Wisdom of the Crowds: data collected by Bill Newsome's monkey study provides input, single cell data, and output to help map neurons utilized in a decision making task. Notes from David Krakauer talk, ISB. JRP.
"What is life? It is an evolved machine powering growth and replication using metabolic free energy... What are the fundamental trends underlying the evolution of biological systems?" - David Krakauer, Santa Fe Institute
One of the great benefits of grad student life is the scientific immersion you get through talks and symposiums organized by your institute or university. Often you don't even need to leave the building to hear about research happening across the country. This week in particular was rich in immersion. On Monday and Tuesday the Institute for Systems Biology held their annual symposium* (this year's theme was Emerging Technologies). Wednesday was the Department of Genome Sciences (at UW) symposium, and lastly Friday was the Molecular & Cellular Biology (my department) Symposium held at Fred Hutch. In sum, there was a ton of opportunity this week to see some great speakers spanning several different fields.
I wanted to share some of what I learned and absorbed.
David Krakauer studies fundamental trends of adaptive phenomena which range from the evolution of computers to the evolution of life. I saw David speak a few years back during my first week of graduate school. At the time, his view of evolutionary biology was so different from my narrow-minded world of functional genomics that I found it pretty inaccessible. Apparently a few years of systems biology and exposure to the likes of Sui Huang and Stu Kauffman has done some good because this time around I found David's ideas much easier to understand. I like David's talks not just for the power of the content. He's an engaging speaker, with slide organization and beautification straight out of an Edward Tufte textbook. He captivated the audience at the start with some impressive drone footage he recently took of the Santa Fe Institute where he is based. After that he dives into a critique of the scientific system as a whole and its reversion to complexity. David makes his point by showing a slide with the publication titles from the recent issue of Nature and Science. In almost every case, the title states something simplistic and linear "Gene X does Y." But is this really a great representation of the world around us? Of biology? If science is a human invention, then perhaps it has been disabled by our own human-ness. We didn't evolve to accept high dimensionality. I think part of the problem here is the story telling we have to do in our publications. I don't think anybody doing systems biology comes out of looking at something and says, "yep that's it - we got one hit, one target, one gene." No, the nature of systems biology is that you reveal the complexity of what you are studying through many layers. But that can get lost in translation I think.
"There are measurements that detect, and there are models that explain. What I mean is, the strength of my opinion has nothing to do with how right it is." - David Krakauer
The 3 Fold Way: thinking about complexity using dynamics, information theory/optimization, and computation. Notes from David Krakauer talk, ISB. JRP.
Atul Butte spoke the first day of the ISB symposium. Atul is an MD who hails from UCSF (recently recruited away from Stanford). Atul is another engaging speaker; he brings props like microarray chips and makes analogies like "this is the match.com for drugs." His science is compelling in that his students access publicly available data through resources like GEO and analyze all these datasets generated by other groups and from that analysis produce greater understanding of diseases or find better uses for drugs developed years ago that were otherwise 'sitting on a shelf.' His first slide lists his Conflicts of Interests (which is filled with text) but he draws our attention to the lower right corner and points out that these are the conflicts of interest that he is most proud of because they are all companies that were started by his graduate students. In fact, more than half of his students have started companies - and his lab dogma is that if you want to change the world you can't just keep writing papers about it.
Atul ends on a powerful note by showing us the health road maps they are building for the 14 million patients in the UC Health system. These health maps are analogous to Google Maps, except if you could see the cars driving on the roads. Instead of buildings and locations, the maps show symptoms and progression of disease and track the movement of individual patients through bins (represented as large circles) such as 'alcohol dependency' to 'cirrhosis of the liver' to small little squares for death. In the interactive version of one of these maps he shows little lines move across the map for hundreds of thousands of patients moving through hospitals and doctors appointments; their electronic medical record pinpointing their trajectory to mortality. For a data nerd, it is inspiring. For a human being, it is horrifying.
Google Maps for Patient Health Records. Talk by Atul Butte at ISB Symposium. Notes by JRP.
Lastly I'll mention that Nels Elde (University of Utah) gave a fantastic talk focusing on the 'generosity' of selfish elements. The concept in a nutshell is this - viruses invade hosts, integrate genetic material into their genomes (selfish elements) and the hosts then use that genetic material for their own benefit (hidden generosity). If you'd like to learn more about his views on evolution, he runs a cool podcast called TWiEVO: This week in evolution.
On the backdrop of this powerful week of talks I was left with the great impression that some incredibly smart people have designed some beautiful studies to reveal amazing things about personalized medicine, neuroscience, and evolution. Biology - and life in general - is complex enough that it's taken an unbelievable amount of work to get this far.
Horizontal Gene Transfer, generosity of selfish genes. Notes from Eugene Koonin and Nels Elde talks at the MCB Symposium. JRP.
* In ancient Greece, the symposium was a drinking party. [Wikipedia]