Tales from the Microbial Laboratory

THE LIST

~a camellia flower, from a tiny plant that my camellia friend gave me two years ago...it's name?  I don't know - does it matter?~

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I've been ignoring my camellias in these pages this winter - I was thinking to myself 'now why is that?' until I realized that it was because they simply haven't had their usual, spectacular year.  It was warm and then that two week period of cold - unusual cold for us - which left many of the buds and blossoms brown and less than their usual selves.  They are recovering though - the buds that were tighter (and hence protected) during the cold are beginning to unfold - and these wonderful flowers of winter and are once again gracing us with their presence.

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I don't write much about science here, details that is - I dance around it, superficially - although I'm sure it often reads like the elephant in the room in almost every post.  When I first started this blog, my intention was to write more about science (hence the name) - but instead it became a retreat from the day-to-day realities of a scientific life.  The challenges, however, of my current job situation has changed this a bit - but I'm still not writing about science - but more about the scientific life itself and it's associated frustrations.  A number of academic friends are struggling right now - with a looming 3-yr freeze on the federal budget and continual cuts in the higher education budget - I can't help but think that we are tossing scientists - educators of all kinds - out on the street.  I don't know what the solution is - but I never thought when I was young that science as a subject would become a luxury, and not be recognized as a priority.

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THE LIST below has been a central focus of the past nine months (except for a month, like January, where I also submitted two NSF grants...).  A hugely frustrating aspect of having one's position terminated when things are going so well (so not a termination due to lack of productivity) is that 'the work' is going great - and how does one let that go?  You can't.  I know that I can't.  The contents of this list - the hypotheses, the data - is why we do this.  It's why it's about something more than just having a job.

I'd like to share THE LIST with you.

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THE LIST

1. work describing a coral pathogen and the role of motility (led by our collaborators in Israel): Published.
2. work describing metabolites produced by a coral pathogen (led by local collaborators): Published.
3. work describing genes involved in nutrient cycling in coral microbial communities: Published (and take a look at the journal cover photo).
4. work describing the bacterial communities in the upper respiratory tract of Atlantic bottlenose dolphins: Published.
5. work describing the phylogeny of a globally-distributed coral pathogen (collaborative with colleagues from Australia):  Published.  
6. work validating the presence of a coral pathogen in the Caribbean and the pathogen's antimicrobial characteristics: Accepted with Minor Revisions (Revised Manuscript Submitted).
7. work describing clinically-relevant bacteria and fungi in gastric, upper respiratory tract and fecal samples of Atlantic bottlenose dolphins: In Review.
8. work describing the genome of a coral pathogen: In Preparation.
9. work describing the proteome of a coral pathogen at two different temperatures: In Preparation.
10. work describing a method to detect and quantify a coral pathogen in environmental samples: In Preparation.
11. working describing the antimicrobial resistance and susceptibility profiles of coral-associated bacteria: In Preparation.
12. work describing the toxicity of a nanoparticle to bacteria: In Preparation.
13. manuscripts 8-12 are all close to submission - in addition to these 4 manuscripts, we have ~12 additional manuscripts where the data is collected, some writing has been done, but they are not close to submission (just yet!).

~~~~~

 

So I've finally found the language to describe my situation:  I lost my job, but not my profession.  This line has helped me, as I try to explain to those not in academia why I am working as much as ever in the absence of a paycheck.  So while I cross my fingers (and toes - and I suggest that you cross yours as well) and go in search of a place for the Microbial Laboratory to land - this list of accomplishments is so important.  It validates us - as academic dysfunction swirls over our heads and goes rushing by. 

 

Hopefully, with a little luck and much hard work, this dysfunction will be behind us - something we only see if we choose to turn and look back.

what? I can't hear you...

 
~The Pointer Sisters on a rainy Saturday morning~

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It's like having eight year old kids stuck inside on a rainy day - what's a Pointer to do?  The storm system sweeping across the country today arrived at this little piece of the Atlantic Ocean coastline last night - bringing with it a dark sky and rain - and sometime later in the day, dropping temperatures.  A rainy day is a bit of a challenge in the Airstream:  while I first enjoyed the sound of the rain on my aluminum home, the reality is that it is LOUD.  Sometimes too loud to carry on a decent phone conversation.  Then - there are The Pointer Sisters.  Having dogs that behave perfectly after running 20 miles or so, rain brings it's own set of Pointer-related challenges.  You see, these are delicate Pointers.  While they desperately wish to be outside, running after squirrels - they really don't like to get wet.  So - when outdoors, they want to be indoors, and vice versa.  So as I type this, two delicate and completely insane Pointers sit at my side, while it's raining so hard that I can't hear NPR on the radio.

Ahhhh... this Airstream Life!

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The upside to such a rainy weekend is that I have manuscripts to submit.  A doctoral student's revised manuscript (accepted with minor revisions) was re-submitted last night at 1:11 am (yes, I've become a night owl) and a second manuscript - a 'new' one - will get submitted this morning (I hope).  This means that I will, most definitely, need to update THE LIST (here is THE LIST as it existed on 30 August 2009).

  Updating THE LIST always feels good.

