Sunday, December 12, 2010

surely NASA has a few grand lying around...

The whole arsenic bacteria discussion is still going strong.  There's a million different angles on it, which I won't go into detail because I don't consider myself at the level of expertise to explain it all eloquently.  I'm sure a simple google search will yield better reviews of the whole matter.  Ed Yong at Not Exactly Rocket Science has reviewed quite a lot of the public criticism, and Derek Lowe at In the Pipeline has a few discussions concerning the chemistry side of things.

All that said....
I had a thought today:  why didn't NASA pony up the money for the experiments that could have* aided the whole paper? 

I don't entirely understand the benefit of NASA's actions.  First they taunt people with a press conference concerning "an announcement" two days prior....obviously they were setting things up for a big event.  Why did they do that if what they were announcing wasn't ironclad?  It doesn't make sense.
So NASA riles up the media for a big announcement....then lets down the general media by "only having Earth based bacteria" in their announcement....and then they further get egg on their face by the weak science holding the "big announcement." 

Now stay with me here...

From Ed Yong's review of the drama:

Nonetheless, later in the day, NASA arranged for a quirky lecture about the findings. After some bizarre goofing-off, [Ron] Oremland addressed a few of the criticisms. He said that lack of money prevented them from doing mass spectrometry experiments. 

Surely NASA could have ponied up the money for these experiments?  They went to all the trouble of announcing their pending announcement....which ultimately disappointed the general media because it wasn't about E.T. or something.  But....the announcement had extraordinary claims to it.  Why raise the awareness if they couldn't shell out a few grand for the experiments to properly back this up?

If this paper had hit Science without all the media being goaded along by NASA, the backlash would have been far less.  It doesn't make sense that NASA would do this....or am I wrong?  I'm not saying that there aren't some interesting findings here, but the whole bent NASA went with just seems
I don't understand why NASA would choose the higher platform for their wondrous belly flop. 

*by could have, I leave the possibility that the experiments could have also proven them wrong as well.  Who knows.

Wednesday, December 8, 2010

Make the bad man stop....

So life almost got back to normal.....
But instead, I'm bogged down with a glorified genetics assignment....

I can't even explain it. 
It doesn't help that my immune system has declared mutiny due to the abusive nutrition and sleep deprivation. 
I just need a few more days...I've promised my brain, my family, and especially the Mr. that I will unplug my brain come the end of next week.  We're due to fly back to the UK, and I dare say I might actually sleep on the flight.

The Mr. has been a saint keeping me supplied with food, tea, coffee, as well as keeping the home from falling apart.  (I did do an ass load of laundry over the weekend.)  I'm fluctuating from moments of rebellion and working on puzzles to the 14 hour work marathons where I feel like some tweaked out albino rat with glowing red eyes that's running on a hamster wheel with no inclination of stopping anytime soon.....

I'm just coming off the latter analogy at the moment. 
Oh thank christ that next semester I won't be taking classes. 

Saturday, December 4, 2010

Thank god that's done....

I made it through my paper writing last night.
I hope that never happens again.  In hind site, I should've worked on pieces here and there throughout the week, but I can't really see where that would've happened.  I haven't had leisurely days at the lab when I might sit down for longer than an hour, and it usually takes 45 min of procrastination to pass before I can hanker down.

Today I'm off to the lab to finish up some stuff....and then start work on another class project.  I have to make a presentation on Thursday, and I am NOT the queen of powerpoint slides.  In fact, I really HATE powerpoint slides.

I think it all started when I took organic chemistry.  I adore my first organic chemistry teacher.  She was fun and taught a great lab.  I think that was probably my favorite lab, despite the 8-10 page write-ups we had to turn in weekly. one hang up was that she used powerpoint slides to teach organic chem I.  It just doesn't translate.  You can't look at pictures and learn it...(at least I can't).  I need to write it.  Drawing the structures ties in the hand - mind connection for me.  There's a term for it, but I can't remember it right now, and it's driving me crazy. ETA: my friend reminded me that it's kinesthetic learning!

Anyway, my point is that I learn by hand writing things out.  I used to have 2-3 copies of every lecture notebook.  One was in class, and the other 1-2 were my re-copying them in the library like a monk.  I'm sure some people think that's tedious, but I nailed every essay exam I had in my microbiology courses.

