unwilling to even accept that.
- On the other hand, those who are at least accepting of the evidence are quick to point out that making changes will not produce immediate results. In this fast-paced, quick reward, instant society that we live in, there's an expectation of instant rewards upon implementation of changes. If barefoot or forefoot running styles lead to injury free running, all I've got to do is lose the shoes and I'm set, right? No one on the side of the barefoot or minimalist running agrees with that (that I've seen, anyway), and all of the anecdotal evidence seems to favor taking time and putting forward a big effort in order to reap the rewards. If you look at the comments of the NY Times article, nearly everyone who has a barefoot story talks about the slow build-up that was necessary to be successful, a fact to which no one on the other side of the fence seems to acknowledge. Once again, if the evidence doesn't support my viewpoint, it must be wrong.

In considering the pros and cons of changing gait and form and possibly running shoes, I've thought about what it would mean to make those changes. First of all, there's never going to be an "ideal time" to think about and implement changes, so those arguing that they don't have time to do it are inherently wrong (and I am among the folks in this camp - I actually made the argument earlier last year that I didn't have time to someone, who argued back that it's a worthwhile venture). Second of all, any changes being made are going to take time and concentration to achieve. One would think that being runners would inherently bias all of us towards this side of the argument based solely on the fact that we're the ones most likely to stick with it and achieve our goals, but a surprising number of folks seem unwilling to work at it for lack of immediate benefits. How can a marathon runner not being willing to put in some work? Maybe they should have been grad students too... that would certainly show what it's like to have to work a long time toward a goal... :-/

In the end, my takeaway from this whole process is that, while it's not been scientifically proven without a shadow of a doubt that barefoot running or forefoot striking is better (and when, in the history of the universe, has anything been proven in such a way by anyone??), there is compelling evidence, both anecdotal and scientific (again, see Runblogger for citations) that running more without shoes and with less of a heel strike can be beneficial for both performance and injury prevention. Physiologically speaking, we are designed to be runners, and - no matter what you argue about our society today - it's possible for everyone to do it at some level. Making a switch in form or running style requires a handful of things - time, patience, dedication, and an understanding that you are not downloading a video on internet, you are training, and training doesn't produce instant rewards. Like anything good in life, you need to spend time working toward the goal rather than expecting to be instantly rewarded.

Finally, if you are interested in making changes, do it scientifically and spend time critically thinking about why and how you are achieving the goal. Are you trying to avoid injury or trying to get faster? Do you have a plan? Can you log your runs - how you felt, how long you went, what worked, what didn't? Having a plan and making observations along the way is key to being successful. I myself wouldn't just go setting up experiments willy-nilly unless I had a goal in mind, and I need to record my observations to know what works and what doesn't so I can be more successful in future experiments. In the same way, noting how changes feel and what effects they're having is important in ensuring success in changing running style.

So, stop making excuses, review the evidence, conduct some experiments, and be patient. You never know what good may come of it until you try!

Familiar Story

2011-06-03T15:39:00.000-05:00

Well, I just want to make it official:

I'm taking a summer vacation from the blog.

As there are a lot of things for me to worry about in the next few months - not the least of which being the push toward getting results for finishing - it's probably better that I don't try to think too much about writing. There may be the occasional post about my running, but I don't have any real desire to force myself to come up with things to talk about. Lots of lab work to do that I just need to do and not really think about.

I'm also turning off my social media for the summer (or trying to, anyway), so aside from updating my workouts on Dailymile I don't anticipate a lot of other activity.

Hope you enjoy your summer!

(I thought this was a "summery" picture!)

Injury Update

2011-05-29T20:28:00.000-05:00

Today I have a quick running post for you, so if you're looking for science unfortunately I don't have any today, although I do have the library's copy of the Handbook of HPLC (2nd edition) sitting nearby, so I may have something to say about that later.

Nope, today I want to talk about my shin splints. I have been working through this particular injury for the better part of the last few months (since about March, by my estimates) and have learned a handful of things along the way. At this point, the long and the short of it is that they are still there and I am still slowly trying to keep running a part of my schedule, along with a number of activities.

On Monday of this last week I went off to the doctor to get a second opinion on my self-diagnosed injury. Although I was pretty sure about what I have, I had been having an increased level of pain leading up to the visit, so I wanted to make sure that I wasn't dealing with a stress fracture. After having discussed the progression of the injury, as well as having several examinations (including, interestingly enough, having a tuning fork placed on different parts of the bone to see if there was any specific pain), he agreed with my assessment that it fit very well with shin splints. No X-ray, but probably none needed. I got a referral to Sportwell, the campus athletic trainers, and have plans to see them shortly.

Now, all of that being said, I have been running. Every day since last Monday. There are several reasons for this, which I will discuss below. In essence, having gotten the confirmation from the doc that it wasn't a stress fracture, I decide that I was ready to start running again. Here are the reasons why:

1) New shoes. One of the reasons that my shins started to hurt was that I went from worn out shoes to a new pair - the increase in the amount of cushioning beneath the shoes seemed to cause the problem. Since I was interested in switching from road running to trail running, I wanted to get a pair of trail shoes. In particular, the pair I decided on was one highly recommended by Runblogger, the New Balance MT101's.

These shoes, unlike my previous pair, are more minimalist and built to help change your running style to a midfoot strike. I'm not exactly sure how my normal gait works, but I was interested to see what would happen.

2) Compression socks. As I mentioned, I bought a pair of compression socks and have been wearing them on longer runs and, whether psychological or physiological, they seem to be working. My legs feel better, and my shin doesn't start to feel sore until later.

3) Terrain. As I've mentioned, I've been running on the grass and trails much more than I would previously. The only time I did run on the track (not even on the road) it started to hurt. Running on more forgiving surfaces seems to help.

4) Cross training. One of the ways I've tried to maintain my fitness was to incorporate a lot of cross training into the mix. Splitting my time between cycling and running has been helpful for me to spend less time on the road (less pounding) while still getting the 45 minutes to 1 hour of activity I need to be functional. I was doing more elliptical training before, but I have a feeling that this contributed to my increase in pain (my leg was getting sore after doing a week with a lot of elliptical work). I've also been doing rowing machine, push-ups, sit-ups, weights, and so forth. Just trying to keep myself active so, when I feel comfortable again, I can ramp of the mileage and still feel food in a cardiovascular way.

So, at this point, I'm actually feeling pretty positive. I've been making sure to stretch, ice, and cross train to make sure that I don't put a lot of stress on my leg. I am hoping that in the next few weeks I can continue to work hard and rehab, so that I will be ready to do a longer race later in the summer and in the fall. I'm not entirely sure what I will do about running a marathon or something like that on the road, but I'm kind of excited about doing something on the trails. Hopefully, I will return to full strength soon!

In Case You Were Wondering...

2011-05-25T08:34:00.000-05:00

Working on everything... busy time... etc. Talk to you soon!

FINALLY...

2011-05-18T20:45:00.000-05:00

... it's summer! Well, it's summer in that my class has ended (passed with flying colors, thank you very much), summer classes have begun, the gym is only open from 11 am - 2 pm (as opposed to being completely closed last summer), and I have made it my goal to make a list of goals to accomplish by the end of summer. Yes, it is a time of great promise and a lot of work needed to be completed! I am excited and somewhat frightened at the same time, because I have a lot to get done before finishing graduate school, but the finish line is coming into view. As I said before, time to push!

That being said, and in the interest of giving a sort of summary before we start moving forward, here are this week's randoms, finishing up with a proposed direction for the blog (not that anyone minds, but I do happen to get enough attention to warrant letting you know "what's up" on occasion).

- As I mentioned, my Immunology class ended today with a final, which I passed with fair ease, considering the lack of attention I have paid to it over the past month or so. To be fair, we haven't had a lecture in nearly a month, and given my propensity to do other things instead of worrying about the class made it a little harder to keep everything straight. That being said, I still think I did pretty well! This now puts me in the position of being about 1/8 completed with medical school (I've finished up about half of the M1 classes, with another half to go). For the time-being, though, I will be focusing primarily on research and will leave classes aside. After I'm finished with the PhD, I will have an "abbreviated" year where I finish the rest of the M1 classes before moving on. I've already devised a system in which I will attend and study for the classes I've already taken (helping to study for boards, etc.) but I won't have to take the exams! Should be fun, whenever that is...

- My research continues to push forward... I'm not really privileged to divulge details, but in essence I'm working through synthesizing and testing derivatives of my conjugate molecules (the design of which is "essentially" here... I say essentially because this figure isn't completely up-to-date, but you get the idea). My hope is to get through a bunch of them this summer and have the relevant data to publish somewhere! I'm also thinking that I will help out a fellow lab mate on the synthesis of a few of her molecules, which should provide some additional opportunity to put some research out there.

- Running is... well, it's not happening. The shin has gotten progressively worse, and I'm still not entirely sure if it isn't actually a stress fracture. I've spent the last few days not running, instead doing biking and elliptical work, in addition to core work, push-ups, and so forth. I still have to goal of getting my weight down this year, and - as I'm not running - I need to focus especially on other activities and developing better eating habits. I need a lot of work on the second part... perhaps I need to take a page out of Suzi Storm's book...

- That being said about the running, I've found that wearing compression socks (I've been using Vitalsox) does seem to have a benefit on my shin... I'm thinking about wearing them under my jeans during the day just to see how I feel during the course of the day. I have also been thinking a lot about shoes, and about how the shin pain started when I started wearing my current pair of shoes, and have been exploring trying a different pair of shoes. I've done a handful of runs in the Vibram Five Fingers on the grass, and thinking that maybe a minimal shoe is better, I ordered a pair of New Balance MT101's (highly recommended on Runblogger and other places... cheap too!). I am hopeful that something good will come from wearing them and running mostly on the trails!

- Hey, it's American Craft Beer Week. If you have the opportunity, and like drinking beer, try out some craft breweries and stay away from those cheap beers. There is a lot of stuff out there!

Well, that's where I am. As far as the blog is concerned, I've got a few ideas, but I think I'm going to go back to a format of focusing on research techniques and topics that I come across as I get my research back on the foreground. I'm really interested in the medical topics I've been studying, so perhaps an occasional foray into medical topics would also be useful. I think I'm going to relegate running and athletic-related posts (aside from those with a scientific bent) to the weekends. Overall, I think it'll be a good opportunity to continue practice with my writing, as well as increasing my capacity to read, understand, and summarize scientific literature.

In the meantime, I'm going to take a break and read a book for a while.

How a Weekly Meeting Should Go

2011-05-16T12:07:00.000-05:00

Me: Well, I was trying out this enzyme, and the reaction worked alright... gel purified, the products were a little diluted... but then I tried this enzyme and got much better results.

Boss: Good.

Me: ... and then I tried it with transcription, and you can see that these products are much better than the previous ones.

Boss: Good. Are you going to order more of the enzyme?

Me: Well, they actually have free samples in the store room, so I'm going to grab a few more while they still have them, so we should be good for a while. If I need more, I can get more.

Boss: Good.

Me: As far as synthesis goes, all of the reactions are working. I've synthesized and conjugated a few products, and I'm going to start testing them soon.

Boss: Good.

Me: ... and... that's it! Just gotta keep going.

Boss: Good!

(not an exact transcript, but pretty close... aside from an exam this week I'm hitting cruising speed and just going for it! More interesting things after the exam is over...)

Everything I Needed to Know I Learned from...

2011-05-12T09:22:00.000-05:00

... not class, that's for sure.

As classes and finals end this week (and for medical school, next week) I've been taking the time to reflect on the last 5(!) years of my graduate education, thinking especially about how much of our learning comes not in the classroom, but through real experience with setting up reactions, analyzing data, and presenting that data to others.

For someone who was very much a "pre-med" student as an undergrad, who focused an awful lot of time on classroom efforts in order to get the best grades possible, entering grad school ended up being quite a shock to my system. I remember coming in thinking about how much I could focus on the only 3(!) classes in the fall, thinking about what research group to join, and trying to adjust to my new location and place here at the U of I.

What I discovered very early on, however, is how much the classes are looked down upon as unnecessary by the faculty, who often have better things to do (i.e. you should be working in the lab) or are so discombobulated that they can't actually teach you anything (i.e. woefully unprepared to teach graduate level courses) or are so focused on the class that they nitpick and prevent you from doing well. Unlike my previous experience in the classroom, the goal didn't seem to be teaching you any sort of skill, nor to make sure that you understand the theory, but rather to give you enough of a basic framework that you can go off and figure out the rest yourself. A good plan for someone who hasn't relied on the classroom for learning, but not for someone who has focused all of his time on getting the most out of the classroom experience.

In the spring of my first year, we were given the opportunity to choose our own classes, as well as to take what is commonly called "doughnut class", as it takes place early on Saturday mornings and, often, also has doughnuts. The doughnut class was supposed to give us a greater exposure to the different facilities and techniques that we could take advantage of in our department, a sort of "practical learning" class that should have been most helpful to those of us who were used to getting some useful info from the classroom. Again, however, those who were in charge had no interest in helping, and a number of opportunities were essentially wasted (although we did get some good info on how to research in the library, among other things...). I'm not exactly sure what could have been done differently, but I would think that a number of relatively basic things could have been covered in a practical setting, i.e. that we actually get to try doing these things instead of just hearing about them. Training on the mass spectrometers or NMR machines, for example, may have been a good use of time. Perhaps that would have helped? My thoughts on the subject have dimmed somewhat, as it has now been 4 years since I took the class, but even so I have the feeling that we could have gotten more out of it.

So, the onus of learning was almost entirely on us to accomplish, through the help of our peers, professors, and the resources that had been made available. While I can understand the idea of "learning from someone else", the catch with that concept is the fact that someone else has to know what you need to do in order to teach it to you. The amount of information you have available is essentially left up to whether or not someone in the lab has previously done the technique you need to do and is willing to teach you that technique.

For example, I have recently had a number of situations in which a senior member of the lab (and one of the few who has been here longer than me) has pointed out little pieces of wisdom that I have never heard before. Now, this is not because she withheld that information, but rather because we have been working on completely different projects in different areas of the lab, with little chance for our projects to overlap. In fact, there have even been chemicals that she has had available for quite a long time that I simply didn't know about. Blame it on what you will (mostly me, it seems), but these little chunks of wisdom would have been more helpful much earlier than now, and some could possibly have been presented earlier than this in a formal setting. There's enough "common wisdom" that it could definitely be put together in a 20 minute Power Point presentation, I would think.

