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but then the red balls and the green balls did different things (the red balls clumped together and the green balls flew around them, I think), so there was some essential difference between a red ball and a green ball; you could change the colours but that difference was still there.
That, at least partly, is because the model you're using is so simplified. It can't hope to explain why the protons stick together, because they shouldn't. They're all positively charged and so should repel each other and fly apart.
(Don't worry yet about why they stick together. Just accept that it gets more complicated later on.)
The terms positive and negative were applied consistently to charge before the discovery of the electron. Unfortunately this turned out to be the wrong way round for easy visualisation.
A rather value-loaded metaphor I think I've just made up is that when you're positive, you attract what you need, and when you're negative, you lose.
But, really, I visualise electrons a bit like little packets of negative charge. And because I know electricity is a flow of electrons, it's therefore logical that it flows from maximum to minimum, ie the negative to the positive electrode.
If an ion is negative, it's because it's got an extra packet of negative charge...
And...read this slowly...you already know that two minuses make a plus. Minus "minus one" is one...if an ion is lacking an electron, it will be minus one unit of negative charge. Therefore it will be positive.
I hope this makes sense... :)
It can't hope to explain why the protons stick together, because they shouldn't. They're all positively charged and so should repel each other and fly apart.
They don't. Two protons can never form a nucleus. That's what you have neutrons for (or rather, that's what neutrons do, if we want to avoid the pitfall of anthropocentrism). If you want a toy model that'll serve you well enough and remain useful pretty far into your studies (if not forever, depending on your line of enquiry), you can think about neutrons as a kind of glue that holds the positively charged protons together.
And by the time that model is no longer adequate, protons, neutrons and electrons should be such familiar mental constructs that they have long transcended the initial toy model.
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