A Test of Common Descent vs. Common Function

(S. Joshua Swamidass) #21

It is common to convince them of the plausibility of common descent, and I do not attempt to change their personal beliefs (though that can happen too). It is fairly common among students. Most of them have never had the science explained from a trusted source in a way they can understand.

(John Harshman) #22

Not the same thing as truth, though, is it? I assume you’re talking about a Todd Wood sort of admission. What have you used to produce such a result?

The argument that you presented here seems quite abstruse and indirect, unlikely to be understood easily. I generally try nested hierarchy, and the responses are usually a) that hierarchy doesn’t exist or b) it does exist but it’s exactly what creation would produce or c) paradoxically, both. One attempts to answer a by demonstrating some obvious tree, with data. I often try Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003; 52:386-402, because the data are very simple and there’s a figure showing it mapped onto the tree. Hasn’t worked so far. As for b, the question is why one would expect such a thing, and nobody so far has an answer, but it doesn’t stop them. And c is just hopeless. Of course, I’m not a trusted source, being a tool of Satan and all.

What’s your approach?


I found the paper on SIFTER quite a few years ago and have been waiting for others to pick up on it. Here is an excerpt from the abstract that relates to what you were saying in the opening post:

96% accuracy is really good. Using evolutionary mechanisms to predict protein function works.

I think it is also worth pointing out that some protein families may not perform as well with SIFTER. As I have been rightfully warned of in the past, we shouldn’t ignore the noise inherent in the process of evolution.

(S. Joshua Swamidass) #24

@Nonlin.org here is a direct test of common descent you have yet to engage.


Didn’t he say he was winding things down here a couple days ago?

Edit: Six days ago?

(Nonlin.org) #26

Did you mean to link to something?

(Blogging Graduate Student) #27

He’s referring to the OP.

(Nonlin.org) #28

How is this a direct test of common descent? From what I see, SIFTER is a new model that is better than other models, all assuming common descent. But how can a model validate its own assumptions? And it’s simply logical that from one set of models one will be better than the others.

In addition, anyone that has ever built a model knows that said model is by definition compatible with its assumptions.

[@moderators deleted spam link]


The same way that all hypotheses are validated: by the results of experimentation. A model using common descent and evolution outperforms a model based simply on similarity. Those are the results that validate the hypothesis.

The SIFTER model is compatible with observations (i.e. facts) which is the ultimate test.

(Bill Cole) #30

We know common descent as a mechanism passes genetic information from parent to children. So as we look at evolutionary trees it explains the similarities.

What is missing is the mechanism that explains the differences which can be independently tested against directly producing those differences successfully without killing the animal.


We also know that each child is born with mutations specific to them. Therefore, common descent and evolution will produce similarities and lineage specific differences. This is the tree-like structure that we often talk about.

Just to be clear, the tree-like structure does not exist within a population. We are all distant cousins to one another so there is a thorough mixing of lineages within populations which destroys any tree-like structure that might exist. However, lineage specific mutations will fix within populations which is what produces lineage specific differences between populations and species.

(Bill Cole) #32

It will also produce differences base on genetic recombination which is not necessarily random.

You have not established that mutation will create the tree like structure we are observing. The structure includes different features between animal groups.


As discussed in other threads, “random” needs some context. I would certainly agree that recombination is much more likely to occur between homologous sections of the genome. What scientists usually mean by random mutations is that they are random with respect to fitness.

Then explain to me how mutations that happen in one species can make their way into a different species if there is no gene flow between them.

(Bill Cole) #34

This is not the issue. The tree structure is built on more then genetic mutation. It is built on unique genes and morphology.


It is the entire issue. There is no way for unique mutations in one species to move to another species because there is a lack of gene flow. This is what produces lineage specific mutations and the tree-like structure.

As discussed earlier, neutral mutations fix by chance. The chance that a specific mutation will reach fixation in a population is 1/(2N). Therefore, there is an extremely high probability that separate species will fix different mutations because the odds of the same neutral mutations independently fixing in two species is extremely low. The only caveat is that over long time periods the probability of two independent but identical neutral mutations fixing in two separate species increases. These are called homoplasies, and they are part of the noise that we expect to see in phylogenies.

(John Harshman) #36

Oh, dear. Is Bill perpetuating his misunderstanding of what common descent is and isn’t supposed to explain wherever he goes? Several years in different online spots and he still doesn’t get it.

(Bill Cole) #37

The claim is that mutation and isolation can create differences in morphological structure and new genes in order to get a hierarchal structure. This is unsupported despite isolation in gene flow.


You are jumping ahead. Would you agree that common descent and evolutionary mechanisms would necessarily produce a noisy tree-like structure with respect to DNA sequences when there is a lack of horizontal genetic transfer?

(Bill Cole) #39

Yes, I agree.

Science-Engaged Theological Argument for Common Descent
(S. Joshua Swamidass) #40

3 posts were merged into an existing topic: Science-Engaged Theological Argument for Common Descent