The glow of a firefly's butt

In the butts of fireflies there is an enzyme (big macromolecule like a protein) called Luciferase. When luciferase is exposed to the common energy currency among life forms, ATP (Adenosine Triphosphate) it glows. The more ATP the brighter the glow. A PhD student in our lab uses this firefly butt enzyme to measure the concentration of ATP in a groundwater samples. Why would she do that? She does it to measure the activity level of bacteria in the water. The more ATP, the more active they are. It strickes me as amazing how useful a bugs butt can be. Who knows what other insect appendages will become useful next?

Leipzig and Ulm in October

The glass structure is a university building they are rebuilding on the site of a church that the communists destroyed.



St. Thomas Church in Leipzig where Johann Sebastian Bach was the choir master for 20 years.



Downtown Leipzig.



This is the Leipzig Main train station. The biggest in Germany!



Biking from Ulm to Blaubeuren in the Swabian Alb, a limestone karst landscape filled with caves, underground rivers, canyons and vampires (I made the last one up).




Blautopf which means Blue Pot. An underground river that runs through a long cave system exits the ground here and makes a river which is really clear and bluish. The flow rate is pretty good and when there is a rainstorm it bubbles up like a hot tub and gushes water out very quickly. The river flows into the Danube River 20 Km downstream.



See it's really blue! I saw a big fish in there too!



Here is a Closter that was built around this mystical site in the middle ages. Science has since disposed of all such mysticism. Too bad. Legends are fun.



I'm up on a cliff looking into the valley. It was a nice warm place for a Sunday afternoon nap in the sun.



Tallest cathedral in the world in Ulm. Built over the course of 400 years in competition with a very similar looking cathedral in Cologne. It is 512 feet tall and you can climb to the top along narrow spiral staircases.





This is part of the old city wall and watch tower along the Danube River. Ulm is a very nice medium sized city with a well preserved old city. It also has only three letters in its name which is impressive! If only all German words could have so few letters. They tend to have very long words in German. English speakers would consider some German words sentences like Schwarzwalderkirshetorten (Black Forest Cherry Cake).







This house is 500 years old, like most of the houses in the fisherman's quarter of Ulm. It is an example of subsidence with one end of the house's foundation in a stream bed. The wood has slowly bent to accommodate the settling and the hotel guests all have levels attached to their beds to ensure no settling is occurring during their stay.



Here we go up the cathedral!

A little city which reminds one of eastern Germany's past

I road the train through this city on the way back to Munich after a weekend visiting some old friends who lead a small church in Leipzig, eastern Germany. The city is called Goeschwitz (pronounced Go-sh-vits) and has some very ugly communist buildings that likely each hold several thousand people in tiny apartments. I learned from living in a similar area of Leipzig (2001-2002) that privacy was discouraged and often families would share apartments and bathrooms were often in the stairwell for everyone to use instead of having a private bathroom.

For some reason I am fascinated as I look at this fading picture of the second world. That other part of the world where individual achievement was discouraged through a range of economic and domestic spying tactics. I like the hills in the background with outcropping sandstone covered with snow. The rocks never cared who was in power. They have been there far longer than us humans and will be there after we leave most likely. Nature resists alignment with a given political or religious view it seems. It just exists, sometimes inadvertently against, sometimes supporting humans, but usually just very quiet and neutral.

The mountains and rivers seem timeless. One can stare at the Urals and resonate with Tolstoy or stare at the Mediterranean and feel with Homer. Our views of earth and the solar system change from century to century, but they remain what they always were before we came. Perhaps this is a good reminder of who God is, unchanging, but the rocks don't give that answer away. If they know the answer, they are hiding it from us.

Trips in Southern Germany

The famous "Neuschwanstein" castle, built by crazy King Ludwig II in a time when there was no longer a strategic advantage to building castles that could be destroyed by modern artillery. Ludwig was one of the last of the Wittelsbach family to reign over Bavaria, the longest dynasty in Europe lasting almost one thousand years! I think he built it 1) for the future economy of Bavaria since it takes in tens of millions of Euros every summer from tourists who line up for hours to pay 9 Euros for a short tour or 2) to get women. Girls love castles. The more beautiful the castle the more girls are into them. Ludwig never married though. He might have been too busy building his castle and he also wasn't deemed fit to rule, so his uncle ruled the Kingdom in his stead while Ludwig spent the family fortune building several ridiculously expensive vacation castles around southern Bavaria. Around 40 he was found dead in Lake Starnberg near Munich, drowned under suspicious circumstances.



Looking out of Neuschwanstein towards Hohenschwangau, the family's more modest castle who Ludwig's father had built after discovering the ruins of a previous castle upon a hill. This castle was very nice as well. We especially liked the Turkish bedroom of the King with a secret passage to his wife's chambers. It seems back then husbands and wives of nobility didn't sleep in the same bed.



