Uncommon or Common Descent?

[swamidass (S. Joshua Swamidass)]

@EricMH

A very well written response.

Thanks, it took some time.

How Many Homoplasies?

@EricMH

A follow on question, you state that evolution predicts homoplasies will be numerous. Could you expand on this? When you say ‘numerous’ is this a raw number or a proportion? 1,000,000 homoplasies is a large number, but not in comparison to 1,000,000,000,000 organisms.

This is unfortunately a to undefined as a question. It all comes down to the mathematical details of the precise traits we are considering.

In Ewert’s Case…

In Ewert’s paper, we are talking about the presence or absence of specific protein families, which is a fuzzy concept. Unfortunately, we don’t have very strong “rate” information about how quickly they can be deleted, or gained, like we do for point mutations. So it is hard to compute a precise number.

@glipsnort however made a great point.

@glipsnort

If so, then it seems to me that this kind of comparison is critically dependent on the completeness and consistency of the dataset, since missing data in more than one species appears as a signal for one of the models.

In this specific formulation, mistakes in annotating proteins, and incomplete genomes will add “noise” to the data that the Dependency Graph will think is a signal, even though its just noise. He suggest the exactly right remedy.

@glipsnort

I would absolutely, positively do – and would insist on an author doing if I were reviewing a study like this – is look at some of the genes that are supposedly missing (in a way not consistent with common descent) and confirm that they are really are missing genes and not missing (or different annotations.

He is right. That is the way to test this further, and build confidence it isn’t just a spurious result. As it is, we do not know for sure at this point. It seems he relied heavily on annotation databases, and that has some real weaknesses. They can be overcome.

Bayes Factors

@EricMH

You also divide a very large Bayes factor by an even larger factor, and state the resulting small ratio is how much more the dependency graph explains, which is a very small number. Is this how Bayes factors work? Is there a way to calculate how much a tree must become non-treeish before a dependency graph is a better explanation? I.e. how many cross clade branches must be added and existing branches removed? 1.7% may seem like a small number, but it still may entail a huge amount of branch addition and removal to transition to a dependency graph.

That is how they work. The numbers are the “error” or the “unexplained information” in the data under each model. If he wrote his program correctly (and let us assume he did), then these are all proportional to “bits” of information that are unexplained in the data. In this data, the dependency graph explained less than 2% (though I’ll round up) of the information that the tree did not explain.

How much of that remaining information (the other 98%) is an unknown design principle? An unknown natural process principle? Stochastic randomness (still governed by God’s providence)? Divine action? We just do not know. It is impossible to know without figuring out a model that makes sense of it.

Remember, trees already explain quite a bit of the data. It is not clear at all how much of the 2% is really fitting a dependency graph, instead of just being impacted by the noise in his data. As a proportion of the data, it is just a small amount. However, there is a lot of data here. It is entirely possible that in terms of individual proteins, that there are actually many examples. Once again, it could just be noise. We do not know yet.

Design or Not?

@EricMH

There is also a sort of question begging going on. If intelligent design is at work, then we would get a large number of horizontal gene transfers and homoplasies, as we do with human driven breeding and genetic experimentation. So, ID also predicts a very high number of transfers and homoplasies.
At what point is the number of transfers and homoplasies evidence of intelligent design instead of evolution? Otherwise, we could just be artificially relabeling evidence for intelligent design as evidence for evolution. How do we ensure this is not happening?

Yes it is begging the question.

This has nothing to do with design vs. no design. Every ID advocate should know that Common Descent IS a design principle. None of this is about ID vs. evolution. It is about an alternative model for origins other than common descent. We already know that God can use common descent to design us.

ID does NOT predict a higher number of homoplasies. It makes zero predictions without specifying a design principle. @Cornelius_Hunter hashed this one out before. In the dialgram below, the more to the bottom of the graph, more homoplasies (and less tree like). The closer to the top the fewer (and more tree like).

A key variable you are missing is the “speed” at which a features evolves (which is often directly measurable). Depending on this parameter, common descent will make different predictions. This isn’t cheating, because we can directly measure the speed in many cases (especially with DNA), and this gives us a way of analytically computing the expectation.

Any how, I think (in my opinion), ReMine’s model corresponds to the blue line, the features used in this analysis correspond to a mixture of slow and fast evolving features, so in this case CD corresponds to the green line. And your model corresponds to the orange line, because it is not specified at all.

So the data ends up fitting CD the best. I should point out that I believe in design too; design by common descent. So in no way does this rule out that God created us. Rather, it tells us that common descent is the best design principle to understand biology.
Signal and Noise - #21 by Swamidass - Faith & Science Conversation - The BioLogos Forum

This was in response to a figure from @Cornelius_Hunter. I had asked him:

1. How did you arrive at the conclusion that Design should have less consistency (at about 0.6) than common descent (at about 0.8)? Walter ReMine (a YEC that rejects evolution) argues exactly the opposite, that design should produces more consistency than common descent (he argues it should be close to 1). Which of you is right? And how do we know?

2. If possible (though I understand this is not likely), can you please show your math. How did you arrive at such precise numbers, with non-overlapping uncertainty?

3. You also point out that you are using an “idealized” common descent model (which presumably does not model any noise). So why should we trust it? Don’t we want a realistic common descent model that includes noise, and would therefore reduce the expected CI?

Signal and Noise - #14 by Cornelius_Hunter - Faith & Science Conversation - The BioLogos Forum

@Cornelius_Hunter had no response. What is exciting about @Winston_Ewert’s work is that he is giving it an attempt. That is respectable. I want to get as far as is possible with the data.

God Can Meddle

@EricMH

There is also a bit of an equivocation. Just because one organism is descended from another does not mean genetic meddling is not happening. So, hypothetically, we could still have common descent in the purely procreative sense, but the genetic record can still be highly indicative of intelligent design, and thus the dependency graph would result. What is interesting, then, is not procreative common descent, but genetic common descent, and the former does not entail the latter.

Of course. None of this is about God’s action. Maybe God is inspiring proteins, just like I already offered you:

@swamidass

To be 100% clear, maybe God did act in our origins, science has not ruled it out.

Questions about God’s action are different than common descent. So there is an equivocation. Let’s stop thinking this is about ID. It is about Common Descent.

@EricMH

To really falsify Dr. Ewert’s result, it is not enough to say A gave birth to B. One must also say that all the genetic material in B is only from A + random variation. There are other sources of variation that would not falsify the dependency graph, such as environmental patterns matching a genetic database of responses that is preconfigured in the DNA.

No one is looking to falsify his result. I’m hoping he will be successful as possible. I wish the best to @Winston_Ewert, and hope he will reveal new things to us about how life arose. We will help him as much as possible. Our exchange was merely the same standards that @sygare, @glipsnort, and myself hold ourselves, our colleagues, and our students. We treated @Winston_Ewert like an equal, and he handled himself well.

@EricMH

So it seems that not only does Dr. Ewert need to do some more work, but proponents of common descent also have to do some more work to explain why the evidence they already have does not improve Dr. Ewert’s case. As it stands, the evidence you offer and Dr. Ewert’s work suggests that common descent + dependency injection or pure creationism are better explanations than common descent + random variation. The question of procreative common descent is orthogonal to the discussion.

Explanations ordered from best to worst:

1. Dependency injection
2. Creationism
3. Random variation

I think you just misunderstood what we are doing here. No one is arguing against anything. We are just trying to give an honest account of the science and be helpful.