Tales from the Microbial Laboratory

~Mmmmm yummy yum yum!~

There is something elegant about the way many flowers decline - as they sit in a glass jar (nothing that one might call a vase) in a sunny window.  These gerbera daisies are now former flowers with petals like rice paper, with stems withered and twisted like twine.  Their color, first a bright almost fire-engine red, now the color of a malbec in your best wine glass.

~~~~~

There are two quotes that might best describe this day.  The first relates to the fact that I was unable to drive my car out of my driveway this morning, thus representing the second time in ten days that I've called a tow truck to come out to Pamdanistan.  This first quote is most likely highly unoriginal, but due to it's appropriateness in times like these, I'll share it with you nonetheless:

When life gives you lemons, make lemon drop martinis.

Now, the second quote is of a more scientific nature - and one that was on the first page of a chapter that a brownie-making and natural products-characterizing doctoral student in the lab showed me yesterday. 

I make no apologies for putting microorganisms on a pedestal above all other living things.  For if the last blue whale choked to death on the last panda, it would be disastrous but not the end of the world.  But if we accidentally poisoned the last two species of ammonia-oxidizers, that would be another matter.  It could be happening now and we wouldn't even know....

Tom Curtis (July 2006) in Nature Reviews Microbiology

~~~~~

So, have you ever thought about how many microorganisms become extinct when a plant or animal (with species-specific microbial communities associated with them) become extinct?  Read here if you happen to care.  But remember this warning:  it will keep you up at night.

~~~~~

And might I leave you this evening with a delightful and award-winning poem written by Lily R., a friend of the three-legged Haiku and to all animals small and large, and obviously a lover of lunch.  Her poem has won her a position in a writing camp this summer - so kudos to Lily!

Our Lunch Room is a Jungle

Tick, tock, tick

The clock strikes twelve.

All the kids run down the hall.

Take your seat and wait to eat.

Now get your lunch box and eat eat eat!

What’s inside? Apples and bananas too!

What’s for you?

Yogurt and noodles

Mmmmm yummy yum yum!

Lily R.
Grade 1

~mowing grass~

This is why we like our hydrangeas down here - since many of them bloom like this one, Hydrangea macrophylla 'Blaumeise', for weeks on end during the summer (I've mentioned this one before here).  This one sits at the entrance to my place, just inside the gate - and it greets me each time I return with wonderfully large lacecap flowers of cobalt blue.  The lower branches are rooting, and this fall I will transplant some of them to other areas which also benefit from the shade of the live oak trees. 

~~~~~

I woke up this morning feeling a bit (actually, more than a bit) overwhelmed by my life at the moment.  Yesterday my day got a bit distracted by a car that wouldn't start first thing in the morning - and a tow truck ride and a few hours later, it had a new starter - so I do have a car for the weekend.  But you know how one little thing, amidst awhole list of things, can just overwhelm you in an instant?  That is how I felt yesterday, as I thought about the mountain of things ahead of me that I need to accomplish.  My architect was out at my place yesterday morning, dropping off the 'builder set' - the set of plans that will go to three different builders by Monday, with bids due back to us by the end of June, in just two weeks.  My architect thinks that the demolition of my place is possible within 4-5 weeks.  Then - there is work and the lab - with five presentations by members of my group looming for a meeting in early July, contigs from a genome trickling (aka pouring) in, manuscripts to submit, manuscripts to write -- and for that matter, to review, edit, you name it!  I've promised a group that I will write four this summer - one on a collaborative dolphin project, and three on our work from the USS Arizona (the latter of which are long overdue, for articles that should be fun and a bit exciting to get 'out there').   There's also a mini-symposium to plan, finding funding for, etc before early September. 

Yes, this morning all of these things were swirling around in my head all at once - which rarely results in anything other than - swirling - and so perhaps I need to just start somewhere.

~~~~~

So - I think I'll go and mow the grass.  Mowing grass is therapeautic - you mow, the grass is mowed.  There is little middle ground, no edits or review process required (or at least I certainly hope not!), and as long as the mower starts (and it should), there should be no major impediments to the process.         

~an old white oak~

This morning I left my parent's home as the sun was rising to head back to Charleston.  About seven or eight miles down the road, at the intersection of Rio Mills and Earlysville Road, I passed one of Virginia's oldest white oaks (Quercus alba) - an oak tree that has been under threat due to expansion of the Charlottesville-Albemarle Airport.  All of the homes that used to be around it are long gone, and a nearby church is scheduled for demolition - but efforts have been made to not disturb this tree, and it seems that a group of individuals in the area have accepted the responsibility of caring for the tree until it's (hopefully) natural end.  It was quite majestic this morning - with the early morning sky all lit up behind it - so I didn't resist the urge to pull off the side of the road and capture an image.

