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.