One theory to explain how alcohol does its damage to the fetus involves hypoxia, or lack of oxygen.

According to the National Institute on Alcohol Abuse and Alcoholism, hypoxia has been called the most common cause of all cell death. In the fetus, hypoxia may play an important role in alcohol teratogenesis (disruption of growth process). Alcohol constricts the blood vessels of the placenta and umbilical cord in humans which will produce profound effects on blood flow. Alcohol can also suppress fetal "breathing" movements.

Certain brain areas such as the hippocampus (plays a role in memory) may be more vulnerable to hypoxia since they are very vascularized and have a high concentration of neurons. A leading FAS researcher, Ernest Abel, has shown that some of the neurons grow too fast and some grow too slow and some do not migrate to the right place in the brain. Some lose direction as to what kind of neural cell they are to become. Most of the effect occurs during the cell's latent or planning period in between growth spurts. It is for this reason that no amount of behavior modification is going to change the behavior of the FAS individual.

Another important finding is that nutritional factors can contribute to alcohol's teratogenic effects. The ability of the placenta to transfer nutrients to the developing fetus can be compromised when the mother is abusing alcohol, even if the mother is adequately nourished herself. Also, by virtue of the fact that the mother is an alcoholic or abusing alcohol, she is most likely undernourished, which in turn leaves her with sub-optimal levels of essential nutrients to transfer to the fetus.

Another, more simplified explanation, is that when a pregnant woman consumes an alcoholic beverage, her blood alcohol content reaches an equilibrium with the fetal blood level since alcohol crosses the placenta freely and enters the embryo or fetus through the umbilical cord.

It takes longer for the alcohol to clear from the fetus than from the mother, however, and the concentration remains high in the placenta long after it has cleared from the mother. This fetal alcohol concentration will adversely affect developing tissues, organs and neural structures.

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