# 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:** 27

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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, 9:24pm UTC](https://discourse.peacefulscience.org/t/winston-ewert-the-dependency-graph-of-life/728/27 "2018-07-21T21:24:18Z")

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> [@sygarte](#):
>
> Thanks Josh. As a matter of fact, I find the module idea very interesting. And I was pleased to see that Dr. Ewert acknowledged what I see as the main objection to the conclusions. He writes:
> 
> > “…the dependency graph model has an advantage over common descent in fitting the data because it can postulate modules to explain otherwise inexplicably distributed gene families…This is why we must also take into account the parsimony or complexity of the model.”

True, however, @Winston_Ewert **penalizes** more complex models. We can debate whether he did that correctly or not, but this objection is not really valid without a careful review of his penalization. I think a better question concerns the fit we would get from an _undirected graph model_ versus a dependency graph (which is a directed graph), using the **same** penalization.

That is an important control to do. If it comes out wrong, it would undermine his argument significantly if the dependency graph model does not do better than the undirected graph. That, it seems, would be a speed bump for his proposal. As a matter of fact, we _already_ know that human diversity data better fits an undirected graph than a tree. So the real question is if the dependency graph does better than an undirected graph, not just better than a tree.

It might be resolvable even if it initially fails this control. Perhaps the penalization function would need to be improved. It is, nonetheless, an important control study to run.

**(side question to @Winston_Ewert, do the numbers in Table 4 include the penalization factor too?)**

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