Kitzmiller, the Universe, and Everything

So your “best evidence” is actually no evidence. And you have no clue about a possible mechanism for the process you imagine.

Yeah, that’s something scientists should be spending their time on.

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I asked Tim to define evidence. He has yet to do this. Do you want to give it a shot?

I most definitely see things differently.

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I know you do and I respect your opinion. The evidence you brought forward with new corn gene was eye opening to me. Any more evidence of this type of evolution you can bring forward would be appreciated.

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You have zero evidence they actually were consciously designed. As always all you have is your religiously inspired personal beliefs.

We know Bill. All you’ve ever offered are your scientifically unsupported personal opinions.

The opening post and link of this thread provides come compelling evidence along these lines. Keep in mind that the protein encoded by T-urf13 is a transmembrane protein. I think the paper by Vakirlis et al. may help to understand just how common (in sequence space) proteins like the T-urf13 gene product really are.

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The problem is the evolution of the new splicing codes by random genetic change.

I think that the actual splicing “code” (which I take to mean the RNA sequence preferences that guide the core spliceosome, accessory splicing factors, and RNA-binding regulatory proteins that control some alternative splicing decisions) is the same in all vertebrates. There is no “new splicing code” described in the cited paper, or probably anywhere in the literature. What changes is the occurrence of particular code “elements” (trying to keep in the vernacular here) across the genome. These changes are well within the reach of random genetic changes.

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Well it’s of a similar nature to many other papers on de novo genes where comparative genetics are used to infer that (and how) novel protein coding genes emerge de novo from non-coding DNA. For example the paper that was discussed here not too long ago about de novo genes in rice.

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And don’t forget this, which fits the same hypothesis with novel genes inserting into the membrane:
https://mbio.asm.org/content/10/3/e00837-19

IMPORTANCE De novo gene origination from nonfunctional DNA sequences was long assumed to be implausible. However, recent studies have shown that large fractions of genomic noncoding DNA are transcribed and translated, potentially generating new genes. Experimental validation of this process so far has been limited to comparative genomics, in vitro selections, or partial randomizations. Here, we describe selection of novel peptides in vivo using fully random synthetic expression libraries. The peptides confer aminoglycoside resistance by inserting into the bacterial membrane and thereby partly reducing membrane potential and decreasing drug uptake. Our results show that beneficial peptides can be selected from random sequence pools in vivo and support the idea that expression of noncoding sequences could spark the origination of new genes.

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Evidence of splicing codes is offered in newer papers and attributed to specific transcription factor proteins. Splicing is active in embryo development and its accuracy seems important as changes have implications in human disease. Random changes may incur purifying selection.

I am not firm on this issue however I think skepticism of random change being responsible for these differences is warranted.

Yeah, but that’s not a problem, is it? As Arthur Hunt points out,

So, the same mechanisms which work well for such things as generating binding sites are at work. When a mutation produces a new splice which is fatal, it won’t be preserved. When it’s neutral, it may be preserved. When it’s beneficial, it likely will. How does this pose any problem? Do any actual biologists claim it poses a problem, or is this just your faith in The Designer talking?

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James Shapiro agrees this may be an issue along with gene expression differences. This is a subject that is not really discussed frequently in evolutionary circles but is an issue when you say transitions that appear straight forward may not be.

As you saw by my comment I am almost sure there is not enough known here for @Art to make a definitive claim. Will see if he does then we can have a discussion.

Random mutation generating useful sequences is not really discussed frequently in evolutionary circles? You are badly mistaken if you think that. And yes, things which are straightforward in concept always are more complex as applied to particular situations, but this does not help you in any way.

I can’t speak to your “almost sure”-ness, but Art’s statements are pretty clear and I do not see what is left for you to argue about.

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I was discussing alternative splicings role in evolution.

There is plenty to argue here as the mechanisms are not completely understood.

Okay, but with which relative activity compared to the natural enzyme?

Right, and that role can be carried out through random mutation and selection. You do not appear to know of any reason why it cannot.

News flash: the mechanisms of biology will never be completely understood. But there is a good deal of difference between an incomplete understanding and no understanding at all.

I don’t really get where you are coming from. You don’t have a positive argument for “design” or manufacture by supernatural beings. Your negative argument rests entirely upon the idea that natural processes cannot do the work – something which can, by the nature of the proposition, never be actually demonstrated. While anyone has the right to think of these things however he wishes, why try to make those positions sound as though they are grounded in science, when they are not? As a free man you may withhold your assent from the sky being blue, fish needing water, the earth being round, or any number of other things. While withholding that assent, in a compelling case, may be absurd, the absurdity of it is greatly compounded when you try to give off the impression that you are driven by reasons which other people ought to find persuasive. Why not just deny evolution outright and have done with it?

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All we need is some activity to let variation and selection increase it.

How can someone who worships Doug Axe, who couldn’t be bothered to measure activity, be so hypocritical?

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I believe mind or design as a mechanistic explanation for some of the features we are observing in the cell is a scientific claim as much as matter induced space-time curvature is a scientific explanation for black holes. I see objections to this as merely ideological. The mind or design conclusion does not support further research but does work as a comparative tool to keep evolutionary claims in check. Since I have been discussing this I have seen a lot of progress pushing evolutionary theory toward testable claims and away from the blind and unguided nonsense.

Sounds like another opportunity for an experiment.