Tales from the Microbial Laboratory

~one step at a time~

~convergence~

Tonight I've sat and thought about how research projects in my laboratory evolve -  how they move in directions, often in disconnected ways, and how sometimes when you sit and look at the work from a distance, with a wider lens, how they begin to converge in a way that is surprising and exciting and new. 

I've felt that way this evening, after sitting through several meetings today, and after editing several sections of presentations from members of my lab, in preparation for an international conference next week. 

I've never had caladiums in my garden before - I've never been tempted to purchase the bulbs, haven't been much of a fan.  But a friend of my Mothers gave her three different kinds last fall, and throughout this past winter she was determined to nuture them (telling me that they were unusual varieties) and keep them going in order to plant them in the springtime (I think she knew that she could have just saved the bulbs - but for some reason, mostly obvious ones, she wanted to keep them growing, to keep them producing new leaves).  I rescued the three pots a month or so ago, and they are now growing in my own garden.  I appreciate them now - they are part of my Mother and something she was looking forward to, and their colors are bright in a heavily shaded area of my garden.  Tonight I marveled at how the bright veins converged in the center of the leaf - how the leaves looked like road maps that mirrored my thoughts on the work in the laboratory.    

~a pineapple lily and insidiousness~

Sometimes there are days that are just plain stressful.

Today was one of those days.

The details are too boring to go into here, details that are common to an academic life in the research sector.  What is it that they say?  Money and space.  That's all it comes down to.

There is little thought of the pineapple lily, blooming away on a warm June day.  There is little thought of such a photogenic little flower - because it doesn't provide my lab money, and it doesn't provide any space.  It doesn't keep the lab stocked with PCR reagants and disposable and sequencing funds.

But this little flower - the pineapple lily's stalk of little flowers - is exquisite in everyway.

But enough of that.  The day ended better than I thought it may have.

~~~~~

And towards the end of such a stressful day, I received an email from my friend over at 3Dsound: Draggin' the Line about something that gives me chills.

It concerns a faculty member at my alma mater, Michigan State University, and at attempt by another to suggest that his studies on evolution are fraudulent.  You can begin this chilling tale by reading the article over at salon.com, and when you're done there - it is well worth your time to head over to here and read the exchange between Lenski and Andy Schlafly.  Of significance is the request by Mr Schlafly for Professor Lenski to make his data available.  From Mr. Schlafly's request, dated June 13, 2008 and posted here:

Submission guidelines for the Proceedings of the National Academy of Science state that "(viii) Materials and Data Availability. To allow others to replicate and build on work published in PNAS, authors must make materials, data, and associated protocols available to readers. Authors must disclose upon submission of the manuscript any restrictions on the availability of materials or information." Also, your work was apparently funded by taxpayers, providing further reason for making the data publicly available.

Please post the data supporting your remarkable claims so that we can review it, and note where in the data you find justification for your conclusions.

I can only say that this sort of request from a non-scientist is chilling - perhaps even insidious.  As 3D mentioned in his email, you 'contact the author of a paper that you don't like', 'demand the author's data', and 'when the author fails to kowtow to your *every* possible request', well, the requestor can 'demand an inquiry into how public funds are being abused'.  It's pretty evident from the exchange that Schlafly had not even read Lenski's work.

It's really worth reading the exchange.  Lenski handled it well (and head over to Daily Kos to read an interesting post about his work - or to NewScientist to read a recent news blurb about Lenski and his research group's discovery -- or better yet, find the primary article if you have access). 

This kind of thing can give well-intentioned scientists nightmares.  Money, space...and now this.

~~~~~

Update, 1 July (morning):  Head over to 3Dsound for some additional comments and links.

Update, 1 July (evening):  Another post that I found interesting on the topic - from over at a Candid World.  Okay, and you've got to take a look at Conservapedia's entry on Richard Lenski.  Absurd.  Oh - and now there is the Lenski Affair (read towards the end - about the censoring). 