~~~~~

My Name is Pam, and I Live in South Carolina

"Life is a game, boy. Life is a game that one plays according to the rules."

 

"Yes, sir. I know it is. I know it."

Game, my ass. Some game. If you get on the side where all the hot-shots are, then it's a game, all right - I'll admit that. But if you get on the other side, where there aren't any hot-shots, then what's a game about it? Nothing. No game.

From Catcher in the Rye

J.D. Salinger, January 1, 1919 – January 27, 2010

~~~~~

I think that all of South Carolina needs to have one giant AA meeting, with all of us acknowledging that we are from the state and that we are all responsible for this embarrassment of leadership.  No matter who we voted for.  Stray animals, hiking the appalachian trail, and 'YOU LIE!" - and who can forget the horse incident(s)?  We need a 12-step program to rid this state of an addiction to idiocy.

The bottomline is that individuals in South Carolina in leadership positions don't really care if kids in this state receive an indecent education.  They don't care if families are struggling to have enough food for their children.  And they don't care about the unemployment statistics (we've even got California beat, but just by a bit), because...they just don't care.

It's all a game to them... 

~~~~~

As John Stewart says, 'Thank you South Carolina'.

The Daily Show With Jon Stewart	Mon - Thurs 11p / 10c
Thank You, South Carolina - Andre Bauer
www.thedailyshow.com
Daily Show Full Episodes Political Humor Health Care Crisis

(Might I add that being unemployed myself generates a very different view of the world?  What is the opposite of rose-colored glasses... perhaps a magnifying lens?) 

I'm including the video below just as a reminder to myself that all of us (aka me) who don't regularly speak up will be left with men like Andre Bauer in leadership positions.  Why isn't being this stupid illegal?

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Okay, just needed to acknowledge the insanity.

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Update, 11:33 pm:  Do not ask me why (yes, insanity I'm sure) but as I was reviewing proposals tonight I had the SC GOP debate on.  Yes - ANDRE BAUER.  Who basically said something like 'he bets most of the people in the audience agreed with what he said' when questioned about the 'don't feed the strays' thing.  Then Henry McMaster said something like 'I'll never apologize for South Carolina, we are a great state'.  Are these guys all INSANE?  Do they see the same stats that the rest of us see?  Are they paying attention to the public joke the state has become in the press?  One of the guys (can't remember who) said one thing he liked about Gov. Sanford was his 'transparency' - yeah, except for when he dropped out of sight for awhile, during a mad dash to Argentina.

Just need to vent.  Really tired of reviewing these proposals.  Not looking forward to a cold, rainy first part of the weekend.  Can I run away from home?  (Wait, I could take my home...and run away!  Now how convenient is that?). 

 

lists

~banana leaves, first frozen, then dried - no salt~

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Long day.  Manuscript edits.  Manuscript review.  The list is obscenely long right now - how can this be? 

