I am trying to understand from a spiritual point of view what distinguishes the dead from the living. I read in Bhagavad Geeta 7.5 that there is an inferior and superior nature of the self. The superior living on the inferior. But what exactly is the difference? I am confused because this implies that only living beings such as humans, animals, cells, etc. have a soul and dead matter doesn't. But then in the Upanishads it is stated that the Self (Soul) is everything.
First, your interpretation of verse 7.5 is almost there, but not quite, which leads to your confusion. It is best to read verses 4-7 together and not separately. Verse 4 refers to the apparent division of Brahman, the Self, when seen through Maya. According to Sankara’s commentary on this verse, the elements referred to in the verse are the subtle elements and not the gross elements (Bhagavad Gita with the Commentary of Sankaracarya, Swami Gambhirananda translator). These are the apparent divisions of Mahamaya.
Verse 5 refers to the fact that it is really Brahman alone that is behind Maya and is the real cause and upholder of the universe. The two verses are meant to contrast that the perceiver of the universe, the individual jiva, is identified with the only real Perceiver of the universe, the universal Jiva, Brahman (verse 5); and that the universe being perceived is due to egoism, one of the eight-fold divisions of Maya referred to (verse 4). Sankara says in his commentary on this verse:
...By anankarah, egoism, is meant the Unmanifest, associated with (Cosmic) ignorance. As food mixed with poison is called poison, similarly the Unmanifest, which is the primordial Cause, is called egoism since it is imbued with the impressions resulting from egoism; and egoism is the impelling force (of all). It is indeed seen in the world, that egoism is the impelling cause behind all endeavor.
Verse 6 and 7 then tries to spell it out more succulently by stating that these two Prakritis are only Brahman.
To understand this more clearly, Sri Vidyaranya Swami says in his Pancadasi 15.7-8 (Swami Swahananda translator):
(Another Sruti says): ‘The supreme Self, though one only, exists in every object. Like the moon reflected in water, though one It appears as many.’ (Amrtabindu Upanishad 12.)
The moon which is reflected in water is faint in muddy water and clear in pure water. Similarly Brahman is two-fold according to the quality of the Vrittis (modification) of the mind.
Does this imply that only living things have souls and dead matter doesn’t? Yes and no. Pancadasi 15.20 says:
Existence, consciousness, and bliss—these are the three-fold nature of Brahman. In objects like clay, stone, and so forth, only existence is manifest, whereas the other two are not.
And verse 23:
The two, absence of consciousness, and misery, and non-existence—these are the three forms of Maya. Non-existence is illustrated by such expressions as ‘the horns of a man’; absence of consciousness is seen in such objects as wood, stone, etc.
What is consciousness and misery? These two are egoism, referred to in Gita verse 7.4. Without these two present, then you have only matter—stone, wood, etc. which are constituted from the other subtle elements referred to in the same verse.
Finally we read again in the Gita (9.4-5, Swami Gambhirananda translator):
This whole world is pervaded by Me in My unmanifest form. All beings exist in Me, but I am not contained in them!
Nor do the beings dwell in Me, Behold My divine Yoga! I am the sustainer and originator of beings, but My Self is not contained in all beings.
So Brahman pervades and sustains all, is omnipresent in all—but Brahman unmanifest remains separate from Maya. This is the eternal divine mystery.
You're right that living beings have soul and dead matter hasn't. Let me clarify your following confusion:
But then in the Upanishads it is stated that the Self (Soul) is everything.
According to Upanishads and Brahma Sutra, Brahman (ब्रह्म) is निमित्तोपादान कारण (material & sufficient cause) for all the creation i.e all these are made from and made by Brahman.
Now when you're refereeing to the self (soul), there are two meanings:
- Individual Self, also called Jivatma
- Supreme self, also called Paramatma
And the verse you've mentioned (7.5) clearly say about Jiva (Individual soul) using
You may find in many scriptures which say 'Only one fourth of Brahman makes up the world.' Aitareya, Taitteriya and Chhandogya Upanishad discuss how the world is made from (and by) Brahman.
the self (soul) is everything is explained with the help of Advaita and Vishishtadvaita Vedanta as follows:
According to Advaita, the Universe/World and the individuality of the self appears because of ignorance (अज्ञान)! and there is only one truth - Brahman (Supreme Self) (You may be aware of Advaita Sound :
ब्रह्म सत्यं जगत् मिथ्याmeans Brahman is the only truth, the world is unreal, and there is ultimately no difference between Brahman and individual self!)
You can read Vivkekachudamani (विवेकचूडामणि) verse 226-231 that demonstrate how everything is verily Brahman. And verse 241-249 states the non-duality of Atman (Individual Self) and Brahman (Supreme Self). Fore more explanation/understanding you can read Aparokshanubhuti.
And hence the clarification to your confusion is explained how the Self (Soul) is everything!
According to Vishishtadvaita, universe/world is real and created by and of/from Brahman (The Supreme Self). In other words, Brahman transforms one fourth of the self into creation as explained earlier. And talking about Jivatma (Individual Soul), Brahman (Supreme Self) dwells inside Jivatma (Individual Self). There is body-soul (Sharira-Shariri) relationship between world and Brahman and between Jivatma and Brahman. So while talking about the Self (Soul) is everything, it should be interpreted as the Supreme Self (not Individual Self). So, Brahman (Supreme Self) is everything because it is in world/universe as well as in Jivatma and everywhere outside them also.
The verses (You've mentioned in question) 7.4 and 7.5 talking about insentient (जड़) and sentient (चेतन) receptively and said are प्रकृति of Krishna which is explained with the help of Advaita and Vishishtadvaita above.
Conclusion: सर्व खल्विदं ब्रह्म । (Chhandogya Upanishad 3.14.1)