# Common design and common descent

**URL:** <https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507>\
**Category:** Side Conversation\
**Created:** [November 24, 2021, 5:09pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507 "2021-11-24T17:09:00Z")\
**Posts on this page:** 19\
**Page:** 1

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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:** [November 24, 2021, 12:46pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/1 "2021-11-24T12:46:56Z")

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> [@An Unpeaceful Peace by Casey Luskin](https://discourse.peacefulscience.org/t/an-unpeaceful-peace-by-casey-luskin/14501/3):
>
> rejecting similarity (and ignoring the very notion of nested similarity) as evidence of descen

actually we can get the same pattern if the designer created a new species by using an existing genome (like he did with Eve if we are talking about creationism). but even if we didnt have any explanation for that hierarchy (which isnt the case as i already showed here in the past), at best we can say that we dont have explanation yet. which is also true in some issues with evolution, and yet i dont see you rejecting it.

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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:** [November 24, 2021, 2:02pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/2 "2021-11-24T14:02:28Z")

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> [@scd](#):
>
> actually we can get the same pattern if the designer created a new species by using an existing genome

In other words, we get the same pattern if the designer carefully simulates common descent. But why would he (it?) do that?

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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:** [November 24, 2021, 3:14pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/3 "2021-11-24T15:14:12Z")

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> [@John\_Harshman](#):
>
> In other words, we get the same pattern if the designer carefully simulates common descent. But why would he (it?) do that?

actually he doesnt. remember that common descent doesnt predict a nested hierarchy, since evolution doesnt necessarily predict a single origin for life. not only that, but common descent also doesnt predict nested hierarchy since it could be that natural selection took place. thus, common descent doesnt predict a specific shape of phylogeny (see the debate about molecular clock for instance).

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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:** [November 24, 2021, 3:19pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/4 "2021-11-24T15:19:27Z")

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> [@scd](#):
>
> remember that common descent doesnt predict a nested hierarchy,

It does.

> [@scd](#):
>
> since evolution doesnt necessarily predict a single origin for life.

Evolution can’t do that. Each origin would produce a separate nested hierarchy. We don’t see that.

> [@scd](#):
>
> but common descent also doesnt predict nested hierarchy since it could be that natural selection took place. t

Natural selection in no way eliminates the nested hierarchy. You are very, very confused.

> [@scd](#):
>
> thus, common descent doesnt predict a specific shape of phylogeny (see the debate about molecular clock for instance).

None of that makes any sense. The molecular clock does not affect the shape of the tree.

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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:** [November 24, 2021, 3:32pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/5 "2021-11-24T15:32:29Z")

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> [@Mercer](#):
>
> The molecular clock does not affect the shape of the tree

yes it does. this is why we can see a different tree by using a different set of genes sometimes.

> [@Mercer](#):
>
> Evolution can’t do that

this is what creationists always says, and yet you disagree with them.

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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:** [November 24, 2021, 4:03pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/6 "2021-11-24T16:03:53Z")

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> [@An Unpeaceful Peace by Casey Luskin](https://discourse.peacefulscience.org/t/an-unpeaceful-peace-by-casey-luskin/14501/20):
>
> > [@Mercer](#):
> >
> > The molecular clock does not affect the shape of the tree
> 
> yes it does. this is why we can see a different tree by using a different set of genes sometimes.

That doesn’t support your claim. You are only demonstrating the depth of your confusion.

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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:** [November 24, 2021, 4:05pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/7 "2021-11-24T16:05:18Z")

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> [@scd](#):
>
> yes it does. this is why we can see a different tree by using a different set of genes sometimes.

No, that has nothing to do with any molecular clock. There are three reasons why different genes can show different trees: 1) the genes actually have different histories (horizontal transfer, lineage sorting, etc.; 2) one or more of the genes doesn’t have a strong signal, and the tree is just noise; 3) the data and analysis method are mismatched. The third option may have something to do with a molecular clock, i.e. if you use an algorithm that assumes a clock when the data are not clocklike. But nobody does that in the past 30 years at least, so no problem.

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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:** [November 24, 2021, 4:18pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/8 "2021-11-24T16:18:11Z")

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> [@scd](#):
>
> remember that common descent doesnt predict a nested hierarchy

Months of discourse about common descent on PS and you have learned nothing.

> [@scd](#):
>
> since evolution doesnt necessarily predict a single origin for life.

True. Evolution happens regardless of the number of origin events.

> [@scd](#):
>
> not only that, but common descent also doesnt predict nested hierarchy since it could be that natural selection took place

You are deeply, deeply confused. Natural selection doesn’t affect common descent. As long as vertical gene inheritance via reproduction, common descent is inevitable.

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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:** [November 24, 2021, 4:58pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/9 "2021-11-24T16:58:00Z")

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> [@John\_Harshman](#):
>
> The third option may have something to do with a molecular clock, i.e. if you use an algorithm that assumes a clock when the data are not clocklike. But nobody does that in the past 30 years at least, so no problem.

even if its true, again, since natural selection can effect DNA sequence, it doesnt necessarily predict a nested hierarchy, since the sequence can be changed at a different rate over time, and thus can give us a different phylogeny. even if all phylogenetic trees were looked like a star phylogeny, evolution would have no problem with that.

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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:** [November 24, 2021, 5:09pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/10 "2021-11-24T17:09:00Z")

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> [@scd](#):
>
> since the sequence can be changed at a different rate over time, and thus can give us a different phylogeny.

This is one of your central misconceptions, that differences in evolutionary rate result in different trees. It just isn’t true.

