Tales from the Microbial Laboratory

hydrangeas

a Wednesday

It was another morning that was shared with the male painted bunting at the feeder, still happy that he has the white millet seed feeder to himself, since others quickly tire of such a simple diet.  The female is still absent from the feeder - seen weeks ago but not since - she is probably staying close to the nest.   

Tonight I feel as if there are many things that I would like to write about, but I sense no theme in my thoughts and I honestly can't imagine that my own personal Wednesday evening stream of consciousness would be of interest to anyone - but here I sit, writing.  It was a full day, a decent day, and there was a meeting of the lab and a poem read and discussions about the research projects of the three undergraduates joining us for ten weeks of the summer.  These students (an example) are always fun:  often it is their first experience is a 'real' research laboratory and they bring with them the enthusiasm that day-to-day science often dampens - in other words, their excitement reminds us why we continue to pursue our hypotheses with such dedication.  They help us to remember why.

So...projects.  One will help to characterize the membrane vesicles associated with a strain of Burkholderia.  Another will focus on a coral pathogen, a strain of Vibrio sp. - and will examine how the well-studied ATCC strain will compare with recently isolated strains from coral reefs off the southern coast of Puerto Rico - the student will learn genomic profiling techniques and approaches to studying anti-microbial activity and an antibiotic resistance assay.  The third student will be trained in molecular approaches to assessing microbial diversity - DNA, DNA, DNA - gotta love it, we most certainly do.  Amidst talks of definable undergraduate research projects we also talked about poetry and the lab's poetry 'plan' and the new plan is that as well as have Katherine present poems to us each week, that we would venture out and be brave and start writing our own and presenting them.  I must say that having a laboratory that discusses genomic profiling and poetry with such growing ease thrills me - there's a feeling of creativity in the room that I just want to breathe in and I laugh to think that my students will get out well-equipped to discuss microbial phylogenetics and membrane transport mechanisms and Kwame Dawes...and other poets.  There's something so perfect about the marriage of interesting science and poetry and today I couldn't have imagined anything more natural that having doctoral students in microbiology willingly volunteer to present poems to one another.

But back to Kwame Dawes.  He read tonight from several of his collections, as well as from a new group of yet to be published poems as part of the Sundown Poetry Series of Piccolo Spoleto.  I've mentioned him before in these pages, and it was a treat to hear him present his work in the small courtyard adjacent to the Dock Street Theatre.  There was a nice breeze and cool shade and the courtyard was full but not too full and this man born in Ghana who grew up in Jamaica and spent time in so many places - this man with a wonderful voice captured the spirit of South Carolina in a way that many ignore - he writes about it's roots and it's people and captures a part of the south that makes you understand where it has been and why and how.  I walked away with a signed copy of 'Midlands', a collection that he read from, and I can still hear his voice although I've been home for hours, and in his words I'm still thinking about a million different things, the least of which is the simple power of words such as these that he prefaced his poem 'Excursion to Port Royal' with, words written by the american poet Ishmael Reed:

i am inside of

history

its

hungrier than i

thot.

So of course this preface made me want to read more about Ishmael Reed, something for another night.  But is that not a wonderful collection of words?  Being inside of history, which of course we all are?  And to describe history as hungry?  But then Dawes went onto read from his collection 'Wisteria' - poems written in the late evenings after interviewing 80 year old african american women from Sumter, South Carolina.  In one poem, he started and ended the reading with the singing of two spirituals - and the words of the songs intermingled with the words of his poem and the breeze in the courtyard and then he read another wonderful poem written about a woman that had passed away just two days ago. 

The power of words.  Driving home tonight I thought about the traditional slave song 'Wade in the Water' and how when I used to swim regularly after work that it was often playing during my first few laps since the young man teaching the water aerobics class (in the open area of the pool next to the lanes for lap swims) always started off with that song.   I used to welcome that song, listening to a word or two each time I came up for a breath of air.  He recently emailed me, since we often spoke before and after his class - asking how and where I was and why I hadn't been there to swim recently.  Tonight I realized that I need to get back to swimming regularly, that I need to get back to the rhythm of that song, and that I need to join my students in writing more poetry myself.  Tonight, while I can't say that I understand the south and what it is all about - while I can't claim to embrace it's history or it's struggles, I realized sitting out in that courtyard, listening to a man with a jamaican accent describe this state so intimately, I realized that I needed to try harder to understand it's true rhythm.

