Tales from the Microbial Laboratory

So.

I learned something today.  Something I was banking on (and literally) - but anyway, I learned that an architect really knows things.  They have insight.

I met late this afternoon with the architect that is helping to design my new home.  My hopefully interesting, environmentally-responsible, small footprint, nice indoor-outdoor connections, little home.  He brought with him four preliminary designs:  the first one was similar to a house plan that I had shown him that I liked (it was two stories - with two of the three bedrooms and one full bath on the second floor - the rest of the stuff is on the first floor).  I liked the first plan - he had modified the home I liked to make it more space-efficient and I was thinking 'okay, this covers what I want' - aren't we done?  But then he showed me the other three plans.

The second plan was a modification of the first one.  There was still two bedrooms and a bath on the second floor - but the location of the master bedroom on the first was different, and it took advantage of both the lot and a southerly exposure.  I liked everything in this plan except for the 'study' - my home office, in other words, that made me think that after awhile I'd feel like I had a home closet - not a home space that I'd actually like to work in (and I like the freedom that I have to work from home - or write from home, more like it).  The third plan was totally narrow and linear - interesting lines, could incorporate everything on one floor but could be two stories as well.  Again, the study/office area felt isolated from the active part of the house, and I couldn't help but think that it would become a space that I would avoid.  But the advantage of the third design was space efficiency and incredible cross-ventilation (especially with a southerly orientation on a piece of land not far from water).  I liked the plan - it was different than what I was thinking about - but it grew on me, surprisingly so.

Until he showed me the fourth plan (now remember that all of this will be close to 20' off the ground.  We're talking treehouse here).  It was completely different from the first plan, and from the house plan that I had showed him that I thought had everything that I wanted.  This house was both simple and fun -- "sexy" was the word he used, and I'd have to say that I would agree.  When he first showed it to me, I was quiet for awhile -  and finally he broke the silence and said 'okay, is this quiet-good or quiet-bad?' and finally I responded 'quiet-good'.  The house was not like anything I had thought about - except that it was perfect in ways that I hadn't even imagined.  We talked through it for awhile, modified it - but I have a feeling that the fourth plan will be the one that we build on from here on out.  It's shaped like a 'T'.  The top of the 'T' will be a master bedroom and bath (that will point towards the live oaks and have windows on three sides).  Then there will be a staircase (remember:  the house is on stilts and I'll park my car and the boat underneath the place) and then a second bedroom, that will essentially be my office (with a closet - so it will be larger than the 'study' proposed in the other plans, a good space that another could use as a bedroom if so desired).  Again, good windows and good cross-ventilation (can you tell that I crave cross-ventilation - open windows and indoor breezes as often as possible?).  Now, the interesting part.  The part that surprised me (in part because I really liked it, and I wouldn't have thought that I would):  the front door takes you into the dining room (just below the top of the 'T").  When you enter the dining room - you can walk straight through (well, after going around a table) and there will be another door that leads out to a covered area that leads you to a separate bedroom and bath - the guest bedroom.  It will be it's own building, connected to the main house by the deck and a covered roof (most likely a screened in area) - when it's not in use, it can be 'shutdown' - so closed up so to speak.  The trunk of the 'T' then will be the dining room, then the kitchen (a linear kitchen that opens up a bit to the dining area and to the living area) - the living area will be at the bottom of the 'T's' trunk.  Again, almost every room will have windows on two (and mostly three) sides.  There still are several things to work through - but we had a great discussion about how to modify his preliminary plan, and I could tell that we each got more and more excited about the design as we continued to talk about it.  It works.  So I walked into this meeting thinking one thing, and walked out being really excited about something completely different.  It was a fun surprise.

