The Internet revolution never truly arrived in scientific publishing. Instead, an old system that was functional in its time was scaled up in a largely cargo-cult manner, producing today’s grotesque, dysfunctional, and extraordinarily expensive publishing ecosystem.
Most scientists tolerate this absurdity because they are insulated from its costs. First, they learn to accept the dysfunction as the inevitable “cost of doing business.” Second, universities pay the subscription bills, so individual researchers working there rarely feel the price and paywalled gatekeeping directly.
Clearly the current publishing model is utterly dysfunctional. The best way to see that is to ask the following question. If the current system is thrown away, and the scientists gather to create a brand new system for publishing, will they build a replica of the current model? Will they beg the journal companies to lock up their papers in exchange for free work of writing, editing, reviewing and most importantly doing the entire research?
The publication system in biology is mindblowingly ridiculous as often pointed out by Mike Eisen. I was planning to buy a biology book published in the 1990s and wanted to check an old review on it before spending my money. The price of the thick book came down to below $20, but the one page review article still costs $32.99.
Now that we are on the very last day of 2021, it is not too late to review the positives of the year. I picked four categories (humor, science, society, technology) and shortlisted a tiny subset from many deserving candidates.
A newly leaked classified document revealed that scandal-ridden Francis Collins plans to change his name to continue running the NIH. He got the idea by observing Facebook CEO Mark Zuckerberg, who is rebranding himself to be a reptilian.
Things are not going well with our friends in biology. In a new paper published in PLoS Biology, a
bigshot from Baylor College of Medicine called for all criticisms of biologists be legally labeled as “hate crimes”. He appears to be upset that people found out about the sponsorship of Wuhan lab by Fauci and Daszak to make new and deadly coronaviruses.
Lately “Sir” Jeremy Farrar, the disgraced director of Wellcome Trust, is not having a good time. In a pair of scathing articles (here and here), British medical journal BMJ criticized his efforts of covering up the origin of the covid virus. If similar articles were posted merely two months back by “fringe” bioinformatics sites like ours, they would be discredited as “conspiracy theories” and blocked by the Silicon valley giants. Given that UK’s oldest medical journal wrote on this topic in its editorial, the wind must be blowing in a different direction.
In the early days of Biorxiv, I was a strong supporter of the fledgling preprint server (see here and here. After using the physics preprint server (Arxiv) in my past life, I thought Biorxiv would become something similar and encourage the biologists to collaborate openly. Although I had lingering doubts about the biologists switching from their secretive mode of worrying about getting scooped to sharing openly, never did I expect the preprint server itself to turn into a gated community.
You may have heard part of this story, where Marilyn Monroe told Einstein - “Would it not be wonderful if we had a child with your brains and my beauty?” Einstein replied promptly: “Yes, but imagine a child with my beauty and your brains!”
The world of software crowdsourcing is experiencing a new threat that is far more serious than the existing nuisances (e.g. dependency hell, heartbleed bug). In it, a malicious programmer included code in a popular and widely deployed Javascript library to steal cryptocurrency wallets. To explain the significance, let me quickly review the history of this model for software development.
For many years, bioinformaticians were defining the publishing trend in biology. This started with the influx of physicists around the completion of human genome project. I remember from early 2000s, when my papers with physicists went straight to preprint servers before publication, whereas the papers with biologists had to go through military-level secrecy. Biologists were not ready to share their papers even with close friends due to the fear of “getting scooped”.
A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.
A couple of warnings before we begin - (i) this article is for entertainment purpose only and no part of it should be considered an investment advice, (ii) we have no financial position in the mentioned companies.
Often I download newly published bioinformatics programs or libraries from the github into my Windows laptop and try to compile them within its Cygwin UNIX environment. Over the years, I noticed that those C/C++ codes tend to fall into two distinct categories -
