When the Universe was first formed it was completely featureless (just a vast patch of hydrogen gas). Over time (billions of years) the hydrogen gas began to clump together to form the first stars, and these in turn created the elements that would form future stars, planets, nebulae and all the other components of today's Universe. The space between galaxies (clusters of stars) contains hot gas. In fact, this gas is so hot (tens of millions of degrees) that it shines in X-rays instead of visible light. By studying the distribution and temperature of the hot gas we can measure how much it is being squeezed by the force of gravity from all the material around it. This allows scientists to determine how much total material (matter) there is in that part of space.
Remarkably, it turns out there is five times more material in clusters of galaxies than we would expect from the galaxies and hot gas we can see. Most of the stuff in clusters of galaxies is invisible and, since these are the largest structures in the Universe held together by gravity, scientists then conclude that most of the matter in the entire Universe is invisible. This invisible stuff is called 'dark matter'. There is currently much ongoing research by scientists attempting to discover exactly what this dark matter is, how much there is, and what effect it may have on the future of the Universe as a whole.
Take a look at this documentary about dark matter and whether the search for it really constitutes proper "science".
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