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After graduation from UCSC, James went on to study at [[St. Vladimir's Orthodox Theological Seminary (Crestwood, New York)|St. Vladimir's Orthodox Theological Seminary]], graduating in 1985 with an M.Div. and again in 1988 with an M.Th. in Dogmatic Theology. In 1989, he began doctoral studies at Graduate Theological Union in Berkeley, but interrupted his studies to spend a year in Russia, working for ''Russkiy Palomnik'' in the publishing arm of the Moscow Patriarchate. During his time in Russia, he was introduced to Russian spirituality and its particular form of monastic life.
He eventually joined [[Valaam Monastery]] as a [[novice]], coming under the spiritual direction of Archimandrite Pankratiy, the monastery's [[abbot]]. Fr. Pankratiy's spiritual father, Elder Kyrill of [[Holy Trinity-St. Sergius Lavra|Trinity-St. Sergius Lavra]], later blessed James to become a [[hieromonk]].
In 1994, James was [[ordination|ordained]] to the [[deacon|diaconate]] and [[priest]]hood, and then in the following year, he was [[tonsure]]d a monastic at [[St. Tikhon's Orthodox Monastery (South Canaan, Pennsylvania)|St. Tikhon's Monastery]], South Canaan, Pennsylvania, receiving the name Jonah.