Orphan genes are yet another topic that seems to lack a punch line. A handful of mutations cause a previously untranscribed region of a genome to suddenly be transcribed. Orphan genes can also be produced through genetic recombination moving a promoter around, or a transposon jumping to a new region. So what next? Why do we see this topic popping up in ID circles?
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And the novel protein product, previously unseen by the cell, immediately finds a novel catalytic or enzymatic task to perform, fitting itself into an existing metabolic pathway or functional complex so seamlessly that the other proteins in the pathway or complex take no notice. Rather like a new bone appearing overnight in the forelimb of a tetrapod. Of course it works! Evolution is smarter than you are.
And no one seems to remember Francois Jacob’s 1977 prediction that the antecedent probability of a novel protein appearing de novo from noncoding sequence was so low as to be effectively zero.
Incredulity is the punch line?
It isn’t possible for Jacob to be mistaken?
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Is it possible he is not 
Then let’s see the evidence that supports Jacob’s claims instead of pretending that it must be true simply because Jacob said so.
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That’s my point. A lack of faith is the only hypothesis that explains why you haven’t managed to come up with a testable scientific hypothesis in 35+ years.
And how can you title yourself a “theorist” when you don’t even have a hypothesis that makes empirical predictions, much less a theory?
That’s a nice poster banner.
Without revealing the top-secret results, what empirical prediction of what ID hypothesis is being tested? The title just looks descriptive to me.
“As seductive as it is, the de novo creation hypothesis is nevertheless plagued by its own difficulties. First, newly expressed (random) proteins have to fold in a compact manner, or at least in a way not interfering with established protein interactions….In absence of a useful function on which to exert a purifying selection, it seems very unlikely that a newly created protein could remain in a genome long enough to acquire a selectable influence on the virus fitness. How the so-called protogene manage to be retained through the intermediate steps eventually leading to a selectable function remains the dark part of any de novo gene creation scenario.”
From here (open access):
No, the mutant allele (even a recessive lethal) hangs around, subject only to drift for thousands of generations. Diploidy allows that, as shown by population genetics.
And where is the research backing this opinion?
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I am (genuinely) sorry, John and T. aquaticus, but I could bat this shuttlecock back and forth all day, to very little useful end. Already indulged myself too much here this AM. It’s fun but gotta run.
Critics of ID who are dismayed by its apparent lack of empirical productivity have good reason to be dismayed, but insufficient reason to badger those of us on the other side of the aisle to stop. Back to work.
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I have always appreciated your willingness to post in hostile territory, and I hope you come back to visit us.
That is certainly a large and lengthy topic, but what I was also dismayed about is the subjects that ID supporters are choosing to comment on. At first glance, orphan genes seem like huge pieces of evidence for evolution because they demonstrate how de novo genes can evolve in genomes. Dragging out a 40 year old mistaken opinion from well before the modern findings in molecular biology really doesn’t budge the needle. We often hear that evolution can’t explain how new genes come about, and yet there are orphan genes, a perfect example of how evolution produces new genes. All I can do is scratch my head.
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So, the Southern corn leaf blight epidemic didn’t really happen.
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We’re badgering you to START, Paul, not to stop.
Come up at least one testable hypothesis before you claim to be a theorist. Your collective lack of empirical productivity is accompanied by a lack of theoretical productivity. The two are intimately related.
That was a reflexive burning, though.
Also, Bucky Dent didn’t hit that homerun, Bill Buckner fielded that ball cleanly, Havlicek didn’t steal that ball …
ID is some powerful medicine 
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Here is the lecture and the eye is discussed in the beginning.
I suppose I remember it and also remember that this hypothesis was definitely falsified in the following 40 years. @pnelson what exactly is your point?
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I think catalytic and enzymatic would be the same thing. You must mean catalytic or otherwise?
fitting itself into an existing metabolic pathway or functional complex so seamlessly that the other proteins in the pathway or complex take no notice.
What does it mean for other proteins in the pathway or complex to “notice”? You seem to be saying something trivial and obvious. Like, if a de novo promoter has a net negative effect on fitness, it should not be expected to evolve. Well doh! But, what if it doesn’t, and instead has a positive effect?
Creationists are very fond of arguing, for example, that most antibiotic resistance evolves by horizontal gene transfer of already existing genes which you presumably think were created. Creationists invoke horizontal transfer of plasmids carrying antibiotic resistance genes as “already existing information” being used by another organism. So it seems you actually don’t have any problem with the concept that a new gene suddenly appears in another organism it was not initially created for, and just so happening to functionally fit into the lifestyle and internal biochemistry of the organism in a way that has a positive effect on reproductive success. ¨
Clearly, if it can some times fit in if delivered through horizontal transfer, it can also fit in if it emerges de novo from non-coding DNA.
You can’t have your cake and eat it too, sorry.
Rather like a new bone appearing overnight in the forelimb of a tetrapod. Of course it works! Evolution is smarter than you are.
Some people are born with six fingers that work. So, yeah.
That was a “prediction” based on a hunch. In fact not really a prediction. There was no model that predicted it. We now know that hunch to be false, as most such hunches invariably are. It’s curious how much work is done by some completely unevidenced assertions invoked by some theorists in the 60’s and 70’s. Fred Hoyle, Hubert Yockey, and Francois Jacob said it - that settles it!
So far you’ve yet to actually say anything that should cause us to think the evidence we have that it happens is all wrong. You’ve tried to give what appears to be just a rhetorical appeal to incredulity (the argument from a sarcastic caricature), and a fallacious appeal to authority.
Meanwhile, evidence keeps amassing that de novo evolution of protein coding DNA is something that occurs.
Great! Let us know when you actually come up with and publish some positive evidence for ID. Not the usual attacks on existing evolutionary theory by cherry-picking and misrepresenting the work of others.
Seriously, the ID “check” has been in the mail for the last 20 years. Isn’t it time you guys produced more than empty propaganda?
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It’s amazing to look at. It’s like a man who is completely unaware of the existence of GPC receptors besides opsins. The whole pathway Behe is talking about there predates the origin of opsins. Organisms had a sense of smell and touch for hundreds of millions of years before they got a sense of sight.
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