# The Argument Clinic

**URL:** <https://discourse.peacefulscience.org/t/the-argument-clinic/15561>\
**Category:** Side Conversation\
**Tags:** Comments\
**Created:** [November 22, 2022, 2:16pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561 "2022-11-22T14:16:20Z")\
**Posts on this page:** 20\
**Page:** 123

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2024, 6:53pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2470 "2024-02-16T18:53:53Z")

</div>

> [@John\_Harshman](#):
>
> I don’t think that the concept of “allele” extends to presence/absence of an entire gene.

Golly.

I do, and have used it that way (presence/absence of THREE genes) throughout my career. No one has ever suggested that my use of “allele” is incorrect.

As for the value of your thoughts, I’ll also note that you think that searching PubMed for “alternative splicing” yields a “comprehensive” list of papers on the subject.

Shall we kill two of your arrogant false claims with a single paper?

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 16, 2024, 6:55pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2471 "2024-02-16T18:55:10Z")

</div>

> [@Mercer](#):
>
> Shall we kill two of your arrogant false claims with a single paper?

Yes, please.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2024, 6:56pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2472 "2024-02-16T18:56:04Z")

</div>

> [@John\_Harshman](#):
>
> The allele that contains the gene can become fixed, eliminating the allele without the gene, and that’s the same as the gene becoming fixed.

Yet you haven’t offered a single case of anyone other than Bill referring to a gene bring fixed.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2024, 7:01pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2473 "2024-02-16T19:01:57Z")

</div>

> [@John\_Harshman](#):
>
> > [@Mercer](#):
> >
> > Shall we kill two of your arrogant false claims with a single paper?
> 
> Yes, please.

[https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1995.tb07227.x](https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1995.tb07227.x)

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2024, 7:12pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2474 "2024-02-16T19:12:20Z")

</div>

> [@John\_Harshman](#):
>
> But that doesn’t make Bill’s use of the term “gene” wrong. The allele that contains the gene can become fixed, eliminating the allele without the gene, and that’s the same as the gene becoming fixed. Of all the things to beat on Bill about, this is the least meaningful.

Bill, as far as I can tell, is trying to deny the existence of orthologs:

> [@colewd](#):
>
> Duplication does not explain the pattern either does polymorphisms inside a population. You are talking about\*\*\* thousands\*\*\* of different functional genes fixed in populations of different vertebrates.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 16, 2024, 7:14pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2475 "2024-02-16T19:14:54Z")

</div>

> [@Mercer](#):
>
> Yet you haven’t offered a single case of anyone other than Bill referring to a gene bring fixed.

Sure, because it doesn’t matter. But here you are:  
[https://www.pnas.org/doi/10.1073/pnas.2535513100#:~:text=Fixation%20of%20an%20unlinked%20duplicate,locus%20(11%2C%2013)](https://www.pnas.org/doi/10.1073/pnas.2535513100#:~:text=Fixation%20of%20an%20unlinked%20duplicate,locus%20(11%2C%2013)).  
Several mentions in there of the fixation of genes. The more important point, though, is that you were attacking Bill for saying something whose intended meaning was perfectly clear, expressed in a way that made sense. Why attack him for that rather than for any of his countless word salad claims?

I fully admit that this entire conversation has been pointless.

> [@Mercer](#):
>
> Bill, as far as I can tell, is trying to deny the existence of orthologs.

Well, at the least he’s trying to redefine them in a way that doesn’t involve descent. Then again, the original definition of homology didn’t involve descent either. He’s merely trying to erase a couple of centuries of science.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2024, 7:20pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2476 "2024-02-16T19:20:53Z")

</div>

> [@John\_Harshman](#):
>
> Several mentions in there of the fixation of genes.

Bill explicitly excluded duplications.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 16, 2024, 7:21pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2477 "2024-02-16T19:21:19Z")

</div>

That quote isn’t saying what you think. Bill is talking about the genes in his favorite Venn diagram, present in some species but not others. He may be trying to deny the existence of paralogs. He also clearly, given his creationism, doesn’t think that any genes in different species are orthologs (in the common, modern sense), but that’s not the import of the quote. By “thousands of genes” he’s talking about different, non-orthologous (and possibly non-homologous) genes.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 16, 2024, 7:21pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2478 "2024-02-16T19:21:56Z")

</div>

> [@Mercer](#):
>
> Bill explicitly excluded duplications.

Not sure what you mean by that or of the context.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 16, 2024, 7:27pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2479 "2024-02-16T19:27:39Z")

</div>

> [@John\_Harshman](#):
>
> By “thousands of genes” he’s talking about different, non-orthologous (and possibly non-homologous) genes.

