Tales from the Microbial Laboratory

"Tracing Cape Romain" by Bob Raynor

 

 "Tracing Cape Romain Archipelago" by Bob Raynor (The History Press, 2009)

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Last Saturday at the Sewee Center there was a wonderful presentation by Bob Raynor regarding his newly released book about his trips around various waterways of Cape Romain - solo trips made on his small sailboat, the 'Kingfisher'.  At the last minute I decided to go and hear him - and I'm glad that I did.

His stories about his sailing adventures in this pristine area were interesting and informative and intimate - but as I listened to him speak, I realized that the hidden gift in his book is that discovery occurs on any scale we want it to:  we can walk on the moon, land a vehicle on Mars, we can roam the wilds of China in search of the yellow Camellia nitidissima or get lost in a bacterial biofilm - and we can use the wind to help us explore a wilderness in our own backyard.  Even in our own gardens is everything we need for a journey of exploration and discovery.  It's all right there, waiting for you.

~~~~~

To learn more about Cape Romain, go here.

To see a description of a wonderful day I had out on Bull Island (a part of the Cape Romain National Wildlife Refuge), go here.

To really find out how beautiful this place is, instead of all of the above just go and find out for yourself. 

~National ALS Awareness Month~

Last Tuesday, on my return from a long weekend spent in Montana, I sat by a man on the Atlanta to Charleston flight who had recently finished writing a book about an inspirational friend, Jimmy Culveyhouse, who is not only fighting ALS, but is also fighting to raise $1M to support ALS research.

May is National ALS Awareness Month.

All of the proceeds for the book, Fighting to Give:  The Jimmy Culveyhouse Story, will go towards fighting ALS and cancer.  The author, Christopher Stevens, lost his wife much too early to lung cancer.  Neither his wife - nor my Mother - smoked.  

Of course this touched me - with my Mother passing away just over a year ago from lung cancer...and with two people in my life, my Father's Mother and a close friend, both losing battles to ALS. 

My friend, Tom, and I emailed almost everyday after his diagnosis - that is, up until three days before he passed away.  For the last several months, he was able to send emails via a voice-activated system.  He chose not to go on a respirator, and shortly after his diagnosis, he visited Johns Hopkins University and an ALS researcher there - and signed documents to donate his body to support ALS research.

I'll order a copy of the book - and I hope you do too.  Help me spread the word, okay?     

   

Black Monday

I'm torn on this one.  My friend Jeff saw this segment last week on Good Morning America and told me about it - it was an interview with author R. Scott Reiss on his new novel, Black Monday.  The novel is a doomsday scenario where genetically-engineered microorganisms are used to destroy (biodegrade) the world's oil supply.      

Now, I'm all for someone writing about microorganisms - even good fiction - and since it appears that Paramount has already purchased the rights to this movie, hell - a genetically-engineered microorganism starring in a feature film...?  Cheap leading...man?  Woman?  Prokaryote?  Yep, I'm all for it.  But do take a look at the video clip.  Reiss' interview is a little too Crichton-esque for me - blurring the lines between fiction and non-fiction... and he suggests that he's speaking for scientists because he's talked to them and read some stuff.   

But two points bugged me.  When asked if it was dangerous to present ideas like this one that could give terrorists ideas, Reiss mentioned that prior to 9/11, he had thought about how flimsy cockpit doors were, and how he regretted not writing a story involving this weakness in airline safety - and that it was 'a writer's responsible to focus the public on issues' (duh).  I think bringing that up was really low.  He's telling you 'to listen to him because if he had been smart, he would have saved us all from 9/11' - while giving credence to this new idea because in the past he'd had an idea that proved true so this could really happen too...when in reality vulnerabilities are pretty obvious to most of us.

But from a scientific perspective, I cringe at flippant statements - statements that are presented authoritatively, as if they were fact - but are much more complicated than the statements suggest.  Reiss mentions in the video that he talked to scientists, and they said such a genetically-engineered microorganism was possible...and then he went on to say that you could go to the internet and buy microorganisms that will clean up a gasoline spill (well, there are all sorts of 'bags of bugs' advertised on the web for cleaning up all sorts of petroleum hydrocarbon mixtures) - and then, THEN he said that bacteria were used to clean up the Exxon-Valdez spill.

"Clean-up' is a relative word.  In most remediation efforts, goals are not generally set all that high - there are 'levels' we try to reach, but let's face it - if microorganisms were able to degrade hydrocarbons to the extent we need them to, petroleum hydrocarbons wouldn't be the most abundant contaminant at many waste sites - there's a background level just about everywhere (and above background in our very own Charleston Harbor).  There have been successes - and microorganisms do degrade certain components of oil quite well  - but you have to be careful.  Since petroleum hydrocarbons/crude oil is such a complex mixture - degradation of these components is often based on what we quantify.  In other words, if you only quantify the lighter oil components - say, the linear alkanes and the standard 53 petroleum aromatic hydrocarbons (PAHs) that are often measured - you might see substantial loss of these compounds - but hydrocarbon mixtures often contain thousand's of different compounds.  It's misleading.  I'd say that alot of folks living in Valdez, Alaska would define 'clean-up' differently than Reiss does.

Now - with respect to genetically-engineered microbes - it all pretty much started here (in the public forum at least) as written about in an online article by Lee at the Institute for Environment, Philosophy & Policy at the University of Lancaster:

