This material world is composed of five principal elements—earth, water, fire, air and ether—and all such elements are emanations from Kṛṣṇa. The material scientists accept these five primary elements as the cause of the material manifestation, but the elements in their gross and subtle states are produced by Kṛṣṇa. The living entities who are working within this material world are products of His marginal potency. In the Seventh Chapter of the Bhagavad-gītā, it is clearly stated that the whole manifestation is a combination of two kinds of energies of Kṛṣṇa, the superior energy and the inferior energy. The living entities are the superior energy, and the dead material elements are His inferior energy. In its dormant stage, everything remains in Kṛṣṇa.
The demigods continued to offer their respectful prayers unto the supreme form of the Personality of Godhead, Kṛṣṇa, by analytical study of the material manifestation. What is this material manifestation? It is just like a tree. A tree stands on the ground. Similarly, the tree of the material manifestation is standing on the ground of material nature. This material manifestation is compared to a tree because a tree is ultimately cut off in due course of time. A tree is called vṛkṣa. Vṛkṣa means that thing which will be ultimately cut off. Therefore, this tree of the material manifestation cannot be accepted as the Ultimate Truth, because it is influenced by time. But Kṛṣṇa's body is eternal: He existed before the material manifestation, He is existing while the material manifestation is continuing, and when it will be dissolved, He will continue to exist. Therefore only Kṛṣṇa can be accepted as the Absolute Truth.
The Kaṭha Upaniṣad also cites this example of the tree of the material manifestation standing on the ground of material nature. This tree has two kinds of fruits, distress and happiness. Those who are living in the tree of the body are just like two birds. One bird is the localized aspect of Kṛṣṇa known as the Paramātmā, and the other bird is the living entity. The living entity is eating the fruits of this material manifestation. Sometimes he eats the fruit of happiness, and sometimes he eats the fruit of distress. But the other bird is not interested in eating the fruit of distress or happiness because he is self-satisfied. The Kaṭha Upaniṣad states that one bird on the tree of the body is eating the fruits, and the other bird is simply witnessing. The roots of this tree extend in three directions. This means that the root of the tree is the three modes of material nature: goodness, passion and ignorance. Just as the tree's root expands, so, by association of the modes of material nature (goodness, passion and ignorance), one expands his duration of material existence. The tastes of the fruits are of four kinds: religiosity, economic development, sense gratification and, ultimately, liberation. According to the different associations in the three modes of material nature, the living entities are tasting different kinds of religiosity, different kinds of economic development, different kinds of sense gratification and different kinds of liberation. Practically all material work is performed in ignorance, but because there are three qualities, sometimes the quality of ignorance is covered with goodness or passion. The taste of these material fruits is accepted through five senses. The five sense organs through which knowledge is acquired are subjected to six kinds of whips: lamentation, illusion, infirmity, death, hunger and thirst. This material body, or the material manifestation, is covered by seven layers: muscle, blood, marrow, bone, fat and semen. The branches of the tree are eight: earth, water, fire, air, ether, mind, intelligence and ego. There are nine gates in this body: the two eyes, two nostrils, two ears, one mouth, one genital, one rectum. And there are ten kinds of internal air passing within the body: prāṇa, apāna, udāna, vyāna, samāna, etc. The two birds seated in this tree, as explained above, are the living entity and the localized Supreme Personality of Godhead, Paramātmā.