Question: What happens at the time of conception? How does an ātmā choose a sperm or an egg cell? Does each sperm cell have an ātmā?
Answer: There are certain mysteries in this universe, which are not known to human beings. Karma, birth, and death are three such mysteries. These mysteries are under the control of Paramātmā, who is the regulator of this universe. How karma gets attached to a particular jīva and how it unfolds in future lives is not known to human beings. They will never be able to have complete understanding of these mysteries, even though science is presently trying hard to understand them.
The mechanism of birth and death, that is, how a particular ātmā takes a particular body, and how a particular ātmā gets a new birth after death, are two major mysteries about life. They can only be known by the sages. There are some hints of these mysteries in śāstra, but there is no detailed explanation available.
The answer to your questions is hinted at in a Bhāgavata verse spoken by Śrī Kapila. (SB 3.31.1)
karmaṇā daiva-netreṇa jantur dehopapattaye
striyāḥ praviṣṭa udaraṁ puṁso retaḥ-kaṇāśrayaḥ
“By the action of daiva or Īśvara/Paramātmā, the impeller, a particular living being, taking shelter of the sperm of a man, enters into the womb of a woman for accepting a body.”
The important words to be noted in this verse are karmaṇā daiva-netreṇa. Karmaṇā means by action, daiva refers to Paramātmā, and netreṇa means “under the guidance” or “being impelled.” So the meaning of this verse is that an ātmā enters into the womb being attached to the sperm of the man. It is not that the ātmā, which is inside the sperm, takes the human body, but a specific ātmā is attracted to the sperm cell, being impelled by Paramātmā. This ātmā may enter inside the womb even without the sperm, if Paramātmā so wills. There are many stories about kings who had no progeny and then performed a yajña or whose wives were given a specific fruit to eat and then became pregnant. In the 6th chapter of the Ninth Canto, we find such a story about King Yuvanāśva:
This king married one hundred wives, but he had no sons, and therefore he entered the forest. In the forest, the sages performed a sacrifice known as Indra-yajña on his behalf. Once, however, the king became so thirsty in the forest that he drank the water kept for performing yajña. Consequently, after some time, a son came forth from the right side of his abdomen (SB 9.6.25–30).
Another interesting story relates the birth of sage Jamadagni, the father of Paraśurāma:
There was a king named Kuśāmba, whose son Gādhi had a daughter named Satyavatī. Satyavatī was married to sage Ṛcīka. Once Satyavatī and her mother both requested Ṛcīka to bless them with a son. Ṛcīka took two pots of rice cooked in milk and empowered them with mantra. In one pot of sweet rice, he infused brāhmaṇa potency, and in the other, he infused kṣatriya potency, because he was a brāhmaṇa himself and wanted a son with brāhminical character for his wife Satyavatī. As her mother was a queen, he wanted a kṣatriya son to be born to her. Therefore, he made two separate pots for them. However, when Satyavatī brought the pot for her mother, the mother thought that the sage Ṛcīka favored his own wife and must have given a special pot of sweet rice to her. Therefore, she asked the daughter to exchange the pots. The daughter, being obedient to her mother and being ignorant of her husband’s intentions, gave her own pot to her mother and ate the sweet rice meant for her mother.
As an outcome, Satyavatī and her mother both became pregnant. As the pregnancy advanced, Ṛcīka Muni could sense that the face of Satyavatī carried the radiance of kṣatriya potency. Upon inquiry, she innocently told her husband that she exchanged the pot with her mother. Hearing this Ṛcīka was upset and said that a kṣatriya son would be born to her. Satyavatī did not like that and begged her husband for a solution Being thus implored, Ṛcīka said that she would have a brāhmaṇa son, but her grandson would be of kṣatriya character. By the grace of sage Ṛcīka, Jamadagni, who had brāhminical character, was born to her. However, his son Parasurāma had the nature of a kṣatriya. Satyavatī’s mother, on the other hand, gave birth to Viśvāmitra who did very severe penances and acquired the status of a brāhma-ṛṣi.
Another such incident is related in the Rāmāyaṇa with King Daśaratha:
As King Daśaratha was originally unable to have children, he reached out to the gods by performing an Aśvamedha, a horse sacrifice, and asked them to bestow a child upon him. King Daśaratha gained this magical substance that would ultimately lead to the birth of his sons.All three of his wives received portions of it. Instructed to divide the potion between his wives, King Daśaratha gave half to Kauśalyā due to her seniority, and the other half to Kaikeyīdue to his fondness for her. Unfortunately, this did not leave any for Sumitrā which caused Kauśalyā and Kaikeyī to each give her half of their portions. As Sumitrā technically received two servings, she bore two sons. Kauśalyā bore Rāma, Sumitrā bore twins, Lakṣmaṇa, and Śatrughna, and Kaikeyī bore Bharata.
Although Lord Rāma is Bhagavān Himself and does not depend on such technicalities, still the stories convey the point that it is not just the semen that carries the soul. Similarly, there are stories that kings would do yajña to get a child (putreṣṭi– yajña). One such example is King Drupada, who did such a yajña to get a son to kill Droṇācārya. As an outcome of this, Drṣṭadyumna and Draupadī were born from the fire of the yajña. Another example is Vṛtrāsura, who was Viśvāmitra’s son. He came out from the fire to kill Indra.
From the above stories, you should understand that a separate ātmā takes shelter of a specific sperm and then combines with the ovum to become a zygote.
Question: If all cells have souls, when a sperm and an egg cell combine, what happens to the soul in the egg cell? [As the body gets the soul from the sperm].
Answer: The soul of the sperm and the ovum remain together in the zygote. The presiding soul of the body also remains there, separate from these souls.
Question: Also, as the zygote divides to form the embryo and then the full body, by what program or mechanism do new souls get into the newly formed cells? Which of these daughter cells has the original soul (from the sperm)?
Answer: The new souls that come into the cells may come from the food eaten by the mother. None of the daughter cells have the original soul, which is separate.
Question: How does the master soul end up in the praṇavāyu area (near the heart), given that it was originally in a cell?
Answer: It was originally not in a cell, but outside, and it is already with praṇavāyu because every conditioned soul is attached to a subtle body, which contains the praṇavāyu. This is hinted at by Kṛṣṇa in Gītā 15.8–10. In fact, in 15.11, he also says that only yogīs can see this and not ordinary people.
Question: Since the souls in individual cells suffer or enjoy according to the karma of the main soul, are these souls karmically linked somehow?
Answer: Yes, they are linked and therefore they end up together in the body provided by the main ātmā.
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