句子结构直观分析：

By ‘indices’ （方式状语）he （主语）refers to （谓语动词。考虑搭配关系，把 refer to 视为及物用法）work （宾语）through connection with, or cause and effect of, the thing to which reference is made.（方式状语）

在 through connection with, or cause and effect of, the thing to which reference is made 中：

1. to which reference is made 是定语从句，先行词是 the thing。

2. through connection with, or cause and effect of, the thing  等于：

through connection with the thing or through cause and effect of the thing

此外，关于网友的两个另外的问题：

1，by ‘indices’还原到句中应该在什么位置；

——句首这个位置，是它最好的位置。因为句子其他地方，结构很紧凑，意思紧密相关，不好插入。

2，the thing to which reference is made 是定语从句吗？有争论说是宾语从句，我十分的不解。

——the thing 是先行词，to which reference is made 才是定语从句。很明显不是定语从句。the thing 是前文介词 through 和 of 的宾语。