Rabbi Eliyahu of Vilna, commonly known as the Gaon (literally "genius") was probably the most influential Jewish leader in modern history. He never assumed any official position of leadership and spent his time in almost total isolation toiling day and night in torah study. He became the undisputed greatest torah scholar and kabbalist in modern history.
Important Note: The Vilna Gaon's Commentary on Yonah is not appropriate for all levels.
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The book of Yonah is publicly read every Yom Kipur in all orthodox synagogues. The simple meaning of the story contains the theme of repentance. However, as is known there are 4 main dimensions of interpretation in the torah. They are 1) "Pshat" (simple,literal meaning), 2) Remez (allusion, hinted), 3) Drosh (not explicit interpretation), 4) Sod (secret meaning, which form the acronym PaRDeS (orchard). The Vilna Gaon on Mishlei (commentary "chemda genuza") explains: "The 4th level of torah, called "Sod" (secret) is the inner and primary meaning. The other lower meanings, are also true, but serve primarily for the purpose of straightening a man in order that he be sufficiently spiritually developed to understand the Sod".
These four dimensions of interpretation exist certainly in the 24 books of the bible but even in the mishna and in the talmud.
Very few people can delve properly beyond the pshat. Only one who has attained mastery in the four levels can be capable of deciphering the hidden code. The Vilna Gaon was such a rare person and offers us a spectacular view of a parallel book of the Yonah story on the plane of "Remez".