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In order for changes to the Bitcoin protocol to be made, 95% consensus must be achieved, otherwise a hard fork would need to occur? Is this the primary reason why changes to the core protocol are so difficult to make?

With regards to consensus mechanism, moving aside whether PoW/PoS/Other is the proper solution, since the vast majority of voting belongs to large mining pools why would they ever vote for PoS or another non-mining solution? It seems even if a superior consensus mechanism exists it is highly doubtful BTC would ever deviate without a hard fork?

I've seen charts online breaking down the mining pool ownership percentage of BTC. I also know some pools have committed to cap their hash power and operations so as not to gain 51%. However, is it possible that a 51% attack could already be occurring and we have no idea? How do we know the mining operations aren't in collusion already and have not already been double spending, etc? If fraudulent activity occurs would we actually ever know?

Thanks!

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In order for changes to the Bitcoin protocol to be made, 95% consensus must be achieved, otherwise a hard fork would need to occur? Is this the primary reason why changes to the core protocol are so difficult to make?

No. Changes are made regularly and you can subscribe to https://bitcoinops.org/en/newsletters/ for updates. Hard forks are not preferred to avoid chain split and other issues but can be used if it's really necessary. Some soft forks are contentious so consensus is a problem which can be solved each time with different solutions. BIP 9 was used for segwit so miners, voting and drama was involved: https://github.com/bitcoin/bips/blob/master/bip-0009.mediawiki

Taproot activation and consensus related discussion: https://www.reddit.com/r/Bitcoin/comments/hqzp14/technical_the_path_to_taproot_activation/

I've seen charts online breaking down the mining pool ownership percentage of BTC

I dont see anything wrong with this mining pool distriibution: https://i.ibb.co/pwxjvtc/image.png

However, is it possible that a 51% attack could already be occurring and we have no idea? How do we know the mining operations aren't in collusion already and have not already been double spending, etc? If fraudulent activity occurs would we actually ever know?

As Raghav mentioned there are lot of users keeping an eye on network activity. You should run your own full node and wait for more confirmations to finalize transactions if you think there is a possibility of miners trying to reorder history. Please refer to Greg Maxwell's thoughts on 51% attacks: https://www.reddit.com/r/Bitcoin/comments/ddddfl/question_on_the_vulnerability_of_bitcoin/f2g9e7b/

And also read about game theory involved in 51% attacks or any attacks on Bitcoin network:

Few things and one case mentioned by Jimmy Song - https://medium.com/@jimmysong/reorg-scenarios-binance-hack-edition-849fc7e7df07

Stratum V2: https://braiins.com/news/stratum-v2-bitcoin-decentralization

Jameson Lopp's thoughts about mining and decentralization: https://blog.lopp.net/are-chinese-miners-threat-bitcoin/

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In order for changes to the Bitcoin protocol to be made, 95% consensus must be achieved, otherwise a hard fork would need to occur? Is this the primary reason why changes to the core protocol are so difficult to make?

Not really - most recent changes have been made by using miner activated forks, which requires miners to vote on proposed changes. Only once a certain threshold is hit (which is very much configurable, and not fixed to something like 95%), the changes are activated.

That said, it is entirely possible to create upgrades without such voting - many other blockchains do it all the time. It's simply a matter of the community agreeing that those changes are valid and not an attempt at an attack.

Even with 95% of miner support, if the broader community feels that recent changes are not in their best interests (such as the somewhat contentious segwit changes), they may choose to fork the chain at a point before the changes (as done by Bitcoin Cash).

You may find the answers to How is Bitcoin governed by mathematics? to be of interest here. Consensus is very different from governance, and one does not imply the other.

With regards to consensus mechanism, moving aside whether PoW/PoS/Other is the proper solution, since the vast majority of voting belongs to large mining pools why would they ever vote for PoS or another non-mining solution? It seems even if a superior consensus mechanism exists it is highly doubtful BTC would ever deviate without a hard fork?

Personally, I'd agree with that - any attempt to reduce the power of miners may result in them attempting to protect it.

However, at the end of the day, if the broader community moves to a different fork, the value will follow it. Any miners left on the other chain will be subject to vastly reduced economic incentives (BCH vs BTC price and adoption being a good example).

However, is it possible that a 51% attack could already be occurring and we have no idea?

One could potentially be happening right now, and our ability to detect it would be limited.

How do we know the mining operations aren't in collusion already and have not already been double spending, etc? If fraudulent activity occurs would we actually ever know?

There are many research groups, exchanges, coin tracking firms, and other entities actively tracking such things - it is fairly easy to detect a double spend after the fact, especially if you were on the receiving side.

Additionally, a double spend attack on BTC would be very detrimental to the BTC price, which is not something most miners would be able to absorb. It is in their best interests to secure the chain, not attack it.

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