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gwern comments on Study shows meditation may have potential to change the physical structure of the brain - Less Wrong
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You are using physical in a rather broad sense.
"Also, if
apt-get updateing my Debian system has any effect at all on a computer's functioning, presumably it must change the physical structure of the computer (that's the only way processing can change). So why would this news about a bug in X.org which makes the monitor explode be news?"Your analogy is not particularly apt, gwern, as the structure of the human brain doesn't have the characteristics which enable a reasonably sharp hardware/software distinction to be drawn in computers.