A highly cited Nature paper that identified a long-sought receptor critical for mediating plant response to stress is being retracted after researchers were unable to reproduce the results. (The Scientist)

The paper in question was the first to identify a receptor for abscicic acid (ABA), which regulates plant stress response. It has been cited some 120 times since its publication in 2006. Scientific experiments are not exact nor always produce results that are set in stone. Even the cleanest and best experiments will find changes in the future as methods and technology improve. But that’s the nature of science. We discover something new and report it, and other scientists test our methods and results. Now I suppose citing the retracted Nature paper is not a real problem unless future studies relied on the assumption that this one paper was correct. Unfortunately, that’s exactly what the problem was.

"It obviously put a big dent in what we’re doing," said corresponding author Robert Hill. "It’s meant that we’ve had to go back and reinterpret data." One graduate student has had to "chop a publication" which was based on the assumption that the ABA receptor was real. "I’ve come to reconcile with the problem," said Hill, adding that he is working to correct it "without hurting too many people."

image: sxc

If I were giving career advice to my son (who’s only four-years-old by the way), I would tell him to consider going into informatics. And if I were really pushy, I’d suggest bioinformatics. With computing power increasing exponentially and the internet offering up overwhelming amounts of information, we need people who can figure out a way to organize it all so the rest of us can actually deal with it. One such person is Stew (pseudonym) of Flags and Lollipops and postgenomic. I’m glad he took time out of his busy schedule working at Nature in the web publishing department to do this genetics interview for us!

1. You work in bioinformatics which I think is the glue that holds the genome revolution together. What kind of role do you think bioinformatics plays?

I’d agree: modern day genetics relies on vast quantities of data that you couldn’t begin to navigate or process efficiently without software of some sort. Nowadays sequence ‘search engines’ like BLAST and genome browsers like Ensembl are standard tools for genetics researchers. On an even more basic level, without sequence alignment algorithms there’d be no complete genomes to search or browse in the first place.

That’s the data processing side of bioinformatics. It’s also got a role to play in creating new data from the old. By doing clever things with existing information you can, for example, take a novel gene, feed it through machine learning algorithms and get back a predicted function based on the sequences of genes that have already been studied, or model a particular process in a cell, or predict which point mutation out of many on a particular gene is most likely to be responsible for causing some disease.

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As you’re reading this, I’ll be winging my way to California for my annual trip back “home”. Fortunately, Dr. Alan Packer of Nature Genetics is here with us in spirit today in the tenth interview of the Genetics and Health interview series. I can imagine that more than one of you out there would like to pick his brain and ask why your paper got rejected!

1. Many scientists are interested in life outside of academia, how did you get into publishing and what do you like best about it? What do you like least?

I have always had broad interests in science—the sort of interests that tend to get pushed aside as one is forced to focus on one or two particular projects. I always liked journal clubs, reading the literature, and thinking about the way journals are put together. As a postdoc, I wrote some science news and book reviews as a freelancer, as an outlet for some of these interests. Toward the end of my postdoc, I spent several months applying and interviewing for academic positions, but didn’t receive an offer. It occurred to me at that point that even if I did receive an offer, it might not be terribly attractive, given how difficult it can sometimes be for young investigators to secure funding for a new research program, especially if one’s publication record (like mine) is respectable, but not spectacular. So I sent an application to Nature Genetics, and luckily they happened to be looking for an assistant editor at the time. I got the job and started a couple of months later.

There are several things that I like about publishing. I work with a very bright group of people, all with very broad interests themselves. I get to read some great science, before most other people get to read it. I get the regular satisfaction of helping to edit and produce a monthly journal (weekly online) that is quite influential. I attend conferences and visit scientists in their labs, where I talk with them about the latest things they’re working on. I do all of these very enjoyable things, and still feel like a scientist, without having to run gels at 10 o’clock at night. While the thrill of getting a result in the lab is unbeatable, all in all it was a good decision for me.

What I like least is rejecting a paper that I know is very good and close to ‘clearing the bar’, but has to be declined because of the fierce competition for space in the journal. We all know how much it can mean for people looking for jobs, grants, promotions etc., and no one likes to give bad news, especially when the work has much to recommend it. I should add that sometimes an acceptance in a journal like Nature Genetics means too much, and I hope hiring and promotion committees are looking less at the perceived quality of the journal and more at the actual quality of the work produced by the author.

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