Friday, April 27, 2012


Yesterday I went on an all-day off road ride in the dunes to the south of Gobabeb, going miles into the interior of the dunes where there are no roads and no people.  We got stuck a few times but dug ourselves out.

Today I did an experiment on 24 natural hypoliths (quartz rocks colonized by cyanobacteria) that showed that cyanobacteria can grow in light levels as low as 0.05% of direct sunlight.  As Chris McKay put it, "this shows they could grow on Pluto, if Pluto wasn't so cold."  I think this will get published in a scientific journal.

But, this is Africa and I know my audience.  Here are some animals:

Ostriches, Springbok and Gemsbok, respectively.  Below is a puff adder.  It was small, but Alacia was wearing flip-flops.

I leave Gobabeb tomorrow for California.  There probably won't be time for me to post to this blog tomorrow morning because I am going to climb a distant dune to watch the sun rise.  So, consider this my last post from Namibia.  I will sign off with some pictures of the NASA team chilling in the desert.

Friday April 27, 2012: We salvage the artificial hypolith experiment

After visiting my artificial hypolith experiment on Wednesday I was pretty discouraged.  But, after a good night's sleep I woke up yesterday realizing that the situation isn't so bad.  When you have sixty tiles laid out on the ground there is no way a rodent can mess up all of them.  Namibian graduate student Alacia Armstrong and I returned to the site to see what we could do.  It looked like this:

After clearing some scattered tiles, we realized that plenty were still in place.  All of those had sand and small pebbles strongly cemented to their undersides, which may be the first step in hypolith colonization.  The cement is known to be exopolysaccharides, a kind of glue that the bacteria secrete to make a biofilm.  Alacia and I carefully photographed the undersides of 22 relatively undisturbed tiles and put them back.  A sample photo is shown below:

Alacia scraped samples off of a dozen of them.  Back in the metagenomics lab in South Africa, Don Cowan's group will analyze their DNA to see if the microbial community sticking to them looks different from that on a fully developed hypolith.  In other words, we are studying microbial succession.  

There was no visible green film of cells sticking to any of the tiles.  If our hunch is correct, there will be visible green in a few more years time.

There was a difference between the percentages of the surface with cemented soil on the marble tiles (68%) and the glass tiles (42%).  The bacteria prefer the marble, which transmits much less light, but they can colonize the glass tiles too.  Half of the tiles were inoculated with local cells in 2010 before being deployed in the field, and there was no evidence that it made any difference two years later.

After that, we replaced the scattered tiles in a new row.  We did not try to excavate the volcano-shaped dirt mound in the center of our array for fear that the rodent wouldn't like it and make subsequent changes.  When we were all done it looked like this:

Now we wait for a few more years!  In the meantime, there are other arrays, in North America and Asia, to check on.  The one in the Arctic can't possibly get disturbed by burrowing rodents, because there is permafrost there.  I wonder if polar bears like to scatter tiles...


Thursday, April 26, 2012

Thursday April 26, 2012: Namibian Sky

In the desert you look at the sky a lot.

That is the Moon and Venus in this photo.

Thursday April 26, 2012: Meet Thulani Makhalanyane

Thulani Makhalanyane is finishing his Ph.D. at the University of the Western Cape in South Africa. I met him here in Namibia two years ago.  His research is on the genomics of the bacterial communities that live in the desert.  His undergraduate degree is in microbiology.

Thulani is in his 20's.  He grew up in the mining town of Klerksdorp, in South Africa.  His father is a school principal and his mother is a nurse.  He has one sister. I asked him about his early influences.  He mentioned that when he was young his father bought a (print) set of the Encyclopedia Britannica.  Thulani is the kind of person who can never look up one thing in the encyclopedia without reading about ten other things before he puts the book down.  He is intellectually curious.

After he gets his Ph.D. he plans to do a post-doctoral research fellowship, and then become a professor in Africa, Europe or America.

I asked Thulani if he had anything to say to Drake students.  He said "They are lucky to have a teacher like you!"  (He meant me.)  I mention this only so I can return the compliment:  Thulani's future students are going to be very lucky indeed to have a teacher like him.  He is warm, gracious, and in love with knowledge.  He is very good at what he does, which is cutting-edge metagenomics and biotechnology, and he is also very good at sharing the excitement of doing it.

Wednesday, April 25, 2012

Wednesday April 25, 2012: The awful truth about my experiment

Two years ago I placed an array of glass and marble tiles in the desert here to see if they would become colonized on their undersides by cyanobacteria.  My main purpose in returning to Namibia was to check on them.  In the photo below you can see how the array looked in 2010.  There were six rows of ten tiles each:

I was so pleased with the project that I put similar arrays on White Mountain Peak in California, in the arctic, in Arabia, and in the Mojave Desert.  Of these arrays, the only one I have been back to is the one on White Mountain Peak.  A marmot had dug his tunnel right through the array and had stolen some of the tiles.  I had to re-do it.

