Tales from the Microbial Laboratory

Oceans

Yes, this morning's walk on Sullivans Island was a wet one - intermittent rain showers and rainbows - that left the Perfect Wood unfazed and happy (and now sore as her 11-yr old frame recuperates from a 2-hr walk).  It was funny - walking on the beach in the rain on the last day of the year, walking through rain showers yet not feeling cold because it was so warm out.

Sometimes I wonder why I'm so drawn to the ocean.  I was raised in the shadow of the Blue Ridge Mountains, in Virginia, and although I call those mountains home, even still - it's the oceans that have captured my curiosity and it's the oceans that calm me now.  I started out enamored with soil - mapping fields in southwest Virginia, growing sunflowers in an alternate cropping rotation with winter wheat in a research station outside of Blacksburg - learning about cation exchange capacity and  partical size and horizons - and while my own garden roots me to the soil even still, as does some of my research - much of what I do now focuses on the study of on-going sea processes.  Walking along Sullivans today, a barrier island that's changing, growing, evolving at a rapid pace each day now - I came across a very large tire that had washed up on the beach, parts of a dock, and metal debris - pieces of metal scattered amongst the bodies of a dead pelican and heron.  Ironically, the dogs respected the newly dead bodies and didn't rush to roll on them - but kept walking, keeping some distance.  As I walked I realized how little I know fundamentally about the oceans - although much of my lab's research is focused there - and how much I need to learn.  There is always so much to learn - but I find myself now in a marine laboratory, without ever having taken a single marine biology course in my life.  It's never too late to learn I hope.

Recently I came across a ScienceBlog - Deep-Sea News - that I think I will enjoy.  They have a 'series' going, '25 Things You Should Know About the Deep Sea' (they're on #14:  The Deep Sea is Not Stable) - that seems really interesting (and should be for all of us living so close to the ocean).  You can find the whole list to date here (I especially like this post on deep ocean diversity - since diversity at the micro-scale is something we study).  However, their most recent post was interesting to me - and they pointed to another site that focuses, to put it simply, on the need for scientists to stand up and defend science - in the political arena (and it refers to a group doing just that, Scientists and Engineers for America - SEA).  This makes me cringe (the whole political arena thing) - and I find myself fitting into this stereotypical Seed Magazine description of a scientist:

What Scientists and Engineers for America seeks to accomplish runs strongly against the instincts of the nation's scientists, however, who have traditionally been much more inclined to write a letter to Nature than sign a check funding attack ads. Scientists have preferred less direct means of influence, like releasing technical reports and studies with thinly veiled policy implications, as opposed to directly confronting political candidates who egregiously misuse and abuse scientific information. Science, they have often argued, must enjoy bipartisan support in order to ensure steady levels of federal research funding. Explicit engagement in politics would inevitably upset this fine balance, prompting politicians to make research dollars contingent on scientists' political support.

Further, Seed states:

Going into the November congressional elections, Scientists and Engineers for America has targeted an as-yet unannounced group of congressional races to try and influence. Whatever happens when votes are cast in November, the group must be sure to handle the issue of partisanship with agility, both in 2006 and as candidates and advocacy groups gear up for 2008. As the stem-cell vote in July demonstrated, Republicans are the most influential foes of science today—but not every Republican. Scientists and Engineers for America should identify science-friendly Republicans as well as Democrats and try to help them in their races. Though the "war on science" has clearly taken place in the context of Republican political rule, the group should reward Republicans who want the party to reform itself.

Perhaps 2007 will be an interesting year for Science (and Scientists).  Here is the Bill of Rights on the Sea website:

