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not from nowhere, but from tissues
, the embryo is material, which means it consists of tissues – ectoderm, endoderm, mesoderm
from which the primary intestine first begins to develop, then the nerve tube, and the chord ( future spine).
there is also a mesenchyme inside, and organs begin to develop further ( skin, etc.)
First, a bunch of identical cells appear from the zygote. After some time, they start the mechanism of specialization (or differentiation, I don't remember the exact name) — in strictly defined parts of the embryo, the cells become different. Then they specialize further and further, and as they develop during this time, they gradually divide into departments. From these parts, different tissues are formed, from the tissues of the organs, from the organs of the system. This process is called the simple term “organogenesis”.
This is if it is straight VERY simplified. In fact, it is easy to Google for the query “human pregnancy” or “human embryo development in utero” (even “human ontogenesis”, but this applies not only to intrauterine development).