Born in Edinburgh, Rutherford was the son of John Rutherford a professor of medicine. Daniel spent his early years as a student in Edinburgh University.

As a student of Edinburgh University, Rutherford was a pupil of Joseph Black. Black was studying the properties of carbon dioxide. In one of his experiments, he discovered that when a candle burned in an enclosed place, it left behind a residue of carbon dioxide. And when this carbon dioxide was absorbed using chemicals, he discovered there was still some other gas remaining. It was then Rutherford who conducted experiments to try to identify this mysterious new gas.

Rutherford was keen on find out more about this gas. So he trapped a mouse in a confined place. When the air ran out the mouse died. Rutherford then burnt a candle in the remaining air. Once the flame also died out, he burnt a piece of phosphorous in the container till it stopped burning. This air was then passed through a solution that absorbed the remaining carbon dioxide. Rutherford had removed oxygen and carbon dioxide from this air mixture. He named the remaining, isolated gas as noxious air or phlogisticated air. He believed that this gas was given out by the mouse while breathing. Today we call the same gas Nitrogen.

Studies on Nitrogen were conducted in the same period by other scientists such as Carl Wilhelm Scheele, Henry Cavendish, Joseph Priestley and Antoine Lavoisier. Rutherford went on to contribute in the field of atomic structure and radioactivity. At the age of 37, Rutherford became the Regius Professor of Botany in Edinburgh. This was followed by him becoming the keeper of the Royal Botanic Garden of Edinburgh.