Uncommon or Common Descent?

Well, there is this from Lynn Margulis, the “godmother” of endosymbiotic theory: "neo-Darwinists say that new species emerge when mutations occur and modify an organism…I believed it until I looked for evidence.” Sounds like skepticism is warranted.

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Are you aware of the definition generated by Szostak and Hazen in their 2003 paper? It is not noise but a sequence that performs a function. Noise is the enemy of this type of information.

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Here is the reason that it does not invalidate the paper and it also still remains a problem for the anomalies between chimps and man.

I apologize for not including this in my original argument :frowning:

You’re confusing entropy with information. An email of random characters is low in information. An email of the same character is also low in information. What we call information is mutual information, which cannot be produced by mere randomness or regularity. Hence, why undirected evolution does not work.


  1. There’s the lungfish whose lung supplements oxygen exchange… and so they spend more and more time in drier environments… exploiting ne e territories… with strong and stronger fins… until the population becomes a tetrapod.

  2. There’s the lizard population that spends more and more of its time burrowing thru loose soils… with limbs becoming smaller… until they are snakes… or a wide variety of other limbless lizards.

  3. And there is any number of colony life forms that eventually differentiate regions of the colony, comprised if differentiated cell forms, to handle more challenging environments.

And we haven’t even mentioned dinos to birds, fish-eating mammals that become whales or otters, or a single population of marsupials in Australia that radiate into multiple niches and become radically different:

  1. Vegetarian moles;
  2. Omnivorous bandicoots; and
  3. Carnivorous Tasmanian devils!

Yeah, that turns out not to be correct if we consider deletions. Deletions can easily delete proteins, and genomic rearrangements can do this on a massive and correlated scale. Keep in mind what he says next:

And incomplete lineage sorting can also create this pattern (dependency graph vs. tree) in the human-primate data.

Can you briefly state what “incomplete lineage sorting” is?


This “information” fixation might get some traction against atheists.

But it makes zero sense when you are discussing information and speciation under God’s control.

Mutual information can be produced by “shared noise,” which arises in undirected evolution. It is easy to demonstrate with simple programs of common descent. The shared noise in genomes that arises from shared history is among the strongest evidence of common descent.

@swamidass, you don’t even have to go that direction.

We dont rely on unguided directions. All our directions are guided!

Sure, that applies in both cases. Mutual information can be produced by “shared noise,” which arises in BOTH directed and undirected evolution.

That isn’t being ‘produced’ per se. It was already contained in the initial random noise. Laws like the data processing inequality, independence conservation, mean nothing deterministic, random, or combination thereof can produce mutual information.

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What would be interesting is to identify the genes and look into this deeper.

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String of mutations…
Not string of organisms.
You are equating all phenotypic change with point mutations. In short, you are assuming you case rather than proving it.


What are you saying here?

In the end, i dont suppose what you mean really matters here. It doesn’t matter whether, semantically speaking, genes do it all or not - - it doesn’t really alter the either/or scenario.

The question comes down to natural vs. Miraculous… and between Young Earth or Old Earth!

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If you look at figure 9 in Winston’s paper you see a module or family with at least 100 genes that is shared between rats and chimps but does not exist in humans and mice. This appears to be very unlikely from a perspective of random gene loss.

How would you explain this from and evolutionary perspective?


If I’m following, Dr. Swamidass is claiming the DG results from gene loss, aka incomplete lineage sorting? Is this the only significant mechanism that is supposed to generate the DG?

I’m trying to get a grasp on what specific changes to the tree are supposedly resulting in a DG, since I believe they can easily be modeled mathematically, and we can get an intuition how helpful they are at explaining away Dr. Ewert’s result. Per my combinatoric analysis above, it seems like a whole lot has to happen to a tree before it resembles a DG.

And despite the 1.7% proportion, it is still the case the Bayesian factor states the DG is 2^{111,823} times better than a tree for explaining the data. That this is mostly an artifact of the dataset size is hard to swallow.

Their can be deletions during meiosis that cannot be repaired. Having this type of deletion fixed in a population would seem to be a very rare event. I don’t think that unique genes are the result of ILS as that would show up as a variation of another gene if I understand ILS correctly.

Winston has identified a real problem with the tree in that it does not explain without rare statistical events gene families occurring outside but not inside taxonomic relationships.

Just thinking out loud I am not sure a tree would ever resemble a DG as they are very different ways to parse the data. The genes being mixed and matched outside the taxa is causing the DG to fit the data better.

[quote]And despite the 1.7% proportion, it is still the case the Bayesian factor states the DG is
times better than a tree for explaining the data. That this is mostly an artifact of the dataset size is hard to swallow.[/quote]

1.7% of the number of atoms in our universe is a boat load of atoms :slight_smile:

Before we go any further, let’s get this settled. We are not explaining away or dismissing @Winston_Ewert’s results. We are taking them seriously. We are treating him with respect, and are here to help.

If we cannot agree on this, I’m not sure explaining more is fruitful.

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However you wish to phrase it, you are minimizing the significance of the 2^{111823} number. If we take the number at face value, it means DG is categorically better than tree, no question about it. However, you claim the number can be produced due to something like p-hacking, where any difference between two theories becomes statistically significant with enough data, thus the number does not mean what it seems to mean. That’s why you throw out the 1.7% proportion as being more indicative of the result’s true significance.

You are also claim that common descent is dissimilar enough from a pure tree that the result does not directly imply common descent is incompatible with the data. However, the extremely large number makes this hard to believe, so you posit a variety of mechanisms that could cause common descent to diverge significantly from a tree structure.

Thus, there is a kind of explaining away of the immediate impact of the paper happening here. I believe you are doing this in good spirit and out of genuine desire to help, but at the same time you are countering the first impression someone comes away with after reading the paper.

So, my goal is to get some sort of “model of the model” that is clearer and easier to work with, which we can use to get an intuition whether the two minimizing factors you propose do in fact apply to the paper’s result. That’s why I proposed the combinatoric analysis, which at least shows the paper has identified the intrinsic weakness of tree like models from a graph theoretic standpoint.