I'm somewhat torn as to whether or not this style of learning is useful. On the one hand, the system of "trial by fire" learning certainly does produce the results that are needed to complete thesis research and continue on to a research career, but at the same time I feel as though you are limited by your own ability to seek out the people who can help you and are at a disadvantage if they are not immediately nearby. There have certainly been opportunities in the classroom to impart this type of advice, but clearly the onus is on the student to seek out that advice rather than being given it.

In the end, it has become clear to me in my years as a researcher that this system, while occasionally problematic, is essentially the way it's "going to be" for the foreseeable future. Despite the importance of learning in the classroom, the faculty will continue to turn their focus away from it in favor of getting students in the lab to produce results and learn through trial and error. It's on the student to seek out the knowledge necessary to complete tasks and present at meetings, hopefully from other students in the lab but (if not that) also from those in other labs. That being said, I should hope that some additional effort be made to increase the effectiveness of those classes we do have to take, to ensure that we get something out of them.

Med school, though... they teach you everything in the classroom. And expect you to memorize it.

Just as a follow-up, I'm curious - to those of you who have been through or are currently going through graduate programs of your own, how important was the classroom learning? Did you find that you got anything special out of it, or did you just see it as a hurdle from getting into the lab? Importantly for those who ended up being faculty members - did you find yourself having to re-learn things from your initial classroom years in order to be able to teach them, or did those pieces of knowledge stay with you through your lab work? Just curious...

10,000 Page Views

2011-05-09T09:49:00.000-05:00

Holy cow, the blog has been looked at over 10,000 times!

I'm gonna celebrate by cleaning my vacuum line and setting up some peptide couplings!

Yay!...?

Time to Push!

2011-05-04T09:35:00.000-05:00

The semester is nearly over, and following my Immunology final I will be solely, 100% focused on getting data and getting my research project completed.

As the onus is on me to get it done, it'll take a lot of self motivation.

So, that is the goal. To push and push hard. To do work. To get results. To get something useful out of it so I can give it to some publisher and say "there it is! Show it to everyone else!".

It's gonna be a tough, but exciting time, and something that I should have done a long time ago.

Ah well. Can't change the past. All I can do is take the "experiences" (i.e. failures) I've had in the past, gather together the lessons I've learned, and say "I know exactly what I need to do and how to do it, so let's do this."

Keep an eye out - good things are coming!

Is Racing Too Expensive?

2011-05-01T20:01:00.000-05:00

This is a post about money. I've been inspired to think about such things by other grad students such as the Insomniac Lab Rat, who is working on paying off school loans and trying to be as frugal as possible while making her way through grad school (although I did see a post about getting a puppy recently... hmm...). Although this is framed in terms of the running (since it's on my mind after this weekend's Illinois Marathon races) it could equally apply to a number of different things - taking vacations, buying technologies like computers, smart phones, etc. - that I have to think about from a financial perspective.

As you may know, graduate students aren't paid incredibly well. We do get a very reasonable living wage (especially for Ur-Paign... bringing it back...) that is able to cover the basic living expenses - rent, food, transportation, University fees, etc. I have many friends who are also able to purchase luxury items for themselves - smart phones, MP3 players, even make monthly car payments - without having to dip too far into savings accounts for payment. Although there are the occasional gripes about having to "live paycheck to paycheck", for the most part it's fine. One important aspect to this is the idea of sacrificing some thing to purchase another. Many of my friends who have these luxury items don't have or do other things - maybe they don't have television (hey, everything's on internet anyway), they shop frugally for groceries, they don't go out all the time, etc. It's about trading off what you don't need for something that you would really like.

My status differs some in that my wife is not a grad student, but rather a registered nurse. Because of this, we (overall) have much more money to play around with. Early on, this was a boon for us, because we really hadn't been in that position before and, therefore, felt it perfect reasonable to continue adding different things to our home without fear of living outside of our means. As we've gone through this process, we've established a certain standard that requires a lot of bills - mortgage, car payment, internet and cable TV, etc. - and those bills need to be paid with the same amount of money that we started with.

When you've gotten to the point that you can pay the bills but not have a lot of extra spending cash, it starts to become a balancing act between haves and have-nots. In the last few years I've have to rethink a number of "essentials" in order to determine what we can and cannot have. Without sacrificing the big things, there are only a small number of luxuries that we can live without. I decided to sell my Blackberry a few years ago, for example, because I didn't feel I could justify paying the extra $30 a month on a data package. While it may have made more sense to get rid of something bigger (i.e. try to live without cable TV for a while), this was one small sacrifice that we could make that would give us a small (if not substantial) piece of the pie back.

What this builds to is that list of essentials and things we can sacrifice. As I've said, cable and internet is probably not something we'll get rid of too quickly, nor is the car or the house. Those things have expenses tied to them that we can't really afford to not pay (i.e. I like having hot water and electricity... not giving those up any time soon... :-] ), which then leaves that short list. New clothes, camping gear, new electronics, and so forth. For example, my computer is almost 3 years old and Windows Vista wasn't really behaving... but instead of trying to buy a new computer, I got a grad student copy of Windows 7 for $5. We're keeping the TV my family bought in the mid 90's (it still works!). I'm wearing a jacket I've had since high school, and probably fixing the zipper on my favorite jacket instead of getting a new one.

The biggest activity that I've had to think about sacrificing is running. Now, I don't anticipate quitting running anytime soon (injuries aside), but there are expenses associated with running that I have to think about avoiding in order to maintain what financial resources I have. I've been hesitant to even consider doing races because of expenses - even the local 5K can get upwards of $25-$30, depending on how early you register. Running marathons, especially the big city races, has become more prohibitively expensive, with races such as Chicago and New York getting into the hundreds of dollars and even smaller races like the Illinois Marathon getting nearer to the $100 mark every year. I've been fortunate to find a handful of races that are closer to $50, but I have a feeling as time goes on those races will continue to become more expensive.

Costs of running shoes and gear aside, I'm finding it more difficult to justify paying the additional money just to do what I would do normally. As I don't have marathoning (or beyond) as a "bucket list", once-in-a-lifetime opportunity anymore (it's more of an activity I enjoy now), I don't really want to spend the extra money associated with running a race. It's really unfortunate, because I really do like the race atmosphere, but hey - I need that money to pay the bills!

So, getting to the point - is racing too expensive? In some ways, it is - the costs associated with getting into the race, getting yourself to the race, and putting in all of the time and money towards training, makes it a very expensive venture. Until I can reconfigure my finances in such a way that makes it more feasible, I don't anticipate doing any additional races anytime soon, which stinks.

I put it to you, readers - what kinds of things have you done to save money as a runner? Finding races that are cheaper? Doing the "Fat Ass" races that don't require fees? Purchasing clothes, gear, food, etc. online?

Think about it.

Illinois 5K Race Report

2011-04-30T11:33:00.002-05:00

Just a quick and dirty race report from my 5K last night.

As mentioned on numerous occasions, I have been dealing with a bit of injury as of late, so I only felt comfortable running a short race (although I could have probably done the 10K...). So, signed up for the 5K. Before the race I shuffled over to the race start for the race, about a mile or so away (the Google maps says it's 1.5, but there was no "as the crow flies" route so it was probably shorter than that). It was a nice warm-up and got me there in plenty of time before the race.

Before the run I ran into a few people I know - one of my church friends, who would be running the 5K and the Half, as well as a gentleman who I met via Dailymile who is a professor here in town who was running the half and the 5K. We chatted a little bit about the race and how small of a world it was, and then hopped into the starting line for the start of the race.

We were off! The first portion of the race had a slight uphill, followed by a 1/2 mile long downhill. It got us moving quickly! I chatted with my friend about the race and the next day's half marathon, random plans for our church group, and so forth. The crowds were large and boisterous, with many college students drinking beers on the side of the road and cheering for friends and random people in the race. We passed the first mile mark in 7:45, about as fast a mile as I've run in a while!

On the second mile, my friend was slowing a little, and for the short term I stayed with him, but was feeling good. We went through Campustown, passing more college students and supporters. We got to the second mile on an uphill at around 8:11, a bit slower than the previous mile, but still quite comfortable. I told my friend that I was going to blow up and go for it, and took off for a fast final mile!

I started passing people at a fast clip, still enjoying the race and cheering on those who I was passing. The crowds cheered us on as we made our way toward the stadium, turning into the entrance ramp at the end of the field. With the crowds cheering us on, we ran 100 yards down the field and then turned back to finish at the 50 yard line at a full sprint! I ran the last 1.1 miles in around 8:00 min, finishing in 24:02! It was a great run and about as fast as I've run a 5K in a while!

This morning I volunteered on the race course, at the 5.5 mile point (right by my neighborhood). The race conditions were pretty decent, although it was pretty windy! We had to redirect a lot of (relatively) angry folks who apparently had no idea that there was a race going on. The runners looked great, and I snapped a number of photos of all of the big groups running by. There were a few characters, including an Illini Darth Vader, Superman, a Purple Man, and Abe Lincoln (who ran last year as well). No Illinois Marathon bee, though... I hope everyone finished up their races well!

One final note - for the race I wore my compression socks, and they were very helpful! My shin felt pretty good for the race, and today I'm having a relatively minimal amount of pain. I did ice it last night, so that still helped. Also, because I ran so hard yesterday and had to stand for a few hours this morning, my quads seized up! I think it was sympathetic paid for all of the racers!

Marathon Weekend!

2011-04-29T13:07:00.002-05:00

Good luck to everyone running the Illinois Marathon here in town, or anywhere else this weekend!

Steven Novella on Dr. Oz

2011-04-27T10:38:00.000-05:00

I've become a regular reader of the Science-Based Medicine blog, and was interested to hear that one of its contributors, Dr. Steven Novella, would be going on the Dr. Oz show to talk about alternative medicine. I listen regularly to the SGU and, knowing enough to know that Dr. Novella is pretty straightforward and no-nonsense when it comes to science and medicine, I was interested to hear how it would go down.

Watching the video (see the links on Science-Based Medicine to get to it), it was peculiar to see the differences between the two (in fact, there were several more than Drs. Novella and Oz) in how they handled both the arguments being put forth by the other and how they presented their opinions. Despite both being trained physicians, each took a different tact when dealing with the arguments of the other - Dr. Novella was straightforward and clear that, in his review of the literature for particular techniques, they did not seem to be effective as prescribed; Dr. Oz, claiming often that Dr. Novella was "dismissive", was dismissive in his own right and claimed that our scientific analysis of certain "Eastern" techniques was not an effective means of determining their efficacy. I may be a little biased (I do like both the SGU and Science-Based Medicine), but the thought that kept going through my head was this:

Wasn't Dr. Oz trained as a doctor? Wasn't he taught science and the scientific method?

As someone who's been in training as both a scientist and a physician, I think I have a slightly different perspective, appreciating science and scientific analysis more than some, but come on now. I'm fairly certain that all physicians have at least some training in scientific principles, and have enough logic and critical thinking skills to distinguish between correct and incorrect conclusions.

I also found it interesting that, when going to "here's what your doctor thinks" about different alternative medicine methods, the experts that he referred to often were critical of the techniques! If he was trying to prove the point that those methods were safe and effective, why show a clip of a doctor saying that it is not safe and effective (or, instead, why it is unproven)? Kind of weird.

I can only hope that, when put into that position in the future, I can be in the role of critical thinker, and not in the role of true believer unwilling to listen to any other evidence.

Running Update - ::: Le sigh :::

2011-04-26T09:11:00.000-05:00

As you can tell by the title, I'm in a bit of a funk with my training.

Well, funk may not be the best word. Let me elaborate.

As I mentioned a few weeks ago, I have been trying to nurse a shin injury (self diagnosed as shin splints) by icing, stretching, and doing a combination of other activities including biking, elliptical, and stair stepping. I had been gradually putting running back into my routine, with occasional runs on the roads but primarily getting on the grass and in the U of I arboretum. I bought I pair of compression socks, and they seemed to be helping me out to run longer with less pain. I was feeling pretty good and confident and started looking into trail races over the summer and fall, with possibly a fall marathon in my future...

After this weekend, however, I'm less certain. I decided to try a few miles on the grass in the Vibram Five Fingers, and while I felt alright on the run the last two days have been fairly sore and painful. Nothing drastic - I can still walk just fine - but significantly worse than before this weekend. I am guessing the combination of several runs on the concrete where I should have been on the trails, combined with the run in the VFF's, are causing this most recent pain, and I honestly can't tell if it's the same problem or a new one. The pain has tended to shift all around my shin, never localized to one spot, so I'm not sure if it's just a similar version of the previous problem or something different.

I have a 5K coming up on Friday night, which should go well (my fitness overall is still good, and I should be able to go 3 miles with my compression socks... I may look like a dork but what do I care?), and then it will be time to re-evaluate my future plans.

Here's what I'm thinking - it's time to focus on weight loss rather than racing. Taking a few weeks/months off from running specifically could actually have some benefit, in that it would help me to focus on strengthening other muscle groups and to probably prevent the overuse injuries that I appear to be fighting with. So, here's the 4-pronged strategy:

1) Upper body strength - use weights, push-ups, and the like to get my arms, shoulders, and chest a little stronger. I have been doing push-ups pretty consistently, but I could do better. Perhaps the 100 push-ups program could be a good thing to follow again.
2) Core strength - start doing crunches again, as well as finding some good core exercises through Runners World or something equivalent to get my core more stable and take some of the "fluff" off of my midsection.
3) Lower body strength - some weights, but mostly focusing on cardiovascular activity like biking, hiking, elliptical, and stair workouts. I am going to use this to keep my fitness up.
4) Better diet. The food I eat is generally alright (given my history with acid reflux, I try to err on the side of caution) but I could do better, particularly when it comes to excessive snacking. Cutting out some of my mid-day and late night snacking, trading off some of my beverages for water, and doing a better job of getting in a variety of food items (more fruits and veggies, etc.) will be significant in helping with weight loss. Just ask my brother.

So, that's the strategy. I'm compiling different core stability and overall strengthening exercises to develop a program that takes 30-40 minutes which I can do a few times a week, hopefully to begin by next Monday.

If you have comments or suggestions, please leave them in yonder comment box so that we all may benefit. I hope to get into good shape and be down to my "ideal weight" for my height (184 lbs for a 6'1" dude) by September 1st. Earlier would be good too!

