# Kitzmiller, the Universe, and Everything

**URL:** <https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427>\
**Category:** Conversation\
**Created:** [February 4, 2020, 1:27am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427 "2020-02-04T01:27:40Z")\
**Posts on this page:** 20\
**Page:** 35

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**Author:** ![Puck\_Mendelssohn](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/puck_mendelssohn/32/11849_2.png) [@Puck\_Mendelssohn](https://discourse.peacefulscience.org/u/Puck_Mendelssohn)\
**Post date:** [February 16, 2020, 9:53pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/693 "2020-02-16T21:53:28Z")

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> [@colewd](#):
>
> 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.

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.

> [@colewd](#):
>
> 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.

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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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 16, 2020, 9:56pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/694 "2020-02-16T21:56:29Z")

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> [@Puck\_Mendelssohn](#):
>
> 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 was discussing alternative splicings role in evolution.

> [@Puck\_Mendelssohn](#):
>
> 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.

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

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**Author:** ![Giltil](https://avatars.discourse-cdn.com/v4/letter/g/5f8ce5/32.png) [@Giltil](https://discourse.peacefulscience.org/u/Giltil)\
**Post date:** [February 16, 2020, 10:04pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/695 "2020-02-16T22:04:51Z")

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> [@Mercer](#):
>
> And beta-lactamase activity can be obtained in catalytic antibodies at a frequency of more than 10^-8

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

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**Author:** ![Puck\_Mendelssohn](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/puck_mendelssohn/32/11849_2.png) [@Puck\_Mendelssohn](https://discourse.peacefulscience.org/u/Puck_Mendelssohn)\
**Post date:** [February 16, 2020, 10:08pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/696 "2020-02-16T22:08:46Z")

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> [@colewd](#):
>
> I was discussing alternative splicings role in evolution.

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.

> [@colewd](#):
>
> There is plenty to argue here as the mechanisms are not completely understood.

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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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2020, 10:16pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/697 "2020-02-16T22:16:36Z")

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> [@Giltil](#):
>
> Okay, but with which relative activity compared to the natural enzyme?

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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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 16, 2020, 10:18pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/698 "2020-02-16T22:18:26Z")

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> [@Puck\_Mendelssohn](#):
>
> 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?

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.

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 16, 2020, 10:23pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/699 "2020-02-16T22:23:09Z")

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> [@Mercer](#):
>
> All we need is some activity to let variation and selection increase it.

Sounds like another opportunity for an experiment.

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2020, 10:27pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/700 "2020-02-16T22:27:50Z")

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> [@colewd](#):
>
> Sounds like another opportunity for an experiment.

Yes, you may recall that I proposed that to @Agauger, who was not interested.

Aren’t there already many such experiments that have been published and you ignore, Bill?

> **[Can an Arbitrary Sequence Evolve Towards Acquiring a Biological Function? -...](https://link.springer.com/article/10.1007/s00239-002-2389-y)**
>
> AbstractTo explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide...

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<div class="post-metadata">

**Author:** ![Puck\_Mendelssohn](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/puck_mendelssohn/32/11849_2.png) [@Puck\_Mendelssohn](https://discourse.peacefulscience.org/u/Puck_Mendelssohn)\
**Post date:** [February 16, 2020, 10:47pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/701 "2020-02-16T22:47:56Z")

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> [@colewd](#):
>
> 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.

It might, if couched in terms which are testable and falsifiable, be, as you say, a scientific “claim.” But there is a good deal of difference between a claim and evidence.

Claims are great for hypothesis formation. If I claim that whales should actually be classified as teleosts rather than as mammals, this is, to use a loose definition, a scientific “claim” because it asserts a state of things which it is within the competency of science to test. But when I do test it, I am liable to be disappointed at how my “claim” fares. Saying that such a claim can be couched in scientific terms says nothing at all about whether it has any actual merit.

> [@colewd](#):
>
> The mind or design conclusion does not support further research but does work as a comparative tool to keep evolutionary claims in check.

But there is no mind or design conclusion. You cannot get there. Your attempts to make a positive argument are all weak analogies rather than evidence bearing on mind or design. Your attempts at a negative argument, even if successful, would only show that our current understanding of evolution is incomplete. Since nobody thinks it is complete, that’d hardly be an earth-mover.

But here again we see your theology holding sway against whatever small scientific impulses you may harbor. Why on earth would the hypothesis of design, even if it met with some sort of confirmation, “not support further research”? When people discovered that point mutations occur in genes, they didn’t say, “well, that doesn’t support further research; we may not ask why they occur, what the chemical processes that cause them to occur are, what factors influence their occurrence, or what the consequences of them may be.” Nobody, in any field of science, EVER says anything like that.

