A Day In The Life III

This year #paperOTD (or paper of the day for any readers not on Twitter) did not go well for me. I’ve been busy with lots of things and I’m now reviewing more grants than last year because I am doing more committee work. This means I am finding less time to read one paper per day. Nonetheless I will round up the stats for this year. I only managed to read a paper on 59.2% of available days…

The top ten journals that published the papers that I read:

  • 1 Nat Commun
  • 2 J Cell Biol
  • 3 Nature
  • 4= Cell
  • 4= eLife
  • 4= Traffic
  • 7 Science
  • 8= Dev Cell
  • 8= Mol Biol Cell
  • 8= Nat Cell Biol

Nature Communications has published some really nice cell biology this year and I’m not surprised it’s number one. Also, I read more papers in Cell this year compared to last. The papers I read are mainly recent. Around 83% of the papers were published in 2015. Again, a significant fraction (42%) of the papers have statistical errors. Funnily enough there were no preprints in my top ten. I realised that I tend to read these when approving them as an affiliate (thoroughly enough for #paperOTD if they interest me) but I don’t mark them in the database.

I think my favourite paper was this one on methods to move organelles around cells using light, see also this paper for a related method. I think I’ll try again next year to read one paper per day. I’m a bit worried that if I don’t attempt this, I simply won’t read any papers in detail.


I also resolved to read one book per month in 2015. I managed this in 2014, but fell short in 2015 just like with #paperOTD. The best book from a limited selection was Matthew Cobb’s Life’s Greatest Secret. A tale of the early days of molecular biology, as it happened. I was a bit sceptical that Matthew could bring anything new to this area of scientific history. Having read Eighth Day of Creation, and then some pale imitations, I thought that this had pretty much been covered completely. This book however takes a fresh perspective and it’s worth reading. Matthew has a nice writing style, animating the dusty old main characters with a insightful detail as he goes along. Check it out.

This blog is going well, with readership growing all the time. I have written about this progress previously (here and here). The most popular posts are those on publishing: preprints, impact factors and publication lag times, rather than my science, but that’s OK. There is more to come on lag times in the New Year, stay tuned.

ladidadiI am a fan of year-end lists as you may be able to tell. My album of the year is Battles – La Di Da Di which came out on Warp in September. An honourable mention goes to Air Formation – Were We Ever Here EP which I bought on iTunes since the 250 copies had long gone by the time I discovered it on AC30.

Since I don’t watch TV or go to the cinema, I don’t have a pick of the year for that. When it comes to pro-cycling, of course I have an opinion. My favourite stage race was Critérium du Dauphiné Libere which was won by Chris Froome in a close contest with Tejay van Garderen. The best one-day race was a tough pick between E3 Harelbeke won by Geraint Thomas and Omloop Het Nieuwsblad won by Ian Stannard. Although E3 was a hard man’s race in tough conditions, I have to go for Stannard outfoxing three(!) Etixx Quick Step riders to take the win in Nieuwsblad. I’m a bit annoyed that those three picks all involve Team Sky and British riders…. I won’t bore everyone with my own cycling (and running) exploits in 2015. Just to say, that I’ve been more active this year in any year since 2009.

I shouldn’t need to tell you where the post title comes from. If you haven’t heard Sgt. Pepper’s Lonely Hearts Club Band by The Beatles, you need to rectify this urgently. The greatest album recorded on 4-track equipment, no question. 🙂


Lemonade Secret Drinker: sober statistics

I read this article on the BBC recently about alcohol consumption in the UK. In passing it mentions how many people in the UK are teetotal. I found the number reported – 21% – unbelievable so I checked out the source for the numbers.

Sure enough, ~20% of the UK population are indeed teetotal (see plots). The breakdown by gender and age is perhaps to be expected. There are fewer teetotal men than women. Older women (65+) in particular are more likely to be teetotal. There has been a slight tendency in recent years for more abstinence across the board, although last year is an exception. The BBC article noted that young people are pushing up the numbers with high rates of sobriety.

There are more interesting stats in the survey which you can check out and download. For example, London has the highest rate of teetotallers in the UK (32%).

I thought this post would make a fun antidote in the run up to the holidays, which in the UK at least is strongly linked with alcohol consumption.

The post title is taken from “Lemonade Secret Drinker” by Mansun, which featured on their first EP (One). It’s a play on “Secret Lemonade Drinker” the theme from R Whites Lemonade TV commercial in the 70s/80s (which I believe was written and sung by Elvis Costello’s father).

White label: the growth of bioRxiv

bioRxiv, the preprint server for biology, recently turned 2 years old. This seems a good point to take a look at how bioRxiv has developed over this time and to discuss any concerns sceptical people may have about using the service.

