It's a protective mechanism by which we can survive our journey to whence we're going -by which 可以去掉 by 嗎？ -整段怎翻? -可寫survive in our...嗎？

It is a protective mechanism that our brain becomes hyper vigilant to the perception of threats around us when we step off the metro or onto a crowded city street.
在步出地鐵或是走上擁擠的街道時，我們的大腦就會對周遭可能發生的威脅特別敏銳，這是一種自我防衛機制。(it是虛主詞，後面的名詞子句是delayed subject）

Because of this protective mechanism. we can survive our journey to a certain place.
因為（大腦）有這種防衛機制，我們外出某地時，才能活著回家。

We are going to xxx.（xxx = a certain place)
We can survive our journey to xxx.
The reason why we can survive our journey to xxx is we are protected by a certain mechanism.
This protective mechanism is that our brain becomes hyper vigilant to the perception of threats around us when we step off the metro or onto a crowded city street.

這些句子壓縮成一句時，使用了「先行詞」＋「修飾語」的方式：
先行詞mechanism後面的修飾語用了by which帶出，是因為we can survive our journey when we are protected "by" a certain mechanism的關係。which = a certain mechanism
先行詞journey後面的修飾語用了to whence帶出，是因為we are going to "a certain place"及our journey to "a certain place"的共同交集是whence。whence = a certain place

「介系詞＋關係代名詞」在兩個形容詞子句裡都是副詞性質的介系詞片語（修飾其述部，並建立子句與前面先行詞的語法關係），我們不能省略介系詞，因為形容詞子句裡沒有關係代名詞which/whence單獨存在的空間。

就是因為有這種自我防衛機制，城市會讓我們的行為粗魯。（本句原文出處的標題：Why does city make us rude ?）

１．不可以的．ｂｙ應該要保留．醬子才可以明確地看出這個關係代名詞在關係子句　裡的角色．
２．這句子寫得不好．其實應該說是很爛：
Ａ）to whence we're going 是廢語．除非你是要賺字數稿費，這種廢語　應該省去．
Ｂ）ｗｈｅｎｃｅ慣例上多用在＂ｆｒｏｍ＂也就是出發地．用在目的地，我還是第一次看到．

再舉個例子們 來解釋我的2B:
3A) I loved whence we came. (O)
3B) I love whence we are destined. (X) 怪異用法...

1.Contrary to what you might think, anxiety is a normal experience. It's a protective mechanism which everyone has - and if we didn't have it, then we wouldn't function ...
2.It’s a protective mechanism by which we can survive our journey to whence (老式英語同:where) we’re going , which makes us all sounds really really rude to us.
3.我不會分析文法，原則上只憑感覺，前一句用 which就夠了，你想要加by都加不進去，因為感覺a protective mechanism --> everyone has ...， – 管他是什詞 – 只是意思平行轉換，感覺上要加 by都加不進去。
4.第二句by which 之前一樣指向三個字 – 一件事，後面就大有不同，我們把by拿掉， … mechanism which we can survive our journey we’re going, 到此感覺還順，但接下來, which makes – 就感覺有點不順了，這裡的which 指前面的一大堆事，其意義已不再是幾個名詞而是:透過之前的機制(By)，我的感覺是是有需要加一個 by的時候了，但加在那，我感覺加在此 - 後面意義也不會變，但老外直覺更快加在前面。英文裡有很多常規 前面既然用了，後面也可省了(有時常規是應加在前面後面需省)。你能讀到這篇文章，你英文可能比我好了，差別在我現在是藉你們的問題學點自己從未想過的理論。