(Okay, I'm a week late about this.  But geez, I've been busy).

~it's snowing bacteria~

No, no, no -- this isn't coastal South Carolina.

(We have daffodils and the ever-fragrant hyacinths in bloom, spinach seedlings showing their faces - and roses budding out like crazy). 

It's the road that my brother used to live on in Vermont (he still lives in Vermont, but just down another road).

In tomorrow's issue of the journal Science (29 February 2008), there will be an article titled 'Ubiquity of Biological Ice Nucleators in Snowfall' [Christner et al., Science, Vol. 29(no. 5867):1214].  Here is the abstract from the Science website:

Despite the integral role of ice nucleators (IN) in atmospheric processes leading to precipitation, their sources and distributions have not been well established. We examined IN in snowfall from mid- and high-latitude locations and found that the most active were biological in origin. Of the IN larger than 0.2 micrometer that were active at temperatures warmer than -7°C, 69 to 100% were biological, and a substantial fraction were bacteria. Our results indicate that the biosphere is a source of highly active IN and suggest that these biological particles may affect the precipitation cycle and/or their own precipitation during atmospheric transport.    

Ahhh!  All of you out there that are tired of the winter's continuing snowfall, might have a bacteria (or two or three) to blame.  This is interesting - imagine what it means with respect to transport of bacteria around the globe!  Look closely at that snowflake...

You can find the 29 February 2008 Science podcast here, if you'd like to hear an interview with Christner.

~a camellia bouquet~

A Monday morning, another camellia's near-perfect bloom.

~~~~~

The morning has started with a flurry of e-mails, and not the kind that one would like to receive.  Yes, I'm in the midst of a firestorm, fortunately not in the center of it, but close enough to the fire to get singed.  Ahhhh...I need to make time to retreat into my lab.  The lab is a good place right now - busy, good-anxious, positive, funny.  The science is good.

~~~~~

So a former neighbor, Scott, sent me a link over the weekend which describes a recent article in New Scientist that made me smile a bit - regarding Amazon River dolphins and behavior and culture and 'gifts' of a very special kind.   From the David Byrne Journal post:

What is culture? In the NS article it’s described as a complex skill (or behavior) that is spread and maintained by social learning rather than being a genetically fostered behavior, or one that the local environment might simply encourage. This description defines by exclusion: culture isn’t the making of things or a certain set of behaviors, but depends on how those behaviors are learned and transmitted. You could have the best table manners in the world, but if they’re merely instinctual, then you’re not cultured. Others define culture as using things or behaviors symbolically — and by that definition these dolphins seem to qualify too. When applied to people, this umbrella definition of symbolic behavior includes codes and prescribed manners of dress, language, religion, rituals, etiquette, morality, cuisine, and on and on. Inevitably, some of those products of culture in dolphins will be invisible to us; we won’t be able to know their religion, if they have one — not now anyway.

It seems that in some populations of dolphins, that the males carry objects - weeds, sticks, clumps of sediment - and that, well, these 'accessories' help the male in the whole mating thing.  As the study goes on to say, the females do not carry these objects - but the fact that they recognize these accessories - and tend to 'go for' the men carrying the most interesting bouquet of seaweed (as an example) - suggests that she too must have some culture to even care.

Later in the post:

In the past, another way of excluding members from the culture club was tool use — for a long time it was assumed that only humans used or fashioned tools. Then chimps were seen carefully choosing thin sticks and fashioning them into tools for extracting delicious honey ants. After that, more and more examples of animal tool use were spotted and acknowledged. Even in dolphins, it turns out. In an inlet called Useless Loop (Useless Loop!!), dolphins pluck specifically shaped sea sponges and use them as protective gear when probing the ocean floor. Some of the scientists who have spotted the sponging behaviors claim it is learned socially — the dolphins teach their kids how to sponge — which qualifies this kind of tool use as a form of culture.

