Last weekend I had a breakthrough with my research that may likely lead to a timely completion of my thesis and graduation. I know I’m projecting my wishes when I think this, but after the months of frustration I feel very excited about this breakthrough. What is this breakthrough I speak of? Sometime soon I’ll write a blog entry about it. None of my friends/family really understand what I do in the laboratory (with the exception of my wife I think) – perhaps a little blog entry would make it easier to comprehend. Anyway, I’m incredibly excited about it.
I’m also smugly satisfied by the amount of programming it took to accomplish this breakthrough! Working in a huge brick building with the giant words “Biomolecular Sciences” on the top of it, I wouldn’t be surprised if I’m the only one sporting a PC running Ubuntu Linux and writing software in python to process data with matplotlib ! I need to get going again, but I just thought I’d record the joy I had when this revelation transcended upon me ^_^
I’m posting this because I wanted to charge my Motorola Razor v3 Phone from a USB port on a PC using one of those standard miniUSB cables, and you wouldn’t believe how hard it was for me to find out how! I didn’t want to do any special software imports or exports or communication with the phone – I just wanted to get my battery charged before it died! It was surprisingly hard to find the software to send power to the USB port for windows. These were the two solutions I came across.
Solution1: Install DriverTool.exe (which will add some drivers) and allow power to be sent to the phone when it’s plugged in.
Solution2: Simply use UBUNTU (booted from the LiveCD or an installation) and plug in the cord. It automatically sends power to the phone, no drivers needed!
I’m in the laboratory right now with a few minutes to kill. To be specific, I have 5×4.5 minutes to kill. I’m in the middle of performing an immunohistochemical reaction on formalin-fixed 4-day-old explanted mouse hearts. I’ve let them incubate with primary antibody for ~48 hours, now it’s time for me to apply the biotinylated secondary antibody (which attaches to the primary antibody and provides a binding site for an avadin mixture I’ll be adding next (to create an “avadin biotin complex”, or ABC)). The problem is that if I apply the biotinylated secondary antibody immediately, it might attach to unattached primary antibody (antibody that’s simply floating in solution). Therefore, I have to thoroughly wash the tissue with a mixture of phosphate buffered saline (at physiological pH) and Triton-X100 (a super-strong detergent). Between my six five-minute-washes, I have time to write.
When browsing through my old blog posts, I realized that my current collection is not complete. I used to write blogs with raw HTML (half a decade ago), then I progressed to custom content management systems, then around age 18 I began using wordpress. No, it wasn’t wordpress – it was something similar though. Oh yeah, it was MovableType (how could I have forgotten? It used a pain-in-the-butt flat file database!). A friend of mine (”majestik”?) was sold on wordpress a few years after that, and convinced to switch (it used a SQL database). Since then I’ve been using wordpress faithfully. SQL databases are easy to manage, modify, and backup. However, I recently began to realize that a lot of my old entries are not here. I don’t know where they are… but they’re not in this database. Hopefully (if I ever find time) I can go through my old backup CDs (and iomega ZIP disks – for the super-old writings) and pull out my old words and post them here. In the mean time, I’ll have to settle for the incompleteness of the current system.
That got me to thinking… How could I visualize the homogenicity of my entries (by date)? I’m sure there’s some kind of wordpress plugin, PHP script, or other tech-savvy method for doing this, but I relied on trust ‘ol python to get me through. I copied/pasted the archive list (click “archives” on the side of the page to see it) which contained the title and date of every entry on record. I then converted the text into an array, isolated the dates, and had python export a text file of only the dates of the entries. I put that into excel, and used the frequency function to generate a histogram of the number of entries per half-year period (this is a fast and useful technique I use almost daily for data in the lab).
