No. When a microwave oven is off, the cooking chamber contains nothing special at all—just some trapped air and perhaps a little light that enters through the window. Even when it is operating, a microwave oven never produces any ionizing (high energy) radiation so there are no long-term effects such as radioactivity present in the cooking chamber when the oven is off. The tomato was simply sitting in a sealed metal box overnight. Since some fruits ripen faster in sealed environments, perhaps that accounts for your observation.
No more so than conventional heating does. Overheating some nutrients can damage them, so that microwave cooking does affect food's nutritional value. But microwave cooking is far less likely to cause serious molecular damage to food than flame broiling or frying.
Apart from the usual precautions with hot food, there is nothing unsafe about food cooked in a microwave oven. You can eat it the instant the microwave oven turns off. The microwaves in the oven are absorbed so quickly that they vanish almost immediately after the oven stops producing them. By the time you get the oven door open, there is nothing hazardous left inside the cooking chamber or in the food. However, a microwave oven tends to heat foods unevenly, particularly if they were initially frozen. Thus you should be careful to stir the food or test its temperature at various places so that you don't burn yourself. You should be particularly wary of solid foods, such as raisin biscuits, that are generally dry but have moist, microwave-absorbing objects inside them. Those moist objects can become dangerously hot and have been known to cause life-threatening burns in people who tried to swallow them without letting them cool off.
That said, a reader notes that the uneven cooking in a microwave oven can lead to bacterial safety problems—if parts of the food aren't heated sufficiently to kill dangerous bacteria, then you could be exposing yourself to those bacteria. He suggests using the microwave oven for reheating only. He also notes that the lack of surface heating leaves the food relatively tasteless, as compared to more conventional cooking.
Just about any cooking damages the cells of the food being cooked, so microwave cooking is nothing unusual. Since our digestive systems destroy cells in the food we eat, cellular damage in cooking is inconsequential. As for the rumors about the unhealthiness of food cooked in a microwave oven, these are simply myths promulgated by people who don't understand what microwaves are and fear them irrationally. The world was awash in microwaves from natural sources long before the developments of electricity and microwave ovens.
While microwave heating could be used to sterilize sewage, it's not the most energy efficient or inexpensive technique. Microwave heating is really only worthwhile in cases where you can't reach the inside of an object directly—as is the case in most solid foods. Since sewage is essentially liquid, it can be heated quickly and efficiently by passing it close to a hot surface. Just about anything can be used to heat that surface—electricity, natural gas, coal, you name it.
But to be even more energy efficient, the sewage that was just sterilized a minute ago and is still hot can be used to heat the sewage that is about to be treated! A well designed thermal treatment facility could employ "counter-current exchange"—that is it could pass the hot, treated material through a heat exchanger to allow it to transfer most of its excess heat to the cooler, untreated material that is about to be sterilized. By recycling the heat in this manner, the facility could avoid having to burn so much fuel. The only drawback with this technique is that the heat exchanger must be leak-proof—it must keep the sterilized material from touching and being contaminated by the unsterilized material.
The fact that sound waves can pass through the cooking chamber's metal walls doesn't mean that microwaves can. These two types of waves are very different and the chamber's walls handle them very differently.
Any type of wave will partially reflect from a surface if passing through that surface causes the wave's speed to change or, more generally, introduces a change in the "impedance" the wave experiences. Impedance is a quantity that relates various parts of a wave to one another—it relates pressure to velocity in sound and it relates the electric field to the magnetic field in a microwave. Since both sound waves and microwaves change speeds and impedances when they encounter the cooking chamber's metal walls, they both partially reflect. The sound that you hear when popcorn pops inside the oven is slightly muffled because the sound is having some trouble escaping from the cooking chamber. However, the impedance change for the microwaves is so enormous that the reflection is complete. No microwaves at all escape from the cooking chamber! The same effect occurs when you hold a large mirror up in front of your face. You can hear what's happening on the other side of the mirror because some sound can pass through the mirror. But light is completely reflected and you can't see through the mirror at all.
When the microwaves bounce around inside the oven's cooking chamber, they experience an effect called interference. Interference occurs when similar waves, or portions of the same wave, follow different paths to the same region in space. As they pass through that region, their crests and troughs ride up on top of one another and they interfere. Sometimes the crests of one wave ride on the crests of the other wave, creating enormous crests—an effect called constructive interference. However, it is also possible for the crests of one wave to ride on the troughs of the other wave, so that they cancel one another out—an effect called destructive interference.
These interference effects are quite visible in wave waves, but they also make themselves apparent in microwaves. In your oven, they lead to regions of the cooking chamber that heat quickly (regions where the microwaves experience constructive interference) and regions that don't heat well at all (regions where they experience destructive interference). Because these fast and slow cooking regions can't be avoided, many microwave ovens incorporate turntables to keep the food moving through the various regions inside the oven. Some ovens use rotating metal paddles to stir that microwaves around inside the cooking chamber, so that the fast and slow cooking regions move about.
Your experience with uneven heating of coffee or milk is an example of this interference problem. The solution is to move the cups occasionally while they are being heated.
While most microwave ovens operate at 2.45 GHz, that frequency is not a resonant frequency for the water molecule. In fact, using a frequency that water molecules responded to strongly (as in a resonance) would be a serious mistake—the microwaves would all be absorbed by water molecules at the surface of the food and the center of the food would remain raw. Instead, the 2.45 GHz frequency was chosen because it is absorbed weakly enough in liquid water (not free water molecules) that the waves maintain good strength even deep inside a typical piece of food. Higher frequencies would penetrate less well and cook less evenly. Lower frequencies would penetrate better, but would be absorbed so weakly that they wouldn't cook well. The 2.45 GHz frequency is a reasonable compromise between the two extremes.
A properly built and maintained microwave oven leaks so little microwave power that you needn't worry about it. There are also inexpensive leakage testers available that you can use at home for a basic check, or for a more reliable and accurate check—as recommended by both the International Microwave Power Institute (IMPI) and the FDA—you can take your microwave oven to a service shop and have it checked with an FDA certified meter. It's only if you have dropped the oven or injured its door in some way that you might have cause to worry about standing near it. If it were to leak microwaves, their main effect would be to heat your tissue, so you would feel the leakage.
Some experiments are so sensitive to electromagnetic waves that they must be performed inside "Faraday cages". A Faraday cage is a metal or metal screen box. Its walls conduct electricity and act as mirrors for electromagnetic waves. As long as a wave has a wavelength significantly longer than the largest hole in the walls, that wave will be reflected and will not enter the box. This reflection occurs because the wave's electric field pushes charges inside the metal walls and causes those charges to accelerate. These accelerating charges redirect (absorb and reemit) the wave in a new direction—a mirror reflection. Just as a box made of metal mirrors will keep light out, a box made with metal walls will keep electromagnetic waves out.
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