So, back to the organic chem.  When I took organic chem II, I had a different instructor.  This guy was awesome.  He had been teaching that class for so long, that he leisurely drew out all the structures while chattering away, and his pace was never hurried.  Despite furiously scribbling down the structures I wasn't as familiar with, this felt like one of the most relaxing classes I took - evar.  The same thing was applicable to my first physics course, and calculus II.  When things are written out, the learning becomes soooo much easier.  Even today I write down notes in classes where the information is provided in powerpoint/pdf format.  Of course, I'm hoping I don't have too many more classes....but I digress.

And I just realized this was one huge digression on why I hate powerpoint slides.  Right.  Off to work now.

Friday, December 3, 2010


So the 2nd digest did not work out.  I knew I should've run that digest at 1am.
Oh well.  I'll just gear up for another big run sometime next week.

I'm trying to get my brain in the mode for cranking out a term paper that's due at midnight tonight....that I haven't really started on.  If I can just get the right ratio of coffee/food I should be good to go.

Ed Yong at Not Exactly Rocket Science (Discover Blogs) has a great write-up of the whole bacterium using arsenic finding. 

And Scicurious has a funny but spot-on review of this paper for your dose of Friday Weird Science.

Lynch, V. (2008). Clitoral and penile size variability are not significantly different: lack of evidence for the byproduct theory of the female orgasm Evolution & Development, 10 (4), 396-397 DOI: 10.1111/j.1525-142X.2008.00248.x

Thursday, December 2, 2010


My labmate just told me what the NASA press conference is going to be on at 2pm today.  She said it was leaked.

I won't spoil it for my 1-2 readers.

ETA:  Ok I will: (See ETA2)

It's not as cool as the gizmodo blurb.

In the paper published today, the researchers report that some of the bacteria could survive on arsenic and incorporate it into their cellular biochemistry. Instead of the usual phosphate-rich DNA, they observed arsenate-rich DNA. Heightened levels of arsenic also showed up in the cell's proteins and fats. The scientists used mass spectroscopy, radioactive labeling and X-ray fluorescence to confirm that the arsenic was really being used in the biomolecules rather than merely contaminating the cells.

Here is where you insert my battle cry.

Yesterday was one of those great days for experiments.  I had one of those long 12+ hour jobs going: up at the lab at 5:30pm....wrapping up about 7pm.... 
And then I had a thought.
I had plenty of energy, despite the lack of sleep the night before.  I knew that to actually see the results, I would have to run some 4-hour gels.  I have to run two sets, so that's an 8 hour wait for the next day.
Somewhere I just thought, the hell with it.  Do ALL the Science!!!

I ran the gels, and at midnight started imaging them.  I got a weird result on one.  But the result is on the cusp of being really cool.
At 1am, I wanted to re-run the digest for the weird result, which would only take 1.5 hours.  As time ticks by, the window of opportunity starts to run thin...waiting until today means the digest might not work right.

This is where the US system fails the PhD student:  I had a class at 8am this morning.
Rolling into bed ~3am doesn't work for an 8am class.  Especially since I have a full day today as well.  In Europe, PhD students don't have classes, at least not required ones.  All you do is your research.  Had I not had a class to interrupt me, I would have kept on until dawn, gone home to sleep for a while, then be back at the lab to happily continue my work.  (There's no sarcasm there.)

Instead, I got ~4 hours of sleep (thank you Spoiled Rotten Cat), and now I'm back after my class.  I'm re-running the digest, hoping it still works.  If not, I can always start the experiment all over again.  That's another 12+ hour job, but it'll be done anyway. 

Either way, I'm running on hopeful happy thoughts right now; sleep deprivation be damned.  It feels good to have a fire lit under my @ss; I've been slogging along with a lot of disappointments lately.

Monday, November 29, 2010

It shall be done!

At the end of my last post I complained about having to work over the weekend...but it's over and done now.  Hopefully the effort will yield some good data.

And today I managed to do something so far yet undone:  Convince my PI that my new scheduling of several up-coming experiments works better!

You see, today my PI wanted me to start a 3-day process that I did not want to start. 
I just like that photo.  It is not a photo of the Spoiled Rotten Cat (SRC). 

