The Four Corners is often thought of as where Utah, Colorado, New Mexico, and Arizona collide. But if you are satisfied with a municipal as opposed to an interstate four corners, you likely can find a quadripoint much closer to home. In my case, I d been searching for the meeting point for four municipalities in New Hampshire — the towns of Hanover, Canaan, Enfield, and the City of Lebanon. In…
On January 24, 2010, Zeke Farwell completed the Long Trail. He had begun just two days earlier, connecting more than 50 segments of trail spanning over 200 miles. Motivated by the longest and most well known hiking trail in Vermont , Zeke often revisited portions of the trails in the years to come. Now I m not revealing a secret FKT , but rather the completion of the Long Trail route on…
The John Maddox Prize has been awarded annually since 2012 to researchers who have shown great courage and integrity in standing up for science and scientific reasoning against fierce opposition and hostility . The prize is a joint initiative between the journal Nature and the Sense about Science charity. Fergus Kane nominated Alexandra Elbakyan, creator of Sci-Hub, for the prize in 2018. While…
Iceland s longest continuous marked trail, some say. Where the night is not, the wind wails, the rain rages, and geysers gurgle. Starting June 15, 2019, I hiked from Skógar to Leirubakki in Iceland. My five day trek covered the following connected trails: Fimmvörðuháls Trail (Skógar and Þórsmörk, 24 km) Laugavegur Trail (Þórsmörk to Landmannalaugar, 63 km) Hellismannaleið Trail (Landmannalaugar to…
Below is the saga of how it took six months and 75 messages for Uber Support to admit a billing error. The issue was quite simple. The receipt indicated that I paid via Uber Credits, however my credit card was charged for the fare. After countless hours of back-and-forth, Uber finally claimed that the receipt is incorrect. However, Uber has still not updated the receipt nor refunded me. On June…
This post discloses an 8-day itinerary for exploring the Big Island, Hawaii. It is based on the expedition performed by Trang and I in January 2019. Of our 7 nights off the resort, we tent camped for six, which kept the combined lodging costs under $250. Warning: these adventures are not for the weak. Instead, these feats should only be attempted by a strong and frugal traveler, who is prepared to…
On Wednesday, June 27, 2018 I woke up in Zurich, having given a presentation at the Central Library the day prior. After 3 trains, I arrived in the French town of Vallorcine to begin my hike of the Aiguilles Rouges, which in English translates to Red Peaks . The beginning of the hike was picturesque with benign terrain (this would change soon enough): The first day was full of day hikers and…
Should citations in scholarly writing appear as author-year snippets, like ( Pantcheva, 2018 ; Zelle, 2015 ), or numbers, like [ 1 , 2 ]? Let s refer to these two methods as author-style and numeric-style . You may have also heard them referred to as the Harvard and Vancouver referencing systems. Author-style Here s an example of author-style from our recent Sci-Hub Coverage Study published in…
In 2015, Simeonov and I proposed that oxygen is an inhaled carcinogen, resulting in greater lung cancer incidence at lower elevations. Our study proved controversial, even evoking criticism from Cancer Research UK , which we responded to elsewhere on this blog . While the link between elevation and lung cancer is an open question, the association between asbestos and mesothelioma is indisputable,…
Today is an exciting day for reproducibility in computational sciences. Continuous analysis awakens with its publication in Nature Biotechnology . Continuous analysis is a method for automatically re-executing a study whenever its source code is updated. Any changes resulting from the update are tracked and visible. Once properly configured, continuous analysis makes a computational study fully…
On February 26, 2016, the first version of an article titled How blockchain-timestamped protocols could improve the trustworthiness of medical science was posted to F1000Research . The paper had two authors: Greg Irving of the University of Cambridge and John Holden of Garswood Surgery. The article describes a method for timestamping clinical trials, so the retrospective existence of a trial can…
Jordan Anaya of Omnes Res — creator of the PrePubMed search engine for biomedical preprints — recently compared bioRxiv to PeerJ Preprints . We agree that PeerJ offers the better technology and user experience. However, bioRxiv has greater adoption in the biodata sciences. In fact, since my last blog post on preprints at the beginning of 2016, bioRxiv has grown by 149% from 2,785 to 6,933…
1,700 days after moving to San Francisco for graduate school, I gave my thesis seminar. We live streamed the seminar on YouTube. The stream peaked at 20 concurrent viewers and had viewers from America, Bulgaria, Brazil, Britain, Canada, Czechia, France, and Israel. Here s a shout-out to everyone who tuned in. If you missed it, the recording (below) and slides are online. After the seminar, the…
As a first year graduate student at UCSF , I took a mandatory course titled Scientific Writing , which helped students apply for the National Science Foundation s Graduate Research Fellowship . I was fortunate to receive the fellowship (Grant No. 1144247 ), which has funded the bulk of my PhD since its third year. At the end of each fellowship year, fellows submit an Annual Activities Report,…
Last June, I released a summary of the recent publishing delays at 3,475 journals. The post attracted lots of attention via Twitter and Nature News , primarily because scientists are frustrated with the sluggish pace of publishing. However, a major question remained. Are publication delays getting shorter or longer? Kendall Powell, writing a feature for Nature News released in tandem with this…
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…
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…
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…
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…
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…
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 Findings In this study, we investigated whether cancer…
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…
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…