Beyond Reasonable Doubt? A Test for Common Ancestry

Our test is based on the expectation that, under evolution, the ancestral sequence of one natural group of taxa will be more similar to the ancestral sequence of a second natural group of taxa, than to any sequence from the first group will be to any sequence from the second. In contrast, a variety of proposed non-evolutionary models either do not make this prediction, or require so many parameters that they cannot be said to make any testable predictions at all.

That is a really interesting premise. I’ll have to think about this…

3 Likes

You are a funny guy. We could use some more of that here.

5 Likes

The issue is the selection of the null hypothesis. The data beats random chance but that tells us very little.

The null model was seperate origins as opposed to common origin of each pair of clades. The “random chance” referred to in the abstract is the chance that the same levels of ancestral convergence observed in the data would be observed in the “seperate origins” null model.

5 Likes

It seems @evograd is correct. You may have misread the paper @colewd.

3 Likes

6 posts were split to a new topic: Side Comments on Beyond Reasonable Doubt: Evolution from DNA Sequences

Evograd, have you looked at the alignments? Do you know if Bojian Zhong can still make them available? (I’m wondering how to reach him/her to obtain the aligned and unaligned sequences.)

Any analysis of this interesting paper would need to start with the alignment methods.

Thanks

1 Like

The discussion topic is universal common descent so for this to be true their must have been a transition from prokaryotic to eukaryotic cells. I agree Winstons paper looks at different line of evidence however it brings common design forward as an inference which this paper also does.

I think this paper proposes a partial and reasonable test for common descent.

1 Like

I have not, nor have I had any contanct with Bojian Zhong, so I’m afraid I can’t help you at all there.

The discussion topic is really more restricted to statistical tests of universal common ancestry, not arguments for or against UCA per se. If you can think of a way to formalise your arguments about splicosomes and other protein complexes into something that can be quantitatively tested, that might be more appropriate.

3 Likes

OK, thanks. I’ll see if I can find him and obtain the data.

1 Like

Here’s why I am worried about the alignments (Bojian Zhong is senior author on this paper):

Notice that the phylogenetic signal from chloroplast sequences was “improved” by editing out GC sites which caused problems with a monophyletic hypothesis.

Such practices are widespread in molecular phylogenetics. These methods rarely elicit critical comment because monophyly is taken as given. One should only use “phylogenetically informative” sites in constructing evolutionary trees.

I should be able to reach Zhong by email later today or tomorrow (traveling right now, but will have some time tomorrow).

2 Likes

The test in the paper seems to be independent of a transitional mechanism. Is this the case?

Yes, the test has nothing to do with mechanisms of “transitions”, it’s just a test of CA versus SA. The “what”, not the “how”.

2 Likes

I then agree with Joshua that the prokaryotic to eukaryotic transition is not a good example based on the papers test method as so many new proteins were added during this transition. Comparing homologous proteins does not explain much.

This does limit the subject to common descent vs universal common descent.

To be clear, they didn’t didn’t edit out GC sites that “caused problem with a monophyletic hypothesis”, they edited out GC sites that were contributing to the unresolved nature of classifications with Chlorophyta. The phylogeny of the classes within Chlorophyta (as well as the monophyly of some of these classes) was thus far unresolved, giving conflicting results and weak support in different studies. Fang et al set out to resolve these conflicts - to find the real phylogeny, regardless of what it was. There’s nothing to suggest that the authors were cherry-picking sites to remove in order to support a particular phylogeny, as you seem to be suggesting.

Their reasoning holds up - if GC heterogenous sites are known to be rapidly-evolving and lacking any useful phylogenetic signal, it stands to reason that they be removed, reducing the noise in the rest of the analysis.

Are you suggesting that these phylogenetically “uninformative” sites are actually some kind of signature of seperate ancestry? Can you elaborate on that?

5 Likes

As I said in the OP, strictly speaking this isn’t about universal common descent because it’s not including all groups of organisms, but it is including a great many groups that creationists/IDers should be concerned with.

Edit: actually I noticed that I didn’t include the line about this not being strictly about universal common ancestry in the OP (I must have deleted it in the final draft), so apologies if that wasn’t clear.

3 Likes

That would be really helpful @pnelson. Thanks.

I’ve been thinking about this study, and have some questions about it. It is not clear they have done the right controls.

@evograd, honestly, I’m not sure this is a valid test. And this is coming from a scientist that affirms common descent. I am no anti-evolutionist. I could be wrong, but it seems it is fairly easy to build a generative model that would show evidence of common descent according to this test. Here is how we could do it.

  1. Define a relatively large convex space in sequence space as “functional” (e.g. a fixed set of differences from a centroid sequence).
  2. Sample sequences uniformly from this functional space to assign sequences to different species.

There is no reason to think it must be a convex space. I’m just saying that here to make it easy to visualize. I’m pretty sure the same finding would apply for any shaped space, as long as it is large enough.

Now, look at the basic intuition here:

the expectation that, under evolution, the ancestral sequence of one natural group of taxa will be more similar to the ancestral sequence of a second natural group of taxa, than to any sequence from the first group will be to any sequence from the second.

Now, in this generative model, which does not include common descent, the same prediction is made. The ancestral sequence will be approximately the “average” of all the sequences in the taxa, and will statistically be much closer to the centroid sequence. So the ancestral sequences will always be closer to one another than the extant sequences are to one another.

Unless I am missing something, it appears that this is a flawed test. Did I miss anything @evograd? What do you think @pnelson?

2 Likes

I think I disagree. The test’s expectation starts from an understanding of sequence evolution, which is a transitional mechanism. It seems they are presuming largely neutral mutation with negative selection in setting the expectation for common descent.

Once again, @evograd, am I missing something? What do you think @Joel_Duff and @pnelson?

Yes, they’re beginning with assumptions about the stochastic nature of sequence evolution, but at the same time their results in figure 4, whereby ancestral convergence increases with sequence length, acts as a somewhat independent confirmation of this implicit assumption.

2 Likes