JeffB and Swamidass: Understanding Evidence for Phylogeny

That’s right.

@jeffb BLAST also implements several heuristics, more heuristics than does SIFTER.

The real question is why this heuristic, of trees, ends up so powerful.

Not exactly, as your further comments make clear. SIFTER is not making trees based on evolutionary phylogeny. It is just inferring the trees directly from the data; the sequences include all the information needed to construct the tree and place the sequences into it.

Not it does not. It is critical to stay on topic here.

We are not testing for design. Instead, we are asking if similarity is fully explained by common function, or if is better explained by common descent.

If the answer is “common descent” that just could mean that God created by a process of common descent.

This is just totally false, both in the conclusion and the reasoning.

BLAST is a very complex algorithm, and much of that complexity enables it to run so fast. It takes a us a several weeks to cover all the key concepts for graduate students to understand how it works. It works fast because it relies on SEVERAL very clever heuristics.

So what? BLAST does not represent common design. We are not discussing design. It does, however, represent sequence similarity.

Here you are revealing some deep confusion.

SIFTER does not rely on information external to the sequences themselves when constructing the tree. What you are proposing is not even possible, because it does not group sequences using external information (e.g. precomputed evolutionary taxonomies), so there is no way to implement what you are suggesting.

More importantly, this is an unbiased test. It would not have been published otherwise.

Why is it so hard to accept this analysis and its conclusions? What I’m presenting here isn’t even in conflict with YEC. Ken Ham thinks that all bacteria are a single “kind,” so maybe they all do share a common ancestor.

I just don’t understand the creativity and persistence of your objections. Are you really confused about this? Or is this really a difficult conclusion to accept? What exactly is supporting your reticence?


Can anyone give me an explanation of how trees are inferred from the data. Is it along the lines of “If we find two sequences with a single difference, we infer the this represents a branch of a tree”?

The most easy to understand algorithm is maximum parsimony (now rarely used on genetic sequences, but provides a nice introduction to the subject of how trees are inferred):

Here’s an explanation for the much more commonly used(but also more complicated) maximum likelihood algorithm:


No, because it’s a mathematical analysis, not human inference in both cases being discussed. That’s why it’s so powerful.

No, it’s orders of magnitude more complex.

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Generally, you compare a whole bunch of different trees under some criterion of fit to the data and pick the one that has the best fit. Parsimony is the simplest one: you pick the tree that requires the smallest number of total changes.

You can’t make a tree out of two sequences. You suppose there’s a branch connecting them through a common ancestor, and that single difference would have to have happened somewhere along that branch. But if you expand that to multiple sequences with variously distributed differences, you can assign those differences to different branches of a tree, whichever branches require the fewest changes. I’m sure there must be some simple graphic explanations somewhere on the web. Try searching for phylogenetics and parsimony.


I’m asking questions. I’ll admit, I hadn’t gotten very far into the supporting material, partial due to time, partly due to their technical nature. I have degrees in computer science, not biology. So I’ve been thinking about this from what I’m familiar with. I’m also trying to ask questions to help me process this from a perspective of comparing common descent with biblical creation (kinds via divine fiat). The word “design” seems to be too ambiguous:

I may not have worded that properly. I do believe this is related to the topic. At least it is for me. Again, I’m trying to determine is how this relates to the question of common design vs biblical creation. And my questions were related to this. Perhaps I was trying to extend this example beyond what it could really accomplish.

Good to know, and confirms what I was considering. I personally can’t speak for the kind boundaries here, but I was wondering if some of the relationships we were seeing was due to them being from a common kind.

Several weeks. Great.
Then I’m assuming it would be a lot longer for a non-graduate student who barely has time to post comments on this site every few days.

Joshua, I appreciate you taking the time on this one. I have made an effort here, despite my limited background and resources. I do feel like I get the general concept, despite my persistently sometime-odd questioning. But a full understanding would take some time. It would take me quite a while to gain enough knowledge to really draw a conclusion that I personally can be comfortable with. And I’m not comfortable with “just take my word for it.” I don’t even do that for YEC experts.

I will say this: I does sound interesting. And I certainly take note of the fact that you find it compelling. I’ll do what I do with anything new like this: make mental note of it, put it in my “back pocket” and watch for future developments on it. Know that I would do that exact same thing even if it was something in YECs favor! I’ve learned it’s good to appreciate new developments, but also not to hold on to them too tightly.

Excellent point, one I have tried to make frequently. You should abandon that term “design”; I suggest “separate creation” as an alternative. “Common design” means nothing.