Hello Newbee_b,
Welcome to the forum.
There is no refutation to be found for this particular argument given in the Shankara Bhashya because Shankara only refuted strong arguments, and this is not one of them. The argument is both circular in nature and it's also a strawman. I'll explain why.
A strawman is a fallacy whereby the the opponent's position is misrepresented and then attacked creating the impression in the unwary that the opponent has successfully been defeated. A circular argument is a fallacy where the conclusion one wishes to prove is already assumed to be true in the premise. Prabhupada's argument contains both fallacies and can be rejected on these grounds.
First, the strawman;
This is not a theory supported by 'Mayavadis' - it is a strawman theory invented by Prabhupada in order to give the impression that his doctrines are more correct. Look closely at this 'theory' and you will see how it is inherently inconsistent and counter to the actual Advaita position. Prabhupada says that the individual soul is separated by maayaa from Brahman, and that after liberation, the individual soul merges back into Brahman; but this is simply not true from the Advaita standpoint. The Self (soul) is not individual, and nor is it separate from Brahman, because it
is Brahman. Further, only Brahman exists in the past, present and future; this is the Advaita view. Even liberation is unreal from the highest standpoint. You must remember that Advaita comes from the top-down perspective, that only Brahman exists; everything else, be they jivas, bondage, world, liberation etc only hold sway from the empirical standpoint of ignorance.
Fundamentally, the Self is Brahman; the Self is not an individual jiva- the condition of being a jiva is superimposed onto the Self through ignorance, but it never actually becomes an individual as Prabhupada mistakenly says; it never actually separates from Brahman (itself!). When the Upanishads speak of attainment of Brahman, they are taken figuratively as if a woman who forgets where her necklace is finds it even though it's always been around her neck. Prabhupada takes the individuality of the self as an a priori assumption, he thinks the Self is
really individual, this is why he can never understand the Advaita view; the living being, the individual jiva, is not the true status of Atman, it is the Atman seen wrongly as a transmigrating, bound, suffering being from the standpoint of self-ignorance.
The Self is not born, it does not die, it does not suffer nor require liberation- and why?
Because it is the immortal, fearless Brahman. Krishna is here revealing to Arjuna the true nature of his own Self. None of us will ever cease to be because the very essence of the embodied being is the immortal Atman, identical to the absolute. Now, keeping this in mind, look at what Prabhupada then says;
Based on the fact that Krishna is referring to Arjuna, the assembled men and himself collectively when referencing the immortality of the Self, Prabhupada concludes that the Self must therefore be eternally an individual. This is a circular argument. Prabhupada already assumes that the Self is an individual, therefore, if Krishna refers to multiple jivas he must be saying that the multiple souls are eternal, and that therefore Advaita is wrong. Prabhupada has missed the deeper import of this verse.
Shankara explains that Krishna uses the collective personal pronoun figuratively because Brahman is the eternal Self of all beings, of all the embodied jivas, and not because there are many Atmas.
There is absolutely no incongruity between the given verse and the Advaita view if the Advaita view is a) correctly understood and b)one does not assume a priori one's own view is correct to begin with.
Look again at what Prabhupada here says;
The circular reasoning is as follows;
1) Individuality is a fact\true (assumption)
2) If Individuality were not a fact, then Krishna would not mention it
3) Krishna mentions Individuality in Gita 2:12
4) Therefore Individuality is a fact
This is extremely poor reasoning. Prabhupada makes the error of not distinguishing between the embodied being and the Atman, therefore when Krishna says 'you' with reference to Arjuna or the others, he assumes straight away that the subject is individual. When Krishna says 'you' what is he really referring to? Advaita says he is referring to the Self as-it-is, the saakshin, Knower of the Field (kshetraj~na) free from the limited superimposition of ignorance which creates the impression of being an embodied, individual jiva. This Self is identical to Brahman (as in the mahavakya that thou art) and therefore the verse should be understood in a deeper sense. Krishna is gradually teaching Arjuna the real nature of the Self because Arjuna takes himself to be an embodied being. He firsts starts by teaching that the Self of everyone is immortal, as in this verse, later (chapter 13) he will go on to identify himself (Brahman) as Arjuna's own Self in 'Know Me as the Knower of the Field in all of the Fields'. The interpretation given by Prabhupada is shallow, and he resorts to strawman attacks in order to sure up his own perceived strengths.
Prabhupada does not question the individuality of the Atman, he strongly believes it, as do many, many people. The Self is one without a second, this is the Advaita view; and therefore we are under no obligation to refute Prabhupada's argument when he assumes a-priori the individuality of the Self. This assumption does not stand scrutiny in Advaita, so neither do any of his arguments require rebuttal. The dualist's (or qualified nondualist's) ideas cannot be addressed by Advaitins, because we admit no duality and their worldview only has relevance in avidyaa.
To sum up my thoughts,
the verse given above from the Gita can be interpreted by both non-dualists and dualists according to their own philosophies, but the verse itself shows no bias for one or the other; despite Prabhupada's distorting strawman and circular reasoning uses to make it
seem otherwise. As I have said, this particular argument requires no refutation because it is invalid to begin with.
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