I buy a box of bolts at the hardware store. They have no manufacturing defects, and no damage. They are still in the box. Are they functional?
Yes - If I take a nut and try to thread it on the bolt, it works, if I try to screw it into a hole, it works.
No - They are not currently holding any parts of any kind together, they don't form any part of any useful machine - they are not functional.
The ENCODE project is using the first definition. 80% of the DNA produces RNA, or has binding sites that bind to regulatory proteins, or some other function that can have a real impact on the cell. Whether or not the RNA is actually used, or if the regulatory sites actually regulate something, or if it actually has an effect on the cell was not considered - and is probably not known yet for most of that 80%.
Most people when they hear 'functional DNA' assume that it has an impact on the organism. The ENCODE project is working on a lower level, asking, 'Does this DNA do something on a molecular level?' not 'Does this DNA make a difference to the cell?'. That is of course the next question, but they are not there yet.
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