(Ahhh...it's what happens when you lose your 'job' but not your 'profession' - the paycheck goes away but the profession is still going full-speed.  Bizarre, I know.  Trust me, I know.)

Did get a fun invite today from former postdoc 'peeps' to fly down to Florida in February to give a seminar (I think they're all worried - hell, I'm worried).

But back to being insanely busy... I have an impossible list of things to accomplish tomorrow (deadline kinda things) already.  Geez.   

 

10 things

~oakleaf hydrangea, after a few months of a southern winter~ 

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Generally when I've been tagged for a meme I run in the opposite direction (much like I do when someone wants to photograph me - pathologically so, I know) - but a week or so ago Whole Life Gardening tagged me and I thought 'why not?'  I've been in a bit of a rut, and it never hurts to think about such things.  So, I'd like to thank 'C.L.' and here goes...

Ten honest things about myself:

1.  I hate wearing shoes.  My toes want to be free (it's from years of living in the south I suppose).  Oh, I hate socks too.  (How did I survive graduate school in Michigan?)

2.  I think I knew that I always wanted to be a scientist.  One of my earliest memories is of being a three or four year old, and being outside with my parents.  They would be weeding their large vegetable garden, and I would be taking the weeds - lambsquarter, for example - and transplanting them into my sandbox.  I remember watching them over the next few days, to see which ones survived the transplanting - and which ones did not.  I was collecting data...even then. 

3.  The past three years have been the most difficult of my life.  Starting with my Mother's lung cancer diagnosis, her death,  the jump into the Airstream, the loss of my job, the Microbial Lab's wartime life, and the recent challenges with my Father.  A friend refers to it as a 'rough patch' - pretty big patch I'd say.

4.  I don't like all of the new varieties of Echinacea being released.  On this planet we're losing biodiversity at a crazy-insane rate every week, and yet we gush over a new variety of Echinacea with a different flower.  When I hear of an extinction (or sometimes the inclusion of yet another organism on the endangered species list) it makes me cry.  I fail to understand why protecting biodiversity is not a higher priority on a global scale - I know, I know - jobs, health care, Haiti, infectious disease, tsunamis... (Disclaimer:  I'm as guilty as the next guy regarding this, with my numerous plant obsessions - so I must lump myself into the 'gusher' category when it comes to new plants.) 

5.  I live in the glorious south and I long for a snow day.

6.  I am a sometimes-arrogant, often-difficult idealist.  I can't help it.  People should be better and should do what's right - but they often aren't/don't.  (Perhaps this is why I like dogs so much?  And find refuge in my garden?)   

7.  I have 188 pages of a novel written.  Single spaced.  (What's stopping me?  I think I need a lawyer to review it before I could even dream of publishing it.  What is it about?  Being a female in science.)

8.  I hate a messy lab (although it's obviously taken a backseat, as many things have, to my current on-going life drama).  And I hate a messy house (aka Airstream).  But my car?  It's a disaster.  Always.

9.   I love choral music.  So many voices - they just blow me away.  Gregorian chants too - these voices are how I'd describe heaven (if I felt any certainty that there was one).

10.  I was raised in a pacifist church (Brethren) and do not understand war.  I've tried to 'understand' it, intellectually that is, but I cannot.

spring?

 

