Tales from the Microbial Laboratory

~happy new year's eve~

A Blessing by James Wright

Just off the highway to Rochester, Minnesota,

Twilight bounds softly forth on the grass.

And the eyes of those two Indian ponies

Darken with kindness.

They have come gladly out of the willows

To welcome my friend and me.

We step over the barbed wire into the pasture

Where they have been grazing all day, alone.

They ripple tensely, they can hardly contain their happiness

That we have come.

They bow shyly as wet swans. They love each other.

There is no loneliness like theirs.

At home once more,

They begin munching the young tufts of spring in the darkness.

I would like to hold the slenderer one in my arms,

For she has walked over to me

And nuzzled my left hand.

She is black and white,

Her mane falls wild on her forehead,

And the light breeze moves me to caress her long ear

That is delicate as the skin over a girl's wrist.

Suddenly I realize

That if I stepped out of my body I would break

Into blossom.

(Image: dried flower heads of ironweed, Vernonia sp.) 

~new wild dog~

How can something so cute...be so terribly bad?

While I was on the phone this evening, she brought a magazine, a shoe, a blanket from my bed, and a large cardboard box into the room. 

Then she got her new yellow squeaky toy and went tearing across the house, back and forth a gazillion times, with Stanley chasing her and the cat chasing Stanley. 

Then she collapsed into an exhausted heap of happy dogness.

Gifts for that Special Microbiologist on your List (2nd Edition)

Somewhat humorously, I have noticed that the search term that most often sends one to this site during the month of December is 'microbiology gifts'.  This is because of a post I wrote last December - listing silly (and some not-so-silly) gifts that might be appropriate for a microbiologist.  Now, I'm a bit late this year with the 2nd edition, but perhaps it will help someone next year figure out a gift for that hard-to-buy-for-microbiologist on your list (and please, if this is me you're shopping for, do skip numbers 1-6 and go right to number 7).

1.  T-shirts, buttons, mugs - you know, stuff.  Over at CafePress.

2.  Over at Twisted Bacteria, I saw a post about the children's book 'Germ Stories' by Nobel Laureate Arthur Kornberg.  Curious adults might like this one too.

3.  A subscription to The Microbiological Update.  Okay, this is QA-QC micro stuff, kinda boring, so don't go getting it for a microbiologist that you plan on having fun with in the future.

4.  Wine (now this can be purchased for a microbiologist that you plan on having fun with) - what about a good Tuscan chianti?  An affordable Argentinian malbec?  What about a nice bottle of wine and a copy of Handbook of Enology: Volume 1: The Microbiology of Wine?  Or what about finding when the next meeting of the International Wine Microbiology Symposium and booking a trip?

5.  Now here's a good one!  A Photographic Atlas for the Microbiology Laboratory.  Looks like it might be nice for someone taking intro to clinical microbiology.  And as for books, you could head on over to ASM Press' eStore and take a look ( there's Joklik's Microbiology: A Centenary Perspective - a collection of landmark papers over the past century, and Bacterial Pathogenomics, editor-in-chief Pallen - which focuses on how genomics has helped us understand how pathogens have evolved and their disease-causing processes).

6.  What about some microbial art? Quite literally...

What about BacterioPoetics (and more specifically, here):

Escherichia coli (E. coli) was discovered in the first decade of the 20th century by the German bacteriologist Theodor Escherich (1857-1911) and according to Wikipedia “the number of individual E. coli bacteria in the faeces that one human passes in one day averages between 100 billion and 10 trillion”. It is the BacterioPoetic conviction that each of these bacteria is a piece of art more beautiful then the “Victory of Samothrace” and as such your poo hosts more art than the collections of all museums in the world put together.

Roughly around the same time Theodor Escherich was making his discovery, James Joyce was working on the sequence of books that have since become the hallmarks of modernism in literature. It is interesting to compare the impact on world culture of E. coli against the Ulysses; Joyce’s masterpiece published in 1921, of which he proclaimed it would take scholars centuries to uncover the riddles hidden therein. Little could Joyce have expected that in the end a work of biology as humble and yet as versatile as the E. coli proved to be far more elusive than the wanderings of Leopold Bloom or the simulation of Dublin in which Bloom lives on, created by a human mind of his scope. E. coli has become the workhorse of molecular biology, the time and resources spent on reverse engineering it by far exceeding the work done on the analysis of Ulysses. But whereas interpretation of Ulysses is the best way to make sure students of literature will never read again, bacteriologists can’t get enough of the E. coli: its mechanism still shaded in mystery, the wonder of its feats of adaptivity never ceasing.

