I have been taking on new mitzvot throughout the past years. I have begun wearing tzitzit regularly and have been working at becoming stricter concerning Shabbat. These activities have come from my understanding of the commandments in the Torah and how Jewish tradition has interpreted said commandments.
I am at a loss, however, for the tradition of wearing a kipah. It seems an entirely human invention. I feel that I have a drive to want to wear the kipah more regularly and even when I leave the house. Unfortunately, I find that the drive to wear it is only to be like others, not to be more in touch with my Jewish tradition and God's law. I feel awkward when I wear a kipah because I feel that I am observing a custom simply to fit in. That said, I also feel awkward about praying without one because I wonder if there is something to the tradition that I might be missing. I am looking for a historical perspective. Is there anything originating from Torah in this tradition, or is it something simply cultural, like the wearing of ties at formal occasions?
You are correct that none of the 613 biblical commandments state that a Jew must wear a kipah. But the logic that flows from your premise requires some fine-tuning.
According to biblical and rabbinic thought, the Torah has been given to humanity. It calls for human interpretation to apply it properly. Were a Jew to fulfill the words of the Bible literally, ignoring subsequent rabbinic interpretation, he or she would be misapplying the Bible, since the Bible itself authorizes the leaders of each generation to interpret it for the use of each new age. We no longer sacrifice goats, we no longer own slaves. By the Torah's own mandate, the sages of each generation are charged with mediating the Torah and life.
From antiquity, Jews covered their heads as a sign of piety and humility. Headcovering reminds us that we are always in God's presence. It marks us as distinct, reminding us that the repair of the world is God's business, our business.
Already by the time of the Talmud, Jewish law required a Jew to wear a headcovering during meals, study, and prayer. Please note that rabbinic law is not mere custom, it is how God speaks to Jews through Judaism. Rabbinic law has the force of divine commandment (like lighting the Chanukah lights and praising God for giving us that commandment even though it is not in the Torah).
By the way, it isn't necessarily bad to want to be like others. The Mishnah commands us not to separate ourselves from the community, and a healthy respect for the opinions of our fellow human beings is a positive virtue to cultivate. That religious Jews wear headcoverings is a pretty good reason to do the same.
So, to summarize: it is a mitzvah to wear a kipah while studying, praying and eating. Wearing it all the time is more than Jewish law requires but is a laudable custom, since it serves to remind the wearer and those around that there is a God who rules the world and that we are commanded to serve God by repairing that world and by loving each other.
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