Random Picture Saturday

2011-04-23T12:14:00.000-05:00

Me, back in 2004(!) working in the summer lab of Dr. Scott Bur at Gustavus. Aside from the hair and the terrible beard, the look is about the same today, 7 years later.

Enjoy!

Living It Up

2011-04-21T19:02:00.000-05:00

This afternoon I went to the U of I College of Medicine Research Symposium to present a poster (which, interestingly enough... got crushed somewhere on the way from the MSP office to the symposium and, thus, looked like garbage. Oh well.) and listen to a handful of talks in between lab work and more lab work. The poster presentation went alright (I doubt I won anything... in fact, the best comment I got was the fact that one of the judges - not a scientist - actually understood what I said, which was nice to hear), but the highlight of the portion I was there was the presentation by Dr. Scott Irwin, MD, PhD, an alum of the my program and currently the director of the psychiatry program at the Institute for Palliative Medicine at San Diego Hospice in California. He spent a good time discussion about palliative care, an area of medicine that is only (relatively) recently being recognized as an important part of medicine.

In short, palliative care is a term referring to treating the pain and suffering of patients at all levels of disease, from initial diagnosis to treatment to cure or possibly death. It seems like something rather obvious - why wouldn't you want to decrease suffering? - but is becoming more prevalent as we as medical professionals pay less attention to the disease and more to the patient. I should note here that a lot of "alternative medicine" folks would say that they are the ones who focus on holistic medicine, while traditional doctors do not, and I am going to say here and now that we should all work towards treating the "whole patient" as opposed to just the disease. For the most part, physicians do, but we all should strive for that no matter what our profession.

Anyway, the point that I'm getting to is something that Dr. Irwin was polling the audience about - what kind of things enrich your life and make it worth living, and how would those priorities change if you were faced with an end of life situation? A lot of folks threw out both the practical - financial stability, being surrounded by family, etc. - and the more conceptual - to be respected, loved, cared for, etc. In essence, we all hope to be respected and loved in our life, and hope to have the same kind of support when we come to the end of our life. It was an interesting discussion, not only because it caused everyone to think specifically about what kind of life the want to live, but because it presented a larger context for us to live in.

What kind of life do we want to have?

I don't mean to be somber about this - quite the opposite, actually. My wife and I have recently been discussing the idea of "living" versus "ticking off the days" - in other words, are we simply watching the days drop off the calender, moving through our day-to-day activities without much thought... or we getting out there and getting involved, meeting new people, doing new things, "living it up" as my old friend Egon used to say? In our analysis of the situation, it was clear - we need to start living!

So, the new life philosophy we have, reinforced by the talk I heard today, is to start living, moving outside the comfort zone and doing things that I would otherwise not have done. Going to the conferences last week and this week to give posters is a part of my new "living" philosophy. Working hard in the lab, producing results, and not being content with just trying is part of my new "living" philosophy. Even getting out and talking to people in the med school and other grad students counts. It's clear that we've been content with our lot in life, and I'm pretty happy with the fact that we're gonna get out there and be active again.

It's time to LIVE IT UP!

APSA Annual Meeting Report. (for the parts that I was there)

2011-04-18T10:07:00.000-05:00

It was quite a meeting... I'm assuming.

Well, no, that's not true - it was a very interesting meeting for the parts that I was there.

Let me back up - this weekend (as I've mentioned numerous times in the last few weeks) was the 7th annual American Physician Scientists Association Annual Meeting in Chicago. It was going to be my first meeting with this organization, and (more importantly) my first chance to even attend a national meeting and present a poster. I was excited and nervous about it, because it would be my first meeting and because I was going to be going essentially by myself. This meant that I would have to make at least a little small talk with others, perhaps even make some contacts with folks so I would have someone to sit with at lunch, etc. The confounding factor in this case was the fact that my family would be in town, so I wouldn't necessarily be there for everything. Unfortunately, this did in fact affect my attendance and how enthralled I became with the conference, but it didn't affect my enjoyment!

Friday morning I drove up to Chicago, intent on getting there at roughly lunch time so I could be there to attend the afternoon sessions. The morning session was a business meeting that, while open to all APSA members, was more geared toward school representatives (i.e. not me). Unfortunately I was far too astute and concerned about my arrival time, and I ended up getting to Chicago about 10:30 in the morning. This left me, of course, with the conundrum of what to do. I met up with another MD/PhD candidate who arrived early, and we spent some time chatting (and I tried not to scare him, me being a 5th year and him being a first year). Since his hotel room and expenses were paid for, he coerced me into going to the hotel restaurant, which had salads at ~$15 a plate and entrees at higher prices than that. I should have just gone to Subway. ::: sigh :::

The conference proper began in the afternoon with a number of talks given by different faculty and professional MD's and PhD's. For example, Elizabeth Lawlor from University of Michigan gave a great talk about her path throughout the US, from post-docs, to clinical positions, to residencies, to... well, a lot of stuff. She offered a lot of great advice about following your passion in research and medicine and finding people who are supportive and offer good wisdom. I have a lot of notes from her talk that I intend to follow. Her talk was followed up by Catherine DeAngelis, Editor-in-Chief of the Journal of the American Medical Association, who talked about conflicts of interest in medicine. It was a pretty interesting discussion of how financial interests and desire to publish questionable research influences decision-making among physicians and clinical researchers, and how industry and marketers can get in the way of good, ethical research. It's kind of scary to realize that a majority of research funding comes from biotech and industrial firms, and how much of an influence they try to impose on researchers and on the journal. She was the best speaker because of how she handled herself in the face of these influences - she kept her integrity and said take this crap somewhere else!

The following talk was given by Constantine Stratakis of the NIH, who is director of the NICHD (child and human development). He gave a very, very brief talk about the strategic vision of the NICHD and what kind of translational and clinical research questions were being addressed. It was such a quick talk, in fact, that I really didn't even catch what he was getting at for a majority of it (my notes are fairly scatterbrained, actually) but I did note that they are still looking for feedback on the strategic vision here. Following his talk, a panel discussion about women in medicine was conducted by a number of physicians, both male and female (the list is on the conference website). The major themes I took away from this talk mirrored those given by Dr. Lawlor earlier in the morning, including continuing to be passionate about your work, surrounding yourself with people who similar goals, finding good mentors, and, probably most importantly, having short-term and long term plans. One panelist mentioned having 1, 3, and 5 year goals, which I thought was a good theme!

The remainder of the afternoon was with scientific talks as part of the joint conference with the Association of American Physicians (AAP) as well as the American Society for Clinical Investigation (ASCI). These included talks by Aaron Ciechanover, a 2004 Nobel laureate who was one of the people to discover ubiquitin-mediated protein degradation; Vishva Dixit, director of molecular oncology at Genentech who talked about death receptors; Webster Cavenee, who talked about developing targeted cancer therapies; and James Downing,who was discussing the genetics of leukemia. They were all very interesting talks! I am planning on looking into several of the speakers for more information on their research topics.

Following these talks, the social activities began... and I went to spend time with the family. That's alright, though... I don't get to see everyone that much!

Saturday, I geared up for my research poster presentation and heard the morning's research talks. A variety of speakers gave talks about their research, with the loose focus being on medical genetics, one of my favorite topics! Harold Varmus, Nobel prize winner and director of the National Cancer Institute, gave an interesting talk about the "state of the NCI" and discussions about how behavior, lifestyle, environment, and genetics influence cancer development, and what types of treatments the NCI hopes to develop. There was also a very provocative discussion about funding for the NCI and NIH, and what needs to be done to increase the funding. The next talk by Helen Hobbs discussed how genetics influence lipid levels in the liver, leading to hepatic steatosis. A particular gene called PNPLA3 has a I-->M mutation at position 148, whose allele frequency follows the prevalence of liver disease. Interestingly, the effects of this allele change are directly effected by whether or not the patient is obese - if you are thin, you won't have these problems! The point - stay thin (or try to, at least).

The following talks continued the medical genetics theme. Janet Rossant discussed the increasing prevalence of stem cells in research and the development of therapies with induced pluripotent stem (iPS) cells (which, interestingly, have only been developed a few years ago). There seem to be a lot of possibilities for therapy with these stem cells! Jeffrey Whitsett, a neonatologist at the University of Cincinnati, discussed disorders of surfactant homeostasis in infants, and how loss of these surfactants can lead to respiratory distress syndrome. The way he figured out what proteins were necessary for surfactant activity? He dialyzed alveolar cells in buffer... for a month. Just left it there. And you know what? He found the proteins and they worked. How about that for science? Erol Fikring discussed some very interesting research looking at vaccines against Lyme disease. He discussed a protein that coats the infective agent Borrelia burgdorferi, which is activated only when ticks are feeding, and how the lack of this protein prevents transmission of the bacterium. Targeting this protein may help prevent transmission of disease!

The poster session came up next, and I think it went pretty well! I had the chance to speak to a small number of people, including physicians and students. They seemed fairly interested in what I was saying, and I was able to answer questions about my research and precedent for my stuff working in other papers. I would like to say I won a poster award or something like that, but I don't think I did... and I'm not sure if I'll ever know! The good news is that it was a good experience for me.

Following the poster session, I unfortunately stopped attending the conference. The unfortunate part is that I wasn't there, but it was just fine since I was able to meet up with my family for the remainder of the weekend! There were a number of other scientific talks and inspirational discussions with different speakers, all of whom were helping us to find our paths in our careers. I'm sad that I wasn't able to attend everything, but glad that I was there for the parts I was there!

My overall impressions? It was a good experience, and a good opportunity to hear from a number of speakers discussing science, policy, and what kind of career paths we can go down. While the socializing aspect was lacking for me, I was excited about discussing my research with others and hearing about the amazing research being done throughout the country. I hope I get to attend this conference next year... as a doctor (at least one kind of doctor). We shall see!

No, I take that back. I will be done with the PhD by next spring! It will be great!

Meet Me in Chicago!

2011-04-13T10:24:00.000-05:00

If you happen to be attending the American Physician Scientist Association meeting (or one of the co-sponsoring meetings, the American Association of Physicians or the American Society for Clinical Investigation) feel free to say hi if you see me! I will be giving a poster on Saturday afternoon which, while probably not terribly exciting, will certainly present the opportunity to "talk shop" about science and medicine!

I'm still thinking about content for the blog, but it's one of those busy times in life when I'm trying to get things accomplished for both med and grad schools, so hopefully soon I will get back to having something interesting to talk about!

Worst-case scenario, I can always talk about running. :-)

See you this weekend!

On the Homestretch

2011-04-09T19:01:00.000-05:00

It's April, meaning that we're rapidly approaching a number of different deadlines and events that we've been thinking about this semester.

In particular, trying to finish up that poster for the APSA conference. I'm feeling a little bit concerned about the level of sophistication on my poster (i.e. it's not very sophisticated) but hey, what other reason do I have to give a poster besides just saying "the hell with it" and giving one? Should be a fun experience.

Again, other deadlines are approaching - the semester ends in about a month, at the end of which I will need to take an exam for my Immunology class. It's been pretty interesting to attend! I'm looking forward to having the opportunity to take it all together and to see the connections between different classes, organ systems, and so forth.

Other deadlines... well, the boss will be leaving in July, so we'll have the deadline of her leaving. The main thing we'll have to worry about it getting things ready for her departure, stuff to ship and stuff to keep, what space we can still occupy, etc. I'm not too excited about this, but hey, we'll do what we can.

Anyway, as always it is exciting times and whatnot. I'm looking forward to the conference next week, and I will be sure to report from it when I'm there!

Data Collection and Other Madness

2011-04-04T20:54:00.001-05:00

Last week I ran a polyacrylamide gel every day of different in vitro splicing assays, looking at the effects of different molecules on my splicing reactions. It was very exciting and very tiring.

I tell you this because it's sort of a reason why I have been relatively absent as of late. I'm in a hurry to collect a good amount of data in advance of the poster session at the APSA Conference I will be attending shortly. Now, more than ever, it's become important for me to push forward collecting data so I can have something to present. I'm sort of using this to light the fire under my butt and get me excited about getting data and analyzing it. I can tell you, if you are familiar with the "data analysis" section of research, that it's pretty mind-numbing. I've been going at it for the better part of the last two hours, and it's making the inside of my head start to melt. I can't imagine doing this more frequently - give me the chance to run a synthetic reaction any day compared to this! (and that's saying something... organic reactions can be pretty tedious themselves).

As far as the rest of my life goes, I had a pretty decent weekend visiting with my brother down here in Ur-Paign (I'm bringing it back!). We had a chance to hit a number of fine restaurants around down, from Das Cafe and Mirabelle in Urbana, to Sun Singer and the Original Pancake Factory in Champaign, and ended the weekend with dinner at Black Dog in Urbana. The crux of the weekend was Wrestlemania XXVII, the pinnacle of sports entertainment and something I had never watched live before. It was pretty exciting! That being said, I don't know if I'm going to order something like that any time soon... maybe next year?

I'm still exercising and training to run the 5K on Illinois Marathon weekend. Shin still hurts, but I went for a short run Sunday wearing my new compression socks, and my leg felt okay! I'm thinking that I will hold off on the running for the most part and focus on cross training, and have the cardiovascular fitness to run the 5K. It's only a few miles! Important side note: if you are in town here and have the time, please please please sign up to be a volunteer! They are looking for about 100 more volunteers on the course, and if they don't get the numbers then they can't have the race! Please go to the website if you can help!

Oh, and I guess med school is still going on, isn't it? Going to need to go study some more, I think. Only a few more weeks until the semester ends!

Okay, back to data crunching... thanks for checking out the blog, and if you've commented on a previous post with advice or suggestions I really appreciate it! To show my appreciation, here is a picture of me with a mustache.

Running Update

2011-03-29T21:49:00.000-05:00

It's been an interesting month down here in Illinois, for a number of reasons. My running hasn't really suffered as a result of that, but because of this shin injury that I've been dealing with. As I think I've mentioned before, near the end of February I bought a new pair of running shoes, which gave me shin pain almost immediately (well, almost is a relative term... it was on my first run in the shoes). I attribute that to the fact that I was switching from a pretty well worn pair of shoes to a brand new pair - the change in midsole and whatnot probably caused my pain. I really should have just stopped running, but why would I do that?

