Things have changed quite a bit in the last decade and especially the last five years in scientific publishing. Starting with open access efforts (notably the PLOS journals, which launched when I was in grad school and have driven a revolution in publishing) and continuing in venues like Retraction Watch and PubPeer, the move toward making science open, clear, honest, and above all accurate is powerful and completely unlike when I started doing research.

Retraction Watch put up a guest post today by Drummond Rennie and C.K. Gunsalus titled If you think it’s rude to ask to look at your co-author’s data, you’re not doing science. In it they talk about how a couple recent and slightly less recent high-profile scientific frauds have broken down, and the failure of senior authors to actually do their part to validate the data and really know what’s going on. They also provide a truly helpful breakdown of approaches to make sure everyone knows what work is being done, that the work is actually being done (and funded, and so forth), and that everyone is credited properly.

If you’re doing, well, science, or any kind of collaboration at all, I recommend this genuinely helpful piece.

One of the most unnerving aspects of biological research is the possibility that your samples aren’t what you think they are. Most of my lab work has involved yeast (cerevisiae) and a smattering of types of bacteria (largely coli and some cyanobacteria). In general, we didn’t maintain the cells by passaging them, and there were some obvious antibiotic and auxotrophic (nutrition-based) markers we could use to tell that the cells were basically what we thought they were.

But as I’ve learned since entering the exciting world of genome analyses, there is just a ton of variation between the “same” organism and strain in different labs…or in the same lab at different times. The “default” E. coli strain, K-12 MG1655, has a neat little mutation in amino acid biosynthesis that easily reverts to wild type, which plays all sorts of havoc with computational models that assume that it’s nonfunctional.

I’m quite interested in how we can account for these kinds of differences and make modeling and predictive tools that are resilient to them.

In their recent paper Hiding in plain view: Genetic profiling reveals decades old cross-contamination of bladder cancer cell line KU7 with HeLa, Jager et al applied a very basic kind of DNA profiling to many samples of a popular and widely used bladder cancer cell line. These are cells that were supposed to have been derived from a fairly mild bladder cancer sampled from a patient in 1980. They’ve been widely used since then to study and model bladder cancer.

Except it turns out that they’re not bladder cancer cells. As Jager and his colleagues discovered, basically all the KU7 cell lines in the world are actually a completely different kind of cell (the most common cancer cell line in the world, HeLa). This apparently started with cross-contamination back at the source.

So what does this mean for studies based on those cells? Presumably we’d want to have a way to mass-tag those publications and all the databases or other informatics resources derived from them with the true identity of the cells used. Is this reasonably achievable, and is there a good way to track areas where the ideas or conclusions drawn from experiments using these misidentified cells ended up?

I’m not especially familiar with the bioinformatics and quantitative bio of cancer biology, so I don’t know how much impact this specific discovery has on large-scale data resources those fields rely on. Presumably this kind of thing is going to keep happening – we’ve certainly seen it in the misidentification and renaming of microbial samples from which enzyme and other metabolic data were derived. It would be handy to have consistent mechanisms in place to add additional metadata to publications so that this kind of “switch” can be tracked and propagated into downstream resources.

There’s more discussion of this discovery and its consequences for publications that used the misidentified cells over at Retraction Watch.