This happens all the time. Take a look at this figure.
Now in part C, there are some black data points and some red data points. What's the difference? What are the authors trying to tell you? Well, here's what the text is trying to tell me I should get from this figure:
As for other EAD sequences studied before, transactivation rises in a nonlinear manner with nY (Fig. 1C, red circles), demonstrating that multiple Ys act together in a cooperative manner.Okay, so the text is telling us to look at this figure to see some sort of non-linear phenomenon. Okay, but presumably these black things mean something also, right? Some sort of comparison? Wait, the legend must know!
To which the paper replies:
(C) Effect of Y number nY on transactivation and simulated binding. Relative transcriptional activity of the EAD peptides (open red circles) was determined under sub-saturating conditions (Methods and Text S1) relative to 10Yn activity (arbitrarily set to 100). Red error bars for the experimental data indicate SEM. The relative Pb(nY) values (filled black squares) are normalized by the Pb for 10Yn [nY = 10, actual simulated (absolute) Pb(10) = 0.43]. The black error bars mark standard deviations among ten independent simulations.Ouch. This highlights the problem with this format: the paper is telling me some relatively high level interpretation, then I look to the figure, but I can't make sense of it, so then I have to look at the legend, which is obfuscated to the point of utter incomprehensibility. Why would you make your reader work so hard?
Here's another more biological example:
The paper tells you that
Ectopic COT expression in A375 and SKMEL28 cells also conferred decreased sensitivity to the MEK inhibitors CI-1040 and AZD6244, suggesting that COT expression alone was sufficient to induce this phenotype (Fig. 4c, 4d, Supplementary Fig. 17).Hmm. Something about Ectopic COT expression. But I don't see any explanation of MEK1, or MEK1 DD (turns out they are negative and positive controls). In fact, just looking at this figure, I would have no idea that this was about overexpression whatsoever. Nor would I be able to tell what's going on with SKMEL28, which isn't even on here (probably in Supp. Fig. 17). And the legend gives us:
ERK phosphorylation in A375 expressing indicated ORFs following treatment with DMSO or 1µM of PLX4720, RAJ265, CI-1040 or AZD6244.Again, ouch! What are all of these different drugs doing? Which is the control (DMSO)? Which one inhibits what? What should I be drawing from this figure? This figure is a bit better than my other example, because the audience of the paper might actually have some notion of what this is all about due to common background knowledge, but the cognitive demands for understanding the point of this experiment for both the initiated and uninitiated are unreasonably high. Just imagine what a few simple annotations or diagrams could do here...
On a more general note, I think that sometimes authors approach their paper as "work" for the reader, that it's somehow good to struggle through a paper to understand it's meaning. Many biology papers with endless combinatorial gels have this quality, like one of those "If Harry can't sit next to Sally on Thursday but wants to sit next to Alice on Wednesday" kind of problems. I think that the notion that this is somehow "good medicine" is ridiculous. A scientific paper's goal is not to be the crossword in the Sunday Times. It's a vehicle for communicating results as clearly and quickly as possible. Our goal as authors is to achieve that result as best possible. It's not an easy task, but that's our job.