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Can someone ELI5 why MBTA has to trust the balance stored on the card in the first place? It seems like this whole issue would go away if they just kept the balance on the server and flagged cards that did not corroborate.

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This is common in truth-on-card transit systems, many of which were conceived before internet connectivity at terminals was a thing. Often the cards needed to work on busses, etc. that didn’t have internet connectivity and couldn’t validate the balances. Even still there isn’t necessarily reliable internet in tunnels, etc.

Newer variants of similar cards are regarded as more secure, such as MiFare’s DESFire line which is used in the SF Bay Area (Clipper).

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