A Day In The Life II

I have been doing paper of the day (#potd) again in 2014. See my previous post about this.

My “rules” for paper of the day are:

  1. Read one paper each working day.
  2. If I am away, or reviewing a paper for a journal or colleague, then I get a pass.
  3. Read it sufficiently to be able to explain it to somebody else, i.e. don’t just scan the abstract and look at the figures. Really read it and understand it. Scan and skim as many other papers as you normally would!
  4. Only papers reporting primary research count. No reviews/opinion pieces etc.
  5. If it was really good or worth telling people about – tweet about it.
  6. Make a simple database in Excel – this helps you keep track, make notes about the paper (to see if you meet #3) and allows you to find the paper easily in the future (this last point turned out to be very useful).

This year has been difficult, especially sticking to #3. My stats for 2014 are:

  • 73% success rate. Down from 85% in 2013
  • Stats errors in 36% of papers I read!
  • 86% of papers were from 2014

Following last year, I wasn’t so surprised by the journals that the papers appeared in:

  1. eLife
  2. J Cell Biol
  3. Mol Biol Cell
  4. Dev Cell
  5. Nature Methods
  6. J Cell Sci
  7. J Neurosci
  8. Nature Cell Biol
  9. Traffic
  10. Curr Biol
  11. Nature
  12. Nature Comm
  13. Science

According to my database I only read one paper in Cell this year. I certainly have lots of them in “Saved for later” in Feedly (which is a black hole from which papers rarely emerge to be read). It’s possible that the reason Cell, Nature and Science are low on the list is that I might quickly glance at papers in those journals but not actually read them for #potd. Last year eLife was at number 9 and this year it is at number 1. This journal is definitely publishing a lot of exciting cell biology and also the lens format is very nice for reading.

I think I’ll try to continue this in 2015. The main thing it has made me realise is how few papers I read (I mean really read). I wonder if students and postdocs are actually the main consumers of the literature. If this is correct, do PIs rely on “subsistence reading”, i.e. when they write their own papers and check the immediate literature? Is their deep reading done only during peer reviewing other people’s work? Or do PIs rely on a constant infusion of the latest science at seminars and at meetings?

Falling and Landing

A great quote from a classic paper by J.B.S. Haldane “On Being The Right Size” (1926).

You can drop a mouse down a thousand-yard mine shaft; and, on arriving at the bottom, it gets a slight shock and walks away, provided that the ground is fairly soft. A rat is killed, a man is broken, a horse splashes.

The paper is available here.


The post title is taken from ‘Falling and Landing’ by The Delgados from their LP ‘Domestiques’.

My Blank Pages

Books about the MRC Laboratory of Molecular Biology are plentiful. If you haven’t read any, the best place to start are the books written by some of the Nobelists themselves: “I Wish I’d Made You Angry Earlier” by Perutz, “My Life in Science” by Brenner. Also, “Sequences, Sequence, Sequences” by Sanger, “What Mad Pursuit” by Crick and even Watson’s “The Double Helix” cover ‘how it was done’ and ‘what the place is like’. After that are the biographies of the Nobelists and their associates. Then comes the next layer, the comprehensive but rather dry “Designs for Life: Molecular Biology after World War II” by de Chadarevian and hell, even “The Eighth Day of Creation” by Judson is substantially about the LMB, since so many major discoveries in Molecular Biology happened there.

If your appetite is not sated after wading through all of those, then there are the books for the insiders.

John Finch wrote a book “A Nobel Fellow on Every Floor” which was enjoyable, if rather selective on who and what was included. The latest book from the LMB Press is a collection of essays entitled “Memories and Consequences: Visiting Scientists at the MRC Laboratory of Molecular Biology, Cambridge”. It was edited by Hugh Huxley and was made available last summer (around the time of his death).
You can get it here

 

memories

The premise of Memories and Consequences is that there were a large number of postdoctoral fellows, mainly from the USA, who spent time at the LMB (in the 60s, mainly) and then went away and had hugely successful scientific careers. At one point in the book, Tom Steitz writes that, of his friends during this period, 40% are now NAS members! The essays cover the time of these visitors in England and how it shaped their subsequent careers.

This is definitely a book to dip in and out of. The experiences are actually pretty repetitive: yes, we drive on the other side of the road; Cambridge is a very stuffy place and Max Perutz liked to be called Max. This repetition is amplified if the chapters are read one-after-the-other. Overall however, the essays are nice reminiscences of a booming time in Molecular Biology and many capture the magic of working at the LMB during this period. Brenner and Crick come to life and even Sir Lawrence Bragg looms large in many chapters filling the authors with awe.