~~~~~

I don't think that I'm ready to be home.  A few days before I left town I met with my architherapist, and he gave me a long list of things to think about, decide upon, and actually do -- appliance dimensions, cabinet 'types', counter tops, where I want tile and where I want hardwood floors (I want to read up on engineered wood floors), lighting...the list is long, but first and foremost is the search for a good mortage.  This I will start 'shopping' for tomorrow.  Then I want to visit a person that a friend knows that salvages tiles - and interesting ones, or so my friend says - so I'd like to take a look and see if I can find something for the two small wall areas in the kitchen.  While I was in Virginia I received the results of my geotechnical survey - and I need to get a copy of this to my architherapist, and there's also the email from the HVAC consultant on the project - who wants to talk with me (and requests an hour in order to do so) - I think he wants to convince me that geothermal is the way to go - and while I'm very interested, I'm concerned about the up-front costs.  I also need to pack - really pack - most of the easy-to-pack stuff is done, but now I need to seriously think about what will make it into the Airstream and what will not - since my architherapist thinks that we'll be ready for demolition in a month or so (we gave a set of plans to one prospective builder about a week ago).  Right now - after months of thinking all of this through - that seems soon - and I'd better start making the more challenging decisions regarding my new Airstream lifestyle:  clothes, shoes, books.  And paperwork.  I need to decide what necessary papers should go with me, and which ones should be packed up and put into storage.  This shouldn't be too difficult - but it's still something that just needs to be done - and it all takes time.  It's nice to be home - but home is such an odd place right now, and a bit overwhelming - perhaps by the time the Airstream is 'home' I'll be relieved more than freaked out by this new adventure.

~~~~~

The New Wild Dog is happy to once again be with Stan and I:  over Christmas I boarded her at a place I was quite lucky to find in Richmond (so on my way to Charlottesville) - at first I felt badly about it, but since I was already bringing Stanley to my parent's home, and since my brother was also showing up with an indoor Shetland Pony (aka Bernese Mountain Dog) -  I just couldn't bear to bring another (new and wild) dog into the mix.  Plus, my mother is just too happy that her daughter (as far as she knows) has only one dog, so I don't have the heart to burst her bubble:  yes, her daughter just can't seem to live in a one dog house and, well, that is just all there is to say.  Honestly?  If it makes her happy to think that, then I'll let her - and the New Wild Dog will go to 'camp' at the Holiday Barn in Richmond.  Now the humorous thing about this is that I was desperate to find her a kennel before I left for Virginia, and in desperation I called a friend in Richmond - who called the Holiday Barn, who had fortunately just had a cancellation.  It ends up that this place is not just a kennel, but a pet resort - and little Dani got four hours of camp time a day with her campmates (I think that Stanley was actually a bit jealous of this).  In fact, this resort was listed by the Travel Channel as being one of the top ten pet resorts in North America (I would find this hilarious if it wasn't so crazy-expensive as well).  Tonight she is all clean and shiny, and miraculously still wears the green bandana she had on her when I picked her up.  She's also quite sleepy (and falling asleep while sitting upright), so I'm guessing all of that camp time must have exhausted her.  She is quite sweet, you know, but is an absolute terror outside - she sees a bird, and if she wasn't on a leash, I'd probably never seen her again.  So there's just a little bit of training to be done...

~~~~~

As I was driving south today, I was listening to NPR when their regular program got interrupted, annoucing the news that Benazir Bhutto had been shot.  I couldn't help but think that this was a day that I might need to remember, a day that the whole world will look back on as a deeply troubling one.  From everything I have ever read about her, she was flawed and shrouded in controversy - but her courage and passion is deeply admirable.  For a country with nuclear weapons, sitting in the middle of an already volatile region - I'll hold my breath while watching what the next few days and weeks and months bring to their country.  But today I found myself sad, driving down the road, sad that she was gone from that troubled region. 

   

