Mailund on the Internet

This is a typical situation for me: I submit a paper to a journal or conference that is just to  under the page limit.  I get review reports back, and each reviewer has a few reasonable suggestions to additional experiments or possible extensions or papers worth referencing.  I want to do the extra work — it is reasonable and I will learn something from it — but there just isn’t room in the paper to write about it!

Right now, I’m editing a paper for Bioinformatics, where the page limit is seven pages.  I’ve done all the work suggested by the reviewers but I’m practically putting it all in the cover letter instead of the paper.  The cover letter is now as long as the paper itself.

What do you do in a situation like this?

The reviewers’ decision is based on the submitted paper, so there is a limit to how much I can remove.  I cannot completely rewrite the paper, since the journal want me to mark up all changes (and I doubt that they will be happy with markups showing that I’ve changed everything).  So with the submitted manuscript being seven pages, I can only make very minor changes to the paper, and I still need to find a way to address all reviewer comments.

It is an impossible task!

I guess I should always leave a page or so for the second submission, but usually I find it hard to get down to the page limit in the first place…

In this letter to Nature, Raghavendra Gadagkar argues that the open access model — that typically means “pay to publish, but read for free” — is doing more harm to research in the developing world than the traditional “publish for free, but pay to read” model.

The reasoning is, that having to pay to publish means that publications are not a result of the quality of ones research, but just as much a result of ones funding, and in developing countries there is less funding.

This is, of course, a valid point, but to conclude from this that the open access model — even if it means you have to pay to publish — is doing more harm than good is, well, just nuts!

First of all, many top journal charges you both for publishing and for reading the articles. With open access, at least, you can read for free.

Secondly, even if the publishing charges are much higher than the reading charge, you only pay when you have a result worth publishing. I don’t know about you, but I personally read a lot more papers than I publish, and most papers I read are never cited in my own work, because they turn out not to be relevant for my own work.

Gadagkar ends his letter with:

A ‘publish for free, read for free’ model may one day prove to be viable. Meanwhile, if I have to choose between the two evils, I prefer the ‘publish for free and pay to read’ model over the ‘pay to publish and read for free’ one. Because if I must choose between publishing or reading, I would choose to publish. Who would not?

Of course we all prefer to publish our own papers, but you cannot, and should not, publish worthwhile research if you are not familiar with the work of other researchers and have read the literature. You cannot choose publishing over reading!

I’m not saying there isn’t a problem with publication charges, but I strongly disagree with the claim that it is worse than the charge for access to papers (and I remind you, once more, that in many cases you get both of the two evils…)

At Genomicron, Ryan Gregory refuses to participate in ResearchBlogging. Why? Because their slogan is Discussing and Creating Peer-reviewed Research. Discussing is fine, but we are not creating peer-reviewed research by blogging about it.

I hadn’t noticed this slogan — it is only on the large icon and I only use the small icons when I use it in posts about published research — but it is not something I worry too much about. I like to read discussions about published papers in blogs, but I am not kidding myself that much research is being created there.

I’ll still use the icon to highlight when I am discussing a paper — and not some more general issue.

Another, older complaint, is that blogging on peer-reviewed research it can be confused for the actual peer-review process:

As a scientist, I take the peer review system very seriously (its several problems notwithstanding) and I do not wish to see blogs perceived as even an approximation of that system. That said, blogs are a useful way to discuss research, and I am happy to see this new development in science communication.

Again, I love reading about paper discussions — it feels like a global journal club — but I agree that the actual peer-review process has very little to do with blog discussions of papers!

Over the last couple of years, I have done a little work on phylogeny inference, including a few papers on neighbour joining.  One thing that consistently happens when you submit a paper on this — and I bring it up because I have just gotten back reviewer reports on such a  paper — is that at least one reviewer will tell you that neighbour joining is not interesting and one should focus on maximum likelihood / Bayesian trees instead.

Sorry to say it, but people do use neighbour joining — I am willing to bet that there are ten times as many people using neighbour joining to infer trees than there are people using the statistical approaches — so algorithmical improvements here do matter!

The statistical approaches are usually more accurate, and they are better at capturing the uncertainty in the inference and such, but they are slow! Not slow as in, “I’ll go get a cup of coffee while the program finish”, but slow as in “I’ll look at the tree when I am back from my vacation”.

Sure, they are fast enough for tens of leaves, but some people infer trees with thousands of leaves.  I recently got an email from a guy who tried with tens of thousands of leaves and ran out of memory using one of my tools — it needed more than 4G so it chocked on the problem (but a student in our lap has now come up with a new algorithm that is less memory expensive so that should solve that problem).

For large trees, forget about ML or Bayesian approaches.  They do not scale (yet).

People do use neighbour joining, so shut up and review the paper for what it is, not what you want it to be. Grrr!

I’ve just become associate editor of a new journal: BMC Research Notes. See the list of editors here. I haven’t received the first paper yet, but I look forward to doing this.