There was a recently published academic paper "Bitcoin’s limited adoption problem" which used a statistic that the network latency is around 15 seconds.

Obviously, this is not true: One can provide a quick argument with Poisson distributions and Jensen's inequality that this means we should be seeing over 1000 stale blocks per year with probability near 1.

I'd like to refute this claim empirically, but have no good source for claiming that the number of stale blocks is small. I can only see the blocks that hit my node and go stale, but I'm assuming that not every stale blocks makes it to my node. Any better sources of data?

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The average block propagation time actually used to be more than 15 seconds before 2016, see the "Block Propagation Delay History" Graph at the KIT statistics website.

However, block latency was reduced drastically with the implementation of BIP152 (compact blocks) and, according to above source, is currently close to ~1 second for 90% network penetration.

As a result of this, stale blocks are much rarer, especially considering that nodes run by miners are likely to be well-connected to the network and would hear about new blocks faster than the average node. I don't know of a comprehensive collection of stale blocks though - see this stackoverflow answer by G. Maxwell why it would be hard to assemble this kind of data.

If that was an important part of their model, this paper may have analyzed a theoretical/historical version of bitcoin that has little resemblance with reality.

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