Tales from the Microbial Laboratory

What happens when you get six scientists in a minivan...for hours?

~~~~~

You get a Wendy's Kid's Meal Dinosaur wearing glass-beaded 'dino trousers' - a dinosaur that makes it way up to the podium during a student's presentation at least week's coral meeting.

Don't ask. 

It was a long drive down.  There were six of us in a minivan.  This stuff just happens.

~~~~~

~a dogless night~

Yes, I've been in southern Florida for the week.

Land of the flamingos - and wonderful tropical flowering plants.  There was a short outing to the Flamingo Gardens - the kind of place that has a 50% (or higher) chance of being pretty cheesy - and ended up being quite delightful.  (More images to come, when it is not quite so late, and I'm not quite so tired). 

But tonight - is a dogless night, since the dogs cannot be retrieved from the kennel until morning - it is unusually quiet.  Dog quiet.  How do people live without dogs?

The lab did well this week - and the homemade eclair-making postdoc even came up with a new lab motto:

...hopelessly misguided but intensely focused....

Yes, that about covers it....about covers us.  There's a new mascot too, but images for that are yet to come.

It's good to be home.

~splitting stars~

It's been a busy weekend, after a busy week, after a busy...oh, this could go on forever.

My July 4th evening was spent seeing the Dave Matthews Band perform - it was the first time that I've seen them perform live - and I'd go into all of the 'six degrees of separation' with Dave and his group and myself, but if a few of my friends were reading this, they'd be rolling their eyes because I'd already told them a dozen or more times.  Needless to say, I had a blast - without a single firework on the horizon.

~~~~~

So tomorrow the lab leaves for Ft Lauderdale, and a meeting that we are excited about being a part of.  It's our first real meeting with the international coral research community - and it's a good time to sit back and think about the direction of the lab's research, and where are we going with respect to what is known and what needs to be known in a broader context.  The lab has five presentations - most of them are printed out as I type this, and ready - but one is taking more time, particularly because of scheduling earlier in the week, and partly because it is the first time that this member of the lab has prepared a poster of this kind.  There is a learning curve.  The interesting part of this is that it is Katherine's poster, the lab's poet laureate - and I've caught myself taking the poetry out of her writing and form, forcing her into a scientific framework that we are all comfortable with - precision and accuracy, no overstating of one's data - ahhhh, it leaves little room for poetic license, as Katherine, even as I type this - forges ahead.

