Uncommon or Common Descent?

[swamidass (S. Joshua Swamidass)]

@EricMH

What would be super interesting is an explanation of how a non-tree can come from common descent with variation.

Evolution Does not Predict Traits are in Trees or Nested Clades

First off, one reason this is so confusing is that it is often falsely stated that evolution produces and predicts perfect nested clades. This is false. Totally false. Obviously false. Homoplasies are observations that do not fit the tree, and evolution predicts that they will be numerous. Not knowing this, some people (e.g. @Cornelius_Hunter and @Nonlin.org ) think that the mere existence of homoplasies is evidence against common descent. This is false. Common descent does not predict that there will be no homoplasies.

How long have we known this? For over 150 years. Wings are an example of a homoplasy. We see them on birds, bats, and insects. That is an example of a trait that does not fit in a tree. So, to be clear, common descent does not predict and never has predicted that traits fall into perfect nested clades.

That doesn’t stop bad arguments from evolution being made all the time. As I explained:

@swamidass

I’d say, in your defense , that a lot of really bad arguments for evolution have been advanced. Nested clades, because it is often advanced as if there are no homoplasies. There are homoplasies, and they are predicted by evolutionary science too. We do not expect, from an evolutionary point of view, for nested clades in nature to be perfect nested clades. In this, Walter ReMine was correct . I don’t doubt that you are correct that others think that nested clades is strong evidence, but often the precise way that argument is advanced is actually in scientific error, even before an anti-common descent rebuttal arrives on the scene.

Empirical Data Demonstrates Homoplasies

So what about empirical data? How do we know this for sure?

We can look at DNA from several humans, and ask if that fits in a tree or not. This is a great control experiment, because we both agree humans arise by common descent (from other humans). So if we see variation in humans that does not fit in a tree arise (i.e. nested clades), that covers what we know from the theory: common descent does not produce data that perfectly fits in a tree.

We see exactly this. For a whole host of reasons, human variation does not fit in a tree. This includes (1) recombination, (2) population structure and migrations, and (3) convergent evolution, especially in HLA, (4) the birthday paradox, and (5) horizontal gene transfer (most commonly lysogenic viruses. Without parsing it out precisely, we just see that a graph fits the data much better than a tree:

@swamidass

here is on example of a study that shows human diversity (which obviously results from common descent) does not show a tree pattern (https://doi.org/10.1534/genetics.115.182626 ). I can produce more examples when you are ready to engage on that. Alan Templeton, a leading population geneticist, argues that not a single human diversity dataset he has examined survives a statistical test to see if it is a tree (private communication).

Other Mechanisms at Speciation

Perhaps the most important additional mechanisms important with speciation (for example explaining homoplasies between humans and primates) are:

1. Incomplete data, especially annotation of proteins (given the datasets that @Winston_Ewert used). This was correctly pointed out by @glipsnort.

2. Incomplete lineage sorting. Given that know for a fact (given the human variation) that variation in a population does not fit a tree, it is no surprise that if we form a new species by partitioning a large population, we expect there to be homoplasies in the final population.

3. I didn’t mention this to @Winston_Ewert , but convergent evolution is also really important. We see this in the human variation data regarding specific mutations: Heliocentric Certainty Against a Bottleneck of Two? - #18 by swamidass. At the level of proteins, convergent gene inactivation would be an easy mechanism to explain a large number of @Winston_Ewert’s modules.

There is more, but those are good starting points, that should be fairly easy to understand. Keep in mind that we’ve already known that the data does not fit a tree. Common descent does not predict the data fits a tree.

How Much Did Dependency Graphs Really Help?

This is perhaps one the of the more important points.

@swamidass

You are saying the 111,823 is large, but that is only (approximately) 1.7% of the unexplained fit (111 / 6308). That means the dependency graph only explains 1.7% more of the data’s patterns than a tree. Not very much. And, as @Winston_Ewert correctly notes, this is not even a real model of common descent.

That means that the Dependency Tree only fits about 1.7% better than a tree. That is not very much. It is a very low improvement, that might vanish entirely if any of the factors we’ve pointed out above are addressed more carefully. A 1.7% improvement on noisy data is not going to be enough to convince people any ways.

I’ve not really even explained all the other relevant mechanisms. There are actually more causes than this, several more come to mind. This, however, should be enough to show you this work only unsettle a cartoon version of evolution, which we already know is false

Respect for Winston

@Winston_Ewert, to be clear, was a professional about this. He wrote:

@Winston_Ewert

For any serious objection to my hypothesis, I probably won’t dispute it in this thread. If its a worthwhile objection I will want to take the time to think about, come up with a hypothesis to explain it, test that hypothesis etc. That will take time. I’m less interested in arguing the point as in understanding the objections to it so that it can guide where work on this hypothesis needs to go.

That is really the right way to think about this. I’m really impressed by his attempt. He has a long way to go, but we are all going to be watching it closely. I wish him the best, and will help him any way we can. Give him time, and tell the polemicists to back off. All they do is hold him back.