We started Haldane’s Sieve back in August 2012, so we’ve just passed our one year anniversary. You can read our first post on our motivations for starting the blog here. We are pretty happy about how well Haldane’s Sieve has done at promoting preprints and a preprint culture more generally in population and evolutionary genetics and genomics.

Overall we posted 430 posts, the majority of which have been abstracts of arXived papers. It’s been great to see so many people starting to experiment with preprinting their work.

We’ve also had 41 guest posts by authors blogging about their papers (see here). This has been a really nice side effect of Haldane’s Sieve; we have gotten more researchers blogging about their work. The main aim of these “our paper” posts has been to allow authors to write about their paper in a more informal setting than a paper, to reach out to other researchers for feedback and to start to publicize their papers to the population and evolutionary genetics and genomics communities.

Over the past year Haldane’s Sieve has had over 600 comments. The majority of preprints have passed without comment, which is fine by us. Not all preprints need commentary, and a reasonable fraction are likely to have little long-term impact (like many papers). However, all of the abstracts posted at Haldane’s Sieve have been visited multiple times (the top ones hundreds of times), and the majority have been tweeted on twitter. Thus all of the preprints have received attention, and have likely had many more sets of eyes viewing them earlier than if they’d never been preprinted.

Some of the preprints get significant amounts of attention, comments, and feedback (both online and offline), which is really heartening to see. We think that many papers have been improved thanks to appearing on the arXiv and at Haldane’s Sieve. Thanks to everyone for their comments. It would be great to have more, remember they do not have to be substantial and could be as simple as asking for clarification on a figure legend. We try to make sure that the authors of preprints get notified about comments, however minor. Every comment helps improve preprints, to encourage others to preprint their papers, and a culture of preprint comments more generally.

Encouragingly, during the past year Genetics, Genome Research, and MBE have all changed their preprint policies to allow the submission of previously preprinted articles (see here). It is great to see preprints are starting to gain more acceptance in evolutionary genetics and genomics.

Here’s hoping for another good year, and we are thinking about extending Haldane’s Sieve in a few different ways over the coming year.

The ease of communication facilitated by the Internet has dramatically affected the process of scientific communication in many fields. Most notably, many physics, math, and economics communities have adopted a system in which new research papers are immediately distributed throughout the world prior to formal evaluation in the form of peer review. This system allows for rapid distribution of “bleeding edge” results among all the experts in a field, allowing them to see and build upon the most recent advances.

This practice has historically been uncommon in biology, where instead results are generally made available to the community (including many people qualified to judge them) only after a delay of generally around six months to a year, during which a paper is reviewed, formatted, and published. We believe this is unfortunate. However, there is growing pressure in some parts of biology (in particular our fields of evolutionary and population genetics) to follow physics and math in posting papers to preprint servers ahead of formal publication.

Some authors have a variety of reasonable concerns about posting their papers to preprint servers. In particular, one worry is that, in a morass of online content, their work will not reach the relevant audience. Others see no benefit in posting their papers prior to review if they will not receive useful feedback. The goal of Haldane’s Sieve is to partially remedy these issues. We aim to provide a simple feed of preprints in the fields of evolutionary and population genetics (though we may later expand to other fields). Thus, instead of checking arXiv, PeerJ, or Figshare for relevant preprints, readers in these fields could simply check Haldane’s Sieve.

What to expect

As described above, most posts to Haldane’s Sieve will be basic descriptions of relevant preprints, with little to no commentary. All posts will have comment sections where discussion of the papers will be welcome. A second type of post will be detailed comments on a preprint of particular interest to a contributor. These posts could take the style of a journal review, or may simply be some brief comments. We hope they will provide useful feedback to the authors of the preprint. Finally, there will be posts by authors of preprints in which they describe their work and place it in broader context.

We ask the commenters to remember that by submitting articles to preprint servers the authors (often biologists) are taking a somewhat unusual step. Therefore, comments should be phrased in a constructive manner to aid the authors.

Authors: Our choice of what to post reflects our interests and knowledge, so we will only post a biased subset of evolutionary, population, and statistical genetics preprints that attract our interest. We will endeavor to be somewhat thorough but we will doubtless miss some interesting preprints, e.g. especially if they are not in the quantitative biology arXiv subfield. If you want us to link to your preprint please drop us a line, our emails can easily be found via our University sites. Alternatively send a tweet to @Haldanessieve.

Why “Haldane’s Sieve”?

A brief description of the name of this site is perhaps in order. When a new beneficial allele arises in a population, the probability that it eventually reaches fixation is influenced by a number of factors. One of these is the dominance coefficient of the allele. The reason the dominance coefficient matters is because early in the life of the allele, while it is at low frequency, it is almost always present in the population in heterozygous form. Therefore all else being equal, dominant beneficial alleles can increase in frequency due to selection faster than recessive alleles, increasing their probability of eventual fixation (or establishment in the population). This effect was noted by Haldane (Haldane 1924,1927) and has become known as “Haldane’s sieve” (Turner 1981; Charlesworth 1992). Analogously, we seek to increase the exposure of interesting papers early in their lifespan, hopefully increasing the probability that they reach their target audience.

A nameless wit has pointed out to us that preprints would really count as standing variation in this analogy and might therefore not be subject to Haldane’s sieve (see Orr and Betancourt Genetics 2001 ). We leave it to the reader to decide whether the analogy holds.

Image

The image of Haldane is from wikipedia.
The image of sieve is from fdctsevilla who kindly uses the creative commons 2.0. It’s surprisingly difficult to find a usable picture of a sieve.

Graham Coop and Joe Pickrell