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Although we use many of their ideas to describe atoms today, such as the existence of a tiny, dense nucleus in an atom (proposed by Rutherford), or the notion that all atoms of an element are identical (proposed by Dalton), some of their ideas have been rejected by the modern theory of the atom.
For example, Thompson came up with the plum pudding model to describe an atom, which resembled a sphere of positive charge with electrons embedded in it. We know now, however, that atoms are mostly empty space with a tiny, dense nucleus.
Another example is Dalton's atomic theory, which stated that atoms are indivisible particles. However, this was disproved by the discovery of subatomic particles.