Tales from the Microbial Laboratory

Another Coneflower

Thoughts on a Day:

Complications:  I need to have someone from the SC Department of Health and Environmental Control's Coastal and Resource Management office come out and flag my properties 'critical area line'.  After faxing a completed form 3902 and a copy of my survey to their office, I found out that it will take two to four weeks for someone to come out to my place and do this.  After this is done, this line needs to be included on the survey - so the surveyor will need to come back out and complete this.

Further Complications:  I have a utility pole dilemma (first, let me just say that I think they all need to be underground for just about a dozen or more good reasons - but I know, it costs money).  So - it means that based on current plans, the location of my existing utility pole might need to change - which means the current one will need to be removed and then the same pole or a new one placed elsewhere.  Elsewhere.  Which is really no where else, because there is no where else it can go because of trees.  Hmmm.  Gotta discuss this one with my architherapist in this week's session.  The whole utility pole thing is complicated a bit by the whole Airstream thing:  I want to hook up the Airstream to electricity to enhance my land yacht living experience. 

To Buy Appliances Now or to Not Buy Appliances Now Perplexity:  So, the local 'where you should go to buy your appliances' store is having a sale where if you buy three or more appliances at once, you get a 20% discount.  That sounds okay to me - except I'd have to get them delivered now.  Today I did decide on a storage facility - a 10' x 20' climate-controlled unit that is pretty close to my place (~2 miles away).  So I could get them delivered there.  I was ready to do this, and had researched the whole warming drawer thing and built-in microwave and convection oven and dishwasher capacity thing (translation:  I basically chose the one that I thought looked best - I'm just being honest here.  That's not totally true, but it's a little true).  But then someone talked to me today about contractor discounts and additional discounts if one is building a potential 'model' home (the whole LEED thing) and so I'm not sure what to do now.  I have until Saturday for the 20% off thing, and Thursday will probably go and look with a friend.

Decisions, Decisions:  On top of the whole appliance thing and the utility pole and the critical area mess, my architherapist sent me two more rough drawings today.  These plans are designed to accomodate the boat.  Which brings me to something my brother said tonight on the phone:  'You seem to always take the most complicated route.'  Which made me think, while I was mowing grass this evening - grass that grew at least six inches today after yesterday's wonderful rain - exactly why is that?  I think he's right.  But what I question is whether it is anything I can truly change. 

Feeding a Wonder Beagle:  So it's probably something I can't change (the whole complicated route thing), which is why I am now feeding the Ancient Wonder Beagle a diet that she seems to be, three months shy of the grand old age of 18, responding to.  She ate her evening meal, took a short nap, went for an even shorter walk, and then came inside and started barking for an after dinner...dinner.  Ground up eggshells (the calcium helps bind the phosphorus), one 10 mg pepcid a day, then a mixture of KD (Science Diet) with lots and lots of water and chicken and barley and sweet potatoes.  Plus a little bit of this great brand of canned food (Wellness) - in venison, etc.  I think the trick is small meals with lots and lots of water.   I don't know how long she will respond to this diet, or how long her kidneys will put up with it, but I have to say that a month ago I didn't think that she would be around for the first day of August.  Yet here she is, snoring at my feet.  Undeniably, she's the world's sweetest beagle.

Never-Ending Treatments:  The first edition to my Mother's etiquette book on 'Living with Terminal Lung Cancer' (hmmm...that sounds like an oxymoron):  Do not ask the person 'How many more treatments do you have?'.  The reality is that there will always be treatments.  Always, until they say there is nothing they can do.  Treatments aren't something that you want to have end.   

Laboratory Richness:  The lab was rich - simply rich - in glimpses of interesting data today.  Baby steps, pieces - possibilities.  The possibility that the bacterial diversity associated with Montastrea faveolata could be as high as 2,200 different operational taxonomic units (OTUs).  The discovery that a coral pathogen isolated in the Indian Ocean has the same antibiotic resistance profile as one isolated off the southern coast of Puerto Rico.  The finding that the production of membrane vesicles by our favorite Gram negative bacterium is influenced by pH, and also by the presence of metals (the latter is a maybe).  (Important) Baby steps.

