Hi, as a prospective lens user and recent eLife author I'd like to share some thoughts on my initial feelings with the user interface. First impressions are essential to acquire new users, so here's what I felt could be improved based on my first 5 minutes on lens!
1. Borders between the different panes should stand out a bit more clearly. If you stick with the 'flat' interface now very much in vogue in web design (i.e. no drop shadows), you should use different background colors. Personally I think that a touch of 3D contributes to function over form without cluttering the interface (see for example http://sixrevisions.com/user-interface/when-flat-design-falls-flat/
1.1 Related to the previous point, it took a bit of clicking to make it clear that the 'contents', 'figures', 'refs', 'article info' are tab controls. I feel that some more feedback to the user is necessary. In the flat paradigm you could again make use of slightly different background colors.
2. The scroll bar for the main text pane with the underlying 'paragraph map' is very cool. However, I expected it to be on the right side of the pane, as we're all used to that location for scrolling. That could be a frustration for other users.
2.1 Took a bit of searching for the scroll button, which should also be made more evident (again a little bit of shadow would help).
2.2 For consistency I suggest replacing the default scroll bar for the right pane (figures, refs...) with something similar to what you use for the main text pane.
3. Anchor icons beside paragraphs. The tooltip appearing on hover should clarify what you mean by 'sharing the link'. I understand that you can copy the Url and send it by email (for example) so that someone else will go directly to that paragraph. However, that is not immediately evident.
4. The leftmost column seems a waste of space for just displaying a back button and a Lens 0.2.0 notice, at least that's what I see on your test article. One would expect to be able to click the browser back button to go back to the original article, while it confusingly (imho) traces back click history within lens. I'm not sure you can provide that behavior, but if you can I would recommend implementing it.
5. Article publication date must absolutely appear below title and authors, and not be confined to 'article info'.
In Safari 7.0 if the window is resized below a width of 1120px the 'refs' and 'article info' tab controls disappear entirely. My suggestion is to change your rules so that when the window is narrower than a given threshold tab names are omitted leaving only the icons (names can still appear on hovering).
This said, I really like lens! Good luck, Lorenzo