Bill of Rights for Scientists and Engineers Effective government depends on accurate, honest and timely advice from scientists and engineers.  Science demands an open, transparent process of review and access to the best scholars from around the nation and the world.  Mistakes dangerous to the nation’s welfare and security have been made when governments prevent scientists from presenting the best evidence and analysis.  Americans should demand that all candidates support the following Bill of Rights: Federal policy shall be made using the best available science and analysis both from within the government and from the rest of society. The federal government shall never intentionally publish false or misleading scientific information nor post such material on federal websites. Scientists conducting research or analysis with federal funding shall be free to discuss and publish the results of unclassified research after a reasonable period of review without fear of intimidation or adverse personnel action.    Federal employees reporting what they believe to be manipulation of federal research and analysis for political or ideological reasons should be free to bring this information to the attention of the public and shall be protected from intimidation, retribution or adverse personnel action by effective enforcement of Whistle Blower laws. No scientists should fear reprisals or intimidation because of the results of their research.    Appointments to federal scientific advisory committees shall be based on the candidate’s scientific qualifications, not political affiliation or ideology. The federal government shall not support any science education program that includes instruction in concepts that are derived from ideology and not science.  While scientists may elect to withhold methods or studies that might be misused there shall be no federal prohibition on publication of basic research results.  Decisions made about blocking the release of information about specific applied research and technologies for reasons of national security shall be the result of a transparent process.  Classification decisions shall be made by trained professionals using a clear set of published criteria and there shall be a clear process for challenging decisions and a process for remedying mistakes and abuses of the classification system.

Mathotiana Supreme

Camellia japonica 'Mathotiana Supreme'.

The outer petals of this crimson camellia are tinged in purple - which becomes more evident as the flower ages.

Finally, Some Time in the Garden.

What a beautiful morning - the light was nice as I looked across at the row of trees on the western edge of my place.  After meeting a former student for breakfast (who spent a summer as a high school student from the SC Governor's School conducting research with us about 10 years ago now), one of those long breakfasts that ends at lunchtime, where we caught up on the activities of the past year, I came home and finally spent some time working in my garden.  It's a bit overwhelming this time of year - frozen back perennials, winter weeds (the impossible Florida betony), dead tomatoes and peppers still in their pots, prickly asparagus stalks - I wasn't quite sure where to start.  So first...I cut back the dead asparagus stalks - and then put the soil (part potting soil and part mushroom compost) from the tomato and pepper pots onto the asparagus bed, added some manure (I haven't amended this bed in years - it was time), covered the bed with about 8 inches of mulched live oak leaves (fresh from the lawnmower bag) - then sprinkle some lime on the bed to compensate for the decaying (acidic) live oak leaves.  The asparagus bed is now ready for spring.  I also pruned back, way back (which is uncharacteristic of me), my antique rose, Mutabilis - it had been growing into a large Savannah Holly and into other near by roses, and had a number of dead lower branches - so now beside it sits a pile of pruned branches almost as large as the rose itself.  I also transplanted my Abraham Darby - it was too close to the Mutabilis, and hadn't been doing well for a year or two - I thought I'd get it in the ground before the rains predicted at the start of the year.  I also made a decision...to call a tree trimming service, one that specializes in live oaks, and get a quote for my live oaks.  I have six large ones in the yard - and I'll probably only be able to afford getting one at a time pruned (I've heard estimates of $1,500 per tree - ouch!) - but I can't wait to see them after a talented trimmer gets a hold of them.  These trees had a rough time during Hurricane Hugo in 1989, and still have some large damaged branches and numerous small 'spurs' - and after every wind event here I spend a few hours picking up small branches from the yard.  So tomorrow morning someone comes by at 8:30 am to give me an estimate.  Keep your fingers crossed that it won't cost the price of a car to get done!

So yes, I haven't been working.  Today was the first day that it felt good - that I was relaxed enough to enjoy the slower pace.  Working in my yard is therapeutic for me - recently, at dinner, I was asked how much time I spent in my yard, and really - it isn't that much time, and anyway, the time is so well-spent, regardless of what I get accomplished.  If something gets done - great, if it doesn't - oh well, it'll get done one day.  I'm by no means a perfectionist in my garden, not even close.  And while wandering the yard I noticed changes:  the larkspur was up and quite tall for the end of December, the arugula was already beginning to flower, which was early as well - and a new blueberry bush was already flowering - with no bees in sight or a companion blueberry to cross-pollinate with.  Global warming...yes, we were experiencing a 69 degree day in the lowcountry...and I came across this post at GardenRant - where they talk about changes in the garden and they cited this article about how southern plants were surviving in Washington gardens now...and how hardiness zones are being modified accordingly. 

