# Howe's Diagram (not really): Round Two

**URL:** <https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105>\
**Category:** Side Conversation\
**Tags:** Science\
**Created:** [August 13, 2021, 10:12pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105 "2021-08-13T22:12:58Z")\
**Posts on this page:** 20\
**Page:** 1

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**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [August 13, 2021, 10:12pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/1 "2021-08-13T22:12:58Z")

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@colewd in a previous thread has refused to comment on whether the organisms sampled and shown in the Venn diagrams below are independently created or not.

![zjom_a_1905958_f0002_oc](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/7/7dd3caa8f0c0a671d53c82bb735211d9a175e99c.jpeg)

That’s a strange decision since the Venn diagrams were made in exactly the same way as the Howe diagram which he claims is better explained by independent creation even though it shows a freaking nested hierarchy.

The organisms in the above diagrams are all _E.coli_, but different strains. **Note how common descent of these strains creates a nested hierarchy pattern matching that seen in Howe’s chart. We also see the same gene loss and gene gain events John showed in Howe’s diagram**. For example, in Venn diagram “b”, we observe that _E.coli_ strains “7.3” and “Nissie 1917” retained 13 ancestral genes, but those genes were lost in strains “K-12 substr. MG1655” and “ATCC BAA-460”. Conversely, “7.3” and “Nissie 1917” individually gained 123 and 723 genes, respectively.

> **[Genomic characterization of four Escherichia coli strains isolated from oral...](https://www.tandfonline.com/doi/full/10.1080/20002297.2021.1905958)**
>
> (2021). Genomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies. Journal of Oral Microbiology: Vol. 13, No. 1, 1905958.

Another similar paper (looking at _Klebsiella pneumoniae_ strains) with the same diagram, showing common descent and gene loss and gain following that descent:

 ![Screenshot_20210813-233653](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/0/0fb113f1f4e8a0157a81cd5b84dc3fb6612295a0.png)

> **[Comparative Genomics of Klebsiella pneumoniae Strains with Different...](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3165360/#!po=36.7257)**
>
> There is a global emergence of multidrug-resistant (MDR) strains of Klebsiella pneumoniae, a Gram-negative enteric bacterium that causes nosocomial and urinary tract infections. While the epidemiology of K. pneumoniae strains and occurrences of...

That’s all guys. Common descent wins.

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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:** [August 13, 2021, 10:29pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/2 "2021-08-13T22:29:03Z")

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> [@Michael\_Okoko](#):
>
> The organisms in the above diagrams are all _E.coli_ , but different strains.

How are you explaining the gene gain/loss in these patterns? Assuming that all these species do indeed share a common ancestor? What Venn diagram would you have expected from the Lenski experiment given this data?

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**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:** [August 13, 2021, 10:32pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/3 "2021-08-13T22:32:51Z")

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> [@colewd](#):
>
> What Venn diagram would you have expected from the Lenski experiment given this data?

I would expect no Venn diagram, because the Lenski experiment began with a single clone and didn’t go on long enough to expect very many genes to be lost or gained. There would doubtless be a few, and they would fit the tree of descent within the clone, but they wouldn’t populate most of the diagram.

> [@colewd](#):
>
> Assuming that all these species do indeed share a common ancestor?

Are you claiming that strains of _E. coli_ do not share a common ancestor? Are you going so far as to claim that even single species are not related within themselves?

> [@colewd](#):
>
> How are you explaining the gene gain/loss in these patterns?

He doesn’t have to. It’s the pattern that counts, and the pattern is explained by common descent.

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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:** [August 13, 2021, 10:46pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/4 "2021-08-13T22:46:46Z")

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> [@John\_Harshman](#):
>
> He doesn’t have to. It’s the pattern that counts, and the pattern is explained by common descent.

Yet in the other discussion you agreed that the pattern was explained by common descent along with gene gain and gene loss.

> The combination of a particular tree of common descent within vertebrates and gene gain/loss explains the pattern in the data.

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**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:** [August 13, 2021, 11:08pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/5 "2021-08-13T23:08:16Z")

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> [@colewd](#):
>
> Yet in the other discussion you agreed that the pattern was explained by common descent along with gene gain and gene loss.

Yes, but the point is that it isn’t necessary, in order to explain the pattern, also to explain the gains and losses. Once again I urge you to think before you type. Or if this is you thinking, I urge you to think better.

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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:** [August 13, 2021, 11:14pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/6 "2021-08-13T23:14:19Z")

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> [@John\_Harshman](#):
>
> Yes, but the point is that it isn’t necessary, in order to explain the pattern, also to explain the gains and losses. Once again I urge you to think before you type. Or if this is you thinking, I urge you to think better.