This morning I am not doing the post (nor the original New Scientist article) justice - I'm distracted and need to be doing other things.  But I did want to make note of it - simply because I enjoy things that change our view of (and place in) the world and our perceptions of it.  It is also quite sweet to think of a male dolphin, scouring his environs for a clump of seaweed - to think of a male dolphin accessorizing as he goes about his day (but then I've always been a sucker for a bouquet of beautiful seaweed). 

Imagine the pressure. 

Imagine what a bouquet of camellias might get him!

~~~~~

Time to get back to it.

~~~~~

(An aside:  I am in conflict about all of this, you do know that, don't you?  Cultural perceptions, expectations - there is something inherently sweet about a bouquet of seaweed, but I recognize that those 'in the know' about where that seaweed is are infinitely more successful then the male dolphin carrying a stick around.  There's something all too familiar here, isn't there?)  

~electricity~

Holly fern.  Cyrtomium falcatum.  A broken branch, early on a cool morning in late January.

~~~~~

I realized recently that when I think of science, rather the history of science - that I generally either daydream about scientists of years and years ago - or am enthralled with the science of the present.

Old discoveries, the first observations, surprisingly sophisticated cave drawings - the origin of writing in Mesopotamia - old things, old things that were beyond bold.  To stand up one day and draw on a wall (which, now that I think about it, I have the freedom to do in my soon-to-be-demolished home).  Then, today's science, science of the minute - what scientists can see today amazes me.

~~~~~

Last week Katherine sent me a pdf of a book review published in Science (2007, Vol. 315:768), a review of Joyce E. Chaplin's The First Scientific American:  Benjamin Franklin and the Pursuit of Genius.

I haven't read the book, but I think that I will.

From the review:

"Experiments and demonstrations were public events," Chaplin comments.  The term scientist was not coined until the 19th century, and many citizens from all professions had a hand in advancing and appreciating scientific knowledge.  For his famous electrical experiments, Franklin collaborated with a lawyer (Thomas Hopkinson), a silversmith (Philip Syng), and a Baptist Minister (Ebenezer Kinnersley).  In contrast to the polarization too often seen nowadays, how refreshing to think of "[m]embers of the clergy preach[ing] the new philosophy of nature."

Wow.  Now that is something.

I've ignored that transition.  The transition from doing science (and having that activity be a part of the popular culture) to being a scientist.  Perhaps I'd rather do it as a normal part of society (which, yes, it probably is - and I'm being sensitive here) - an activity which others can contribute to - than to do it isolated in a laboratory with other scientists.

It's just something to think about.

I submitted a manuscript today for review.  I hope it's a decent contribution.  I hope the submission process will go smoothly. 

I hope that a lawyer will be ask to review it, or perhaps a silversmith.

But I doubt it.

~~~~~

Words of wisdom:

Either write something worth reading or do something worth writing. Benjamin Franklin

Words of even greater wisdom:

Beer is living proof that God loves us and wants us to be happy.  Benjamin Franklin

      

(A Sniffing and Pondering) Stanley and an Acceptance Speech

Stanley can't help but sniff the air on this wondrous and crazy-warm December day, all the while pondering the significance of Al Gore's shared Nobel Prize with the Intergovernmental Panel on Climate Change, the words Al delivered in his acceptance speech, and the fact that the very leaves that littered the ground all around him fell from a tree [Triadica sebifera (L.)] considered to be a highly invasive species in the southeastern United States.  (In case you didn't know, Stanley does ponder quite a bit).

~~~~~

Read below the fold for a copy of Gore's acceptance speech.

~dead-end questions~

The morning started with a commotion on the front deck - shrill sounds that I didn't recognize at first, but then I looked out - and a foot or two away was a hawk that had swooped down on the deck and captured a bird.  I responded in an automatic, impractical and foolish way:  I opened the front door, hoping to save the bird that was now covered by the wings of the hawk.  The hawk took off, landed in the grass under the live oaks, and Stanley ran down the steps, causing the hawk to fly over the fence, across the tidal creek where it landed on the opposite bank.  During all of this, I heard the shrill, terrifying cries of the captured bird.

