Tales from the Microbial Laboratory

~a winter's afternoon, Circular Quay~

~~~~~

On the way back from Cairns, flights got backed up - supposedly from Typhoon Nuri - which resulted in a 12-hour layover in Sydney last Saturday. 

It was a two-way thing.

Ugh.  A 12-hour layover added to an already long travel itinerary.

Cool.  A 12-hour layover in a wonderful city! 

So Qantas escorted us back through Customs (checking us back into the country), gave us a voucher for cabfare - and off to Circular Quay we went.  A winter's afternoon in Sydney - spent along Sydney Cove.

~~~~~

The cab dropped us off right down at Circular Quay - right at Sydney Cove, which as far as I could tell - was a great spot to be dropped off.  From this point you could hop on a ferry to just about anywhere in the harbour - and boy did we find a great place for lunch.  All within earshot of some live indigenous music.

I hate seeing Gustav head towards the Lousiana coast.  I'm mad at myself for contacting a friend and colleague only last night regarding lab space - to see if he needed room in an ultralow temp freezer for anything.  He could have fedexed it to us last week.  I did offer work space, if it comes to that - in the weeks and months following the storm if he needs it.  I hope it doesn't come to that.   

~~~~~

We only (perhaps foolishly) walked by Sydney's Museum of Contemporary Art -- I think this bonus day caught us so off-guard that we didn't actually think we do anything, if that makes any sense at all.  Later, I read that one of the main exhibits was 'The 2008 Biennale of Sydney:  Revolutions - Forms that Turn' - and I'm guessing it would have been fascinating to see.  As for the signs in front of the museum - ugh.

'Tis the season.  Yep, the tropics might give us a busy few weeks - right now we're keeping an eye on Hanna, with several computer models having her going further north of Charleston, while two models have her going much further south.  We're pretty much in the middle of the two divergent tracks.  I guess that means we pay attention, right? 

~~~~~

The Sydney Harbour bridge was quite beautiful - with a hotel at her base that I must say would be a fun place to stay for a weekend.  The park at the base was nice too.  You could walk the bridge - the top evidently has a walk way and I think I read that it takes a few hours to walk the whole bridge.  You could also take the stairs up at the end of the bridge - and there was a nice lookout there too.  (If you look closely at the image below - or click on it to enlarge it - you'll see folks in the upper right-hand corner walking - as well as one of the lookout locations).

The garden is a mess.  I desperately need to mow grass - we had quite a bit of rain while I was gone - and there are quite a number of small branches down from the live oaks - we must have had some wind too.  During this time of year it's a bit hard to be motivated in the garden - the humidity is high, storms linger out in the Atlantic - tall grass and a few branches seem trivial in the big picture.  Instead I think about where I'll need to take the boat if Hanna gets closer and stronger, and if the Airstream can weather a storm.  The Airstream can handle wind - but not a tidal surge - it'd end up floating down Highway 17 somewhere, or drifting out in the marshes.  Or better yet, just turning upside down and landing a few yards away.

~~~~~

Now these guys had spectacular views of the Sydney Opera House and Harbour Bridge...and this was the only sailboat I spotted on the water all afternoon.  (And I'd have like to hop aboard.  I need to go for a sail).

Okay, so I'll mow the grass.  I'll ignore the less-than-motivating tropical season - and mow the grass.  And I'll also find out if the stuff that I have in storage (stuff=most of my possessions) are covered for flood damage.  All in the name of 'storm preparation'.  Maybe I'll also stock up on wine.  It couldn't hurt.