When I first downloaded the book, I read the chapters by those whose work I am most familiar. I didn’t even know that Dick McIntosh had spent not one but two sabbaticals at the LMB. Tom Pollard, Harvey Lodish etc. followed. I then read the other chapters when I had more time.

The best chapters were those by Harry Noller and by Peter Moore who gave the right amount (for my taste) of personal insight to their stay at the LMB. I would recommend that the reader skips the chapter by William Dove and Alexandra Shevlovsky, who tried to be a bit clever and didn’t quite pull it off. Sid Altman’s chapter has previously been published and I actually witnessed him read this out (more-or-less) verbatim at the DNA50+1 celebrations – which was far more enjoyable than it sounds.

In short, I enjoyed the book and it’s worth reading some of the chapters if you have a leaning towards the history of science, but there are plenty of other books (listed above) where you should start if you want to find out what life is like inside the Nobel Prize Factory.

I’ll leave you with three quotes that I enjoyed immensely:

“I remember seeing copies of the journal Cell, where we all yearned to publish (though, I noticed, not the really great scientists, like John Sulston or Sydney Brenner). I would shudder and turn away; Cell was for other scientists, not for me.”
Cynthia Kenyon

“Like many others who worked at the LMB in that era, I still think of its modus operandi as exemplifying the blueprint that all scientific research establishments should aspire to emulate. Pack the very best scientists you can find into a building, so densely that they cannot avoid talking to each other, and encourage them to interact in every other way you can. A canteen or dining room might be a good idea. (The facility itself need not be luxurious, and indeed, it is probably better if it is not.) Give those scientists ample staff support, and all the money they need to get on with the job. Stir well, and then be patient because good science takes time. My subsequent career has taught me that this recipe is much harder to execute than it is to describe. I still wonder how the MRC managed to do it so well for so long.”
Peter Moore

“I learned that protein chemistry didn’t need me, that King’s College High Table was for tougher folk than I, and that Sydney talked but Francis conversed.”
Frank Stahl

A comprehensive guide to LMB books is available here

Don’t worry, book reviews will be a very infrequent feature as I hardly have any time to read books these days!

The post title is from My Blank Pages – Velvet Crush from their LP Teenage Symphonies to God. Presumably a play on the Dylan/Byrds song My Back Pages.

A Day In The Life

#paperoftheday #potd

A common complaint from other PIs is that they “don’t read enough any more”. I feel like this too and a solution was proposed by a friend of a friend*: try to read one paper per day.

This seemed like a good idea and I started to do this in 2013. The rules, obviously, can be set by you. Here’s my version:

  1. Read one paper each working day.
  2. If I am away, or reviewing a paper for a journal or colleague, then I get a pass.
  3. Read it sufficiently to be able to explain it to somebody else, i.e. don’t just scan the abstract and look at the figures. Really read it and understand it. Scan and skim as many other papers as you normally would!
  4. Only papers reporting primary research count towards #paperoftheday.
  5. If it was really good or worth telling people about – tweet about it.
  6. Make a simple database in Excel or Papers – this helps you keep track, make notes about the paper (to see if you meet #3) and allows you to find the paper easily in the future (this last point turned out to be very useful).

I started this in 2013 (for one full year) and am trying to continue in 2014. I feel that this is succeeding in making me read more than I would have otherwise done.

My stats for 2013 were:

  • 85% success rate. Filling that last 15% will be tough.
  • Stats errors in 48% of papers! Most common error was incorrect use of Student’s  t-test.
  • 68% of papers were from 2013 and 22% were from 2009-2012.

The big surprise was which journals I read most:

  1. J Cell Biol 13
  2. PLOS One 12
  3. Nat Cell Biol 10
  4. PNAS 10
  5. Curr Biol 9
  6. Mol Biol Cell 8
  7. Nature 8
  8. Dev Cell 7
  9. eLife 7
  10. Nature Methods 7
  11. Cell 6
  12. Neuron 6
  13. Traffic 6
  14. J Cell Sci 4
  15. Science 4

I thought that Cell would be much higher and PNAS would be much lower. Since where we publish is dictated by who is likely to see and read the paper, this list was thought-provoking.

*I think this was a colleague of @david_s_bristol who suggested it, sometime in 2012.

The post title is of course from A Day in The Life – The Beatles from the LP Sgt Pepper’s Lonely Hearts Club Band. For the first line…