So now I just need to see if the enthusiasm holds.  I think it will.  Tonight in the dark I stood out in the front garden, by the gate, and tried to imagine a 'T'-shaped home, and it actually fits.  It fits the live oaks - in fact, it takes advantage of them.  Just as it should.

pure possibility

Is the dream of a flower...better than the flower?  Is a dream of a garden, as good as any garden?  The County Clerk's post today made me think about my garden, anybody's garden really - and what it is in the moment and how we see it in our minds.  I'm guessing that the way my eyes translate my garden is different than how another might see it (i.e., partially unmowed with chaotic areas and a little wildness thrown in).  I think it's something about the process of growing a plant -  over one season, over multiple seasons - that makes the translation of what is possible a language that we cannot easily explain.  But what we see is pure possibility.  I feel certain of that.

The Phrase of the Day:  "Impendance mismatch".  From an editorial by DeLong (Nature Reviews Microbiology, 2007, 5:326).  It's defined as 'an inadequate (or excessive) ability of one system to accomodate the input from another."  It's what's happening in genomics right now - where we're beginning to generate sequence data at a rate that is just mind-boggling - but what's even more mind-boggling is how to actually process the data, to make sense of it - and to actually use it, as DeLong says, to "confirm a functional hypothesis."  In other words - the data is no longer a dream, we can have it in our hand (or on our servers) - but what next, what then?

Today was so full - so full of life - that I don't think I can talk about it, or at least I shouldn't.  But a meeting, one that I had with several colleagues yesterday - came closer to fruition today, and closer to our own 'impedance mismatch.'  Much of the data that we are now generating for bacteria and their communities is at multiple layers of complexity:  we look at the genome (or metagenome), the proteome (or metaproteome) - and now, the metabonome (or meta-metabonome?).  We're initiating this summer with colleagues a small metabonomic study:  with a single microorganism, our favorite coral pathogen, grown under two different temperatures to a single growth phase.  A simple experimental set-up for what will prove to be a complex analysis:  the use of NMR to develop profiles of the metabolites generated by this organism under two different growth conditions.  A chemical profile you might say, an expression of the communication potential of that organism, or the metabolic potential, a way to perhaps later find that organism in a more complex sample.  We've already generated the proteome of this organism (more or less) and it's full genome sequencing is underway - so now the metabonome.  One organism and alot of data, but nothing in comparison to what we are beginning to examine at the community level. 

Impendance mismatch here we come.

 

 

bronze fennel

Oddly, the bronze fennel (Foeniculum vulgare subsp. vulgare 'Rubrum') is actually producing flowers this year - most years, the black swallowtail caterpillars (there are some nice caterpillar pics here) devour this poor fennel and I rarely see flowers.  Perhaps this year's lack of rain is playing a role.  Perhaps.  There is an increased chance of rain in the forecast for the next few days.  Unfortunately, all of the pop-up showers have thus far been kept away from right along the coast due to the sea breeze - I hope this pattern changes soon.

Today was busy, and I'm tired tonight.  Random thoughts:  I'm oddly enamored with all of the new colors of Heuchera coming out - like these I just saw in the Wayside Gardens catalogue.  They are perfect for places in my garden, shady spots that look nice with some color.  Ellis Hollow has got me thinking now about trout lilies, yes, a new plant Genus to obsess about - and just in time (a grant is due).  Speaking of grants, a pre-proposal that I submitted about a month ago has been selected for development into a full proposal.  A good thing, yes - another thing on the list, yes.  The lab had a coral 'pow-wow' today (okay, that's probably not PC) - related to the diversity aspects of the project - I think it was good but it made me realize how anxious I am about getting some of this work out - getting it published.  But...back to the garden.  I decided tonight that I could live on tomato sandwiches.  Good bread (toasted), slices of tomatoes (any and all kinds available), light on the mayo (or roasted garlic instead), salt, pepper.  Happiness.  Looking at the basil tonight, it's time to make pesto.  The first batch of the summer is always a treat.  A friend sent me a CD this week with a ton of new music on it - MP3's - helps me get through days spent glued to a computer and writing.  What would we do without music?  I'd never get anything written, I know that for sure.  It's time to get a watermelon; I haven't had a watermelon yet this summer.

