How to: Amazon’s Kindle 3 for Academics and Students

by Luke Muehlhauser on September 23, 2010 in How-To,Resources,Reviews

A friend of mine told me the iPhone is the invention that has most changed her daily life since the World Wide Web. After using Amazon’s Kindle 3 for a while now, I can give it similar praise. As the New York Times wrote, “New Kindle leaves rivals farther back.”

Obviously, it’s not an iPad. It doesn’t do color, touch-screen, games, video, etc. And that’s the whole point. The Kindle is for reading, and it is designed to do that one thing very, very well.

As the new TV ad shows, reading outdoors on the iPad is a pain, but you can read the Kindle anywhere because the dynamic screen is literally printed with ink, just like a book. Even indoors, reading on the iPad gives me a headache after a while – for the same reason that reading a computer monitor for a few hours will make you drowsy. But reading hour after hour on the Kindle is like getting lost in a great novel.

The battery lasts for over a week, and it will fit in your back pants pocket or the pocket inside your suitcoat! And, a warning: seeing an entire book appear on your Kindle literally 5 seconds after clicking ‘Buy’ is addicting. Don’t get carried away and go broke!

This technology is a godsend to academics and students, who have hundreds or thousands of pages to read – papers from JSTOR, classic or contemporary academic books, modern textbooks, and so on. Now you can pack all of them into your pencil-thin Kindle and read them at the beach or the park.

My Kindle 3 Tips

First, you can stock up on classic texts from Homer, Aristotle, Shakespeare, Aquinas, Hume, Galileo, Newton, etc. for free, which are already available for free from the Amazon store. Just search Amazon’s site for the titles you want, click ‘Buy Now,’ and they’ll be delivered wirelessly to your Kindle.

You can also buy thousands of recent Kindle-formatted ebooks (or Audible-formatted audiobooks) and have them delivered immediately to your Kindle. Unfortunately, ebooks are not much cheaper than the paper verison.

On your Kindle, organize your texts into collections. Hit Menu -> Add New Collection and give it a name. On the Home screen, highlight a book, hit the right-arrow and choose Add to Collection. Once it’s added, click Home and move another.

For reading, I adjust your view. Hit the Aa (text) button to switch the orientation and the text size. I prefer landscape orientation for reading PDFs, and portrait orientation for reading Kindle-formatted documents (including reformatted PDFs). Also, check word definitions in-text by using the arrow keys to move the cursor to the word for which you want to see a definition. The definition will pop up automatically.

Next, convert your PDFs. You can read PDFs on the Kindle just fine, but there are three reasons to convert them anyway. First, the text-to-speech feature (Shift+Sym) can’t read PDFs, so if your eyes get tired then you’ll be glad you converted your PDFs first. Second, the Kindle must show the PDF as formatted, which sometimes isn’t very readable on the Kindle’s small screen. If you convert your PDFs, the Kindle can re-format paragraphs to match your desired text size and screen orientation. Third, the Kindle cannot search text within PDFs.

You can convert PDFs by emailing them to with the subject ‘Convert’. But these PDFs can only be so big, and sometimes Amazon’s conversion service is slow. For that and other reasons, I highly recommend you download Calibre.

Calibre is an extremely well-designed and easy-to-use ebook management program that is free on Windows, Mac, and Linux. It recognizes over 30 ebook readers, can convert dozens of formats, and much more. Watch the video tutorial. You will be impressed.

During installation, you can tell it your ebook reader is the Kindle 3, and it will automatically configure itself to convert to the right format, to deliver converted documents to your Kindle via email, and so on. Then you basically just drag and drop all the PDFs you want to read on your Kindle into the main program window, fix the author and title tags, highlight all the books, click Convert Books -> Bulk Convert to convert them all to Kindle format (MOBI). Then if you have your Kindle plugged in, you just click Send to Device, or else you can send the converted files to your device wirelessly by email.

Calibre has a lot of other awesome features, such as downloading news from hundreds of sources and converting them for easy reading on the Kindle. It can also download the metadata and cover images for your books automatically. One thing, though: Calibre can’t convert DJVU files, so for those I convert to PDF first with a free PDF printer like Bullzip.

