I'm reopening this thread because (cats and dogs notwithstanding) it is by far the most useful discussion I have encountered on the Internet after extensively exploring the topic of popup footnotes.
I'm currently reading a scholarly book with lots of footnotes in it, and I find it interesting that while this book does not display any popup footnotes in my primary e-reader, which is Marvin for iOS, nor do any footnotes from this book get displayed as popups in iBooks or Kindle or Kobo on iPad... they do get displayed as popup footnotes in Moon+ Reader Pro on Android. Moon must be doing it "intuitively/heuristically", as discussed previously in this thread, because there's nothing special in the coding to generate the popups – none of the stuff Elizabeth Castro talks about in
her blog entry on popup footnotes. Just simple back-and-forth links of the variety Hitch quoted in this thread.
In fact, Moon+ Reader Pro seems to be giving you the best of
both worlds: it first pops up a footnote, but it also gives you the option to subsequently press the "Open" button, and then you get transferred to the book's endnotes section where it may be more comfortable to read some of the more extensive footnotes. See the 2 screenshots from Moon, attached below.
I can understand both of what Psymon and Hitch are saying on page 1 of this thread. They both have a point, even though they claim the opposite. On the one hand, as Hitch says, it may be more comfortable to read longish footnotes in an endnotes section, without the need for scrolling in a pop-up window. On the other hand, as Psymon says, in texts with a huge amount of footnotes (say, a couple of footnotes in
every sentence of the text, as in that particular
Walden edition by Thoreau that Psymon coded for the web), popup footnotes are not just about "looking cool", but they're infinitely more usable. Sorry, Hitch, but in cases like that, it's just
not true that "a tap is a tap, and you need 2 taps in both instances". Yes, but as the screenshot from Moon+ Reader Pro documents, with a popup footnote (or at least with some of them), you might still be able to see the snippet of text to which the footnote is directly attached,
at a single glance – and that makes all the difference, from the point of view of usability and user-friendliness. It's the difference analogous between working on a desktop computer with a single monitor attached to it, and on a computer with 2 (or more) monitors attached. Or it's a difference analogous to seeing two application windows at the same time (some Android devices lately), versus having to run each app in full-screen all the time (iOS). Sometimes, it can be invaluable to be able to
see two related things at a single glance.

Sorry, but for Psymon's particular edition of Thoreau's
Walden, I can't imagine any reader would be delighted at being forced to jump back and forth, back and forth, back and forth between the main text and the endnotes section all the time. For a text like this, popup footnotes really seem ideally suited
functionally speaking, and it's not primarily about "looking cool".
<aside>I'm a big-time Emerson, Thoreau et al. fan; in fact, the -erson in my "Faterson" nickname is a bow to Emerson, while Fat- is a reference to my no. 1 favorite writer, Leo Tolstoy (and his last name means "Fat" in Russian), who happened to be a big-time Emerson and Thoreau fan, too.</aside>
Personally, I find it distracting to have to be switching back and forth between the main text and the endnotes section all the time – even in books that
don't feature an enormous amount of footnotes like that
Walden edition does. So, I find Moon's "intuitive/heuristic" treatment of footnotes to be the ideal remedy. What's my solution on the iPad, though, where Marvin is my e-reader of choice? Well, I have
three instances of Marvin installed on my iPad: the standard, universal Marvin for iOS, then the no-longer-developed Marvin for iPad, and Marvin Free as well. Whenever a book has lots of footnotes, I load it into both full-fledged Marvin instances. I read the book's main text in the standard Marvin for iOS, while I keep the endnotes section of that book permanently open in Marvin for iPad. Then, to read footnotes, I keep switching back and forth between the two Marvins, using iOS's 4-finger sideways swipe gesture. If that sounds crazy, believe me: I find it less annoying or time-consuming than having to tap on footnote marks all the time, and then having to tap again every time to return to main text. Just swiping with 4 fingers in one direction, and then swiping once more in the opposite direction, seems so much faster and easier, because you don't need to keep aiming with your finger, in order to hit the (typically smallish) footnote marks precisely. I even set up two different font colours in the 2 Marvins, so that the main book text displays in one color, and the footnotes to that same book in a different color, which makes it easy for me at any time to tell which Marvin I'm currently looking at.
I would still prefer if Marvin displayed footnotes in popup windows, though. Upcoming functionality like that in Marvin has already been announced, but I'm afraid it would require special EPUB 3-like coding of the type Elizabeth Castro wrote about.

