Marked by/marked with

In the literal sense of the word “to mark”, the difference is obvious:

something is marked with markings (= symbols, added visuals) by the painter(s) (= the person or persons who made the markings).

Passive voice: The stone is marked with hieroglyphs by unknown ancient Egyptian carvers.

Active voice: Unknown ancient Egyptian carvers marked the stone with hieroglyphs.

•

So what if one uses “to mark” in a metaphorical sense?

I would use by when the thing that follows is the trigger: an emotion, such as scorn, that drives a person to behave differently than he otherwise would.

The politician’s speech was marked by scorn for the rival party.

= The politician or his speechwriter had so much scorn that they just couldn’t write a speech in which the rival party was refered to in a polite, respectable tone.

Scorn is here the driving force.

•

I would use with when the thing that follows is something that can be seen, heard, or sensed: not the driver of the markings, but the way the markings are visible, audible, or sensible.

The politician’s speech was marked with scorn for the rival party.

= You can just hear the scorn in the words of the speech.

Scorn is here the output. The politician’s speech was full of scorn for the rival party.

I think there is a little more to it than the passive.

(i) It was marked by a hard, sharp object - "by" introduces the agent and the agent does the action of the verb.

(ii) It was marked with a red X - "with" introduces an item that is now combined with, or accompanied by, the subject.

The objection might be:

A: “How was that cut mark on the door made?”

B: “It was made by the murderer.”

Pedantically, B is inaccurate as murderers tend not to be sharp. It should be

B’: “It was made by the murderer’s knife.

Compare:

(iii) He dug the garden with a spade.

(iv) He dug the garden with a song in his heart.

(v) He dug the garden with his wife.

All are correct and describe what/who was with him whilst he dug. In (iii) the reader assumes the instrumental, (he may have been holding a spade whilst operating a rotivator) but not with (iv) and (v).

For a simple rule of thumb you could follow this: "Marked with..." refers to nouns. Specific words that exist and "mark" the text, literally.

• "His speech was marked with anger."
• "John, you bastard, I'm sick of suffering your crap in this hellhole."

You can see specific angry nouns: bastard, suffering, crap, hellhole. "Marked by..." refers to a characteristic or person which did the marking. It's not any specific noun but a quality you can infer about the whole text.

• "His speech was marked by anger."
• "John, I've had enough, I'm at the end of my patience and I'm done with this."

There's no specifically angry noun, yet the text is still "marked by" anger. In another context "marked by" could be substituted with "shown by" or "revealed by". Again showing a quality of the whole context. Whereas "marked with" is more likely to refer to "soiled with" or "polluted with".

• "The birthday was wild fun, marked by cheering and playfulness and the host singing a tribute to her mother."

• "The birthday was disappointing, marked with some fights and the kitchen catching fire."

The latter describes the specific markings. The former describes characteristics. So "by" is used more in passive voice and "with" used more in active voice. More information available here:

https://pediaa.com/difference-between-by-and-with/