Arthur Koestler, in an appendix to The Thirteenth Tribe , notes:
T. E. Lawrence was a brilliant orientalist, but he was as ruthless in his spelling as he was in raiding Turkish garrisons. His brother, A. W. Lawrence, explained in his preface to Seven Pillars of Wisdom:
The spelling of Arabic names varies greatly in all editions, and I have made no alterations. It should be explained that only three vowels are recognized in Arabic, and that some of the consonants have no equivalents in English. The general practice of orientalists in recent years has been to adopt one of the various sets of conventional signs for the letters and vowel marks of the Arabic alphabet, transliterating Mohamed as Muhammad, muezzin as mu'edhdhin, and Koran as Qur'an or Kur'an. This method is useful to those who know what it means but this book follows the old fashion of writing the best phonetic approximations according to ordinary English spelling.
Clearly the problem is not a trivial one.