Get a reading light. The Kindle is not backlit – that’s why you can read it for so long without a headache – so if you’re reading in the dark you need a light just as you would with a book. I bought this one, which runs on batteries and clips onto the Kindle.

Also, load up your Kindle with music. The Kindle is not a media player, so this feature is really meant for background music for reading. You can only pause and play (Alt+Space) your music or skip (F) to the next track. Kindle will play tracks in the order you added them to the ‘music’ folder via USB. I mostly put ambient music on my Kindle. You probably have tons of music on your phone, anyway.

Install the Kindle app on your computer, phone, iPad, etc. It won’t be as nice to read on those screens, but you’ll have your books available there.

Finally, create bookmarks, notes, and highlights. To add a bookmark, just hit Alt+B. You’ll see the corner of the page get “earmarked.” Hit Alt+B again to un-bookmark it.

When reading, I create very short notes and highlights on the Kindle, because working with the Kindle’s tiny keyboard is obviously not as fun as doing the same thing on a computer. Later, I open these notes on a computer so that I can type my longer thoughts into a text document or an article I’m preparing or whatever. (For example, I highlight a passage I want to quote in an essay I’m writing.)

To highlight a section, move the cursor to the start of the passage you want to highlight, hit the center button to start highlighting, move the cursors to the end of the passage, and hit the center button again to finish (or hit Back to cancel). Highlights appear lightly underlined.

To write a note, move the cursor to the right place and just start typing to create a note. I usually only type one to five words that will jog my memory, then choose Save Note. Notes are shown with numbered superscripts.

To access all your highlights, notes, and so on (with links to the original text) on your computer, just visit and sign in!

The basic model Kindle is only $140.  You can add unlimited 3G (cell phone towers) connection for a total of $190. If you prefer a bigger size so it’s easier to read PDFs natively, you can get the 9.7-inch DX model for $380.

Now, what am I missing? What’s your favorite Kindle tip? And why the frack can’t I hit Alt+NextPage to jump ahead 10 pages?

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{ 32 comments… read them below or add one }

The Atheist Missionary September 23, 2010 at 4:26 am

My eureka moment with the Kindle was in March of this year at about 6:00 a.m. on a beach in Trelawny Parish, Jamaica. It took me about 90 seconds to download that morning’s National Post (one of Canada’s national newspapers) for less than it would have cost me to buy a hard copy at home. That was pretty sweet.


Luke Barnes September 23, 2010 at 5:36 am

Hmmm … very tempting.

What do PDF’s look like after you convert them? What happens to the figures?

Also, I’ve heard that you can’t make notes/highlight on PDF’s directly. Is this true?


Bill Snedden September 23, 2010 at 6:27 am

I’ve not had much luck with reading PDFs natively, that is, without conversion…the type is much too small to be read on my Kindle 3. I’ve only converted a couple of PDFs and they seem to work pretty well. The only caveat there being that I’ve not attempted to convert any PDFs with graphs or other “illustrative” figures. IIRC, Amazon pretty much tells you up front that those things won’t be converted.

If you like Sci-Fi, the website has dozens of short stories by contemporary authors that can be downloaded and added to your Kindle. They also add new ones quite regularly. It’s a great way to discover new authors.

I’ve got a couple of Kindle blogs/tip pages bookmarked on delicious

You can download an excellent guide to free downloadable content from feedbooks here. After adding the guide to your Kindle, you can search through it for content and download to your Kindle with a simple click. The guide also has a link that allows you to download updates as they become available.


lukeprog September 23, 2010 at 6:52 am


For people who read lots of PDFs with math equations, I would recommend the DX so you can read PDFs in original PDF format without having to “nudge” the screen along each line with Shift+Arrow key. When PDFs are converted, the figures and ligatures often do not survive well. And I suspect that on the regular-size Kindle, some PDFs will be too large in their original format to be readable in ‘fit-to-screen’ mode, even using the Kindle in lanscape mode. Many, many philosophy papers can be read just fine this way, and don’t suffer much from conversion either, but astronomy and physics papers are another matter. Here is a good video on PDFs on the Kindle. I forget whether or not you can highlight passages of the PDF; I’ll check later.


lukeprog September 23, 2010 at 7:01 am

Good tips, Bill Snedden!