~~~~~

So I couldn't help tonight, while thinking about a poet immersing herself in a scientific world, to think about another poet who often wrote (surprisingly often) somewhat obscure poems about science and the love of science - and in particular, to that poet's poem about a man who burned down his home so that he could buy a telescope in order to explore the skies.

~~~~~

The Star-Splitter by Robert Frost

"You know Orion always comes up sideways.

Throwing a leg up over our fence of mountains,

And rising on his hands, he looks in on me

Busy outdoors by lantern-light with something

I should have done by daylight, and indeed,

After the ground is frozen, I should have done

Before it froze, and a gust flings a handful

Of waste leaves at my smoky lantern chimney

To make fun of my way of doing things,

Or else fun of Orion's having caught me.

Has a man, I should like to ask, no rights

These forces are obliged to pay respect to?"

So Brad McLaughlin mingled reckless talk

Of heavenly stars with hugger-mugger farming,

Till having failed at hugger-mugger farming,

He burned his house down for the fire insurance

And spent the proceeds on a telescope

To satisfy a lifelong curiosity

About our place among the infinities.

"What do you want with one of those blame things?"

I asked him well beforehand. "Don't you get one!"

"Don't call it blamed; there isn't anything

More blameless in the sense of being less

A weapon in our human fight," he said.

"I'll have one if I sell my farm to buy it."

There where he moved the rocks to plow the ground

And plowed between the rocks he couldn't move,

Few farms changed hands; so rather than spend years

Trying to sell his farm and then not selling,

He burned his house down for the fire insurance

And bought the telescope with what it came to.

He had been heard to say by several:

"The best thing that we're put here for's to see;

The strongest thing that's given us to see with's

A telescope. Someone in every town

Seems to me owes it to the town to keep one.

In Littleton it may as well be me."

After such loose talk it was no surprise

When he did what he did and burned his house down.

Mean laughter went about the town that day

To let him know we weren't the least imposed on,

And he could wait—we'd see to him tomorrow.

But the first thing next morning we reflected

If one by one we counted people out

For the least sin, it wouldn't take us long

To get so we had no one left to live with.

For to be social is to be forgiving.

Our thief, the one who does our stealing from us,

We don't cut off from coming to church suppers,

But what we miss we go to him and ask for.

He promptly gives it back, that is if still

Uneaten, unworn out, or undisposed of.

It wouldn't do to be too hard on Brad

About his telescope. Beyond the age

Of being given one for Christmas gift,

He had to take the best way he knew how

To find himself in one. Well, all we said was

He took a strange thing to be roguish over.

Some sympathy was wasted on the house,

A good old-timer dating back along;

But a house isn't sentient; the house

Didn't feel anything. And if it did,

Why not regard it as a sacrifice,

And an old-fashioned sacrifice by fire,

Instead of a new-fashioned one at auction?

Out of a house and so out of a farm

At one stroke (of a match), Brad had to turn

To earn a living on the Concord railroad,

As under-ticket-agent at a station

Where his job, when he wasn't selling tickets,

Was setting out up track and down, not plants

As on a farm, but planets, evening stars

That varied in their hue from red to green.

He got a good glass for six hundred dollars.

His new job gave him leisure for stargazing.

Often he bid me come and have a look

Up the brass barrel, velvet black inside,

At a star quaking in the other end.

I recollect a night of broken clouds

And underfoot snow melted down to ice,

And melting further in the wind to mud.

Bradford and I had out the telescope.

We spread our two legs as it spread its three,

Pointed our thoughts the way we pointed it,

And standing at our leisure till the day broke,

Said some of the best things we ever said.

That telescope was christened the Star-Splitter,

Because it didn't do a thing but split

A star in two or three the way you split

A globule of quicksilver in your hand

With one stroke of your finger in the middle.

It's a star-splitter if there ever was one,

And ought to do some good if splitting stars

'Sa thing to be compared with splitting wood.

We've looked and looked, but after all where are we?

Do we know any better where we are,

And how it stands between the night tonight

And a man with a smoky lantern chimney?

How different from the way it ever stood?

~RIP, CatDaddy~

Evidently CatDaddy wasn't immortal afterall.

He was a member of the lab, quite literally, for about seven years.  A not-so-uncommon contribution of CatDaddy to the workings of the lab could be uncovered in expressions such as 'The good news is, CatDaddy is fine, the bad news is - that the GC-MS is...'.

He was a good fish.

~a science day~

I haven't planted my sunflowers yet, but I have alot of them that have reseeded from last year, haphazardly and happily, in my vegetable beds.  I have alot of sunflower seeds to get in the ground, packages that I purchased from various places last season and didn't plant - so as soon as I get out there, to pull up the sugar-snap peas (that are long past their prime), the now-bolting lettuces - and as soon as I harvest the small patch of red potatoes that I planted - it'll be time to plant sunflowers in their place.  But for now, I'll be grateful for the ones that came up on their own - as if they knew that I had a difficult spring and wasn't able to get seeds in the ground myself.

~~~~~

Today was a good 'science' day - one of those days when I ignored the work that I really had to do (a reality that will haunt me tomorrow) and instead talked with my lab, found myself standing in front of the lab sink, just standing - looking around and soaking in everyone else's enthusiasm.  A new master's student came running in with a gel that showed excellent results - a first step in developing a method to detect (and hopefully quantify) a coral pathogen that seems to be just about everywhere now:  the Red Sea, the Indian Ocean, the Carribean, and the Great Barrier Reef.  This student has been working with the eclair-making postdoc on this - and, well, so-far, so-good.  Then a doctoral student in the lab showed me an article she had found, an article about an organism that she is working with now with respect to hopefully novel and broadly-acting anti-microbial activity - demonstrating a similar isolate from the same Genus (a quite interesting and poorly understood Genus) that also produces an anti-microbial (this organism was isolate from a tunicate, if I remember correctly).  This one article lead us to looking through a series of articles - all fitting in perfectly with this student's 'story' and fueling enthusiam for - stuff.  Again, the eclair-making postdoc will help clarify aspects of this - related to the organism's sequence analysis (which, I'll summarize, is FUNKY aka potentially interesting-as-hell).  There were additional discussions about projects, about life frustrations and life expectations -- there was a sense of discovery, anticipation, frustration, confusion - there was a sense that the lab was just where it should be, that it was going just where it needed to go - and that at the very least, at the end of the hour, the day - the week - that something would be learned.  I can't help but think that the lab reseeds itself, month after month - coming up here - there, unpredictable, surprising - and that like the sunflowers in my garden, knew that I had a difficult spring and took it upon itself to just...bloom. 

