Smith, S. A., Cranston, K. A., Allman, J. F., Brown, J. W., Burleigh, G., Chaudhary, R., ... & Williams, T. (2014). Synthesis of phylogeny and taxonomy into a comprehensive tree of life. bioRxiv, 012260.
This week Sam Church will lead our discussion about inferring THE tree of life, and the challenges, hope, and possibility that come with this undertaking:
"I thought about doing a paper that would be really great for my learning and my thesis and challenging or whatever, but then I remembered it was thanksgiving, and we should read papers that make us happy to be alive and doing science all the time. This paper, which maybe people are already familiar with, makes me excited about research. I think it is great and raises cool questions, such as...
What is our end game for this great big tree we are building?
What is phylogenetic conflict? We work hard to eliminate it with our research, can we justify that given this paper?
What does this paper tell us about current sampling practices? Do we agree with the perspective it provides?
What can we gain by going open source? What do we lose? What else besides phylogenetic relationships would be amenable to going open source?
What would you do if you had the tree, and you knew it was completely correct and perfectly sampled? What questions could you ask then?
I also think the methods are really compelling, and if people are cool with digging into them, I think that would be fun. I especially like the critical thinking they present about data curation, how we make, report, and read a tree, etc. Maybe we could even look at what it would take to submit some trees to the database...? I bet you everyone in the room has a tree they know a lot about that might not be represented, and it would be great to learn the format."
We will be meeting at our normal 11 o'clock in the MCZ Labs 4th floor Seminar Room, where there will be snacks and coffee! As a reminder this is not a regular meeting week for us, but because of the Thanksgiving holiday we have decided to have journal club this week instead of next week.
This week Sam Church will lead our discussion about inferring THE tree of life, and the challenges, hope, and possibility that come with this undertaking:
"I thought about doing a paper that would be really great for my learning and my thesis and challenging or whatever, but then I remembered it was thanksgiving, and we should read papers that make us happy to be alive and doing science all the time. This paper, which maybe people are already familiar with, makes me excited about research. I think it is great and raises cool questions, such as...
What is our end game for this great big tree we are building?
What is phylogenetic conflict? We work hard to eliminate it with our research, can we justify that given this paper?
What does this paper tell us about current sampling practices? Do we agree with the perspective it provides?
What can we gain by going open source? What do we lose? What else besides phylogenetic relationships would be amenable to going open source?
What would you do if you had the tree, and you knew it was completely correct and perfectly sampled? What questions could you ask then?
I also think the methods are really compelling, and if people are cool with digging into them, I think that would be fun. I especially like the critical thinking they present about data curation, how we make, report, and read a tree, etc. Maybe we could even look at what it would take to submit some trees to the database...? I bet you everyone in the room has a tree they know a lot about that might not be represented, and it would be great to learn the format."
We will be meeting at our normal 11 o'clock in the MCZ Labs 4th floor Seminar Room, where there will be snacks and coffee! As a reminder this is not a regular meeting week for us, but because of the Thanksgiving holiday we have decided to have journal club this week instead of next week.
thetreeoflife.pdf |