Not yet but you should remain hopeful 
I give up. I spent a chunk of my time trying to push this back towards useful discussion, and no one listens. The timer is back on.
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If it arises and goes away what’s the point?
No, not interested in putting the work in for that. I think it is evident to everyone who understands the discussion. And it does not seem possible to word it simply enough for @colewd or @Giltil to understand. Professional workers in the field don’t seem able to, I have no reason to believe I would do any better.
If it arises, then your claim that it cannot arise is false.
Dan is trying to help here. I am putting you on notice that you are not holding yourself to the same standards you are asking other people.
The useful part has already happened. The part where the creationists realize they were wrong all along hasn’t happened, but don’t feel that was your fault. Thanks for trying.
Dude you are confused. I never made this claim… We’re done.
Ah, OK. Bill believes novel functional proteins of enormous complexity can arise thru unguided evolutionary processes. He just admitted it. For some reason, we all thought he was saying otherwise. Boy, do I ever feel stupid now.
I didn’t say it would be easy!
You wrote this was discussion was important. Is it important enough to be be worth turning it into something useful?
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I don’t recall asking anyone to write a summary of this entire 350 post discussion, but my memory is not what is used to be. Maybe you could be a dear and cite where I did that.
Say, didn’t I ask you a math question just above? Did you ever answer it? I’m sure you don’t want anyone to think you’re avoiding questions.
It is useful. We don’t need the creationists to understand it for it to be useful. Thankfully, because that will never happen.
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So your direction is complexity. But in fact, evolution doesn’t have an overall direction, it just has circumstantial responses to local conditions. Some lineages have become more complex, many others have not. And there are reasons for why it does what it does.
The fact that some lineages become simpler isn’t “wrong” evolution. Evolution is not a theory that says complexity must always increase under all circumstances. Complexity either increases by chance if it does not have a fitness cost, or it increases if it is beneficial. But there is no reason to think complexity increase must always be beneficial, and that it is “wrong” evolution if it is not beneficial.
When and where it is beneficial depends on environment. There’s a perfectly good explanation for why the LTEE favors simplicity over complexity. Many of the adaptations E coli carry are towards surviving in the human and mammalian gut. New types of food are added, temperatures change, some times other species of bacteria are present, there are novel diseases etc. etc.
Some of those adaptations have no use in the synthetic flask environment, where the primary selective pressure is replication speed due to direct competition for a limited resource. That’s pretty much it. Carrying extra genes around to break down proteins or carbohydrates they never see in Lenski’s flasks costs energy to maintain and replicate every new generation, but since they’re not needed, and it just takes time to copy them every cell division, they can be discarded. That’s not wrong evolution, that’s expected and sensible evolution.
If there was often new challenges introduced to that environment, if things were not held constant, if new possible food sources were occasionally added, or new predators and diseases introduced, there would be the potential for adding new adaptations to face them. But there isn’t.
I love this!
Regarding gpuccio’s method, I haven’t yet seen any good argument that falsify it. On the contrary, I have noticed that several people here showed that they didn’t understand his reasoning. For exemple, they didn’t grasp that the prerequisite for calculating the FI of a given protein is that said protein must have been around through deep time (For example, see @Rumraket’s comment at 265).
But this is ludicrous, because then what use is it to ask for a demonstration of evolution producing high amounts of FI if we need to wait for multiple geological periods before we can estimate the FI for the protein?
Also, what the flying fork does how conserved the protein is going to be over this period of time, have to do with whether it is likely to evolve?
I point of distinction here: They can understand without necessarily accepting. THAT IS USEFUL.
It’s hard to get there, but that’s the sort of thing we would like to achieve.
And relevantly, what does FI really tell us here?
The question is if new complex proteins can evolve. Could a 132 amino acid protein with a useful function evolve? Yes, it could. Bsc4 evolved.
How conserved this protein is going to be over the next 200 million years is relevant to what? Why should that matter? Either the function can evolve or it can not. Whether it subsequently changes a lot is meaningless and irrelevant. Completely and utterly meaningless. The function evolved, it’s useful, it participates in DNA repair.
If in 200 million years an alignment of all homologous proteins of Bsc4 show them to be only 5% conserved, what the heck does it matter? Why?
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The math was simple and I thought you would be able to answer it yourself. You resorted to a logical fallacy in the end which is either an issue of misunderstanding of the discussion or honesty. I will give you credit that you misunderstood the argument. I gave you a private forum to work it through the offer is still open.
Do you realize this is a very tentative conclusion according to your paper?. There are other possibilities.
All conclusions in science are tentative. It is always strictly possible for future observations to overturn previous ones, so this excuse of yours is bad.
There are other possibilities.
All of which, given the evidence we have, are much more remote. You can’t just dismiss good data you don’t like with “it’s tentative”, even if you stick the word “very” before tentative.