"Numbers" doesn't go by that name anymore, it's now called operators. The only reason it says "numbers" in the forum blocks is because it hasn't been updated since the name was changed.
But anyway...
Numbers/operators has a lot of different functions. You have blocks for addition, subtraction, multiplication and division, a block to pick random numbers, and lots more. The "and" block allows you to put two "boolean" blocks, which means it can only be either true or false and are the hexagonal-shaped, into a single space. It checks if both of the things are true. The same goes for "or", except it checks of only one is true. Then there's more that you won't need unless you're into more advanced programming.
Variables are really useful. Basically, you first need to create a variable. Then you can use the "set" or "change" blocks to change the number in it (by default it's 0). This is really useful if you're making lives or scores. Lists are like variables, except they can hold many different numbers/letters.
Pen you won't use much. Basically, it draws marks on top of the background, but it's really useful if you're making a paint program. The "pen down" block is like putting a pen on a piece of paper, and "pen up" is like taking it off. When the pen is down everywhere the sprite moves it draws the pen mark. You can change the size and color of the lines it makes. The clear block clears all marks on the background, and the stamp block makes an exact copy of the sprite.
I hope you can understand this. It's hard to describe entire sections.
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For the pen blocks, you could view Lanie's Pen Paint and study the scripts...
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For variables, you're invited to watch an introduction to using them featuring Scratch Cat: http://scratch.mit.edu/projects/Larry828/940874.
The project is called "Use a Switch" and shows how to create a variable with only two values (ON and OFF) and then use it to turn the Starfish into an astronaut!
All the scripts appear on the screen as they are needed, so you get to see how things work.
And if you enjoy it you can download it to study it some more.
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