You’d have to assess that by experimentally assessing each functional domain. Which is work you and Gpuccio haven’t done. So you have no justification for the number of sequences you’re plugging into the equation as the number of sequences that meet the minimal threshold for function.
By transposition, that’s what transposons do.
What about the sequences without “homology”.
Yeah what about them, do you know the number of sequences that meet the minimum threshold for function for those? Nope, not in this case either.
It’s critical to the point he is making. He is saying preservation is not an indicator or rarity in sequence space. To show this he needs to use a highly preserved protein as an example.
This question is difficult to answer because the phrase “significantly complex new protein” is ridiculously vague. Nevertheless, there are a multitude of examples of proteins (and other functional elements) either entirely or partially derived from transposon sequences. I submit for your edification, the RAG1 and RAG2 proteins (of V-D-J recombination fame), which are both derived from a DNA transposon.
To be honest, @colewd, your comment doesn’t make any sense to me. Even a highly-conserved protein is a representative of but one of what we can expect (based on many studies, including those explained to you over and over here) to be hundreds of orders of magnitudes of other sequence families that perform the same biochemical function. A sequence alignment isn’t going to tell us anything about all of these other sequence families, nor will it tell us much about the numbers of related functional sequences.
This is certainly true for many proteins. The evolutionists smoke and mirrors game is to show a single protein and say that is representative of all proteins. Some proteins are preserved some are not.
Preservation absolutely points to a lack of substitutability in the specified function. How much is open for debate and will be seeing differently depending what paradigm you are accessing the data with.
This is circular reasoning. You first need to establish there are other sequence families and this is true in all cases. Prp8 is highly preserved over hundreds of millions of years and there is no defined ladder for it to climb as it is part of a large protein complex.
I think you have actually helped Gpuccio’s case and we will see if there is correlation between preservation and sequence flexibility.
@colewd, it’s been shown for enough protein functions to take as a general rule. The onus is on you (and @gpuccio) to demonstrate, experimentally (and not by special pleading) that PRP8 is unusual in this respect. In so doing, you must keep in mind that the high degree of conservation you are claiming breaks down when we look at the functional modules in PRP8.
So, show us some wet-bench experimental measurements that prove your case. That would be a welcome addition to this discussion.
Comparing a 300AA protein with a 2000AA protein is comparing apples and oranges. You have the burden to demonstrate that the causal process can do the job. The longer the sequence and the higher the preservation data the less likely it is to work. Mind does not have the limitation your mechanism or causal process does.
No, real experimental results show us just the opposite, at least when it comes to protein length. There is no strict or even approximate length dependence when it comes to the frequency of function in sequence space.
Of course, the very protein Bill is so obsessed about, Prp8, is another example of a transposon derived fusion protein. The problem is Bill doesn’t accept inferences about past events when it comes to evolution. He wants to observe it in real time, otherwise it doesn’t count. Except when he can use those inferences in some weirdly conceived argument against evolution. Then he will immediately switch around on a dime and accept inferences about past events based on phylogenetic studies when he argues that Prp8 is very conserved in vertebrates.
No it’s not. FI = -log2(total functional sequences/all sequences).
I repeat - TOTAL function sequences. When you pick out one consensus, you deliberately arrive at a value that we all know, BY DEFINITION, is false, because you are deliberately throwing out all but the consensus.
This is coming from a guy promoting that very thing. A just-so story based on an inference from some weird calculation of a bitscore extrapolated from the level of preservation seen in a domain fusion protein. Back in ancient geological epochs, floating minds came to the Earth and wished the prp8 protein into existence, with multiple transposon-derived RNA binding and editing domains.
Actually, Axe, Behe, and @Agauger have implied that scientists have this same mysterious telekinetic ability, to magically create sequences or replace (transmute) extant sequences just by studying them.