~~~~~

Yes, it really is a beautiful structure.  We've all seen images of it so often, and I thought that might dim my view of it - but it didn't.  It was stunning.  It also backs up to the Royal Botanic Gardens (which, surprisingly, I did not visit - because I honestly didn't know they were there until the cab drive back to the airport).  If I had known, I would have loved to have visited the Centre for Plant Conservation & Research, which I've read a bit about since my return.  Their big story is that of the Wollemi Pine - or 'dinosaur tree'.  Here's the official australian site and here is a link to some photos of this tree.  You can even purchase them now for planting in the US.  A bit of a background (from Wikipedia - do read the whole story there, it's a very interesting one!):

Wollemia is a genus of coniferous tree in the family Araucariaceae. The Australian species Wollemia nobilis is the sole species in the genus Wollemia and was discovered in 1994 in a remote series of narrow, steep-sided sandstone gorges near Lithgow in temperate rainforest wilderness area of the Wollemi National Park in New South Wales, 150 kilometres-west of Sydney.

In both the botanical and popular literature, the tree has been almost universally dubbed the Wollemi Pine, although it is not a true pine (genus Pinus) nor a member of the pine family (Pinaceae), but rather is related to Kauri and Araucaria in the family Araucariaceae. The oldest fossil of the Wollemi tree has been dated to 200 million years ago    

(Too cool.  It is related to the Kauri pine - an image of which I showed here).

Would it be...tempting fate to say that it wouldn't surprise me at all if a hurricane came our way this year?  It's been such a tumultuous year - that I almost expect it.  I almost feel guilty saying that, with Gustav bearing down on Lousiana, and the Atlantic filling up with storms.  I think I'd almost just shrug my shoulders and say 'well, yeah...' - but perhaps I also need to improve my attitude a bit, don't ya think?  So I'll pause for a moment...

...and go through my INBOX and dig up my first graduate student, R, and his email that contains the 'go away hurricane' song that he used to sing as a kid in Puerto Rico.  So, with all credit to R:

Santa Maria, Libranos de todo mal
Amparanos Senora, de ese terrible animal

Temporal, Temporal, Alla viene el Temporal
Temporal, Temporal, Alla viene el Temporal
Que sear de mi Borinquen, Cuando llegue el Temporal
Que sera de mi Bohio cuando venga el Temporal

(I know, I'll ask R for a translation and get back with you.)

~~~~~

I'm just showing you this image - of the Observer Hotel - because I liked it.  And because my good friend from graduate school, Bill, used to always say that we scientists were 'trained observers' each time we did something blatantly...stupid.  So in honor of Bill, and all of the stupid things we've done - I'd love to stay in that hotel one day.  It was constructed in 1848 - and (no surprise) seems to have it's own resident ghost.  More reason to stay, don't you think?  As for Bill, I owe him one this trip.  I had fedexed my two poster presentations to my hotel in Cairns, and they didn't arrive by the time I had to leave Monday morning for my oral presentation (and one of the poster presentations was that same afternoon).  So he said he'd walk me to a printers after my morning session - and on the way there in INSISTED that we stop off at his hotel to drop off his computer bag - so I groaned and we stopped - and there, in the front of his hotel, was a fedex truck with both my posters inside.  Yep, that was a relief (and yes, lessons learned).

So it's just strange to think that outer bands of Gustav are crossing our shoreline today.  Mostly bringing just wind, a few really quick showers.  These storms are huge, and Gustav isn't all that big a storm (in terms of size).  But here it is, reaching us. 

~~~~~

Several hours were spent at the Market at The Rocks.  What a nice market - only open on Saturdays and Sundays I believe - and right across from a near-perfect Irish Pub, The Mercantile.  My friend and I both felt it was perfectly reasonable for Qantas to reimburse us for the shopping we had done during the afternoon - since if we had not been delayed, we wouldn't have had the opportunity - but not surprisingly, we didn't get a chance to ask (nor would we have - but it was a good running joke to justify the splurges, like the beautiful pashmina scarves...).  So yes - you got it - me, the consumate non-shopper, chose shopping over going to the Art Museum or touring the Opera House.  And I had a blast doing it.  Shopping and an irish pub - maybe it was the combination?  Anyway, after a few beers and a few packages - it was time to head back to the airport and a 14 hour flight to LAX.  In an almost full plane.  In LAX, it took almost four and a half hours to get processed back into the country, fill out the form for a lost piece of luggage (the posters!) and rebook flights to the east coast.  No wonder I'm still tired.

