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According to this list of the Patimokkha Rules,

Using water, or getting others to use it, knowing that it contains living beings that will die from that use, is a pācittiya offense. (Pc 62)

So, does this refer even to microbes in water? If so, how would a monk boil water for food and/or tea without committing an offense? Or even drink water without committing an offense?

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The common answer is that microbes and smaller life forms are exempt from Buddhist classifications of sentient life forms.

I'd like to make a more nuanced point.

At the time it was written, this rule probably had mosquito larvae in mind.

Practically speaking, even abiding by this ontological line in the sand is difficult if the only source of water is infested with mosquitoes or the numerous life forms of tropical Asia. Most monasteries therefore often rely on lay helpers to perform water boiling and several other life tasks that might break the vinaya if a monk were to perform it.

To an outside observer this can appear dogmatic or a farce, and depending on the individuals involved sometimes it is so, but not always so. It aids in cultivation of zeal, and respect for the expectation placed on the monastic.

The whole of the spiritual life is doing one's best in trying conditions.

The Bodhisattva vows reflect this,

However innumerable sentient beings are, I vow to save them.
However inexhaustible the defilements are, I vow to extinguish them.
However immeasurable the dharmas are, I vow to master them.
However incomparable enlightenment is, I vow to attain it.

In traditional Asian cultures the laity often view these small inconveniences the monks undertake, like waiting around for a lay person to give them potable water as resolve strengthening sacrifices the monks make in the pursuit of the holy life. It also gives the laity a meritorious role in the life of the monastic, and keeps them inter-dependant.

This can also be a very instructive exercise in patience and virtue when applied correctly.

For example, if a novice monk is alone and thirsty in the forest, it must be very tempting to drink a cup of water after pushing aside the larvae on top of the forest pool.

This simple physical act is not so simple in the mind of a monk, given the vinaya. It leads him weigh his life against that of the organisms in the water.

In this way the monk comes to directly feel the enormous burden human life places on the planet, and the numerous beings and life forms including plants that we inadvertently or unavoidably destroy or disturb in order to live.

Thus chastised, the monk will truly consider the cup of water a precious cup of life, and endeavour to uphold the ideals of the holy life so stiffly purchased.

The rules are meant to aid the holy life, not become obstacles or rituals. The Buddha reveals this pragmatic distinction here:

AN 3.83: Vajjiputta Sutta — The Vajjian Monk {A i 230; Thai 3.85} [Thanissaro]. A monk who is having difficulty following all the Pāṭimokkha training rules can boil them all down to these three: the training in heightened virtue, the training in heightened mind, the training in heightened discernment.

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