~another day spent in the Blue Ridge~

The day was a grey one - a colorless, cloudy sky was all we saw as we crossed Swift Run Gap on our way to lunch in the Shenandoah Valley with a close family friend.  We were visiting the spouse of a friend who had died a number of years ago now of Lou Gehrig's disease (or ALS) - and sitting there with her, telling stories about her husband, I couldn't help but miss his tenor voice booming from some part of the house, and his deep laughed that warmed you up from the inside (I always described him as someone who had the ability to warm up even the coldest of rooms).  I remember once arriving at his home and Pavarotti was playing loudly and his wife was calmly saying (aka yelling) for him to 'turn that stuff down' and then he looked at me, and then back to his wife and said 'but Alice, dear, we have a guest that also believes that Pavarotti should only be listened to loudly'.  Tom and I emailed (me, using my fingers and a keyboard, him using a voice-activated system) up until three days before his death.  I miss him still, every day, but the stories that he left behind for us to still tell (over and over again) are wonderful ones.

~~~~~

Every family has little stories, odd symbolic reminders of the past, and on a pond where Swift Run Gap drops down to the Shenandoah Valley is one such reminder for my family.  For ever since I could remember, there have been two pink flamingos standing in the middle of a small pond (I thought that there used to be a small island in the middle, but perhaps not?) - and during one such family trip over the Blue Ridge and into the valley, my brother's then-spouse noticed the flamingos and exclaimed while pointing them out to us 'I didn't know they lived this far north' and those of us in the car couldn't do anything but agree (at least for a second or two) and then start laughing.  Now, whenever we find ourselves on this road, we see the pink flamingos and ponder their remarkable survivability during the colder-than-southern-Florida-winters.  And then we laugh and remember that drive years ago.   

~~~~~

Just as today was about to end - the sun come out and we saw a wonderful sunset over Fray's Ridge, just behind the two sour cherry trees and the bluebird house (that is home to several 'batches' of baby bluebirds each summer) in my parent's back yard.  The light in the oak forest was next to perfect for fifteen minutes or so - and after I watched the sun set, I went inside to find my Mom at the dining room window, watching the growing shades of pink and blue filter through the trees.  This is my last evening in Virginia for this holiday season, and tonight I feel grateful that my family was all together, that my Mother was happy and even happier because she cooked Christmas Day dinner for her family, just as she always does.  That is all she wanted:  for things to be normal, for us to eat too much and still ask for a piece of one of her homemade cakes (german chocolate or six-layer yellow cake with chocolate frosting or fruitcake), for people to disperse when it was time to clear the table, and for my brother to wear his new sweater all day and to walk around in her new and soft and warm slippers, and to tell my Father to keep certain boxes because she might need them next year.  I don't want to think about how she will feel tomorrow morning as we all drive off to our other lives, the deep snow of my brother's home in Vermont, the busy streets of my niece's life in Boston, and the salt air of my soon-to-be demolished home in South Carolina.  But at least for four days and five nights we kept cancer once again outside in the cold, hopefully shivering in the woods behind the house -- and we'll keep it there for as long as we possibly can.    

~no two are alike~

There was no snow for our part of the Blue Ridge mountains this Christmas morning - but as I was walking the dogs behind my parent's home, I couldn't help but thinking that these lichens are quite like snowflakes, since I can't imagine that any of them are truly the same.  They cover the striated bark on my Mother's sour cherry tree - a blizzard of flakes, each a slightly different size and shape and color.

~~~~~

I awoke early this morning, and while everyone else was still asleep - I collected all of the dogs (including my brother's shetland pony aka bernese mountain dog) and went for a walk down the path behind my parent's house.  The sky was clear, it was barely light - and the moon was still bright.  Christmas morning is the perfect time to go for a walk in the woods, don't you think?  I was lucky when the dogs were enamored with a scent to my right because to my left five white-tailed deer when racing down the side ridge - I was glad to not have to either yell to get the dogs to not run off to the next county, or to have had to go off running after them (it was my own tiny Christmas miracle).  By the time we made it back to the house - everyone was moving around and the day had begun.

~~~~~

This is my brother's mountain.  Not literally, not according to any legal or binding documents - but ever since we were young, when we drove by this tiny mountain, he said that when he grew up, that he would build a home on the very top, with a long driveway meandering down to the main road.  It's nice that no one has broken our illusion...since over the years no one has carved a drive up this hillside, and no home has been nestled into the oaks up on top.   No door has closed.  It is still my brother's mountain, it is all still possible - and possibilities are all that matter...perhaps?

~~~~~

Since March and my Mother's diagnosis, my brother and I have spent more time than usual wandering these hills, these hills of our childhood, and their familiarity is comforting to us:  we are a part of these mountains, of these roads and the rocks collected from them - and we're part of many of the people's lives that still live here.  I thought today about a poem, a poem about rivers - and it perhaps captures, if only in a small (and much less significant way than perhaps it captured for Hughes), how I feel about these hills. 

The Negro Speaks of Rivers by Langston Hughes

I've known rivers:

I've known rivers ancient as the world and older than the

     flow of human blood in human veins.



My soul has grown deep like the rivers.



I bathed in the Euphrates when dawns were young.

I built my hut near the Congo and it lulled me to sleep.

I looked upon the Nile and raised the pyramids above it.

I heard the singing of the Mississippi when Abe Lincoln 

     went down to New Orleans, and I've seen its muddy 

     bosom turn all golden in the sunset.



I've known rivers:

Ancient, dusky rivers.



My soul has grown deep like the rivers.

