People keep food diaries. You then have them limit particular things or add in particular things. It is not going to kill them but you can measure it. As long as the study is large enough and the controls are ok you can usually draw some trends.

The big one for me is amount of salt per day. Someone on Ars years ago (when they actually kinda were good at instead of a leftest rag) looked into how much salt do we need. They literally could not find any study on it. The original 2000mg per day was apparently made up. Everyone else based their numbers off that. In the 1970s a lot of health advice was made up to sell programs, seminars, and books.

Want to lose weight? Stop eating things with sugar in it. Limit your fruit portions to one small fruit per day (lots of sugar in them). Eat heavy meaty protein heavy foods. Limit that to 20-40g per day Limit yourself to 900-1200 calories per day. Drink 40-80oz of water per day instead of soda, juices and milk. You will probably lose weight. However, do not take advice from me find a dietitian who knows what they are doing (not weightwatchers they just want to sell you a program).