Making Microbes Work

Tonight I'm trying out Blogger on my phone as I'm sitting in my research lab. I'm trying out something new with a reactor and I want to see how it preforms before I leave for the night. Microorganisms aren't terribly speedy though and watching this digital multimeter record a new voltage (at 1 microvolt incriments) isn't thrilling. I wish I could crack a whip and yell "Mush! Mush!" as one would to a dog-sled team and instantly reap the rewards of more power.  Pity things don't work that way.

Bad Project

I'm a bit behind - one of my labmates told me about this video today but it's pretty awesome.  A parody of Lady Gaga's Bad Romance, the Hui Zheng lab at Baylor College of Medicine put this together for the 2011 Molecular and Human Genetics Retreat (and won 1st prize!).  





While the ideas expressed in the video apply largely to those working on a PhD (I want to graduate in less than five years but there ain't no getting out here) they can also apply to anyone who's every inherited a project from someone else (I want good data...but I got a project straight from hell).

Research Posters

Made my first research poster two weeks ago.  I had never made a poster before (grade school posters don't count!) so I spent a while browsing the internet looking for tips.  These are the most helpful websites I found for me.

Scientific Poster Design
I like this PowerPoint from Cornell University because it gives text sizes for different parts of the poster (page 33) but it also has some nice tips on image file types and colors.

Advice on Designing Scientific Posters
Swarthmore College's Department of Biology did a really awesome job of putting together tons of information on scientific posters.  Their information includes sections to include and what to include in them, tips such as "posters with 800 words or less are ideal," when to use serif and sans serif fonts, and much more.  I think it's definitely worth a once-over if you're creating a poster.  I love their idea of having a button to press for a ten-second overview of the poster - great for when one wanders away from the poster.

I'm conflicted on the recommendation to color coordinate with the poster.  Clashing is obviously bad, it's always bad, but actually trying to match your poster?  It seems really weird to me.  I think a complementary color would be fine.

Other suggestions from the site include a coin envelope of business cards attached to the poster and 8.5" x 11" copies of the poster as handouts.

PhD Posters
Gallery of completed posters.  I think you can never look at too many posters to get ideas for them.

Poster Sessions Flickr Group
Gallery of many, many completed posters.  I'd rather see close-ups of the posters but that doesn't seem to be the intent of this group.


The above sites were just what I used to get ideas on creating my poster.  Do you have any recommended sites for poster creation?

Coxie's Replacement

The next phase for my research is beginning just as Coxie's replacement is coming out of the machine shop.

Newest reactor, still needs a name.  Suggestions?

I'm going to try and take this little reactor on a plane in the morning to St. Louis University.  Wish me well!

Hectic Day

In one of my recent posts I mentioned that I respond well to bribery, especially in the form of cookies. I probably should have mentioned in that post that all the students in the lab received cookies shortly before our advisor flew to Mexico for a week.

The cookies were the incentive to keep our microbes live and well, not to mention have a bunch of stuff ready to share in the weekly meeting. My weekly meeting occurs every Tuesday afternoon for an hour. It takes the full hour because I either have an experiment that goes really well (which gets my advisor very excited about what I can publish) or one that goes really poorly (which confuses my advisor and causes us to spend significant time troubleshooting the problem).

My advisor came back yesterday. Regularly scheduled meeting was today.

I have two different experiments running right now: one is doing great, the other not so much. The two experiments, combined with the fact that I was out of town since last Friday and didn't get a chance to assemble my data over the weekend like I normally do (I got back in town last night at 11:30), meant that I was frantically sitting in the lab all morning trying to put together information to show my advisor. I finished just in the nick of time by looking through my lab notebook during class and skipping breakfast & lunch.

The hectic pace of earlier today has left me feeling unmotivated to continue working on a take-home midterm I have due Thursday. I must pull myself together! While I'd love for this midterm to complete itself I doubt it will happen.

Classes, the Unnecessary Evil

I've always thought that the purpose of graduate school was to become very specialized in one topic.

For a bachelor's degree you learn a lot in four (plus or minus) years and it covers a wide variety of topics. For a master's degree you hone in on one topic from your bachelor's and specialize; becoming the master of that area. And finally for a doctorate you become really really specialized in one area from your master's degree.

I think the following comic from PhD Comics says it well with the following graph:

"Piled Higher and Deeper" by Jorge Cham
www.phdcomics.com

It's so true. And if you don't already subscribe to PhD Comics you should. Seriously.

Throughout that period of school you take a lot of classes. Because the bachelor's degree is so general you have a wide variety of options to chose from. The same, more or less depending on where you do your master's at, goes for the master's degree. But by the time you get to your doctorate all your research is cutting-edge - or at least to new to have classes devoted to the topic. So you take the classes that you think will help you pass the qualifying exams or the few that you find interesting.

Classes then become this evil, time-consuming thing that helps to foster procrastination. Why work on that journal article when you have homework to do? So few classes are applicable (at least for me) that it's almost a waste of time. Professors don't like teaching them because they take away from time they could be writing grants, students don't like taking them because it takes time away from research.

Classes at the graduate level are one of the really big differences between the educational system in the United States versus Europe. Here in the US it's classes and research until you fill the credit requirements and then just research. In Europe, or at least the UK, it's research-based where students work mostly towards the end goal (thesis/dissertation) without having to fiddle around with classes.

I'd like to just get these classes done so I can focus on my research! Especially right now when I'm trying to learn MATLAB (and failing, sigh) but still have a large "to-do" list accumulating. Perhaps this is just me complaining but how do you feel about class-work at the graduate level?