Charles September 23, 2010 at 7:16 am

I am writer and avid reader, but I have so far held off. The chief problem I have with these devices is that I use books for research in addition to reading them, and I can always find the passage I’m looking for faster if I have the physical book. I don’t like that I can’t lend or sell books I buy or being locked into a single vendor for media. I’ve been sitting on the fence for quite some time.


Jason Berberich September 23, 2010 at 7:53 am

I’ve had my Kindle 3 for a few weeks and have been very happy with it so far. I have Calibre installed on my Mac at home, but haven’t had the time to convert any of the PDFs I’ve collected over the years or configure its web news-fetching feature.

At the moment, I’m mainly using my Kindle to read my way through my Instapaper archive. Instapaper, if you’ve never used it, lets you save a copy of web content for later reading. It works great for long-form content (including many of the items Luke links to) and can be set to automatically deliver a Kindle-formatted periodical daily or weekly to your device. It’s a great way to read long content from the web.


lukeprog September 23, 2010 at 8:46 am


Good tip! I’ll have to try that.


pjPonzo September 23, 2010 at 8:58 am

I’ve converted HTML stuff (with lots of math) to .prc files so they can be read by Kindle 3:

They look pretty good :^)


inajeep September 23, 2010 at 9:57 am

I use my Kindle daily and agree with all your pluses. The only minus I like to make you aware of is for students or technical readers. I browse by chapter, index or flip through to find specific sections of information (in my case, application development) so any electronic method makes that process cumbersome. Reading sequentially end to end is wonderful via the kindle or any e-reader. It remembers the last page looked at per book. I have not purchased as many books in the last year of owning a kindle than the last 5 years.


MarcC September 23, 2010 at 10:15 am

Wow, that was an excellent write-up, and the comment thread is equally valuable. Thank you all.

To get your highlighted text and your typed-on-the-Kindle notes to your main computer, please remember the special-purpose page, which contains all your highlighted text and all your typed notes, with pointers back into the original text.

It is just my personal opinion, of course, but I consider the path superior to the Twitter path (for me) because of the book marks on the page that allow me to open the e-book instantly to that text on my Kindle-for-PC software. Sometimes when I look back at my highlighted text or my typed notes, I wonder what the heck I was thinking and I want to look at the surrounding passage in the e-book. Via the page I can do just that with a single click (which automatically opens my Kindle-for-PC software, opens the e-book, and puts me on the page where the highlight or note is).

The highlighted text and notes can be copied and pasted to other applications from the web page.


lukeprog September 23, 2010 at 10:30 am


You’re right! I’ve edited the OP. Thanks.


lukeprog September 23, 2010 at 11:44 am

Luke Barnes,

Highlighting on PDFs is hit and miss. It depends on how the PDF was prepared. You can highlight on PDF, but let’s say it’s a scanned PDF with no OCR. Then you’re just highlighting images. Or, if the PDF is prepared weirdly then you can highlight exactly the words you want, but when you go to ‘My Clippings’, the words you highlighted are not the words stored there. You could add a note just fine, though, such as ‘wrong equation, page 13.”


Dan Nelson September 23, 2010 at 1:28 pm

great post about a great device and service. ever since they added text search to the “Kindle for PC” software, i’ve been logging large numbers of hours in cross-reference heaven.


Jake de Backer September 23, 2010 at 1:29 pm

This question may very well betray just how little I’ve covered the literature on this device, but can you upload word documents as well as PDF’s?

And somewhat tangential; I have thousands of Philosophy, Theology and Science (Articles, Debate transcripts, Book reviews, Books, etc.) PDF’s/Word.doc’s. If any of you are looking to exchange some material and increase the size of your digital library, please email me directly @ Thanks.



Martin September 23, 2010 at 2:34 pm


There are tons of software programs that convert Word and PDF to Kindle format.


lukeprog September 23, 2010 at 2:41 pm


Yes, like the Calibre mentioned in the original post.


drj September 23, 2010 at 2:54 pm

If you plan on using your Kindle for reference books (like math, or computer science, etc), DO NOT get the small Kindle. I made that mistake, and I find the device absolutely pathetic for the task.

One semester I tried using an ebook on the kindle instead of an actual text book – never again.

The larger kindle might be better, but honestly, screen size is only one of the issues for me. The other biggy is that navigation through books is just extremely kludgy and slow, even using bookmarks and tables of contents.

