By virtue of their electrical properties, tubes generate a special waveform when they're saturated, which is why tube engineering has tremendous tonal advantages over solid state or DSP solutions, particularly for crunch and lead sounds. Tubes enter the saturation zone gradually or softly, which lends tube-driven tone its trademark yet totally unique character.
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Very good question. I have been wanting to know this too. I think being able to create your own songs using what theory you know is a very good thing to practise at. Also just improvising and always trying to improve your technique is always a good thing. Being able to use scales is useful but i think learning to be able to use them in interesting and different ways is the most important thing.