This is a claim that one piece of evidence is sufficient to confirm a hypothesis. It turns out we can explain divergent gene patterns in prokaryotic cells because of HGT. This is common descent plus HGT.

There is no equivalent explanation in vertebrates. Why did you let Michael push this deception of not providing a citation and demanding an answer?

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**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [August 13, 2021, 11:29pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/7 "2021-08-13T23:29:22Z")

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> [@colewd](#):
>
> > [@Michael\_Okoko](#):
> >
> > The organisms in the above diagrams are all _E.coli_ , but different strains.
> 
> How are you explaining the gene gain/loss in these patterns?

That’s totally irrelevant Bill. All I have demonstrated is that common descent reproduces the Howe pattern, completely refuting the arguments you have been throwing about in the name of Sal’s flower. Gene loss and gene gain were also clearly evident.

> [@colewd](#):
>
> Assuming that all these species do indeed share a common ancestor?

Those aren’t different species. They are different strains of the same species, which is _E.coli_.

I am also not “assuming” common ancestry here. Do you even know what a strain is?

> [@colewd](#):
>
> What Venn diagram would you have expected from the Lenski experiment given this data?

The same diagram, but with few gains and losses due to the nature of the ancestor and the length of the experiment. Something like this:

![zjom_a_1905958_f0001_oc (1)](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/c/c579f5220f24567f37cead582e4d186fa6140dbd.jpeg)

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**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:** [August 14, 2021, 12:10am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/8 "2021-08-14T00:10:55Z")

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> [@colewd](#):
>
> This is a claim that one piece of evidence is sufficient to confirm a hypothesis.

It is not. You mistake the quantity of evidence even in that one diagram, much less all the other evidence people have mentioned to you and you have ignored.

> [@colewd](#):
>
> It turns out we can explain divergent gene patterns in prokaryotic cells because of HGT.

Not nested hierarchical patterns. You are confused.

> [@colewd](#):
>
> Why did you let Michael push this deception of not providing a citation and demanding an answer?

It wasn’t deception. You should be able to answer, as you claim to be able to tell that the Howe diagram is the result of separate creation without reference to anything other than the diagram, you should also be able to tell whether these other diagrams are also, without advance knowledge of the identities of the taxa being compared. Your inability to work with the new diagrams suggests that your claims about the previous one are not warranted. And that was the point, amply shown.

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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:** [August 14, 2021, 12:24am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/9 "2021-08-14T00:24:04Z")

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> [@John\_Harshman](#):
>
> It wasn’t deception. You should be able to answer, as you claim to be able to tell that the Howe diagram is the result of separate creation without reference to anything other than the diagram, you should also be able to tell whether these other diagrams are also,

Can I pull quotes in the future without a citation when we are having a discussion?

Are you going to claim that the diagrams were prokaryotic vs multicellular eukaryotic was not relevant to the discussion?

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**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:** [August 14, 2021, 12:27am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/10 "2021-08-14T00:27:56Z")

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> [@colewd](#):
>
> Can I pull quotes in the future without a citation when we are having a discussion?

You have, you will. But that’s not at all the same. This was a test, a blind experiment. The result of the experiment is clear.

> [@colewd](#):
>
> Are you going to claim that the diagrams were prokaryotic vs multicellular eukaryotic was not relevant to the discussion?

Yes. It wasn’t relevant. When comparing gene presence and absence, it doesn’t matter whether the organisms involved are prokaryotic or eukaryotic, unicellular or multicellular. If the diagrams show nested hierarchy, the explanation is common descent. You can make all the vague, whiny noises you like, but it doesn’t change the facts.

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**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [August 14, 2021, 12:44am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/11 "2021-08-14T00:44:33Z")

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> [@colewd](#):
>
> Are you going to claim that the diagrams were prokaryotic vs multicellular eukaryotic was not relevant to the discussion?

You want multicellular eukaryotes? Cool. Look at the Venn diagram below and tell me whether the compared organisms were independently created or not?

 ![ezgif.com-gif-maker (1)](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/b/b9ce535b6225f1e76fd9e1e706368615f11d5979.jpeg)

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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:** [August 14, 2021, 12:54am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/12 "2021-08-14T00:54:33Z")

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> [@John\_Harshman](#):
>
> You have, you will. But that’s not at all the same. This was a test, a blind experiment. The result of the experiment is clear.

What was clear is evolutionary biologists are continuing to push prokaryotic micro evolution is the same as multicellular macro evolution.

