Friday, 28 September 2012

Self publishing "failed" thesis chapters on Figshare

Sometimes in life, things just don't work out, and this is especially the case when doing scientific research. Experiments fail, you ran out of time/money, you didn't collect as much data as you wanted, you get a boring negative result, the conclusions are littered with caveats, or maybe the idea was just a duff one in the first place? Unfortunately, one of my thesis chapters ended up suffering from pretty much all of these problems, but is that time I spent on it now wasted?

Perhaps not. The Web site Figshare was set up by a "frustrated Imperial College PhD student" and it looks great (not that I'm biased you understand). It's a "community-based, open science project", allowing "researchers to publish all of their research outputs in seconds in an easily citable, shareable and discoverable manner".

Despite the fact that I felt this chapter was not of the expected quality, rigour, and interest required by a peer-reviewed journal, there are still elements I think would perhaps be useful in the public domain (particularly to aquarists). More importantly though, by putting it in the public domain, an editor, a reviewer, or even myself, doesn't have to make that subjective decision. This is a bit like the PLoS ONE model of publishing, expect without the all-important peer review stage to check that the science is sound. Seeing as I don't really have any strong conclusions other than "more work is required", I can't see much of a problem there.

A hybrid Synodontis catfish. Image used with permission (Mike Norén).

The study is on investigating a simple way to find out if an aquarium fish is a hybrid or not. Hybrid fishes are quite commonly sold in the ornamental trade (especially African Synodontis catfishes), and this has implications for biosecurity agencies who have a responsibility to know which exotic organisms are entering their country. There is also the possibility of fraud, with these "fakes" often passed off as high-value species such as Synodontis granulosa. Finding experts experienced enough to know what they are is hard, and often all they are able to do is make an educated guess based on a photo. One solution is using DNA.

Given a good reference library, mitochondrial DNA with tell you who the maternal species is, but will not itself give you an indication that the fish is a hybrid, or what the paternal species is. Enter nuclear DNA. Microsatellites or SNPs are the best options, but these are too expensive and time consuming for a simple at-the-border test.

What I tried to do was see if a single nuclear gene could give me what I wanted. Results were mixed. It worked nicely for the control (hybrid danios bred in the lab), and some purchased hybrids too. However, for various unexplored reasons, it didn't work so well for the Synodontis (which was really the aim here).

Anyway, see for yourself at Comments are welcome; if they are about self publishing, add them to this blog, if they are about the manuscript use the comment feature on Figshare, and if they are on catfish hybrids, then please add them to the PlanetCatfish discussion thread on the subject.