Minkowski refers to Hermann Minkowski, the early twentieth century German mathematician-physicist who described time as a fourth dimension. Supported by "The Constant".
Minkowski Spacetime is the most common frame of reference for spacetime, with three physical dimensions and a single time dimension, and it is used in general relativity. Closed timelike curves (CTCs) existing in Minkowski space explain many of the mysterious features of the island, why it can't be found or seen, etc. CTCs were linked to the Lost universe through clues from the ARG Find 815.
This connection is posited as evidence by the proponent of the HEMA theory.
With the appearance of the character of Daniel Faraday, and The Maxwell Group all named after famous scientists, this could hint that the mysterious faction to which Minkowski belongs are more like scientists than the philosophers who currently inhabit the Island.
Minkowski is named after phenomenological philosopher and psychiatrist Eugène Minkowski, who studied the "subjectivity of the lived time", and was described as having made "the first serious attempt in psychiatry to reconstruct the other person's lived experience."