Wade in the water (children)
Wade in the water
Wade in the water
God's gonna trouble the water

If you don't believe I've been redeemed
God's gonna trouble the water
I want you to follow him on down to Jordan stream
(I said) My God's gonna trouble the water
You know chilly water is dark and cold
(I know my) God's gonna trouble the water
You know it chills my body but not my soul
(I said my) God's gonna trouble the water

(Come on let's) wade in the water
Wade in the water (children)
Wade in the water
God's gonna trouble the water

Now if you should get there before I do
(I know) God's gonna trouble the water
Tell all my friends that I'm comin' too
(I know) God's gonna trouble the water
Sometimes I'm up lord and sometimes I'm down
(You know my) God's gonna trouble the water
Sometimes I'm level to the ground
God's gonna trouble the water
(I Know) God's gonna trouble the water

Wade in the water (children)
Wade out in the water (children)
God's gonna trouble the water

a Tuesday

I was greeted this morning by the male painted bunting at the feeder - I'm sure that he was thinking 'it's about damned time' because the feeder had sat empty for awhile.  I finally remembered this weekend to pick up some white millet seed (their favorite from my experience).  This is the fourth year in a row that I've had a pair nesting in my yard - and while my intentions have been to be an active member of the Painted Bunting Observer Team, I've failed miserably at my PBOT duties.  Over the past three years, I've always felt that I had the same pair return each year to nest - but this is the first year that I feel as if I have a different (younger) pair (offspring perhaps?).  They've just behaved differently, it's hard to explain.  I think that you can get to know a bird - if only from a distance.  I just don't feel as if I know this pair yet.

Today the laboratory was paid a very generous visit by a Professor Emeritus from Tel Aviv University.  He was in the states for a meeting, and was taking a side trip to visit a cousin in Charleston - so he had contacted me months ago about spending the day with my research group.  His laboratory was the first to isolate and characterize the coral pathogen that we are now sequencing the genome of - our first full genome of a microorganism.  This organism is becoming more and more interesting to us each day:  it's being found more frequently in coral-associated microbial communities, it's temperature-dependent virulence and susceptibility to anti-microbials is fascinating - and I'm eager to see it's similarity to other important Vibrios - cholera, vulnificus, shiloi.  The discussions today were interesting, illuminating, puzzling, comforting - when a senior scientist comes to visit your group, it's always useful to gauge their response to your on-going studies, new data, and hypotheses - especially on something like our coral project which is a field I've only recently joined.  At the end of the day, I felt good - we all felt good - and eager to get on with it.  As one of my doctoral students said as we were all leaving the place we'd gathered for lunch:  we're on the edge of a whole lot of discoveries.  I do believe that is true.  The lab's postdoc heads tomorrow up to Rockville, Maryland, and the J. Craig Venter Institute to generate test metagenomic libraries of our coral microbial communities.  A test library alone will generate more sequence data than the laboratory has ever obtained before.  It's going to be quite a summer.

Now I need to grab the dogs and spend some time in the garden.  Today was warm and it's still dry.  We desperately need rain, although none is predicted in the near future.  A nice summer thunderstorm would be a welcomed end to the day.  But that will have to wait for another day to end.     

Japanese Irises

Before heading to Bishopville, South Carolina, on Saturday - a friend and I stopped off at the Sumter Iris Festival.  I had not been before, and for the most part, I'm not much of a festival-goer, but Pete had said that it would be worth the drive just to see all of the japanese irises in bloom, and he was most certainly right about that.  The Swan Lake Iris Gardens were worth the drive all itself...and I love the fact that the garden was an accidental one.  According to their website:

Swan Lake-Iris Gardens began in 1927 as a private fishing retreat for Hamilton Carr Bland, a local businessman. At the same time he was developing the 30 acres of swamp on what is now West Liberty Street, he was landscaping the grounds of his home with Japanese iris. They failed miserably, and after consulting expert horticulturists from as far away as New York, he ordered his gardener to dig up the bulbs and dump them at the swamp. The following spring, they burst into bloom. The accidental garden, referred to by Southern Living magazine a "lovely mistake," has since been developed into one of the finest botanical gardens in the United States.

