Nonspecific Citations

The point of this post is to introduce the term nonspecific citation.

A common problem with antibody is non-specific binding: while the antibody may be targetted to grab on to protein P, it actually also grabs X, Y, and Z, which are somewhat similar to P.

A nonspecific citation is when paper gets cited as an example of a broad class rather than for its specific ideas.

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In the case of a review article, it might make some sense: if you are just mentioning the field, you might as well cite my review of bioimage informatics. Even here, though, you could cite other reviews.

In the case of the research articles, though, it is often more of a throwaway citation: we need to mention work in the area of cell image analysis and I have a fairly recent paper on this, so you cite that. Or you cite somebody else’s work as it does not really matter the specific contents of that citation.

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There are intermediate levels of specificity.

Maybe you are writing a paper that somehow touts the general usefulness of local features and you write a sentence such as:

Local features are useful (or SURF has been used) in many context such as A [paper], B [paper], and cell image analysis [my work].

Then there is the completely nonspecific:

Recent work in bioimage informatics […, my work, …] …

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This will of course lead to a citation Matthew Effect: if you are highly cited, you are likely to get even more citations by getting more nonspecific citations.

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Whenever I have a paper I really want to read that is not open-access and to which my institution does not have access, I generally get it by asking the author for a preprint. It has never been a problem and has even led to some good follow up discussions.

On the other hand, if I am not looking for a specific paper but just something in a general area to get acquainted, then it whether something it open access or not may make me choose to read (and then subsequently cite) one paper instead of the other. In fact, just seeing an IEEE link will be enough for me to not even click through to the abstract.

Maybe if open access does have an advantage in getting citations, it’ll mostly come in the form of nonspecific ones.

Friday Links

1. On Schekman’s pledge to not publish high-profile. I almost called this a balanced view, but then realized that I probably used that phrase to refer to Derek Lowe’s work at least twice in the past. The man is smart and balanced, what can I say?

2. An interesting meeting report (closed access, sorry). Two highlights:

While discussing mutations that predispose to cancer, Nazneen Rahman (Institute of Cancer Research, UK) rightly reminded us that people make big decisions and have parts of their anatomy removed based on their genotype.

[…]

Jeanne Lawrence (University of Massachusetts Medical School, USA) convincingly showed that her lab was able to silence one entire copy of chromosome 21 in stem cells in vitro. Trisomy 21 or Down’s syndrome is caused by an extra copy of chromosome 21. […] Lawrence and colleagues inserted XIST (human X-inactivation gene) into chromosome 21 in stem cells with trisomy 21. They then showed using eight different methods that a single copy of the chromosome had indeed been silenced.

3. A good explanation of Bitcoin, the protocol

4. Interesting article about wine & technology in The Economist (which is one of the few mainstream magazines whose science coverage is worth reading [1]).

[1] Actually, I think it’s the only one who can be consistently trusted, but I enjoy anything by Ed Yong wherever he publishes and been reading some excellent articles by Carl Zimmer in The Atlantic.

People do read your thesis

Last week, @proflikesubstance wrote that you should Publish papers. Your thesis means nothing:

Get the papers out. Don’t focus on an arcane document that will gather dust for the next 50 years until the departmental office needs space and throws the old ones out.

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I didn’t even get the bound copies of my thesis. It’s a PDF sitting on a department server (it’s open access!).

Thus, this image of a thesis as a big block of paper, gathering dust in a hard-to-reach library section is out of date. It is a document, widely available, sometimes even read. During my graduate studies, I did read a few theses by others.

Because things are now electronic, people will read your thesis. Probably not PIs (who will read the executive summary, ie, the papers), but graduate students will (and, incredible though it may seem, graduate students are people too). The median paper is probably read by very few people too, by the way.

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My thesis is a staple thesis: short intro, review, paperpaperpaper, paper [yet unpublished], short “conclusion”, software paper as appendix.

Have your cake and eat it too.

I did, however, enjoy being able to write without any page limits and put in more details than made it into the final version of the papers. I also put in some side comments that I thought were cool but on the periphery of what the chapter was about. In some ways, I had the opportunity to write down the type of thought I would now cut out of the paper and put on the blog.

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This is not to say that you shouldn’t publish in peer-reviewed outlets. You should (as I said, my thesis is a staple thesis, almost all of the content is available in peer-reviewed literature too). But we shouldn’t use bad or out-of-date arguments, like nobody reads your thesis, for it.

You should publish because your résumé looks better with publications than with a thesis. Theses are like assholes, everybody has one (everyone who is applying to the sort of academic jobs we are discussing).

So, write your thesis and publish.

Friday Links

1.How genetic engineering ruined dogs

2. A Professor is unhappy that his PlOS One paper ended up in a commercial book

This is the old copyleft and viral licensing discussion from software: GPL or BSD?

I am posting because I found it interesting, not because I agree.

I actually found it a bit naïve that the guy did not know what open access really meant. If one is publishing in an open access journal, one should know what CC-BY means.

Still, when will someone propose a version of the GPL for scientific papers?

3. A scientist associated with a certain idea that is gaining traction says that ambitious young researchers should try to find the major flaws in that idea! This is what being a good scientist is.

4. From a post about the IMF & Academia:

Just as Canadians know much more about the US, than Americans know about Canada, bloggers know much more about academia than academics know about the blogosphere.

As with the previous link, my purpose here is to about the scientific aspect, not the politics.

5. Melatonin for sleep dysfunctions in children.

As a biologist, my initial thought is that taking a hormone is probably more likely to have side effects than a small molecule (ie, traditional drug). Small molecules have side effects all the time, but hormones should be expected to be all over the place, especially in children. However, it seems calling it natural makes many people feel the opposite (also lowers the regulatory burden because this feeling is codified in law).

6. An interview with me (in Portuguese).

How Long Does Plos One Take to Accept A Paper?

How long do papers take to review?

Too long.

No, seriously, how long? I did a little measurement.

I downloaded the 360 most recent papers from Plos One (as of Friday). They are all annotated with submission and acceptance dates, so it was easy to just compute the differences.

The plot below is a histogram (one bin per day) in grey with a Kernel density estimate as a solid line.

Histogram of acceptance times

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The result is it takes about 3 to 4 months to get a paper accepted, but with substancial variance.

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Looking at the figure, I had to ask who the poor people were who published that paper which was longest in revision.

Alternative Sigma Factor Over-Expression Enables Heterologous Expression of a Type II Polyketide Biosynthetic Pathway in Escherichia coli by David Cole Stevens, Kyle R. Conway, Nelson Pearce, Luis Roberto Villegas-Peñaranda, Anthony G. Garza, and Christopher N. Boddy. DOI: 10.1371/journal.pone.0064858

Submitted on 29 March 2011 and accepted on 22 April 2013, this paper was 755 days in revision.

The fastest acceptance was only 19 days. However, this being Plos One, it is possible that the paper had been reviewed for another Plos journal, rejected with positive reviews on significance grounds, and had those reviews transferred to Plos One. After this, acceptance followed without a new round of peer review.

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This is a gimmick. There is perhaps a paper to be written where this is extended to see what areas of research/keywords/&c matter to acceptance time. If I had more free time I might write that paper.

The code for the above is available on github.

UpdateFollowup with all PLoS Journals.