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gwern comments on The lymphatic system is found to connect to the Central Nervous System - Less Wrong Discussion
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Fulltext: https://www.dropbox.com/s/2mmdmty3nxfe5u8/2015-louveau.pdf / http://sci-hub.org/downloads/e18c/louveau2015.pdf
It's worth remembering the functions of the lymphatic system, and that important discoveries tend to be made first.
After reading the paper, NeuroscientistNews, HN & Reddit comments, it sounds as if for the most part the new tube wouldn't be directly affecting the brain as the flow is brain->lymph-tube, unless something has gone wrong, possibly being a new cause of various mental disorders as the flow reverses and causes problems.
So it sounds as if an upload which ignored the new tube would work just fine as a normal healthy human mind - in the worst (best?) case, the uploads might not be able to reproduce observed rates of schizophrenia or autism.