The reason the immune system can reject organs is because the way it recognises hostiles is by assuming that everything that isn’t itself is the enemy. It looks at certain molecules (called antigens) on the surface of cells, and if those molecules aren’t the molecules its expecting to see, it declares war.
The immune system doesn’t innately know what *not* to kill though – it has to be trained. This happens very early on in fetal development, but it happens *after* the chimera process normally occurs. When it happens, any antigen that’s currently part of the body gets put on the “treat this as self” list. If the body is a chimera, then every kind of antigen found gets put on that list. Every cell in your body (except the bacteria) is descended from a cell that was present when the immune cells were taught who you were, and so expresses the same antigens and is tolerated by the immune system.
Also, fun fact – all women are a little bit chimera-ish. As you may be aware, there are things called the X and Y chromosomes. In humans, men have one X and one Y in each cell, and men have two Xs. However, having two Xs actively being used at once causes problems, so during development (before the immune system is trained) every cell switches one of its Xs off at random, meaning that 50% of the cells express one X and 50% express the other. That’s passed on to all cells they create too. It’s not full blown chimera, but it’s not entirely dissimilar – half a women’s cells are expressing different genes to the other half, even when doing the same job.
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