# Winston Ewert: The Dependency Graph of Life

**URL:** <https://discourse.peacefulscience.org/t/winston-ewert-the-dependency-graph-of-life/728>\
**Category:** Office Hours\
**Tags:** Design\
**Created:** [July 21, 2018, 2:51am UTC](https://discourse.peacefulscience.org/t/winston-ewert-the-dependency-graph-of-life/728 "2018-07-21T02:51:30Z")\
**Posts on this page:** 1\
**Showing post:** 14

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [July 21, 2018, 6:17pm UTC](https://discourse.peacefulscience.org/t/winston-ewert-the-dependency-graph-of-life/728/14 "2018-07-21T18:17:35Z")

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> [@Winston\_Ewert](#):
>
> For any serious objection to my hypothesis, I probably won’t dispute it in this thread. If its a worthwhile objection I will want to take the time to think about, come up with a hypothesis to explain it, test that hypothesis etc. That will take time. **I’m less interested in arguing the point as in understanding the objections to it so that it can guide where work on this hypothesis needs to go.**

Same here. This thread will be open indefinitely though. This is a place where you can figure out what type of experiments might convince skeptics. Even if it takes months to get that analysis done, we will still be interested. Coming to agreement on the experiments ahead of time will help us understand the results when they come. And this also gives you a forum to make negative results known too, which also will build trust in your work.

> [@Winston\_Ewert](#):
>
> My question for you is: what mechanisms do you see as good candidates?

I can see a few:

1. Incomplete sorting (which seems to be at play in the human data).
2. Deletion and large scale genome rearrangement.
3. The Birthday paradox.
4. Introgression and/or hybridization after speciation.

Now, there are ways to test to what extent these things are affecting your results. The primate lineages are a good place to focus, because we have the most data there, and is most salient because it deals with human origins.

Once again, there seem to be ways to test your theory on the data versus these mechanisms. However, it seems that as written that it is not specified clearly enough to do this yet (at least as a third party reviewer). Though we can, for example, start to apportion specific cases into the different classes I just mentioned based on some tests of the data.

> [@Winston\_Ewert](#):
>
> I’d be curious to know which data you think has the best chance of falsifying my hypothesis.

This, also, is where the human data becomes important. I think we both agree that humans are monophyogenetic. So if your non-tree model fits better than a tree model, that is an important failed control. Without getting into the details yet, we **_already_** know that tree models fail on human diversity data. There have been several papers put out demonstrating this. We should get into the weeds on this I am sure, but that seems to indicate that common descent in the real world does not produce a tree, so your tests themselves are not demonstrating that your model is better than common descent. **Where am I going wrong in that reasoning?** And do you want to see some examples of what I am talking about?

> [@Winston\_Ewert](#):
>
> Here I’d like to know what you are referring to since selection of any sort didn’t enter into the analysis. Perhaps something about genes drifting through sequence space in a neutral fashion?

Selection is not really the issue I’m referring to here. That has to be considered carefully too.

Instead, I’m referring to, for example, synonymous mutations in proteins. It seems (though I could be wrong), you’ve restricted this to gene families. If that is the case, you are glossing over mutations more likely to be neutral. That seems to be a real problem. As this is actually where the nested clade evidence is stronger (at least from my assessment).

If I am right (and I may not be), it seems this is a direct falsification of the conceptual argument being put forward. It seems that “design modules” must be defined to be non-neutral, and you **_may_** have an explanation for why they almost fit in a nested tree. However, that **_does not_** explain why more neutral mutations (it is a relative term) might fit more tightly in a nested three than design modules. That seems to be a looming problem for your proposal. I don’t think you can make your case without dealing with this head on. It seems to be a direct falsification of your proposal, unless I’m missing something here.

> [@Winston\_Ewert](#):
>
> I will also note that BioComplexity would love to publish an official critique to my paper if anyone is interested.

Thanks for the offer. **I’m more interested in real dialogue with you.** I want you to have the best model possible, and get credit for retracting it if its wrong. If it is wrong, maybe the next idea you come up would work. Dialogue like this, I’ve found, is a much faster way to help you out.

I’m not looking for a publication out of this, but to really help us all figure this out together. In a way, think about this forum like a “micro publication,” or a “public peer-review.” It is a public thread. If desired, I can even get a DOI for it so you can reference it.

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