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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:** [November 24, 2021, 5:23pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/11 "2021-11-24T17:23:49Z")

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> [@John\_Harshman](#):
>
> This is one of your central misconceptions, that differences in evolutionary rate result in different trees. It just isn’t true.

so whats that?:

![](https://us1.discourse-cdn.com/flex016/uploads/peacefulscience/original/2X/c/cf3534c11b768f28385e0f0528daf04a38979bae.gif)

as you can see, different evolutionery rate can indeed result in a different tree.  
(image from lee et al. 1999)

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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:** [November 24, 2021, 5:43pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/12 "2021-11-24T17:43:27Z")

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> [@scd](#):
>
> as you can see, different evolutionery rate can indeed result in a different tree.  
> (image from lee et al. 1999)

I can’t see anything there. All you show is two trees, which seem to have problems for unknown reasons and that come from an uncited reference. (“lee et al. 1999” is insufficient.)

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**Author:** ![AlanFox](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/alanfox/32/3495_2.png) [@AlanFox](https://discourse.peacefulscience.org/u/AlanFox)\
**Post date:** [November 24, 2021, 5:46pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/13 "2021-11-24T17:46:46Z")

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[https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(99)01603-1](https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347%2899%2901603-1)

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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:** [November 24, 2021, 5:51pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/14 "2021-11-24T17:51:04Z")

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from the paper:

"In another study, the mitochondrial cytochrome b gene implied a similarly absurd phylogeny of mammals, regardless of the method of tree construction. "

and:

“The most reasonable conclusion is that this is no coincidence: rather, these functionally related parts of the mitochondrial genome have undergone concerted, adaptive evolution and lost their historical signal.”

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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:** [November 24, 2021, 5:55pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/15 "2021-11-24T17:55:13Z")

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Paywalled, unfortunately.

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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:** [November 24, 2021, 5:56pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/16 "2021-11-24T17:56:26Z")

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The most reasonable conclusion is that the mitochondrial signal has been lost for deep nodes. But I can’t see the paper so can’t really comment.

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**Author:** ![AlanFox](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/alanfox/32/3495_2.png) [@AlanFox](https://discourse.peacefulscience.org/u/AlanFox)\
**Post date:** [November 24, 2021, 6:40pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/17 "2021-11-24T18:40:16Z")

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[Here’s](http://www.filogenetica.org/bibliografia/filogenetica/caracteres/functional_Phylogeny.pdf) a PDF

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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:** [November 24, 2021, 7:44pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/18 "2021-11-24T19:44:28Z")

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Thanks. The relevant papers are actually Naylor, G.J.P. and Brown, W.M. (1998) Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences, Syst. Biol. 47, 61–77 and Andrews, T.D., Jermiin, L.S. and Easteal, S. (1998) Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins? J. Mol. Evol. 47, 249–257, the actual sources of the trees and analyses referenced. I have the first, though not the second. I’ll look.

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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:** [November 24, 2021, 9:01pm UTC](https://discourse.peacefulscience.org/t/common-design-and-common-descent/14507/19 "2021-11-24T21:01:56Z")

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> [@scd](#):
>
> actually he doesnt.

Then we have no reason to expect the nested hierarchy.

> [@scd](#):
>
> remember that common descent doesnt predict a nested hierarchy

Yes it does. Common descent predicts a nested hierarchy.

> [@scd](#):
>
> since evolution doesnt necessarily predict a single origin for life

This statement doesn’t follow from the former, the word “since” in the sentence is misplaced and the logical relationship between the concepts in the two statements is completely mangled.

Allow me to spell this out more correctly:  
It is true that evolution doesn’t necessarily predict a single origin of life. That is, it being true that evolution is something that happens to living organisms does not entail that life arose only once. Nobody here disagrees with that. You could in principle have life originating multiple times, and each originating event giving rise to a different type of life that evolves. Thus evolution would be true, in the sense that all life evolves, but it does not all share common ancestry, and it came from different originating events.

Thus the reason we think common descent _is_ true, is _not_ that we think evolution is true(that living organisms evolve over time) or that there _was_ a single origin of life.

Rather, we think common descent is true _because we have the evidence we expect of common descent_ (and we do _not_ expect on any competing hypothesis), **a nested hierarchy.**

Please get your logic and evidence in order and try to properly understand why we think the things we do.

We think all life on Earth shares common ancestry _because we have the evidence expected of common ancestry._

We also think all the life that shares common ancestry originated in one originating event.

We do _not_ think there _could not_ have been other such events, we just haven’t been able to find any evidence of descendants of other originating events.

So we simply say that there appears to have been _at least_ one originating event, and all known life seems to be related through a bottleneck of one species, the last universal common ancestor, which itself can trace it’s ancestry back to that one originating event.

Does it compute? I think it does. At least it should. Thank you.

> [@scd](#):
>
> . not only that, but common descent also doesnt predict nested hierarchy since it could be that natural selection took place.

Given what we know of genetics, natural selection “taking place” does not give any reason to doubt the nested hierarchy. As best we can tell, there is an overwhelming abundance of underlying genetic ways to produce the same or similar anatomical/physiological solutions, which is why we have an actual nested hierarchy, instead of just lots of basically identical organism.

While convergence _does_ happen, it is very limited in extent and can always be identified against an overwhelming background of nested hierarchy in many other kinds of data. For any one set of genes (or anatomical attributes) you can find with a few convergently evolved residues or character states, we can find many thousands or even millions of others that exhibited a strong nested hierarchy.

> [@scd](#):
>
> thus, common descent doesn’t predict a specific shape of phylogeny (see the debate about molecular clock for instance).

Common descent doesn’t have to predict a _specific_ phylogeny, to predict _a_ phylogeny.