My reaction - as automatic as it was - was indeed a foolish one.  I'm guessing that if it happened again, that I'd once again rush to the door in a silly attempt to save the captured bird.  A few minutes ago, I heard Stanley outside - rushing down the front stairs - and when I went out to see what was up, I saw that he had chased a raccoon up one of the large oak trees, and that he was frozen, perfectly still, focused on the animal up on the branch over his head.  I called him - and he (reluctantly) came indoors.

Tonight I've been reading, writing, and thinking.  The grant is due in nine days.  I've read many interesting things, but I've yet to have a vision, and I've been uncomfortable, until a few moments ago, about why - and then a simple (and most likely obvious) thought popped into my head:  the dolphin respiratory tract microorganisms that we are 'seeing' and keep referring to as related to 'human pathogens' - well, it isn't that way at all.  I have been hung up on everyone else's questions.  The questions have distracted me. 

Why are you finding organisms in dolphins that are similar to those associated with humans?

How did the bottlenose dolphins become infected with human pathogens?

Is the antibiotic resistance of the dolphin microorganisms due to exposure to antibiotics from humans?

Questions, that in my conversation with several individuals today, kept getting me off-track.  I knew differently, intuitively, but I nonetheless encouraged these conversations.  So as I read some tonight, I was feeling awkward - and then I realized that I needed to shed these questions, dead-end questions, that everyone was asking, to shed the day's conversations, and come up with my own question and internal dialogue. 

So I thought about my response this morning, my rush to save the captured bird - as you all know, as I have trouble accepting, the hawk was just doing what a hawk does.  I could have just as easily cheered the hawk on, been relieved that it had captured it's lunch - my perspective was just skewed and biased.

It is much more likely that we humans have dolphin microorganisms associated with us.

What I need to read up on is evolution.  The evolutionary age of cetaceans versus Homo sapiens - not just the age, but the how of evolution.  So it's hypothesized that we showed up about 200,000 years ago (granted, our ancestors showed up much earlier).  An estimate.  It is also believed that cetaceans - dolphins, whales and porpoises - are descendants of land-living mammals.  You know, the whole coming-up-to-the-surface to breathe thing.  It seems that one of the the earliest hypothesized ancestors of the cetaceans are the Pakicetids:  these animals, often referred to as the earliest whales, were possibly around 52 million years ago.  So what I need to understand is how the Pakicetids evolved - and how they evolved in relationship to Homo sapiens.  I need to understand the phylogenetic tree of humans, relative to the cetaceans. 

All of this thinking and reading probably will end up being a sentence or two in the proposal, if it's included at all.  But it's important to the process:  there is most likely a relatively stable percentage of microorganisms associated with humans - and associated with dolphins - that have co-evolved with these two very different mammals.  But do you want to hear something interesting?  A recent article in Nature (Dethlefsen et al. 2007.  Nature 449:811-818) - which discusses the co-evolution of human-associated microorganisms (from more of an ecological perspective), states that only four of the fifty known bacterial phyla dominate humans - so low diversity at the phylum level - but there is substantial diversity at the species/strain level.

In bottlenose dolphins we are seeing a very similar relationship.  Surprisingly similar.  These two mammals - with such distinctly different lifestyles - share remarkably similar phyla:  the microorganisms that we are finding associated with bottlenose dolphins comprise three of the four phyla found associated with humans.

I don't know about you, but I find this really fascinating.  And to think that it took a hawk on my deck early in the morning to make me think about things a bit differently.

~~~~~

The roses are still happy in the garden.  The pale yellow of Mermaid is towering over everything, who'd get near those thorns anyway.  This morning I realized that over half of my roses were covered in flowers - yes, December, and a warm Autumn, in South Carolina.