~~~~~

Merry Christmas everyone.

~Saturday, December 22, 2007, 1:08 A.M. EST~

A favorite evening - Winter Solstice Eve - because after tomorrow each day begins to slowly grow longer... and how nice is that?

Almost every year since I've lived in Charleston, my friends out on Johns Island, at Pete's Herbs, have held a wonderful winter solstice gathering.  Unfortunately circumstances prevented it this year - and I must say that I'll miss being out by a fire, listening to classical music filtering through the pines - and I'll miss drinking more glog than is good for me while talking to people that I often just see once a year.  Tonight I'll have to take the New Wild Dog out for a walk, with the Stanley joining us - and watch the dark clouds race over the almost-full moon.  One day, when I'm not traveling to Virginia for the holidays, I'd like to have a solstice gathering of my own - in my new home, sitting out on the deck under the circle of live oaks - and talk about what it must have been like, wondering what the sun was, many, many years ago.

Happy Winter Solstice from the Microbial Laboratory

(Credit:  microbial artwork by the lab's senior graduate student, who will know who he is if he reads this).

~a citrus gift box~

It's been difficult this Christmas, deciding on gifts for my mother.  She has told both my brother and I that she wants us to get her nothing - she's been adamant about it - and we just nod, knowing that of course, we'll get her something...but what?  Practical is for the birds, during this year of lung cancer -- so my brother and I decided upon one of those services that send flowers to a person each month of the year.  In January she'll receive a white amaryllis, in February daffodils, and you get the picture.  The gift is optimistic - flowers always are - and when it came time to chose whether we wanted the 3-,6-, or 12-month subscription, of course we had to chose the one that lasted the entire year.  My brother and I also wanted to give her some small gifts - things to open on Christmas morning - and so today I went to work on those.  I couldn't resist making this 'citrus gift box' straight from my own garden:  one Meyer's lemon (just starting to turn yellow) and five satsumas.  This will make my mother laugh, and I can see her now, shaking her head as she tells her friends what I gave her. 

The other gifts I've been working on for awhile now - slowly scanning in slides, a few at a time, taken during my childhood - and today I printed out five images and framed them for her.  There is a photograph of her holding my brother, who looked less than one - they're sitting in a chair with my father's family farm as the back drop.  Another is of my mother, when she was about 25, putting an ornament on a small red cedar - and then one from a few years before that, of my mother and father on their honeymoon (my father is looking h-a-p-p-y).  Then there are two of me - one with me wearing cherry red tights and white mary janes, a pleated blue skirt and white sweater - and a big football helmet.  I'm hiking the football to one of my brother's friend, and behind me are a row of older boys from my childhood (including my brother on the far right) - all of them tolerating this little girl in the middle of their game (I have to wonder:  was there some foreshadowing going on...?).  The final image is of one of my birthdays, with me and a cake baked by my mother - surrounded by my best childhood friend, my brother and his close friend, and a cousin.  We looked as if we wanted cake, but we also looked like we were imagining what we were going to do after the cake, and I can't help but think that it was something...bad.

I'm glad that my citrus was ripe - hell, I'm glad that my citrus was even alive - because my mother will open the box and know that it is from her daughter - yes, the one that she has never quite understood, and whose contradictions have always puzzled her.  The one in the red tights demanding to play football with her brother and his friends, and the one who grows everything, just like her mother.       

~a new member of the pack~

Okay, I might be biased (already!) but I just think she is the sweetest thing ever. 

Stanley feels like Santa Claus came to visit a week early.

According to the rescue folks (Dogs Hope, Midland, NC) she's ~2 years old.  Most likely she was a teen mother.  She's a small English Pointer - at 42 lbs.

We're happy to be a pack again.

 

~submission~

Pronunciation:

\səb-ˈmi-shən\

Function:

noun

Etymology:

Middle English, from Anglo-French, from Latin submission-, submissio act of lowering, from submittere

Date:

14th century

1 a: a legal agreement to submit to the decision of arbitrators b: an act of submitting something (as for consideration or inspection); also : something submitted (as a manuscript)

2: the condition of being submissive, humble, or compliant

3: an act of submitting to the authority or control of another

(according to here)

~~~~~

The grant was submitted 17 minutes prior to the deadline.

It is now in the control of another, it will be inspected.  For months.  Ahhh...the external review process.

All I can do is stand in the middle of my kitchen. 

It takes me a few days to recover.

This week I walked out of the grocery store, failing to pay for my groceries.

Obliviousness.

They called me as I was walking out the door - I went back and paid.

I need time in my garden.

I need to roll in the grass.

With abandon.

~a deadline~

19 hours, 17 minutes.