~above Barron Gorge, Queensland, Australia~

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Yes, I was wandering around Australia again today (only in my mind of course) - although the warm wind and brief bit of sun here in South Carolina today were wonderful.  It's funny how spring happens:  it's nowhere near, seems like an impossibility - and then there is a warm afternoon when winds are strong and from the south - and suddenly the daffodils are four inches tall and popping up everywhere (it is late January, isn't it?  why should this observation surprise me so much?).  Spring reminds me of that moment when dogwood flowers turn from that early color when the petals first start to emerge (a pale, pale green) to a bright white, an event that each year I'm determined to witness but miss when I turn my head for only a second.

~~~~~ 

 

~keyboards~

~ Barron Gorge National Park, Queensland, Australia~

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No - I wasn't at Barron Gorge today (although it would have been nice) - instead I was trying to troubleshoot the 'blue screen of death' on my PC, talking with my electrician (I am happy to report that while my PC's screen is still blue - my electrical issues in the Airstream are resolved).  Oh... and the check engine light is on in my car (but something not terribly traumatic and it's scheduled for repair next week), the left front headlight is burned out, and, yeah, when it rains it pours (and thankfully it isn't raining).  I am happy to report however that the Airstream once again has water..BIG news.  I was able to repair the pipe myself (with the help of a very nice man at the Ace Hardware).

So I'm posting this from a macbook that I'm not particularly fond of (I hate hate hate the keyboard).  

This image of Barron Gorge happened to be on the desktop of my mac, saved on the desktop during my visit to Australia over a year ago now.  Boy does wandering around Australia sound like alot of fun right now.

I've had no time to wander the blogosphere (my apologies) and I miss it - the time will come again, I'm sure of it - just like spring will come again.  I was talking with my father today, and I told him that I really wanted spring this year and that I felt like it would never arrive, and he sweetly assured me that it would - as it always does.  And to not worry.  That is reassuring, isn't it?  The dependability of certain aspects of our lives?  Spring will (eventually) arrive.

Much to write, but as I've already said - I do hate this keyboard.  So instead I'll go back to daydreaming about wandering around Barron Gorge... in the springtime. 

a mosaic

~an elephant ear leaf, after the cold~

~~~~~

Tired, busy, glad it's a weekend (but with much still to do).  This 'new' life...

~bored pointers~

~the Pointer Sisters, bored on a rainy day~

~~~~~

It was your classic rainy day today - the sky was almost touching the ground, keeping things dark and wet.  The Pointer Sisters kept wanting to be outside (in theory) - and when outside, wanted back inside (they're fragile creatures, you know).  You know the drill (annoying?  yep.).

I've got a to-do list a mile long, and I'm trying to wade through it - but this week it's felt like wading through pluff mud:  one leg trying to take a step forward, while the other ones sinks further into the mud.  I think I'm making progress, but it's muddy progress - not the sense of clarity that feels good.  By the end of the day tomorrow I need to have scores in for 16 fellowship applications - a long night is ahead of me.

But I just returned from a wonderful dinner at a friend's home - with a few of us sitting around a table lit with candles, catching up on challenges and funny stories and reality and life.  I'm so grateful for my friends during this tough time (a 'rough patch' as my one friend calls it).

a sweet reflection

~Annabelle Lee and her reflection~

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Annabelle is such a sweet and crazy dog girl - and yesterday she was at her crazy-best when she became enamored with her own reflection in the window (look closely, and you'll see that she's nose-nose with herself).  Look at that tail - she was obviously happy with what she saw!

She's something really - all muscle and bone - and I don't believe that I've ever seen her tired.  During our last visit to the vet, for her annual checkup, the vet said she had the heart of a long distance runner.  I certainly believe that. 

(I have six of these windows - and my goal a year ago was to use them to make a coldframe - obviously a goal that got pushed to the side when bigger life issues intervened.)

~~~~~

I got another proposal successfully submitted today.  A full six hours before the deadline.  This one felt good, really good - and I actually had time to read over the entire proposal three times prior to submission - a rare luxury.  The Supporting Data in the proposal represented years of hard work by members of the Microbial Lab, and it was a treat to tell such a nice story.  It started with our discovery of a coral pathogen in the Caribbean, it's relationship to other strains of the same organism from other coral reefs - followed by a discussion of the organisms genome (which we recently sequenced) and the influence of temperature on this organism's proteome.  (I know, I know - you all are just dying to read it).  So.  It felt good - like a job well done, which as we all know - always feels good.

Now I've got to review 24 EPA proposals for a panel review.  And review a manuscript for a journal.  And edit three manuscripts written by members of the Microbial Lab.

It hit 70F here today.

(This unemployment is exhausting!)