So, since then, I've been doing a combination of different activities - biking, stair stepper, rowing machine, elliptical, and so forth - interspersed with runs. While my mileage has decreased, I've actually been pretty consistent in my workouts, meaning that my overall fitness seems to have been retained. On various occasions I've done 1-2 mile runs during my workouts that have been fairly quick (according to the indoor track, anyway), and for the most part the runs I've been on lately have been pretty successful.

In the short term, I've been trying to dedicate more time to running in the Arboretum on campus, which gives the dual benefit of reducing the impact on my legs, as well as giving me a different place to run! It's meant that I've gotten up to almost 5 miles during a run, which has been good for me both mentally and physically. I'm planning on dedicating more of my miles to the trails in the surrounding towns (Mahomet, Kickapoo, etc.) in the hopes of doing a trail marathon or ultra sometime soon (perhaps this one?).

As far as goals for the year, my current strategy involves doing shorter races for the "short term" and then trying to build up my mileage on the trails. There are a number of trail races around here that I can go run in, which should satiate my need to do longer distance runs. As far as the injury goes, I'm trying my best to ice and rest when possible, spend more time doing things other than running, and I bought a pair of compression socks to see if they have any positive effects on these shins. I've heard good anecdotal evidence for compression gear, but we shall see if they are helpful to me.

Overall? Good news, I'm still running and exercising. I'm not quite happy with the fact that I can't do as much longer distance running, but that I'm going at all (and losing weight too!) is a good thing.

Hopefully I'll have some race reports to share with you soon!

Putting that Liberal Arts Degree to Good Use

2011-03-27T20:53:00.000-05:00

Guys, this afternoon I was working on my poster for the APSA Conference in Chicago next month, and in a spur of the moment example of genius/madness, began to think of different ways to present my poster and/or my thesis when the time comes.

I could, for example, follow the Hipster Science philosophy and present my poster as a beat poem, complete with bongo drum, or as a spoken word song set to the three guitar chords I actually know how to play.

Or, in a more dramatic turn, I was thinking of turning my poster (or, even better, my thesis defense) into an epic poem, a la The Iliad or The Odyssey. Starting off my defense by invoking the muses and describing my thesis research as a "long, arduous journey that lasted nearly a decade..." creates the perfect tone and sends the message that I went through a lot of personal exploration and discovery on my search for results and insight into my project. Organic synthesis is a lot like fighting the Cyclops, right? The only question is whether I should start it like the Iliad, whose first word is... say it with me... "anger".

Another possibility mentioned today was that I should present my poster as a carnival barker, trying to get people to come to see the spectacle that is my research. I've been growing a goatee that I could easily turn into a mustache... "Come one come all! Come see the spectacle so wondrous that you won't believe your eyes nor trust your senses ever again! You'll never be the same!"

Of course, the old standby - interpretive dance - is always an option.

In any case, it would behoove me to use some of that liberal arts learning I received as an undergrad to spice up my presentation a bit.

Additional suggestions to make my presentation and/or defense more "interesting" are welcome!

Conference Posters - Best Format?

2011-03-25T13:12:00.000-05:00

Folks, I have a question!

I am currently working on a poster for the American Physician-Scientist Association Meeting next month up in sunny/windy/sometimes horrifying weather Chicago, and I am hoping to get some advice on putting together a poster for the event! I know I'm pretty far behind the game as far as conference posters go (I will admit - true confession! - that I am not someone who goes to a lot of conferences and gives a lot of posters), so I am wondering the following things from those of you who have given posters in the past:

- One big poster, or slides?
- How much background material? My current poster (the one I did a few years ago at our MSP Symposium) has 1/3 of the poster devoted to background, which I'm pretty sure is too much.
- Poster arrangement - 3 columns? Should those sections be separated physically (i.e. barriers between sections) or is it okay to just use the headers to keep them separated?
- Should I take advantage of one of the many powerpoint styles, or just keep it blank?
- Umm... what "X-Factor" do you think would be helpful to make this a good poster?

Please leave your feedback in the comments!

Also, this:

Plans, Trips, and So Forth

2011-03-21T11:59:00.001-05:00

It's been a whirlwind of activity here lately, which is partially why my day has been so scatterbrained and unproductive. At least, that's what I'm going to say is the reason why, anyway. A few bits of news and activity have put me in this place, and I'm only now (around lunch time) getting my brain back into the correct frame of mind for work.

- I had all of my meetings with the different people in the department who would be helpful to me once the boss leaves - committee members, the MSP office, and finally the head of the department - and the general consensus is that there should be funding and space available for us to finish up our work and graduate (the first time, for me). The reason I put an emphasis on should is that the department head is still being relatively vague about whether or not all of that will be in place this fall. I understand that weren't not quite at the point where all of that is figured out, but come on now - you say that you're "committed to the students" but still not committed enough to tell us with certainty that we can finish in our space and be funded? It's bothersome, that's for sure. Regardless, we plan on remaining in this space until finishing up, hopefully getting some good results along the way.
- The side note to this, which I guess I didn't mention yet, is that I will have to take an additional year beyond what I had expected in order to finish both degrees. Everyone universally agreed that it would be in my best interest to focus on research until I'm done with it, rather than taking extra time by completing classes at the same time. There is precedent for that route, but the difference is that most of the people who do that a) have external funding, b) have multiple people working on the project, and c) have compiled enough results (probably due to a and b) to be able to do more "administrative" work on their projects, finishing up the following summer. As someone who is in charge of only himself, I don't have the luxury of delegating tasks, so I'm stuck doing the work myself and finishing it all as best I can. This means taking a semester (at least) off from classes. Hopefully I will be able to get back into it in the spring, finishing up the rest of the classes the following fall.

- This past weekend we had a lovely visit with some friends out in North Carolina, where my former roommate (and, near as I can tell, identical twin) is finishing up his degree at UNC in a synthesis lab. We sampled a lot of great food (both purchased and prepared by our hosts), enjoyed a number of different activities and scenery, and discussed future job prospects. It's interesting to see another perspective on someone getting closer to finishing school, figuring out where you want to go and what kind of work you want to do. Hopefully his job prospects will work out and they'll be able to stay in the area - she has quite a music business going down there, the area is extremely nice, and they seem to be quite happy there. Also, I should note - the campus and surrounding area in Raleigh-Durham-Chapel Hill is extremely nice, full of trees and gardens and sunshine and happiness which is in stark contrast to Illinois, which is mainly prairie. I was happy for the change!

- Running progressing slowly and steadily. I was able to get out for a number of short runs this week, with somewhat minimal damage to my shin. I say minimal because the pain was there, but not very extreme (a fairly dull pain), and I could tolerate and treat it without having ill effects later. As I've mentioned, it's most likely shinsplints, so I'm going to continue treating it as such. I'm planning on getting back to the Arb this weekend, in the hopes of getting out to the trails outside of town soon. I'm not running any races in the Illinois Marathon at this point, and am planning on volunteering. Better get on that...

- Research is still research, and now that the excitement and frustration surrounding everything has died down a little I can focus again. I have plans to get some things tested before the APSA Conference next month, at which I will be presenting a poster. I'm also planning on presenting at the U of I Med School research symposium, so I'd better get that registration in if I want to give a poster.

- FYI - Allen and Sons has great Carolina BBQ. If you are ever in the area, go find it.

- Also, one thing I remembered from the trip that I should mention. There's a place called the Patterson's Mill Country Store that, among other things, has a collection of old pharmaceuticals and chemicals on display. Among the random assortment of miracle cures and mixtures are a number of chemicals with some very familiar labels...

We have, in fact, several bottles with the same labels as these "antiques". It was quite funny to see these bottles and realize that we have many of the same chemicals, from the same company, with the same labels! Pretty funny stuff.

A Small Request

2011-03-13T21:16:00.000-05:00

Folks, I am still dealing with some shin pain, and I'm looking for advice about it. A few days ago I ran a ~5 miler through the U of I Arboretum which, while relatively benign on my legs, still gave me some shin pain by the end. I'm fairly convinced it's not a stress fracture (it hasn't been painful outside of running) but it's getting to be a bit annoying and I'm looking for ways to treat it.

Currently the treatment is icing it occasionally (every other day, mostly), taking ibuprofin or the equivalent, and trying to do activities other than running (yesterday's run at the Arb was the longest run I've done in about 2 weeks). I'm wondering if compression socks/sleeves would be helpful, or if some other remedy is going to be better. I'm contemplating getting a referral to the athletic trainers again to address this problem, but would be happy to avoid it if necessary (primarily due to lack of time).

Any advice is appreciated! Keep on keepin' on, friends.

Bikram Yoga (or: Sweating Your Face Off)

2011-03-09T21:31:00.000-06:00

As I've alluded (I almost said "eluted"... silly scientist...) to previously, I'm working through another injury and thinking of different ways to keep myself in shape until I heal up and can get out to do more miles on the road. In try different things, this past weekend my brother invited along to a session of Bikram Yoga, a special brand of yoga in which you sweat, and sweat a lot.

Developed in the 1970's, this particular type of yoga (named after the originator), is special in that it follows a series of 26 poses over 90 minutes, taking place in a room somewhere around 105F with ~40% humidity. While this may be to "facilitate deeper stretching and prevent injury", the main thing it did for me was make it really dang hot and sweaty! To start, you enter the studio in silence in an effort to reach a more meditative and spiritually centered state. I will admit that, as a first timer, I spent the first few minutes being a little fidgety and thinking about the different things I would be doing the remainder of the day. But, that's just me.

The session was initiated by an enthusiastic instructor who energetically spoke out commands for each of the exercises. Unlike your stereotypical yoga session, with people sitting in silence on mats while the instructor gets them to think about deep concepts, this form of yoga was much more involved, including a lot of dynamic stretching and poses that forced me to get far outside of my flexibility comfort zone. Much of the initial challenge involved poses that I, as a runner, was not used to doing, requiring me to maintain my balance and, probably most (embarrassingly) challenging, hold my arms out for long periods of time. There were a number of poses that I, as a first timer, simply couldn't get to, but you could tell that some people were enthusiasts as they easily moved from pose to pose. Even my brother, only a month-long veteran, was doing a very good job at achieving the level of flexibility required to fulfill each stretch requirement.

One of the main concerns with this type of activity is the fact that a) it's hot, b) it's humid, and c) you're twisting your body into contortions that could be very negatively affected by a and b. They address this by suggesting stopping and sitting down if you're dizzy or lightheaded, but I can see how it could become a problem if someone passed out in the middle of a pose. Especially one that required balancing on a single foot with everything else twisted and contorted above it.

So, what's my thought on this activity? It was certainly challenging, and not just because my body wasn't used to twisting into pretzels. Despite being someone who feels it's necessary to be moving a long period of time before feeling fatigued, I can say that my heart rate was up and I sweated more than I ever had in my life before that (with the possible exception being the 2007 Chicago Marathon). Having to hold different poses for 30 seconds to a minute was actually quite challenging, and I think it stretched and pulled muscles that wouldn't normally be worked by running. I think it may be an interesting exercise (pun intended) to incorporate this activity or something like it into a regular running routine, if only to change the pace a little (pun intended again) and introduce some activity to muscle groups that wouldn't normally get it.

And, as is evidence of any good work out, I was definitely feeling sore the next day!

Will I do it again? Maybe. Until then, I will be back on the roads. Hopefully.

Fending for Yourself

2011-03-08T21:17:00.000-06:00

I'm going to cut straight to the chase here - we in the research group are in an interesting position, because our boss is going to be traveling off to a different school in the fall. Unfortunately, she's not going to be maintaining a lab after this semester, so all of the students in her lab are going to need to figure out where they need to go. Some have clearer paths (the younger folks need to join new labs) while others need to spend time figuring out which way to go.

For me, the answer is pretty straightforward - FINISH! While I'm not quite there yet, I'm on the homestretch and need to spend the next few months figuring out how long the homestretch is going to be, what I'm going to be doing during said homestretch, and so forth. One of the issues is that, because the boss will be gone and I will still be here, I (and my fellow upperclassmen) are going to need to establish that a) we need to get paid and b) we need the space to work in to make sure that we can finish. The money thing shouldn't be an issue, except for me, because my funding has been coming from the department. I am going to need to talk to a number of professors and the head of the department to ensure that money that was going to go to me still does. I'm sure the "please fund me so I can finish up" argument will be a good one, but you have to cover your bases here, you know? After that, it will be a matter of making sure we have the space to work in. There are processes going on that should solve that problem, but worst-case scenario we're going to have to fight off the vultures, as it were, to make sure that we can continue to work in our space until we all finish.

It's interesting to think about - what would you do if presented with the problem of having to finish in a limited time, limited space, with limited support? Speaking to both my parents and my in-laws, both are surprised at the relative lack of support for people who don't have an adviser keeping an eye out for them. One of the people in my lab relayed the story of how, as she was starting before our boss got here, the prof who was waiting for her lab space was hounding her nearly every day to get out so he could take over. Why is it that, when they present to us the idea of our community being collaborative and supportive, it actually becomes cutthroat and competitive? It's a big problem, and will continue to be one for us until we can establish that we're going to be there until we're done and you can't take our space. Hopefully, we will establish a support system that will ensure that we can continue working within our space until the year finishes out and we all move on to bigger and better things (for me - anatomy and the like).

The next year is going to be an exciting and difficult one, for many reasons. Do I take med school classes in the fall or hold off so I can finish my thesis? What do I do in spring next year if I'm not enrolled in med school? How am I going to be funded next year? Will I have to continue tutoring or be a TA? Will we have to compete for laboratory space with a new professor, or will they be too enamored by the other lab space that's opening up down the hall? It's going to be an ordeal, that's for sure, but I'm sure it will at least provide a lot of "life experience".

Stay tuned to see what happens!

Trehalose-Based Click Polymers for Nucleic Acid Delivery

2011-03-06T21:05:00.000-06:00

It is a busy time over here in Illinois! I just spent the weekend up in Chicago after a week in which I had to do two presentations and take an exam for Immunology, so I was happy to relax a little. I got to see some good art at the Art Institute of Chicago and eat way too much food at restaurants such as the Bongo Room (which I highly recommend if you're in Chicago any time soon!).

Anyway, one of the presentations I did in group meeting this week was on non-viral gene delivery of DNA. It's a pretty interesting subject, so I figured I'd take you through the design of the project and what they were trying to accomplish.