It's still out tonight, there's not even a hint of a breeze.  The insects are loud, and the moon is bright.

acceptance

There's always a point in the summer when, after days or perhaps weeks of denial, I realize that the heat and humidity have won.  I accept the discomfort, recognize the limitations of the warm days - this year it seemed to have happened earlier than usual, perhaps due to the drought that is this year's companion to the heat of summer.  Spider webs have been collecting in the garden - without rains or the winds from storms to disrupt them - they slowly (or not so slowly) get made and becomes works of art in themselves.  They become permanent fixtures in the garden and I walk around them, accepting their presence.  And now that I've also accepted the summer's heat, I'll adjust - and again go out into the garden, without the expectation of a cool breeze.  The ritual of summer in the south. 

I remember when I first moved to the Gulf Coast of Florida, for a postdoctoral fellowship - a move that took me from central Michigan (and a farmhouse that didn't have air-conditioning in it's hundred years of existence) to the panhandle of Florida in mid-July.  During my first few weeks at the laboratory, each day I'd say to a colleague 'Boy, it's hot today, isn't it?' - until finally someone looked at me and said 'Pam, this isn't hot - it's just what it is'.  So now I find myself accepting the heat of the summer - or at least trying to - and once that acceptance is complete, the days seem less oppressive, less over-bearing.  It seems just like what it is supposed to be.

So I resign myself to watering.  The garden is large, I can't water everything (I simply don't have time) so decisions have to be made and I hope for rain.  The Ancient Wonder Beagle wasn't so eager this evening to eat her chicken and rice, which makes me sad.  A friend's mother passed away last night, and today there were emails and phone calls - plans had been made.  All we can really say is how sad it truly is.  Tonight I need to work late - a grant is due soon, or my part of one - and I've got to present a lecture to a class on Thursday (one that I keep worrying that I will forget to attend - the curse of the research appointment).  There is too much going on for it to be summer and so warm (the acceptance is not quite complete).

A poet from last week, Tyehimba Jess, one that Katherine introduced us to - can be heard here reciting some of his work from a collection called Leadbelly.  She read from two of his poems, and I find myself hesitating here - with respect to presenting one of them, primarily because of language that offends me, language that I don't want to propagate.  So I hesitate - but the poems are powerful and emotive, so I present them here and I also recommend that you listen to the poet reciting his own work.  It is a treat.

John Lomax Writes Home, 1934 by Tyehimba Jess

Leadbelly is
    a nigger
to the core
of his being...

He is a killer.

He tells the truth only accidentally...

He is as
     sensual

as   a goat,

and when he sings

to me

my spine

     tingles...

sometimes

     tears

          come.

Penitentiary
wardens all tell me
I set no value on my life
in using him as
traveling companion.
Don't be uneasy.
He thinks I freed him.

I am bringing him

to New York.

<><><><><><>
Leadbelly Writes Home, 1934 by Tyehimba Jess

martha:

lomax is carpetbagger
to the core.
truth slides itself
slicked up and sideways
out his mouth,
dressed up in the way
he wants to see the world.

so i let him brag on
how "he freed me"
'cause the fastest way
to a white man's heart
is through his lies,
the fastest way out
of his grace
is truth.

a day

One of the crinums opened up this morning.

The Ancient Wonder Beagle enjoyed her breakfast of chicken and potatoes and softened kidney diet.

The phone rang at 8 am (I'm still at home) and it was a colleague, saying that the core group of us needed to get together for an urgent meeting.  Was I available at 1 pm?  (Thank goodness for caller ID).

I get an email from a student in the laboratory, he's visiting a lab in Gaithersburg, getting access to a piece of equipment that will help him characterize the membrane vesicles that his microorganism of study is producing.  He writes:

hey, so the hotel i am staying at is filled with 1500 or so librarians, all for a 5 day conference discussing and doing librarian things, among other things, awarding the Newberry award. anyways, also, leaving dupont circle metro station tonight they are engraving part of a Walt Whitman poem, here is the part from it, though i guess only the first few lines will be on it...

Thus in silence in dreams' projections,
Returning, resuming, I thread my way through the hospitals,
The hurt and wounded I pacify with soothing hand,
I sit by the restless all the dark night, some are so young,
Some suffer so much, I recall the experience sweet and sad,

anyways, thats my quasi-update, and yes pam, i am writing.

tomorrow is FFF.