Not to shabby, huh? Note the transition between ScottIsHot.com and SWHarden.com (I lost my original domain name (which I never intended to use anyway) due to a billing error and was forced to get a different one as a result). It appears that my reliable blog record begins at 17 and ends at 20 – that’s only about 3 years. I remember writing my first few regular blog-style posts. I don’t think I knew what a blog was back then, but I felt like writing just because. I was sitting at my desk in my room with a newly-built FreeBSD webserver. I had a simple blue-background website with some kind of reddish logo at the top that I drew in Gimp (I was new to open source software and excited to use it). I remember thinking about what to write, and decided to write about how I felt about starting college soon. I also vividly remember the day I decided to stop writing. I was sitting at my desk in a dorm room in Tennessee (I’d already completed 2 and a half years of college) and thought to myself “I’m completely overwhelmed, I feel like I’m going to flunk all of my classes, and I have absolutely no time to do this anymore”. See that tiny little excuse for a bar at age 22.5? That’s this week’s post. I wonder if that bar will ever grow to match the rest… [ponders] Okay, back to labwork!
~5 hours pass ~
I just finished giving a presentation on the conformational plasticity of the human prion protein throughout oligomer and fibril development. It’s weird; graudate school is supposed to be harder than undergraduate, but why do all of these classes seem to be the same (or less) difficulty? CORE class is different: It’s easy, but the material is abstract and requires total memorization (which is incredibly difficult since there are only two tests per semester). The class I’m referring to is a seminar course. All I do is get a paper…
Sometimes it’s the smallest decisions that impact your life the most. “Come on Scott, just pick something”, I remember thinking to myself a year and a half ago as I browsed through UCF’s graduate catalogue website. “This one will work”, I 
told myself as I clicked the “Molecular Biology and Microbiology” link. I didn’t really care what I studied, and I’d only be fooling myself if I tried to act like I wanted to study anything. The fact is that the whole graduate school idea was a surprisingly haphazard academic crutch – something I had to rely on because my career was crippled when I received my rejection letter from dental school. It was never my intention to apply to the Molecular Biology and Microbiology program. Why did I? Because I didn’t know what it was.
When I perused the other options in the field, I was discouraged because I knew I wouldn’t be able to enjoy any of them. Marine biology, conservation biology, general biology, ecology – I know what these are, and they’re ridiculous. What am I going to do with a graduate degree in marine biology? Beside, there’s no way I could sit through any more classes listening to some professor tell me about why environmentalism is so much more important than constitutionalism. The Molecular Biology and Microbiology seemed interesting only because I’d only taken one microbiology class before, and had never taken a molecular class (I didn’t even know what molecular biology was!).
That careless mouse click will either become a horrible blunder or an incredible opportunity for my future but it’s still too early to tell. I don’t know where I’ll be able to go from here, but I hope it’s somewhere. I know one thing for sure – I have absolutely NO interest in molecular biology. In summary, molecular biology studies protein-level biological processes. A gene in DNA is transcribed into mRNA, then translated into a protein which goes off and does something incredibly boring in the cell. The monotony of studying the subject in any detail is brain-numbing.
| “Does protein A interact with DNA at location B, resulting in increased production of protein C when is transported by mechanism D to the cell membrane where it interacts with ligands E, F, and G to form a protein-coupled receptor for extracellular proteins H and I so that simultaneous binding releases protein subunit J which then binds to calcium ion channel protein K allowing calium to influx signaling proteins L, M, and N to become activated by further release of calcium by calcium-activated-release-receptors so that protein kinases O and P can phosphorylate proteins Q, R, and S allowing them to dimerize and be transported into the nucleus so they can act with nuclear T and U to form a transcription factor, binding to the DNA to stimulate translation of gene V which is then rearranged as mRNA, with exons W and X switched and introns Y and Z becoming degraded?” |
While other students in the program are memorized by concepts similar to the one I described, I sit in class listening to rotating professors ramble in a manner reminiscent of incessant static on an empty radio station wondering if anyone would 
clap a few times if I stood up and screamed “I hate DNA!”. On second thought, quite a few of the students are heavily invested (intellectually) into the subject, and I’m sure they’d become quite hostile toward me. I’m not exaggerating that example either. Just google image search for molecular biology signaling mechanisms. This is an example result (the type that students like me are expected to memorize in large numbers). See how every little circle (representing a protein) has a random-seeming name? Try memorizing 100s of those little abbreviations (if you’re lucky enough to have to memorize proteins whose names actually stand for something) in bulk. I can just look this stuff up if I ever need to study it, why do I have to memorize this?