Much Needed Stress Relief:  I'm really glad that my order from Lazy S'S has been shipped, and that it should arrive this week.  Their customer service has been excellent (in case you were wondering).  Now we'll see what their plants look like (I've been to their nursery before, when they had a retail operation - but I've never ordered from them and had anything shipped.  I'm optimistic though.).  Knowing that these plants are coming will keep me from heading out and buying one of these.   

~~~~~

It's time to walk the beagle for awhile, to carry her down the stairs and to the good grass under the six live oaks where it's dark and cool and where she can wander easily and smell the history of the day.

 

coneflower

 

rain

It's a rainy evening.

I like the sound of that.  We haven't been able to say that for a long while - we haven't been able to say that it's been a rainy night, the kind where you have to grab something to put over your head when you go running out the door and down the stairs in order to convince the dogs that going outside isn't so bad afterall.  Stanley runs to the front door and sees the rain and turns back, after about the fourth time he goes running down the stairs with me.  Silly Stanley.

The garden is happy.

~~~~~

This website is amazing:  Linus Pauling and the Race for DNA.  I've read about this story many times before - but this narrative documenting the 'drama behind the race' - complete with scanned images of many of the manuscripts published, is just excellent.  I was wandering the web this afternoon, looking for information on something related to DNA, and came across it.  If you are having a rainy evening too, I recommend that you spend some time there.  There are images, like the one included at the left, of infamous 'Photo 15' - sodium deoxyribose nucleate from calf thymus (Structure B) taken by Rosalind E. Franklin and R.G. Goslin (May 2, 1952).  There it is - the infamous maltese cross.

Even now, the story is still a fascinating one.

~~~~~

While the storms move toward the coastal marshes, and the beagle snores loudly - it's time for me to write. 

   

a wall of figs

The fig tree has gotten large.  Surprisingly large. 

Each fall I think to myself that I need to remember to find out how one should prune a fig tree.  Each fall I forget to find out.

So this afternoon I googled 'pruning figs', and found this site which said:

Figs:  prune severely for size control (you’ll still get plenty of fruit), or allow them to become big tropical-looking trees -- and get even more fruit. Your choice.

I like having choices.  A big tropical-look tree it is!  There's room for it.  Plus it's branching pattern is beautiful in the late fall, after the leaves have fallen.  I don't think I have the heart to prune it now.

~~~~~

I saw a butterfly today that I couldn't identify - I tried to find it in my book, but I couldn't match it with anything within the book's pages.  ~~  There was also a bird, an unfamiliar one, checking out the purple martin house - it seemed anxious to buy.  ~~  A rabbit, a silly, silly rabbit - went racing across the yard in the middle of the day, to (and through) the side fence.  Stanley was out in the yard - Stanley, a lover of braised rabbit - except the braising, or really the baking, isn't really necessary in Stanley's version. 

Lucky rabbit.

~~~~~ 

Biological diversity fascinates me.  It always has - and it's something that I've always respected, and the more I learn about different ecosystems, the more it makes sense that a stable ecosystem is a diverse one.  I was happy to read a week or so ago about a news release by the U.S. Fish and Wildlife Service stating that they were to review eight endangered species decisions.  The Endanger Species Act has had a rough few years - and the eight species being evaluated are occurring because, as stated in the news release:

The U.S. Fish and Wildlife Service today announced plans to review and take further action, as appropriate, for eight decisions made under the Endangered Species Act, after questions were raised about the integrity of the scientific information used and whether the decisions made were consistent with appropriate legal standards.

Hmmmm.

The species under review are:

The Service had already begun reviewing the following decisions. The original date of publication is also included.

• White-tailed prairie dog, 90-day petition finding (November 9, 2004)

• Preble’s meadow jumping mouse, 12 month petition finding/proposed delisting (January 28, 2005)

• 12 species of Hawaiian picture-wing flies, proposed critical habitat (August 15, 2006)

The decisions requiring additional review and the dates of their original publication are as follows:

• Preble’s meadow jumping mouse, final critical habitat (June 23, 2003)

• Arroyo toad, final critical habitat (April 13, 2005)

• Southwestern willow flycatcher, final critical habitat (October 19, 2005)

• California red-legged frog, final critical habitat (April 13, 2006)

• Canada lynx, final critical habitat (November 9, 2006)

I know that there are alot of sides to each species being protected - many voices (such as this one).  Each organism that becomes under the watchful eye of the ESA soon becomes a political token.  I'm generally familiar with the arguments.  Some of you might be groaning at the thought of even trying to protect the Arroyo toad.  But if it is 'the bringer of life giving rain', I say that I wish they liked coastal marshes.

Anyway, I like toads.

~~~~~

It is predicted that commercial and seafood stocks may crash by 2048.

It has been estimated that 12.5% of the world's plants will soon be critically rare due to deforestation and non-native species.