So, really, now it's time to mow grass.  And make a plan.  I've avoided it long enough here I do believe.     

~"I want more wine."~

I don't think that I ever imagined diving on the Great Barrier Reef.

I'm not certified to dive.  That's a nutty thing, I mean - my lab studies Caribbean corals and we've hung out around sunken ships.  We talk about bottlenose dolphins. 

In other words, there has been opportunity.  I love the water - so, I suppose, there has been little to no impediment to my learning how to dive.

I just never did it.

(Which is ashame.  I know, I know - I still can).

So a friend and I go out on a boat to snorkel on the GBR.  Onboard was a woman who had taken the same boat out a day before, and who had dived for the first time.  She was persuasive.  More than persuasive, she was enamored with what she saw down there.  How could we resist?  We were on the other side of the planet - and it was the Great Barrier Reef, for Christ's sake.  I'd like to say that I was brave while they were loading me up with weights and the tank and everything else required - but I wasn't, I was pretty terrified.  Then they shuffle you over to the end of the boat, and tell you to step off the end (yeah, right) - which I did, and thanks to bouyancy control I came back up to the surface quickly.  They had two horizontal bars at the end of the boat - one about a foot down, one perhaps five feet down - and they allowed you to get comfortable breathing at the first bar and then they moved you down to the second bar.  Unfortunately my mask was leaking pretty badly, so I had to come back up to the surface and get equipped with a different one.  It worked better. 

As quickly as I was back in the water, I was back down to the second bar - and before I had much time to think the 'dive buddy' that took you down had grabbed ahold of my left arm and was taking me out and further down.  We were down for about 30 minutes to a depth of about 6 meters.  The other person being taken down was having problems with her ears - she couldn't clear them and started to panic - so we went back up to the surface where a small boat came to get her.  However the 'dive buddy' and I went back down -  and all I can say is that it was amazing.  I'm thrilled that I did it.  There were giant clams and schools of angelfish over a foot tall, royal blue starfish and a large turtle hiding amongst the corals (partially seen in the imagine above, if you look carefully at the top center).  The corals themselves were just all sorts of colors, exquisite shades of golds and greens and blues - the images that I captured with a little disposable underwater camera don't come close to doing them justice.  But I love the images nonetheless.

~~~~~

And I'm back.  Sorting through a full INBOX and neglecting a pile of mail on my kitchen counter.  Trying to wrap my head around work and where I was -- (which wasn't such a good place to be) -- still in denial that my grass is a foot high and that rabbits have taken up residence (much to Stan's wishes, and perhaps to mine - since more rabbits generally mean fewer large snakes).  The tropics are active and today meetings started up - yes, meetings.  What do you do?  I go to meetings. 

But today there was some talk of science.  We talked about a predominant band in a protein gel (a 'hypothetical' protein), about a student's two outlines for manuscripts, and about how we need to come up with a plan for distinguishing phylotypes of an organism we are studying - there were talks behind closed doors and talks in the hallway, talks in my office and one in the parking lot.  Yes, I am back.  Today during lab meeting Katherine read to us a wonderful poem - a poem about a wooden creature who wanted to do more than what was expected of her.  Perhaps, last Friday, I did more than what I expected of myself - and yes, I want more wine too.

(What a treat it was to see this new world through my own eyes, and not through descriptions and images shown to me!) 

~~~~~

Not Paint and Wood by Martin Espada

I saw her at Neruda’s house,

carved a century ago

to keep vigil over the waves

from the prow of a ship,

with great brown eyes

and hair in a whirl,

now hovering silently

above the poet's table.

That night at the bar

she appeared at my elbow,

the same eyes, the same hair,

not paint and wood but flesh.