Don’t get me wrong – I admit and agree that the field can be important for medical research. It’s easy to convey how the study of molecular signaling pathways that influence disease is important. Yes, this field is a major component of medical research, especially cancer and neurodegenerative diseases. It’s just… [sigh] why does it have to be this boring. If this were my life – my future – perhaps I could learn to enjoy it, but it’s not. I don’t want this. I’d rather work at Mc. Donalds (Burger King, actually) than peruse a job studying molecular mechanisms of biological processes. Knowing this isn’t my future makes it that much harder to endure it. What is my future? When I was in high school and in the beginning of college, I was good at computers, electricity, engineering, programming, and logic-type stuff. I know that if I pursued this path, I would have excelled quickly, and gotten a job I enjoyed. Somewhere along the line I got screwed up thinking I had the grades to get into medical school. I have conversations with undergraduates at UCF in the cafeteria occasionally, and I’m sure I come across as mean when I tell them how hard it can be to get into and how it’s never a bad idea to have a backup plan. I wish someone firmly told me the same thing when I was in their position. My classmates, parents, friends, and even academic advisors were all like “yeah you can do it reach for the stars” blah blah.
A major component of my graduate work is thesis-based research. I’m incredibly thankful that the classroom-style component of the degree was finished after about a year. From here, the major component that stands between me and graduate is the completion of my thesis research. Basically, I have to discover something novel (and relevant) by designing an experiment, gathering results, drawing accurate conclusions, and presenting my work (in the form of a manuscript) for review by the scientific community (randomly selected reviewers from many universities). There are ~20 labs in the molecular biology and microbiology program I could have joined, and I was lucky enough to find the one that didn’t study either molecular biology or microbiology! I’m doing higher-level (pathology/physiology) studies investigating the effects of diabetes with the cardiovascular neural system. Yeah – the heart as brain cells on it, weird huh? Actually I should call them neurons, because a brain cell is a neuron in the brain, and I study the neurons on the heart.
Graduate school is like 3D video rendering. It’s hours and hours of work (like designing 3D models for a computer animation) followed by awkward periods of extreme boredom (waiting for the 3D animation to render). In actuality, my “work” is reading-type research study, confocal time, and immunohistochemistry (IHC) solution preparation. My “extreme boredom” comes from the short periods between experiments when I’m waiting for a batch of tissue to complete IHC. Yeah, I know I could always use my free time to start new experiments, but then when the original experiments begin to become more labor-intensive, the newly-started experiments will 
also require this labor-intensive work, and I’ll perform poorly on both of them (I try to maintain only about 4 simultaneous projects). Anyway, the reason I mentioned this is because I do have some free time (in blocks of 20 or 30 minutes a few times a day) and I would like to be able to write again. I’ve written ~1.4 million words over the years (about 7), but stopped abruptly 2 years into college (my undergraduate work was overwhelming).
I’m really sad that I stopped writing though – many amazing things happened over those two years that I wish I documented. I moved to another state, studied biology (which is INSANITY to most of the people who knew me prior to the move, who would have put big money that I would have continued a live of computers and engineering), met a cute girl, and even got married. Is this time lost? I wrote in a pen-type journal, not sporadically and in no where near the detail of this web log –the greatest accomplishment/creation/manuscript of my entire life (thus far).
Although I would desire to write regularly, I have so many other obligations. Coursework, thesis work, marriage, and planning my future are all hovering around me at the same time. Whenever I take time out of my schedule to work on one of these, it’s at the detriment of all the rest. I feel like a small piece of saran wrap trying to cover a wet bowl – It’s being stretched tightly, to the point where it seems like it might break, but at the same time the edges aren’t sticking very well, and there’s a good chance the whole thing will have to be wadded up and thrown away so the whole process can start over.