I've spoken before about coral reefs (here's a nice overview).

All of a sudden I feel like I am on a soap box, and that was not at all my intent as I sit here on a Sunday evening, after a full day spent packing and researching appliances, and making a small patio out of concrete square pavers for the Airstream (a temporary and quick 'patio' - a patio fit for an Airstream - unlike the lovely stone patio in Pam's beautiful Austin garden - hopefully that patio will be built later, after the new house is a reality). 

After a day spent walking up and down my steps about 200 hundred times, I'm not sure that I'm up for being on a soap box.

I know, you're relieved.  I don't blame you - I even bore myself sometimes most of the time.

~~~~~

During last week's Democratic Debate held in Charleston and the whole YouTube approach - I was thrilled to see that Mossy got some fun airtime.  Charleston's definitely been feeling pretty full of herself lately.

But that's for another time.

(But it is a surprisingly wonderful city.  Take a walk with Joan - she'll show you the streets).

~~~~~

architherapy

I had a tough session with my architherapist today.  It was grueling.

The last set of drawings I saw I really liked - and I think I had wrapped my head around them, could see myself walking the rooms and the hallways - and then WHAM!  He thought of something a bit different. 

But I didn't like the changes.

The problem is Spirit.  She's 21' long - but the trailer is 24' long - and since I want her to be able to stay underneath the house, both the angle of the drive and the size of the area underneath the house needs to acccomodate her.  The plans that I like didn't have sufficient 'underneath' space (partly due to the angle of the house - facing due south - and the fact that the house has narrow, rectangular-sized spaces, not squares) - so we have to modify our current plan to accomodate the boat.  His latest set of drawings did this - but put the third bedroom (aka office space) into an area that felt closed-in to me - and isolated this room from the guest bath, making it difficult to transition into a bedroom if ever necessary (say, with another owner, etc).  But this is important space to me, I like to be able to work from home - I like where it was in the prior plan - open, with windows on three sides.  So we talked through it, and by the end of the hour - I think that my architherapist and I came up with a possible solution.  We'll see how it translates onto paper.

Oh, and we talked about where the dog food should go.  No problem is too trivial for my architherapist.

Which necessitates the need for plants (to relieve post-architherapy session stress, plus the Airstream needs to be 'landscaped', doesn't it?), so an order was placed at Lazy S'S Farm Nursery (located in my hometown of Charlottesville, Virginia). 

Hydrangea macrophylla 'Jogasaki' Double Pink Japanese Hydrangea 

Hydrangea macrophylla 'Izu No Hana' Double Lacecap Japanese Hydrangea

Hydrangea paniculata 'Tardiva' Panicle Hydrangea

Salvia cleistogama Closed Sage

Salvia koyamae  Yellow Groundcover Sage

Salvia nemorosa 'Blauhugel' Blue Hill Sage

Salvia nemorosa 'Carradonna Sage' Caradonna Sage

Coniogramme emeiensis 'Variegata' Variegated Chinese Bamboo Fern

Dryopteris celsa  Log Fern

Phlox divaricata ssp. laphamii Wild Blue Phlox 

Phlox paniculata 'LSS Vincent' Garden Phlox

Erythronium americanum Dog Tooth Violet/Trout Lily

Storms are approaching and I'm hoping for rain - although it seems that the storms, coming in from the northwest, are being hindered by the sea breeze.  ~~  I'm still getting emails, even now, lingering reactions and responses from a busy day.  ~~  It looks like I might be able to attend a bat viewing party afterall, a second one in Oklahoma, in September, one where my colleague would bring me in to present a seminar to their Petroleum Institute.  That would be fun - I'd dust off the work about that sunken ship - and 'talk oil' to a group that really knows oil.  Perhaps it would motivate me to get those three manuscripts written in preparation.  ~~  It seems that the coral community DNA that we sent up to JCVI is cooperating - the shearing was successful, our collaborators are sending it back to us for the next stage - our first step in generating a metagenomic library.  ~~  There's been interesting sequence data from one of the clone libraries; interesting antibiotic resistance data from a set of coral isolates.  ~~  Forward progress.         

~unmasking~

The mexican sunflowers are happy in the garden - it is warm, beyond warm - and the sun is strong.  With much optimism, I have planted Kentucky Wonder pole beans this week, as well as cucumber (Marketmore 76), yellow crookneck squash, giant scarlet zinnias, sunflowers (misc), and garden heliotrope (Valeriana officinalis).

