Zoom, zoom, zooming away

It's vacation time, meaning that I'm going to be away for a while.  No lab, no papers, no reading, no pipeting...  How exciting is that?  Plus I get to soak up the sun, drink lots of wine and beer, and do some awesome shopping (I hope).  Doesn't get much better than that...

The one downside to my vacation is that the timing is horrendous.  My project in lab has stalled because I can't clone anything, but just now my cloning is starting to work.  In an ideal world, I would get all of it done before leaving, but that's not quite possible.  Sigh.  The second bad thing is that one week after returning from vacation, I have a department-wide presentation to give.  While Super PI doesn't seem to think that it's very important, it is important to me, so I need to work on it a lot before leaving so that I don't look like a complete fool upon my return.

Anyway, I'm excited to be gone and looking forward to a lovely vacation.  İAdiós!

Organizing journal articles: Why must this be so painful?

I have a confession: I hate reading scientific papers.

And that's generally a problem because I'm a scientist, and the primary means of communication in the scientific world is via publications.  Still, I can't help but hate to read them.  Why?

Because they can be so incredibly dry.  Sometimes, I can really get into papers, and I can really enjoy reading them.  But the majority of the time, I just have difficulty keeping my interest (I blame Facebook).  What's even more problematic is that I cannot always remember what was done in papers that I absolutely must remember so that my PI doesn't think I'm a complete idiot.

I'm not sure if it's just me, but I just find it difficult to read papers sometimes.  Don't get me wrong, I can certainly read a paper, comprehend every word, and discuss the paper in its entirety to anyone.  I'm not stupid.  At the same time, I just find it difficult to spend an afternoon reading papers.  Maybe there are too many distractions, or maybe I just need to smack myself in the head.  But what is wrong with me?

I think that my main problem is organization.  I accumulate papers but I don't really read them thoroughly.  The folder on my computer of papers is several gigabytes, organized by first author, year, and article title.  But ask me to find a particular paper, and I'll probably just go to PubMed.  Then what's the point of saving and "organizing" all of these papers?  I'm still figuring that one out...

When I'm about to give a presentation or talk about science with someone, I generally mop up my act by reading several papers, looking at figures, and writing down some notes.  My problem remains that I cannot seem to maintain the knowledge, and that's a problem.

In the past, I've tried a few different strategies:

1) Writing small reviews of each paper I read.  I'll make a word document for every paper I read, summarizing the main findings and the figures, as well as my "verdict" (whether the paper is good or bad).  This i helpful to some degree, as it helps me both in going through all papers very thoroughly and making a judgment on the content of the papers.  On the other hand, it takes a lot of time and isn't particularly productive - I still forget a lot.

2) Just reading a lot.  The problem I've found with this is that reading a lot of papers is just overwhelming (sometimes).  I guess that I've overcome this by reading review articles and using that as a jumpoff-point for reading other articles.  That has seemed to be rather successful.

3) Organize papers into categories.  I've tried this several times, and it's never successful.  No matter how many folders I make or how carefully I catalog my papers, I can never find the exact one I want and eventually end up just going to PubMed - what's the point in that?  I've also tried programs like Mendeley, which I found to be frustrating.  Mendeley is a bloated program that takes to long to load, isn't fast enough, and doesn't have enough options for me.  I found it to be counter-productive.  I have yet to find a worthwhile paper-organizing software program.  Papers looks good, but I use Windows...

4) Print papers and make notes on them.  It seems that every professor has a cabinet full of old papers that they have scribbled on for their future use.  In my personal experience, I don't find having physical copies of papers to be helpful - it's more of a waste of space.  Plus, it wastes trees, and who needs that?  Electronic copies are also frustrating because it's more difficult to read on a screen.  Still, I find it better than having a gigantic pile of papers.

Is there something better I should do?  The answer is definitely.  I need to find a solution that works for me. It's wasteful for me to hobble along as I have been - and it's also kind of ridiculous that I've gone this far in my scientific career without figuring this out.  My newest idea is to read papers and draw little interpretations.  I love working in Illustrator, and maybe drawing out the main points of papers will make it more memorable - plus, it's never a bad thing to have these little graphics at my disposal!  We'll have to see how this little experiment goes...

A Necessary Evil: The Office Coffee

Is that warm coffee or a
steaming pile of crap?

It's one of the most deceiving entities in the department.  Sure, it may look friendly and like it might put you in a better mood, but, in reality, it is truly sinister.  After the first encounter, it may take a while to show its evil side, and it will likely have you coming back for more, time after time.

The coffee in this department is horrendous.  And I'm sure this isn't just a phenomenon of this department either.  On more than one occasion, I have had serious stomach issues after drinking the brown concoction, and you would think that this would steer me from ever drinking it again. But does it?