I walked away from the festival with an Iris ensata Pink Dace, Flamingo Frolic (I couldn't find an image of this one - but it's a large flower, white, with purple veins originating from a yellow center), and Geisha Obi.  They were a bit picked over when I got there, since it was late in the afternoon on Saturday - but I think that this will be a great start.  They'll need moisture, so I'm planting them around a bird bath that I try to fill up with water regularly, so I'm hopeful that they will do well.  I did get them planted today.  I don't know terribly much about Japanese Irises, so here are some links I found, while roaming around the web last night:

• The Society for Japanese Irises
• Japanese Iris Photographs by L.R. Fortney
• National and International Iris Societies

   

little bowls (Magnolia grandiflora 'Little Gem')

a Monday at home (planting)

I tell myself that I don't have a holding bed, I mean - I haven't purposefully dug up an area and designated it as such.  But yesterday morning I was looking at the area under one of my live oak trees, and I'm thinking that I'd better get planting and transplanting - still in pots was a satsuma, another chaste tree, a copper plant, japanese irises (note the plural), a beautiful white swamp iris, a variegated abutilon (Abutilon pictum 'Souvenir de Bonn') and recently obtained 'passalong' plants from a friend living on the Gulf Coast of Florida - in the ground (but in the right spot?), a few ferns and hydrangeas.  My goal for the day:  to get all of this sorted out!  Perhaps with a margarita in hand (it is a holiday, right?). 

But what a nice day to spend in the garden - the tobacco jasmine mingles with the lacecap hydrangeas, the magnolias are in bloom (my large southern magnolia has so many blossoms on it this year that you can smell them throughout the entire front garden), and the blueberries are ripening.  Plus, it's a Monday and I'm at home!

Time to plant.

Pearl Fryar's Topiary Garden (Bishopville, South Carolina)

When you drive into Bishopville, South Carolina, you immediately know that there's something different about the place.  The main street is like alot of other small town main streets in South Carolina, except that it looks a little more hopeful, more optimistic - and there in the center of Main Street is a neat brick median planted with four evergreen topiaries, and not just your everyday topiaries.

A few months ago, I was fortunate to be able to attend the opening of the documentary, A Man Named Pearl, about Bishopville topiary artist Pearl Fryar.  Since I've lived in South Carolina, I've heard alot about this man (all good) and although I've always thought I'd love to see his garden up-close, I simply never made the two and more hour drive to Bishopville.  The documentary about his life is being released into a few markets soon (I've heard Charleston, Charlotte, Knoxville, and Indianapolis, but I'm not sure) and the hope is that it will get picked up for broader distribution at some point.  I most certainly hope all of you get the opportunity to see it.

As for me, seeing his garden in person was everything I thought it would be and much, much more.  I thought about it on the drive back to Charleston - and all I could come up with is that this man is simply everything that is written about him.  He's the real thing.  He's a man who forty years ago started cutting the shrubs around his house differently.  He's a man with a vision bigger than his three acres of land, bigger than Bishopville, and bigger than the state of South Carolina.  So here's how it goes:  you drive into Bishopville, you see the topiaries on Main Street, then you stop and ask where the topiary garden is.  A guy on a bicycle at the gas station tells you that you need to turn around, and take a right immediately after the town's only cemetery.  After the turn, you can't miss it.  At the turn you notice a few small, subtle topiaries (that you hadn't noticed driving into town), then you turn and you start driving down Broad Acres Road and you look up and well, everybody's right:  you can't miss it.  There, a bit up the road, on the left, is a 'yard' like no other.  Yes, 165 Broad Acres Road.  How could you miss it?

So, everything I'd read said that Fryar was always working in his garden, and that he loved when folks stopped by, and that he'd stopped whatever he was doing to talk with you.  So here it was, almost 5 pm on a Saturday evening, and there he was, working in his garden with another man.  There was that tractor that he was always riding around on in the documentary, and there was a ladder (he always kept a ladder close by).  They were planting annuals in a huge heart-shaped trench that he had dug into  the lawn - it  was just under the words 'Love, Peace, and Goodwill' that he had already planted.

