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Now your point is correct - if we aim for a 1cent transaction fee, then a hodl output worth less than 1 cent is effectively worthless (with some caveats). I'm happy enough with that - I see the network as a place for 10cent+ transactions. I think other technologies and second layers are more suitable for sub-cent transactions.
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By my rough calculation, a block of 50 HOdlcoin is only worth about 6 or 7 cents. If you HOdl that block, you must pay between 14-17% at today's HOdl/BTC rates. I think that is overly steep at this stage and more than a bit destructive to the current ecosystem. It will effectively drive out any of today's small time miners. At some point, I do think it could be worth looking at a target fee such as you have proposed, but I do not think that day is today.
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Is it too soon for another change? No, I think either HODL is improving or its dying.
I believe that depends on your definition of improving. It seems to me that you are attempting to progress HOdlcoin which is not the same as improving it.
To continue with that thought, if I mine with a pool (let's use optiminer's as the example), and my payouts come in 50 HODL each payments, those are worth (at the moment) about 10 cents usd. Optiminer's pool sends the payment to me, and a 1 cent fee is incurred (which is destroyed). So that's 1/10th the value of the payment. I will assume the pool is not likely to be absorbing those costs out of the goodness of their hearts. So let's say they get passed on to the miners. Now my payment of 50 HODL has cost me 5 HODL on top of the pool fee (1%, or .5 HODL) I was already paying which effectively brings the pool fee to 11%. Who among us wouldn't die laughing if a pool advertised an 11% fee?
Now I HODL those 50 in the wallet, and another 10% is taken in transaction fees? So by the time I get paid for mining and get my nuts safely hodled away, I actually get a value of 39.5 HODL out of a block of 50. 21% in fees for every 50 HODL is straight out nuts. Not to mention the compounded loss when you start talking about interest lost on the coins that are taken up in fees.
So ok, yes, you can mitigate this some by pools upping the minimum payout amount so that the percentage of the total payment that is taken by the 1 cent fee is less, but then the pool is now holding on to my HODL that could be earning interest in my wallet. Meanwhile, in my wallet, I'm having to mimic the pool's payout scheme when I HODL by waiting until I have a substantial balance to HODL in order to minimize the impact the fee will have as a percentage of my HODL transaction. And the longer I wait, the more interest I lose out on. You also put massive pressure on HODL'ers to choose the longer term deposits, because doing short term deposits will cost more in transaction fees (re-hodling every say 30 days to keep your HODL somewhat liquid would cost you the transaction fee 12 times a year instead of 1 with a yr HODL). And voila, we're back to everyone having to HODL for a year, only now it's not a requirement, it's the only economically sensible thing to do.
If you really want to implement something like this now you need to write it to scale to the current value of a HODL, maybe updating the fee amount once a month (or week, or day, whatever is reasonable). And right now 1 cent per transaction is highway robbery.