Uncommon or Common Descent?

[Ashwin_s]

@gbrooks9

You seem oblivious to the idea that a long string of little mutations is the more successful version of evolution

You are correct. I am oblivious to this idea. Perhaps you could elaborate… cite a few of the success stories… how a “long string” of specific mutations led to a novelty.

[colewd (Bill Cole)]

We, here at Peaceful Science, focus in on the common descent of man . No one cares whether bacteria share a common ancestor.

If you look at figure 9 of Winston’s paper you will see a problem with the hypothesis of chimps and man sharing a common ancestor. You have two cases of multiple gene losses that need to be explained. First there is about 50-100 genes that rats share with chimps and not humans and there are about the same amount that humans share with monkeys and not chimps.

[swamidass (S. Joshua Swamidass)]

@Argon

No one cares whether bacteria share a common ancestor.

Well… I care. At least that provides some interesting challenges with detection. This isn’t to say that many bacteria can’t be grouped into trees of solid relationships. It’s just that the ultimate grounding of any tree is currently up for grabs, as is the question of whether there is a single root.

Humans and mammals are easy cases, in comparison.

How about this: no one in society is fighting about the common ancestry of bacteria. That is reserved for the common ancestry of man.

@colewd

We, here at Peaceful Science, focus in on the common descent of man . No one cares whether bacteria share a common ancestor.

If you look at figure 9 of Winston’s paper you will see a problem with the hypothesis of chimps and man sharing a common ancestor. You have two cases of multiple gene losses that need to be explained. First there is about 50-100 genes that rats share with chimps and not humans and there are about the same amount that humans share with monkeys and not chimps.

And we have already given the primary explanation for this: incomplete sorting.

[swamidass (S. Joshua Swamidass)]

@colewd

I think the real answer is we don’t know. The big problem with the evolutionary hypothesis is trying to figure out the origin of new functional information. Large amounts have appeared suddenly as you point out and there is no explanation for the source of this.

Not really. Functional information is poorly defined concept, and every definition I’ve seen can be demonstrated to form in the lab or in realistic simulation. It comes down to a misunderstanding of information theory. Remember, noise = information.

[colewd (Bill Cole)]

And we have already given the primary explanation for this: incomplete sorting.

So why can’t you use this to invalidate the whole paper since gene loss is his primary target?

[Guy_Coe]

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.

[colewd (Bill Cole)]

Not really. Functional information is poorly defined concept, and every definition I’ve seen can be demonstrated to form in the lab or in realistic simulation. It comes down to a misunderstanding of information theory. Remember, noise = information.

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.

[colewd (Bill Cole)]

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.

Uti- lizing gene families rather than sequences ignores small deviations from the tree easily explained by convergent evolution or incomplete lineage sorting.

I apologize for not including this in my original argument

[EricMH (Eric Michael Holloway)]

@swamidass

Remember, noise = information.

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.

[gbrooks9 (George)]

@Ashwin_s

You are correct. I am oblivious to this idea. Perhaps you could elaborate… cite a few of the success stories… how a “long string” of specific mutations led to a novelty.

@Ashwin_,

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!

[swamidass (S. Joshua Swamidass)]

@colewd

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.

Uti- lizing gene families rather than sequences ignores small deviations from the tree easily explained by convergent evolution or incomplete lineage sorting.

I apologize for not including this in my original argument

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:

@Winston_Ewert

As for 2, I do have deletions in my model. But I’m curious about how you see large scale genome rearrangement playing into this. Since I’m just looking at the presence or absence of gene families, I’d think a rearrangement wouldn’t do anything interesting there. But presumably you know something about that which I don’t.

@swamidass

Large scale genomic rearrangements can create correlated deletions in multiple branches of the tree. One test for this is to see if modules are correlated with synteny. I expect they are. If so, that gives a fairly straightforward reason for why the data shakes out this way.

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

[EricMH (Eric Michael Holloway)]

@swamidass

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?

[gbrooks9 (George)]

@EricMH

What we call information is mutual information, which cannot be produced by mere randomness or regularity. Hence, why undirected evolution does not work.

@EricMH,

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.

[swamidass (S. Joshua Swamidass)]

@EricMH

What we call information is mutual information, which cannot be produced by mere randomness or regularity.

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.

[gbrooks9 (George)]

@swamidass

Mutual information can be produced by “shared noise,” which arises in undirected evolution. It

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

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

[swamidass (S. Joshua Swamidass)]

@gbrooks9

Mutual information can be produced by “shared noise,” which arises in undirected evolution. It

@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.

[EricMH (Eric Michael Holloway)]

@swamidass

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.

[colewd (Bill Cole)]

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

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

[Ashwin_s]

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.

[gbrooks9 (George)]

@Ashwin_s

String of mutations…
Not string of organisms.

@ashwin_s,

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!