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The only feasible way I can come up with to protect the blockchain against transaction flooding, is to make such attacks economically unfeasible.
This means higher transaction costs on the blockchain. Moving the bulk of the transactions on the Lightning network and only clearing large numbers of them on the blockchain at once.
This moves the attack surface to the Lightning network. Correct me of I am wrong but an attack on the Lightning network would only affect a particular payment channel not the network as a whole.
What do you think?