Some theologians have believed that souls are newly created within a developing baby, while some believe that souls were created before time and are added to babies while the body develops.
There is considerable debate about the timing of ensoulment during fetal development, with some claiming the moment of conception, some the moment of implantation, some the formation of the heart, some the formation of the nervous system and brain, the first brain activity, the ability of the fetus to survive independently of the uterus (viability), and still others the time of quickening. Others place the time of ensoulment at the moment of birth (post-fetal). The presence or absence of a soul is factored into considerations of the moral nature of abortion, particularly whether it is or is not morally equivalent to infanticide and murder, and to discussion of the souls of clones and identical twins, which necessarily separate after conception.
In the Roman Catholic Church since the Middle Ages, ecclesiastical penalties for abortion have differed based on varying views of ensoulment. St. Augustine made a distinction between a fetus with a rational soul (fetus animatus) and one without (fetus inanimatus), and said that a human soul cannot exist in an animal or unformed body. Writing about Exodus 21 (c. 415), he said:
"The law does not provide that the act [of abortion] pertains to homicide, for there cannot be said to be a live soul in a body that lacks sensation, if it is not yet formed in flesh and so not yet endowed with senses."
This stood as the Christian position for over 1000 years, being incorporated into the Decretum Gratiani. Around 1211, Innocent III, when asked if a monk was guilty of murder for helping his lover get an abortion, stated that the soul enters the body of the fetus at the time of quickening (when the mother first felt movement of the fetus), and that abortion before quickening was not murder. St. Thomas Aquinas, Doctor of the Church, wrote in the 1200s that a developing human embryo has first a vegetative and then a sensitive, or animal soul, before dissolving and being replaced by an intellective, or human soul:
"Therefore it must be said that the intellective soul is created by God at the completion of man's coming-into-being. This soul is at one and the same time both a sensitive and nutritive life-principle, the preceding forms having been dissolved
The 1311 Council of Vienne officially confirmed the view of Thomas Aquinas.
In 1588, Pope Sixtus V issued the first Papal Bull (Effraenatam) which subjected those that carried out abortions at any stage of gestation with excommunication and punishment by civil authorities. In 1591, Gregory XIV modified the law so that the penalty did not apply until the fetus became animated.
In 1679, Pope Innocent XI publicly condemned sixty-five propositions as "at least scandalous and in practice dangerous", including:
34. It is lawful to procure abortion before ensoulment of the fetus lest a girl, detected as pregnant, be killed or defamed.
35. It seems probable that the fetus (as long as it is in the uterus) lacks a rational soul and begins to first have one when it is born; and consequently it must be said that no abortion is homicide.
In 1869, Pius IX rescinded Gregory's animated fetus exception in the Bull Apostolicae Sedis, and re-enacted the penalty of excommunication for abortions at any stage of pregnancy. The distinction between animated and unanimated fetus remained in canon law until the second codification in 1917.
According to the Catholic Encyclopedia:
The early Christians are the first on record as having pronounced abortion to be the murder of human beings, for their public apologists, Athenagoras, Tertullian, and Minutius Felix (Eschbach, "Disp. Phys.", Disp. iii), to refute the slander that a child was slain, and its flesh eaten, by the guests at the Agapae, appealed to their laws as forbidding all manner of murder, even that of children in the womb. The Fathers of the Church unanimously maintained the same doctrine. In the fourth century the Council of Eliberis decreed that Holy Communion should be refused all the rest of her life, even on her deathbed, to an adulteress who had procured the abortion of her child. The Sixth Ecumenical Council determined for the whole Church that anyone who procured abortion should bear all the punishments inflicted on murderers. In all these teachings and enactments no distinction is made between the earlier and the later stages of gestation. For, though the opinion of Aristotle, or similar speculations, regarding the time when the rational soul is infused into the embryo, were practically accepted for many centuries still it was always held by the Church that he who destroyed what was to be a man was guilty of destroying a human life.
"And if men strive together, and hurt a pregnant woman, so that her fruit [children] come out, and yet no harm follows; the one who hit her shall surely be fined, according as the woman’s husband shall impose upon him; and he shall pay a fine as the judges determine. Nevertheless, if any harm follows, then you shall pay life for life, eye for eye, tooth for tooth . . . "(Exodus 21:22-23)
This fine can be compared to the death penalty described in nearby verses like Exodus 21:12, 15, and 17 for other offenses.
"Before I formed You in the womb I knew You, And before You were born I consecrated You; I have appointed You a prophet to the nations." (Jeremiah 1:5)
"For he will be great in the sight of the Lord, and he will drink no wine or liquor; and he will be filled with the Holy Spirit, while yet in his mother's womb." (Luke 1:15)
"But when He who had set me apart, even from my mother's womb, and called me through His grace..." (Galatians 1:15)
These verses??? do not describe ensoulment or a similar act occurring in utero. Rather, they describe a special act of anointing or setting apart, which does not take place for regular people not specially identified and set apart by God. This leaves open the possibility that ensoulment may already have taken place prior to the special anointing described in these verses.
In Psalm 139 of the Bible, the psalmist describes God as purposefully forming him as an embryo in his mother's womb:
"You wove me in the womb of my mother, I will thank You, for with fearful [things] I am wonderful; Your works are marvelous, and my soul knows [it] very well. My bones were not hidden from You when I was made in secret; when I was woven in the depths of the earth. Your eyes saw my embryo; and in Your book all [my members] were written; the days they were formed, and none [was] among them.This verse is often cited as supporting the concept of the embryo being fully human once conceived.
Also at issue is the Bible's usage of the phrase breath of life. Some who support the right to abortion hold that this means that life begins with the first breath. They point to the use of this phrase with reference to Adam:
"Then the Lord God formed man of dust from the ground, and breathed into his nostrils the breath of life; and man became a living being" (Genesis 2:7).
Clearly, it holds that Adam had no living existence until that first breath. However, there is no Biblical indication whether this same process applies to newborns created in utero, especially if "breath" is considered to include the oxygenated blood which the mother supplies through the umbilical cord.
The early Church father, Tertullian (160–220 CE), wrote: "Now we allow that life begins with conception because we contend that the soul also begins from conception; life taking its commencement at the same moment and place that the soul does" ([A Treatise on the Soul, chapter XXVII]http://www.ccel.org/ccel/schaff/anf03.iv.xi.xxvii.html).