We nod for yes and shake for no.
Why and how did this come about ?
Don’t know how it came about, but be aware that this is not universal. Different cultures have different gestures - including head movements - to indicate “yes” and “no”.
A nod is a minimal bow. A bow is pretty much universal human body language for acquiescence, for pretty obvious reasons.
The origin of the head shake is in doubt amongst scholars, but if you’ve ever watched a parent trying to feed an infant something it doesn’t want you’ll no longer have any doubt as to where it originated.
Here in Greece a ‘yes’ is shown by tipping the head slightly to one side. Given that the accompanying word is ‘né’ this can be confusing.
A ‘no’ is anything from barely raised eyebrows to tipped backwards and then forward head accompanied by a shoulder shrug and clicked tongue.
I once worked at a computer programming company in NJ, which acquired a branch office in India. A few guys from the Indian office came to us so that we could introduce them to various aspects of what our software did and how it worked.
At many points, we’d notice them slowly shaking their heads from side to side. We interpreted this as, “No. That makes no sense. I don’t get it.”, so we naturally went into more detail, with deeper explanations. It spiralled down pretty badly for a few days until we learned that in their culture the head shaking was a sign of satisfaction, and they were understanding everything clearly all along.
Yeah, shaking your head side to side (as we would for no) is India for agreement. It’s confusing until you get used to. Then you find yourself doing it. I hate cross-cultural infections. 
I think in Arab cultures no is a sharp jerk of the head back – like recoiling from something.
I was recently in Bulgaria, and had heard that they nod for No and shake (or something like it) for Yes. I thought this might be a bit outdated, or a myth, but it really did cause confusion a couple of times, bearing in mind that not many people speak English there:
Them: (in Bulgarian, I’m guessing at the meaning) Do you want the room?
Me: (nodding) Yes, I’ll take it.
Them: So… do you want it or not?
I found it surprisingly hard to suppress my nodding. Maybe it’s a game they play with foreigners, pretending to be confused. They must be aware of the issue.
All of which makes it likely that Blake’s suggested origin of a baby refusing food is incorrect. Babies refuse food the same way the world over, and, as has been shown, shaking the head for no is purely a cultural thing.
But it’s still a good guess and the most logical one I can think of. When you don’t like something on or near your face your natural instinct is to shake your head back and forth. Similar is shaking your head back in forth if something doesn’t make sense to you or you disagree with it and you’re trying to shake it out of your head.
More confusing still is the occasional American usage, “he shook his head yes,” which means he nodded.
What you say is probably true only for people from the southern part of India. And to be precise, although similar, the shaking of their head in agreement is not exactly identical to the ‘No’ shake of our heads. The difference is very subtle though and unless one is observant it can, and does, get mistaken for the opposite.
The best way to describe it would be to imagine a piece of paper held in front of the face touching the nose. If the tip of the nose was painted such that it left a trace on the paper, in the case of a ‘no’, our nose would perhaps create a straight line on the paper because of the strict side to side shake. In the case of person from southern India, a shaking of the head side to side saying ‘yes’ would perhaps leave an arc with the ends pointing upwards.
With the guys from work that I’ve seen this in, it’s sort of like a bobblehead doll on your dashboard as you go over a bump. Actually it may be a bit different in different guys, but I get exposed to so many Indians in separate situations that I frankly lose track of where they’re from. And if they tell me where they’re from, when they meet up with the others then they nitpick and subdefine it so as to totally lose me. They also can disagree with what means northern and southern India, etc.
This is a new one to me:confused:
You got it!
Rather than “shake” and “nod”, some Americans say, “shake yes” and “shake no”. I don’t know if it’s a regional thing or what - I can’t recall that I’ve ever actually heard anyone say it, but you see it quite often in print here.
I’ve seen the “shook his head yes” thing in print. Drives me batty. To me, shake=no, nod=yes. But others differ.
Ah, sweet truthiness. Ignorance perpetuated!!
By the way, did you know that the word “golf” is an initialism for “Gentlemen Only, Ladies Forbidden”?
I said it was a “good guess” and I haven’t seen anything or anyone come up with something better explanation.