I think your discussion has been exemplary of a positive ID discussion.

Underlying the discussion is defining distinctions.

To me, it looks like you both are agreeing to the possibility to subtle selections in deep time.

One view (Zachriel’s?) would suggest it is just more supportive evidence of MET.

However, another view (FMM’s?) if it is too subtle it becomes supportive of front loading.

Allow me to suggest the distinction between the two views is foresight. If the subtle, deep time selection pressures are too subtle and too deep it may suggest being influenced by a future need.

Of course, I suggest a direct link to the future need is via interconnect quantum effects. Slight pressures from the future influence the quantum effects in superposition to “randomly” choose a path that provides consistency in the universe.

Whether the foresight comes indirectly from an intelligence or directly from orchestrated Quantum Mechanics, I suggest the distinction of these views from MET is foresight.

I hope this comment is helpful to your discussion.

fifth monarchy man: Actually it’s those with the variant that have the kick me sign and it's put on them by their own HM.

That's not quite what you said. I appreciate the clarification. But again, there is nothing to stop a mutation from disabling the mechanism itself so that it has the beneficial function and not the detrimental function.

fifth monarchy man: The HM could conserve information that would become vital in a periodic climatic event. Like an Ice age or prolonged drought.

Now, you are positing that the ultraconserved regions are conserved because they are historically selected.

Yes, evolution can keep various genes that were previously useful around for long periods of time. But eventually they drift and degrade unless selected. We have significant data on this, and it doesn't appear to support such long-term storage without evolutionary drift, or even progressive adaptation.

fifth monarchy man: Because the climate of earth is so variable the HM would be constantly needed and tend not to degrade.

But it is unstable in so many different ways. That which might be useful in one environment might not be useful in another. And a designer would have no way to predict the long-term environment an organism might find itself in.

Zachriel: No, you have a speculation, not an answer. It's not an answer unless you can provide the data to support your speculation.

fifth monarchy man: Is there a specific reason you are calling it speculation and a not prediction?

I said it was a "speculation" as opposed to an "answer". As to it being a prediction, it's rather vague. If you could tell us what observation to make, then you would have a solid prediction. There's nothing wrong with proposing ideas.

But you really need to look at your concept *critically*. Do you understand how evolution works, and why your idea appears contrary to the evidence? It's important in science that you try to determine and answer objections, and not rehash stale arguments without significant new evidence or insights. Consider it a courtesy.

fifth monarchy man: A selectable difference does not lead to ultraselection. For ultra selection you need an ultraselectable difference.

An ultraselectable difference just has to be something that exerts consistent selective pressure. It doesn't have to mean the organism is not viable. Though as you suggest above, it might mean strong but intermittent selection.

fifth monarchy man: Is this your prediction?

I would suspect that there are selectable difference in the mice that were not apparent in the study, as indicated in other studies. However, I am not wed to that concept and am open to other possibilities.

Those with the original gene put a "Kick Me" sign on their rivals so they never get the girl. Either way, it's a selectable trait.

Actually it’s those with the variant that have the kick me sign and it's put on them by their own HM.

You have proposed nothing that would tend to maintain the conserved region over geological time.

Perhaps I have not made my self clear enough on this point.

The HM could conserve information that would become vital in a periodic climatic event. Like an Ice age or prolonged drought.
In such a case any advantage an organism had lost due to the HM would be regained over night. Leaving the original gene and it’s conserver dominant once again in a population.

Because the climate of earth is so variable the HM would be constantly needed and tend not to degrade. As to exactly what information this would be I can once again I can only speculate but the possibilities are immense.

I would even say that we could look at organisms that evolve rapidly in response to climate fluctuations only to return to their original state after the crisis for clues.

More possible research flowing from a spur of the moment prediction on an internet blog.
Science is cool

No, you have a speculation, not an answer. It's not an answer unless you can provide the data to support your speculation.

Is there a specific reason you are calling it speculation and a not prediction?

I agree we need to do research that’s what you do in science.

[I Predict]That there are selectable difference in the mice that were not apparent in the study. However, I am not wed to that concept and am open to other possibilities.

A selectable difference does not lead to ultraselection. For ultra selection you need an ultraselectable difference. Is this your prediction?

Peace

fifth monarchy man: A hypothetical pheromone produced by the Hibernation Mechanism in response to variation would make an organism less sexually attractive. So if the HM or the gene itself evolved to produce the pheromone on it’s own it would be selected out.

This was your original proposal.

fifth monarchy man: Perhaps organisms with the original gene release a pheromone that renders those with the variant slightly less attractive to the opposite sex.

Those with the original gene put a "Kick Me" sign on their rivals so they never get the girl. Either way, it's a selectable trait.

On the other hand, if the Hibernation Mechanism produces a pheromone that makes the same organism less attractive if its a variant, it would be a selectable and detrimental trait. This is the conservation mechanism.

But…

The pheromone, the response in potential mates, and the relationship (which would tend to become decoupled) between the conserved region and the Hibernation Mechanism (which being detrimental to the organism would tend to stop working) are all subject to evolutionary change. You have proposed nothing that would tend to maintain the conserved region over geological time.

Perhaps there is some other type of Hibernation Mechanism, something more akin to gene conversion. But this is also inadequate.

Zachriel: The evidence is consistent with what we would expect if ultraconserved regions are subjected to ultraselection.

fifth monarchy man: No That prediction has been falsified. In order for there to be ultra selection a gene must perform some vital function. Knocking out the ultraconserved gens had no effect on the mice.

