While continuing to research Tool's style of music I have come across some terminology that is helpful to understand, especially when trying to perform their songs on guitar.
Question 1) What is a "Minor Scale Fragment"?
Answer: There are three different kinds of minor scales (natural, harmonic, and melodic). A "fragment" of one of these scales could be playing the notes from the scale in a different pattern other than 1,2,3,4,5,6,7. The fragment could be in an order like 123 234 345 456. Depending on the minor scale (natural, harmonic, and melodic) the notes and their fragments will give a different feel to the scale or song.
*Natural Minor Scales have a pattern of Whole Steps and Half Steps like this:
*Here is an example of a D Natural Minor Scale
*Harmonic Minor Scales have a pattern of Whole Steps and Half Steps with an augmented second (one and a half steps) that looks like this:
*Here is an example of a D Harmonic Minor Scale
*Melodic Minor Scales are different from the other two minor scales because it has one pattern ascending the scale and another pattern descending the scale.
*The Ascending Pattern in whole steps and half steps looks like this:
*The Descending Patter in whole steps and half steps looks like this:
*Here is an example of an ascending D Melodic Minor Scale