After being hunched over my bench for ~7 hours on Sunday, the last thing I wanted to do was start another big process.  In fact, my back has been aching all day.  I'm not a spring chicken. (I'm what is called a "non-traditional student.")

Anyway, I managed to convince my PI that I'll actually get MORE work done if I shift it around like so.....
And it actually worked. 

I still managed to get a boat-load of stuff done today...

Most of it is to organize part of the extra stuff I'm doing.  You see, it has recently come to light that the DLM isn't just dumb, but pretty much completely incompetent.  About 1.5 weeks ago, this became painfully known to my PI.  This was much to the satisfaction of the other grad student and myself, as we were worried that PI would think we were training the kid horribly.  We weren't; we tried to make idiot-proof protocols, but there's only so much you can do.
So the PI now knows that somehow they were duped into taking on this kid.  Thankfully the MRU is funding his one-year masters program thing.  But now my PI is stuck with him, and he's working (well, kinda) on part of project that's funded by a grant that's under review soon.  Because I have done similar experiments, I can pitch in and help out. 

And this has pretty much turned into my PI and me doing all of DLM's work...because PI doesn't trust the kid anymore.  At.  All.  He's pretty much been demoted to making buffers and cleaning the lab. 
I honestly don't know what the PI is going to do.  The DLM certainly couldn't defend his thesis.  I asked him about one of the papers (our lab's own) which is the foundation for his thesis, and apparently he can't recall too much about it. 

I suppose the PI is going to let the system work its magic.  Come the late spring, he'll have to defend, and when he doesn't pass, it isn't necessary for the PI to take him back.  I don't know how all the money or administrative jumbo works, nor do I care.  I'll be grateful when I get done doing double duty for this kid. 

Until then...I'm trying to steam ahead to the end of this semester.  I have two papers and one project for classes, plus a ton of work for this grant review.  Hold onto something bolted down; it's going to be a bumpy ride! 

Wednesday, November 24, 2010


Over at Neurotic Physiology and other bloggers over at Scientopia have posted "what are you thankful for?"  This includes an item, a person, and an idea.

I really like this concept, and maybe if you had contacted me a week ago, I would have a thoughtful, meaningful answer to these questions.* (the reason for this is below)
Instead, you get my half-assed answers:

My item that I'm thankful for:  coffee and the old coffee maker given to me and the Mr. when we move to the town where the MRU is.
My parents bought us a super nice espresso maker as an actual wedding gift, but as we were packing up, my mom found an old drip coffee maker they never used.  This thing has a timer, and THAT is priceless.  A lot of times I have to get up at about 4am for some long experiments.  There's something entirely comforting about having the coffee ready as soon as I drag myself out of bed.

The person I'm thankful for:  easily this could go to the Mr., as he keeps everything sane in the household.  However, I think that as far as my academic career's one of my non-advisor mentors.

In confession, my PI is an amazing scientist, but is also one of the busiest.  I can't say my PI is the most encouraging person, and that's ok.  Some of my classmates have very enthusiastic and animated PI's, and they benefit from the overflow of that effervescent passion.  While I would have loved to have landed in such a situation, I'm ok with the reality I have.  My PI is often too busy, and they tend to run the lab like the business that it is.  When I have times of low morale, it's good when I have to go to another facility for some experiments.  At that location I get to see one of my committee members, who is also the enthusiastic and passionate type.  Our conversations give me inspiration, and they fire me up for my ideas and my research.  In that regard, I am very thankful. 

As for my idea...
A friend once joked, "If you don't feel like a complete fraud who's in over their head, you're not stretching your abilities enough."  
I think one of the bigger mental challenges that grad school has presented is the sense of being overwhelmed.  I feel like I have more contact with various specialists in many different fields, and while talking to them you have to know exactly what they're talking about.  And most of the time it feels like I have to wing it, and then later read up on it.  

I bought a chemistry model kit after a discussion with one of our collaborators, a biochemist who knows all sugars backwards and forwards.  I could follow the discussion, but I knew that I needed to be able to look at several different molecules, regardless of how they were presented on the page, and know what from what.  It's like having to learn to think like a microbiologist, a biochemist, and a geneticist all at the same time.  When I feel overwhelmed, and "in over my head," I remind myself that this probably happens to every grad student at some point.  Unfortunately, due to the unique structure of my program, I'm kinda isolated and don't have the constant camaraderie that my peers benefit from, so this is only a guess.  The alternative is that I'm just a complete idiot...