FFF stands for field flow fractionation.  Or something like this.  It's exciting.  We hope it works.  I think that it should.

My architect calls.  There is someone local who can certified both Earthcraft and LEED homes:  CIA Inspections.  You see, to do this, there needs to be a buy in from the beginning, all stages of building need to be approved and certified.  And (of course) there's a cost for the inspection - $600 for Earthcraft, $3,000 for LEED.  The LEED requires lots of paperwork, and the local certifier actually acts as a liason between Charleston and the LEED folks in Atlanta.  And for what?  To say that you are Earthcraft and/or LEED certified.  Some tax benefit, but minimal.  So you're doing it to set an example - for the good of the planet.  So why, you ask?  I'm still thinking about that one myself.

Oh, and gorgeous wood floors can be found at Mountain Lumber.  Other interesting products - such as plyboo (laminanted bamboo plywood) can be found at Bettencourt Green Building Supplies.  But what is it about dark woods that I'm drawn to so much?  I love the granary oak - the imperfections, the warmth of the wood.  I think I want a lighter look - lighter floors.  But boy - walnut, and other dark woods - those are my favorite.  Why is this?

I wander around the lab, put away a little glassware, talk to an undergraduate about microorganisms showing up on a petri plate (which end up, as the day progresses, to be better than we first expected), talk to another about her written qualifiers (which she just turned in last Friday) - background lab chatter.  Another undergraduate shows me gorgeous data:  a gel he has run, using a method called REP-PCR that helps to distinguish between strains of a microorganism that are the same Genus and species.  His gel is both well-done technically as interesting scientifically.  It's win-win for him, and he's happy.  Another undergraduate is learning something new - DGGE or denaturing gradient gel electrophoresis.  The undergraduates look busy - and they're all learning.  Quickly.

I call my Mom, after her appointment with her oncologist.  The x-ray shows that her lungs haven't changed.  No improvement, no worsening.  But her blood pressure is high and she must go on additional medications - and if they don't work, she won't be able to take one of her chemotherapeutic agents next Monday.  This all disappoints her - in this world of cancer, one desires no change in anything, as if holding one's breath will stop time.  But eventually one must exhale.  She's good though - one of her sister's is coming to visit from out of town tomorrow - just for the afternoon, and she will enjoy that.

I attend the urgent meeting.  After 45 minutes I still wasn't sure what was so urgent.

A colleague called me about meeting to discuss metabonomic experiments - fun experiments with a swanky NMR.  We'll meet on Wednesday.  I"ll look forward to this meeting.

I respond to e-mails regarding a grant that I've been asked to participate in, due soon, in just a few weeks - and I've been asked to take the lead on the micro component.  I agree.  I need to get busy.  But this afternoon I have an opthamology appointment, a pre-scheduled check-up and I go and wait, and wait and finally after waiting for 90 minutes I have a 10 minute appointment and I'm done.  I'm close to Whole Foods and thinking about some good fish for dinner.

I come home and let the dogs out and as I'm walking with the Ancient Wonder Beagle, I notice that orange tape is everywhere.  The survey of my place must have been done today.  Hopefully completed.  Another thing down.  The Airstream is ready for pick-up, and hopefully my friend Pete will help me haul her back from RV World later this week.  On Friday I meet with the architect; we'll sit and look over his first sketches of my new home.

The Ancient Wonder Beagle gobbles up her chicken and rice dinner.  She's thinking (I'm pretty sure) that having a failing organ isn't so bad as long as freshly cooked chicken is involved.  I take her outside, she walks around, and then I bring her back inside and she goes to her bed and sleeps. 

I harvest blueberries.  About five cups or so.  I need to harvest more tomorrow.  I water the peppers and eggplants recently planted.

The gardenias are still blooming.  The garden is fragrant as the warmth of the day fades.   