No.  Nearly every morning, you can find me filling my mug with the crap.  I try to improve it by adding some creamer and sugar, but I've found that this is useless based on the following careful testing:

One creamer package:  No change in flavor
Two creamer packages: Slight change in flavor, but not appreciably better
One packet of sugar: No change in flavor
Two packets of sugar: Oh dead god, what the hell just happened to my coffee?!
One creamer and one sugar: Slight improvement (synergistic effect, I suppose)
Two creamers and two sugars:  Modest improvement; too sweet and barely recognizable coffee flavor

I've basically found no solution to making that coffee bearable, but it doesn't stop me from drinking it almost every day. Sure, there's a coffee shop upstairs, but that costs money and, as a graduate student, I have too little money to justify spending it on coffee.

The best solution I've found is to buy flavored creamer and attempt to mask the flavor with something like hazelnut or Italian sweet cream (I don't know what it is, but I don't care because it is delicious).  The problem with this solution is that I use way too much of the flavored creamer to make that coffee even recognizable anymore.  Plus, it's got a ton of sugar.

My newest solution: black coffee.  If it's so bad, I shouldn't drink it, so maybe (maybe) if the coffee disgusts me morning after morning, I will wean myself from it and drink something better, like water.  The caffeine kick sure helps, especially during those long lectures, meetings, and presentations, so I'm afraid that I may just have to learn to live with the coffee.  Plus, it's free - I'm sure not going to complain about that.

The Slump

You know that all-to-familiar time during your research when absolutely nothing will work?  I've been going through this for about the last month, and it has worn on me extensively.  It has gotten to the point where even a simple plasmid mini prep won't work.  I'll check my antibiotics, use fresh media, make brand new compentent cells, but when it comes to the simplest of all, I cannot perform a mini prep.  I've determined that it is not a problem with the kit my lab uses because I'm not able to isolate any plasmids even using the "old school" methods of phenol-chloroform extraction.

In the past, I've gone through periods like this when I'll have a bad week, but it's never been this bad before.  Every time it happens, it makes me wonder how so much could go wrong.  After all, it is science, and we're supposed to have a method to our madness (emphasis on supposed to).  How can it be that a simple process that I was able to perform only a couple months ago has completely escaped me now?  Especially at a time when I need it to work the most...

Through my (admittedly limited) experience, I've found that there are only a few ways to drag myself from the pit of desperation:

1) Start several experiments and hope that one of them works.  This is my method of choice, mostly because I like to multi-task in the lab.  The important thing for me to remember is to make sure that none of these experiments are high-priority (I don't need these results right now with this experiment) and that at least one of them will work.  It never hurts to have a confidence booster, in my opinion.

2) Stop. While I find it hard to do, sometimes it just helps to stop and do nothing for a short period of time.  Usually this makes me feel even less productive and more depressed, leading to a vicious cycle.  I've found it can be beneficial sometimes, though, to just take a coffee break and stop worrying.

3) Read. Diving into the literature can never hurt, and reading can really take your mind off the sucky things that are going on in the lab.  I like to read reviews particularly when I'm stuck experimentally because it's less intense and allows me to relax a tad.  Reading more hardcore papers can also make you feel like your problems in the lab are quite insignificant compared to the 736 Western blots required for that awesome Nature paper.

4) Start over.  Like really start over.  New media, new cells, new antibiotics, new reagents, new pipet tips, new underwear, new music.  I find it's easier for me to pick up mistakes when I have to start over from the beginning.

5) Swallow your pride and ask for help.  Sure, a mini prep is a ridiculously simple task that a trained monkey (probably even a zebrafish) could do with one hand.  Still, it never hurts to ask for help and advice because there are probably people across the hall that have run into the same problem.  Even if not, it's nice to complain to others as a catharsis.

And that's where I'm stuck.  A month later and my mini preps still won't work.  I've tried all of my tips from above, and nothing seems to work.  All seems like it should be just dandy with a *%$! mini prep, but, alas, it is not.  As with all other times in the lab, I will plod along until one day, my ability to isolate plasmid DNA will magically reappear.  Until then, I will continue to complain about it... because that's what I do.

Post-slump update: My minipreps are all in working order again after I finally figured out that the media was an old formulation and didn't support plasmid replication for some reason unknown to me.  Lesson learned, I guess.  There is still hope for me!

An Introduction

Yes, yet another blog written by a graduate student.  When I created this, I knew that it would exist among the swath of other similar blogs.  At the same time, I consider it a fun outlet and opportunity for me to be creative, regardless of whether others read my posts or roll their eyes.

I'm a second-year graduate student, studying viruses and loving every second of it.  I've survived the first year curriculum, the qualifying exam, and the tribulations of absolutely nothing working in the lab.  I have enough experience in science to (usually) know what I'm doing at this stage, but I'm learning and maturing each day.  My dream is to be a successful principal investigator, and while the journey might be tough, I'm going to continue working my hardest to achieve that goal.

There is also more to me than just science:  I love traveling, graphic design, technology, eating good food, running and exercising, and reading.  I'm also the guy in the department that you will hear blasting the Spice Girls (every Friday), Britney Spears (mostly Saturday mornings), and Paula Abdul (Tuesday afternoons).  I sing along to the radio sometimes, I wear funky glasses, and I have an adorable car.  Overall, I like to think I'm quirky... a quirky virologist.