Unfortunately, after the explosion on Saturday things continued to all go downhill.  (By the way, my PI said she had never seen or heard of an anaerobic culture causing a glass 1L bottle to explode, but perhaps the bottle had been compromised in some way which lead to its demise.)
I had been harvesting cells for both some anaerobic cultures and some VERY slow growing aerobic cultures.  I was on my feet pretty much all of Saturday and Sunday, and I still hadn't started a paper that was due on Monday.  Monday rolls around, and I'm on track.  I think, I'll get this stuff sorted and that experiment started....and then I can get home and start on my paper.

And about halfway through the day, my PI and I were looking at the data, and slowly....but then very surely, we realized that all of that work was for naught.  Despite harvesting all the cells that I had, it wasn't enough.  There was no way of knowing this until we got there.  I think I saw genuine sympathy in my PI's face.  I was exhausted, and I understood that I was about to be cheated out of my Thanksgiving Day weekend.

Frustration and anger gripped me all day Monday, and I realized I had to snap back into it to churn out a paper by 10pm that evening.  Tuesday I woke in a zombie state and sat through another class.  More stuff surfaced that I have to get done.  The numbness helped in my resignation that there will be no rest until I board a plane for the UK in late December.  The project manager of our grant has requested a review of all data on the 16th, and due to the DLM, we are scrambling to get his data.  (There's more to that story, but that's another post.)

So sometime around 10pm tonight, the Mr, the Spoiled Rotten Cat and I will trek up to my parents for Thursday and Friday, and then we'll be back on Saturday for me to continue harvesting cells.  I'm ok with this now, but earlier I'm not sure I was.

Saturday, November 20, 2010

Things that explode and my new definition for "frisky."

This is not the explosion that occurred, but I would have preferred this:

I have some big experiments coming up, and I need a TON of culture to complete them.  By a ton, I mean 3-4 liters.  This includes my anaerobic cultures.

I spent the week cultivating some awesome dense and fast growing starter cultures of about ~80ml.  I call these "frisky" because if I take a syringe full of nitrogen, and push the needle into the bottle, the culture spurts into the syringe before I can plunge all the nitrogen gas in.  I tend to put personalities to my cultures, and for whatever reason, the first time I saw this happen I thought, "well that's frisky."

The culture is producing hydrogen gas, and it grows so fast that there's TONS of pressure in these small bottles.  I use a small amount to re-inoculate smaller starter cultures, and hope to relieve some of the pressure.

Then, under nitrogen gas, I open the bottles (they sound like champagne bottles popping), dump the culture into my large 1 liter jars, and seal it up.  These are then incubated at 85 degrees C.  Dumping ~80ml of culture into ~1 liter dilutes the culture, and I'm thinking that by ~24 hours, these bottles will be ready for harvest.  Easy peasy.

Today I'm well rested, well fed, and walking up the stairwell.  I should explain that our lab is in a bit of shambles, and we're in the process of moving soon, so the high temp incubators are in the hallway.  The moment I turn down the hallway....I smell it.

Instantly I know that something absolutely wrong has happened with the anaerobes.  
Basically, they ferment the sugars at a high isn't a good ferment like beer, it's an evil waft you get when you have food gone wrong in your fridge.  And it's still 25 feet from where I'm standing.  THAT is how horrid it is.

And in the back of my head, I knew something like this could happen.  I just thought that it would have taken more time.  
The leak of culture is so bad that it's triggered the sensors to go into error mode, and the heat has shut off.  I open the incubator, and thankfully only one of the four liter bottles have exploded.  I still have 3L left (which is sufficient for my experiments).  

But this wasn't a leak.  This was an all out explosion.  The rubber stopper is still lodged in the neck of the bottle, with the cap in place.  There are bits of shattered glass EVERYWHERE.  I think that must be a LOT of pressure.  

And I should've known better.  There should have been more head space in the bottles, but I'd been having problems with oxygen getting in the media, so I decided the less, the better.  
Fortunately, because the incubator shut off, the temperature dropped, the remaining culture quit growing, so they didn't go 'splody as well.  

