# Mini-thought experiment about the nested hierarchy

**URL:** <https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139>\
**Category:** Side Conversation\
**Created:** [May 9, 2019, 7:30pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139 "2019-05-09T19:30:52Z")\
**Posts on this page:** 20\
**Page:** 1

<div class="post-metadata">

**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [May 9, 2019, 7:30pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/1 "2019-05-09T19:30:52Z")

</div>

Consider this a PSA about the “nested hierarchy.” This post is an unattended roadside display: I won’t be back to respond to replies, because I am a bad person who, according to John Harshman, “flounces” off like an irresponsible pixie. (Seriously: I shouldn’t even be posting this, if you could see the barely-polite emails from my Discovery Institute co-workers about my unfinished projects…but I can’t help myself, at least not this afternoon.)

First, some leftover business from the Gould: Evolution as Fact and Theory thread. T. aqua wrote:

> Why would an information retrieval system need to be a nested hierarchy? This makes no sense.

Look at the file structures of your computer, or whatever device you are using to read this. Nested hierarchies. The Library of Congress classification system? Nested hierarchy. Almost any data storage system one can conceive? Nested hierarchy. The groups-within-groups logic, arranged in most-to-least inclusive sets, is superbly suited – maybe even optimally suited – for information storage and retrieval.

John Harshman didn’t complain about that, but he did say that, in my own “vague way,” I denied the reality of the nested hierarchy, seeing it as “merely a matter of convenience.”

Actually, this is what I said, about which John failed to comment:

> My nominalist interpretation [of the hierarchy] is supported by many thousands of anomalous character distributions, typically dumped into a bin labeled “not phylogenetically informative.”

Time to set up my little display; there is lemonade in the cooler, as long as it lasts.

Below is the standard three-domain hierarchy of life on Earth. The node on the right, marked by an arrow, represents the Last Eukaryotic Common Ancestor (LECA).

**Ask yourself this question: given that LECA is inferred to have possessed chromosomal segregation machinery (for mitotic and meiotic cell division), what would the nested hierarchy predict about the character distribution of such essential cellular machinery throughout the domain Eukarya?** Homologous or not homologous?

 ![28%20PM](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/2/27aae24135b46354f1e0e4cbca16dc2867867418.jpeg)

Write down your answer, then go here:

[https://www.g3journal.org/content/7/10/3337](https://www.g3journal.org/content/7/10/3337)

---

<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:** [May 9, 2019, 7:41pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/2 "2019-05-09T19:41:02Z")

</div>

What is the point of any of this if you will neither read nor reply to responses?

---

<div class="post-metadata">

**Author:** ![pnelson](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/pnelson/32/876_2.png) [@pnelson](https://discourse.peacefulscience.org/u/pnelson)\
**Post date:** [May 9, 2019, 7:43pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/3 "2019-05-09T19:43:35Z")

</div>

Okay – have to add one anecdote (true story).

When I was a college student, I kept myself alive by working as a reference clerk at this library:

> **[Main (Oakland) - Carnegie Library of Pittsburgh](https://www.carnegielibrary.org/clp_location/main-oakland/)**
>
> Located in the heart of Pittsburgh's Oakland neighborhood, Carnegie Library of Pittsburgh - Main serves as the primary, full-service resource for current and historic materials and information for Pittsburgh.

Millions of volumes. Great place, which gave me borrowing privileges in research library of the Natural History museum next door, where I first met the work of Soren Lovtrup, Leigh Van Valen, Joel Cracraft, and many others whom John Harshman will know.

Anyway, someone used to telephone the reference desk regularly, and ask, “Hey, do y’all still have that _ **little green book** _? You know the one I’m talking about…”

Of course, we didn’t. Now, do books naturally fall into a nested hierarchy?

Who knows? The experiment is probably impossible to do. But do we need a nested hierarchy to organize and retrieve them in a sensible way? Hell yes.

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 7:45pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/4 "2019-05-09T19:45:47Z")

</div>

> [@pnelson](#):
>
> The Library of Congress classification system? Nested hierarchy.

Will inferring the hiearchical order from the contents of books reproduce the same hiearchy to a high degree of statistical significance, and will ANY of those inferred hiearchies reproduce the actual hiearchy used by the libriarians?

Clearly the answer here is no.

---

<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:** [May 9, 2019, 8:01pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/5 "2019-05-09T20:01:36Z")

</div>

> [@Rumraket](#):
>
> Will inferring the hiearchical order from the contents of books reproduce the same hiearchy to a high degree of statistical significance, and will ANY of those inferred hiearchies reproduce the actual hiearchy used by the libriarians?

They will create a similar pattern. What you don’t have in a library is control of sequences building diversity.

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 8:04pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/6 "2019-05-09T20:04:05Z")

</div>

> [@colewd](#):
>
> They will create a similar pattern.

Prove it.

---

<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:** [May 9, 2019, 8:04pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/7 "2019-05-09T20:04:47Z")

</div>

From the cited article:

" We suggest that the large numbers of apparently lineage-specific genes in the chromosome-segregation machinery are because a very wide range of sequences must be able to carry out similar essential functions in chromosome segregation. TRGs in the chromosome-segregation machinery are either under weak selection, allowing them to drift rapidly until homology is unrecognizable, even over relatively short evolutionary distances; or some of the functions of chromosome segregation-machinery components may simply be very easy to evolve and thus TRGs that arise _de novo_ can readily evolve roles in this process."

---

<div class="post-metadata">

**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [May 9, 2019, 8:04pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/8 "2019-05-09T20:04:58Z")

</div>

> [@pnelson](#):
>
> Look at the file structures of your computer, or whatever device you are using to read this. Nested hierarchies.