Sunday Morning

Did you hear Mary Chapin Carpenter this morning on NPR's Weekend Edition Sunday speak of 'The Learning Curve of Gratitude'?  Don't just read it - listen to her audio.  While I was on the NPR website, I came across another similar essay written by Ruth Knamps:

There are those who want to give my life more importance than the tree, but I don't believe them. They think there is a special place for me somewhere for eternity, but I don't believe them. I believe my tree and all other living things believe and feel in their particular living ways. I want to work on being as good a human as I am able, just as my tree does her job with grace and elegant treeness.

Well said, Ruth.  Elegant treeness!  I just love it.  If we could all strive to live life that way.  Like my beagle, really.  The Ancient Wonder Beagle isn't doing so well - good days followed by a bad day when I think to myself that this is the turning point, that it'll be time very soon to make the decision.  I hate making the decision.  I truly appreciate the ability to stop pain and suffering though.  Yesterday she wasn't good for much of the day - she refused food in the morning, then slept and slept - the sleep of someone far away - and when she got up and I took her outside, she was unsteady and unsure.  Her kidneys, the kidneys of a dog only a few months shy of 18, are failing.  Of course it's heartbreaking, and in my head I think about what I will need to do (I always try to have a vet come to my house if it is at all possible) - so I think about what I will do if she seems like she is in pain and it is a Sunday and the traveling vet is off - I dread the thought of taking her to the emergency vet clinic which is generally busy and hectic on weekends.  But as I settle in to the reality of this, shortly before I was leaving for a dinner out, she gets out of her bed, walks into the kitchen, drinks a bunch of water and starts barking for dinner, like always.  This morning she ate her breakfast and seems comfortable and not at all like yesterday.  Another day.  So what kind of tree would the beagle be?  Most definitely a live oak.  Solid, steady, remarkably long-lived.  Perhaps live oaks are filled with elegant dogness.  I'm not sure that we will ever know.

Homemade blueberry whole wheat-oatmeal pancakes for breakfast.  With blueberries picked just this morning.  What is it about pancakes that are so decadent?  Oh yeah, the syrup.

I've never really had a favorite dining establishment in Charleston - so many of them are good - you've got the fried shrimp at Bowen's Island that is such a treat, the sesame tuna at Cypress, the best non-thai pad thai at Mustard Seed, oh - then the thai  pad thai at Basil's and well, the list of good places to eat around here is a long one.  But I think that now I have a favorite - FIG (for Food Is Good).  I've been going there for awhile, not often, but regularly - and last night I dined there and it was just amazing.  Simple-amazing.  They focus alot on local foods and foods in season - and the simplicity of their entrees just makes every place else seem fussy and overdone.  I think that FIG is really beginning to stand apart from many of the other eating establishments here.

It's a warm morning.  'They're' saying it's 84 degrees out, but that it feels like 90.  I watered a bit - mostly the peppers that I planted only late this week - a strange collection:  the sweet Italia and Italian Gourmet, the mild Anaheim, and the medium hot Ancho/Poblano.  Another one as well, but I misplaced the tag - I think it's a chili of some kind.  They like heat, so I don't think that they'll mind this late planting date.  The tomatoes are coming in - Sweet 100's and Sungolds and Matt's Wild Cherry and Ildi (the latter are doing much better than last years attempt) - no brandywines yet, but soon.  The basil is large enough to start harvesting, and today I really need to dig up the rest of the potatoes.  Beans need to be harvested too.  I think that the figs are only a few weeks away - the tree is just covered with them, enough to share with the mockingbirds.

Rambling thoughts.  I have alot to do - I'm starting to pack, slowly - going through those drawers and kitchen cabinets that you'd rather ignore.  I'm now looking at everything in my home in a new light, asking the question 'Is this Airstream worthy?' which really is about size as much as importance.  It's an interesting exercise, finding out how much of what I have around me is really so unnecessary day-to-day.  I think that I'll learn for this.  The new house thing is progressing, but it's for another post.  As is an update on the lab - it's abuzz with activity - we're all feeling the anxiousness associated with pending data acquisitions - large amounts of it - and the three undergraduates interning with us for the summer are running around, learning new things - making genuine contributions - and it all feels good.  Another research group has recently advertised for a postdoctoral fellow to conduct research on the exact same corals that we are working on - with many of the exact same questions being asked.  Yikes.  I think I told some folks in the lab last week that I didn't think that they needed to sleep anymore.  They could eat dinner, but only on the run.  We're were laughing about it really, about how much of what we can do could be just eliminated from our lives.  Of course, we don't really mean it - I didn't mean it (at least I don't think I did) - but that's what competition does for you.  There's much to be done.  Much to be learned.

