[link to original on tumblr]
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What I found interesting is that - when notated - that phrase forms a cross:
I should note that this phrase doesn't occur on the first beat as my notation would seem to suggest; it actually occurs on the third beat of the first measure the bass is in. I'm not sure of the key, but based on what I know of the guitar part, I think it's Bb major.
I first ran across this idea of inscribing crosses in music while reading John Eliot Gardiner's Bach: Music in the Castle of Heaven. He illustrates how Bach does this in Christ lag in Todes Banden, BWV 4:
I'm not sure if Brian Wilson was aware of this sort of thing, but I've read a few things where he talks about how he wanted the music on Pet Sounds to be spiritual. In the liner notes to the 1990 CD re-issue, he says, "Carl and I were into prayer. We'd pray together, and we prayed for light and guidance through the album." That quote is included in the comments about "God Only Knows," but it seems that it could apply to the title track and its inscription of the cross too.