Forget cockroaches.  Bacteria will be the only organisms left if we manage to launch a warhead too many or if any doomsday scenarios actually occur.  It's a good thing - without bacteria we wouldn't be alive.  Bacteria control nutrient cycles and help us make cheese, but they can also kill us (it should be noted that pathogenic bacteria make up a minuscule portion of the known bacteria).  Their astounding diversity has allowed them to become the earth's dominant life form.

Even our bodies are not our own.  The average person has five pounds of bacteria (1.2 kg) in their intestinal tracts and on their skin - and bacterial cells outnumber our own cells by a factor of 10 to 1.  This difference is more pronounced on the genetic level.  While the human genome encodes approximately 25,000 unique genes, the bacterial community in our intestines alone produces an astounding 9 million.  Some scientists have even proposed that the human is a "super-organism" and these bacteria play a major role in our health.  Scientists have postulated that bacteria may cause syndromes as diverse as irritable bowel syndrome, colon cancer, and yes, even autism. 

One major misconception is that bacteria are inferior or unevolved when compared to higher animals.  Although they may be simpler (in the context of size and structural complexity), bacteria have also spent the last 3.5 billion years evolving to inhabit niche habitats.  So a better way to think of bacteria is how we think of humans - perfectly adapted and at the pinnacle of evolution.  And they can survive conditions that we can't even imagine - I've isolated bacteria from hot springs so acidic that they can dissolve a cow within two weeks, and I've worked with bacteria that can eat methane and breathe sulfur.  If we find bacteria on other planets, it will probably be because we sent them there - even NASA clean rooms are not sterilized enough to kill every bacteria.

Even more astounding than the diversity we've discovered is the diversity that we can't discover - it is estimated that up to 99.99% of all bacterial species cannot be isolated in a pure culture using current technologies.  Imagine if 99.99% of birds were invisible, and you begin to see the problems that microbiologists face trying to catalog life's dominant form.  In a gram of soil there are as many as 10 billion bacterial cells - more than the Earth's human population.  Go to deep salt mines, oxygen-free caves filled with sulfuric acid, and the bottom of the ocean; look inside rocks, trees, your mouth, and nuclear waste dumps; in all of these places you'll find bacterial life.

While here at the MPI, we've tried to discover more information about a small subset of these soil bacteria, those that consume methane.  Although this order of bacteria was discovered in 1904, we still don't know very much about them.  For example, we know that they can consume atmospheric methane (23 times more potent as a greenhouse gas than carbon dioxide) but we're still not sure exactly how - the leading theory is that some bacteria contain an isozyme which allows them to consume methane at a lower concentration than cultured species, but we still have not detected this isozyme in nature.  On a more general note, we're not even sure what percentage of soil bacteria can consume methane, nor do we know how many types of methanotrophs there are.

As we discover more about microbial ecology, we realize how little we know - but also that these organisms determine many more aspects of our lives than we thought possible.  In the 18th and 19th centuries, scientists began to catalog life's macroscopic diversity, providing us with a good overview of how the environment is structured.  We are now beginning to discover life's microscopic diversity, and while bacteria may be less exciting than, say, tigers or lions, this knowledge will deepen our understanding of earth's fundamental ecological processes.  We will probably discover unexpected benefits along the way (how many pharmaceuticals were developed from plants?), but the most exciting aspect is its audacity.  At it's most basic level, we're extracting information from dirt and using it to understand the world around us.  How cool is that?

As an added bonus, here's a video of the fireworks in Marburg (yes, the soundtrack is Star Wars as played by the university orchestra), courtesy of Tour de Flener. 

Marburg held (one) of their annual city festivals this weekend, and it wasn't quite what I expected.  Normally, Marburg is a nice, quiet, reserved town (with some students to make life interesting of course) in the middle of the German equivalent of Kansas.  We don't even get the high speed trains.  However, for the festival (hereafter 3TM - Drei Tage Marburg) the town transformed itself.  Most of the walkable sidewalks in the old city were converted into a market (stands selling Wurst, beer, and kitsch - the usual), and the town somehow managed to find space for no less than nine open-air stages, with a very nice mix of music (oompah bands to Latin jazz fusion/reggae).  For me, the highlight was the conversion of the castle park (where the defenses used to be, now a rarely visited park) into a sort of mini-festival ground.  With no less than 4 stages, 6 beer tents, various fried food stands, and an exhibit about math/geometry within a 2km radius, it made for some pretty nice and eclectic wandering.  Where else can you build a small bridge without any glue (yay friction!), order a half liter of Hefeweizen, and stroll between a jazz quartet and a German rock/pop band? 