Up to 1980, no one could be sure in any country with a Western-type legal system whether patents could be granted to any living organism, which claimed to have been made by humans. Up to then, animal varieties and any biological processes which underpinned the production of animals and plants fell outside the ambit of patenting. However, there was legislation to protect plant varieties in several countries–for instance, in the USA, the 1930 Plant Patent Act (PPA) covers asexually reproducing plants, and the 1970 Plant Variety Protection Act (PVPA) covers sexually reproducing ones. The UK 1983 Plant Varieties Act comes under the aegis of the Ministry of Agriculture, Fisheries and Food, not the Patenting Office, and covers the reproductive materials of plants. There is also the 1968 International Union for the Protection of Plant Varieties. ⁸

But in June 1980, the situation altered with the decision of the US Supreme Court in the case of Diamond v. Chakrabarty. Chakrabarty, a scientist, who worked for General Electric, submitted an application to the US Patent Office in 1972 for a new strain of the bacterium, Pseudomonas. The novel bacteria were intended to clean up oil spills in water by degrading the crude oil, then ingesting the degraded material, with the bacteria themselves, in turn, forming part of the normal food chain. Chakrabarty did not use rDNA techniques in producing the new strain. He relied on other techniques. Plasmids from separate organisms–each able to degrade one of the important hydrocarbons which constitute crude oil–were bred into a single bacterium, thus combining all their superior properties in a single strain of super bacteria. The Patents Office rejected the application for a patent on the organism itself on the grounds that the 1930 (PPA) and 1970 (PVPA) Acts showed that Congress had not meant living organisms in general to be patentable, and was simply making special arrangements in providing protection for plants. But the Court of Customs and Patent Appeals (CCPA) rejected this interpretation, arguing that ‘the fact that micro-organisms, as distinguished from chemical compounds, are alive, is a distinction without legal significance.’ The US government in 1979 itself lodged an appeal against the CCPA’s decision. The crucial issue before the Supreme Court was whether ‘a living organism which otherwise complies with legal requirements for patentability nevertheless [is] disqualified because it is alive?’ A five to four majority upheld the line argued by the CCPA, deciding in favour of patentability.

Two assumptions stood behind such recognition of patentability: that artefacts can be biotic or abiotic, and that the products of biogenetic technology qualify as biotic artefacts. Given these assumptions, it was expected that a favourable decision in the Chakarbarty case would clear the way for the numerous products of the biotechnology revolution which were rapidly coming on stream but which were held up until the Supreme Court had pronounced on the Chakrabarty case. After all, the rDNA organisms–be they animals, plants or microbes–compared with those produced by other forms of biogenetic technology, embody even a greater degree of artefacticity. It stood to reason then that rDNA organisms, their products and procedures are all patentable as they are paradigmatically human-designed, human-made, and are not the products of nature.

So microbiologists have been engineering microbes for years - they're the perfect subject.  In fact, if I recall correctly - the very same organism that Chakrabarty patented years ago was given last minute approval to be used in Prince William Sound after the oil spill - they were desperate, and they pushed the approval through.  But the debate over the effectiveness of adding microorganisms in Alaska was debated for a long time (and is still being debated in some circles) - and this brings up the big problem in Reiss' novel:  So what if you have a genetically-engineered microorganisms that degrades oil?  Can you get it to survive out there in the big cruel world?

So I haven't read the book yet - but I would be curious as to how Reiss has 'engineered' his microorganism to survive once introduced into the environment (or if he even goes into this at all).  He's got himself a couple of obstacles.  First, if he's introducing his strains into an oil reservoir - you're talking about an environment that is generally anaerobic with aerobic events occurring.  Second, you're introducing your strains into an environment that is generally already rich in well-adapted sulfate-reducers (that can often biodegrade components of oil themselves) as well as other indigenous microorganisms - which is a little like adding a flightless bird into an aligator pond and suspecting the bird to thrive.  My point is this:  while Reiss is talking about genetically-engineered microorganisms - I'm thinking 'sure, the engineering we can do' - but it's the ecology that we still are really naive about.  How was he going to engineer that?

So my curiousity may get the best of me, and I might have to read the book.  But like I said at the beginning - I'm torn.  I think it's great when microorganisms get attention - especially regarding their amazing metabolic diversity - but I hope it's not at the expense of misleading those who take Reiss' text as statements of fact.  I'm not a fan of Crichton - and this isn't saying that I don't like science fiction - I love it.  But enough of this for now.  It's definitely no Black Monday for me - I'm not in the lab today - I've got some serious gardening plans and I'm hoping to catch Hillary Clinton later this evening (although I suspect the event is not 'open').  I'd like to hear her speak.   

Light Summer Reading

About the Author:  Tiny blonde-haired 5th grader who had a slight history of being difficult (something was ominous, upon reflection, about that "D" in Conduct in 1st grade - but come on, Mrs. Gibson was a real pain-in-the-ass).  She got kicked out of Brownies in the 2nd grade for refusing to make the mandatory Brownie pledge - because she and her best friend thought it was unethical to look into a mirror surrounded by greenery and pretend it was a lake (they demanded an actual lake for the event, but the request was refused).  After that, her Brownie purse got turned into a spy bag, where detailed notes of her brother's annoying behaviour was thoroughly documented).  Hence, no Girl Scouts or those brightly colored badges were in her future.  The year she wrote this piece, she got suspended from the 5th grade Bible Class because she and her best friend skipped it one day, and got caught smoking cigarettes outside the classroom behind a grove of red cedars.  It was raining and the teacher came out yelling for them and slipped in the wet Virginia red clay. 

The only teacher she liked was her 5th grade English teacher.