He likes for me to be still,

she grinned. I don't like to be still.

I want to climb the steps

at Macchu Picchu.

I want to talk about poetry all night.

I want more wine.

~~~~~

Martin Espada teaches at Amherst.  His most recent collection was a Pulitzer finalist.  Gary Soto has said, "Martín Espada has chosen to go outside the self-absorbed terrain of most contemporary poets into a landscape where others—bus drivers, revolutionaries, the executed of El Salvador—sit, walk, or lie dead 'without heads.' There's no rest here. We're jostled awake by the starkness of these moments."

~~~~~

You see, Neruda collected figureheads and wrote a series of poems about them.  (I'd love to visit that collection one day!  Is that possible?).

Here is one such poem.

To a Ship’s Figurehead (Elegy) by Pablo Neruda

From: ‘Canto general’

From the sands of Magellan we salvaged you, exhausted

voyager, immobile

beneath the storm your sweet twofold breast so many times

defied dividing itself between your nipples.

We lifted you again over the Southern waters, but now

you were the passenger in darkness, of angles, one

with the wheat and the metal you guarded

on the wide water, enveloped by oceanic night.

Today you are mine, goddess whom the giant albatross

grazed with its wingspan extended in flight,

like a cloak of music conducted in rain

by your blind wandering eyelids of timber.

Rose of the sea, bee more pure than dream,

almond-woman who from the roots

of a holm-oak peopled with cantos

made yourself form, force of the nest-filled foliage,

mouth of tempests, delicate sweetness,

that could go conquering the light with its thighs.

When the angels and the queens born with you,

covering themselves with moss, slumbered, fated

to the immobility the dead guard with honour,

you climbed to the narrow prow of the ship

and angel and queen and wave, you were the earth’s tremor.

Man’s shudderings climbed to your

noble tunic with its apple-wood breast.

while your lips oh sweetness! were moistened

by other kisses worthy of your wild mouth.

Beneath strange nights your waist let

fall the pure burden of the ship into the waves

cutting a path through the sombre extent

of overturned flame, of phosphorescent honey.

The wind opened its bag of tempests,

the unbound metal of its groans,

and the light at dawn received you trembling

in the ports, kissing your moist diadem.

Sometimes the trembling vessel heeled

when you halted your path through the sea,

like a heavy fruit that breaks off and falls,

a dead mariner whom the spume,

and the pure motion of time and ship, receive.

And you alone among all the faces

submerged by menace, plunged into barren sadness,

received the scattered salt-brine on your mask,

and your eyes retained the salty tears.

More than one wretched life slipped from your arms

into an eternity of funereal waters,

and the touch of the dead and the living

wore away your heart of ocean timber.

Today we have salvaged your form from the sand.

Finally you were destined for my eyes.

You slumber, perhaps, a slumberer, perhaps you are dead, a dead one:

your motion has finally forgotten the sighing

and the wandering splendour has ceased its journey.

Anger of ocean, blows of the heavens have circled

your proud head with cracks and fissures,

and your face rests like a conch,

with wounds that mark your swaying brow.

For me your beauty holds all of the perfume,

all of the wandering corrosion, all its dark night.

And in your raised breast of lamp or of goddess,

swelling turret, immobile love, life lives.

Salvaged, you sail with me, until that day

in which they let fall what I am into the spume.

~~~~~

 

~Cairns~

~~~~~

Flying into Cairns was quite spectacular - with those mountains edging up right to the sea.  We had been flying in the clouds - and finally we moved down below the clouds, revealing a sea - the coral sea - that was simply beautiful.

~~~~~

This is an area that I want to learn more about.  Oh, for all sorts of reasons, but mostly because of the coral research that we do, some of which is focused on a coral pathogen that is tormenting this area - how strange to work on something here on the East Coast of the United States that has such relevance to a place on the other side of the planet.

