notes in a shoebox

Quantum Forest

Category: research

If one were to invent scientific journals today

While taking a shower I was daydreaming about what would happen if one were to invent journals today, with a very low cost of publication and no physical limits to the size of a publication. My shower answer was that there would be little chance for a model like traditional printed journals.

One could create a central repository (a bit like the arXiv) taking submissions of text format of the article + figures, which are automatically translated to a decent-looking web format and a printable version. This would be the canonical version of the article and would get assigned a unique identifier. The submitters would get to update their article any number of times, creating versions (pretty much like software). This way they could fix any issues without breaking references from other articles.

When R, or any other language, is not enough

This post is tangential to R, although R has a fair share of the issues I mention here, which include research reproducibility, open source, paying for software, multiple languages, salt and pepper.

There is an increasing interest in the reproducibility of research. In many topics we face multiple, often conflicting claims and as researchers we value the ability to evaluate those claims, including repeating/reproducing research results. While I share the interest in reproducibility, some times I feel we are obsessing too much on only part of the research process: statistical analysis. Even here, many people focus not on the models per se, but only on the code for the analysis, which should only use tools that are free of charge.

Publication incentives

(This post continues discussing issues I described back in January in Academic publication boycott)

Some weeks ago I received a couple of emails the same day: one asking me to submit a paper to an open access journal, while the other one was inviting me to be the editor of an ‘special issue’ of my choice for another journal. I haven’t heard before about any of the two publications, which follow pretty much the same model: submit a paper for $600 and—if they like it—it will be published. However, the special issue email had this ‘buy your way in’ feeling: find ten contributors (i.e. $6,000) and you get to be an editor. Now, there is nothing wrong per-se with open access journals, some of my favorite ones (e.g. PLoS ONE) follow that model. However, I was surprised by the increasing number of new journals that look at filling the gap for ‘I need to publish soon, somewhere’. Surprised until one remembers the incentives at play in academic environments.

On the destruction of a trial of genetically modified pines

The media in New Zealand briefly covered the destruction of a trial with genetically modified pines (Pinus radiata D. Don, vulgar name Radiata pine, Monterey pine) near Rotorua. This is not the first time that Luddites destroy a trial, ignoring that they have been established following regulations from the Environmental Protection Agency. Most people have discussed this pseudo-religious vandalism either from the wasting resources (money, more importantly time, delays on publication for scientists, etc) or from the criminal activity points of view.

I will discuss something slightly different, when would we plant genetically modified trees?

Academic publication boycott

The last few weeks there has been a number of researchers calling for, or supporting, a boycott against Elsevier; for example, Scientific Community to Elsevier: Drop Dead, Elsevier—my part in its downfall or, more general, Should you boycott academic publishers?

What metrics are used to compare Elsevier to other publishers? It is common to refer to cost-per-article; for example, in my area Forest Ecology and Management (one of the most popular general Forestry Journals) charges USD 31.50 per article but Tree Genetics and Genomes (published by Springer Verlag) costs EUR 34.95 (roughly USD 46).

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