Tales from the Microbial Laboratory

World Ocean Day

How Much Oil Has Leaked Into the Gulf of Mexico?

Found here.

jumping into the fray

I've been watching the oil spill, sneaking glimpses like sneaking pieces of chocolate - a curious, even addictive appetite, a past history of experiences - yet reluctant to jump in, to make a call and say 'I'm available if needed'.

But tonight I watched this video, and it isn't about the science, it's more about having a social conscience.  I received an email, a few emails were sent - the word 'team' was tossed around.  We'll see - the work that needs to be done requires big money, varied expertise - willing investigators.  But I hope something comes of it - I can't stand just sitting by, watching, waiting for more video. 

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A good source of information can be found here.

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eloquence

From the 7 May 2010 issue of Science (Vol. 328. no. 5979, pp. 689-690):

Climate Change and the Integrity of Science

We are deeply disturbed by the recent escalation of political assaults on scientists in general and on climate scientists in particular. All citizens should understand some basic scientific facts. There is always some uncertainty associated with scientific conclusions; science never absolutely proves anything. When someone says that society should wait until scientists are absolutely certain before taking any action, it is the same as saying society should never take action. For a problem as potentially catastrophic as climate change, taking no action poses a dangerous risk for our planet.

Scientific conclusions derive from an understanding of basic laws supported by laboratory experiments, observations of nature, and mathematical and computer modeling. Like all human beings, scientists make mistakes, but the scientific process is designed to find and correct them. This process is inherently adversarial—scientists build reputations and gain recognition not only for supporting conventional wisdom, but even more so for demonstrating that the scientific consensus is wrong and that there is a better explanation. That's what Galileo, Pasteur, Darwin, and Einstein did. But when some conclusions have been thoroughly and deeply tested, questioned, and examined, they gain the status of "well-established theories" and are often spoken of as "facts."

For instance, there is compelling scientific evidence that our planet is about 4.5 billion years old (the theory of the origin of Earth), that our universe was born from a single event about 14 billion years ago (the Big Bang theory), and that today's organisms evolved from ones living in the past (the theory of evolution). Even as these are overwhelmingly accepted by the scientific community, fame still awaits anyone who could show these theories to be wrong. Climate change now falls into this category: There is compelling, comprehensive, and consistent objective evidence that humans are changing the climate in ways that threaten our societies and the ecosystems on which we depend.

Many recent assaults on climate science and, more disturbingly, on climate scientists by climate change deniers are typically driven by special interests or dogma, not by an honest effort to provide an alternative theory that credibly satisfies the evidence. The Intergovernmental Panel on Climate Change (IPCC) and other scientific assessments of climate change, which involve thousands of scientists producing massive and comprehensive reports, have, quite expectedly and normally, made some mistakes. When errors are pointed out, they are corrected. But there is nothing remotely identified in the recent events that changes the fundamental conclusions about climate change:

(i) The planet is warming due to increased concentrations of heat-trapping gases in our atmosphere. A snowy winter in Washington does not alter this fact.

(ii) Most of the increase in the concentration of these gases over the last century is due to human activities, especially the burning of fossil fuels and deforestation.

(iii) Natural causes always play a role in changing Earth's climate, but are now being overwhelmed by human-induced changes.

(iv) Warming the planet will cause many other climatic patterns to change at speeds unprecedented in modern times, including increasing rates of sea-level rise and alterations in the hydrologic cycle. Rising concentrations of carbon dioxide are making the oceans more acidic.

(v) The combination of these complex climate changes threatens coastal communities and cities, our food and water supplies, marine and freshwater ecosystems, forests, high mountain environments, and far more.

Much more can be, and has been, said by the world's scientific societies, national academies, and individuals, but these conclusions should be enough to indicate why scientists are concerned about what future generations will face from business-as-usual practices. We urge our policy-makers and the public to move forward immediately to address the causes of climate change, including the un restrained burning of fossil fuels.