This lake is near the base of Zugspitze, the highest peak in Germany. It is great fun driving along the winding switch back roads through the Alps!



This is Karlsruhe, which means "Karl's rest". The city was built by orders of King Karl, after he fell asleep in the woods here on a hunting trip and decided it was so nice that he should build a city. The city is extremely well organized with 36 or so streets radiating from the central palace. This picture is looking west towards France across the Rhine river and the Rhine Graben (= grave in German). A graben is where the earth is being pulled apart and infilled with sediment, in this case the sediment is coming from the Black Forest and the Swiss Alps. France is slowly drifting away from Germany. Depending on which German you talk to, this may be good thing ;-)

The Rhine Graben is part of the large European Cenozoic Rift System, along which one finds extinct volcanoes with plains of basalts and historical earthquakes such as the 1356 Basel earthquake which flattened buildings 250 km away (http://en.wikipedia.org/wiki/Upper_Rhine_Plain).

Starnberger See

Southern Bavaria has many beautiful lakes with views of the Alps on a clear day. This lake is called Starnberger See, which means roughly Star Mountains Lake. I went there on Sunday to relax and swim to beat the heat. You can reach some of these lakes with cheap public transit less than one hour from Munich. The water was clean and cool and refreshing too.

The Scientific Method and You

“Maturity is perseverance in the face of uncertainty”

This was spoken by scientist at the beginning of his talk at a conference in San Francisco last year for the annual meeting of the American Geophysical Union. He was referring to uncertainty in forecasting flooding in watersheds. As a non-modeler, experimentalist and field worker my research and work has taught me that uncertainty is everywhere, but the only way to learn and move forward is to persevere in spite of this uncertainty.

This philosophical statement goes well beyond research and covers all areas of life. I’ve heard it said that two world wars and a great depression is what forced the young countries of America and Canada to grow up. I have experienced personal tragedy and hardship which has had the same effect on me. Perhaps it is only in trouble that we grow?

During my masters, I encountered problems growing and replicating a virus I was working with in the lab. I lost about one month of my life to this problem which came out of nowhere when I thought everything was finally working well. I was totally discouraged. This failure drove me to do a couple good things though. The first was to seek counsel. I talked to a former TA who was a post-doc and experimentalist about my problems. She told me something I have never forgot. “Peter, in science we ONLY learn when we fail”. The second thing I did was to sit down and think about why the virus wasn’t infecting the host bacteria and what I experiments I could do to figure this out. This forced me to use my imagination, something I wouldn’t have done if everything worked as planned. I eventually ended up talking to a researcher in our department who quickly suggested an effective solution to my problem and I was back on track to graduating!

I think progress can be measured by considering how far I am towards reaching my objective or goal. Hypotheses are like the specific outcomes we imagine or predict. Hypotheses are designed to be “falsifiable” or easily disproven if not correct. A failed hypothesis does not mean a failed objective. Failed hypotheses are the only way we learn what we need to learn to achieve the objective. An objective might be to “compare the transport of bacteria and viruses through groundwater”. A hypothesis would be “bacteria will be transported faster and further than viruses” and this would be based on previous experience or theory. The hypothesis can still fail while the objective is achieved.

So why do we need hypotheses in science? Making a hypothesis that turns out to be correct, based on a theory or conceptual model developed from experience, validates the theory or model. When this happens (and it is published in a rigorously peer reviewed journal) we take a step towards the complete understanding the natural world. I don’t believe that complete understanding will never be achieved by humans, however on average people in developed countries live twice as long today as they did 200 years ago because of thousands of these steps.

In an essay he wrote on evolution, my father, a biology and math teacher at a high school in northern Ontario once said “science is the formalization of learning through experience”. I always told my students this at the beginning of the semester to break down their fear of formulas and jargon. If science is the formalization of learning through experience then scientific maturity could perhaps be defined as persevering in learning through as many experiences as you can obtain in your field. Many people associate science with arrogance. In fact it takes quite a bit of humility to admit you don’t know the answer and maturity to persevere until you find it.

There is also a difference between professing science and doing science. Professing always looks into the well lighted past and communicates that to people enlightening or in-forming them. Doing stumbles forward into the future and uncovers new areas of light. Both are important.

Living in Munich

The mountain "Untersberg" near Salzburg.

Going up Untersberg in an Arial Tram

I'm not sure if this is edelweiss

There is a huge drop off behind me of about 1000 m. I wish I brought my base jumping gear..

Looking south over the Austrian Alps

High Alpine meadows with limestone and karst terrain. The sign said that infiltrating water takes about 60 days to exit the mountain in springs below. That sounds like someone's PhD project.

The peak of Untersberg

A church in Salzburg.