I was reading recently about applications of "click" reactions to a number of biologically relevant molecules, in the hopes of finding some molecule type that would be of interest to the group, and came upon a section in this review that was discussing building polymers that could interact with nucleic acids and deliver them into cells. This is particularly interesting because the molecules use non-viral gene delivery instead of using viral vectors. One of the problems with using viral vectors for gene therapy is the fact that they can potentially lead to health problems associated with the particular virus being used, so finding ways to deliver nucleic acids without having to use a virus may be useful as a therapeutic method down the road.

The work, done by Professor Theresa Reinke's group (previously at University of Cincinnati, now at Virginia Tech) is explained over several papers in which they analyzed the properties of these structures to determine why they acted in the manner that they did. The initial study looked at the properties of different polymers consisting of three regions: a trehalose sugar, an amide-triazole region, and a polyamino region.

Trehalose is a disaccharide that was chosen because it is biocompatible, increases water solubility (due to having many hydroxyl groups), and has been shown to have properties that prevent it from aggregating with serum proteins. This is pretty important, as one of the main concerns with their polymers would be potential aggregation, leading to blobs of material that could not pass through cells. The amide-triazole region is formed by using click chemistry to attach alkynes and azides together. Essentially, this means that they could easily put together different pieces of material and control how much polymer was made. Each of these functional groups is important to the polymer, as they would be necessary to interact with the DNA they would be delivering. Finally, a polyamino region was incorporated to include a bunch of positively-charged functional groups to interact with the negatively charged backbone of DNA, promote formation of the complex, and provide a surface that could interact favorably with the outside of cells (a necessary property for transfection).

Before I get too technical (if I haven't already), imagine it like this - you have a piece of DNA you want to get into the cell. It can't get in on its own (the cell surface and DNA are both negatively charged), so it requires a delivery device to get it to and through the cell surface. This polymer is able to form structures that encapsulate the DNA and help bring it into the cell. Cool? Cool. (I feel like I need some pretty pictures like I Can Has Science, but I wouldn't want to do any upstaging, would I?).

The molecules that were synthesized contain 1, 2, or 3 secondary amines per polymer repeat. This property was the variable, and Reinke's group determined what effect this change had on the properties of the molecules. To summarize a number of experiments - it appears that having three amines per polymer repeat produces the most favorable properties for these polymer structures. A look at the structure of these polymers by TEM reveals that the polymer with 3 amines gives nice, spherical aggregates of a fixed size (about 400 nm) that do not increase aggregation over time in different biological media. This is an important property, because it will ensure that the cargo is small and uniform enough to get into the cells.

More important, though, is whether or not they can get into cells and have biologically relevant activity. A number of assays, including monitoring the uptake of a fluorescein-labeled DNA and a luciferase-reporter assay, revealed that the polymer containing 3 amines continued to show the best properties, consistently producing high transfection rates, high fluorescence, and good luciferase activity. This again indicated that, for whatever reason, the properties of this particular polymer were favorable.

Examination of a number of other properties revealed that, despite the good activity, the best polymer carrier seemed to have problems with cytotoxicity. Essentially, it caused more cells to die than the other polymers, but showed a better profile than a common transfection agent, Jet-PEI.

I'm glossing over some of the finer points, but in sum the results of this research show that the group was able to produce a polymer that fulfilled their goals - binding to and complexing DNA, then delivering it efficiently into cells. Later work by the group has produced a number of positive results and further evidence for the efficacy and cellular uptake of their polymers, and right now they're working toward a major goal (and the goal of many people) of developing efficient means of transferring biologically relevant material across the cell membrane into diseased cells. I, for one, hope that they are successful soon.

Hopefully this has been a relatively reasonable insight into the development of particular type of non-viral gene carrying tool for basic science research and potentially therapeutic activities. If not, feel free to browse by again sometime, when I will probably relate to you how my own research and other activities are doing (I could certainly tell you about my recent experience with Bikram yoga, and maybe I will!).

Citation: Sathya Srinivasachari, Yemin Liu, Guodong Zhang, Lisa Prevette, and Theresa M. Reineke. "Trehalose Click Polymers Inhibit Nanoparticle Aggregation and Promote pDNA Delivery in Serum". J. Am. Chem. Soc., 2006, 128 (25), pp 8176–8184

Hipster Science

2011-03-01T19:30:00.000-06:00

It's kind of this thing I heard about, but now it's gotten all popular so I don't like it anymore.

Go have yourself a look.

Next up will be Hipster Medicine.

"I like retroviral therapies because they're retro"

"I was using conjugate vaccines before they got all popular"

Or, "My hero is Edward Jenner, because he was using cowpox innoculations to vaccinate against smallpox before they went mainstream in Britain in 1840".

In other news, congrats to CBC blogger Excimer for making the rest of us look bad and finishing his PhD! He now goes on to fame and fortune out at ETH in Zurich. Way to go!

Stuff and Things... and Stuff. And Things.

2011-02-26T12:08:00.000-06:00

I'm in the throws of studying for an exam, so I'll give you a list of things that are going on for me.

- If you're a fan of Futurama, like I am, you may remember the episode where Fry enrolls in Mars University with Gunter, the hyper-intelligent monkey. If you have seen the episode, you know that all of the intelligence is in his tiny bowler hat. At one point, when given the choice between his animal nature (in the form of a banana) and civilized society (in the form of the hat), he eventually figures it out, proclaiming "the hat goes on the head! It's so simple!". The point of this story is that I've been thinking of that particular moment a lot lately in my research. A lot of things are starting to come together for me, and the good results I've been getting lately have come from fairly simple concepts that I have tried before with mild success. Call it a necessity to gain experience before moving forward, or whatever, but a lot of "it's so simple!" moments have been coming lately.
For example, I have been using maleimide-thiol reactions to conjugate peptides and oligonucleotides, with middling success. One of the issues is how to reduce the thiol, which can oxidize to form disulfide binds in air. I originally tried using dithiothreitol (DTT), which sort of worked but had the problem of reacting with the peptide. Following that, I attempted to use TCEP, another reducing agent that had the potential benefits of being unreactive toward my peptide and could stay in the reaction without interfering with anything. Except, of course, it reacted with everything and wasn't useful at all. I recently went back to DTT, and figured out why it wasn't working before... I didn't get enough time! Duh! After letting it act as a reducing agent overnight, I got almost complete conversion in 2 hours rather than overnight. Just that simple! It's really hilarious to think how much thinking I put into this, with the best result coming when I just did the easiest thing. Funny how things work.

- If you've had a look on that Dailymile widget I have on my blog (go ahead and look now... see it? Good), you may notice that I have been struggling a little bit this week with shinsplints. I think it's because of having spent a lot of hours on the roads lately, along with switching to a new pair of shoes. I was in a lot of pain a few days ago, so I iced it, took some Alleve, and rested for two days. This morning, I did a few light miles on the track, putting in some time on the stairmaster in between miles. Leg felt alright, so no worries there. The new plan? Split my time between easy and infrequent miles, and other activities like the bike, stairmaster, and so forth. My race plans are not scrapped yet, but I think I may have to re-frame my goals. If I run the 5K in 2 weeks, I may just go for it, and if it starts to hurt just back off, but we'll see. As far as the Illinois Marathon goes... well, it won't be the marathon, that's for sure. Unless something changes, of course. Maybe the 1/2, 10K, or 5K, whatever I feel like doing at the time. I'm going to get some trail running started once the weather warms up a little bit more, and I think I will be doing most of my longer running on softer surfaces this summer. Could lead to a 50K later this year! We'll see...

- Med school exam on Wednesday. I took a practice exam yesterday, without having studied at all specifically for this exam (aside from the requisite reading and reviewing on a daily basis), and got almost all of the questions right on the first try. Those that I didn't get right, most of them I got right on the second try (i.e. I had two possible answers and picked the wrong one first), and only a few were completely wrong. Good sign, I think. Need to study this weekend, though...

- I need to do a lit presentation next week for group meeting - yesterday I did a talk on in vitro splicing assays, the conclusion of which is that my group can't use those assays for studying myotonic dystrophy. What should I talk about this week??

That's all I've got right now. I'm sort of waiting for my wife to finish taking the GRE, after which I will go and do my studying. Good stuff!

Mid-Day at the Gym

2011-02-22T13:59:00.000-06:00

Just musing about running at the gym, something that happens occasionally but not too often.

On the rare occasion, I take a trip to the gym over my lunch hour in order to pound out a few miles in a climate-controlled environment, helping me to avoid the foibles of running in winter weather and having to run in the dark after work. While often time consuming because of the different preparations I need to make - be sure to eat something a few hours beforehand, drop off that sample on my way over, take the 10 minute walk to get there, change, don't forget a pit stop, and then finally get going - I do like running at the gym because it gives me an opportunity to do something that I wouldn't normally do on the run. People watching.

Aside from having a measured distance in which to run, the biggest enjoyment I get from running on the track in the gym is the sheer variety of people I can look at. Now, don't get me wrong - this isn't some sort of creepy stopping and staring thing... not that I would have the opportunity to do so, as I tend to avoid the treadmills and instead do laps around the track. This is more me going in circles, sometimes passing folks, having others pass me, and getting a few seconds for every minute to think about that one person on the treadmill or elliptical machine or the one who's working on his beach muscle - what are they here for? Are they training for an event, trying to improve their fitness, or just working on a visual for presentation at the next Friday-night bar outing?

There are a variety of people at the gym, and given that it's a college gym I see a wide range, from those who are simply there to work on appearances (who are usually the best dressed of the bunch, or wearing shirts for their upcoming or recent bar-crawls), to those who are really there for a work-out (who are often wearing the race t-shirts that I sometimes get), to those who have recently come back to athletics and are finally taking advantage of the facilities available to them as employees of a University. Even within each category, there are finer and finer subcategories - the professors or long-time employees doing their daily routine, the frat guys who legitimately want to be in shape for intermurals but would also be happy with looking good for the sorority ladies, the occasional guy who goes to do an interval session when he doesn't feel like running outside. Yes, after doing so many runs by myself on the roads, it's nice to have something to look at.

So, if you have the opportunity, head to the gym for your run. It may be boring to run around a track as opposed to traveling through the outdoors, but there's still plenty to see. And possibly make up stories about.

Also, stay away from treadmills. You can fall off of those.

The Minute I Move from Minnesota

2011-02-20T21:32:00.000-06:00

Okay, so it's been 5 years (give or take).

And we've gotten our fair share of snowy days and school cancellations. (BTW - canceled has one l and cancellation has two l's - what's up with that, grammar?)

But this winter has by far made me the most jealous of my homeland in the past five years. It's been a winter of epic snowstorms, and I want in, dang it. Nevermind the fact that I would probably have been sick of it months ago, or that I would probably never want to shovel again after this winter, or that I probably would still have gone to work regardless of the snow.

When you're from Minnesota, and you see a map that looks like this:

While your current forecast looks like this:

You tend to get a little jealous of all that snow.

Good news, though - at least it's not going to be below freezing with no snow.

That's just lame.

Quick Post: How to Evade the "When Are You Graduating" Question

2011-02-18T15:57:00.000-06:00

Sometimes, when I go home, I get asked by family members either "what are you working on", "what do you want to do when you're done" or "when are you going to graduate?".

The "what are you working on" question is the most complicated, since I always feel like I need to have visual aids in order to explain it. I could point them to the group website, or just carry around a poster with me, but I usually am able to get away with "therapeutic molecules for RNA splicing diseases, like spinal muscular atrophy or cystic fibrosis". Most people know cystic fibrosis, so I've got that going for me. Further clarification can be gained if they understand "RNA" and "splicing", and in fact I was able to teach a whole group of family members about splicing using Twizzlers and marshmallows. Pretty simple, pretty smart.

The "what do you want to do" question is tricky, but at this point I've been able to manage with "here are my interests, so studying in field x would be best for me." Since I haven't been exposed to medicine as much as research, it makes that question a little easier to answer with "I'm not sure". I have a feeling it will get more complicated, but at the same time easier to answer, once I get into the med school full-time.

By far, these days the "when are you graduating" question is the easiest. The short answer is, of course, "not for a while", since it won't be for a while. I can't help that - I'm getting two degrees! Good for me! The follow-up to that question, usually some variation of "wow, that's a pretty long time" can usually be further answered with my favorite response:

"Hey, it's a steady job. In this economy, these things are hard to come by!".

Just think about that next time you go home for the holidays are bothered with questions about when you'll be getting a "real job". Just saying.

Science-Blogging Win, Science-Reporting FAIL, and Why Am I Not in the Spotlight Yet??

2011-02-15T20:01:00.001-06:00

Friend of the blog and commenter Sharon of I Can Has Science? (the best possible name for a science blog) has seemed to gain some notoriety and standing in the science community this week, becoming the main critic of a product called Brazilian Blowout (which originally had formaldehyde as an active ingredient) on an NPR Health Blog. Citing her recent post on the product, the crux of the article is how she doubts that the product will be up to snuff without the active ingredient.

People in the comments, however, were frustrated by the fact that, as a PhD candidate, she may not have the proper experience to comment on such an issue. To a certain extent this is true - as stated (quite clearly) on her blog, she is an organometallic chemist who wanted to look at research outside of her field. The big point of the blog is to step outside the comfort zone and report new subjects in a straightforward, easily understandable way. So, in fulfilling her role, she is learning about the science behind these subjects just like everyone else is.

The real problem with this is the fact that the NPR blogger went to her as an authority, citing a quote from her blog as a comment and not doing any additional reading into the fact that she may not be the person to act an authoritative figure on the subject. *EDIT* I suppose the other, more pressing issue here is the fact that the title of the article is "Chemist Doubts Hair-Straightener With Formaldehyde-Free Formula" while she only said that she "wasn't sure" what the active ingredient would be. It's headline grabbing and misconstruing what she said. Seriously. *END EDIT* Not to put her down (I rather enjoy her posts and have on several occasions had additional insights into her topics, being of a more biochemical and medical nature), but if you're a reporter looking for a person to discuss this subject, why pick a blog post by a grad student and use it as an authoritative comment? Seriously, journalism is not as thorough as it used to be.

So, to sum up:
- Science Blogging Win for I Can Has Science, specifically for clearly explaining and discussing this new product.
- Science Reporting Fail for NPR, for taking a line from a blog post and acting as though the person is an expert in the field
- Why am I not in the spotlight? As a friend of mine suggested, perhaps I should "Invent a "surfactant-free" soap under a pseudonym. Write a blog post about it. Send the link to NPR 100 times." Maybe that's the path to stardom?