Biology is conservative. The function and perhaps even the definition of creativity is to come up with novelty. In terms of burn-rate bacteria are surely more creative than, say, elephants, lemurs or even fruit flies because all these animals evolve much slower than the 3,5 hour it takes the E. coli to iterate a new generation. But bacteria are also impressive for the quality of the novelty they introduce.

Or microbial art climatology: 

[...] The practice of microbial art climatology starts with immersing (a sample of) the art works (submergence) in an environment with a lot of micro-organisms (ditchwater). Micro-organisms will settle in and on the art works in great numbers and by doing so provide the key to the microbial art climatological analysis. In the end, the quality of the art work is determined by the type of organism that it attracts [...] Determination is the most essential part of the microbial art climatology. It needs to be carried out with the utmost precision. If you cannot distinguish a Ciliate from a Gastrotrich you will certainly not be able to tell a good 'hard edge' from a mediocre 'colourfield painting'. An incorrect determination can cause a lot of damage to both museum and- private collections. Eventually, it might disrupt our overall view of the course of art history. The art climatologist should assume full responsibility for his determination. [...]

7.  But lets face it.  Most of the microbiologist that I know don't want clothes or books or wine (wait, skip that last one) - what we want are new toys.  Bigger (well, actually smaller), faster, toys with increasing resolution.  As for me, I'd love a gift certificate for ~1M for a shopping spree at 454 Life Sciences.  I'd probably start with the Genome Sequencer FLX System with has the capacity to generate about 100 million bases per 7.5-hour instrument run.  I'd need to purchase alot of the supporting software as well.  Now that would keep the lab busy - yes, I know, we can still send out, but wouldn't it be easier to just walk down the hall, or over to the next lab bench?  I'd also very much like an atomic force microscope - no, no - it's not that expensive, but for a quarter of a million I could get everything that I want (I'd like to be able to examine samples in liquid - so a few accessories would be required).  Oh, and a new scanning electron microscope would be nice, especially if it were coupled to EDX (like this one).

~~~~~

For prior and subsequent years:

The 2006 Edition.

The 2008 Edition.

The 2009 Edition.

         

~a governor's home and geothermal thoughts~

It would be nice to have known Thomas Jefferson, and to have been able to say 'hey -- Tom -- if you could, when you get a minute, would you design me a place?' and then you'd laugh over some agricultural faux pas and drink a few glasses of wine and talk about things, like where your land is and how many bedrooms you needed - and that would about cover it.  Except that everybody has budget issues, since it seems like even Virginia's Governor Barbour never got around to building the dome on his place in Barboursville.  From the Virginia Landmarks Register, 4th ed., 1999: 

Until it burned on Christmas Day, 1884, James Barbour's home at Barboursville stood essentially as completed ca. 1822 from designs supplied by Barbour's friend Thomas Jefferson. Jefferson's drawings called for a dwelling with a recessed portico on the north front and a three-part bay sheltered by a portico on the south front, with dome above -- a scheme resembling Jefferson's Monticello. The dome, however, was not built. Even in its ruinous state, the house presents a romantic image of the Jeffersonian ideal, a compact but architecturally sophisticated classical villa in a carefully contrived landscape setting. The great grassy oval in front of the house was originally a racetrack. James Barbour (1775-1842), a statesman and diplomat, held many public offices, including governor of Virginia, secretary of war, and minister to Great Britain. The stabilized ruins are now the centerpiece of one of Virginia's first large-scale wineries.

So - '...a romantic image of the Jeffersonian ideal, a compact but architecturally sophiticated classical villa in a carefully contrived landscape setting...' - works for me.  Except that I'm not building in the foothills of the Blue Ridge, and Thomas Jefferson doesn't live down the road from me (but I wish he did).

~~~~~ 

But all I can say is thank God for my architherapist.  Truly.  I can't complain for a minute.  I think that he is trying to keep me on tract to build a 'compact but architecturally sophisticated classical' home at the beach.  A contemporary beach house, so to speak.  I'm at the stage though where I need to be actively involved in the process, decisions need to be made, and a big one will get started on Wednesday, and that's when I have an early morning phone discussion with the HVAC consultant on the project (yes, it's all part of the LEED process - we need HVAC and Structural Engineering consultants to contribute to the design and building process).  My architect has told me that the HVAC consultant is going to try and convince me that geothermal is the way I need to go for my heating, cooling, and hot water needs.  In fact, I asked if he would send me something to read on geothermal, so the consultant sent me the following overview ('The Geothermal Concept') to review prior to our conversation on Wednesday:  Download geo_conceptca002_december_28_2007.pdf