In vertebrates, which simply don’t have thousands of such genes.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 16, 2024, 7:33pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2480 "2024-02-16T19:33:56Z")

</div>

> [@Mercer](#):
>
> [https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1995.tb07227.x](https://www.embopress.org/doi/abs/10.1002/j.1460-2075.1995.tb07227.x)

Thanks. I see that the phrase “alternative splicing” does not appear in that paper (though several close equivalents do). Not sure how that’s a big problem. And I’m not sure what other arrogant false claim that paper refuted. The allele in question is of a single gene, though one of its introns does contain an insertaion that itself contains viral genes.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 16, 2024, 7:36pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2481 "2024-02-16T19:36:03Z")

</div>

> [@Mercer](#):
>
> In vertebrates, which simply don’t have thousands of such genes.

Yes they do. Every gene the zebrafish has that the mouse doesn’t is non-orthologous to any mouse gene. I will grant that most of them probably have paralogs in the mouse, but that doesn’t seem relevant to Bill’s statement.

---

<div class="post-metadata">

**Author:** ![Dan\_Eastwood](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dan_eastwood/32/2368_2.png) [@Dan\_Eastwood](https://discourse.peacefulscience.org/u/Dan_Eastwood)\
**Post date:** [February 16, 2024, 11:46pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2482 "2024-02-16T23:46:42Z")

</div>

> [@John\_Harshman](#):
>
> Was there supposed to be a “not” in that sentence?

Indeed! Fixed.

> [@colewd](#):
>
> I think where you see different gene patterns and different chromosome counts you can infer separate ancestry.

What you think doesn’t matter. The math says you are wrong.

> [@](#):
>
> These differences are evidence against a reproductive connection. This implies many origin events as the different patterns exist between many vertebrate species.

To the best of my understanding the difference are the result of more-or-less random deletions or HGT. These difference, once present in the genome, follow the predicted nested heirarchy from that time on.  
Your hypothesis _“This better explains the data that does not follow the reproductive patterns”,_ or _“separate origins”_ has been disproven.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 17, 2024, 12:32am UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2483 "2024-02-17T00:32:44Z")

</div>

> [@John\_Harshman](#):
>
> > [@Mercer](#):
> >
> > In vertebrates, which simply don’t have thousands of such genes.
> 
> Yes they do…

No, they don’t, because Bill’s same/different dichotomy doesn’t exist. This is why we have terms like ortholog, paralog, and homolog, which still have fuzzy boundaries.

> [@John\_Harshman](#):
>
> Thanks. I see that the phrase “alternative splicing” does not appear in that paper (though several close equivalents do).

So searching only for “alternative splicing” and no equivalents is incompetent.

> [@John\_Harshman](#):
>
> Not sure how that’s a big problem. And I’m not sure what other arrogant false claim that paper refuted.

It refutes your arrogant claim that the paper you cited (apparently without bothering to read it), trying to support the preconceived notion alternative splicing isn’t common, was “comprehensive.”

---

<div class="post-metadata">

**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 17, 2024, 1:42am UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2484 "2024-02-17T01:42:26Z")

</div>

> [@Dan\_Eastwood](#):
>
> What you think doesn’t matter. The math says you are wrong.

Hi Dan  
There is no mathematical model in the literature that reconciles this. I am not sure what you mean that the math says I am wrong.

> [@Dan\_Eastwood](#):
>
> To the best of my understanding the difference are the result of more-or-less random deletions or HGT. These difference, once present in the genome, follow the predicted nested heirarchy from that time on.  
> Your hypothesis _“This better explains the data that does not follow the reproductive patterns”,_ or _“separate origins”_ has been disproven.

Horizontal gene transfer is a mechanism primarily between prokaryotes. While it may be a contributing explanation it is much rarer in vertebrates.

There is currently no model of how random deletions can explain the data. To build a model you need to build up empirical data that gives you the frequency of gene deletions in a population along with the probability of a gene deletion being selection positive, neutral or deleterious.

The other problem is how do new genes get produced by the reproductive process. I don’t currently know of any evidence for this in vertebrates.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 17, 2024, 1:53am UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2485 "2024-02-17T01:53:50Z")

</div>

> [@Mercer](#):
>
> No, they don’t, because Bill’s same/different dichotomy doesn’t exist. This is why we have terms like ortholog, paralog, and homolog, which still have fuzzy boundaries.

If you look at the diagram Bill keeps referring to, it’s referring specifically to orthologs.

> [@Mercer](#):
>
> So searching only for “alternative splicing” and no equivalents is incompetent.