Nail Bitting vs Sickness

This fall I've been pretty sick. The current score is Research 0, Sickness 3. Basically I've been sick for the last three weeks and it's been a pain. The urge to sleep all day, the puffy sinuses, the throbbing headaches, and let's not forget my nose.

What gives? I'm usually really healthy. In fact, I'm usually the one who picks something up, walks around with it for a few days with no symptoms giving it to everyone, and then marvelously gets over being "sick" in a matter of hours. I'm the carrier! I don't get sick! I've attributed this tendency to my hearty Minnesota blood but uh, that seems to have failed me now. Plus there was this article last week in the New York Times about how my body may not have been "making the normal amount of inflammatory agents. "

So what's this different about this year as opposed to all the previous ones? This year I suspect my nail biting habit may be playing a part in my ceaseless illness. I'm a horrible nail biter, especially in times of stress (can you say graduate school?). Countless times I have bitten my nails down to bloody, painful stubs. Countless times my eyes have welled up with tears because of how much it hurts to try and grasp something with a finger who's nail I've bitten down too far.

I can't say that nail biting is a particularly good way to relieve stress but it is a good distraction -- hold on, I've got a hang nail -- but it does pass the time. Thankfully I've been biting my nails less and less. I'm attributing it to better time management. For the first time for as long as I can remember I have finger nails that I can use to scratch/open/use and it's amazing. I am a bit fixated on them - they look so pretty now! And I'm sure George is sick of hearing "look at my finger nails! Aren't they pretty?!?!" But perhaps biting my nails was a blessing in disguise.

I started noticing something about when I got sick this fall. It always seemed to occur a day or two after I bit a couple of nails down. I was hoping to find statistics on the number of times nail biters get sick as compared to non-nail biters but all I found in my very scientific Google search was this article from a dentist. According to Dr. Connelly:

Your fingers are pretty much involved in almost everything you do. Even with frequent hand-washing, your fingers are still dirty. Your fingernails are almost twice as dirty as your fingers. Since fingernails are not the easiest places in the world to clean, there's all manner of germs and bacteria underneath there-- germs you really don't want in your mouth. And when you bite your nails, you are inviting these germs into your mouth (and chewing them, etc.) Plus, bitten nails can be jagged, and may cut the gums, allowing these undesirable germs to easily access your bloodstream. [emphasis mine]

What he said makes sense and truthfully it's a little scary. But perhaps decades of biting has helped me build up an immune system that can take on anything! Or perhaps it's just a coincidence that I'm getting sick when I bite my nails after going cold turkey in the summer. In any event, it's one more reason why I really need to keep these nails looking pretty.

"Look at my finger nails! Aren't they pretty?!?!"

I do hope George never tires of me asking him what he thinks of my nails. Especially if not biting them keeps me healthier!

Research vs. Sickness

I'm onto my second sickness of the fall season and let me tell you, it's really putting a hamper on my research. I feel so listless and tired that it's hard to scrounge up the motivation to get out of my apartment to go to my research lab.

Today I slept in past when I would have normally gotten up to start my day and so I didn't get any new papers read. Bummer. Then while I was at my school's research lab my pain killers that I took before going to class wore off and I couldn't take anymore so I went home to sleep.

It appears that my ability to research is no match to me being sick. You would think I would be more inclined to work on my paper or find more articles to read but that is not happening tonight. It's hard to focus and keep my eyes open. Plus I just set a towel on fire in my apartment and melted the top of my George Foreman in the process. Oops.

I hope I get better real fast otherwise I'm going to have to suck it up and just go work in the lab till I get caught up. And I don't want to do that!

Research: 0 Sickness: 1

Coxie Pt. 2

Hello world, meet Coxie.



What you see in the picture are three microbial fuel cells. The one on the red is a microbial fuel cell (MFC), the one on the green is a microbial desalination cell (MDC), and the one on orange is top secret for now, formerly a MDC.

Coxie was acting up today. I made some modifications to the test plan this week and that could be the reason for the misbehavior but I won't know till the week after next. Ah, research.

Coxie

A few posts ago I mentioned that I was reading through How to be a Good Graduate Student. In that article it was suggested that I should have "30-second, 2-minute, 5-minute and 10-minute summaries of your thesis ready at a moment's notice." I am not at that point yet but I'm getting there. I'm mostly not there yet because I'm still in the beginning stages of my work.

This past weekend I was at a perfect place to practice this idea: MSOE's greek reception. MSOE is my alma mater and the annual greek reception was a way for me to show support for my sorority, Alpha Omega Epsilon, and help with fall recruitment.

While there I was able to share with my sisters some of what I have been working on. I've been picking up where another student left off with desalination using microbial fuel cells. One of my sisters mentioned my habit of naming inanimate objects and decided that my three microbial fuel cells needed a nickname. "Ballcock" was suggested due to my fondness for toilets and thus my cells were named. I think my sisters were trying to come up with something embarrassing for me to say and ballcock does fit that definition. Now the name has been shortened to Coxie and that's not so bad to say at all. :)

I haven't had the opportunity to use Coxie yet (explaining where the name Coxie came from to my research advisor doesn't seem very professional) but someday I will be discussing my research with a colleague and the term will slip out. Ah, well.

Where to start?

So much has happened since I last updated. Mostly, I registered for classes and began my research.

I'm taking two classes this term: environmental microbiology and pollution dispersion processes. Hopefully taking classes and working won't be too bad here. When I was working on my masters it was pretty easy to take classes and work but I'm not sure what this school will be like.

I'm working on two different tracks with my research. I've picked up where another student left off with microbial desalination cells and am putting together a literature review on enzyme biofuel cells.

The research appointment officially started last Monday. I didn't realize I would be starting so soon! Classes don't start till this week.