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Proteins are the machinery of living tissue that builds the structures and carries out the chemical reactions necessary for life.
We can look high or we can look low in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system.
Irreducible complexity is a problem for Darwinian evolution. Whenever we see these complex functional systems we realise that they have to be designed.
As the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows.
Biology has progressed tremendously due to the model that Darwin put forth. But the black boxes Darwin accepted are now being opened, and our view of the world is again being shaken.
Many people, including many important and well-respected scientists, just don't want there to be anything beyond nature. They don't want a supernatural being to affect nature.
Throughout history there have been many other examples, similar to that of Haeckel, Huxley and the cell, where a key piece of a particular scientific puzzle was beyond the understanding of the age.