Archive for May 1st, 2010

In defence of author-pays business models

Saturday, May 1st, 2010

"Science in the open" has a very nice piece on the "author pays" publishing model.

There are several good points in the post, but in particular I want to address this one:

The more insidious claim made is that there is a link between this supposed light touch review and the author pays models; that there is pressure on those who make the publication decision to publish as much as possible. Let me put this as simply as possible. The decision whether to publish is mine as an Academic Editor and mine alone. I have never so much as discussed my decision on a paper with the professional staff at PLoS and I have never received any payment whatsoever from PLoS (with the possible exception of two lunches and one night’s accommodation for a PLoS meeting I attended – and I missed the drinks reception…). If I ever perceived pressure to accept or was offered inducements to accept papers I would resign immediately and publicly as an AE

I am an AE at PLoS ONE myself, and that is work I do for free.  Like any other editorial or reviewing job. It is part of academic life and basically just expected of scientists. I have never been paid to review or to serve as editor, so I really have no interest in making money for any publisher. The financial gain for me is exactly the same if I accept or reject a paper.  I get exactly nothing in either case.

If the author pays model was a scheme to earn money from papers that cannot be published elsewhere, it seems a bit dumb to leave the decision of whether a paper should be published with people who have nothing to gain from accepting papers over rejecting them.

As a side note, you usually have some author fees at most high tier journals as well.  They will charge you both to publish and then to read the papers.

Another point that is rarely raised is that the author pays model is much more widely used than people generally admit. Page charges and colour charges for many disciplines are of the same order as Open Access publication charges. The Journal of Biological Chemistry has been charging page rates for years while increasing publication volume. Author fees of one sort or another are very common right across the biological and medical sciences literature. And it is not new. Bill Hooker’s analysis (here and here) of these hidden charges bears reading.

I guess one of the reasons that this discussion pops up again and again is PLoS ONE's approach to papers. That is just PLoS ONE, the other PLoS journals are a very different story, by the way.  At ONE the philosophy is to publish anything that is considered sound science. There is a lot of science that is solid enough, but where the results are not that ground breaking.  Those are hard to get published, but that doesn't make it bad science.

A prime example is negative results. The reason we have to worry about publication bias is exactly because we are more likely to publish positive results over negative results.  We need to know about the negative results as well, but they are usually too hard to get published.

At PLoS ONE, and also BMC Research Notes where I'm also an AE, negative results are welcome.

This doesn't mean that we will accept any paper that is submitted.  Not at all. The methods used must be of the same standard as required everywhere else. The statistics just as solid. The impact of the discoveries are just not a criteria.

If you don't believe me, try to go to the journal and read some of the papers.  I think you will find that they are usually of the same quality as you would find elsewhere.

Horizontal gene transfer and alien invaders

Saturday, May 1st, 2010

From Science Daily:

Researchers at The University of Texas at Arlington have found the first solid evidence of horizontal DNA transfer, the movement of genetic material among non-mating species, between parasitic invertebrates and some of their vertebrate hosts.

Genome biologist Cédric Feschotte and postdoctoral researchers Clément Gilbert and Sarah Schaack found evidence of horizontal transfer of transposon from a South American blood-sucking bug and a pond snail to their hosts. A transposon is a segment of DNA that can replicate itself and move around to different positions within the genome. Transposons can cause mutations, change the amount of DNA in the cell and dramatically influence the structure and function of the genomes where they reside.

I heard about this in February where I was at a meeting where Cédric gave a talk.

What they have found is families of transposons in different branches of mammals that doesn't seem to have been inherited from further up the phylogeny.  Some distantly related mammals have them, but their close relations do not.  They appear to have just popped out of no where (so Cédric calls them "space invaders").

They seem to have entered the genomes at roughly the same time, a time where the ancestors of those species have lived in the same area, and what points to horizontal gene transfer is that parasites that would have fed on these animals do have the same transposon family.

His talk at the meeting was recorded (all the talks were) but I haven't yet found the videos online so I guess they are still being processed or something.  When I find them, I'll let you know.