I did write a post about Miracle Mineral Solution once. And Splenda. Does that count?

Valentimes Day

2011-02-14T09:25:00.000-06:00

Well hey, Happy Valentines Day folks.

I have somewhat mixed feelings about Valentines Day. While on the one hand it makes sense to have a day on which we profess our love for our sweethearts, shouldn't that be every day? And who was this St. Valentine, anyway? Some sources claim that his origins may not be as clear as they seem...

That being said, I never miss an opportunity to dote on my sweetheart, and having had 12 years to do so now (many of them with an assist from my folks, who always came through with some fresh flowers when I had no money and/or didn't plan ahead) I feel as though I have had plenty of experience doing something nice for my wife. This year I gave her a card suggesting that she get ready to get on the "love train" (whatever that means... are we going somewhere?), cooked her an elaborate dinner, tried my hand at making creme brulee, and bought her some delicious Askinosie chocolate (and it's really good chocolate - just ask her). She reciprocated by getting me a pair of cufflinks and a tie clip, some excellent accessories to go with the new suit I received for Xmas.

Unfortunately we don't have anything planned for the big day, as I have to work tonight and she has to attend her kickboxing class, but that's okay. As I've said, I would rather have a nice dinner, enjoy some chocolate, and shine my new cufflinks than worry too much about adhering to what has essentially become a greeting card holiday.

If you have someone special in your life, don't wait for a commercial holiday to say how much you care about them.

Wait until the day after that holiday, when all of the candy is 50% off.

And for goodness sakes, don't buy them a gun for Valentines. That's just dumb.

Running Update - Goals, Weight Loss, and Plans

2011-02-10T10:56:00.000-06:00

Well hey, although I have discussed (to a certain extent) running recently, I don't think I've done it directly, so I think it's a good time to do it.

Running for me has actually been going well, overall, although it's not without it's issues. This year I signed up for an account on Daily Mile (as you can see on the right), which has both its perks and its problems. On the one hand, it's very nice to be able to use the tools they provide - mapping out routes for accurate distance, or letting it add up your mileage and give a good idea of how your training is going - and it's great to get motivational comments from people who are following your training. On the other hand, having those numbers produces a certain competitiveness and drive to continue putting up said numbers, to the point that I feel bad if I haven't done a run and have done something else instead that doesn't give a number (i.e. ridden on the bike for 40+ minutes). This issue was actually addressed on a recent episode of Geeks in Running Shoes, with the advice that you simply don't worry about it, but it's hard to ignore how good it feels to see those numbers go up.

The biggest issue I'm having these days is not the weather (evidenced by my Daily Mile photo), nor the fact that it gets dark outside early (although it has been getting later and later until the sun goes down... and there are plenty of ways to get around the problem of running in the dark as discussed on a recent Runners Round Table episode), nor the motivation to get out to run. It's this hamstring issue. The pain I've been having for the past several years doesn't seem to want to leave me alone, and no matter what I do the pain doesn't go away. I've been more aggressive with stretching (which is what got me out of the injury rut last year), but it seems as though no matter what I do it doesn't go away. I'm also dealing with a bit of runners knee (self diagnosed), which has come on most likely because of increased mileage and because my shoes have probably seen better days (although one could argue the fact that they are probably more suitable for running now than they were when they were fully cushioned, but that's a different argument entirely).

This leads to another plus/minus issue I have to deal with - weight loss. With all of the running I've been doing, I'm actually doing much better weight-wise than I was a year ago. Although I biked a lot last winter, I still got up to 220 lbs by the spring and felt pretty gross for a while. Since then, having run a 1/2 and full marathon last year and spending more time on the roads this winter, I'm actually hovering around 200 lbs, going as low as 196 lbs after my runs. I've felt really good and fast during the runs, so I want to maintain this feeling! The problem is that the more I run, the more pain I have in my hamstring and knee, and while I could bike more often than run I feel like I need to run for the weight maintenance and for those numbers in my training log.

Weight loss is also an issue lately because I've gotten back into the habit of snacking a lot while I'm at home. One of my goals for this year was to curb that, but a combination of stress and needing something to keep myself occupied while studying at home has turned me back into a snacker. I'm trying to eat healthier snacks (we buy veggie trays and Triscuts and popcorn) but it's still peppered with unhealthy things (mostly chocolate). I think I could curb the running and save myself some knee pain by substituting (at least partially) with biking, but I would need to change my eating habits substantially to compensate for the reduced calorie burning.

Finally, the goals end up being an issue. If I can't run as much, then I can't do the mileage necessary to train for a marathon. My knee pain and several other issues have made me rethink my goals for this year, and having some discussions with my wife cemented for me the idea that I can take time away from running marathons exclusively, instead focusing on other races and distances that will both take less time (1/2 marathon, 10K, 5K, etc.) and be less stressful (trail ultra runs, which should take less of a toll on my hamstring than road marathons). My initial goals for this year were to win my age group in the race circuit (need to sign up for the running club!), break four hours in a marathon, and run a 50K trail race. I've got eyes on the first and third goals, but perhaps I can wait on the second one for a while. There's nothing saying I can't continue running marathons in the future, except for the lingering pain that could turn into something bigger, so it may be for the best that I wait a little while before tackling that goal. I mean, hey, I'm only 27, right? There's plenty of time to run marathons.

So, I think the redefined goals for this year are as follow:
- Substitute a percentage (25-50%) of my running workouts with biking or something else cross training
- Run more races that are shorter distance, and aim for the Illinois Half Marathon or 10K this spring
- Maybe run a marathon this fall (and focus in on running marathons that I have not run before)
- Shoot for a trail ultra in the late summer/early fall
- Reduce the hamstring pain to a minimum
- Stop snacking so much so as to maintain weight

So, there you go. Running: updated.

Study Habits, Homework, and the Like

2011-02-08T13:32:00.000-06:00

One of the mantles I've taken up in the past few months or so, which I think I've mentioned at one time or another here, is that of a chemistry tutor for undergrads in a "living learning community" on campus. A few nights a week I show up, sit around in a room, and occasionally help the kids with their chemistry problems (recent problems - isoelectric point; recent successes - isoelectric focusing [basically the same thing]). For the most part the students are with it as far as their homework and studying goes, but occasionally you'll get the student who hasn't really looked at the material looking to have a lot of stuff explained. Fortunately I can usually point them in the right direction or, as recently happened to me on Sunday, I can say "come back in 15 minutes and I'll have an answer for you", which I usually do. It shows how I can usually figure out a problem if I've learned the concept before, but (unfortunately) it takes a few minutes before I can fully remember how to do the problem.

Anyway, having spent a bit of time now working with students in various capacities (tutoring, being a teaching assistant, etc.), as well as being a student myself, I've used some of that time thinking about study habits that are effective and those that aren't that effective. Most effective study habits revolve around constant low-level radiation... er, um, exposure to... yeah, exposure to different topics over longer periods of time, and changing it up every once in a while so as not to burn out on a particular subject. My main problem in undergrad was that this ended up taking a lot of time, especially when other, more appealing things took precedent, meaning that I ended up having to shrink this drawn-out process into a more compact time-frame. I've heard that there are studying extolling the benefits of not cramming, i.e. spending small amounts of time with different subjects and switching between them over a period of time, so I'm fairly certain this is the right way to go.

All this being said, here's a short(ish) list of what I think are good and effective studying habits for getting your homework done and remember all of the big important info for your exams.

- Study early and often - don't wait until the last minute (i.e. don't cram!) to begin actively engaging yourself with the material. A 15-20 minute review of the lecture after you've gone to it will be more helpful than trying to remember what the professor said six weeks from now.

- Don't cram! My wife, as an undergrad, ended up spending three straight days awake to finish projects and papers and to study before her finals one semester because she waited too long to start them. I've been a little more straightforward with her as she studies for the GRE, which I think has helped (she is lucky in that she is a pretty iron-clad memory, so she can get away with this more than others, but I think that this is the exception rather than the rule).

- Read the textbook (or lecture outlines) before looking at the material. I've heard a number of professors extolling the text as a means to fill in the gaps not covered in lecture, only to have students look at each other dumbfounded as if to say "we have a text?". Previous knowledge (not necessarily understanding, mind you) can make the lecture material more easy to digest and will produce questions that you can have answered in class.

- Take advantage of resources (professors, TA's, tutors, Chemistry Learning Center, etc.). If you don't understand something, get clarification rather than waiting until the end of the semester to unload the "I can't fail this class what can I do to pass" email.

- Try to limit the distractions in your study area. I've heard before that there are associations made with studying/memorization that can help with memory recall, but this can work against you if the only way you can remember the Krebs cycle is when you are listening to Destiny's Child (or Snoop Dogg or whatever the kids are listening to these days... what is it, anyway? I have no idea...). Strive for an environment in which you can occasionally take breaks with email, Facebook, etc. but not have it ringing in your ear the entire time. My biggest flaw nowadays is having access to all of these technologies I didn't even have in college (didn't get an MP3 player until grad school) - now I can't seem to put them down, and it definitely affects my study habits. As a guy who's going to be in school for a while longer, this is a problem!

- Make a plan and stick to it - my best friend in college (well, my best non-human friend) was my assignment book, because it gave me a list of reasonable goals to achieve. I didn't say "I have to study", I said "I have to read a chapter of chem, answer these 10 calc questions, write a 2-page essay, etc.". I heard a story on NPR last night whose main focus was on the fact that it's easier to solve a problem once your means for solving that problem are identified, i.e. you give it an endpoint. Saying "I need to study" doesn't give quantifiable goals, just a big problem looming over your head. By giving it goals that can be achieved by known methods in a certain time-frame, you put a face to that name and make it easier to come to a good conclusion. Homework done, more time for silly cat videos.

In conclusion, studying is an important part of learning, and by following these suggestions (or at least pondering the utility of these suggestions) it may become a task that's much more reasonable than staying up all night cramming the night before an exam. It may not be as exciting as that, but I'd rather be rested and refreshed before my exam than jittery because of all the 5 Hour Energy I just downed. Just saying.

Taking Advantage of Your Resources - Library Edition

2011-02-04T10:45:00.000-06:00

Just a quick post, since I wanted to mention my thoughts on this.

Too quickly these days we tend to go straight to the almighty Google for our information. Don't know a fact? Google it. Don't know how to run a flash column? Google it. The internet, along with associated sites that are being developed by scientists to aggregate protocols such as OpenWetWare (and other sites that we've put up at the links page on our group website), provides an excellent resource when you're unsure how to do a certain technique or need a piece of information.

BUT there's a tendency for too much information when you need a particular technique. I myself, for example, am looking for ways to purify oligonucleotides by methods other than gel or HPLC, since I haven't had a great deal of success with using them for whatever reason. Another grad student in my lab suggested Prep TLC, a technique which is fairly easy to do and may solve my problems associated with not knowing where my product is eluting.

So, I went to look it up... and wasn't too happy with the results. With the abundance of information available, it's difficult to suss out the good info from the random protocols and websites that, technically, match with my search but don't give me the information that I want. There was one site with great pictures and positive feedback on using Prep TLC to purify oligos, but because it is a company that synthesizes custom oligos they can't say how they did it. Not helpful for me. I also found book chapters on Google books, which is nice but only certain pages were available, and I was implored by the Google to purchase the book for $200.

I was then reminded this morning that I should check the Chemistry Library to see if they have the book. Turns out they do! Along with a handbook for HPLC! And, since I'm a graduate student, I get to take the books out for months and can check them out again unlimited times! Importantly, the book has exactly what I'm looking for and the information I need to get my work done.

The point I'm getting at is that we often overlook the resources available to us in favor of the quick and easy fix (i.e. the Google). Depending on your location, you probably have more resources available to you than you think, and if you're anything like me you need some poking and prodding to get the information you need from those resources. When trying to solve a problem, whether it is a technique you need to learn or troubleshoot, or needing some more information on a particular reaction, don't go straight to the internet for help, but look for resources you may not think about, like the library. Who knows, you may find the exact thing you need without nearly as much sifting necessary to find that same piece of information through all of the crap on the internet.

And hey, books, right? Who knew?

Have You Seen This Weather?

2011-02-01T22:03:00.000-06:00

Apparently there's a big ol' blizzard happening all over the place! It's so bad that they ended up canceling classes down here at the U of I tomorrow. Holy cow!

Anyway, down where we are, rather than snow, we've had hours of sleet and hail. Not only did this give everything a nice layer of ice, but those hail pellets kind of hurt!

How do I know? Well... I went running in it. Not the best idea!

When Life Gives You Lemons...

2011-01-31T13:50:00.000-06:00

... throw them back!

It's been an odd day here. Over the course of the weekend I went from optimistic (reactions are starting to work!) to fretting (there's a paper that looks similar to what I'm doing and the HPLC is getting clogged up!) to optimistic again (the paper actually supports our strategy and I have a solvent method for the HPLC to get it fixed up) to today, where my optimism has been shattered (well, not really shattered, but definitely punctured slightly) by a string of problems.

First off, it appears that either I am a doofus or someone else got all up in my business, because when I got here this morning the speed vac pump was off. This wouldn't have been a problem, but it appears that it may have not been on from the time that I supposedly turned it on. I'm not sure what happened (whether someone decided it needed to be turned off or I was just not thinking) but the result ended up being me turning it on this morning, causing a mess and having half of my solvent into the cold trap. Not a good start!

Following up that gem, I went to try and unclog the HPLC. I have been having problems with it ever since I started trying to purify click reactions on it. Going to the literature, it appeared that I shouldn't have any problems, but some combination of the product or starting materials or copper salts ended up causing an aggregate in the column, and no manner of solvent combination has been able to get it out. I tried polar and non-polar solvents, and even the magic solvent that should have taken care of the problem (isopropanol) didn't have an effect. I'm now waiting for a repair person from the electronics shop to come over and give it a look (there's a problem with leakage as well, so it was going to require some repair to begin with, but even so - I have a lot of compounds that I want to purify that I can't until this is fixed!). The only good news (and example of making lemons with lemonade) is that it may force me to look into other purification methods, including prep TLC and gel purification techniques.

I wanted to go get some lunch at Sandella's on campus, and it apparently closed down! What??

After this string of annoyances, I'm trying to re-evaluate my plans and make sure I have a new strategy that takes into account these issues. Like I said, if the HPLC is down, then I have to come up with new purification methods, which may end up being easier than what I had been doing.

