Alphabet's first half is beginning to muddle fundamental theory (7)
I believe the answer is:
atomism
'fundamental theory' is the definition.
The definition suggests a singular noun which matches the answer.
'alphabet's first half is beginning to muddle' is the wordplay.
'alphabet's first half' becomes 'atom' (I've seen this in another clue).
'beginning to' indicates taking the first letters.
The initial letter of 'muddle' is 'm'.
'atom'+'is'+'m'='ATOMISM'
Can you help me to learn more?
(Another definition for atomism that I've seen is " ancient philosophical theory".)