With reference books you’re often going to be flipping back and forth between pages and sections and its just too slow and awkward.. I don’t think a larger screen can fix this.

I also find myself getting frustrated at how difficult it is just to get a feel of where you “are in the book”.

It is great for novels though, or any other book where there will be few diagrams, or where its unlikely that you will need to jump around in the text a lot. Its also great for philosophy books. Having most any book from the public domain available on demand is amazing.


lukeprog September 23, 2010 at 2:59 pm


Yes. The Kindle is not for reference books or large books in general, at least not yet. But it’s pretty useful for journal articles that don’t have lots of symbols in them, or with a narrow enough text column that the original PDF can be read comfortably on the Kindle screen without panning.


Jeff H September 23, 2010 at 4:06 pm

Dammit, Luke, you’re making it very hard for me to resist the urge to go and buy one of these things! I used to tell myself that I didn’t like the fact that it couldn’t read PDFs and whatnot…but that excuse is gone now. And I wanted to be able to surf the Internet with it (at least to some extent)…and now it can. And of course, it was too expensive…but now the price isn’t even that bad.

These companies are constantly figuring out ways to make me spend my money…


lukeprog September 23, 2010 at 4:17 pm



Hermes September 23, 2010 at 4:19 pm

Kindle owners: How detailed are the Oxford American Dictionary entries? Is it comparable to the paper edition, or a subset?

Can you flip through and/or search the dictionary itself?


lukeprog September 23, 2010 at 4:26 pm


Looks pretty detailed to me, but I don’t have the paper one to compare. Yes, you can search or browse the two included dictionaries independently. They’re listed as books on your Kindle like everything else, but also pop up when you move the cursor through a page in another document.


TaiChi September 23, 2010 at 5:10 pm

Thanks for this write-up. I think I’ll have to get a Kindle, now that I know there’s Calibre to convert my PDF’s.

By the way, if anyone wants to convert a scanned image PDF to text, you can do it via cometdocs.


lukeprog September 23, 2010 at 5:14 pm

Cool, I also like and


TaiChi September 23, 2010 at 5:17 pm

Oh, I should add: I do that by changing the PDF to an ODF, and then export from open office as a PDF.


Hermes September 23, 2010 at 5:41 pm

Thanks Luke. That’s too bad.

Along those lines, I was reading a review of the paper edition of what is bundled with the Kindle, and it also looks like a pale substitute for the Concise OED let alone the full OED ($$$). The full OED doesn’t seem to be available in a Kindle edition, and the Concise OED Kindle edition is not as complete as the paper edition of the Concise OED (25% smaller; 180K words in Kindle vs. 240K for paper), though all things considered it’s the best of the lot.

I looked to see if my second choice — The American Heritage Dictionary — was available in Kindle form, and it looks like the answer is no.

Along the way, I did see a few people switching to a Webster’s edition, though I don’t know if that says more about the weak Oxford offering than it does about the strength of Webster’s. I don’t bother with Webster’s if either some variant of the OED or the American Heritage are available, but that doesn’t seem to be an option. I’d opt for paying more for the limited Concise OED Kindle edition given the current options.


Luke Barnes September 24, 2010 at 1:33 am

Thanks Luke.


Jorgen Sundberg October 12, 2010 at 12:38 pm

Great tips, thanks so much for the post!


theuns November 11, 2010 at 6:40 am

For any academic user – and this is many kindle clients, the current collection method does not work. If I upload 50 articles to my kindle, it takes way too long to organise these by assigning them one at a time to the collections.

If I had access to the operating system I could do this in a few hours…

Ideally I would want to do this using a simple tool on my Laptop or internet.

I propose that we hack our way out of this limitation if amazon does not play ball…

Also I will recommend that academics do not use the kindle due to these limitations. It will just frustrate you…



TaiChi January 19, 2011 at 9:35 pm

Chrome now has an extension to send web-page text to your kindle account:

Pretty nifty, especially if you want a blog post to be read to you.


sam32 March 31, 2011 at 1:43 pm

You can convert your kindle clippings into Microsoft Word, Excel & PDF files. The website is for free, it’s called

I’m a student and I use this all the time to create study notes, on my kindle – it’s all too easy!


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