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Mendeleev grouped the elements in series according to their properties and atomic weight. His rule of thumb of giving priority to chemical properties, among other effects, left him with spots where he couldn't insert any of the elements known in his time -- germanium ang gallium come to mind. In group IIIa between aluminum and indium, and in group IVa between silicon and tin, there should have been two other elements, with properties intermediary between those of Al and In, respectively Si and Sn. Given that no such elements were known at the time, he left the spots empty, predicting that they will be discovered in the future, and called the two missing elements eka-aluminium ("similar to aluminum") and eka-silicium ("similar to silicon"). As it happens, he was right!

Those empty spots are where the question marks go. Of course, using a question mark is not mandatory -- anything that can be understood as "something is missing here" will do.

As a side note, these two were by far not the only "missing" elements when Mendeleev initially published his Periodic Table. Many of the places of transitional elements, discovered later, would have been "question marks", including all transuranic and transplutonic ones (which are artificial, synthesized only in the 20th century), as well as most the heavier radioactive elements in the main groups (francium, radium, polonium, astatine, radon etc.).

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