In other news, apparently there's a blizzard coming to our little down, which is nice because I've been jealous of my home state and the east coast for getting so much snow! (I know, I know... probably would feel different if we had it here, but still! It's in my blood).

Back to the grind...

The Effects of Beards on Distance Running Performance

2011-01-28T17:29:00.000-06:00

There's been a lot of talk recently about American marathon runner Ryan Hall. Not only did he recently leave the his coach and teammates, but even more recently he arrived at the Houston USA Half Marathon championships sporting a tremendous beard. This has prompted people to wonder many things, not only why he would sport such as epic beard, but will it have any effect on his performance this weekend, should he keep it?

Bearded runners have had their moments throughout running history, and for the most part have been met with successes. A recent article looks at some of the best of all time (i.e. the last 20-30 years or so). I'm pretty sure the last American winner of Boston, Greg Meyer, was sporting a pretty sharp looking beard as well. The question, though, is how does the beard affect performance? Clearly a beard may be necessary for an American to win Boston, but is there any science behind it? A quick search on Pubmed for terms such as "beards and running", or "facial hair and exercise" don't seem to yield any particular results. I implore those of you with scientific backgrounds to let me know if you find anything!

As a means of starting this scientific topic, I present to you a quick glance at my own marathon performance as it relates to facial hair. The sample size is small (n=6) but it does seem to indicate potential "performance enhancing" properties of having a beard versus some other type of facial hair. So, in order:

Sample 1: Chin beard and sideburns; Marathon time: 4:11:14

Sample 2: Chin beard and sideburns; Marathon Time: 4:49

Sample 3: Chin beard and sideburns; Marathon Time: 4:10

Sample 4: 2-week full beard; Marathon time: 4:19

Sample 5: 6-week full beard; Marathon time: 4:01:06

Sample 6: Chin beard, mustache, sideburns; Marathon time: 4:13

So, what does the data tell us? Unfortunately, not much. I wanted to have the trend be that the more facial hair I have, the better I do, but it doesn't seem to be a linear curve. Although I will point out that the 6-week beard did perform much better than the 2-week beard, but there may have been other factors (primarily the fact that Chicago 2008 SUCKED) involved.

My preliminary conclusion is that advanced beards do have some mild effect versus less advanced and/or chin beards, but I need a larger sample size and better training to verify this claim.

Thoughts on further studies would be appreciated.

(Also I'm trying to get an excuse to be allowed by my wife to grow a beard, so scientific data would be helpful in convincing her!)

The Great Weight Debate*

2011-01-26T12:17:00.000-06:00

(Or... "Making Good Food Choices"... or... "Why I Am Eating Veggie Nachos for Lunch")

A recent post over at Science-Based Medicine entitled "Why We Get Fat" continued an ongoing debate about the reasons why we as a country (and world, really) seem to be continually moving in the direction of increased weight gain and obesity, despite the myriad of diet fads and meal plans and engineered diets that put us in a state of ketosis and, probably most importantly, the ever increasing scrutiny with which we analyze why we are getting more obese. The content of the post - a particular journalist citing why carbohydrates are the cause of our problems - is less important than the overarching fact that we don't seem to know both why obesity rates are rising (and they are, despite arguments to the contrary) or how we can combat this epidemic. Lifestyle changes seem most ideal, but as a society we want it done and we want it done now, opening the door for these fad diets and potential obesity drugs.

It is my personal opinion that the calories-in/calories-out model is the best way to determine weight gain and loss. In a simple way, it describes that you require a certain level of calories for function on a daily basis - consume more than that requirement, and it gets stored for later; consume less than that requirement, and the energy will need to come from another source (i.e. your stored energy). It's a simplistic model that focuses on energy consumption which, scientifically, makes a lot of sense. Where many of these fad diets can come in, claiming that a certain macronutrient - fat, carbohydrates/sugars, protein, etc. - is the cause of our problems primarily stems from the fact that a) we often consume a lot of these particular nutrients, and b) if we create a deficit of the particular nutrient without replacing it with something else, we're going to cause a deficit that leads to weight loss. Occam's razor, people - if you reduce a macronutrient, you reduce the total number of calories, and you reduce the weight. Makes sense, I think.

As runners I think we're acutely aware of this phenomenon. Starting off an exercise program often leads to weight loss simply because you are introducing a large deficit to the system that, because of previously established eating habits, is not initially replaced by calories consumed. Those big gains (or, rather, losses) eventually level off as you adjust to your new lifestyle and begin consuming additional calories to make up for deficits (i.e. you start to get hungry after working out). I myself have been a runner since I was 12, and the only time I ended up losing a lot of weight in the past 15 years was when I was training for my first marathon, when I increased the number of calories I consumed substantially but had not yet gone through the adjustment to my diet. Since then I've run 5 more, without significant weight loss (in fact, I've gained weight during training on occasion) because my body knows what's coming and adjusts accordingly. Running or exercising for weight loss, under circumstances in which you've been doing it for a while, requires additional changes in diet and/or exercise routine to see new losses.

The question then becomes how those adjustments can be made. As I've mentioned, it doesn't seem like cutting any one particular nutrient will lead to sustained weight loss (i.e. keeping the weight off), so a different plan of attack involving careful choice of what and how much you eat will lead to the most positive results. My brother's dramatic weight loss this past year using the Insanity program came as a result of not only working his ass off every day (and holy cow, I was training for a marathon and I was dying after a "rest week" workout) but by using the accompanying nutrition guide to plan out meals that had a good combination of macronutrients as well as a good portion size. Without having to cut out a particular nutrient (but cutting out "empty calories" like beer, chocolate, etc.) he was able to sustain and maintain a substantial weight loss that could be relatively easily maintained as long as the diet was adhered to.

In the end, I think the real challenge here lies with the individual, not with the principles behind the diet. There is a great deal of evidence to suggest that control of calorie intake, not through restriction of certain foods but by acknowledging that foods have a certain number of calories, leads to the best and most sustainable results. This not only allows for a better control of diet, but can also highlight how certain foods can be substituted in and out of a diet depending on the desired outcome. I think my favorite example of this is energy density - in simple terms, how many calories a certain volume of food has. My favorite example is comparing a baked potato to a serving of french fries - having a full baked potato loaded with fixings ends up giving you the same number of calories as a small serving of fries, due to how the foods are prepared (i.e. deep frying puts more calories in the food). You can get a smaller number of calories from a food with lower energy density, but feel full because you've eaten a larger volume of food. This can produce that energy deficit, making your body rely on previously stored nutrients (i.e. body fat), helping you lose weight. It's simple!

To the point - why did I eat the veggie nachos? Because I got beans instead of meat! Fewer saturated fats, lower cholesterol, and I still feel just as full. Simple choice, but one that can have lasting benefits both on the road and in the lab.

*This post is primarily opinion but my opinions are generally backed by anecdotal and published evidence. Get into the literature (I suggest starting at Pubmed) if you're unconvinced about the calorie thing. I'm pretty convinced, but that's because I'm a fan of science!

Re-Introduction

2011-01-23T21:52:00.000-06:00

Well hey folks, I've come to the realization that I've been getting a bit more traffic here as of late, so it may be worthwhile to write a quick "hey how are ya" post explaining who I am and what I do!

(also it'll be a good way to kill my last twenty minutes of tutoring, to which no one has come for help tonight)

So, let's see - I'm a late-20's Leo (although, depending on your classification system, I may be a Cancer) MD/PhD candidate runner husband who grew up in the suburbs in Minnesota but now lives in the cornfields of Illinois. I've been enrolled at the U of I down in Urbana for ~4.5 years (i.e. half way through my fifth year), where I currently split my time (about 75:25) between thesis research and medical school. My research interests (as listed on the short "about me" blurb on the left) focus on chemical biology, organic synthesis, and genetics, and I spend a little bit of my time on each of those subjects while conducting lab work. I'm about 1/2 way through the first year med school course load, with the hopes that sometime soon I can finish the rest of that and move on to M2. What do I want to be when I grow up? A doctor, probably. Not sure what kind yet, although I've been shadowing in family practice and think that working with patients is interesting and exciting! Maybe focusing on genetic diseases?

As I said, I'm a runner - I've run 6 marathons, 3 half-marathons (2 official, one unofficial but I followed an official course), and a whole slew of 10K's, 5K's, and trail races. I have several goals this year, including 2 more marathons (maybe), a 50K (more likely), and winning the race circuit in my age group (most attainable). My marathon PR is 4:01:06, and I hope to be able to break four hours!

I'm also a husband, having been married for nearly 5 years and having dated the same young lady for almost 12! I am an old man when it comes to relationships.

What do I write about? Well, originally I was going to focus solely on research topics and the grad school experience, but more recently I've branched out into a number of areas, primarily running-related, with the occasional story about how gross it can be to be a runner (see the archives if you're interested). Sometimes I write about diseases I've been studying (or, in the case of acid reflux, I actually have) or discuss my experiences shadowing in the clinic. Other times it may be about what kind of things you can do to be a better co-worker in the lab. Looking back at my original "manifesto" in blog post #1, it's really about chemistry, medicine, life in grad school, and anything else you care to know about!

Thanks for reading, tell your friends, etc. Only you can help to make me a little bit more internet famous.

On Finding a New Path

2011-01-21T16:17:00.000-06:00

Any of us who are involved in research have a very good knowledge of the fact that the best laid plans are often met with multiple road blocks and obstacles, requiring many changes in order to make it through those problems and come out the other side with something interesting and important to the advancement of science.

In other words - sometimes things don't work, so you need to come up with a new plan.

One of the big themes that seems to have taken hold of this blog is the continuous need to change and redirect the path toward the ultimate goal, whether it is finishing a thesis, planning a set of reactions, or otherwise. I'm once again re-evaluating my plans and making observations that will help me move forward with what I'm working on, both in the lab and in other parts of my life.

For example, I've spent a good amount of time fighting with PCR, a technique that, while well laid out and relatively easy to perform, is not without its nuances, requiring a certain level of understanding of each parameter in order to change and adjust and find a method that works. Even at times when you think you've figured it out, it can change on you in an instant, necessitating further manipulation to get the desired products you want. We recently acquired a new PCR machine (thanks mostly to me!) and I was excited about the prospect of having the machine available and at the ready for use. Until, of course, I couldn't get my reactions to work. No matter what I tried, no products. I tried different templates, different annealing temps, different extension times, different enzyme mixes, different primers... pretty much every parameter I could try. I went through different tutorials, all with no avail. Thankfully, all of my meticulous analysis led me to this site, and reading through it I figured out the best way to get my results - reduce the annealing temperature to the point that, while I would get side products, would give me the products I wanted. A little gel purification, and I have my product and my method to make more when necessary. By re-analyzing my methods, I found a way to the conclusion I want!

Quite often looking back at your previous data can give you clues about what's going wrong. Another example - I work with conjugation reactions such as the maleimide-thiol addition, which should be straightforward but, again, are not without their little quirks. I've been having issues with it, and I couldn't figure out why... until I looked back at some of the data. Turns out I'm adding too much reducing agent, which in turn is reacting with one of my starting materials! This may be all I need to do to fix it... we shall see. In any case, by reviewing my data and changing my path, it may provide the results I need to move forward with my research.

These are only a small number of examples, but hopefully it's clear how important continuous re-evaluation of methods and results is in order to be successful as a researcher. And this doesn't just apply to research! Training for a marathon is a great example of this - sometimes sticking to a training plan is a great thing, but if you're not able to reach your weekly mileage goals it is necessary to step back, re-evaluate, and change your path before you end up getting too fatigued or, worse, injured. I'm actually a fan of trying out different training methods, incorporating things I've learned from previous campaigns in order to come out the other side a better runner and to put forth a greater effort on race day. As I've mentioned, I'm looking at the Hanson's training methods this time around, changing around things to make them work for me and synthesizing their methods with my previous experiences, hopefully leading to lack of injury and a good race time. We shall see how this strategy ends up doing!

All in all, my advice is to go back at regular intervals, see what works and what doesn't, and to re-direct your path toward the way of least resistance. It will make life easier and will probably get you those results that you've so desperately been looking for! At least, that's what I want to have for me...

Whoops

2011-01-20T08:49:00.000-06:00

Well, looks like I missed the blog's 2-Year-Annual-Blog-o-Versary on January 4th.

I thought it was later...

So, Happy Birthday to my little slice of internet.

Here's to another year!

On the Benefits of Undergraduate Research

2011-01-15T13:06:00.001-06:00

This morning I had the chance to have coffee with a former undergrad, as well as the labmate who was in charge of her before I took her under my wing a few years ago. My undergrad, who I will call Julie (since that's her name) graduated this past spring (almost a year ago!) and has moved on to bigger and better things in life. She chose to go into a medical field, currently working in physical therapy and starting up with physician's assistant school in the fall. I'm pretty proud!

It's interesting to think about how important doing research as an undergraduate can be to future endeavors. Depending on what your chosen career will be following your undergraduate schooling, getting that research experience can play an important role in determining where (and if!) you get in. As the ebb and flow of funding continues to determine how many people can get into chosen programs, having better and more interesting experience than everyone else is key to getting the proper training for your future career.

My experience as an undergraduate researcher, for example, relied a lot on the variety of different activities, which has both advantages and disadvantages when applying to graduate programs and even jobs. I did research stints in several different areas, ranging from pure chemistry to immunology laboratories, doing different things such as ELISA assays and attempting chemical syntheses. This, of course, was on top of the course-work I had taken during my undergrad years, which, while important, is only the minimum required for entry to the next level of education. The good part of this variety was the fact that I could say that I had tried a different number of techniques, rather than sticking to a single set of required tasks (i.e. just doing peptide couplings). The disadvantage, however, was the fact that I had one of those "knowledge that's a mile wide and an inch deep", meaning that I didn't spend enough time with a single project to really see it to its conclusion. There are students who work in our lab right now who have spent several years(!) working on the same project, with the hope that they will get the results necessary to publish their work. Unless they are doing many different things, however, it's possible that they will be stuck with the "single technique" experience.

Having spent time thinking about this on occasion, my overall recommendation is to find a variety of different experiences as an undergraduate. This will not only make your resume and applications look more appealing to those recruiters who are trying to get the best people possible for their jobs or programs, but will help you to better understand what your interests are and what kind of doctor/grad student/employee you want to be. For me: research in 2 different labs over the summers of 2004 and 2005; shadowing experiences in different areas including ophthalmology and oncology; work experience in a restaurant and in a factory (ask me about that one sometime); experience as a teaching assistant and tutor; and a good academic record with a number of accolades. As I've mentioned, the only thing I'm not happy with was the fact that I didn't spend enough time with my research experiences (especially the one at my undergrad institution).

