Saturday, April 27, 2013

PALEONTOLOGY AND MICROBES – WHY MY FATHER FINALLY ACCEPTS BIOCHEMISTRY AS AN HONORABLE CAREER



The world is a big and fascinating place. There is simply so many interesting things to do and learn about that choosing a career can be a daunting task and one that we often have to decide about at a young age.  As a parent, I always tried to expose my son Griffin to as many things as possible and always encouraged him to try many different activities, and he did --- skateboarding, rock climbing, and snowboarding to name a few.  I told him to find his passion and follow it and that just because his father is a paleontologist didn't mean he had to be one.  It never occurred to me that he would actually take that admonition seriously. But he did.  

Griffin is graduating soon and will be heading off to graduate school.  He asked to do a guest post at Land of the Dead and I told him fine.  So here it is, his own thoughts in his own words, including the profanities.


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My name is Griffin and I am the son of Supreme Leader Dr. Dan Chure. While in my first semester at the University of Utah, four years ago, I came out to my parents as a biochemist. While my mother was very accepting, my father was crushed by the news. What had he done wrong? Why did his son not devote his life to theropod dinosaurs of the Nugget Sandstone? Was it his fault? These are all questions I am sure plagued his mind as he lay sleepless every night. 

Family gatherings often resulted in terse words between us. When afforded the opportunity to talk about my undergraduate research on the biochemical assembly of the bacterial flagellar motor, he often asked “But how does this relate to dinosaurs?” before flipping over the dinner table, storming out of the house, and leaving my mother and I in tears.


The bacterial flagellar motor1 – a common source of familial contention.

After much struggle, my father finally accepted me as his son again and is planning on attending my graduation this Friday. However, this was only after I showed him that microbes have quite a fascinating (and impressively old) fossil record.  

Many species of bacteria can form biofilms – large, multicellular masses that can grow almost anywhere (agar plates, tops of ponds, teeth, etc.) In forming these massive biofilms, small grains of sediment can be bound and cemented between layers of cells. Given much time, biofilms can form large sturdy structures, known as stromatolites2.



Prime prokaryotic real estate, underwater stromatolites in Shark Bay, Australia3.

Given time, some sedimentation, a pinch of pressure, and a few heaping loads of interesting chemistry, stromatolites can fossilize. These fossilized stromatolites can be 3.5 billion years old4. That's right - fossilized life from the fucking Precambrian.



Close-up of Precambrian stromatolites in Siyeh Formation, Glacier National Park5.

Okay, so maybe these fossils aren’t as “pretty” as a skull of an Allosaurus fragilis specimen pulled from the Morrison formation (I can speak paleo too), but they are pretty damn cool. 

A typical bacterium such as the ill-famed Escherichia coli is about 2 microns long by 1 micron across. Objects on this size scale are not readily visible without the help of microscopy. Light microscopy is one of the most commonly used tools for studying bacterial cells. However, it cannot be used to look for fossilized cells in hard, unforgiving sediments. Transmission Electron Microscopy and Scanning Electron Microscopy allows us to look at cells in excruciating detail with the resolution of a few nanometers, which is exactly what’s needed to look at bacterial fossils.

Most bacterial fossils are of cyanobacteria – a special type of bacterium typically larger than most other prokaryotes – and are responsible for oxygenation of the atmosphere. 


A transmission electron micrograph of a preserved chain of cyanobacterium Palaeolyngbya from Bitter Springs Chert, Australia6.

“But Griffin!” you shout at your screen, “All bacteria look the same, so how can one even classify them by fossils alone?” Bacteria can often look similar to the untrained eye but they by no means look the same. However, due to the limited number of fossilized cells available, it can be difficult to assign classification by morphology. DNA and proteins are not typically rugged enough to survive the extreme conditions of fossilizations and typically degrade. However, certain biomolecules such as lipids, which make up the cell membrane, and various pigments can remain stable especially when chemically modified. Leaving all the interesting quantum mechanics behind, infrared spectroscopic studies of the bacterium pictured above shows that the DNA and proteins have degraded leaving only geochemically modified lipids and pigments behind. The lipid composition and metabolites present in that chemical fossil can be enough to understand the organism’s metabolism and assign Linnaean classification.

Amber also sometimes preserves fossil bacteria. The earliest report of bacteria in Baltic amber dates back to 1929. The specimens were extracted by dissolving the amber in turpentine, centrifuging the liquid, and examining the concentrate under 800 X magnification.  A surprising bacterial flora was seen, ranging from micrococci (1 micrometer in diameter), to short rods (2-3 micrometers), longer rods (5-8 micrometers), and spiral forms. Paleontologists have a terrible obsession with naming and classification so these various bacteria were assigned to Bacillus elektroni, Longibacillus elektroni, and Spirillium elektroni.  Not very creative when it comes to those species names!7  Later, clusters of spherical bacteria (Succinococcus) were found8 as well as unnamed bacteria inside the body of a nematode worm preserved in amber.  Attempts to revive the latter bacteria were unsuccessful9, although other crazy paleoclimatologists have revived 50,000 year old microorganisms from ice cores from glaciers.  And people accuse me of “playing God” just because I manipulate a few genes of living bacteria. 

Well, this concludes my little journey through the small world of tiny bacteria fossils. This September I will enter the PhD program in Biochemistry and Molecular Biophysics at CalTech in Pasadena.  That got my father upset all over again but I simply told him to grow up. I reassured him that he will still have his beloved ancient bones and teeth that he and his friends (oops…I mean colleagues) can play with and he can leave it to me to do the stuff that is important.   

 
Portrait of the biochemist as a young man and a bit of a smart ass.
 

IMAGE SOURCES AND REFERENCES

1. http://en.wikipedia.org/wiki/File:Flagellum_base_diagram_en.svg
2. Riding, R. (2007). "The term stromatolite: towards an essential definition". Lethaia 32 (4): 321–330. doi:10.1111/j.1502-3931.1999.tb00550.x.
3. http://www.sharkbay.org/assets/images/strom13.jpg
4. Allwood, Abigail; Grotzinger, Knoll, Burch, Anderson, Coleman, and Kanik (2009). "Controls on development and diversity of Early Archean stromatolites". Proceedings of the National Academy of Sciences 106 (24): 9548–9555.
5.http://www.nature.nps.gov/geology/cfprojects/photodb/Photo_Detail.cfm?PhotoID=204
7 Blunck , G. 1929. Bakterieneinschlusse im Bernstein.  Centralblatt fur Mineralogie, Geologie und Palaontologie (Abt. B, no. 11): 554-555.
8 Katinas, V. 1983. Baltijos Gintara.  Vilnius: Mokslas. 111 pages.
8 Poinar, G.O. Life in Amber.  Stanford University Press, Stanford CA: 350 pages

1 comment:

  1. Congratulations on your graduation, Griffin!

    ReplyDelete