~~~~~

The Coral Sea.  I need to learn more about the Great Barrier Reef and the Coral Sea Islands.  But not tonight, later.  I'm still tired and in need of a night's sleep that mirrors those generally obtained by folks in this time zone...instead of wondering...is it time for lunch yet?

   

~~~~~

Sweet Dreams.

~jet lag~

Okay, so I'm feeling a little loopy, but this really cracked me up.  One of my student's sent it to me (and yes, the one that sends me this kind of random stuff regularly - which I really appreciate.  I refuse to ask him when he has the time to find it).

~~~~~

~arrivals~

~~~~~

I'm home.

(What day is it?)

Tired, but my head is still filled with fantastic images.

(I went for my first dive EVER on the Great Barrier Reef!).

Sleep - yes, sleep would be nice.

(Typhoon Nuri backed up flights on that side of the planet - so there was a 'bonus day' spent at Circular Quay in Sydney).

Check out Xavier Rudd.  Hear a bit of him here.

(The Dan tore up two dog beds at the Paw Plaza Hotel.  Evidently The Dan and The Stan were put into separate kennels one afternoon, and The Stan howled until they put them back together.  That made me smile.  There has been all sorts of rain here along my bit of the coastline - my grass is tall and green and most likely snake-filled, much of the garden looks as if it needs staking, and there are lots of over-ripe tomatoes still clinging to the vines).

But Australia!   

~looking out towards Low Isles~

~the rainforest~

~~~~~

This is a big place. Not quite sure where to start. Head out to the Great Barrier Reef tomorrow, then head for home.

It's an amazing place.

~~~~~

Update, 27 August 2008:  According to "Plants of Tropical North Queensland:  the Compact Guide" (John Beasley, 2006) this seems to be the Queensland Kauri or Kauri Pine, a primitive member of the Araucariaceae family linked to Gondwana. 

This ancient supercontinent (according to Wikipedia):  "included most of the landmasses in today's southern hemisphere, including Antarctica, South America, Africa, Madagascar, Australia-New Guinea, and New Zealand, as well as Arabia and the Indian subcontinent, which are in the Northern Hemisphere. The name is derived from the Gondwana region of central northern."

These are the largest trees in Queensland - and although the leaves are not needles, they do have parallel veins and the fruit are large cones.

~have a little fun while I'm gone~

The garden grows.

The 'Little Gem' magnolia is in bloom - spreading it's own version of lemon across the back garden.  The hydrangeas look thirsty and the roses are holding on tight for cooler evenings - some of the gingers are over 7' tall and look as if they still aren't done growing.

There's a few waves, popping up off the coast of Africa.

August.

~~~~~

~stick this on your blog and smoke it~

Ahhh, graduate students.  Sometimes I just want to completely ignore proper protocol and cut and paste some of their emails in here.  As for tonight, I'll paste a subject heading - which was in reference to this MIT discovery, which is nicely summarized below:

Until now, solar power has been a daytime-only energy source, because storing extra solar energy for later use is prohibitively expensive and grossly inefficient. With today's announcement, MIT researchers have hit upon a simple, inexpensive, highly efficient process for storing solar energy.

Kudos to them I say.

~~~~~

Which leads me to another email (from the same graduate student as above) that was making the laboratory aware of developments in bringing the Large Hadron Collider on-line.  It seems that the first attempt to circulate a beam will be on 10 September.  If you want to read a wonderful article - At the Heart of All Matter:  The hunt for the God particle - or, as the National Geographic article (published March 2008) states:

The preferred name for the God particle among physicists is the Higgs boson, or the Higgs particle, or simply the Higgs, in honor of the University of Edinburgh physicist Peter Higgs, who proposed its existence more than 40 years ago. Most physicists believe that there must be a Higgs field that pervades all space; the Higgs particle would be the carrier of the field and would interact with other particles, sort of the way a Jedi knight in Star Wars is the carrier of the "force." The Higgs is a crucial part of the standard model of particle physics—but no one's ever found it.

Theoretical physicist John Ellis is one of the CERN scientists searching for the Higgs. He works amid totemic stacks of scientific papers that seem to defy the normal laws of gravity. He has long, gray hair and a long, white beard and, with all due respect, looks as if he belongs on a mountaintop in Tibet. Ellis explains that the Higgs field, in theory, is what gives fundamental particles mass. He offers an analogy: Different fundamental particles, he says, are like a crowd of people running through mud. Some particles, like quarks, have big boots that get covered with lots of mud; others, like electrons, have little shoes that barely gather any mud at all. Photons don't wear shoes—they just glide over the top of the mud without picking any up. And the Higgs field is the mud.

So I really recommend that you read the National Geographic article.  It's a pretty good one.  And when you are done, reward yourself by watching the video below.

(I know, I seem like a gardener here - but at heart, I'm pretty much a geek).

~~~~~

This weeks poem was presented in between comments about lemonade (and the lack thereof), and slices of a Piggly Wiggly cake decorated in red roses with the inscription "Love, Peace and Microbes", a rough run through of a talk by an undergraduate (who latered 'WOW'ed' us all in her formal presentation) - and then, somewhere in there, was this poem that Katherine read to us.  It's a lovely one I think.

Three Naps at Walker Point by D. Nurkse

I slept, when I woke
I had built this cabin
with its shade garden,
flagstones, and screened porch
overlooking Burnt Coat Harbor.

I dozed, when I came to myself
we were middle-aged, our children
called from an inner room—
you stirred and tiptoed out,
agile as the breeze.

I drowsed and at twilight
I remained in the dream,
in the cursive slope of the letters
that would contain it, caught
in the maze of reflected masts,

so I bit back panic and listened
for the bell from the ocean.

~~~~~

I'll try to check in from Australia - perhaps share an image or two.  This is a part of the planet that I have never visited - and I'm guessing that it will be a visual pleasure.  And the reef - I can't imagine getting to see that reef.

~the GBR, off Cairns~

   

~an Emperor~

Curcuma petiolata variegated 'Emperor'

This one is worth growing for the variegated leaves alone, and for the lovely little quality of not minding a bit of shade.

The edges of the leaves remind me of a watercolor painting.

(I was wondering today if it would be possible to divide mine this fall.  I'd like to spread this one around a bit).

~~~~~

And then the flowers appear, low to the ground - and unpretentious.

(But pretentious all the same). 

The flowers are like icing on the cake - because the leaves contribute as much as one needs to contribute in a garden.

I like how my early August garden looks - and much of this is due to plants like this Curcuma - lush, green, and happy.

I need to think about filling in spaces with more gingers.  They love our heat and humidity - and while other things are fading a bit, they just seem to be coming into their own.

~~~~~

So there has been a list of things that I want to write here, but I've simply been too busy.  I head to Australia in a few days for a meeting - it'll be my first trip to that interesting land, and I'm looking forward to it (except for the fact that I have quite a bit to do before I'll feel ready to step foot on the plane, that is, planes:  Charleston to Charlotte to San Francisco to Sydney to Cairns.  Once I get there though, I'll be staying in a hotel with views of the marina, the city, the water and the mountains - a week with those views doesn't seem half bad, so I'd best not whine for abit.

~~~~~

As for life, my Father, Brother and I chose my Mother's gravestone today.  It was another step in this...this whole thing - but while we felt good choosing something nice, it was another step in the acceptance of our loss.  I know that it was strange for my Father, because in reality he was picking out his own gravestone as well - and his one requirement was that it was of the same granite that his Mother and Father's gravestone was made of.  Theirs is a beautiful stone - in the same cemetery where most of my long-gone relatives are buried.  I know that my Father now feels better with this taken care of.  I'm not sure how I feel.  There is a part of me that wants to resist completion of these milestones - to slow down the process a bit.  But I know that is a bit foolish. 

~~~~~

I'm tired.  More, hopefully, tomorrow.