On the basis of a single paper? What if most papers do mention the exact term?

> [@Mercer](#):
>
> It refutes your arrogant claim that the paper you cited (apparently without bothering to read it), trying to support the preconceived notion alternative splicing isn’t common, was “comprehensive.”

It could be comprehensive without including every paper in the literature. So one counterexample shows little. You have to establish that the search misses a large fraction of such genes.

> [@colewd](#):
>
> The other problem is how do new genes get produced by the reproductive process. I don’t currently know of any evidence for this in vertebrates.

The presence of non-coding sequences in chimpanzees that are orthologous to proposed human ORFans is just such evidence.

---

<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [February 17, 2024, 3:03am UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2486 "2024-02-17T03:03:29Z")

</div>

> [@John\_Harshman](#):
>
> > [@Mercer](#):
> >
> > So searching only for “alternative splicing” and no equivalents is incompetent.
> 
> On the basis of a single paper?

No, but it was an instant indicator of incompetence.

> [@John\_Harshman](#):
>
> What if most papers do mention the exact term?

Irrelevant, because you claimed it was “comprehensive.” That’s objectively false. It’s very amusing that your ego won’t let you admit that.

Do you know that you can do searches for more than one term? For title/abstract searches that include one term and don’t include another?

Oh, and as further evidence of incompetence and/or unethical cherry-picking, in their database they cited a much more recent paper and concluded that there was no evidence of functional splice isoforms.

> [@John\_Harshman](#):
>
> It could be comprehensive without including every paper in the literature.

You claimed to know that it is comprehensive. Again, your flailing is amusing.

> [@John\_Harshman](#):
>
> You have to establish that the search misses a large fraction of such genes.

No, _ **you** _ have to establish that it was comprehensive. Your claim, your evidentiary burden. You’ve also claimed that more comprehensive reviews with higher percentages were wrong, remember? You’ve touted this utter crap paper as the gold standard.

---

<div class="post-metadata">

**Author:** ![CrisprCAS9](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/crisprcas9/32/9145_2.png) [@CrisprCAS9](https://discourse.peacefulscience.org/u/CrisprCAS9)\
**Post date:** [February 17, 2024, 3:24am UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2487 "2024-02-17T03:24:04Z")

</div>

> [@colewd](#):
>
> There is no mathematical model in the literature that reconciles this.

The ‘mathematical model’ is called division and multiplication. This isn’t science, this is grade school math.

---

<div class="post-metadata">

**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [February 17, 2024, 4:51am UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2488 "2024-02-17T04:51:25Z")

</div>

> [@Mercer](#):
>
> No, but it was an instant indicator of incompetence.

It’s only incompetence if it produces poor results, which has not yet been demonstrated. Now, a useful citation would be to a better review. Do you have one?

> [@Mercer](#):
>
> Oh, and as further evidence of incompetence and/or unethical cherry-picking, in their database they cited a much more recent paper and concluded that there was no evidence of functional splice isoforms.

I have no idea what you mean by that one.

> [@Mercer](#):
>
> You’ve also claimed that more comprehensive reviews with higher percentages were wrong, remember?

No, I don’t remember. Then again I don’t recall claiming that the review in question was comprehensive either. What reviews are you talking about? I also don’t recall anyone mentioning them. What I’m doing is trusting that Larry Moran knows what he’s talking about, failing evidence to the contrary.

---

<div class="post-metadata">

**Author:** ![colewd](https://avatars.discourse-cdn.com/v4/letter/c/ecd19e/32.png) [@colewd](https://discourse.peacefulscience.org/u/colewd)\
**Post date:** [February 17, 2024, 1:17pm UTC](https://discourse.peacefulscience.org/t/the-argument-clinic/15561/2489 "2024-02-17T13:17:42Z")

</div>

> [@John\_Harshman](#):
>
> The presence of non-coding sequences in chimpanzees that are orthologous to proposed human ORFans is just such evidence.

Hi John  
This is based on the inference of common descent and the inference that the ORFans are non functional.

The evidence that is not available is reproduction generating a novel functional gene sequence. Given the vast quantity of differences this should be possible if there is indeed a working mechanism in the reproductive process.

regarding alternative splicing

[https://doi.org/10.1016%2Fj.csbj.2020.12.009](https://doi.org/10.1016%2Fj.csbj.2020.12.009)

[Previous page](https://discourse.peacefulscience.org/t/the-argument-clinic/15561.md?page=122)

[Next page](https://discourse.peacefulscience.org/t/the-argument-clinic/15561.md?page=124)