What I'm interested in right now is to learn about all of the disadvantages of geothermal, so I can ask the right questions on Wednesday.  From what I've read thus far, here are the main disadvantages (and questions):

• higher initial costs than conventional systems (so the question is, how much higher?  and how much more efficient are they than conventional systems?  what is the cost-recovery time?)
• open-loop systems have more potential problems than closed-loop systems, since they bring water into the unit, which can result in clogging, corrosions, etc.  (do you recommend an open- or closed-loop system?)
• since open-loop systems require large amounts of clean water to be effective, this often limits their use to coastal areas, or areas near lakes, rivers, etc.  The used water must also be returned to the environment safely (so an open-loop system would possibly be one done in a coastal area, so - what is the typical repair historys for such a system?)
• closed-loop systems often use an anti-freeze solution to keep the loop from freezing (this is probably not an issue in coastal South Carolina, right?)
• there are all sorts of added issues if refrigerant is needed - toxicity is a concern, corrosion issues (for copper piping) is a possible problem, and repair issues are problematic.
• accessibility to terminal units is critical for repair - so architects, builders, structural engineers, etc all need to coordinate their efforts - and the units need access to both electrical and plumbing service.  (what is the repair history on similar units?  will the loop joints be heat-fused, which is supposed to reduce repair frequency?
• back-up heat systems are required in cooler regions (so how cool is 'cooler'?  we're supposed to get down to the upper teens by sometime next week...how will such a system operate during the colder than normal or warmer than normal periods?)
• the area needed to lay the piping system can be quite large (how large is 'quite large'?  what happens when a 'repair' needs to be done on the underground section of the system?  what is the average cost of repairs, and how many repair people are even out there in Charleston County?  how will the system interfere with my evolving 'landscape plan'?)
• what tax credits are available for geothermal installation in a new residential home? (it looks like a $300 credit, which seems sort of...minimal, doesn't it?).

Some useful links (while I'm at it):

• Alternative Energy Resources in South Carolina
• State Energy Efficiency Index:  South Carolina (not too impressive)
• South Carolina Incentives for Renewables and Efficiency (for geothermal)
• South Carolina Incentives for Renewables and Efficiency (comprehensive list)
• Santee Cooper Residential Green Power
• The Case for Geothermal (from gladwell.com)
• Financing an Energy Efficient Home
• Southface Fact Sheets and Technical Bulletins
• Southface:  Sustainable Design, Construction, and Land Development (Guidelines for the Southeast)
• building science.com
• BuildingGreen.com (LEED credits)
• BuildingGreen.com (ground-source heat pumps: tapping the Earth's mass)

~~~~~

But back to Governor Barbour's place.  I went there the day after Thanksgiving with my brother, to visit the Barboursville Vineyard.  It was just a beautiful setting - with vines covering the hillsides around the home - with the home itself surrounded by large boxwoods and a few southern magnolias.  What a gracious home - and it reminded me so much of Monticello - a slightly smaller version, and no, it isn't on a mountain top - but the style was distinctly Jefferson.  I can't imagine heating those rooms, but the reality is that they were probably always cold in the winter (hence the Christmas Day fire, right?).  But to design and build a home whose bare bones are so elegant, so perfect - is definitely a wonderful thing, and while I don't AT ALL think that a plaque will be in front of my home one day like the one that says 'Governor Barbour's Mansion' - I still hope that it will be a place that will seem cared for, designed, perhaps thought through, and definitely responsible. 

There is much learning yet to be done though.  Talk about a steep learning curve...

historical rendering of Barboursville, Barboursville Plan and Elevations (and here)        

~views of a fading amaryllis (Papilio)~

 

~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.

~a Sunday in Virginia~

I made my way up I-95N yesterday, with Stanley and the New Wild Dog in tow - to spend a few days with my family.  This morning started off foggy, then changed by late morning to much needed rain for this region of Virginia.  But in the late afternoon, as my brother and I were driving to a holiday gathering of my father's side of the family - the clouds began to race quickly past the tops of the mountains, and by dusk, when the almost full moon was rising, the sky was a deep blue and clear.  I find myself trying to remember every detail of this time spent with my family, one that could easily be the last one in which we are all together - and the early morning fog filtering through the woods that surround my parent's home, and the racing clouds, and the big white moon - are all things that I want to remember.

~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).