But boy, are those cultures dense.  Here's a comparison of an un-inoculated culture (with some oxygen in it, hence the orange/pink tinge to it) next to one of the surviving bottles:

So yah....I'll be cleaning and cleaning....and cleaning again.  I've notified my PI, and I'm worried that I might have damaged the high temp incubator.  The sad thing is...I showed up ~17 hours after I inoculated the culture.  Had I been a little sooner, it might have been avoided.  And I'm curious as hell if it made a huge bang or anything.  Tiny shards of glass were stuck ALL over the incubator.

I'm also lucky.  If I had arrived earlier, I could have removed the bottles, and that one particular could have continued to grow and produce gas and pressure while sitting out on my bench.  In which case, it could have exploded near me, spraying glass and the bog of eternal stench onto me.

I also hope the smell dissipates a ton before Monday.  I'm about to become quite unpopular in my department.

Thursday, November 18, 2010

A good day

Today was one of those days that strangely turned out for the better.
There's a TON that needs to be done in the next month, and it almost feels overwhelming.  I was trying to get things going while working with the anaerobes when the nitrogen ran out.  Thankfully I was able to call someone up and get another for tomorrow morning. 

Then something strange happened.  With half of the work unable to be done, everything else got done!  I got just about everything I'd been meaning to do over the course of 6 hours...and then I didn't stop.  I organized my entire bench, updated the lab books, and managed to step out on campus for a cup of coffee. 

In the early evening, I had the option of going to a discussion panel, but I found that I wanted to continue the flow of things and set to task some things I had been putting off.  Today I truly did ALL the science!

If only everyday felt as easy and flowing as today.  I guess I get overwhelmed with the "so much to do" thought that sometimes I go into overload and my brain shuts down.  When things were automatically taken out of the to-do list by necessity, everything was so much easier. 

I even get to sleep in until 7:30am tomorrow!  THAT is awesome.  I'll probably be at the lab all weekend, but Thanksgiving is on the horizon.  The Mr. and I are looking forward to driving to my folks' house with the Spoiled Rotten Cat.  It feels good to be optimistic occasionally.  It's going to be awesome to walk into the lab to my clean bench.  And with the nitrogen tank delivered tomorrow, I can finish off the other half of all the science. 

Thursday, November 11, 2010

I try...

In the spirit of having consistent posts....

I'm waiting on the autoclave, so to kill time:
There's always one in every lab I think.  I've only been in two, so I don't really know. 
And I always try NOT to be that one.  You know, the dumb labmate (DLM).

This does not include the learning curve that new members have when they're integrated into the lab.  Everyone goes through it.  After a while, you find your groove, and you understand how things work.  As you continue to run experiments, you start to trust your instinct.  Unless being in the lab is your *first* non-class lab experience. 

The DLM was in chemistry as an undergrad.  He took some basic micro, so he's been introduced to the principles.  And I encourage asking questions.  I've told the undergrads to ask as many as they want, as that's what I did as an undergrad.  That goes with the territory.

But the DLM doesn't seem to be getting it.  At. All.

Exhibit A: The DLM is asking a ton of questions as usual about a certain protocol.  I didn't write it, so today he's asking the another labmate who did.  I'm not paying too much attention, but I hear this:
DLM:  So do I leave the lid on?
Labmate:  Yah.
DLM walks away.
Me:  Leave the lid on what?
Labmate:  The centrifuge.

*cue the confused look on my face*
When is it ever a good idea to leave the lid off a centrifuge when working with culture? 
I wouldn't care so much...but tomorrow I'm rolling into work early just to babysit the DLM through what is most certainly a straight-forward TCA extraction that should take 20 minutes to complete.  The sad thing is, I know there will be tons of commonsense questions, on a procedure he's already done. 

Part of me knows it isn't being dumb, but more lazy. 
Over the weekend, one of the keys to a room the lab uses was missing.  Often someone will accidentally leave the key in the room.  DLM called me to ask if I had it.  I didn't, but I suggested he simply call security and have them let him into the room. 

Without missing a beat, the first thing he said was:  Do you have the number for security?
That's laziness on a grand scale there.  The brain hurts from the laziness.  Security numbers are posted in every room and on the lab doors.  Everyone knows this.  And yet he though I would just have it handy on my laptop or something.  WTF?

Wednesday, November 10, 2010

The worst pun evar....