I plant.  I pack.  I weed.  Today I swam (for the first time in a long while, and it felt like -- like something I need to do regularly again.  It's the breathing I think, the rhythm of the breathing).  I write.  I edit.  I prepare food for the Ancient Wonder Beagle.  I sit in the Airstream.  Today I found myself opening storage areas under the sink and the living area's 'couch' and thinking that they were spacious.  That was positive.

I meet with my architherapist late tomorrow afternoon.  He has given me 'homework' and tomorrow will be important:  we need to decide where the stairways will go, how I will enter the house and from where - meaning that a decision on decks and porches should probably be made.  I want porches wrapping around the whole place, but I don't know if that's in my budget.  He and I emailed back and forth numerous times today -- where is the drive?  between which trees?  what about the setback from the tidal areas?  have I heard anything back from FEMA regarding flood zone?

an invitation to a bat viewing!

I have really good colleagues - scientists that I've met along the way, that I often only see annually (or less) in some city - where we all gather to meet for some reason or another (but generally to present our research).  Today I received a delightful email from a favorite colleague, one that I haven't spoken with in almost a year, since we were both in Vienna for a meeting. 

He's one of those individuals who is both very successful and remarkably kind.  If I had any sense at all, any, I'd find a good vintage beverage, catch a flight and spend an interesting evening with he and his spouse, their family and his friends and colleagues...viewing bats. 

Hello All: As many of you may know, I am planning on hosting a bat viewing trip on Thursday, August 9.  You will see by the attached directions (from the OKC area - adapt as necessary) that the bat viewing area is a private ranch in northwest Oklahoma.  I did receive permission from the very gracious caretakers of the property for this expedition. We should gather (at least) between 6:30 - 7:00 pm at the Whitlaw Ranch main gate.  We will proceed from there and wait for the show to start.  Please ignore the caving instructions on the attachments since we will NOT be caving on this trip.  Follow the instructions about litter, potties, and snakes etc, but for the record,  I have never even seen a snake on the ranch.  It will be necessary for all visitors to sign a liability waiver (also attached).  It specifically refers to caving, but completion of this form is required.  You will not be allowed on the premises without it.  Bring some knock around garb, a lawn chair, cameras/video stuff, a vintage beverage or something to drink, and perhaps some snacks.  FYI, you are more than welcome to bring whomever you wish - kids, spouses, colleagues, students, etc., so share this message if you would like. However, respect for the property should be emphasized and I do need to get a head count. So let me know in advance if you are coming and how many are in your party.  I have been going there for years and the bat spectacle has never failed to impress. For a small glimpse of what it might be like, take a look at the attached photo.  I'm looking forward to the trip.  J--

PS: If you can't make it, I certainly understand.  Rest assured that you will be missed and we will probably go again next year.

The e-vite came complete with a map on how to get to the ranch as well as the liability waiver.

I love bats.  Isn't the photo he sent us a fun one?

Maybe next year, the Airstream and I should head on down to Oklahoma -- don't you think?  It would perfect.  I should plan on that.

~silly and completely non-productive airstream distractions~

So.  There are Airstream Party lights available.

Jeff thinks that I need to register somewhere (like the Airstream Store).   That made me  laugh throughout the evening (until I had just finished cleaning out a few rows of climbing sweet peas in order to plant Kentucky Wonder pole beans - and a 2' snake came wiggling out of the soil in the darkness).  I can see my Mother's face now:  her only daughter is registering at the on-line Airstream Store, and she's included on her 'list' an Airstream Cocktail Shaker.

There is Airstream apparel.   

There are Airstream Christmas Cards and Airstream Needlepoint Pillows.  This is almost too much.

I've gotta write now.  Really, I do.  There's much writing to be done.

Airstream ringtone anyone?

My thanks go out this morning to John B. over at Blog Meridian (it's always an interesting visit there - and yes, he's already finished Deathly Hallows!) - he commented on my Ry Cooder post sometime during the night, letting me know about the Pat Metheney album, American Garage (1979).  Not only does it have Airstreams on the cover, but there is a song 'Airstream' among it's soundtracks.

If I was even remotely savvy with typepad, I'd link directly to an MP3 here.  But I'm not.  So go here and take a listen.