Sadly, the weather did not cooperate as much as I would have liked - although the fest lasted from Friday to Sunday, Sunday was mostly rained out (which helped keep me inside and grading papers), so I only got to experience the fest for one day.  I also didn't get to go on Friday, as Erica left for the US on Saturday so we had a nice going-away party for her in Mainz.  Continuing my theme from last week, that marks my last visit to Mainz (my second home in Germany), and since Erica has left I'm now forced to realize that yes, my time in Germany will come to an end soon as well. 

However, had I made it to the fest on Friday, I could have experienced that rarest of all occurrences - free beer (and given to me by the mayor, no less!).  It's one of Marburg's fun traditions that for the start of the fest they bring a keg of beer to the Marktplatz and tap it at 11 AM (too early for me) while dressed in traditional clothing.  Since I missed this event, it looks like I'll just have to find a way to come back next year...

New research from Mitchell et al. (Nature, July 2009) seems to indicate that higher animals (i.e., those of us lucky enough to have a central nervous system) aren't the only ones able to prepare for the future based on current environmental conditions - bacteria (E. coli) and yeast (S. cerevisiae) can do it too.  While it seems odd, the basic principle has been recognized for years.  Indeed, the lac operon in E. coli activates the genes needed to digest the sugar lactose, but the lac operon is activated only by lactose.  This mechanism makes good sense from an evolutionary perspective - proteins are expensive to produce, and if the cell does not need them (i.e. there is no lactose to digest) then producing them is wasteful.  While direct links like this one are easy to uncover, more subtle ones have remained a mystery - until now.

The biggest misconception that we need to get rid as higher mammals is the concept of memory - bacteria are unicellular organisms, so there is quite literally no way for them to develop a nervous system (or even a single neuron!), so any response and regulation has to be encoded directly into their genome.  That's where the second misconception comes in - individual bacteria don't really matter, and since their doubling time is about one hour, the number of offspring that can be produced in a short amount of time is high - as is the corresponding number of mutations and selection pressure. 

Here's where we come to the experiment.  Imagine that every time an E. coli culture is exposed to lactose, exposure to glucose follows.  Over time, the bacteria whose genes encode for the appropriate regulatory response (every time you see lactose, make the enzymes needed to digest glucose) will have a significant survival advantage over those that don't.  Think Pavlov's dog - every time the bell rings, it was conditioned to salivate.  With E. coli, lactose is the bell and glucose enzyme production is the salivation. 

Why might this be useful?  E. coli and Homo sapiens (that's us!) have a long history (not just related to contaminated beef).  In fact, most E. coli strains are helpful and make it easier to digest food.  But they have to get into our intestines somehow, and that environment is variable.  The sugars present in the stomach (where the bacteria enter) are different from those present in the large intestine (where the bacteria spend a lot of time), so if the stomach sugars can prime the bacterial cells to digest the sugars found in the large intestine, they'll have an easier time surviving in the new environment. 

The most fascinating implication of this study is how old the conditioning pathway is.  Eukaryotes (everything ranging from amoebas to humans) split from the bacteria (and archaea!) about three billion years ago, and since this genetic conditioning response is found in both bacteria (E. coli) and yeast (eukaryote), it is likely that the age of the pathway predates both - so "planning" for the future (anthropomorphism is a bad idea at the unicellular level) may actually be one of the oldest complex processes that there is.

For the scientifically-minded, here's a link to the original article.  Sadly, it is not open-access.

Now that my in Marburg is coming slowly to an end, I'm starting to do things for the last time.  These final experiences are helping to drive home what I've done in Marburg and help to show me how fond I've become of this city (it really does feel like home now).  Yesterday I had two of these final experiences: volunteering at the retirement home and my last Aikido training session.  Volunteering at the retirement was sort of like "Tuesdays with a Racist Eastern European Murray", but I'm glad that I was able to give him someone to talk to (read: at) for a few hours a week, as the rest of the residents were not able to carry out a complete converstation.

