And some crosses with blind cave fish also lead to sight even though it’s partial.
There is no reason this cannot happen in nature. Blind cave fish are capable of breeding with sighted variants of the species as well as other populations of blind cave fish.
They genes related to sight which were not effected by the mutation that caused blindness helped in regaining sight. You are clutching at straws here.
Sorry about that … would causal role be better?
Yes… why not? It’s not as if the definition of function you support is not arbitrary.
In late February, I gave a talk about this question to an online ID research seminar (private group), which is relevant to this thread. Right now, there is no one in the Discovery Institute offices in Seattle – well, no one who cares to answer my email help requests, anyway – but later today, I should be able to get a staffer up there to post the pdf version of my talk. I’ll then post the link here.
I am afraid you didn’t understand the abstract correctly. The meaning it conveys is that if the functional portion of the genome exceeded 25%, then you would have to postulate an IMPOSSIBLE fertility rate for the human population to maintain a constant size from generation to generation. IOW, according to Graur’s analysis, above 25% for the functional fraction of the genome, you will go toward extinction rather than evolution. Hence Graur’s famous statement that « if ENCODE is right, then evolution is wrong ». Please see table 1 of the paper to see the magnitude of the problem.
If that were the case, then it would be consistent with Graur’s definition of function.
Hmm. Now this is where I have to make sure I’m understanding the whole idea of “function” correctly. If the sequences in question result in the formation of a physical structure of the organism (eyes), should they not be considered “functional” even if they do not perform the “function” that we usually associate those structures with (seeing). That is to say, would there not still be mutations that could occur in these sequences that are subject to positive or negative selection. (e.g. if the eyes became enlarged so it made it more difficult for the fish to swim)?
If >25% of the genome is functional then, according to Graur’s analysis, the human species could not have avoided extinction without having produced an unreasonable number of offspring per couple. That is correct, but irrelevant.
As has already been explained, this does not require that evolution is true. It would remain the case if the human species was just one of a number of “kinds” that had been magically created by a god.
No… Graur’s definition is dependent on actual evolutionary history. It has nothing much to do with causal roles except to the extent that some specific functions bare selected for or against.
Though it’s true that Friars definition of function would be a subset of all the genes which play some causal role in an organism.
It doesn’t matter what physical structures genes form in Graur’s definition. The only thing that matters is whether it is selected for/effects reproductive fitness For example if change in the shape of an elephants trunk does not change its reproductive fitness, then the genes responsible for that shape are not functional .same for Genes that determine the shape of your nose, or the color your eyes etc.
This seems to be demonstrating confusion associated with ambiguity of the term “sequence”. The sequences in question are presumably related to development of the brain. As such, if we stick with Graur’s defintion, there are almost certainly mutations in these sequences that will be deleterious. e.g. that would lead to the related structures of the brain being highly underdeveloped, or not developing at all. So, again, these sequences would still be functional, even if none of the alleles that are currently present in the population are subject to selection one way or the other.
In your example, there will be variants of the sequence subject to positive selection. So it meets Graur’s defintion of function.
See above. A mutation that led to the trunk or eyes not developing at all (e.g. deletion of the entire sequence) would clearly be deleterious. I will remind you again of Graur’s actual definition of function, which is not what you keep using (with emphasis added by myself):
A genomic segment is considered to possess a selected effect function if at least one out of all the possible mutations that can affect its sequence is deleterious
Deletion of the entire segment is included among “all of the possible mutations that can affect its sequence.” No?
How long is the sequence? Is there a limit o the length of such a sequence?If a chromosome has one useful gene, then the loss of the chromosome would be deleterious… does that mean the entire chromosome is functional?
This is not my question by the way. Ford Doolittle also asks a similar question. Let me quote it below:
If a short region localized at the 3′ end of a long ncRNA is under selection to interact with a specific site on another molecule, does that make the whole molecule ‘functional’? What if experiments showed that most of the upstream part could be harmlessly deleted? Would, by similar logic, the presence of one functional gene on a chromosome render the whole chromosome ‘functional’?
It would mean the chromosome as a whole is functional. That does not mean the whole chromosome is functional. Similarly, that a sequence is functional does not entail that every single nucleotide is functional (ie that there is at least one way the nucleotide can be mutated that affects fitness).
I have no problem answering those questions, TBH:
No.
It would mean that upstream part is non-functional.
It could, but your claim wasn’t even about hybridization, and you claimed that it had indeed happened in nature. Why not just retract the claim, since it was false?
All that means, to me, is that a gene can be functional in one genetic environment and nonfunctional in another. And you still haven’t managed to define function.
Well, in the case we’re discussing here, the sequences in question don’t result in formation of a physical structure in their native genetic environment. Eyes only result when the blind fish is crossed with a different population that hasn’t had the same mutations deactivating other eye-forming genes. Is “does something” or “exists” enough to consider a structure functional? If a gene results in a useless feature, is that gene functional? Is the useless feature functional?
Actually I remember reading an article which mentions a lake with light falling on one side and the other side being in the darkness… the portion under the light had fish with sight… It’s been a few years since I saw it, I am trying to trace it. I will share it when I do.
However, the main point remains. Let me make it even simpler. Assume a cave fish with sight entered a dark cave. In this environment, every mutation that effects sight would be neutral and not deleterious. So the genes that confer sight to the fish are non-functional even if they are in working condition.
Would you agree?
Whether a feature is useless or not depends on the environment.
In a causal sense, the gene is functional.
But, per Graur, the issue of function does not pertain just to this particular allele of the gene, but to all possible alleles, and not even just the one’s that have actually arisen. That’s how I read it. So the useless feature may well serve no function, but that does not mean the gene itself is junk. For instance, the allele that causes eyes to develop may be deleterious because it wastes biological resources on structures that produce no benefit. That would make the sequence (as defined by all its variants) functional, because a deleterious form exists.
And, therefore, also in the sense that Graur uses the term “function”.