I've just opened
a thread in Marvin's GitHub for this issue.
Another potential solution for this would be
split window, but I know of no e-reader app per se that offers this feature. (It definitely
is possible technically: see the excellent Olive Tree Bible app for iPad that allows you to open and simultaneously display 2 Biblical editions in a split window, so that you can, for example, view the same text passage in 2 different Bible translations at a single glance, and when you scroll in one portion of the split screen, the other portion of the split screen scrolls along correspondingly.) I have
suggested this functionality to Marvin's developer, with no result so far. With a split-screen, for example in portrait orientation, a user might perhaps (by adjusting a slider) devote the top two thirds of the screen to the book's main text, and the bottom third of the screen to displaying the footnotes section. That is, the split-screen should be capable of simultaneously displaying two different sections from the same EPUB file. The top portion of the screen might be permanently displaying the book text, and the bottom portion of the screen might be permanently displaying the footnotes section. Both portions of the screen would be individually scrollable. (It would perhaps be too much, too futuristic to ask the footnotes section to scroll automatically depending on what footnote marks are visible in the top portion of the screen in the book's main text – but it
might be doable.) Split-screen functionality like this would nicely emulate the look of a printed book: after all, in a printed book, you get to see the book's main text in the top portion of the printed page, and footnotes (as their name suggests) at the bottom.
Yet another option (that would be the
fourth footnotes option, right?) would be to display footnotes in the same way that e-ink Kindles have always, and highly ingeniously, displayed dictionary definitions: you tap a word, and its definition pops up at the bottom (or top) of the Kindle's screen. In the same way, you might tap a footnote mark, and the footnote would
temporarily pop up at (you guessed it:
) the foot of the page. No need for a popup bubble/window, and no need to keep switching between the main text and the footnotes section, either. If you ask me, this might be the
best of all solutions: because unlike with a popup bubble that often ends up obstructing the (full) view of the passage to which the footnote is attached, you'd get to see the
context of the footnote,
and the footnote itself,
at a single glance, every time.
To sum up: there appear – in theory – to be 4 possible ways of displaying footnotes in e-books. Only option #1 currently works reliably, but is rather unwieldy; option #2 is not widely supported as of late 2014; and options #3 and #4 don't seem to be available in current e-readers:
- put footnotes in an endnotes section (either at the end of the book, or at the end of each chapter)
- display footnote in a popup bubble/window
- display footnotes using a split-screen, giving the user the flexible option to adjust the dimensions of the two sub-windows with a slider
- display the footnote at the bottom (or top) of the screen whenever the corresponding footnote mark is tapped in the main text.
What would the ideal, supremely intelligent e-reader app do? Why, of course: it would support
all 4 of the footnote display options listed above, leaving it up to the user to choose whether he or she prefers to view footnotes using method #1, #2, #3, or #4. Don't force the
same way of displaying footnotes on
everyone. Each of us is different. In fact,
I as a single reader might prefer a
different way of displaying footnotes from book A to book B to book C, or even
inside a particular book. For a heavily annotated book, like Psymon's edition of
Walden, I might prefer method #3: see the footnotes section displayed permanently at the bottom of the screen. For a different book with fewer, but still many footnotes, I might prefer option #4: pop up the footnote at the bottom of the screen whenever I tap a footnote mark. And for a book with very few footnotes, I might find the option traditionally used nowadays, #1, perfectly satisfactory. An intelligent e-reader app should be flexible enough to let me change my preferrred way of displaying footnotes
on the fly, from #1 to #4 to #3 or vice versa – whatever the reader might find appropriate for any particular book, or even a particular
section of a book. (Some chapters of a single book might be heavily annotated, and others might not. Or I might be interested in exploring footnotes related to certain chapters of a book, while choosing to ignore footnotes related to other chapters of the same book if those chapters aren't as relevant for my needs.)
As to the footnote marks controversy, that is: using
superscript versus using
square brackets, I have had bad experience with superscript. Using plain superscripts often results in unequal line heights throughout the book text, which makes the book look ugly. (Moon+ Reader is guilty of this, too, as can be seen in the screenshot below.) If you attempt to fiddle with the superscript via CSS properties (the vertical-align, etc., tricks that Psymon provided)... well, the effect might still not be what you intended to see, especially on simple e-ink e-reader devices including the plain black-and-white Kindles.
I would, therefore, decidedly prefer to use footnote marks of the [23] variety instead, no superscript. I'm going to ask my client as to what type of footnote marks he prefers. If the client insists on superscripted footnote marks despite the dangers of doing so that I'll have explained to him... well, it's going to be the
client's choice, then, and not mine, and the client would bear responsibility for any undesired consequences that design choice might entail.
Finally, a cautionary note on Psymon's dismissal of potential issues related to having to load and reload a large endnotes file all the time, when repeatedly moving from main text to endnotes and back. Please don't underestimate this, Psymon. This is definitely a potential issue not just on low-powered, old reading devices, but there's a noticeable delay in loading a
huge separate new file inside an EPUB (even if it contains nothing but 100% pure text!) even if you're reading on a recent iPad using a superb EPUB e-reader like Marvin. I would strongly discourage anyone from putting 1000+ footnotes into a single endnotes file – dividing that endnotes file into several endnotes files (one endnotes file per each book chapter, for example) might be the way to go. For me, though, the alternative option discussed earlier seems preferable: just put the footnotes directly at the end of the same internal EPUB file that contains the chapter of the book text to which these particular footnotes relate. That has the
huge advantage of never having to load a new file when moving between main text and footnotes/endnotes; and as I said, this is definitely a relevant consideration even on powerful computers like the iPad tablets. So as not to disrupt the flow of reading the main text, the solution is easy: simply put a tappable "Continue to Chapter X" hyperlink just above the start of the endnotes section at the end of each chapter (each internal EPUB file).
So, my current dilemma is whether to bother, in the e-book I am currently producing, with popup footnotes-specific coding Elizabeth Castro mentioned, or whether I should just stick to traditional coding that Hitch recommended. Based on the discussion in this thread (and I don't believe much has changed since the summer), it appears that in late 2014, employing popup footnotes-specific coding is just not worth the bother, because the popup footnotes functionality still isn't as widely and universally supported as we'd like to see. Please correct me if the conclusion I have reached here is wrong.

Thank you.