So he stopped, and talked with us.  He tells us that we can walk around as long as we'd like and take as many pictures as we want.  This man in Bishopville made this garden out of mostly unwanted plants, he doesn't use fertilizers or pesticides, and he rarely waters (and we get hot and dry here).  All of the sculptures and fountains in the garden he has made from just things he found 'laying around'.  He has numerous plants, such as short-needled evergreens, that really shouldn't be growing in his garden (much less thriving).  He's really into mentoring young kids now, because he feels that anybody can take anything and make it something special.  If that's not true with gardening, I don't know what is.  He feels that if you work hard enough at something that you love, that eventually, someone will take notice.  I guess he was right - because he smiled a big smile when I told him that I had seen the opening of his documentary in Charleston (he immediately asked if I had liked it), and then he went on to tell us about how the Garden Conservancy was working with him to see that his garden is cared for and that it will be preserved in the future (Pearl Fryar's Topiary Garden Fund of the Garden Conservancy).  The pride he takes in the place is etched in his face, and his passion for his garden is beyond anything I have ever seen.  If you're experiencing a bit of the gardening doldrums, or any kind of doldrums for that matter, go visit this man.  He is about as contagious a person as I have met in my life.   As for his garden, I'll show you a bit of what I captured, but just know that the real thing is so much better.

     

a day

Convincing a friend to join me in a whirlwind tour of rural South Carolina today, the first full day of Spoleto, wasn't as difficult as I thought it would be.  The day was filled with black water and bald cypresses, swans, more japanese irises than I thought existed, and the most passionate gardener that I have ever met.  It was nice driving through the corn fields (dry as they were) and small towns - sometimes I forget how much of my existence resides within a mile of the Atlantic Ocean. 

More to come on irises and topiaries. 

the Cordyceps Fungus (from Planet Earth, the BBC Series)

'bird by bird I've come to know the earth'

Once upon a time there was a bluebird pair who decided to take up residence in the lower right condominium of a purple martin house.  The caretaker of this purple martin house had lowered the house in the fall in order to clean it out, and amidst the events of the early spring, she had neglected to raise the house to it's full height on the pole  So there the house sat through the winter and early spring, resting on a snake guard made of wire mesh with sharp edges that the caretaker prayed would protect any bird families that would take up residence there.

One day, the caretaker noticed that a male bluebird was sitting on the top of the purple martin pole, as if standing guard.  Soon, a female bluebird was seen there as well - and they both after a few days were discovered to be entering and exiting the purple martin house with some frequency.  Again, the caretaker was busy and days went by and then a week or more and suddenly small beaks could be seen through the lower right doorway (if the caretaker stood on a large clay pot to take a look).  Two beaks actually.

So the caretaker panicked.  Her garden is a renowned snake emporium, the Lower Awendaw Snake Emporium to be exact (at least in her own terrified mind) - and she couldn't bear to see these bluebird babies become an evening snack for some wayward snake simply fulfilling it's own ecological destiny.  That simply was not acceptable.   

So one evening, she decided to move the purple martin house up a few feet so that the snake guard would be more effective.  She didn't want to move it too far up the pole, because she didn't want to disturb the baby bluebirds or anger the doting parents - but according to wire mesh snake guard lore, it was best to have the guard about two to three feet below the house.

Fortunately, after moving the snake guard, all seemed good.  There was one incident of a gruesome nature that involved a four foot snake and a dog, and the caretaker can gladly say that the dog won (but she just came in on the 'tail' end of this event, quite literally).  But one day, as quickly as the bluebirds appeared, everything fell silent.  There was no longer the male bluebird sitting proudly on the top of the purple martin pole, taking turns with the female bringing food to the two babies.  There was also no longer any starving cries coming from inside the lower right doorway - and it seemed much too early to just assume that the young ones had just up and flown away.  For a week or more, the caretaker feared the worst:  that a snake had learned to manuever around the sharp edges of the wire guard through some fantastic acrobatic feat.  After a day or so, however, she was looking up over her head, into the live oak canopy above, and she saw the male bluebird and then the female - flying around in an area of the yard opposite of the purple martin house.  There were no little ones in sight.

