So the Universe rests on imperfection, who would have guessed?

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The Dharma, incomparably profound and minutely subtle,

Is rarely encountered, even in hundreds of thousands of millions of kalpas.

We now can see it, listen to it, accept and hold it,

May we completely realize the true meaning of the Tathagata.

This (or a close variation) is the verse chanted before Dharma talks in Zen centers through out the world. The line about the rarity of being able to encounter the Dharma is often taken as some kind of self-aggrandizing hyperbole. A kalpa is an eon of very long time with several colorful analogies, such as the length of time it would take for a butterfly's wing brushing up against Mt. Everest to erode it to smooth ground   But the article, "This One Imperfection In Nuclear Physics Allowed Earth To Exist" by Ethan Siegel, explains how the rarity is literally true, because of the crazy quilt of conditions that must occur in order for planets to arise and for life on those planets to appear.

Of course, it begs the question of how those early sages of India were able to conceive of the inconceivable eons of time and the innumerable numbers of galaxies as many as the sands of the Ganges River that are the context for this one precious life, a couple thousand years before Giordano Bruno was burned at the stake for daring to propose that the universe is infinite.  

The article describes the rarity like this:

In order to create a rocky planet that's teeming with life, the Universe needed to create large amounts of the heavy elements required for life's processes. To make many of those elements, such as Tin, Iodine, Selenium, Molybdenum, Zinc, and Copper, you need supernovae to have occurred many times in our galaxy's past. To get many more, such as Iron, Calcium, Cobalt, Sulfur, and Potassium, you need stars massive enough to create them....The only reason we can exist, today, is because one tiny imperfection in the early Universe allows the stars to grow hundreds of times as massive.

 

Since we are only able to appear on the basis of that one original "imperfection" then all appearances can be said to be the continuation of that imperfection, which gives credence to Zen master Dogen's phrase, ‘Shoshaku jushaku,” which according to Shunryu Suzuki Roshi in his book Zen Mind, Beginner's Mind, means “'to succeed wrong with wrong,' or one continuous mistake.”

Buddhism is the religion of the science of mind, or the psychological religion.  I recognize that is a controversial claim, even for some Buddhists, but it is stated from a perspective in which it is a valid statement, so instead of saying why it appears invalid from one perspective, I would ask that the critic make the effort to stand, if only for a moment, in the spot where the view makes sense. Here are a couple Tibetan Buddhist perspectives adopting the Buddhism is a science of mind approach.

Buddhism, as the science of mind, empirically observes, investigates, and analyzes mind with its mental states, conditions, and phenomena, that comprise all our cognitions, thoughts, emotions, feelings, views, desires, joys, etc. (i.e., the Tin, Iodine, Selenium, Molybdenum, Zinc, and Copper of our mind). This empirical study of mind was Carl G. Jung's definition of the science of psychology (i.e., "psych" = mind; "ology" = study or science).  In other words, Buddhism explores the universe as mind not as matter.  What we are now discovering by Western Science's exploration of the universe as matter, not mind, is that there is a confluence and congruence of findings.  Over the preceding 400 years,(Bruno was killed by the Catholic Church in 1600 C.E.)  the exploration of the universe as matter has grown to include such previously inconceivable (at least to the West) ideas as infinity, laws of cause and effect, unseen forces of gravity, the strange nature of light (constant speed and indeterminacy as wave or particle),  dark matter and dark energy, etc., all of which have their analogues in the discoveries of Buddhism's exploration of the universe as mind.

The classic early Buddhist scripture The Dhammapada begins in the first two verses from this startling vantage point:

1. Mentation is the precursor of things; mentation is the ringleader; mentation is the producer.

If mentation is corrupted, just so the voice, just so the act,

Thereupon unease is enabled, just as the wheel follows the transporter’s (e.g., ox or man) foot.

2. Mentation is the precursor of things; mentation is the ringleader; mentation is the producer.

If mentation is clear, just so the voice, just so the act,

Thereupon ease is enabled, just as the shadow follows and does not depart.

Here, "mentation" (Pali and Sanskrit, mano & mana(s)) means the cognitive activity of mind, and "things" (P. dhamma, Skt. dharma) means both discrete things and the thingness of all phenomena.  So we find many variations in translation from the strict to the loose, from the prosaic to the poetic, such as:

All the phenomena of existence have mind as their precursor, mind as their supreme leader, and of mind are they made.