I just had the worst (or best) pun ever.  I was explaining to my labmate how my advisor suggested using the same media for two of my anaerobes.  This would theoretically simplify things.  Making the media is generally a pain in the neck as I don't have an anaerobic chamber.

Actually, we do have one at the lab, but my advisor is loathe to set it up, as we don't have the space.  Instead everything is made by boiling oxygen out while flushing with nitrogen gas.  Hence, working with boiling liquids while trying to pour it into bottles, which then bubble out at you as the nitrogen does its thing....all while trying to work as quickly as possible to prevent oxygen getting into the a pain in my @ss. 

Thankfully I've also become more comfortable working with syringes.  All inoculation and addition of any nutrients, etc. are done by syringe into the sealed bottles of media.  I admit at first, I had a lot of torn gloves and thanked my luck that I hadn't stabbed myself.  I'm naturally accident prone and clumsy, so getting the hang of working with needles took some time.

I really didn't want to relive the scene from Four Rooms.

But I digress....

For whatever reason, both organisms prefer* different media types, despite what is in the literature.
Continuing the discussion with my labmate...
Me:  Ya know, I think I would save a lot of time and frustration if I just abandon the thought of finding a happy medium and make two separate ones.

Immediately thereafter my labmate laughed a bit, and I groaned to myself.

(*By prefer, I mean grow quickly.)

Wednesday, October 27, 2010

The Graduate Research Paradox

I'm starting to think about spring semester, and I've hit a bit of a conundrum. 
You see, this summer was mostly squandered away waiting either for cultures to arrive or to get equipment to work with anaerobes.  By the time everything was good to go, it was August.  And classes have plagued my productivity ever since.

I would LOVE to tell classes off next semester and just get down to the brass tacks of my research. 
I may be able to.  You see, my first semester I took 10 credits (3 classes) while working as a research assistant for my lab*.  I was paid by a grant completely unrelated to my thesis, so I was paid as a tech instead of having to TA.  I didn't know (and no one the graduate office bothered to tell me) that I really only had to take 4-6 credits at the 600-level.  In the end, it kinda works out, as of now, I only have to take 1 more class, and 2 more seminars.

My reasoning for putting off taking that 1 class in the spring are: A) The class offered doesn't really apply to my area of specialization and B) I have my qualifying exams + thesis proposal defense in May.  I would rather prepare for my exams, as well as get some serious research done for my preliminary data/ have a solid proposal defense. 

I think my advisor will go for it. 
A better class becomes available in Spring 2012 (I missed it last spring), so there's always that.  I wonder how many other graduate students do this?  I know that the exams are going to be tough.  One of my classmates has a mutual committee member, and she said that his exam was insanely difficult.  This particular member has already told me that he'll be testing me on possible genetic manipulation that I might use in my research.  Genetics is not my strong point.  In theory I'm ok, but I've had very little practice with it.  All the more reason for me to really prepare. 

And now...instead of working on some new ideas, I have to wade through another assignment due on Friday.  It isn't that I don't enjoy my classes; I just wish they would quit taking up so much time.

*I should clarify that my particular PhD program doesn't have rotations.  You basically have to be approved and brought on to a lab prior to starting.  If the lab takes you on, but doesn't have funding, you can always TA your way through (though I haven't heard of this happening).

Wednesday, October 13, 2010

Running ragged...

I'm just now getting to a post I've had in my head since Sunday.  That's lame, but things have been rolling fast for the last several days.  It's been so pathetic that during the morning drive to work with the Mr., we had to itemize our evening. 

I've been kept busy ironing out issues with my anaerobic cultures.  Those who have worked with them know and understand the suckiness that goes with that...those who haven't worked with anaerobes will continue to live on in ignorant bliss. I was boiling media and dealing with syringes full of sodium sulfide, I was thinking this was FAR better than sitting next to Mouth-Breather-Boy with severe halitosis in the lab meeting for a solid hour.  I will not complain about making anaerobic media again.  Halitosis Mouth-Breather-Boy?  Or stinky anaerobic media?  Pick your level of hell. 