But theology, specifically Christian theology, says exactly that, except whenever it claims the opposite. I could not count the number of times I have seen people write about how God is unknowable, inscrutable, ineffable, et cetera, and then follow that up by explaining what God is like. Inquiry cannot stop at the design hypothesis; in fact, it cannot produce any confirmation of the design hypothesis without going beyond it, by demonstrating that processes do indeed exist which can account for the phenomena design is said to be responsible for.

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**Author:** ![Art](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/art/32/3805_2.png) [@Art](https://discourse.peacefulscience.org/u/Art)\
**Post date:** [February 16, 2020, 10:48pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/702 "2020-02-16T22:48:23Z")

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> [@colewd](#):
>
> Evidence of splicing codes is offered in newer papers and attributed to specific transcription factor proteins.

Do you have citations or other pointers?

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 17, 2020, 12:05am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/703 "2020-02-17T00:05:09Z")

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# Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning[Genes (Basel)](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6722613/#). 2019 Aug; 10(8): 587.

Published online 2019 Aug 1. doi: [10.3390/genes10080587](https://dx.doi.org/10.3390%2Fgenes10080587)

PMCID: PMC6722613

Review Article

Free Access

# Regulation of alternative mRNA splicing: old players and new perspectives

[Heidi Dvinge](https://febs.onlinelibrary.wiley.com/action/doSearch?ContribAuthorStored=Dvinge%2C+Heidi)

First published: 01 June 2018

[https://doi.org/10.1002/1873-3468.13119](https://doi.org/10.1002/1873-3468.13119)

PMID: [31374967](https://www.ncbi.nlm.nih.gov/pubmed/31374967)

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**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 17, 2020, 12:41am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/704 "2020-02-17T00:41:05Z")

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> [@Puck\_Mendelssohn](#):
>
> But there is no mind or design conclusion. You cannot get there. Your attempts to make a positive argument are all weak analogies rather than evidence bearing on mind or design.

The analogy being weak is your opinion. I just think we disagree here. A mind is capable of complex design and this is the problem we see when we examine the cell. There is really no other known mechanism to explain this observation.

> [@Puck\_Mendelssohn](#):
>
> Why on earth would the hypothesis of design, even if it met with some sort of confirmation, “not support further research”?

This is just where it is right now. Hopefully in the future we will have room the understand Mind as a mechanism in more detail. Some guys are currently working on this but the supporting data is immature.

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**Author:** ![Puck\_Mendelssohn](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/puck_mendelssohn/32/11849_2.png) [@Puck\_Mendelssohn](https://discourse.peacefulscience.org/u/Puck_Mendelssohn)\
**Post date:** [February 17, 2020, 12:54am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/705 "2020-02-17T00:54:47Z")

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> [@colewd](#):
>
> The analogy being weak is your opinion.

Well, if you like. But it IS weak, and even a strong analogy isn’t a compelling argument. To have a scientific theory you’re going to need a good deal more than an argument by analogy that seems compelling to you and useless to those you are hoping to convince. Do bear in mind that biologists have been rejecting this for decades now; you need something else.

> [@colewd](#):
>
> A mind is capable of complex design and this is the problem we see when we examine the cell. There is really no other known mechanism to explain this observation.

But no known mind is capable of having designed the cell, as human minds were late to the party. So you have no actor and no mechanism. Meanwhile, the observation (I assume you mean the observation that cells are complex) is completely consistent with naturally-originating complexity.

> [@colewd](#):
>
> > [@Puck\_Mendelssohn](#):
> >
> > Why on earth would the hypothesis of design, even if it met with some sort of confirmation, “not support further research”?
> 
> This is just where it is right now. Hopefully in the future we will have room the understand Mind as a mechanism in more detail. Some guys are currently working on this but the supporting data is immature.

But since you need to demonstrate that a mind capable of doing the work exists before you are justified in identifying the work as having been so performed, if “right now” we can say nothing about that mind, you are dead in the water. The supporting data are not so much immature as absent; there simply are no known minds capable of doing the work.

Bear this in mind, too: we do not know of ANY case of a mind that is not of natural biological origin. To get minds before biology is almost certainly impossible; certainly a theory which depends upon pre-biologic minds has a heck of a lot of explaining to do.

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**Author:** ![Faizal\_Ali](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/faizal_ali/32/12416_2.png) [@Faizal\_Ali](https://discourse.peacefulscience.org/u/Faizal_Ali)\
**Post date:** [February 17, 2020, 1:44am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/706 "2020-02-17T01:44:06Z")

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> [@colewd](#):
>
> Some guys are currently working on this but the supporting data is immature.

Could you describe some of this work? Or give some citations to it?