If you are an undergraduate student or have been one, what kind of experiences have you had? Did they help with your applications or job searches? Let everyone know!

Okay, Here's the Deal

2011-01-14T08:58:00.001-06:00

Not a whole lot going on here blog-wise, but I thought I'd let you know a few things.

1) Undergrads are back on Monday, which means I start tutoring again the following week. Time to brush up on my general chemistry for another semester of saying "um... well, let's look at your lecture notes... do you have your text?... what page are you reading?... oh, here's how you get the answer. ::: 5 minutes pass ::: OH That's how you should have done that problem!"

2) Med school has started up already. Immunology. And I will be shadowing a few more times in the family med clinic this semester. Fun stuff. Ask me what I want to be when I grow up! I'm working on it.

3) "Marathon training" officially started up this week. Actually, I take that back. It apparently should have started two weeks ago, but I didn't have the training plan in hand yet, so I just didn't worry about it. I've kept my mileage up, though, so I am getting into it at the correct mileage volume, so that's good. The plan I'm going to use is the Hanson's plan laid out in RunnersWorld last month. It calls for more miles during the week, but the long run peaks at 16 miles, which may be better for my hamstring than those 20+ mile jaunts. Plus, I've run 6 marathons, so I'm pretty confident about my ability to get through one mentally, despite not having gone the distance in training. I've run over 20 miles plenty of times!

4) Research is moving along. More to say on that later.

5) Looking for interesting things to talk about on the blog that relate to anything I'm interested in, science or otherwise. Any thoughts?

More to do today, so I'm off to do it. Good times.

All That's Old Is New Again

2011-01-10T14:44:00.001-06:00

I've been running for something around 15 years now, and in that time I've run races ranging from the 5K to the marathon. Although I never really paid attention to my times early on, I've been finding recently that websites such as Athlinks have been doing the job for me, accumulating different races that I've run in the past and letting me see how my times have changed since I ran cross country back in high school.

The result? Looks like I've been slowing down! Surprisingly, though, there are a number of races that have times much faster than I could have imagined. For example, I've run two official half marathons, one in 2004 and one in 2010. This last year I ran the Illinois Half, a completely flat course, in just under 2 hours. Pretty good, right? Well, it turns out my half marathon PR, set back at the Gary Bjorklund Half, is 1:47. That's a pace almost a full minute faster than the pace this year! Holy crap!

This trend of slowing down isn't absolute (I've actually had some random times in which my pace sped up dramatically despite races around it matching the trend), and while I feel like I'm getting faster and losing weight these days, I have no clue of whether or not I'll have the opportunity to get back to that form. Holding an 8:17 pace for 13 miles sounds like a daunting task now, considering how difficult holding a 9:09 can be for 26 miles. Can I make that change and get back to that form? Perhaps.

The point I'm leading to is highlighted by this particular example - it's really easy to look back on past performances and wish that we could continue to be that way, but it's really difficult to recreate those experiences or events after they've already happened. Graduate school has shown me, more than anything else, that you can't focus on how great you were in the past, since it's your current performance that determines what works and how well you do. Despite the fact that "this reaction worked before", if it isn't working now it doesn't matter how well it worked before. In the world of research, just like in athletics, you need to continue having the positive results in order to succeed, and there's no guarantee that whatever worked before will continue to be that way in the future.

Take detailed notes, and be sure to remember what made these things successful, whether they be that great race performance or that reaction scheme that worked perfectly, so when you have to recreate them they can continue to work. That way, if they don't, then you at least have a reference to go back to when experiments are not going the way you want them to.

Or something like that.

Gastroesophageal Reflux Disease*

2011-01-07T17:03:00.000-06:00

Otherwise known as... acid reflux.

Not just something that causes you to screw up your performance on Saturday Night Live, acid reflux is something that affects a large number of people throughout the world to varying degrees, ranging from mild discomfort to pain that can cause one to seek medical assistance (as it did to me this week).

Gastroesophageal reflux, which I'll refer to herein as acid reflux, is a common condition that leads to dyspepsia (heartburn) and affects abotu 40% of the US population. It is defined as the flow of the stomach's contents back into the esophagus. How does this happen? Well, under normal conditions a ring of muscle called the lower esophageal sphincter (LES) acts as a valve between the esophagus and stomach. When you swallow, muscular contractions cause the LES to relax, letting the contents of your esophagus go into the stomach. When you have acid reflux, however, the LES relaxes on its own (it has a mind of its own!), which allows the contents of the stomach to go back into the esophagus. There are factors that may help allow this relaxation to occur randomly, including a hiatal hernia (when the upper part of the stomach gets above the diaphragm). When you have acid reflux, symptoms include burning pain behind the breastbone, "gnawing" upper abdominal pain, hoarseness, difficulty swallowing, and an acid/bitter taste in the mouth.

Probably the most common cause of acid reflux in the general population is dietary and lifestyle choices. Certain foods and medications have the ability to trigger the LES to relax, causing reflux and heartburn. These foods include caffeine, peppermint, spearmint, alcohol, citrus foods, tomatoes, chocolate, spicy or fried foods, onions, and carbonated beverages (basically - all of the good things). Medications like estrogen, progesterone, tobacco, Valium, and Beta-blockers also can cause symptoms. Conditions such as being overweight and being pregnant (not exactly a condition, but anyway...) can also cause symptoms.

How would you treat acid reflux? The easiest thing to do is to change your diet and lifestyle! Avoid those foods that I mentioned above (or limit them to once or twice a day, at most); eat smaller meals at more frequent intervals rather than large meals; change your habits regarding tobacco and alcohol; and try to change your lifestyle if possible (i.e. stop being pregnant all of the time!).

Another treatment route is medication, with some caveats. Taking antacids provides short-term relief, but can be problematic in the long-term and produce side-effects like diarrhea, altered calcium metabolism, and magnesium accumulation. Certain medications can also provide longer-term relief. For example, histamine receptor (H2) blockers like Zantac inhibit acid secretion in the stomach, which can reduce the acid produced and relieve the symptoms. They act relatively quickly and can be a good treatment when diet and lifestyle changes aren't helping. Strong drugs, called proton pump inhibitors, inhibit the enzyme necessary for acid secretion and essentially stop any acid production. They take longer to work, but they can be very effective once they've gotten going. There's concern among the medical community about possible problems associated with completely turning off acid production, but these have not been accurately defined as of yet.

For the most part, treatments like these can help stop the effects of acid reflux. More severe cases require additional analysis and treatment, ranging from diagnostic X-rays to endoscopy to surgery. Fortunately, if treated early these treatments can probably be avoided.

Acid reflux, while a potentially uncomfortable problem, is rarely a life-threatening condition (just a lifestyle threatening condition!). It is a common disorder that can actually act to keep you in check and make sure that you stick to a better diet and better lifestyle choices. So, avoid those buffalo wings and eat the celery instead!

*All information was taken from the McKinley Health Center handout "Gastroesophageal Reflux Disease (Hiatal Hernia and Heartburn)", from the University of Illinois.

Sharing Equipment

2011-01-05T22:00:00.000-06:00

I know stuff like this is equivalent to beating a dead horse, but I want to talk again about a common thing that you learned about in kindergarten - sharing. Specifically, sharing lab equipment.

This afternoon I signed up for NMR time. There are protocols involved in signing up, most of which involving making your reservation online ahead of time for a short period (usually 20 minutes) and getting in and out within that time frame. That's how it should work, of course, but there's always the possibility that something happens and it takes a little longer than that to get everything finished up. As long as you're not going way over your time (which I've been on both sides of), if you go over a few minutes occasionally it's alright. I understand.

Today, the gentleman ahead of me signed up after I had already signed up, likely in the few minutes before my reservation was supposed to start. He then proceeded to go 5 minutes into my time. Now, as I mentioned, it happens, and I had 14-15 minutes of needed time for my spectra anyway, so I wasn't too frustrated or anything. He left, I got set up, and... he didn't change the standard. First sign he might not have known was he was doing. Again, another little thing, but I can understand. I do my thing, and I start finishing up my time. As soon as the clock strikes 4:50 (the end of my time) though, the same guy from before comes back to the computer I'm sitting at and just stares at me. Baffled, I finish up and walk out without saying anything.

So, he went over his time and he expected me to finish up on time, to the point of staring me down because I'm not done right at the end of my time?? Seriously?!

It baffles me sometimes how people don't seem to have respect for common equipment that everyone uses. This guy today didn't seem to understand that someone else besides him was using that equipment, and that the same rules apply to everyone. He needs to finish up on time so everyone else can get their work done on time too. For every person who respects the fact that there are pieces of equipment everyone needs to use, there are those who don't seem to understand that we all need to use that equipment, so clean it up when you're done and finish up when you're supposed to finish up!

I don't want to turn this into too much of a rant, so instead let's move it in a different direction. What to do if you're using a piece of lab equipment that everyone uses? Be sure to note if something is off when you use it - not cleaned up beforehand, calibration or background levels are off, etc. Most pieces of equipment come with a log book, so you can go to the previous user to see what was going on before you got to it. After you're done with it, be sure to reset and clean up what you've been using so that the next person can use it without having to spend a lot of time cleaning up. Importantly, be sure to note if people aren't taking care of the instrument, and bring it up in meetings, with advisers or staff coordinators, etc. Lab equipment or space that has been messed up is no good for everyone, so those who are in charge will make certain that future situations don't occur. Be consistent with the people who are making the mess, too... often times, if they don't already get it, it takes a while before they will get it.

So, if you're in a situation like I was in tonight, where someone isn't following the rules and expecting you to bend to them, be sure to tell them that they need to follow the rules too! By doing so, everyone can get their work done and no one needs to be a jerk.

Feeling a Little Too Connected...

2011-01-03T16:17:00.000-06:00

Facebook, Twitter, Blogger, Hotmail, Skype, Youtube, Google, Daily Mile, Active, etc. etc. etc....

That's only a small number of the different services that I am subscribed to online. And sometimes it gets a little overwhelming to think about all of the different things that have my contact information and browsing information and personal information and on and on and on...

Sometimes I wonder how important it is to have all of these different means of communicating with people other than face to face or over the phone. There are those (many of whom I follow on these different social outlets) who champion the idea that we can bring ourselves together virtually and, often, physically via these means of communication. To that point, I agree that it makes life a lot easier when trying to develop relationships with others from around the world. I just signed up for Daily Mile and, thanks to a shout-out from a certain podcaster, I'm now getting a flood of emails from people around the country and the world who have added me as friends due to his recommendation alone. In the future this may facilitate actual friendships with those people, and that's great!

At the same time, I always feel like I'm putting a little too much of myself out there on these various channels. While Facebook, for example, has primarily been a tool for communicating with friends with whom I have been in the same physical location, other outlets like the blog and the Twitter have been used more for a public persona to communicate with people whom I haven't met yet. I started off being a little more anonymous, but as time as gone on it's become easier to communicate more personal info (or, rather, harder to not do so). Again, not sure if this is such a bad thing, but it does lead to something else that bothers me sometimes...

... and that is the nature of these things to be constantly plugged in. If I'm sitting down, I'm almost always on internet. A great majority of the time it's not for any sort of substance (just checking Facebook/Twitter/etc.), with only a small portion being for work or other personal things (i.e. looking for Xmas presents or textbooks). This is annoying to my wife (who combats this by spending all of her time in books instead) and annoying to me because it's become pretty difficult to disconnect.

The internet is a pretty great tool, but it can be pretty hard to get away from it when you're waiting to see what thing someone is saying to you next.

As part of my resolutions, I'm going to work harder on disconnecting from the tubes of the internets from time to time, especially when interactions with others would be more ideal. I'd rather go out or to a friend's house than spend all night chatting online - not because I don't value communicating and making friends with people online, but because that deserves its own time that doesn't interfere with those people who are physically nearby!

What do you think? Are we too "plugged in" with all of these social media outlets, or is it the wave of the future (today!) that we should embrace, developing personal relationships that way instead? Or is a combination of the two most ideal?

Thoughts appreciated!

New Years Resolutions: 2011 Edition

2011-01-02T12:52:00.000-06:00

Happy New Year! I hope the year has gone well for you so far. I know, I know... it's only been 2 days, but I'm certain that you're already well into your year, working on all of the important things and contemplating breaking your resolutions... er, um, I mean, sticking with them!

Like every year for the past 7(?) or so, I'm going to make my resolutions part of the public record. Believe it or not, I had a blog before this one (a Livejournal, which has since been deleted... thank goodness) and I've spent a long time working out the important resolutions to put forward each year, some of which are slam dunks and others requiring more effort (and not always being met with success). After some thought, here are some goals I hope to achieve this year:

Make it 28. I always start the resolutions with a relatively easy and attainable goal.
Along with number 1, make it to 28 by bettering my eating, sleeping, and exercise habits. While I don't necessarily think that my exercise and health are too much trouble (considering all of the running), I still think I can improve my health by eating less, sleeping more, and keeping my exercise relatively consistent. Specific addendum - less snacking!
Running goals: 2 marathons (one spring and one fall); one trail ultra race (probably a 50K somewhere down here... I'll be checking out the local running club and related sites for relevant races sometime over the summer?); win my age group in the race circuit standings (without much effort I have gotten in the top 3 over the last two years... I think it's time to win it!)
Publish my research and/or co-author a paper with one of my co-workers
By the end of the year, be as close as possible to finishing my thesis research
Bump up my weekly average time in the lab to 52 hours per week (for the last two years I've averaged around 50... 52 is good because it's an extra few hours per week [attainable] that will still provide for greater feelings of success if I get a higher average)
Read at least one academic article per day every day of the year
Review my coursework and/or research at least one hour per day
Save enough money to be comfortable over the summer months with a smaller paycheck
Well, I can't really think of a 10th one, so let's just get out in left field... go one at least one camping trip. And win the lottery.

Okay, so I think that's a good start. I'm going to follow some others' advice as well (in particular that of The Insomniac Lab Rat) and try to start and maintain good habits in and out of the lab. I think it should be a good year!

In other news, it's almost been 2 years since I started the blog! I probably should think about what I'm going to do with it in the future, huh... we shall see!