everyone has won and all shall be given prizes said the dodo in Alice and Wonderland

This is one of my mentor Fred Cross's favorite quotes and I think it makes some sense when applied to scientists:

'First it marked out a race-course, in a sort of circle, (`the exact shape doesn't matter,' it said,) and then all the party were placed along the course, here and there. There was no `One, two, three, and away,' but they began running when they liked, and left off when they liked, so that it was not easy to know when the race was over. However, when they had been running half an hour or so, and were quite dry again, the Dodo suddenly called out `The race is over!' and they all crowded round it, panting, and asking, `But who has won?'

This question the Dodo could not answer without a great deal of thought, and it sat for a long time with one finger pressed upon its forehead (the position in which you usually see Shakespeare, in the pictures of him), while the rest waited in silence. At last the Dodo said, `Everybody has won, and all must have prizes.' '

how we should select our graduate students

interesting piece of analysis by orion weiner using ucsf data link here. it is fantastic that someone was able to do this, and it confirmed some of my suspicions that i've had from sitting on the stanford bio dept grad admission committee. i would posit another way of interpreting the results. it isn't that any of the scores of the admitted students (except number of years of research experience and subject gres) are useless, but that at the top programs, like ucsf, the students scores are above where they start being predictive. another case is nih grant scores - if i recall correctly, there is no correlation with grant score and productivity (sum of impact factor points or some such metric), up to a point, estimated around 30% or so. after the 30th percentile, things get predictably worse though... i suspect something similar is going on with our students, where beyond the 30th percentile things would get predictably worse. so, all in all, we may be doing as good a job as we can on the committee. yeah! perhaps we can do it faster next year...

network nonsense continues. an amazing post by Lior Patcher http://liorpachter.wordpress.com/2014/02/12/why-i-read-the-network-nonsense-papers/

http://liorpachter.wordpress.com/2014/02/12/why-i-read-the-network-nonsense-papers/

I always wondered how long this network stuff would go on after meeting Barabasi at a NATO school on complex systems. It just keeps going and going and certainly seems to have lasted far longer than I had thought it would. Part of it, usefully, seems to have merged with the big data tsunami hitting just about everything. Still, though, it seems to me this is mostly about the statistics of artifacts, scale-free... whatever that means. Most biological interactions are probably meaningless, e.g., see the collected works of Sandy Johnson at UCSF on targets of specific transcription factors. So, even if the nodes and edges were all real, it is unclear how informative the statistics of neutral evolution interactions might be in gaining biological insight.

amanda amodeo defends her phd!

a fantastic effort on identifying histones as the molecular basis of the titration mechanism sensing the dna-to-cytoplasm ratio prior up until the mid-blastula transition in frogs.

why we do science : the man who loved numbers

i reread the book 'the man who loved only numbers' by Paul Hoffman over the holidays. it is a wonderful book and a reminder of why we do this. it is so fun and so engrossing. lessons sometimes forgotten in the competitive world of molecular and cell biology, where the competition often is not about who has the ideas, but rather who gathers the most funding and implements fastest. still, it is possible to have a lot of fun solving problems.

i must say though, that the title is just wrong. after reading the book it would be impossible to describe Paul Erdos as only loving numbers. he clearly loved his mother, first and foremost, his collaborators and all children, the 'epsilons as he called them. he just didn't love money, institutional positions or official praise - the usual motivations of many in the higher echelons of our academy and beyond. after his 30's, i don't think he held any official university position, with the duties responsibilities and steady paycheck that this brings. so the image that emerges, is of a man who loved many people and was loved by many. my quibbles with the title aside, this is a highly recommended book.