Thursday, January 31, 2013

Uprooting the Tree of Life

Arabidopsis thaliana flower
image - European Research Commission

Hello and welcome to Tom Paine's Ghost. It has been some time since last I wrote a post of any depth. My life has been a whirlwind for the last year and I am only now watching the dust settle. Luckily I still have a big smile on my face. I am currently in Raleigh, North Carolina for my inaugural Science Online conference (if you use twitter look up #SciO13). If the wind doesn't blow me to Kansas I will finally get to meet some big-time science bloggers I've been following for years. The people at this conference are heroes of mine, writers for big international publications, renegades of open-access science journalism, and brothers and sisters-in-arms in the ranks of science. They are people who live and breath science and tell the world about it in compelling new ways. I am delighted to be here and finally to interact with them in the real world!

But before I go live-blogging the Science Online conference I'd like to re-commit to my own blog. To do that I'd better bring you up to date on me my life and where I am now.

At the beginning of 2013 I began a postdoctoral research position in the Biology Department at Emory University. I am continuing to pursue my interest in chromatin structure though I have shifted from test-tubes to whole organisms. As a graduate student at Colorado State I expressed human brain proteins in E. coli and explored how they affect chromatin structure outside living cells in test tubes. Scientists call this kind of work "In Vitro" which is Latin for in glass (glass = test tube). Now I'm working in a plant biology lab that just happens to be interested in chromatin structure as well. The beautiful little plant we work with is commonly known as "mouse-ear cress." Its Latin name is Arabidopsis thaliana.  I can't tell you how much difference it makes to my mood to grind-up plants instead of e. coli for a living.  Now the smell of fresh cut grass wafts from my mortar and pestle while I used to smell that fecal smell you get when you grow up gallons of modified gut bacteria.  It's been a nice transition.  Though I have re-entered science through academia I plan to continue to blog right through. That being said please keep in mind that the opinions expressed here on Tom Paine's Ghost are mine and the authors' I choose to share and do not necessarily represent the opinions of my home institution.

My personal history aside, I have to tell you about a lecture I attended my first week in the Biology Department at Emory.  Charles Kurland, a professor of molecular biology and evolution at the Uppsala University in Sweden came to give a departmental talk hosted by our in-house national academy member - Bruce Levin. During the course of Dr. Kurland's talk I realized he was proposing some radical reshaping of the phylogenetic tree of life.  His overarching claim is that contemporary consensus on structure of the deepest branches is wrong. He claims that his algorithm for sequence comparison does not jive with the accepted models.  This debate may sound esoteric but in this case the conclusions would change biology textbooks across the globe.  It involves the three most ancient roots of the phylogenetic tree of life - The bacteria, the eukaryota, and the archaea.

Common consensus in biology says that the last universal common ancestor (LUCA) of all life was bacteria-like and that this proto-bacteria gave rise to some archaeal ancestor which then gave rise to the first eukaryotic ancestors. Charles Kurland asserts this is not the case.  Professor Kurland uses data from his genomic comparisons to infer the existence of a common ancestor that gave rise to eukaryotes, and then bacteria, and archaea.  At first this seems incredibly counter-intuitive because of course eukaryotes are "more complex" than bacteria and archaea. But Maybe they are just smaller. There is no good reason to think that those organisms have not been evolving in parallel to all other life all along while remaining happily resilient in their tiny forms.

Kurland's hypothesis shakes up the tree of life in several other profound ways.  For one he thinks that all living organisms, the current "crown of phylogeny" as he calls it, is only one bush of biodiversity in a long lineage of expansions  and contractions of life over deep geologic time. He points to the bizarre morphology of the ediacaran fauna as evidence for previous crowns coming to be then dying almost completely due to global climactic events.  Kurland supposes the organism at the base of the current crown of phylogeny to be only a "Most Recent Universal Common Ancestor" (MRUCA) not THE FIRST organism. With this model we would have to accept that it will be impossible to ever theorize about the genetic make up of the first organism on earth because we can never reach past that bottle neck. During his lecture he also pointed out that if random genetic mutation holds steady for all living things over time, then every gene in existence would be fully saturated with mutations within 100 million years. This means that there would be zero sequence similarity between organisms living more than 100 million years from each other.  To me, one of the most fascinating aspects of living things is that when it comes time to reproduce, to replicate the genetic information, it seems that certain genes demand a more rigorous fidelity than others.  Some of the most widely shared genes among all organisms are copied with the most precision and fidelity. Seems like a chicken and egg scenario though.

The other major change to biological consensus Kurland's hypothesis brings to bear is basically a big middle finger to the endo-symbiont theory.  Kurland claims that because the genes for the mitochondrial ribosomes exist and bacteria and mitochondria does not necessarily mean that mitochondria are the remnants of an endosymbiotic bacteria engulfed by primordial life to give rise o the energy-rich cells we all know and love.  Having met Lynn Marguilis before she passed away I know she would take great offense to this suggestion. I wonder who in the community will come to her theory's defense.

Overall the boom/bust cycle of the entirely of life on earth does not seem so far-fetched to me but throwing out the endosymbiant theory seems a bit hasty and at least worth examining further.

All and all a great way to start off my re-entry into science.  Having shaken me to my roots I am forced to accept the fact there there will never be a text book of science ever written that is completely "up-to-date." The minute it goes to press there is bound to be new discoveries overturning old ideas before the ink dries.  Yet another reason to BLOG ON!


Monday, January 28, 2013

Biocentric perspective

Lawrence Krauss "science teachers should get paid more"

I had the privilege of meeting Lawrence Krauss last summer at Chautauqua Institution. I like him more every time I hear him speak. His ideas in the video below are no exception. But I am wondering if PZ has a point when he says "You can't buy good teaching." I do think all teachers should be paid more. However, in my opinion the free market has no place to operate in the classroom. If it did we might have home-ec sponsored by coca-cola, and social studies funded by Halliburton. No thanks.