Yesterday evening I returned to the 2010 Namib array.  The tiles lie flat on the ground about a quarter mile off the road, miles from the nearest humans.  I was the only person on earth who knew their coordinates. 

The array wasn’t exactly as I left it.

I couldn’t believe it.  A burrowing rodent had tunneled right through the array, flipping tiles over, scattering them and burying them.  Some of the glass ones were even broken!  How could that be?  Of the sixty tiles I had left there, I couldn’t even see half of them.

Bad luck?  This was the only rodent burrow in sight.

Slowly the horrifying truth seeped into my shocked, jet-lagged brain.  This was no accident.  It could not be a coincidence that the first two arrays I put in place, on two separate continents, were both disturbed by rodents.  Rodents must be attracted to these arrays.

Maybe they think the glass tiles shine like water.  Maybe they like the human scent.  Maybe something about the geometric, checkerboard-like pattern offends their rodent sensibilities.   But the experiment depended on the idea that, once they are put in place, Mother Nature will treat these tiles just like she would any natural stones.  She doesn’t.  She selects them for special treatment.

It’s a good thing I still have my day job.

And I had just finished putting five more arrays of tiles in the desert here, of twelve tiles each.  Three rows of four.  Will those get vandalized too?  Should I go back and put the tiles farther apart from each other?

Looking more closely at the wreckage of my experiment, it appears that a little bit of data can be salvaged.  A few tiles on the left-hand side of the array are still in position.  Turning over the marble ones, I found sand and small pebbles cemented to the surface of the marble.  This, according to Don Cowan, is due to extra-cellular polysaccharides secreted by bacteria.  In other words, the bacteria produce a kind of glue that binds sand to the stone’s surface.  There was no sign of any green film of cells, though.  Don and Chris McKay think that maybe the production of these polysaccharides is the first step in hypolith colonization.  If so, then it obviously takes a lot longer than two years to make a hypolith.

The glass tiles, in contrast, appeared smooth and clean without anything sticking to them.  Probably too much light gets through them for the bacteria to be comfortable.

All this is very preliminary.  I will return to the site later today to re-analyze it stone by stone.  Don’s group will collect a sample of the polysaccharide- bound sand for genetic analysis.  I still haven’t decided what to do going forward, but I am inclined to leave the mess exactly as it is now.  The wind and rain should even out the dirt pile.  We might still learn something from this array, if we are patient. 

(Update on Friday April 27:  Mary Seely, Director of the Gobabeb Centre, says rodents here like to begin their burrows on a firm, not sandy, surface.  She believes they like the way the array feels hard underfoot.  Maybe in the future I should space the tiles out more.  However, all is not lost.  See my post from April 27 - we still got lots of good samples and data from this experiment, and expect to get more in the years ahead.)

Monday, April 23, 2012

Tuesday April 24, 2012: Happy Birthday Elise!

My wonderful daughter Elise turns twelve today.  Happy Birthday Elise!  I will see you on Sunday.  Love, Daddy

Tuesday April 24, 2012: What we are doing here

A lot of what we do here is drive along east-west trending roads stopping periodically to dig shallow holes, collect soil samples, measure the temperature and humidity underground, and turn over rocks.

The western side of the Namib Desert has lots of fog but essentially no rain.  The eastern side has more rain, but less fog.  Here at Gobabeb there is a little of both.

All of us are here to study the bacteria that live in the soil and under rocks, and how they survive such an extreme environment.  Each of us has a different focus:

Professor Don Cowan’s South African team uses a powerful technique called metagenomics which essentially means studying the DNA of whole communities of bacteria probably consisting of hundreds of different species.  You don’t isolate and culture the individual species; you just study the collective DNA of the whole sample.  That way you learn about its genetic diversity; and how its ecology works.

NASA Scientist Chris McKay says “Follow the Water.”  He and his team are interested in whether the microbes are getting their water from fog, rain, or groundwater.  Is the water reaching them by coming down from above, or up from below?  There are chemical and physical techniques you can use to answer these questions.

The University of Edinburgh’s Sophie Nixon wants to know what chemical reactions the bacteria use to live when there is no molecular oxygen (O2) present.  She is especially interested in reactions that use iron.

Like everybody here, I am interested in the cyanobacteria that colonize the undersides of rocks.  How long does it take them to colonize a new surface?  What light levels do they prefer?  Why are some rocks colonized and not others?  That is why I am placing glass and marble tiles in the desert; to see when and if they become colonized by cyanobacteria.

Although we’re here for science none of us are unaffected by the majestic scenery and the presence of herds of big animals running around in the wild.  Yesterday on the road we saw zebras, ostriches, springbok, and warthogs.  I will try to post some good pictures but it isn’t easy.  The animals are very shy of us and they run fast.