If I compare the data (e.g. letters) in those files they don’t produce a nested hierarchy. However, DNA sequences do produce a nested hierarchy. The two aren’t comparable.

> [@pnelson](#):
>
> **Ask yourself this question: given that LECA is inferred to have possessed chromosomal segregation machinery (for mitotic and meiotic cell division), what would the nested hierarchy predict about the character distribution of such essential cellular machinery throughout the domain Eukarya?** Homologous or not homologous?

It would differ for each example. Different cellular machinery can emerge in each lineage and later become essential. What we would predict is if there is a homologous gene that it would carry a phylogenetic signal.

---

<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:** [May 9, 2019, 8:21pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/9 "2019-05-09T20:21:32Z")

</div>

> [@John\_Harshman](#):
>
> or some of the functions of chromosome segregation-machinery components **may simply be very easy to evolve** and thus TRGs that arise _de novo_ can **readily evolve roles** in this process."

Looks like an assumption. Random change can find complex function. Whats the real mechanism causing this? A mind can find functional sequences.

---

<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:** [May 9, 2019, 8:26pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/10 "2019-05-09T20:26:00Z")

</div>

> [@colewd](#):
>
> Whats the real mechanism causing this?

They mention that in the part you snipped out. They’re easy to evolve because the sequences are not very constrained by selection, i.e. all manner of sequences will work. Now of course this is a hypothesis that needs further testing. But you really ought to read and try to understand the things you opine about.

---

<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:** [May 9, 2019, 8:34pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/11 "2019-05-09T20:34:39Z")

</div>

> [@John\_Harshman](#):
>
> They mention that in the part you snipped out. They’re easy to evolve because the sequences are not very constrained by selection, i.e. all manner of sequences will work.

So you think this is good for evolutionary mechanisms. Now we have unguided random change and you are proposing that finds function in almost infinite sequence space.

How about considering a deterministic mechanism?

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 8:38pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/12 "2019-05-09T20:38:32Z")

</div>

Hey Bill you working on proving it, or are you satisfied with just claiming something without having the slightest clue if it is true?

---

<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:** [May 9, 2019, 8:42pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/13 "2019-05-09T20:42:26Z")

</div>

I am satisfied that my statement is true. I don’t feel the need to prove it as we can get tother examples that work better or are closer to biological nested hierarchies.

We have gone 15 rounds on this before and it comes down to throwing assertions at each other.

We cannot eliminate common descent or common design as explanations for the pattern so we have a stand off.

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 8:44pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/14 "2019-05-09T20:44:55Z")

</div>

> [@colewd](#):
>
> I am satisfied that my statement is true.

Based on what?

> I don’t feel the need to prove it

I understand that you don’t, but isn’t that a problem? Couldn’t I just say the opposite?

_I am satisfied that your statement is false, and I don’t feel the need to prove it._

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 8:47pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/15 "2019-05-09T20:47:39Z")

</div>

> [@colewd](#):
>
> We have gone 15 rounds on this before and it comes down to throwing assertions at each other.

No, I once literally tested one of your assertions and proved it false before your very eyes when I showed that three sets of ten similar sequences designed to merely be similar by randomly mutating the same template did not reproduce the same nested hiearchy at all.

Clearly your intutions about this are false and I demonstrated this to you. Your reaction at the time was that you appreciated the work and needed to think about it. Now you’re back, having somehow magically forgotten about it, and are repeating the same basic mistake all over again.

---

<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:** [May 9, 2019, 8:54pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/16 "2019-05-09T20:54:08Z")

</div>

> [@Rumraket](#):
>
> I am satisfied that your statement is false, and I don’t feel the need to prove it.

The problem is Rum my statement is subjective so you cannot prove it is false until you nail down what similar means. Similar can merely mean two nested patterns.

This was really tangential to my argument anyway as computers that come from similar designers are a closer match than library books as they process coded information.

---

<div class="post-metadata">

**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:** [May 9, 2019, 8:57pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/17 "2019-05-09T20:57:41Z")

</div>

> [@colewd](#):
>
> The problem is Rum my statement is subjective so you cannot prove it is false until you nail down what similar means.

Science doesn’t need to prove any of your science-free woo is false Bill. You need to demonstrate your “common Design” claims are true. Since you haven’t demonstrated **any** sort of Design in biological life, let alone common Design, looks like you failed again.

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 8:58pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/18 "2019-05-09T20:58:18Z")

</div>

And now you’re just not making sense I’m sad to say. Your previous response which I objected to, while wrong, at least made logical sense. This one is incoherent and looks sort of like a collection of only half-way related concepts and ideas.

---

<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:** [May 9, 2019, 9:06pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/20 "2019-05-09T21:06:23Z")

</div>

> [@Rumraket](#):
>
> No, I once literally tested one of your assertions and proved it false before your very eyes when I showed that three sets of ten similar sequences designed to merely be similar by randomly mutating the same template did not reproduce the same nested hiearchy at all.

This does not make any sense to me. I initiated a private conversation if you want to work through this.

---

<div class="post-metadata">

**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [May 9, 2019, 9:08pm UTC](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139/21 "2019-05-09T21:08:21Z")

</div>

I’m sorry Bill I don’t mean to be an asshole but I just don’t have the patience for it. Like you probably are, I too am bored of trodding this same ground all over again for the gazillionth time.

[Next page](https://discourse.peacefulscience.org/t/mini-thought-experiment-about-the-nested-hierarchy/6139.md?page=2)