But on this Sunday morning, the beagle is asleep on her bed, after gobbling up her breakfast - and the two large dogs look like throw rugs on the cool kitchen floor.  The cat is rustling around in a box that is waiting to be packed.   I have portions of a grant to start working on - and more reading on this whole house thing to do.  I missed my morning walk on Sullivan's - I chose to sleep in instead.  Sunday mornings are for doing what you want to do. 

 

a Day of Mourning

Tomorrow has been declared a Day of Mourning for the City of Charleston - at 8 am a processional, complete with approximately 150 fire trucks - will follow a route from downtown Charleston by the site of the fire and by the fire stations of those lost - ending up at the North Charleston Coliseum where tens of thousands are predicted to be present for a memorial service.  It's been a sad week for this community, and while I've thought about rambling on in this space about the bluebird parents, my tomatoes, how my place is getting surveyed tomorrow, and about a grant that was rejected (the latter would be a rant more than a ramble) - my heart just hasn't been in it.  Tomorrow I won't be attending the memorial service.  Instead I'll be giving talks to undergraduates from Claflin University about how exciting microbial ecology is (exciting beyond words...right?).  I'll be thinking about the families though - about how overwhelming all of this must be for them, and hoping that the remarkable community support that is being shown is helping them through these difficult days.  What is it about a trajedy that brings the best in a community to the forefront?  Is there a way to sustain that feeling throughout the following weeks, months, years?  Yes, it's been a sad week here in Charleston - but also remarkable in so many ways.    

bravery

This evening I was thinking about what I could say about the tragic fire that occurred here yesterday evening - about what I could add to everything that has already been said.  I don't really have many words.  The names and photographs of the nine firefighters that perished in the fire have been released.  The list is a sad one to read.  Today has made me reflect on how I have taken firefighters for granted, and it has made me think about the dangers they face routinely.  Would anyone have predicted that a warehouse filled with sofas and chairs could be so deadly?  I know, it's a combination of factors - but the description of the fire, and how quickly it erupted into 'tornados' of flames has been hard to imagine.  But it happened, and the lives of dedicated individuals were lost.  I know that I will try, from here on out, to feel more day-in and day-out gratitude for firefighters and what they do.  It truly is remarkable bravery.

variegations

Variegated...ginger, solomon's seal, peppers, flowering maple, cuban oregano, hydrangea, spider lily, hostas, artemesia, and Farfugium (in no particular order).  Is any variegated leaf the same - doubtfully, but today they reminded me of a day in the UP of Michigan, fly fishing on the rivers that Hemingway wrote of - seeing trout for the first time - with colors that were a simple kind of beauty that words don't describe so well.  Sometimes I look at an individual variegated leaf and it reminds me of a watercolor painting - colors blending in a way that doesn't seem possible.  How does a plant do this?  I know, I know - pigments, genetics - but really, how? 

Creel by Robert Wrigley

for Greg Pape

We sentimentalize the weaver, the hands

that love and bind methodical and true,

wicker tightly wound on ribs. Fronds

of fern too, and rainbow trout blue

and gold and rose, are likewise woven,

fishermen looping the air with their lines.

What is weaving but a kind of love

for what holds: the tines

of branches locked among leaves, sure

elegance of burlap on the bundled roots

of a transplanted sapling, and if you’re

fishing, that dark nest at your hip boots’

top, nestled variegations of trout

and leaf, ribs and whitely layered flesh—

streams falling all ways down and out,

the cold fabric of the river, a mesh.

 

Cypress knees (emerging)