Firstly, thanks to Richard Sever (@cshperspectives) for posting the data below. The first plot shows the number of new preprints deposited and the number that were revised, per month since bioRxiv opened in Nov 2013. There are now about 200 preprints being deposited per month and this number will continue to increase. The cumulative article count (of new preprints) shows that, as of the end of last month, there are >2500 preprints deposited at bioRxiv. overall2


What is take up like across biology? To look at this, the number of articles in different subject categories can be totted up. Evolutionary Biology, Bioinformatics and Genomics/Genetics are the front-running disciplines. Obviously counting articles should be corrected for the size of these fields, but it’s clear that some large disciplines have not adopted preprinting in the same way. Cell biology, my own field, has some catching up to do. It’s likely that this reflects cultures within different fields. For example, genomics has a rich history of data deposition, sharing and openness. Other fields, less so…

So what are we waiting for?

I’d recommend that people wondering about preprinting go and read Stephen Curry’s post “just do it“. Any people who remain sceptical should keep reading…

Do I really want to deposit my best work on bioRxiv?

I’ve picked six preprints that were deposited in 2015. This selection demonstrates how important work is appearing first at bioRxiv and is being downloaded thousands of times before the papers appear in the pages of scientific journals.

  1. Accelerating scientific publishing in biology. A preprint about preprinting from Ron Vale, subsequently published in PNAS.
  2. Analysis of protein-coding genetic variation in 60,706 humans. A preprint summarising a huge effort from ExAC Exome Aggregation Consortium. 12,366 views, 4,534 downloads.
  3. TP53 copy number expansion correlates with the evolution of increased body size and an enhanced DNA damage response in elephants. This preprint was all over the news, e.g. Science.
  4. Sampling the conformational space of the catalytic subunit of human γ-secretase. CryoEM is the hottest technique in biology right now. Sjors Scheres’ group have been at the forefront of this revolution. This paper is now out in eLife.
  5. The genome of the tardigrade Hypsibius dujardini. The recent controversy over horizontal gene transfer in Tardigrades was rapidfire thanks to preprinting.
  6. CRISPR with independent transgenes is a safe and robust alternative to autonomous gene drives in basic research. This preprint concerning biosafety of CRISPR/Cas technology could be accessed immediately thanks to preprinting.

But many journals consider preprints to be previous publications!

Wrong. It is true that some journals have yet to change their policy, but the majority – including Nature, Cell and Science – are happy to consider manuscripts that have been preprinted. There are many examples of biology preprints that went on to be published in Nature (ancient genomes) and Science (hotspots in birds). If you are worried about whether the journal you want to submit your work to will allow preprinting, check this page first or the SHERPA/RoMEO resource. The journal “information to authors” page should have a statement about this, but you can always ask the Editor.

I’m going to get scooped

Preprints establish priority. It isn’t possible to be scooped if you deposit a preprint that is time-stamped showing that you were the first. The alternative is to send it to a journal where no record will exist that you submitted it if the paper is rejected, or sometimes even if they end up publishing it (see discussion here). Personally, I feel that the fear of scooping in science is overblown. In fields that are so hot that papers are coming out really fast the fear of scooping is high, everyone sees the work if its on bioRxiv or elsewhere – who was first is clear to all. Think of it this way: depositing a preprint at bioRxiv is just the same as giving a talk at a meeting. Preprints mean that there is a verifiable record available to everyone.

Preprints look ugly, I don’t want people to see my paper like that.

The depositor can format their preprint however they like! Check out Christophe Leterrier’s beautifully formatted preprint, or this one from Dennis Eckmeier. Both authors made their templates available so you can follow their example (1 and 2).

Yes but does -insert name of famous scientist- deposit preprints?

Lots of high profile scientists have already used bioRxiv. David Bartel, Ewan Birney, George Church, Ray Deshaies, Jennifer Doudna, Steve Henikoff, Rudy Jaenisch, Sophien Kamoun, Eric Karsenti, Maria Leptin, Rong Li, Andrew Murray, Pam Silver, Bruce Stillman, Leslie Vosshall and many more. Some sceptical people may find this argument compelling.

I know how publishing works now and I don’t want to disrupt the status quo

It’s paradoxical how science is all about pushing the frontiers, yet when it comes to publishing, scientists are incredibly conservative. Physics and Mathematics have been using preprinting as part of the standard route to publication for decades and so adoption by biology is nothing unusual and actually, we will simply be catching up. One vision for the future of scientific publishing is that we will deposit preprints and then journals will search out the best work from the server to highlight in their pages. The journals that will do this are called “overlay journals”. Sounds crazy? It’s already happening in Mathematics. Terry Tao, a Fields medal-winning mathematician recently deposited a solution to the Erdos discrepency problem on arXiv (he actually put them on his blog first). This was then “published” in Discrete Analysis, an overlay journal. Read about this here.

Disclaimer: other preprint services are available. F1000 Research, PeerJ Preprints and of course arXiv itself has quantitative biology section. My lab have deposited work at bioRxiv (1, 2 and 3) and I am an affiliate for the service, which means I check preprints before they go online.

Edit 14/12/15 07:13 put the scientists in alphabetical order. Added a part about scooping.

The post title comes from the term “white label” which is used for promotional vinyl copies of records ahead of their official release.