But I also ran across an interesting post at Island of Doubt titled 'Have we oversold climate change?'  that I found very thought provoking.  No, he doesn't say that climate change isn't occurring - but he does discuss the 'so what' of overselling climate change (and I agree with him):

Of course, here on the Island of Doubt, uncertainty isn't a bad thing. I look forward to a world transformed to anticipate climate change by shifting away from expensive, dirty, centralized, fossil-fuel-based economies in favor of clean, affordable, decentralized, more equitable, energy-distribution networks, regardless of how hot it gets. I say it's a win-win scenario. If we haven't oversold climate change, great. If we have, that's just fine, too.

If we do make it through this most challenging period of change and put the brakes on global warming -- there's no guarantee we will -- then I doubt history will condemn us for jumping the gun. We will have made the world a better place.

The site he directs his readers to (that is connected with the University of Colorado-Boulder) - is a discussion about a recent American Geophysical Union meeting, a meeting rich in climate folks.  I went to an AGU meeting a few years ago - they're interesting meetings for a microbiologist interested in geochemistry.  Anyway, this site has a very interesting discussion on climate change - and the 'climate' at AGU with respect to this topic.  I'll quote directly (from J. Kranes):

To sum the state of climsci world in one word, as I see it right now, it is this: tension.

What I am starting to hear is internal backlash. Sure, science is messy and always full of tension between holders of competing positions, opinions and analyses. That has always been the nature of science, and of course extends to climate science. Tensions come out at meetings, on listservs, on letters pages, and in the press. But these tensions normally surround a particular paper, or a particular question. While much more broadly-based tensions have existed for years on the state of understanding on global warming, they haven't really been tensions internal to the climsci community, but tensions between the climsci community and interested outsiders.

What I am sensing now is something much broader and more diffuse, something that has less to do with particular components of the science in the field and is much more about how the field is composing itself.

What I see is something that I am having a hard time labeling, but that I might call either a "hangover" or a "sophomore slump" or "buyers remorse." None fit perfectly, but perhaps the combination does. I speak for (my interpretation) of the collective: {We tried for years – decades – to get them to listen to us about climate change. To do that we had to ramp up our rhetoric. We had to figure out ways to tone down our natural skepticism (we are scientists, after all) in order to put on a united face. We knew it would mean pushing the science harder than it should be. We knew it would mean allowing the boundary-pushers on the "it's happening" side free reign while stifling the boundary-pushers on the other side. But knowing the science, we knew the stakes to humanity were high and that the opposition to the truth would be fierce, so we knew we had to dig in. But now they are listening. Now they do believe us. Now they say they're ready to take action. And now we're wondering if we didn't create a monster. We're wondering if they realize how uncertain our projections of future climate are. We wonder if we've oversold the science. We're wondering what happened to our community, that individuals caveat even the most minor questionings of barely-proven climate change evidence, lest they be tagged as "skeptics." We're wondering if we've let our alarm at the problem trickle to the public sphere, missing all the caveats in translation that we have internalized. And we're wondering if we’ve let some of our scientists take the science too far, promise too much knowledge, and promote more certainty in ourselves than is warranted.}

I found this really interesting - and very relevant to so many scientific pursuits - we immerse ourselves into terrority that is filled with uncertainty, imperfections.  Our approaches each have their own biases.  To the 'best of knowledge' we say - and for the most part, most of the scientists that I know are very well-intentioned.  But are climate scientists in a bind?  If the worst case scenario doesn't come true (a scenario that some of their data supports) - will the public cry 'foul' and being even less likely to support policies that will benefit the planet anyway?

Too much serious thought for a day spent in the garden...and a post that was interrupted by a phone call from my brother - waving to me from the webcam of the Hog's Breath Saloon in Key West.  Creep.

???

So 'Saddam to be hanged by Sunday'?  How barbaric is that headline?  Before the Eid religious holiday you say?  Nothing says 'Happy End of Ramadan' like a hanging...

Does anyone feel good about this?

5:15 pm update:  His execution will possibly occur by 10 pm tonight.