But on to my original idea for the post.  Cooking.
I love this.  You can buy this apron at  LOVE this comic.  Seriously.  Go to the beginning and kill a day reading up to what's current.  =)

In my household (again, it's just me, the Mr., and the spoiled rotten Cat), we love to cook.  Well, not the cat, though if we let him I'm sure he'd want to.  The Mr. and I take turns cooking though. feels like everything that I make that he likes, has onions in it.  Loads of 'em.  I'm one of the afflicted that if I make one slice into a raw onion, I'm in pain and crying my eyes out. 

I remember I was in Organic Chemistry II when my professor got to sulfenic acids, and in particular syn-propanethial-S-oxide which is released when you slice onions.  I loved that class...he was always telling us fascinating tidbits about every day organic chemistry.  I also loved his relaxed pace as he wrote out every equation on the chalkboard while we scribbled frantically to write everything down.  But I digress...

I loath the painful side of chopping onions, so I had an idea.  I won't claim originality on this.  Around 2007 I had a short-lived blog known as 1420Mhz, and on my blog roll was a fellow undergrad's blog known as 90%true or something.  (I should probably look that up.)  On one post, he was chopping onions with his lab goggles on.  I remember thinking at the time, "THAT is awesome...."  
So....during the most recent move from one apartment to another in the city my MRU is in...I stumbled across an old pair of lab goggles.  Normally I had some super awesome sleek lab glasses that I loved and need to find another pair of, but one day I forgot them, and bought the big bulky goggles out of necessity (have them or lose points on my lab grade).  Turns out that day I didn't even need them, and threw them in my backpack.
And this summer I found them again...and now they are awesomely used in my kitchen.  Technically, since they were never used in a lab that's ok.  
I even hang them up in the cupboard.  
The Mr. usually laughs at me for wearing them, but chopping onions is bliss.  I was preparing meatloaf without a care in the world, and I thought that this should be shared.  It's a very odd sensation to smell the onions without your eyes watering.  The smell almost triggers a Pavlovian wincing of the eyes, but after a while it's nothing but awesome.  I highly recommend it.  Just make sure you use them early in the day, and not ~1hr before entertaining:  those who have worn them know the super stupid outline imprinted on your face lingers after your lab class for at least 30 minutes. 

Thursday, October 7, 2010

I'm not insane -- my mother had me tested.

It's been a lovely crap-tastic week.  It always feels like no matter what I do, in whatever order, I'm not doing things fast enough or efficiently enough.  Of course it's been 24 hours since I started the de-icing process, and I'm just now finished hammering, heating, and mopping up the mess. 

Oddly enough I'm looking forward to having no social engagements and a full Saturday & Sunday to get stuff done in the lab.  And that's just sad.  I'm at the stage when I'm starting to get annoyed with classes because they really interrupt things.  I think I only have one next semester, and then after that I just go to two more seminars over the following two years. 

It IS Thursday...which means a new episode of Big Bang Theory!!!  Initially the over-used laugh track really put me off, but Sheldon Cooper won me over.

While I'm not one of those sci-fi obsessed geeks, I love the terminology jokes that are bantered around.  I don't get a TON of physics, but I can appreciate it (I liked Feynman's Six Easy Pieces).  And where else is the word protocol thrown about more in a non-military setting?  It's a show when I can revel in my nerdiness within the household....and by household I mean my husband and our spoiled-rotten cat. 

My husband has ~2 years of what the UK calls a "bioscience" degree, but then quit because he's more art/music orientated.  He gets the gist of my work, but I feel no compulsion to bore him with minute details of the day-to-day (I'll save that for when I defend my thesis a few years down the road).  In this respect, most of my social interaction is with non-science people (and thusly turn to the blog world for science-y interaction).  The Mr. will sit through Big Bang Theory, but usually it's out of hanging out with me, rather than wanting to watch it.  I've had to explain what a Ren Faire is, and whether or not online gamers or comic conventions "really look like that," so his dislike is more from lack of commonality than anything else. 

That said, one of my best friends told me about Big Bang Theory, and she's not what I would consider science-y oriented.  I contend there's some mass appeal beyond the nerd community...I'm guessing it might be the witty sarcasm/ quick dialog insults a la Will and Grace sort of humor.   

Either way, it's this time of the week that I get to sit down with a snack, giggle at the jokes, and enjoy that someone out there is catering to my demographic for once.

If this is dis-jointed, it's because it was written over several breaks from various other things in the lab.  I really should end this and figure out which fire to put out next.

Wednesday, October 6, 2010

I know the game so well....

