A Newbie question about the Favorite Bookshelf

The easiest method is probably to use pocket holes. That's not the only method.

I recently built a similar set using dados cut into the side, but you'd have to construct the sides slightly differently, and that method requires other tools you probably don't have.

The other traditional method is to install shelf pins. This requires some fairly precision drilling, easy with a drill press or a doweling jig.

The thing you shouldn't do is try to screw or nail through the sides and into the ends of the shelves. That will fall apart, possibly with books on it. That's bad.

End grain had very little strength to hold anything: glue, nails, screws. It's covered in that book, but I have also conducted the experiment personally. Nails into end grain have about the holding power of bubble gum in July.

I really need to educate myself better on woodworking terms. I mean, I gather that "end grain" refers to the end of a board. But does that apply even when the end has been cut from the middle of a longer board?

EDIT: Ok, to satisfy my curiosity, I looked at a lot of Ana's bookshelf plans. If I'm understanding both you and her correctly, she instructs to attach shelves in exactly the way you recommended against (if you don't own a Kreg Jig). Since I own one it's not an issue anymore, but I have a few builds at home from my pre-Kreg days that contain shelves fastened this way. So how long til I'm crying and refastening them with the Kreg?

That kind of joint is called a butt joint. They are the weakest joint you can make. I can't tell you when they'll fail, but it's sooner than you would like in most cases.

End grain is just the surface of the board that runs perpendicular to the direction of the grain. They are the cuts across the tree, rather than down its length. You can cut a board in half, and it will still have end grain at the ends.