「で」をどう翻訳するか？

Last week, I was at Tamagawa University for a meeting. I had to walk across the campus to get to the building where the meeting was being held. That's when I saw this nice tree in bloom.

• 花咲く (はなさく) (v5) to bloom; (definition from Edict)
• in bloom 真っ盛りで、咲いて (definition from Eijiro on the Web)

× By the flowers on this tree, I know spring is near.
◯ By seeing the flowers on this tree, I know spring is near.
◯ Because of the flowers on this tree, I know spring is near.

You know, I think many Japanese learn early on to say things like "I went there by train".

× By that, they want to translate で as "by" in many cases.
◯ Because of that, they want to translate で as "by" in many cases.

However, many of those cases should be "because of", not "by". If you want to use "by", you probably should follow it with a verb+ing, not a noun.