It had no discernable effect on the mice. That doesn't mean it didn't lead to a selectable difference in the wild.

fifth monarchy man: As David said “there must be another answer”.
I have got mine.

No, you have a speculation, not an answer. It's not an answer unless you can provide the data to support your speculation.

fifth monarchy man: What’s you prediction?

That there are selectable difference in the mice that were not apparent in the study. However, I am not wed to that concept and am open to other possibilities.

You before: Neither it nor the organism requires the conserved region to generate a pheromone

Me Before: I’ll grant that such a thing is possible

After further thought I need to retract my previous concession.

A hypothetical pheromone produced by the Hibernation Mechanism in response to variation would make an organism less sexually attractive. So if the HM or the gene itself evolved to produce the pheromone on it’s own it would be selected out.

Therefore it looks like if a HM like I describe was frontloaded into a genome it would tend to remain there and functioning, all things being equal.

Peace

The hibernation/conserved system is therefore subject to natural selection.

Yes this is Mike’s problem with the prediction. My response would be that this could be overcome if such a mechanism were beneficial in the medium /short term. For example if the hibernation mechanism also conserved genes that were helpful in the event of a climatic event like a unusual flood or drought.

the hibernation gene should tend to evolve over time to decouple from the conserved region, or be deleted entirely

Yes and the mechanism would tend to keep that from happening producing results much like we see in the ultraconserved genes

Neither it nor the organism requires the conserved region to generate a pheromone

But if the two are linked like a lock and key any mutation would tend to disable the mechanism long before it evolved the ability to produce a pheromone on its own. And if no pheromone is produced the organism functions normally.
I’ll grant that such a thing is possible . But that does not hold for the other possible mechanisms I mentioned.
Do you agree?

The evidence is consistent with what we would expect if ultraconserved regions are subjected to ultraselection.

No That prediction has been falsified. In order for there to be ultra selection a gene must perform some vital function. Knocking out the ultraconserved gens had no effect on the mice.
As David said “there must be another answer”.
I have got mine. What’s you prediction?

Of course, you're admittedly just speculating. If you find any evidence of some alternative mechanism, please let us know.

I will.
In the mean time I’ll be happy just knowing that you won’t be able to say that ID makes no distinguishing predictions anymore.
Peace

fifth monarchy man: Perhaps organisms with the original gene release a pheromone that renders those with the variant slightly less attractive to the opposite sex.

So, the hibernation gene detects changes in the conserved region and generates a selectable change in the organism.

The hibernation/conserved system is therefore subject to natural selection. Meanwhile, the hibernation gene should tend to evolve over time to decouple from the conserved region, or be deleted entirely. Neither it nor the organism requires the conserved region to generate a pheromone.

There's nothing you have suggested that would tend to maintain the conserved region in the face of selection. The evidence is consistent with what we would expect if ultraconserved regions are subjected to ultraselection. Of course, you're admittedly just speculating. If you find any evidence of some alternative mechanism, please let us know.

Umm, you just said it might create a sexual pheromone.

No it's the hibernation mechanism that might create a sexual pheromone not the gene it conserves. The gene itself is with out function hence the need for a mechanism to conserve it. Is this really unclear?

Much of biology is about sex and sexual attraction. The birds and the bees.

All the more reason for a frontloader to harness it to protect unexpressed genes.

why is it always like pulling teeth with you?

Peace

Let me just address the first theme, from my own perspective. I don't look at biology from the point of view of an engineer, judging its excellence or lack thereof from a standpoint of "efficiency" or "elegance" or "design." I'm not saying that none of those things is present in biological systems, or that I'm not impressed by the design in biology, I'm just saying that I don't start with the presumption that a system which exhibits inefficiency or kludginess is unexpected.

I think this is a weakness of strong design-based thinking, and I think it has created confusion on your part. The presence of a second copy of a gene seems "wasteful" to you, and so you are surprised that duplicates are retained in genomes, asking if the retention is "theoretically odd" solely on the basis of your judgment regarding "wastefulness." But the retention of many duplicates is not theoretically odd at all, at least because no useful theory begins with the assumption of extreme fine-tuning of cellular metabolism, and especially not of eukaryotic genomes. I would suggest that you have overemphasized the importance of "efficiency," and I suspect this is because the perspective of ID lends itself to such imbalances in consideration of biological phenomena.

Also, you asked whether a new gene would need to have its own regulators in order to be useful. This depends on how the new copy gets used. Sometimes the usefulness of the extra copy is precisely its boosting of expression of the protein (an example here is human amylase). Sometimes the usefulness of the extra copy is in regulating the activity of the first copy, such that the regulation of the expression of the two different genes will be very similar. An example of this is summarized on my blog; the idea is that the duplication relieved an adaptive road block in evolution.

Finally, I note that while gene duplication does not necessarily lead to selectable "wastefulness," there are lineages where it does appear that control of genome size has been a strong evolutionary influence. Birds are a famous example, and Zachriel mentioned bacteria in a comment on the other thread. On the flip side, some lineages appear not to care at all about excess DNA – plants are content with multiple copies of the entire genome, and some amphibia carry around 40 times as much DNA as humans do. I conclude that "efficiency" on the genomic level can be an evolutionary influence, but that it is a mistake to simplistically overemphasize it.