JeffB and Swamidass: Understanding Evidence for Phylogeny

Truthfully, I could have given a more educated response on #1. Correct, it’s not intended to ‘Model God’.
#1 really served to, as I mentioned, get some dialog going.
You have a lot of visitors here, and for some of them that might be their first impression at the first pass on that article. So if anything it serves as a chance to clear that up. To word this one better, the first step in this process is to trust the question: Is this really a good test of descent vs. God’s direct design? Personally I haven’t strongly settled on that answer. And that’ s a hindrance (BUT, let’s table that topic).

As for the other points: I really didn’t believe strongly on #3, and really don’t care either way on #4. So those are worth dropping.

#2 is where I really want to focus on. So I’d like to proceed with that.

But to do so, I first want to respond to this:

Actually you make a valid point when you accurate described what we call a dependency graph. Those certainly are different from nested hierarchies. In fact, I’m glad you mentioned those. I have a follow-up post related to that (that would be Part (2) ).

Understand that I’m using an analogy for sake of communication. When I mentioned nested hierarchies for software, I meant something along these lines:

The first branch could be:
Console apps, web services, user interfaces.

User interfaces could be branched into
Webpages, phone apps, desktop apps.

Desktop apps (written in C#) could be branched into:
WinForms, WPF, UWP

I meant branching like that.
So again, following that analogy, if I were to write a program to scan existing machine code, and wanted to use existing apps, organizing them this way, and using that as a heuristic would improve the performance of my algorithm.

For example, if an app had code that functions as an event queue (mouse events for example), then only searching other user interfaces would be the best approach to find that match.

Getting back to #2 above (since again, that’s really what I want to focus on), I can see the value of using nested hierarchies, regardless of whether or not there was an actual ancestral relationship between them.

(LASTLY: Since I wrote this, I noticed there were some other posts. Just fyi, I have not had the time to read those yet, so this is just a reply to Joshua’s response.)