Where do thoughts arise?

Bhikkhus, in dependence on an element there arises a perception, there arises a view, there arises a thought.
SN 14.13

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Bhikkhus, sensual thoughts arise with a source, not without a source; thought of ill will arises with a source, not without a source; thought of harming arises with a source, not without a source. And how is this so?

In dependence on the sensuality element there arises sensual perception; in dependence on the sensual perception there arises sensual intention; in dependence on the sensual intention there arises sensual desire; in dependence on the sensual desire there arises sensual passion; in dependence on the sensual passion there arises a sensual quest.

In dependence on the ill will element there arises perception of ill will...

In dependence on the cruelty element there arises perception of harming...

In dependence on the renunciation element there arises perception of renunciation...

In dependence on the non-ill will element there arises perception of non-ill will...

In dependence on the harmlessness element there arises perception of harmlessness. In dependence on the perception of harmlessness there arises intention of harmlessness; in dependence on intention of harmlessness there arises desire for harmlessness; in dependence on desire for harmlessness there arises passion for harmlessness; in dependence on passion for harmlessness there arises a quest for harmlessness.

SN 14.12

Like everything else THOUGHT boils down to energy, and the "id" is the source of all psychic energy, from the instincts through to higher intuition. Id = the reservoir of all mental energy: id to the flow of libido, the life force, into ideas which define our identity by inflating thought bubbles, which deflate into mortido, the death wish, which dissolve into the so-called Void or Sunyata, from where the Ideal Self or Non-Self arises. (tried to keep it brief, if you want more google, cordery poems.

"'All phenomena are rooted in desire.[1]

"'All phenomena come into play through attention.

"'All phenomena have contact as their origination.

"'All phenomena have feeling as their meeting place.

'All phenomena have concentration as their presiding state.

"'All phenomena have mindfulness as their governing principle.

"'All phenomena have discernment as their surpassing state.

"'All phenomena have release as their heartwood.

"'All phenomena gain their footing in the deathless.

"'All phenomena have Unbinding as their final end.'

"On being asked this by those who have gone forth in other sects, this is how you should answer."

Rooted Sutta

Following Dhammapada several translations of a verse;

“ Mind is the origin of events. They have mind as the chief, and are mind-impelled.

“ All experience is preceded by mind, led by mind, made by mind.

“ Mind precedes all mental states. Mind is their chief; they are all mind-wrought.

“ Mind precedes all mental states. Mind is their chief;

Just as our sense organs have their definite natural functions (the eyes see, ears listen, nose smells, skin feels or the tongue tastes) the natural function of mind is to generate thoughts. It is doing for what it is made for. But we must not necessarily cling to all of its thoughts. We can watch or observe or witness them by standing apart, non-clinging to them. As our detachment grows the mind produces less and less and less thoughts. One day it is all silent. That is the Buddhahood.

Karma is most certainly created by thought! The Buddha described three doors of action through which karma is generated (see the Upajjhatthana Sutta as one example of this teaching). One door is body (i.e. actions done with the body), another door is speech (verbal expression, writing, etc.), and the last door is mind. This final door is characterized by any desire, thinking, planning, etc. Karma literally means action. It's a kind of moral momentum. Acting in one way strengthens and ingrains a certain behavior. Ruminating about something in your mind gives just as much strength to it as action. It habituates you to that pattern.

As to where those thoughts are coming from, well, that's tougher to pin down and it's really not so important from a meditative standpoint. You'll be hard pressed to point to one thought and say this came from this or that came from that; moreover, it's just going to distract your concentration. Think of your mind as one of those snow globes. All of those little flakes flying around are instances of karma, maybe some deeper expression of your subconscious (us yogacara folk call that alayavijnana), or whatever. It's your job to first let them settle. Worry about examining them later.

Sensation [in combination with perception] is the mind conditioner. Based on sensations further thinking and pondering arises which intern to fabrication. Fabrications lead to further experiences which give rise to sensation and cycle continues.

According to Abhidhamma thoughts are heart based.

What you need to realize is the one place where Buddhism & psychology does not agree. Psychology treats mind as a permanent thing and thoughts as its product. But as to Lord Buddha Mind & Thoughts are the product of a process. And as to Buddhism Mind is not a single thing.

Let me explain...

What is this process?

There are six receptors (aggregates) with a human (Eyes,Ears,Tongue,Nose,Body,Mind), These capture Light,Sound,Taste,Smell,Touch,Logic.

What gets captured creates it's own unique process called "Sanskara". Which then go on to feed its content (Liking,Hating or Neutral feelings) to a process called "Vinyana". These are six versions of possible Vinyanas that comes to existence when the aggregates come to contact with it's own version of input (Eyes with light,Ears with sound,Tongue with taste,etc). But a Vinyanas are only created if the being is aware & the aggregates are not damaged. Vinyanas are not with a permanent existence, these are born with the aggregates functioning and they cease with the end of process.

Thoughts are the mind,its process of occurring and ceasing is the mind. But Mind is not a place or a thing but a product of a process which cease to exist with the end of it's creator (the set of thoughts that created it in the first place)

I understand this explanation can be a bit hard to understand so here's a link read and learn this fully: "A Comprehensive Manual of Abhidhamma" (edited by Bhikkhu Boddhi)

**Sanskara - Sanskara is the thing that is capable of creating another set of aggregates (receptors) for a being. It has got its name from the meaning " The thing that is made as an result of many others combining which has the ability to create the components that makes it again.So simply without sanskara there's no next life."

**Vinyana - If you compare the concept that we call "Mind" to "Vinyana",it is essentially the same thing. But the difference is there are six possible Vinyanas that gets created every time the aggregates come to contact with it's own version of input.

Thoughts are created by the mind's natural activity. It's what the mind does. It's like a muscle or hair follicle. What matters is our attachment to that thought. Karma is simply energy and attachment and by attaching ourselves to the thoughts of a temporary vehicle (our body and mind), we are destined for suffering.

If you're a fellow geek, you may get a lot out of the research from Dr. Fred Travis. He studies the brain and has done a lot of research on meditation and brain activity. He basically shows that meditation helps us rise past lower states of consciousnesses by disconnecting that "word = object" mentality. See Youtube, Brain Plasticity and Transcendental Meditation with Dr Fred Travis.

Letting go of karma is thus attaining a higher form of humanity.