Satoshi Village the blog of Daniel Himmelstein

The preprint in 2015 and what comes next

2015 was a year of the preprint. While posting manuscripts prior to peer review and journal publication has long been practiced in physics, preprints are just catching on in the biosciences.

Last year, labs started universally preprinting, and preprints were billed as the solution to accelerating an ever more laborious publishing process.

To give some context, PeerJ PrePrints and bioRxiv both launched in 2013. Prior to 2015, PeerJ published on average 1.2 preprints per …

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Electromagnetic pulses and slime molds

Recently I listened to a great podcast on the threat posed by electromagnetic pulses (EMPs). EMPs are short bursts of energy that can fry electronics. Large scale EMPs can be triggered by solar flares or high altitude nuclear detonations. A hefty nuclear EMP could destroy unprotected electronic equipment within a thousand miles radius. The podcast motivated me recount my strange story involving EMPs and slime molds.

Arguing the unforeseen

The year was 2010. I was …

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Publication delays at PLOS and 3,475 other journals

On April 22, 2015 my research was formally accepted to PLOS Computational Biology. 68 days later the article has yet to be published. My current project builds on the forthcoming study and would benefit from its publication. Frustrated, I decided to investigate whether such delays are commonplace at PLOS.

Publication and acceptance delays at PLOS

I started by retrieving all PubMed records for the 7 PLOS journals. For each journal, I randomly selected 1000 articles …

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My application to OpenCon 2015, the best conference ever

Below I have posted the written portions of my application to OpenCon 2015, which was called the best conference ever by a 2014 attendee. This open science gathering will be held from November 14–16 in Brussels, Belgium. I have ordered my responses from practical to philosophical and mundane to radical.

For the events you checked, please explain how you plan to participate.

Last year I went to the Bay Area Open Access Week event …

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The Cancer Research UK Reassessment of our Lung Cancer versus Elevation Study

We would like to thank Cancer Research UK for their cancer related advocacy and their coverage of our recent publication. However, we find several aspects of their interpretation troubling.

First, we find it unwise to discount our study because it analyzed counties rather than individuals. As Professor Pearce explains, much of our current understanding of cancer risk arose initially from ecological studies:

Historically, the key area in which epidemiologists have been able to “add value …

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Elevation, Oxygen, and Cancer of the Lung

For the past two years, Kamen Simeonov and I have been working on a project codenamed The Lung. Today is PeerJ Publication Day and the results of our research are now online:

Simeonov KP, Himmelstein DS (2015) Lung cancer incidence decreases with elevation: evidence for oxygen as an inhaled carcinogen. PeerJ 2:e705 DOI: 10.7717/peerj.705


In this study, we investigated whether cancer rates varied with altitude. Our primary focus was lung …

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My Friendship Network

One network, with which many of my readers are familiar, is Facebook. At its core, Facebook is a network (graph) of users (nodes) connected by friendships (edges). Each user exists and experiences content within the confines of their Facebook subgraph, the portion of the network consisting of their friends. When analyzed properly, an individual’s friendship network paints a historical picture of his or her social engagement.

Here I’ve created my Facebook friendship network …

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Innovation in Medical Education Forum

During the first week of October in 2013, I traveled to Guatemala. The Universidad Francisco Marroquín (UFM) hosted a forum of 30 innovators and medical professionals to envision the future of healthcare and medical education. The forum produced suggestions for a new medical degree, based on embracing disruptions, which would initially coexist with the current medical program.

UFM is well positioned to innovate education. Founded under free market ideals, the school is characterized by an …

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