And no - I haven't actually moved into the Airstream yet.  There are a few things left to do...like complete the design of my new home (there's a meeting scheduled for Friday with my architherapist, and hopefully this will get us close), find a builder (I have been talking seriously to one person already), demolish my current abode (my friend has recommended a guy who sounds perfect for this, since we're trying to recycle/reuse as much of the current structure as possible) - you know, all of that stuff.   I'm currently focused on forward progress - as long as things keep getting accomplished, I think we're on track.  I'm sure that you'll know when the big moment arrives, and I move back to living on the ground.  In an aluminum box.

(There will probably be this large sigh and a quietly spoken 'what the hell have I done?' coming from this tiny part of the lowcountry).

I was speaking with someone recently about this whole Airstream adventure, and about how so much comfort and security we get from our possessions.  Our possessions insulate us from the world.  But he used a word that I had not yet used, about how so much of our identity is wrapped up in what we surround ourselves with.  I'm having the most difficulty parting (temporarily) with my paintings and books.  Most of my paintings have been taken up to my parents home in Virginia, for safe keeping - I could have scattered them throughout friends homes here, but it just seemed easier to store them in a safe place somewhere in my parent's home in Virginia (so no lingering hurricane season worries). 

But I have yet to pack a single book.

In that recent conversation, I was asked something like 'what books will I choose to take with me, and which ones will I pack up?' . I simply don't know.  I thought about it last night - and I took my flashflight and went out to the Airstream, looking around - and there are a few ledges (window ledges more or less) where I could stack some books I think.  But not many - 10 or 20 is being optimistic.

A few poetry books I think.  Neruda's 'The Art of Birds'.  Mary Oliver, Louise Gluck.  A few gardening books - my one on salvias (a current obsession), my antique rose book. 

Deciding on which books won't be easy.  So I repeat to myself:  This is temporary, it is okay.

I'm shedding, slowly.

But last night, as I was speaking with my Mother on the phone, I think it really struck her for the first time that her daughter was moving into an Airstream.  She said something really interesting, something positive.  She said that you will probably find that you have more time, less responsibility, since you will have a less complicated home.  She is right, I do realize that - and in fact, that is what I am hoping for.  But it made me feel good that she came up with that on her own.

~~~~~~~~~   

Oh, and of course, if I continue along this path, I have no doubt that I will download this 'Airstream' ringtone for my cell phone.  And please, if I do this, will someone see that I get help?

(But it does sound better than the one that I have never changed on my phone since purchase - perhaps it is not such a bad idea?  Yes, it is indeed a slippery-slope, isn't it?).

~~~~~~~~~

Back to writing.

comfort flowers

Zinnias are comfort flowers - perfect to plant at the end of a hectic day.

[One student wasn't getting a signal - so wasn't getting detection - with a sample injected on our GC-MS...the GC-MS that just had a service call within the past several months.  Another might be needed.  The postdoc was frustrated, trying to work through some sequence data that didn't look good:  trying, ultimately, to troubleshoot whether it was something we messed up on our end (and if so, what?), or whether the folks doing the sequencing messed up (ditto).  Another study underway - a short study, data due in tomorrow.  Another study (and collaboration) proving to be a disappointment).]

So as the evening grew dark, I planted several rows of 'California Giant' zinnia seeds (scarlet).  I also filled in the gaps in the rows where I planted sunflowers several weeks ago (I got surprisingly poor germination - unusual, these guys are easy).  I love planting annuals in the middle of the summer season - if I keep them watered through August, they're usually gorgeous in September and sometimes until late October.  Halloween with the moon vines still blooming - that's what I call a growing season.

It's a still night, the air refused to move - and at one point I spotted a spider flying through the air, and when I moved to look at it's acrobatic feat from another angle, I could see a thread from the base of the purple martin house to the fig tree.  This observation makes me wonder about the true productivity of my own day, in comparison to that of the small spider.  They're amazingly hard-working, amazingly resourceful.  I wonder if it's all worth it - the spider works so hard for food, I work so hard for...something different.  Food of another kind I suppose.

Now it's time to start editing a draft of a manuscript that my laboratory is writing - a review of coral microbiology.  Our deadline is now the end of August for a (surprisingly) quick turn around (it helps to be collaborating with the editor) and an October publication date.  That would be nice.  There are too many manuscripts to keep track of right now - there was a meeting today on another (and still another) that I am writing - progress was made, but sometimes I think that I need to stay home for six months, alone, chained to my small wooden chair and a computer moniter.  Then, just maybe, I could put a dent in all of this.  Next, after corals, dolphin respiratory tract microflora.  Then that ship that sank out in Pearl Harbor (three manuscripts on this one).  I think I need a real vacation.

But tonight I planted zinnias and sunflowers, and feel much better.