We are what we think. All that we are arises with our thoughts. With our thoughts we make the world.

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

The important point here is that mentation (manas, also known as the 7th consciousness in Mahayana analysis), as the basic cognitive activity of mind, can be either corrupted or clear, and when it is corrupted all manners of antithetical conceptions and oppositional dualities arise that are taken as literal, fixed, and substantial.  This is what Buddhism calls the primordial ignorance, or in the words of Siegel's article "a tiny imperfection," in the arising of consciousness that leads to the 'creation' of the universe and life on a planet.  But there is the inherent possibility that what begins as corrupted and the source of all unease (dukkha) in life, can become clear and the source of ease (sukkha).

The Treatise on the Mahayana's Arousing of Faith (date unknown, translated into Chinese in 553 C.E. by the Indian monk Paramartha (499-569 C.E.)) contains an outline for how the universe appears (using the mind paradigm, not matter paradigm) that was elaborated on by Zen master Guifeng Zongmi (780 – 841 C.E.) and used by him to establish his taxonomy of the teachings (panjiao) of Buddhism.   In Zongmi's Treatise on the Origin of the Person (原人論 Yuan Ren Lun), based on the Arousing of Faith, the universe is the One True Mind and "initially there is only one true numionous nature, that is not born, does not die, does not increase, does not decrease, does not become, and does not change.  

The "big bang" of the appearance of consciousness occurs with the bifurcation of this unity into enlightenment, i.e., the clear mentation of the Dhammapada, on the one hand and unenlightenment, i.e. the corrupted mentation of the Dhammapada, on the other.  The word corrupt is used, not in a moral sense, but in a phenomenological sense of having a "broken" view of the phenomenon of thingness. This broken view is what is called "false conceptions" or "false thinking" and is taking the bifurcated view of consciousness as substantially existing and seeing things as fundamentally separate rather than unified.   Zongmi cites the Flower Garland Sutra's version of the Buddha's calling out upon his enlightenment:

“Children of the Buddha, there is not one of the multitude of beings who nevertheless does not completely possess the Tahtagata’s innate awareness and wisdom. Yet by means of false thinking and clinging they nevertheless do not verify getting it."     

The analogy to this question of unity or separation in the Western science of taking the universe as matter has been revealed through the changing nature of the theory of the universe from mechanics to quantum physics. Once things were taken as essentially separate, independent, and discrete things, and now their nature is seen as energetic fields of potential and actuality of non-thingness.

When the big bang of mental bifurcation takes place, the "world of birth and death" begins to appear, and by natural evolution, consciousness flows in a stream of ignorance called unenlightenment that reverberates into the condensation of subject and object (i.e., inner and outer orientations) and with further evolution becomes discrimination, continuation, attachments, conceptual elaborations, karma, and the fruit of karma in varying degrees of suffering within the six paths of birth and death (i.e., hell, ghosts, animals, humans, titans, and celestials).  

The Dhammapada's promise of clarifying mentation is seen by the Zen of Zongmi as the promise of enlightenment which begins (and ends) in the mind of enlightenment (bodhicitta) that first appears as a dawning intuition or intimation, then as a faith or trust in it's actual possibility, then as turning toward it as a path to cultivate, then the practical acts of cultivation, experiencing the fruit of that cultivation, and ultimately having one's own realization of enlightenment with its unassailable clarification of what had previously been thought of as broken ("mentation corrupted") and the manifestation of the mind of suchness.  As Zongmi points out, this teaching of the manifestation of the One True Mind, indistinguishable from one's own Buddha Nature, is the One Vehicle.         

"That Which Is The One Vehicle's (Ekayana) Teaching Of Manifesting Nature clarifies for everyone having sentience that everybody has the root enlightenment of True Mind.  Beginningless is how it comes, and it always abides clear and pure.  Its luminosity does not darken and is completely and constantly aware.  It is also called Buddha Nature, and is also called the Inner Tathagata (tathagatagarbha)."

So we can appreciate how this Dharma teaching is incomparably profound and minutely subtle and why it is so rarely encountered, even in hundreds of thousands of millions of eons, because, in the context of the universe as mind, the evolution of consciousness is synonymous with the evolution of the universe, and only after the process of evolution comes to the realization of its own nature can we see it, listen to it, accept and hold it, and completely realize the true meaning of the Tathagata as the coming and going of True Suchness.