We also call for an end to McCarthy-like threats of criminal prosecution against our colleagues based on innuendo and guilt by association, the harassment of scientists by politicians seeking distractions to avoid taking action, and the outright lies being spread about them. Society has two choices: We can ignore the science and hide our heads in the sand and hope we are lucky, or we can act in the public interest to reduce the threat of global climate change quickly and substantively. The good news is that smart and effective actions are possible. But delay must not be an option.

P. H. Gleick,^* R. M. Adams, R. M. Amasino, E. Anders, D. J. Anderson, W. W. Anderson, L. E. Anselin, M. K. Arroyo, B. Asfaw, F. J. Ayala, A. Bax, A. J. Bebbington, G. Bell, M. V. L. Bennett, J. L. Bennetzen, M. R. Berenbaum, O. B. Berlin, P. J. Bjorkman, E. Blackburn, J. E. Blamont, M. R. Botchan, J. S. Boyer, E. A. Boyle, D. Branton, S. P. Briggs, W. R. Briggs, W. J. Brill, R. J. Britten, W. S. Broecker, J. H. Brown, P. O. Brown, A. T. Brunger, J. Cairns, Jr., D. E. Canfield, S. R. Carpenter, J. C. Carrington, A. R. Cashmore, J. C. Castilla, A. Cazenave, F. S. Chapin, III, A. J. Ciechanover, D. E. Clapham, W. C. Clark, R. N. Clayton, M. D. Coe, E. M. Conwell, E. B. Cowling, R. M Cowling, C. S. Cox, R. B. Croteau, D. M. Crothers, P. J. Crutzen, G. C. Daily, G. B. Dalrymple, J. L. Dangl, S. A. Darst, D. R. Davies, M. B. Davis, P. V. de Camilli, C. Dean, R. S. Defries, J. Deisenhofer, D. P. Delmer, E. F. Delong, D. J. Derosier, T. O. Diener, R. Dirzo, J. E. Dixon, M. J. Donoghue, R. F. Doolittle, T. Dunne, P. R. Ehrlich, S. N. Eisenstadt, T. Eisner, K. A. Emanuel, S. W. Englander, W. G. Ernst, P. G. Falkowski, G. Feher, J. A. Ferejohn, A. Fersht, E. H. Fischer, R. Fischer, K. V. Flannery, J. Frank, P. A. Frey, I. Fridovich, C. Frieden, D. J. Futuyma, W. R. Gardner, C. J. R. Garrett, W. Gilbert, R. B. Goldberg, W. H. Goodenough, C. S. Goodman, M. Goodman, P. Greengard, S. Hake, G. Hammel, S. Hanson, S. C. Harrison, S. R. Hart, D. L. Hartl, R. Haselkorn, K. Hawkes, J. M. Hayes, B. Hille, T. Hökfelt, J. S. House, M. Hout, D. M. Hunten, I. A. Izquierdo, A. T. Jagendorf, D. H. Janzen, R. Jeanloz, C. S. Jencks, W. A. Jury, H. R. Kaback, T. Kailath, P. Kay, S. A. Kay, D. Kennedy, A. Kerr, R. C. Kessler, G. S. Khush, S. W. Kieffer, P. V. Kirch, K. Kirk, M. G. Kivelson, J. P. Klinman, A. Klug, L. Knopoff, H. Kornberg, J. E. Kutzbach, J. C. Lagarias, K. Lambeck, A. Landy, C. H. Langmuir, B. A. Larkins, X. T. Le Pichon, R. E. Lenski, E. B. Leopold, S. A. Levin, M. Levitt, G. E. Likens, J. Lippincott-Schwartz, L. Lorand, C. O. Lovejoy, M. Lynch, A. L. Mabogunje, T. F. Malone, S. Manabe, J. Marcus, D. S. Massey, J. C. McWilliams, E. Medina, H. J. Melosh, D. J. Meltzer, C. D. Michener, E. L. Miles, H. A. Mooney, P. B. Moore, F. M. M. Morel, E. S. Mosley-Thompson, B. Moss, W. H. Munk, N. Myers, G. B. Nair, J. Nathans, E. W. Nester, R. A. Nicoll, R. P. Novick, J. F. O'Connell, P. E. Olsen, N. D. Opdyke, G. F. Oster, E. Ostrom, N. R. Pace, R. T. Paine, R. D. Palmiter, J. Pedlosky, G. A. Petsko, G. H. Pettengill, S. G. Philander, D. R. Piperno, T. D. Pollard, P. B. Price, Jr., P. A. Reichard, B. F. Reskin, R. E. Ricklefs, R. L. Rivest, J. D. Roberts, A. K. Romney, M. G. Rossmann, D. W. Russell, W. J. Rutter, J. A. Sabloff, R. Z. Sagdeev, M. D. Sahlins, A. Salmond, J. R. Sanes, R. Schekman, J. Schellnhuber, D. W. Schindler, J. Schmitt, S. H. Schneider, V. L. Schramm, R. R. Sederoff, C. J. Shatz, F. Sherman, R. L. Sidman, K. Sieh, E. L. Simons, B. H. Singer, M. F. Singer, B. Skyrms, N. H. Sleep, B. D. Smith, S. H. Snyder, R. R. Sokal, C. S. Spencer, T. A. Steitz, K. B. Strier, T. C. Südhof, S. S. Taylor, J. Terborgh, D. H. Thomas, L. G. Thompson, R. T. TJian, M. G. Turner, S. Uyeda, J. W. Valentine, J. S. Valentine, J. L. van Etten, K. E. van Holde, M. Vaughan, S. Verba, P. H. von Hippel, D. B. Wake, A. Walker, J. E. Walker, E. B. Watson, P. J. Watson, D. Weigel, S. R. Wessler, M. J. West-Eberhard, T. D. White, W. J. Wilson, R. V. Wolfenden, J. A. Wood, G. M. Woodwell, H. E. Wright, Jr., C. Wu, C. Wunsch, M. L. Zoback