~~~~~

Take a look, just for the fun of it, at the Aquatic Ape Hypothesis.    

stacking wood (and thoughts on resolution)

Today I moved a pile of wood that was underneath my home to the back of my yard, along the fence.  The wood was from trees in my garden that came down as a result of Hurricane Gaston, just over three years ago now.  Much of it has been burned - but quite a bit remains - some logs too large and in need of splitting (that will be most likely enjoyed in a bonfire one day). 

My stacking skills are adequate, but definitely not elegant - and I'm sure that my brother in Vermont would comment on both the technique and appearance of my stack (while being quietly relieved that he didn't have to help me do it).  This weekend my 'goal' at home is to start dealing with all of the stuff underneath my home - in my  garage of sorts.  Getting this stack of wood moved was an important component of the 'stuff' that I wanted to deal with.  Dry wood, and dry wood that came from trees downed in my own garden from a hurricane - I consider that a precious commodity.

Moving the wood today wasn't something that I had been looking forward to - it wasn't that much wood though, and it just needed to get done.  It felt good to be doing something purely physical, after a week of meetings, grant preparations, and hours spent hovering over an IT guy as he worked on my corrupted hard drive.  Today, after the wood was moved, I grabbed my camera to take a photograph of the stack - where I found myself zooming in closer and closer to the wood.  As is obvious on these pages, I tend to take more macro images than anything else.

It hit me, while taking these images, that it should be no surprise that I am a microbiologist.  When I look at things, I can't seem to get close enough - and when I'm playing with my camera, I generally get so close that the images become out-of-focus - and I don't mind the blurry images, they still provide information, a new 'view' of an object and what the object is all about.  In the laboratory, we're always operating at the edge of resolution - cramming our lenses into our experimental samples as closely as we can, never quite finding ourselves as close as we'd like to be.

Ultimately, we always want to be closer.  We stare into our blurred results - for hours, for days - sometimes for weeks and months - trying to see something that we hadn't seen before, something new, something deeper.  We work with organisms that are several microns in size - and become frustrated (as one student is now) due to struggles in our hunt for something that requires nanometer scale resolution.  Where are those zinc oxide nanoparticles?  They have to be in there somewhere...or not.  We want to find them - not finding them suggests that they are either there, and we can't resolve them - or they are not there (and we have no controls on that observation).  We keep looking.

What can we resolve?  These images are from one of the laboratory's past publications, where a doctoral student in the laboratory studied the cell surface of Pseudomonas aeruginosa using atomic force microscopy (AFM).  I think that these images are beautiful - they show changes in the cell surface of this organism, and reflect changes in the surface lipopolysaccharides during growth on a hydrophillic, compared to a hydrophobic, substrate (what you're looking at, in the right column, are sections of the bacterial cell that are ~0.5 microns in size - with a micron being one millionth of a meter).  In AFM, a microscale cantilever (with a sharp probe at the end) moves along the sample's surface - and to simplify the description, the probe's movement is recorded digitally - and the resulting digital images are characteristic of the surface of the object.

This image was the sum total of five days spent at the Advanced Photon Source at Argonne National Laboratory.  Several years ago now, a graduate student and I were fortunate to receive a grant for five days of beamtime.  It was one of those 24/7 kinda things - beamtime is precious and regardless of the time of day, there were people wandering around, waiting for a sample or peering intently at a sample or simply pacing nervously - it's a place filled with scientists asking big questions - and here we were, simply there because we were curious about the localization of metals within (on?) a bacterial cell.  Each of the squares in the image represents the same bacterial cell (the rod-shaped Burkholderia sp. - yes, this one) - and each square shows the localization of a different metal within that cell.  Unfortunately, these data did not conclusively answer our question - and this figure is just something we pull out from time-to-time, primarily when we want to reflect on how fascinating microorganisms are - but the first time that I saw this image - I realized that it's difficult to get the desired resolution:  while this is amazing, it couldn't resolve a fundamental question regarding the localization of metals (surface-associated?  inside the cell?  both?), which would require a different approach and a beamline with even more resolution.  The beamline exists - perhaps one day we will answer our question.  I hope so - but until then, we will use different methods - but just knowing these views are available makes us want to cram our lenses even closer inside of our question. 

