By ‘indices’ he refers to work through connection with, or cause and effect of, the thing to which reference is made.
刘老师这句话我问过你，可是我今天再看又有了新问题，所以抱歉又来打扰。
关于方法状语 By ‘indices’，大家之前说它是修饰 refers to的，但我心中的疑问是，它是修饰做后一个单词 made的。
把它放在句中是：
he refers to work through connection with, or cause and effect of, the thing to which reference is madeBy ‘indices’.
我的想法是By ‘indices’是作者着重强调的，所以才会把它从最后提到最前面。
“make reference tothe thing：参考某事
变被动语态后：
reference is made tothe thing
the thing 成为先行词后：
the thing which reference is made to =the thing to which reference is made”
蓝色部分是你之前帮我剖析的，这里我的弄不知道的是，make的主语是什么呢，换言之reference是通过什么产生的呢？
我想的是reference是made by indices
主动语态是：indices make reference
所以这句话的理解就是：
他指的是通过与事物的关联或者通过事物的因果的工作，‘indices’给事物制造了reference。
By ‘indices’ he refers to work through connection with, or cause and effect of, the thing to which reference is made.
网友把By ‘indices’（借用索引），理解为is made 这个动作的施事者（主动语态的主语），所以把它放在句末。即：
He refers to work through connection with, or cause and effect of, the thing to which reference is made by ‘indices’.
第一说明：By ‘indices’放在句首，它肯定是修饰主句的谓语动词（refers to），说明refers to 的方法，不可能瞒山过海去修饰一个定语从句的。从结构上即可看出来，这不应该存在争议的。网友理解失误。
through connection with, or cause and effect of, the thing... 两个介词共有一个宾语 the thing。
through connection with, or cause and effect of, the thing... 等于：
through connection with the thingorthrough cause and effect of the thing
我依据颜色英汉对应翻译：
By ‘indices’ he refers to work through connection with, or cause and effect of, the thing to which reference is made.
【翻译】借用“索引”，他指的是通过与所指事物的联系或因果关系而进行的工作。