Mailund on the Internet

A little while back, I posted a few thoughts about the differences about post doc life and PI life.  A different perspective is posted here: Mentorship styles.

The point of view is of a grad student just starting out.  It is very optimistic.  I like that, but find it a bit naive, but go read it just for the different perspective!

(Just so I don't insult anyone: by naive I only mean less experienced and perhaps too optimistic. I am not saying that the post is simplistic or anything... please don't take it the wrong way!)

I have to get up at 4am tomorrow to get on the train for this symposium in Copenhagen. I so do not want to get up that early...

It looks like a very interesting meeting, judging from the program, and I do not want to miss it. I even had to cancel a talk I was going to give at CLC Bio myself to get there, but when I saw how early I had to get up to get there, I considered staying away...

I hate getting up early. I've gotten used to getting up around 6 am -- otherwise I simply cannot manage to do all the things I plan for the day -- but since I never manage to get to bed before midnight, four in the morning is a bit scary.

I wonder if my alarm clock will even allow me to set such an early time for the wake up time?

How do you calibrate the molecular clock -- where you need a few known sequence divergence times -- when you only know a few speciation times?

Yesterday at a meeting (I'm not sure I can tell you which meeting; I'm not sure how open it is supposed to be :-/) we discussed the divergence time of human-orangutan and human-macaque. We need the sequence divergence time to calibrate a CoalHMM model for figuring out some speciation and population genetics parameters of ancestral species.

No definitive answer came up at the meeting, but there was a short discussion by email after the meeting. This paper was sent around, where the divergence times were estimated to 25MYA and 13MYA, respectively, although the last of those numbers is actually the calibration point used in the analysis, so it is an assumption more than an estimate.

The problem is, the 13MYA used for the calibration is based on fossil evidence, and as far as I can see, that would make it an estimate for the speciation time between human and orangutan. We need the sequence divergence time. Speciation time and divergence time can vary with millions of years (if the effective population size is large enough).

If 13MYA is the divergence time between human and orangutan, we get a speciation time that is unrealistically recent.  If the divergence time is 18MYA instead, as we assumed in this paper, we would get a speciation time around 12MYA which would match the MBE paper.

But how do you figure out the divergence time needed to calibrate the clock?  Is there any way to get it, rather than the speciation time, from fossil evidence?

For our purposes, I suppose we can just as well work with speciation times for our calibration, but not everyone is using CoalHMMs for their analysis, so how do you deal with this problem?