Are atoms real?

The chemistry list serve has brought up some interesting discussion around how we know atoms exist if we cannot directly observe them.

One of the responses to this was an activity using boxes with mystery items inside them.  By using a scientific method or process, students are given the task of determining what they think is the most likely item to be in the box.  So the question remains how you could teach this concept of theoretical certainty using a visual simulation.

One of the online resources that was sent out was a link to a flash animation that sort of mimics the Rutherford experiment but it's not about atomic structure, it's about using a similar methodology to determine the shape of an unknown mystery object.  The link is here.

I have added the link to Chemistry as Flash - Rutherford Remake.