Today was one of those days that I was going to get a ton done.  Seriously.  I got to work an hour early for a meeting, got my stuff was going to be awesome.

After a productive meeting with my PI and a fellow professor in our department, I felt hopeful.  Said professor has taken pity on me, and is offering time and his post-doc's expertise to help with isolating/quantifying some compounds of interest.  Sweet.
The catch was that said professor is going to leave town I need to summarize the protocols popular for these compounds.  Knowing how these things go....this was gonna take some time.  But hey!  It's cool.  I had my cultures in check: bring on the work!

Or no.
I was quickly reminded I needed to hunt down some cultures and start them growing for something else.  No biggie. 
Our lab is split between two smaller labs, as my PI is slightly new to the MRU we're at, and I'm told the MRU is renovating a shiny brand new should be finished in a year (or so they say).  My bench & desk are in one small lab area shared with one other post-masters student who has stayed on as a tech.
The other lab down the hall has the other current PhD student, and all of the undergrads. 
I rarely use the fridge in the other lab because I'm rarely there....but there might be the chance I'll find an old plate of the desired culture.  As I'm digging around...I notice everything is wet. 

The freezer part of the fridge has been frosted over for some time.  I noticed in July it was a little difficult to close the fridge, but it would still close.  But now, I sense that something is very wrong.  The reagents don't look cold.  I ask a nearby undergrad what's up with the fridge.
Ungergrad:  Oh, the frost over the freezer blocks you from closing the door all the way.
Me:  So it isn't getting cold enough?
Undergrad:  Yah
Me:  Did you just notice this today?
Undergrad:  No.  Probably earlier this week.

WTF?  Earlier this in 2-3 days ago.  There's stuff that we use in there.  Stuff I use occasionally for gels and what-not. 

Immediately my day has shifted.  Trying to cram everything into the fridge in the lab space I'm at...locating a cold room to store other stuff.  Then start the de-icing process of hammering away at the freezer, borrowing a hair dryer from another lab so I don't damage the coils in the freezer.... 
I'm annoyed because if someone had told me this on Monday, I could have taken care of it.  It wouldn't have cut into the day so terribly. 

But I know why the undergrad didn't mention it to anyone.  She didn't want to get stuck doing it herself.  Maybe she had a class to run to, or homework to finish...or whatever.  I did that kinda crap when I was an undergrad (well, kinda - I stayed and helped for 2 hours when a freezer went down). 

So I sent an email to the lab group:  hey, if something is broken/not functioning/etc., even if you don't have the time to fix it, no biggie.  Just let us know.  I'd rather have an undergrad shoot me a "oh by the way...I think the fridge in room #xxx is acting funny..." email sooner rather than later. 

As a grad student I accept that I'm cheap labor and part of my duties are the mundane lab maintenance that undergrads aren't required to keep up.
But...A) some of those reagents could be worthless from spending ~24 hours about 4°C
And B) I could have soooo easily done this Monday or Tuesday of this week.  Not today. 

I was planning on catching up on sleep this weekend anyway.


I'm a 2nd year PhD student in molecular biology.  My blog is just my way of throwing my hat into the science blog ring instead of remaining a nameless commenter on my favorite science blogs.

I got the idea for Do ALL the Science! from a friend who first introduced me to Hyperbole and a Half, which is AWESOME.  Since I've been reading Hyperbole and a Half, all the posts make me laugh until I cry. 

Recently, one of her posts was stretched out to the science world by another one of my favorite bloggers, Scicurious
While I was trying to think of a name for the blog, said friend suggested: DO ALL THE SCIENCE!
I hope that both Allie (creator of Hyperbole and a Half) and Scicurious attribute the title of my blog as the complement intended.  (But no, I am not going to run off and email both about it.)

My undergraduate years were spent focusing on microbiology and biochemistry.  I still work with microorganisms in my graduate research, and I'm learning more biochemistry as time goes on.  (I was one of the weirdos who LIKED organic chemistry/ biochemistry, mmm'kay?)  Mostly my blog is for ranting about life in science, life in academia, life as a grad student, and the weirdness in between. 

While I realize the pseudo-anonymity is just that, I appreciate my right to it.  If you're a close friend, please keep this in mind while commenting.  I'm just another cog in the MRU machine for now.