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Arndst studied medicine and zoology at the University of Breslau. Even as a student, several companies invited him to take part in various expeditions. In this way, Arndt ended up exploring the Hohe Tauern, Corsica, and Norway.
In 1920 Arndt was appointed as a volunteer of the Zoological Institute at the University of Breslau. There he published his first research findings.
In 1921 Arndt changed jobs and became an assistant at the Zoological Institute in Berlin. In 1923 he was instrumental in the large-scale hydrochemical study of the North Sea. He became curator in 1925, and an "ordinary professor" (ordentlicher Professor) in 1931, when he converted to Judaism. From 1926 Arndt was an editor of Fauna Arctica. In 1938 he was appointed to the International Zoological Nomenclature Commission.
Having made some criticisms of the Nazi régime, including the statement "This is the end of the Third Reich, and the guilty can now be brought to punishment", Arndt was denounced in 1944 and sentenced to death on 11 May. Despite many appeals for clemency from academic quarters, Arndt was executed on 26 June 1944 at Zuchthaus Brandenburg-Görden. He was 53 years old.
He was the author of nearly 250 scientific publications on systematics, anatomy, the distribution of sponges, helminthology, oceanic fauna, museology, animal toxins, et al. With August Brauer, Fritz Römer and Fritz Schaudinn, he was an editor of "Fauna arctica : eine Zusammenstellung der arktischen Tierformen mit besonderer Berücksichtigung des Spitzbergen-Gebietes auf Grund der Ergebnisse der Deutschen Expedition in das Nördliche Eismeer im Jahre 1898".
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