I’m sorry but this reads to me like it’s been written more to sound like it’s technical and sophisticated than to actually convey a substantive point of any real value.
A protein is the product of an encoded description; the position of the stars in the night sky are not. Neither are the locations of islands on the open sea. Neither are weather patterns and tornadoes.”
I’m reading it and it just raises the question: So what? What does that have to do with how protein coding genes evolve?
Try reading any of David Abel’s publications if you find yourself wanting more of that.
Taking a look at this thread, I am surprised at the definition of FI that everyone seems to be using. In a long thread at The Skeptical Zone last December (see here) gpuccio and numbers of other people debated whether there was any sound argument for gpuccio’s assertion that 500 bits of FI could not be produced by ordinary evolutionary forces such as natural selection. You could argue that if the definition of FI were that there is a function, and it exists only in a small subset of the sequences, one a fraction less than 10^(-150) of all sequences, then natural selection cannot reward changes that get close to, but not into, that set.
Actually it finally became clear in that discussion that gpuccio was not assuming that there was no function outside of the set. So I would have said that in such cases there were possible paths for natural selection and mutation to take to get into the set. But for such cases gpuccio was asserting that natural selection would just not be strong enough to do the job. I disagree with his reasoning for saying that, but I was at least happy to have that matter cleared up. However in this PS thread you all seem to be using the definition that function is zero outside of the target set.
The definition of FI used by Jack Szostak in 2003, and corrected a little by Hazen, Griffin, Carothers, and Szostak in 2007, is the one gpuccio said he was using. However that definition has FI be computed for each possible sequence: it is minus the log (to the base 2) of the fraction of all sequences that have a value of function greater than or equal to the value in that particular sequence. There is in that definition no assumption that function is only nonzero in one subset of the sequences, and that function is zero elsewhere. I do not know why gpuccio has changed his definition to have zero function in most sequences. You are all accepting this modified definition of FI. Maybe you should not.
A very important point, because obviously if a single mutation in a larger non-coding sequence acts to change the sequence to recruit a transcription factor and produce a translatable open reading frame with a biological function, then pretty much the entire sequence existed before the mutation that made it functional.
And that sequence in turn has evolved approximately neutrally, potentially for millions of generations until the mutation that made it functional occurred. That means the sequence didn’t just pop into existence as if a tornado in a junkyard, rather it also evolved iteratively by mutations. It could even have been drifting from some previous functional gene, like an ancient transposon or another type of pseudogene. That means the “initial condition” in that lead to the origination of this de novo gene isn’t random either, and itself was largely the product of natural selection.
At what point does ANYTHING happen at the genetic level that could really be accurately compared to the tornado in a junkyard? It seems to me there’s never any such thing occurring.
Well I agree with you their @Joe_Felsenstein. There is no reason to think 500 bits of FI is inaccessible, and have said it several times.
Have you ever considered the chance that vibrating air molecules would assemble a tornado. The probability is really small. Yet it happens often.
Should we conclude the tornados are intelligently designed? Why aren’t the ID proponents pointing to tornados as examples of intelligent design?
Or maybe when you have an energy flow, and a homeostatic process is part of that energy flow, what appear to be highly improbable arrangements can occur more often than we would otherwise expect.
I’m not sure how many non-creationists are accepting this definition, except to the extent that they are doing so provisionally with the idea of providing @gpuccio the rope he needs to hang himself.
Last comment I’m posting from UD. Maybe Upright Biped will join the conversation here.
478
[Upright BiPed]
Faizal Ali,
“The problem is the inclusion of the latter under the category “semantic” information is the point in question. The large majority of experts who do not accept the creationist argument also do not accept the creationist claim that the physical and chemical interactions of the molecules involved in biological processes are directly analogous to sort of semantic information involved in, say, a written novel or a computer program.”
No, sorry, it is not in question. The physics of symbol systems remain the same regardless of the medium, or its origin, and your attempt to dismiss the issue as a “creationist claim” displays an embarrassing lack of knowledge regarding the recorded history of the issue. You are likely unaware of this because you have not educated yourself on the literature. Additionally, empirical science is not established by consensus; it is established by what can be demonstrated and repeated. I would think you might have been aware of this, but I could be mistaken. In any case, if you find someone who as shown that the genetic material is not rate-independent, or that the process is not irreversible, or that no distinctions need be made between laws and initial conditions, or perhaps if you find someone who has solved the measurement problem, or any of the other physical observations recorded in the physics literature regarding symbol systems over the past half century, then be bure to let us know.
Until then, I plan to stick with the science. You are free to continue otherwise.
Ahh yes thanks for bringing that up. I now recall that one of Gpuccio’s arguments in response to various criticisms, was that, if the protein in question had evolved from some other functional protein, then it simply doesn’t exhibit 500bits of FI.
So we pointed out that then his case rests on this idea that there’s some protein that is an isolated target in sequence space, and we asked him to show that such a sequence exists. He then insisted on reverting the burden of proof and claimed it’s our job to show that protein X could have evolved from protein Y, and until we do that we should automatically assume the function is isolated and that evolution is impossible until proven otherwise.
I’m sorry, but it is in question. And so is it’s relevance to evolution.
You are likely unaware of this because you have not educated yourself on the literature. Additionally, empirical science is not established by consensus; it is established by what can be demonstrated and repeated. I would think you might have been aware of this, but I could be mistaken. In any case, if you find someone who as shown that the genetic material is not rate-independent, or that the process is not irreversible, or that no distinctions need be made between laws and initial conditions, or perhaps if you find someone who has solved the measurement problem, or any of the other physical observations recorded in the physics literature regarding symbol systems over the past half century, then be bure to let us know.
Until then, I plan to stick with the science. You are free to continue otherwise.
This wall of substance-less but technical-sounding fog left me still wondering what it has to do with evolution or the evolution of protein coding genes.
I think we are letting @gpuccio lead us through this, warts and all. There are (at least) four different forms of FI we have come across, and it is not clear what the rules are for switching between these.
This is, I believe, the definition that the biologists here will resort to, as the discussion proceeds. Certainly, this is the usage we have used often (while perhaps not in so many words) in other threads on PS.
Thanks for dropping in and for the pointer…
@Upright_BiPed is already here 
.
Consider the source. What more do you expect?
Maybe he will actually respond here instead of UD.
I would be very interested in seeing your explanation. Don’t be coy.
I have the same question about foxes. As I recall nearly every species has a unique chromosome count, and outside of Arctic-Red fox hybrids, I believe all the species are reproductively isolated. And there appears to be the same reproductive barrier between foxes and Canids. Is this ID and if so is it at class or species level or both?
The reason I think this would be a good test case is because it is a less loaded question and it involves specimens easily relatable to the lay person. (If I had the money, i’d probably fund this ‘pet’ project.)
And maybe not. If he was going to, why hasn’t he?
We had another loooong discussion about the 500-bits-rule on theskepticalzone in this thread with almost 2000 comments: Does gpuccio’s argument that 500 bits of Functional Information implies Design work? | The Skeptical Zone
Excellent. What journal? That at least should be no secret.
Likewise, any thermodynamic system will have the same sort of complexity.
I anticipate the claim that a thunderstorm has no function.
How about navigation? (@swamidass was headed that way already)
It was a long setup, but we finally got there. 