But yesterday, the caretaker learned that there is indeed an advantage to working from home, because one happens upon events that they would not normally notice.  Perhaps it's because the dogs are sequestered inside during work days, dreaming of being free in the garden, or perhaps it is because the caretaker isn't roaming the place, digging here, planting there.  But suddenly, from the deck, the caretaker noticed once again the male bluebird on the top of the purple martin pole...with a baby bluebird.  Before long there was a flurry of flying bluebirds, the female stopped by, and then the second offspring.  Yes, it appeared that the two baby bluebirds had made it after all.

Which brings me to poetry, and Pablo Neruda.  This morning while I was procrastinating the inevitable (i.e., work) I was roaming my favorite sites and happened upon a post mentioning Neruda over at A Lake County Point of View.  I marvel at Pablo Neruda, for a million different reasons, the first of which is that he wrote love sonnets with such clarity and force that they bring you to your knees.  My favorite, perhaps, is The Infinite One, of which he writes (a partial verse):

For me, you are a treasure more laden

with immensity than the sea and its branches

and you are white and blue and spacious like

the earth at vintage time.

In that territory,

from your feet to your brow,

walking, walking, walking,

I shall spend my life.

I mean, my God - 'walking, walking, walking' -  (men, read this man, study him, and as for me - I shouldn't be reading his poetry late on a Friday evening) - words that he not only wrote but lived by.  He not only wrote beautiful love sonnets, but he wrote them about a woman that he truly loved, he felt the immensity of all of her.  But then...Pablo distracts me further, because he writes of the sea with such intensity, and of flowers with such passion (as the County Clerk makes mention of), and (yes, there's a point to all of this) of birds.  Pablo was a birder.  This man rich in odes and sonnets also wrote 'bird by bird I've come to know the earth'. 

The Poet Says Goodbye to the Birds from Arte de Pajaros, 1966 (The Art of Birds) 

by Pablo Neruda

A provincial poet and birder, I come and go about the world,
unarmed,
just whistle my way along,
submit
to the sun and its certainty,
to the rain’s violin voice,
to the wind’s cold syllable.

In the course
of past lives
and preterit disinterments, I’ve been a creature of the elements
and keep on being a corpse in the city:
I cannot abide the niche,
prefer woodlands with startled
pigeons, mud, a branch of
chattering parakeets,
the citadel of the condor, captive
of its implacable heights,
the primordial ooze of the ravines adorned with slipperworts.

Yes yes yes yes yes yes,
I’m an incorrigible birder,
cannot reform my ways -
though the birds

do not invite me
to the treetops,
to the ocean
or the sky,
to their conversation, their banquet,
I invite myself,
watch them
without missing a thing:
yellow-rumped siskins,
dark fishing cormorants
or metallic cowbirds,
nightingales,
vibrant hummingbirds,
quail,
eagles native
to the mountains of Chile,
meadowlarks with pure
and bloody breasts,
wrathful condors
and thrushes,
hovering hawks, hanging from the sky,
finches that taught me their trill
nectar birds and foragers,
blue velvet and white birds,
birds crowned by foam
or simply dressed in sand,

pensive birds that question
the earth and peck at its secret
or attack the giant’s bark
and lay open the wood’s heart
or build with straw, clay, and rain
the fragrant love nest
or join thousands of their kind
forming body to body, wing to wing,
a river of unity and movement,
solitary
severe birds among the rocky crags,
ardent, fleeting,
lusty, erotic birds,
inaccessible in the solitude
of snow and mist,
in the hirsute hostility
of windswept wastes,
or gentle gardeners
or robbers
or blue inventors of music
or tacit witnesses of dawn.

A people’s poet,
provincial and birder,
I’ve wandered the world in search of life:
bird by bird I’ve come to know the earth:

discovered where fire flames aloft:
the expenditure of energy
and my disinterestedness were rewarded,
even though no one paid me for it,
because I received those wings in my soul
and immobility never held me down.

— Pablo Neruda


translated by Jack Schmitt,
University of Texas Press, 1989