Some really nice conglomerate interbedded with sandstone along the back of Salzburg. Conglomerate is when there is a mixture of bolders, pebbles and fine matrial forming a consolidated rock together. Geologists say it is "poorly sorted" (by size). According to the textbook I read (Davis, Sedimentology) conglomerates are formed by turbidites which are submarine landslides. Usually material deposited in rivers, lakes and oceans (continental margins) are grouped by size. This is because the finer the material, the longer it stays suspended according to Stokes Law of gravitational settling.

The old city of Salzburg (founded more than 1000 years ago) and the fortress above. Salzburg was a rich and powerful city, because of its Salt (Salz) and the fact that it was a powerful seat of the holy Roman Empire.

Mirabelli Palace gardens (Scene from Sound of Music).

Sunset over Salzburg.

My home street.

I have been living in Munich for almost two weeks now. I have an apartment that I share with three other guys (yes the kitchen is messy), but I have a big room with two windows overlooking a little street with a street car, cafes, a bakery, pubs and a fruit market. I have a one hour commute to work every day, on street cars, subways and bus, in north Munich at the German Research Center for Environmental Health. I like the peole I work with. Although there is no airconditioning in our building, it is not Tennessee or Bangladesh so I can't really complain too much.

Munich is a really big city (2.5 million people) in the center of Europe and very close to the Alps. Last Saturday, I visited Salzburg and did some mountain climbing (assisted by an arial Tram ;-). Salzburg is a very beautiful city nestled in a valley at the base of the Alps.

Right now my work consists of going to meetings where I learn about the different projects and people connected with this institute for Groundwater Ecology where I am a Marie Curie Postdoctoral Fellow. I also have plenty of work to do publishing the chapters of my recent dissertation at the University of Tennessee. I think I'm also remembering and learning German a lot these days which is coming back to me well. My office neighour is is from Banlgadesh, and I like surprising him with expressions and greetings I learned. I think he likes it, because he always laughs a lot when I say something.

My girlfriend Sarah is doing Geology field camp in Turkey (http://sarahsgeologicadventures.blogspot.com/) this summer so you should check out her blog too.

For the Children of Bangladesh

http://inside.unicefusa.org/goto/Peter.Knappett

I did my PhD research on sanitation and drinking water quality in rural Bangladesh from 2008 through 2010. The frustrating thing about doing a very specific research project was that there were clearly many needs around us that were just as urgent as clean drinking water and sanitation. These include education (literacy is only 55% in Bangladesh), instruction in hygiene and family planning, transportation and city planning and flood control. Out of the many organizations operating in Bangladesh, UNICEF is very widespread and effective at tracking progress and targeting specific areas of need and opportunities for positive change.

What was exciting to see is that only a few dollars makes a big difference in Bangladesh. A man in Char Para, the village I work in, got his rickshaw stolen. We were able to get him another with only 40 dollars! Without this he would have lost his livelihood, which wasn't much (1-2 dollars a day), but enough for him to provide for his family.

One of the people that worked for us while in Chara Para (25 Km east of Dhaka) was Kousa, a really smart, athletic 15 year old. He liked working with us and he learned a lot about drinking water from us in the process. Kousa's family is very poor and although Char Para has a school with teachers, Kousa had to drop out of school at age 8 and go work with his father for a local businessman in a textile factory in his village. These factories are very dark, loud and hot and not very safe. I think that's one reason why he liked working with us outside for a change. Kousa has so much potential to accomplish things (he learned English quickly), and yet because he has very little schooling he couldn't read or write very well in Bangali or Enlgish.

UNICEF in Bangladesh is very aware of kids like Kousa and could do more to help them with our help. What is crazy is that Kousa has worked very hard for 7 years full time only making 1 dollar a day. For 400 dollars, he could have learned to read and do math and gone onto college to become an accountant (national occupation in Bangladesh) like some others in the village.

I'm giving my dissertation defense at the end of April (University of Tennessee at Knoxville) and dedicating the written dissertation to the children of Bangladesh. I'm going to wear my Langi (Bangladeshi man skirt) every day to school (UTK Dept. Earth & Planetary Sciences) from now until the goal of 500 dollars is reached.

Peter Knappett
March 24, 2010

Moving to Munich, Germany

This is possibly the real reason why I'm moving back to Germany... the baking!

The Munich Rathaus (City Hall) with a life size Glockenspiel with little dancers.

One of the many royal palaces in Munich.

Big Church.

The Institute for Groundwater Ecology, my new home.

The German Museum. It is a huge museum containing many inventions from the past 1000 years.

I went on this Nightwatchman tour of the old city center of Munich and heard stories and legends from centuries past. One true story is that they used to bury many people within the city walls, and when the bodies decomposed it caused pollution of the groundwater where people extracted their drinking water! Yuk!