~a Friday evening film short courtesy of the Microbial Lab~

So, for those of you anxious for a Joy update...here's a little 'film short' to kick off your weekend...featuring an improved Joy and the immortal CatDaddy, grooving to Hendrix and Catfish Blues.

Catfish Blues

Well I wish I was a catfish,
Swimming in, lord, the deep blue sea.
I'd have a, all you pretty women,
fishin' after me, fishin' after me,
fishin' after me. Yeah.
Ohh yeah, ohh yeah, ohh yeah, ohh yeah.

When I went down, my girlfriends house.
And I sat down, lord, on her front step.
And she said a, come in now Jimi.
My husband just now left, just now left.
Ohh yeah, ohh yeah, ohh yeah, ohh yeah.

Well there's two, two trains runnin',
but there's not one, lord, that's goin' my way.
You know there's a one train runnin' at midnight.
Other one leave just for a day,
leave just for a day.
Ohh yeah, ohh yeah, ohh yeah, ohh yeah.

~a bastion of scientific intellectualism~

So it appears that Joy the goldfish (an emotional purchase of mine from the Walmart goldfish mines...), named after Joy-the-former-doctoral student (who is, as I post this, helping out a current graduate student with a functional genomics study at the University of Oklahoma) - is floating upside down.  The eclair-making postdoc (who made another batch of eclairs last week and may I just say:  WOW) cleaned out the tank really well (with some help from others I think) - but that was before this video was made (and downloaded onto YouTube, where - perhaps I shouldn't be so surprised here - there are a number of videos posted on goldfish floating upside down).

Anyway, here is Joy - and some of the lab (aka 'bastion of scientific intellectualism') watching Joy (and while I could make fun of them here, and I am - I am guilty of Joy-watching as well, an understatement, so what can I say?).

We'll keep you posted on her health status.  She's been getting peas (fresh from a student's garden), she's fasted, been quarantined, and is now back into a clean tank getting food pellets that sink. 

Yeah, you're thinking, so THIS is what they do. 

Pamdanistan, an evening

Oh, it's just another whacky evening in Pamdanistan.

The duck's neck is, well, unstuffed, suggesting not such a good duck state - however the quacker is still in good form, so The Dan feels the need to keep it with her at all times...which often means getting her nose and her duck as close to the cat as possible.  (The cat obviously feels that if she doesn't make eye contact with The Dan, that perhaps he will simply go away.  The cat is always right).

~~~~~

Back in the lab today, a salsa-dancin' doctoral student successfully defended her proposal for her dissertation research in front of her committee - a 50 minute seminar followed by almost two hours behind closed doors with her committee.  It's a critical few hours for a student - marking their successful transition from being a doctoral student to being a doctoral candidate...another step in the centuries old tradition of conferring the doctoral degree.  The student works hard to prepare - the lab works hard as well, reviewing presentation materials, asking questions and more questions, sitting in on practice seminars, and scrutinizing her materials to the last detail for typos or grammatical errors - rearranging the presentation's overall organization or even the wording on a single slide.  By the end of our many practices, I often feel that anyone in my group could get up and give the talk - and I like that sense of community, of one person's goal becoming a goal that we all share.

So while the salsa-dancin' student was frantically preparing at the last moment, the group met for their weekly laboratory meeting - with Katherine, the lab's poet laureate beginning a discussion on her community-wide evaluation of the antibiotic resistance and susceptibility profiles of her coral isolates.  The lab rambled on for awhile first, ordered a cheese pizza, and then:  the eclair-making postdoc, who often is referred to as Mr. AngryPants, accused one of the graduate students of 'harshing his mellow' -  over the past week the eclair maker has managed (after many months of struggling) to develop what is looking like a reliable protocol for obtaining good quality DNA from coral mucus.  (If this doesn't mean anything to you personally, just trust me on this one - it should).  After months of being cranky (as you might imagine a Mr. AngryPants could be) - he has been smiling, not groaning, making progress, and almost appearing, dare I say...optimistic?   All-in-all its a good thing, and we're happy.  Breakthroughs!  Successful defenses!  Nobody could do any of that harshing our mellow today, no way.  We'd dare them to even try. 

~~~~~

So, back in Pamdanistan, The Dan and The Stan are presenting a somewhat solidified front: 

'We are dogs, we might even be spoiled dogs, and we'd appreciate a large-dog sized greenie each evening after dinner.  It's the least you can do, since you abandon us for long periods of time each day.  As dogs, we feel that we are not intuitively connected to the plight of the coral reefs or instinctively interested in the upper respiratory tract microbial communities of the bottlenose dolphins, and we are, quite frankly, sick of all of the background chatter about corals and dolphins.  *yawn*  As dogs, we're thinking that adding a few pheasants or quail to the place would do it a world of good.  And while you're at it, if a heron could land inside the fence just once or twice a week, we'd really appreciate it.  But first - let's start with those greenies.  Because it's tough being a dog - dealing with the cat and all of her personality quirks, putting up with your ups and downs of having a life in science - and hey - the guest bedroom ceiling has caved in.  We're dogs, but we have our standards.  We can't get a driver's license - so come on, greenies aren't asking for much.  And stop harshing our mellow while you're at it.'     

~microbial treats~

Happy Halloween from the Headless Microbial Asylum Laboratory! 

If you happen by our laboratory door, please do knock:  there will be plenty of treats -- slants of Bacillus anthracis, vials of Clostridium botulinum, and Erlenmeyer flasks overflowing with happily growing Yersinia pestis -- and perhaps even homemade glazed doughnuts made by Wesley-the-Postdoc. 

If you don't find us in the laboratory, then it must mean that we have been released for our one hour each day...and that we are wandering the streets of James Island, bumping into the trunks of live oaks and young trick-or-treaters...while spreading our own very special and infectious brand of Halloween cheer.

 

thoughts (ever so random)

Today was nutty.

I can't write about much of it here, but just trust me when I say that it was nutty.

I had to talk with someone about what inspires me.  My first response was everything - but then I realized that I wasn't answering the question.  I was asked what inspires me about Charleston, about my work, about my life.  I got to talk with this person about science, it's low profile in the Charleston community, and why I felt that was.  I got to show her a piece of equipment in the building where my laboratory is located - to show her a piece of equipment where there were only four or five other laboratories in the US with the same capability.  She just looked at this facility and said 'Swanky' and I said 'See' and she said 'I had no idea.'   Is that good?  Good to be a low profile scientific community, or is it a reflection of something broader regarding education in general here?  I don't know.  She asked if I thought it was because we're a southern city.  She asked if it was because scientists often aren't good promoters of their work.  I said, once again, I don't know.  She asked about what it was like being a female scientist.  I had alot to say on this one, but I'm tired of that conversation so I didn't answer her.

Overall, I enjoyed the questions that she asked me.  But again, I didn't have many answers.

But something she asked me, something that was really interesting (because of it's personal relevance) - was the question about whether I have anyone outside of work to talk to about what I do.  The answer is:  sort of, but not really.  It's not meant arrogantly when I say that I tend to not talk about it because they wouldn't understand.  It's just what it is, a reality of what I do.  I talk with friends and family about the edges of my work life - about the students in the lab, about broader issues and challenges with colleagues, but rarely do I really talk about the science.  I wouldn't, over dinner, chime in 'hey, the CHAO1 index of diseased Montastrea faveolata is over 2200, isn't that AMAZING?' - but then, I think most of us don't talk about the core of our work with others.  I don't think I can say that it is any worse for a scientist than anyone else.