Aikido is another activity that I will miss - although it's a martial art, it's not very violent and focuses more on practical techniques and defeating your opponent (not that I ever expect to use it in a fight...) as painlessly as possible.  The intructor was quite friendly, as were the others who took the course, and I plan to continue when I start at the University of Michigan in the fall.  More than the class itself, I'll miss the walk back from the gym to my room - it's late enough that there's almost no other pedestrians and I can enjoy the old city at night.  It's also nice to walk around on a summer night without having to worry about personal safety, so this is another small habit that I will have to adjust when I get back to the US.  It's these little routines that I've gotten into which have helped Marburg feel more like home to me, so giving them up is a gentle reminder that it's time to head back and starting looking towards the future. 

We were quite sad that we would not be able to celebrate the Fourth of July (no fireworks?), but Germany decided to accommodate us in a big way - "Rhine in Flames" (it just sounds odd in English, I know) happened on the fourth of July, and it was one of the greatest spectacles (in the best sense of the word) that I've yet experienced.  When it started, we found ourselves on an Autobahn pull-out that was almost perched over the Rhine across from two ruined castles and facing down the fleet of around sixty large and fully decorated ships (we would have been on one, but at 60+ Euro per ticket...).  When the fireworks started, it was still dusk - so we got to watch the fireworks explode against the setting sun over moodily lit (since Germans don't shy from the Gothic, all of the castles and churches were lit with torches and blood-red spotlights) castle ruins.  Sadly, we could only see the first part of the fireworks from here, so it was off to the next stop after the first 30-minute show.

We watched the last half of the fireworks from the Niederwalddenkmal - a relic of Germany's Imperial past, and a sweeping monument of a half-naked Germania brandishing a sword in victory at the defeated French from the cliffs near Rudesheim.  Sadly, we were not the only ones with this idea, so to get a clear view we were "forced" to climb onto the monument itself and watch from there.  After setting off three more sets from more ruined castles/monasteries/what have you, a barge made its way into the middle of the Rhine and let loose with a world-ending cataclysm of red, white, blue, and green (almost our flag...) fire.  Since the Rhine makes its way through a mini-canyon, we then felt the vibrations for another good minute or so, and the show came to a close.  

The next morning (after sleeping in for a bit), Erica and I took a walk around town and enjoyed my last weekend in Mainz (it's very odd to think that I won't be back in the city again).  I finally got around to seeing the Chagall windows in St. Stephan's church, which lived up to my (probably too high) expectations.  I'm glad that it was my last experience of the city, as it will leave a lasting impression. 

That's not the only thing we had on tap for the day though: as a birthday gift Erica's roommate gave me 10 Euro to spend in the Weisbaden Casino - the same casino which "inspired" Dostoevsky to write his novella "The Gambler" after winning some (and losing more) at the city's roulette tables.  Roulette seems to be the only game that Wiesbaden really has, and those of you with an even elementary knowledge of statistics will not be surprised that I did not leave with anything.  However, going to the casino was worth it just to look inside - Wiesbaden was never bombed during the war and the room remains almost exactly as it did in the 1850's - full of dark polished wood and burnished bronze.  As a memorial to Dostoevsky, "his" roulette wheel stands in a corner.  It was certainly a lot of experiences to pack into one weekend, but e

Astoundingly, today marks the start of the one-month countdown to leaving Germany.  The last few months (since April in particular) have flown by - it seems like only yesterday that June had started, and we're already coming up on the first weekend in July.  A lot of this relativistic(ish) passage of time has to do with the fact that I have a lot more on my plate than I had at the start of my Fulbright grant, and all of these responsibilities (I hate to call them that because I really enjoy most of them) keep my days full and help to pass the time.  This weekend shows no signs of letting up: some other Americans and I are having a 3rd of July (no, that's not a typo) BBQ before heading down to watch fireworks over the ruined castles of the Rhine on July 4th.  For the 5th Erica and I are going to the casino in Wiesbaden with her roommate (it's the first chance we've had to celebrate my birthday last month), and on Monday I have to start grading the final papers from my Academic Writing Course.  If that weren't enough, there's an open-air movie in Marburg tonight, and since the chance to experience that happens so rarely... you get the idea.

However, the fact that I only have a month left has put me in a bit of reflective mood and helped me realize what I will miss about Germany - and (more interestingly for most of you) what I'll be glad to get away from.

Things I'll miss: