REAL NS is a problem for common descent, fitness peaks, in Eukaryotic evolution

[Faizal_Ali]

@colewd

It shows deviation from what common descent would predict.

John Harshman disagrees. I wonder which of you I should believe?

[T_aquaticus]

@PDPrice

To my knowledge, I don’t know why the same techniques and principles being applied in cladistics to produce these nested hierarchies couldn’t theoretically be applied to any large dataset of different things with varying levels of similarity to one another.

The same techniques can be applied. What we will be looking at is the statistical support for those trees. That’s the difference.

The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of “cladistic hierarchical structure” (also known as the “phylogenetic signal”) in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al . 2001; Klassen et al . 1991).
29+ Evidences for Macroevolution: Part 1

You can put any set of objects into a phylogeny, but the real test is the amount of phylogenetic signal that can be found in that tree. If there are numerous and obvious violations of the tree, depending on the character used, then there is very little phylogenetic signal. Phylogenetic signal is a measurement of how well those objects fit into a tree, and it is that measurement you need to make.

@PDPrice

And I don’t view it as an evidence of common descent because it begs the question to begin with. The method only has validity if you assume common descent.

You have already stated that you will not accept any evidence for common descent, so your claims ring quite hollow. You are also wrong. The method does not assume common descent. You can arrange any set of objects into a tree, even those that don’t share common descent. What matters is the measured phylogenetic signal. In the case of known genealogical processes and known genetic relationships, they return very high measurements.

[Faizal_Ali]

@T_aquaticus

You have already stated that you will not accept any evidence for common descent, so your claims ring quite hollow. You are also wrong. The method does not assume common descent. You can arrange any set of objects into a tree, even those that don’t share common descent. What matters is the measured phylogenetic signal. In the case of known genealogical processes and known genetic relationships, they return very high measurements.

My example with the cars was an attempt to illustrate the concept of phyogenetic signal in a simplified manner. I hope it was accurate enough.

[colewd (Bill Cole)]

@John_Harshman

Sorry, but no. Common descent predicts a certain number of convergent losses of genes. Homplasy exists. The point is that it’s much rarer here than homology.

Based on what predictive model?

[John_Harshman]

@colewd

Based on what predictive model?

Based on the observation that gene gains and losses happen, that there is a tree of descent, and that gains and losses happen at particular places on that tree, and that if gene loss is stochastic, there will be occasional multiple losses of the same gene.

Now, what predictive model tells you to expect the pattern of gain and loss frequencies shown in that figure?

[colewd (Bill Cole)]

@John_Harshman

Now, what predictive model tells you to expect the pattern of gain and loss frequencies shown in that figure?

The model that a mind was behind the pattern we are observing. Re use of components is a design pattern. This is the model Winston will be building as the gene and protein data bases mature.

You cannot model non deterministic events. This is why the grand claims of evolution will never be a scientific theory until you find a deterministic mechanism. That mechanism is between your ears. Matter itself and its properties cannot explain the pattern.

[scd]

@Faizal_Ali

That God could have created “kinds” with the appearance of having evolved thru common ancestry

thats the point- it doesnt necessarily looks like common descent. he can just create groups of animals: reptiles, mammals etc.

[T_aquaticus]

@colewd

You cannot model non deterministic events.

Quantum physicists across the world just facepalmed in unison.

@colewd

This is why the grand claims of evolution will never be a scientific theory until you find a deterministic mechanism.

You will never gain credibility if you repeatedly play dumb after being shown these mechanisms over and over and over.

[John_Harshman]

@colewd

The model that a mind was behind the pattern we are observing. Re use of components is a design pattern. This is the model Winston will be building as the gene and protein data bases mature.

Sorry, Bill, that isn’t a model. It makes no predictions. Why, under that model, should patterns requiring one change on the standard tree so greatly outnumber patterns requiring two changes? Why is the fit to the standard tree so good?

@colewd

You cannot model non deterministic events.

I’ll inform all the people who simulate stochastic processes that everything they do is invalid, then. Good to know.

[T_aquaticus]

@scd

thats the point- it doesnt necessarily looks like common descent. he can just create groups of animals: reptiles, mammals etc.

Romanes said it best:

For, be it observed, the exception in limine to the evidence which we are about to consider, does not question that natural selection may not be able to do all that Mr. Darwin ascribes to it: it merely objects to his interpretation of the facts, because it maintains that these facts might equally well be ascribed to intelligent design. And so undoubtedly they might, if we were all childish enough to rush into a supernatural explanation whenever a natural explanation is found sufficient to account for the facts. Once admit the glaringly illogical principle that we may assume the operation of higher causes where the operation of lower ones is sufficient to explain the observed phenomena, and all our science and all our philosophy are scattered to the winds. For the law of logic which Sir William Hamilton called the law of parsimony—or the law which forbids us to assume the operation of higher causes when lower ones are found sufficient to explain the observed effects—this law constitutes the only logical barrier between science and superstition. For it is manifest that it is always possible to give a hypothetical explanation of any phenomenon whatever, by referring it immediately to the intelligence of some supernatural agent; so that the only difference between the logic of science and the logic of superstition consists in science recognising a validity in the law of parsimony which superstition disregards.
–George Romanes, “The Scientific Evidences of Organic Evolution”, 1882
The Project Gutenberg eBook of The Scientific Evidences of Organic Evolution, by George J. Romanes, M.A., LL.D., F.R.S.

What you are pushing is superstition.

[colewd (Bill Cole)]

@John_Harshman

Sorry, Bill, that isn’t a model. It makes no predictions. Why, under that model, should patterns requiring one change on the standard tree so greatly outnumber patterns requiring two changes? Why is the fit to the standard tree so good?

It’s not a good fit. It’s a fit in your imagination. You have no model of how convergence occurs. The evidence is overwhelming that a mind was involved in the pattern. You can arbitrarily rule out design but this is not going to last,

Physics will soon hit the same wall as biology has with the observation of translated sequences. Why not lead and really acknowledge what you are observing?

[scd]

@John_Harshman

Now, what predictive model tells you to expect the pattern of gain and loss frequencies shown in that figure?

its very simple: we see it in designed objects all the time. we can find the same engine in different cars but not in others or the same gps etc. but in general we do see hierarchy.

@John_Harshman

Common descent predicts a certain number of convergent losses of genes

how much? where is the limit that common descent cant explain?

[T_aquaticus]

@scd

its very simple: we see it in designed objects all the time. we can find the same engine in different cars but not in others or the same gps etc.

But do those losses follow the same tree in your model? You need to show that.

[T_aquaticus]

@colewd

It’s not a good fit. It’s a fit in your imagination. You have no model of how convergence occurs.

The model is natural selection, mutation, speciation, and vertical inheritance. How many times have we stated this?

@colewd

You can arbitrarily rule out design but this is not going to last,

You arbitrarily rule out design all of the time, and for the same reasons. When you observe the planets moving about the Sun you rule out gravity fairies pushing them in their path because we have a natural mechanism that explains the motion.

[Faizal_Ali]

@scd

thats the point- it doesnt necessarily looks like common descent. he can just create groups of animals: reptiles, mammals etc.

And he also could not. If he did not deliberately set out to create all “kinds” such that they look exactly as if they evolved from common ancestors to each other, there is essentially zero chance he would have done so just by chance.

So the options are 1) common ancestry is true. 2) God deliberately created a universe in which common ancestry would be the correct scientific conclusion from the evidence.

Those are your options. Either one leads to the conclusion that according to science common ancestry is true.

[colewd (Bill Cole)]

@T_aquaticus

The model is natural selection, mutation, speciation, and vertical inheritance. How many times have we stated this?

These are not models. Real models can show how the prediction works. Dawkins built a model. The problem was that it required design to work. I have explained this to you many times

[colewd (Bill Cole)]

@Faizal_Ali

And he also could not. If he did not deliberately set out to create all “kinds” such that they look exactly as if they evolved from common ancestors to each other,

This is a false assertion. You need to move on.

[Faizal_Ali]

@colewd

This is a false assertion. You need to move on.

Wrong. The assertion is correct. If you disagree, please provide the evidence to support your claim.

@colewd

These are not models. Real models can show how the prediction works.

Is it again time for us to ask you to provide the model that explains how living things were “designed”, so you can yet again fail to provide an answer?

[T_aquaticus]

@colewd

These are not models. Real models can show how the prediction works.

That’s exactly what the model does. You ignore it every time it is given.

If you want a real, living example of the model at work, I suggest you go to my thread on rock pocket mice:

The Rock Pocket Mouse: A Model for Natural Selection

I thought it would be helpful to use a specific example of natural selection for those having issues understanding how it works. Coat color in pocket mice is one of those examples. The paper I will be working from is found here: First, let’s look at the environment where these mice are found. They are found in the southwest deserts of the US, and the vast majority of their range is made up of light brown dirt and rocks. However, there are isolated areas where recent volcanic eruptions have created areas with dark black basalt rock. Interestingly, when we look at the distribution of coat color in pocket mice it matches the environment they are found in: [image] The black mice are found in islands of black basalt rock, and brown mice are found in the sea of brown desert between those islands of volcanic rock. I don’t think it is a stretch to state that camouflage is playing a strong role in the distribution of coat color alleles. The scientists in the paper also looked at in…

It shows how convergence works. Read the abstract of the paper linked in the opening post.

[colewd (Bill Cole)]

[quote=“Faizal_Ali, post:158, topic:8218”]
Wrong. The assertion is correct. If you disagree, please provide the evidence to support your claim.
[/quote
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