^* To whom correspondence should be addressed. E-mail: [email protected]

Michael Specter: The danger of science denial

The List, Updated

 
~redwing Euphorbia~

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Thank goodness I don't go through the whole pollen allergy thing - because around here right now, there's a layer of the stuff on everything.  It makes you wonder what it's elemental composition is, and if it wasn't around, what ecosystems might collapse!

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The Microbial Lab's mission moves forward - with the submission of two manuscripts over the past few days to the open access journal PLoS Pathogens.  It was the first time that we have submitted to PLoS - and I'm looking forward to the fast turnaround for reviews.  We wanted this work - focused on the genome and proteome of an emerging coral pathogen - to be published in an open access journal for easy accessibility to the broader coral research community.  Now just cross your fingers and toes that the reviews go well - it was our 'first' genome and proteome (and we've become quite attached).

THE LIST was last updated on the last day in January 2010 - and then there was this much earlier update on 10 August 2009.  Progress has indeed been made.  The Microbial Lab's Life during Wartime continues on, and I must say that with 10 manuscripts either published or in review since early last summer, that getting an even dozen submitted within a year seems possible to me now.  That will be the new goal of the Microbial Lab during this wartime year. 

In the meantime, I might go out into the garden for awhile, with the pollen, and weed.  
  
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THE LIST

1. work describing a coral pathogen and the role of motility (led by our collaborators in Israel): Published.
2. work describing metabolites produced by a coral pathogen (led by local collaborators): Published.
3. work describing genes involved in nutrient cycling in coral microbial communities: Published (and take a look at the journal cover photo).
4. work describing the bacterial communities in the upper respiratory tract of Atlantic bottlenose dolphins: Published.
5. work describing the phylogeny of a globally-distributed coral pathogen (collaborative with colleagues from Australia):  Published.  
6. work validating the presence of a coral pathogen in the Caribbean and the pathogen's antimicrobial characteristics: Published.
7. work describing a method to detect and quantify a coral pathogen in environmental samples: In Revision.
8. work describing clinically-relevant bacteria and fungi in gastric, upper respiratory tract and fecal samples of Atlantic bottlenose dolphins: In Review.  
9. work describing the genome of a coral pathogen: In Review. 
10. work describing the proteome of a coral pathogen at two different temperatures: In Review. 
11. working describing the antimicrobial resistance and susceptibility profiles of coral-associated bacteria: In Preparation.
12. work describing the toxicity of a nanoparticle to bacteria: In Preparation.
13. manuscripts 8-12 are all close to submission - in addition to these 4 manuscripts, we have ~12 additional manuscripts where the data is collected, some writing has been done, but they are not close to submission (just yet!).

International Year of Biodiversity

2010 International Year of Biodiversity

IUCN Red List of Threatened Species™

(on the left)

my official last day of winter

~cedar waxwings, hanging out in the tops of the popcorn tree~

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There has been an unusual number of robins hanging out in my garden over the past few weeks - large birds compared to the more common goldfinches and nuthatches and sparrows - and an unusual thing about them, that I haven't noticed before either is that they have been enjoying the berries on my large Savannah Holly.  These berries are typically reserved for the annual visit of the cedar waxwings - and finally, yesterday morning, they arrived - pushing the robins out (at least for awhile), taking up residence in the top of the popcorn tree (chinese tallow) and taking turns flying the short distance to the holly to enjoy the berries.

This morning I was thinking about the robins, and was hoping that they sensed warmer days and had decided to fly south a few hundred miles more.  Personally, in my own garden calendar, I have decided that this last day in February is the last official day of winter - and that spring begins tomorrow, no matter what.  I will ignore the two days in the forecast for next week, with predicted highs only in the 40s - and I will ignore that one night predicted to be just below freezing.  This morning I noticed crocisma coming up - and most certainly I did not notice the crocisma yesterday morning - one entire clump of daffodils in in bloom, another type of daffodil should be in full bloom next week - the hyacinths are showing color, buds are swelling, and one protected hydrangea is leafing out.  If they can ignore days in the 40s, then so can I (ignoring biology of course, and how responses to day length often trump all else if some species).

This afternoon I plan to work in my garden, in celebration of the garden's last official day of this dreary, cold, and miserable winter.  Let spring officially begin!

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~the South Carolina Aquarium~

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Yesterday I had an interesting day - a new experience as a scientist - as I was invited to speak to a group of middle and high school teachers on the topic of 'Ocean Acidification' as part of a continuing education program focused of 'Ocean Awareness Day' focused on oceans and a changing climate.  The event was coordinated by a number of folks, including the SEWEE Association, the SC Aquarium, and COSEE SouthEast (Centers for Ocean Sciences Education Excellence) - the southeastern group serves North Carolina, South Carolina, and Georgia.

It was a small group of teachers - about 12 from the three states - but they were interesting and quite passionate and they raised some issues that just baffled me.  At the beginning of the workshop, they were asked to list some questions/concerns they had about the topic - and one said that a few students had approached her when she started teaching climate change science, stating that like evolution, it was - more or less - against their religion.  The insinuation, which was not surprising, was that it was against their parents politics.  When did science and politics and religion get so messed up...and entangled in education?  The other interesting point that was raised by another speaker, a climate extension specialist, was that the southeastern United States is an anomaly with respect to current climate change models - thus making it difficult when folks from this part of the world say, tonque-in-check, 'See?  Al Gore was certainly onto something, wasn't he?  It's been sooooo warm in Charleston this winter...'.

You see, what many folks forget is that everything, and I mean EVERYTHING- including global climate patterns, is based on what is happening right here in Charleston, South Carolina.

Remember that.  

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~moon jellies~

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You must love it before you are moved to save it.

Sylvia Earle, Oceanographer

(a TED prize winner)

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Yesterday was a nice day.

I finally was seeing the Florida invasive and infectious organisms that had invaded my body over the previous week retreat, and it was nice to feel a bit more human again (it was one of those flu-like illness where at some point, late at night, you pondered whether you would ever feel well again).  It was also nice because as I found myself talking to the teacher workshop - I realized, despite all the craziness, how lucky I have been.  While talking with the workshop folks, one teacher asked what I studied - and I told her that right now, we were working mostly on corals and bottlenose dolphins - and she laughed and said "How'd you manage that?" - she had a point.  I'm unemployed, and my near future is a bit uncertain - but amidst it all I have an invitation to the University of the Virgin Islands in St Thomas to discuss areas of possible collaboration, the publications we are having released have been received well (with more to come), and last Friday we received ~113 Mb of sequence data (for those of you who don't regular talk in Mb language, 1 Mb=1,000,000 bp) - metagenomic libraries from the upper respiratory tract of eight bottlenose dolphins.

It's a stressful time, but it sure is interesting.   

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~little white fish, captured by the flash~

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Don't these guys look like flashes of bright metal?  After my talk, and after I enjoyed lunch with the workshop participants, I walked around the Aquarium for the first time in a long while.  Unfortunately for me (but fortunately for the Aquarium), it was crowded - but I still enjoyed stopping at my favorite tanks - the moon jellies, the large ocean tank - and the outdoor exhibit with all of turtles swimming around.

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~little white fish, captured in low light~

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Of course I became enamored with these little white fish - and while I like them looking as if they are shiny, metallic objects - I think I like even better this out of focus image.

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~turtles, hanging out~

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It was so crowded that I didn't get the Genus and species information on most of these guys - but that didn't stop me from enjoying them.  The turtles were quite playful, and photogenic - and although my images weren't as focused as I would have liked, the patterns on these guys are so amazing that it doesn't seem to matter.

Tomorrow, in the afternoon, I'm attending a loggerhead turtle planning meeting (with these guys) - I want to get some samples from them, to cryopreserve for microbiome analysis at a future time.

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Another view...

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...and another.  This one I really liked - with the reflection of the glass ceiling overhead - I thought the contrasting patterns were interesting.

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~the Ocean tank~

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I'll end this with two images of the ocean tank - the large tank essentially in the middle of the aquarium.

Oh, and by the way - happy last day of my winter! 

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fun

Now, these guys are fun!

~a sunken ship, leaking oil, and being a happy camper~

~U.S. Naval Historical Center photo G-387565, obtained from here~

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Pearl Harbor Day is always a bit of an odd day around the Microbial Laboratory.  Although it's fearless leader was raised a pacifist, and it's members are much too young to think much about something that happened 68 years ago - we are still tied to the ship that has come to be a symbol of that day, and of our country's resilience.  I've spoken of this tie before (and even before that).  You see, my lab has collected a large amount of data describing the oil that is leaking out of the memorialized vessel - and so sometimes on this day we get a bit of attention because of our past involvement in the project.

Now this is always nice attention (of course it is) but it's also a bit stressful because I still have two or three manuscripts to write describing what we learned.  They've been lingering much too long, and while others are pondering the significance of this day in our Nation's history, I'm kicking myself in the butt for not having submitted manuscripts on this work for publication already.

  For a fascinating look at the history of the USS Arizona and on-going preservation efforts, I recommend that you spend some time here.

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As for me, well, I should get writing (and if it were only that easy).  But alas, yesterday's funky state has gone viral, at least in my little world - this morning the Airstream's electricity blew, and I have calls in to several electricians with no call backs yet.  I'm posting this because of an extension cord that is connected to the power in the falling-down house - and this evening I've been alternating between plugging the cord into the computer, the TV, and the Vornado.  Fortunately for me I always liked camping (although I must say, tonight is testing my limits).

So if you're in the neighborhood, please do drop by - there's a fire going outside, and if you have the ingredients for s'mores, all the better.

Happy Pearl Harbor Day.