This has already been addressed in the above discussion.
What are you thoughts on Ann Gauger’s tacit admission that if ENCODE is right, ID is wrong?
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Part of your problem is your failure to distinguish the task of determining the specific function of a DNA sequence that is believed to be functional, from that of determining whether a sequence is functional. Determining the latter is valuable, and does not in any way require determining the former.
Why should it be restricted to only functions that effect reproductive fitness?
Didn’t evolution start out trying to describe why organisms got to be the way they are? So why eliminate a large part of what makes an organism the way it is from function?
It’s an arbitrary and quite restrictive definition. Why should it be that way?
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Let’s try to get a little more concrete. Name a function that doesn’t affect reproductive fitness and explain why it ought to be called a function. Consider the eyes of a blind cave fish. They’re a part of the way it is. Are they functional?
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The “selected effect” criterion of genomic function is indeed problematic:
“Selection is neither sufficient nor necessary for function. It is a very useful proxy to relevant functions, but an imperfect one and not the only one.” (page 21)
Is there a criterion you like better? Or is it like Winston Churchill’s view of democracy?
I stopped reading that paper when they began by equating “junk” with “not protein-coding”.
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Same genes are active in giving sight to cave fish which can see … and when blind cave fish come to environments suitable for sight, the regain the ability in a few generations.
So why shouldn’t it be seen as functional?
Edit: interestingly enough different mechanisms lead to blindness in cave fish in different populations…
I’m going to need a citation for that.
And you will need to provide a definition of function under which the eyes of blind fish are functional. Are you including “things that are useless now but might come in handy at some unknown time in the future”?
I have no trouble with the idea that a sequence might be functional in a real sense without conferring a selective advantage. In developed countries, for example, mutations whose sole effect is to produce near-sightedness or slightly higher intelligence are likely neutral or deleterious, respectively, at present. I would expect such cases to be pretty unusual, though.
[Edited: higher intelligence is deleterious, not lower. Which I would have typed the first time if I had been more intelligent.]
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Where does embryo development become part of the function equation?
https://www.sciencedirect.com/science/article/pii/S0960982207022622
The above paper shows that blind cave fish can regain sight upon cross breeding with other populations.
I.e this is because blindness in this species of Cave fish is caused due to different genetic mutations in different populations. When interbreeding occurs, the genes that are not impaired help in restoring sight to future generations. However these same genes were useless to provide sight in the parents genome.
I am talking about genes here. Sight depends on many genes and mutations in some can lead to blindness.
So, the fish have genes that have a function, but is not able to express the same due to certain mutations.
Why shouldn’t these be considered functional?
Has any IDer acknowledged that even if we accept ENCODE’s hopelessly broad definition of “function” there’s still 20% of the human genome with NO function whatsoever?
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Cetaceans still carry the unexpressed Tbx4 gene for hind limb development. Does that mean we should say whales have functional hind legs?
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That’s not what you were claiming. It appears I was right to demand evidence. And I don’t see how this advances your argument in any way.
Again, you will have to provide a definition of “functional”. You can’t just say “genes that have a function” without explaining what that means.
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Not true. If we accept ENCODE’s definition, there’s 20% of the genome for which function hasn’t yet been found. Big difference. But why should anyone accept ENCODE’s definition?
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That looks like a proposition meant to save a hypothesis rather than a hypothesis with merit.
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How is it different. The fish regain sight because they still retained genes that were needed for sight.
They have a causative function/a possible causative function in conjunction with other genes (as demonstrated in the cross bred fish).
Agreed.
On the other end of the spectrum, there can be rare deleterious mutations in junk DNA, such as a random mutations producing a weak promoter sequence that results in dysfunctional gene regulation. These would be rare, and possibly lost in the noise of genetic drift.
There’s no known function under any currently accepted definition of function. Of course IDers will claim the function is merely unknown, like all the rest of their evidence for ID is unknown. But they’ll find some evidence one day, just wait, really, they mean it. The check is in the mail.
They shouldn’t. 
You said “when blind cave fish come to environments suitable for sight, the regain the ability in a few generations”. But that isn’t what happened. What happened is that crosses in the laboratory, some, I might add, with fully sighted surface fish, ended up with functional eyes. That’s nothing like what you claimed.
That’s your definition of “functional”? So a gene that does nothing in its current genetic environment is still functional as long as it could do something in some other genetic environment? I think you’ll have trouble finding anyone to agree with that definition. And you will also have to clarify what “causative function” means. (Hint: never use a term as part of its own definition.)
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