No wonder I cram my macro lens into the throats of flowers and come up with images like this.

So what was Stanley doing while I was thinking about all of this?  While I was moving a pile of wood, he was pondering the realization that he lived in a household that was rejected by a dog rescue group.  He was outraged, of course.  And troubled - even a bit sad.  He thought back over his days on Johns Island as a young stray, battling parvovirus - and how he now sleeps on beds, runs on beaches, and dreams of Airstream vacations.  How dare they!       

   

a saturday morning frost (and perhaps a freeze?)

This morning there was a heavy frost covering the garden on the northwest side of my place - there was frost on the mexican sunflowers, frost on the cabbages, frost on the wisteria - yes, an unwelcomed (but unavoidable) and most definitely undeniable frost.

Online, I saw that at 8:42 am it was 37.4 degrees farhenheit.  According to my much less sophisticated assessment of the temperature:  at 8:02 am when I walked across the garden hose on the front deck, it crunched. 

I covered a few things last night:  two still happy (and producing) chilli peppers, the marigolds, the satsuma and two Meyer's lemons (all three in the ground), the large cardamon ginger (Alpinia calcarata) and bromeliad (both in pots on the deck) - a few other things I threw into the back of my car late last night, just to be safe.  We are supposed to reach 70 F by Sunday afternoon. 

This cool air is only temporary.

~~~~~

Thoughts following me around this morning....

I was waiting for this:

The U.S. Fish and Wildlife Service decided that federally protected mussels can live with less water from Lanier, which could allow drought-stricken Georgia to keep more water in the drying lake.

I find all of this a very slippery slope (I mentioned this before - and the relationship of the drought to the Endangered Species Act). 

Yes, water is HUGE.  Quality water.  I think that it will be the issue of the future.

The sterility of the (healthy) human lung...is this just an assumption?   All of the data that I can find on this is based on diseased lung samples - and I feel like I must be missing something, but after a phone conversation yesterday, perhaps I am not.  So -- I'm working on a grant related to the microbial diversity of the upper respiratory track of wild bottlenose dolphins - from preserved samples from animals located in the Charleston Harbor (SC) and the Indian River Lagoon (FL).  This is a revision of a grant that was not funded several years ago - a proposal that received good reviews except for one haunting one:  If we don't know the microbial diversity of a healthy human lung, why should we start with the dolphin?   Excellent (albeit annoying) point.  Human subjects are hard to work with (paperwork, paperwork, paperwork...as it should be) but christ, wild bottlenose dolphins aren't exactly a breeze either (more paperwork, paperwork, paperwork...as it should be).  But I have to work through this one review -- and there are two ways to go.  Move away from the possibility that dolphins are sentinels of human health in the marine environment, or simply say that it is most likely a false assumption that human lungs are sterile - confront the dogma.  There's advantages/disadvantages to both approaches.  Moving away from the link is easy - we're focusing on upper respiratory track fluids of the dolphins anyway (not the lung specifically) and the anatomy of the dolphin (something I'm getting a crash course in) is very different from the human (resulting in different niches within the organisms for microorganisms - and different pathways for travel).  But (isn't there always a but?) - the preliminary data that we have obtained suggests relatedness to a funky suite of known human pathogens.  The preliminary data is eye-opening.  Wes, the eclair-making, tool-sharpening postdoctoral fellow, has been obsessed with this dataset for awhile now - for good reason - and it's hard to not look at it and think about the relationship between a cetacean swimming around in Indian River Lagoon and us.  And everything that I know about microbiology tells me that the human lung - the healthy human lung - contains a modestly flourishing microbial community.  I can't ignore that.