> [@John\_Harshman](#):
>
> Yes. It wasn’t relevant. When comparing gene presence and absence, it doesn’t matter whether the organisms involved are prokaryotic or eukaryotic, unicellular or multicellular. If the diagrams show nested hierarchy, the explanation is common descent. You can make all the vague, whiny noises you like, but it doesn’t change the facts.

Even if the reproductive processes are different? Even if the cellular structures are different. You are claiming equivalence based on a pattern?

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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:** [August 14, 2021, 1:02am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/13 "2021-08-14T01:02:30Z")

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Michael  
The burden is on evolutionary biology to show this pattern is consistent with the LUCA and LVCA hypothesis. If this is not addressed credibility is lost. A pattern as the only evidence is not going to hold up IMO. You need to explain the how the changes occurred or change the starting points.

No one at this point is arguing the common ancestry of bacteria. They are biologically apples and oranges with multicellular eukaryotes.

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**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:** [August 14, 2021, 1:07am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/14 "2021-08-14T01:07:12Z")

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> [@colewd](#):
>
> What was clear is evolutionary biologists are continuing to push prokaryotic micro evolution is the same as multicellular macro evolution.

That’s what someone in my recollection has referred to as the “labeling fallacy”. The diagrams don’t care if they come from prokaryotes or eukaryotes, from microevolution or macroevolution (however you think those terms may be defined). Their similarities are clearly the result of similar processes, and similar conclusions may be drawn from them.

> [@colewd](#):
>
> Even if the reproductive processes are different?

They are not, in any way that matters here.

> [@colewd](#):
>
> Even if the cellular structures are different.

They are not, in any way that matters here.

> [@colewd](#):
>
> Your are claiming equivalence based on a pattern?

You are so far out of your depth that you are reduced to random sputtering. Thanks to @Michael_Okoko for a most elegant demonstration of your position’s vacuity.

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<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:** [August 14, 2021, 1:11am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/15 "2021-08-14T01:11:21Z")

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> [@John\_Harshman](#):
>
> They are not, in any way that matters here.

Please explain.

> [@John\_Harshman](#):
>
> You are so far out of your depth that you are reduced to random sputtering. Thanks to @Michael_Okoko for a most elegant demonstration of your position’s vacuity.

You support asking for yes or no answers based on an incomplete reference? This reminds me of Washington politics. John, you need to support your claims more than an assertion based on a pattern.

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<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:** [August 14, 2021, 3:55am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/16 "2021-08-14T03:55:11Z")

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

The same evolutionary processes happen in both of them. The differences don’t affect that. What more needs to be explained?

> [@colewd](#):
>
> John, you need to support your claims more than an assertion based on a pattern.

I have, and I do. This is more random sputtering.

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<div class="post-metadata">

**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [August 14, 2021, 9:36am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/17 "2021-08-14T09:36:32Z")

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> [@colewd](#):
>
> No one at this point is arguing the common ancestry of bacteria. They are biologically apples and oranges with multicellular eukaryotes.

This is woefully incorrect, but since you want multicellular eukaryotes no problem. The Venn diagram below shows two multicellular organisms:

![ezgif.com-gif-maker (2)](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/0/06237fcc8c64fd19b0970ae540c225d328a6a258.jpeg)

Remember this was made exactly the same way as Howe’s diagram, so it should be too easy to say whether they were made separately or not. Which is it?

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**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:** [August 14, 2021, 10:55am UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/18 "2021-08-14T10:55:20Z")

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Guys forget it. Just forget it. This is Bill Cole. There’s a 5000 post thread on theskepticalzone where 3-4 people try to explain things to him. Elementary things like the more distantly related the more divergent, common descent predicts consilience of independent phylogenies(including an outright demonstration of this), the patterns of gene gain and loss corroborate the same tree, etc. 5000 posts to no avail.

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<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:** [August 14, 2021, 12:53pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/19 "2021-08-14T12:53:44Z")

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> [@Rumraket](#):
>
> Elementary things like the more distantly related the more divergent,

That one, at least, is not true.

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<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:** [August 14, 2021, 1:10pm UTC](https://discourse.peacefulscience.org/t/howes-diagram-not-really-round-two/14105/20 "2021-08-14T13:10:04Z")

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To a first approximation it’s close enough. And you can generally show this just by looking at close family relationships, like parents and their children, vs grand-cousins and the like. Descent with modification accumulating along branching lines of descent. Yes rates of evolution can vary due to both changes in mutation rates and the effect of selection, so that some independent lineages retain more similarity over longer timescales, while others can diverge much more radically in the same amount of time. The point is, even these plain and simple things we can see in our own family trees everyone can understand Bill would become mysteriously incapable of wrapping his head around.

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