3.2.6. Afflictive and Cognitive Obstructions
“Sentient beings are buddhas.
Nevertheless, they are obscured by adventitious stains.
When those are removed, they are buddhas.”
— Hevajra Tantra
I have come to see this part of the journey not as a task of acquisition, but of gentle removal — like patiently cleaning a window so that light can pour through unimpeded. Even now, so far along this path, I find myself amazed at the sheer subtlety of the mind’s obstructions. They are not merely stains of anger or greed, obvious enough to detect and purify. There are deeper patterns, woven so tightly into consciousness that they pass unnoticed, shaping how reality appears before we ever have the chance to question it. This chapter is my attempt to unravel these veils — to trace the gradual dissolution of afflictive and cognitive obstructions that conceal the luminous nature already present.
The work of the alchemist has now become a delicate process of purification — removing the stains that obscure the mind’s intrinsic clarity. Even an arahant, fully liberated from personal suffering, carries the subtle residues of karmic history. Though these residues no longer bind or deceive, they still ripple quietly through the continuum of mind.
It is important to recognise the different goals along this path. Those who follow the solitary vehicle — from sotāpanna through to arahant — seek emancipation from suffering. They successfully eliminate the seed of self, so that the thought “I exist” never arises spontaneously again. Freed from ill-will, greed, and delusion, they experience the world without the prison of self-concern. Yet, in the analogy of The Matrix, they remain within the system’s fabric, simply no longer mistaking it for a personal domain.
The Great Vehicle shares much with this solitary path, but with one luminous difference: bodhicitta, the earnest wish to awaken for the benefit of all beings. As the bodhisattva cultivates this motivation, it becomes a living seed within them, even present during sleep. Eventually, a further aspiration arises — called the special quality — a resolve to become a buddha specifically to maximise their ability to guide others.
Thus, the goal of the bodhisattva enfolds and surpasses that of the solitary vehicle. Their journey still begins by dismantling coarse afflictions — those rooted in intellectual habits of selfhood — but it continues far deeper. They work through subtler karmic patterns laid down across countless lifetimes.
Layers of purification
Imagine trying to repair a computer. First you uninstall corrupted software, akin to eliminating the notion of self. But deeper faults lie in the operating system itself — hidden scripts that subtly distort every process. This is like the innate afflictive obstructions, patterns imprinted by vast karmic histories. The bodhisattva on the Path of Meditation gradually uproots these, moving towards a state where no conditioned phenomena remain to stir perception. By the eighth bhūmi, even these deepest afflictions fall away, leaving only the most elusive obstacles: cognitive obstructions.
A helpful metaphor is the seed. We are rarely perpetually angry or grasping; these tendencies lie dormant until the right conditions awaken them. The coarsest seed is the belief in a self. Its removal liberates an arahant from personal suffering, unveiling a reality undistorted by self-regard. Yet, this only addresses the grosser habits of mind.
Two types of afflictive obstructions
- Intellectually acquired afflictions are ideas we hold about ourselves, shaped by memory and personal narrative — beliefs about who we are, formed across this lifetime. These dissolve entirely for an arahant or a bodhisattva reaching the Path of Seeing.
- Innate afflictions are subtler. They represent the deep continuum of conditioning — impressions from countless lives that automatically shape perception. Like instinctive fears of danger, these do not require teaching; they spring from the mind’s long entanglement in cyclic existence.
When the bodhisattva attains the eighth bhūmi, they clear away the last of these afflictive obstructions. With nothing left for the mind to grasp, it rests naturally in non-dual awareness. The world appears luminous, objects glowing as expressions of the mind’s intrinsic clarity. Yet, even here, phenomena still arise, subtly tinted by residual imprints.
The cognitive obstructions
These are the faintest habits of perception that prevent total omniscience. The final three bhūmis are devoted to dissolving these, until all distortions vanish and the mind realises perfect buddhahood.
This work becomes ever more refined — shifting from strenuous effort to a tender, almost playful exploration. Eventually, even the yearning for success must be relinquished, for that too is a veil. The true miracle is that, layer by layer, these obstructions fall away, revealing what was always here.
So the alchemist’s work matures from vigorous striving to a subtle art of letting be. As the afflictive stains are cleared, the cognitive habits that once seemed inseparable from reality come gently into view, ready to dissolve. Each stage brings a quieter joy, a growing intimacy with the luminous ground of being that was never absent, only hidden.
This text is excerpted from the upcoming book Citrinitas: A Course in Modern Alchemy. The complete volume will include additional study guides, glossaries, and extended teachings. Learn more about the book here.