Lights

Cat in the Box

Haiku refuses to let the celebration end - there's still a box, there's still crumbled up wrapping paper!!  There are still ornaments on the tree that I haven't managed to reach!  Come on - it's still a party! 

Blackbirds in the Chinese Tallow

Happy Holidays

Happy Holidays from the Microbial Laboratory! 

May you have a holiday season rich in beneficial microorganisms, with reduced use of anti-microbials (toss that anti-bacterial soap!), and abundant diversity!

Yes, several days ago the lab prepared test-tubes of 'paint' (microorganisms isolated from coral reefs) and applied them to canvases (glycerol artificial seawater agar plates).  Look closely at our 'microbial palette' of 'fat fluffy white' and 'orange yellow fat' and 'dull gold'...

Traditions

MOM'S CINNAMON ROLLS

2Pkgs. or 2 T. dry yeast
1 T. sugar
1 c.lukewarm water
1 c. milk
1/2 c. sugar
6 T margarine or butter
3 eggs beaten
1 tsp. salt
6 to 7 c. flour
butter, melted
brown sugar
cinnamon
nuts. opt
Dissolve yeast and 1 T sugar in lukewarm
water. Scald milk; add butter, sugar and salt.
Cool to lukewarm. Add 2 cups flour to make
a batter. Add yeast and beaten eggs. Beat
well.  Add remaining flour to make a soft dough.
Knead lightly and place in greased bowl.
Let rise until double in bulk. Roll out and
spread with melted butter. Sprinkle with
brown sugar and cinnamon as desired.
Roll up as a jelly roll. Cut in one inch slices;
put cut side on greased pan.
Let rise about 30 minutes. Bake for 20 minutes
at 375. When cool, frost.

Caramel Frosting
1/2 c. butter
1 c. brown sugar
1/4 c. milk
2 c. 10x sugar
1 tsp. maple flavoring or
1 tsp. vanilla
Melt butter; add brown sugar and cook
over low heat for 2 minutes, stirring constantly.
Add milk and continue to stir until mixture
comes to a boil. Remove from heat and cool.
Add flavouring and 10 x sugar until right consistency.
Beat by hand until smooth.
( I half this frosting recipe and apply a thin layer of frosting)

Makes enough to share.

Nests

Yesterday, starting early in the morning, I began to make cakes.  I ended up making only one cake - but delivered it to a friend that I hadn't seen in a long, long time - and so this morning, here I find myself again, making cakes. 

Anyway, I was listening to NPR yesterday morning, half listening, half measuring - when I heard a familiar voice that made me smile:  it was someone that I had met this past October in Washington DC (I mentioned this person before).  He's a museum curator (of invertebrate zoology) - and I took the opportunity to email him, reflecting on our discussions of how one can integrate microbiology with his invertebrate world (while incorporating mules into the sampling protocol - long story, but one must have research goals, right?).  The story was quite fun (you can still listen to it here) - and better yet, find this last minute gift idea - a sleepover at a museum.  Now...how fun would that be?  Although it had hints of the Lincoln Bedroom - it really isn't the same at all.  Not in the slightest.  A night in the Hall of Mammals - it can be yours!

So upon reflection - yesterday was a perfect day.  Time is perhaps our truest of gifts.  Yesterday was about lowering ones cake-baking expectations and spending time talking instead to an old friend - it's about using a perfectly acceptable excuse (when one isn't really necessary) to touch base with a new friend - and enjoying the passionate response:  

...why not undertake a project where the landscape surveyed is not just geographically delimited, but also organismal, ecological, and ontogenetic!  What I'm thinking is an exploration of the microbiota across a comparative "landscape" that is organismal (larval Lepidoptera =caterpillars, external and internal), geographical (comparing tropical/temperate systems or cold/hot or wet/dry), evolutionary (comparing parallel lineages of larvae with convergent lifeways), ecological (comparing larvae with different feeding modes) and ontogenetic (from egg to adult).  This approach is dripping with serious hypotheses...would require pooling essential expertise of 3-4 persons, would co-investigate a megadiverse insect lineage and megadiverse microbial ones, and would uncover a real richness of unknown and undoubtedly life-critical beasties living on or in my critters!

Back to the cake.