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**Author:** ![Faizal\_Ali](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/faizal_ali/32/12416_2.png) [@Faizal\_Ali](https://discourse.peacefulscience.org/u/Faizal_Ali)\
**Post date:** [February 17, 2020, 1:45am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/707 "2020-02-17T01:45:03Z")

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> [@Puck\_Mendelssohn](#):
>
> Bear this in mind, too: we do not know of ANY case of a mind that is not of natural biological origin. To get minds before biology is almost certainly impossible; certainly a theory which depends upon pre-biologic minds has a heck of a lot of explaining to do.

Yes, that is the “chicken/egg” problem I have raised several times. Bill doesn’t understand why it’s a problem.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [February 17, 2020, 1:46am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/708 "2020-02-17T01:46:19Z")

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> [@colewd](#):
>
> A mind is capable of complex design and this is the problem we see when we examine the cell. There is really no other known mechanism to explain this observation.

Good old one note Bill. The evidence-free disembodied mind and the magic POOF just won’t die. 🙂

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**Author:** ![Puck\_Mendelssohn](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/puck_mendelssohn/32/11849_2.png) [@Puck\_Mendelssohn](https://discourse.peacefulscience.org/u/Puck_Mendelssohn)\
**Post date:** [February 17, 2020, 2:15am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/709 "2020-02-17T02:15:12Z")

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> [@Faizal\_Ali](#):
>
> Bill doesn’t understand why it’s a problem.

Well, he may. But his solution to it is not the sort of thing people like to speak of, when they are claiming the merit of science for their speculations. God goes from “He Whose Name Must Be Proclaimed Everywhere” to “He Whose Name Must Not Be Spoken” when the claim that ID is science is the point under discussion.

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**Author:** ![Puck\_Mendelssohn](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/puck_mendelssohn/32/11849_2.png) [@Puck\_Mendelssohn](https://discourse.peacefulscience.org/u/Puck_Mendelssohn)\
**Post date:** [February 17, 2020, 2:21am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/710 "2020-02-17T02:21:09Z")

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And, further to that:

One of the most important things to do in evaluating a legal argument is to tear it down. Nobody who knows what he is doing goes into advocacy without already having subjected his own arguments to the most withering skepticism. It has to be done; otherwise one is unprepared to face the things one will hear in response. And when one’s conclusion is – as it surely ought to be for these ID arguments – that it’s just not going to work, one looks for something else.

But the difference between argument in court and argument “in the wild” is that in the wild, you can walk through the buzzsaw, have nothing left of your position, and just keep talking as though nothing has happened. You can wake up the next morning and start all over again, as people voicing these horrible ID arguments have now done for decades. Litigation is a whole different matter. We have referees and we have finality; so you have to convince someone who is not your adversary that you’re right and the adversary is wrong, and if instead your adversary wins, the argument is all over. If you’re the DI, you can spend the next fifteen years blogging about what a lousy job Judge Jones did, but you can’t win the case after you’ve lost it. It forces one to focus, to drop the losing arguments, and to meet the kinds of evidentiary standards that will carry the day. On the one and only occasion that ID was tested in this fashion, the result was hilariously bad.

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**Author:** ![scd](https://avatars.discourse-cdn.com/v4/letter/s/6f9a4e/32.png) [@scd](https://discourse.peacefulscience.org/u/scd)\
**Post date:** [February 17, 2020, 8:53am UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/711 "2020-02-17T08:53:18Z")

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> [@Puck\_Mendelssohn](#):
>
> If the hubcap and colander were made by aliens instead, they would still bear various earmarks of manufacture,

> [@Puck\_Mendelssohn](#):
>
> Hubcaps and colanders are plainly manufactured.

so bottom line you can detect design base on the image alone. this is my point- we can detect design when we see such an object like a flying saucer. so can you tell me what is the different from a motor and why you conclude something different when you see a motor?

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**Author:** ![Roy](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/roy/32/3799_2.png) [@Roy](https://discourse.peacefulscience.org/u/Roy)\
**Post date:** [February 17, 2020, 12:03pm UTC](https://discourse.peacefulscience.org/t/kitzmiller-the-universe-and-everything/9427/712 "2020-02-17T12:03:48Z")

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> [@Giltil](#):
>
> When you blast the human sequence of astrotactin 2 (accession number in Uniprot is O75129) against pre-vertebrates such as cephalochordates, you get a moderate bitscore of 366. But when you blast it against cartilagenous fishes, you get a much, much higher bitscore of 1853. So, as far as astrotactin 2 is concerned, the transition to vertebrates is associated with a big information jump of 1487.

That’s not the transition to vertebrates, it’s both of the transitions from the common ancestor to extant vertebrates and from the common ancestor to extant cephalochordates.

You are _assuming_ that all the changes took place in the vertebrate lineage and there were none in the cephalochordate lineage - but the known variation among cephalochordates contradicts this assumption, and renders your assertion that the big information jump is associated with the transition to vertebrates unproven. It could be associated with the transition to _modern_ cephalochordates.

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