Clade

[Loudmouth]

(Sorry, I am actually testing your ability of teaching. If you can not teach me, then there is probably few you can teach)

"I do not intend to learn biology in this thread. "--juvenissun

The only thing you are testing is our patience.

 

[sfs]

[I missed this post before.]

I do not understand the specifics. So I can not evaluate if it practical or not. I am trying to find out:

May I learn the the following:
1. How to identify the positive selection in humans (by the mutation rate)?
2. What is the positive selection in that particular study?

1. By the reduced diversity, relative to the amount expected based on the mutation rate.
2. Who knows? It's an open scientific question, awaiting someone to pursue it.

In order to see if the study has any practical value, I need to know the practical implication. I am not going to read the papers. If you could not (or would not) make an simple explanation which I can understand, then you can simply stop. But the question in my OP is not answered either.

Sorry, but the student doesn't get to announce that he's not going to do the assigned reading and then blame the teacher. If you don't do the reading, you fail.

 

[juvenissun]

It's a somewhat subtle analysis. The best description of it is in the paper itself, which you can read here. We worked quite hard on making the paper clear, going through more than 100 drafts. I'll be happy to answer questions about it.


Many people have read and understood the paper.

If you said so, I will read it.
But, you are going to answer my questions about the paper, don't go away.

 

[sfs]

If you said so, I will read it.
But, you are going to answer my questions about the paper, don't go away.

I don't aim to go anywhere for a spell.

 

[juvenissun]

I don't aim to go anywhere for a spell.

It is immoral to have me read your paper. I do not even have genetics 101.
But, for sake of learning something new, I will try. It is going to be slow.

 

[PsychoSarah]

It is immoral to have me read your paper. I do not even have genetics 101.
But, for sake of learning something new, I will try. It is going to be slow.

If sfs isn't around to answer your genetics questions, I can help a bit.

 

[Dizredux]

It is immoral to have me read your paper. I do not even have genetics 101.
But, for sake of learning something new, I will try. It is going to be slow.

Immoral?

Dizredux

 

[CabVet]

It is immoral to have me read your paper. I do not even have genetics 101.
But, for sake of learning something new, I will try. It is going to be slow.

No, that's not immoral. Immoral is to dismiss evolution without knowing what it is.

 

[lasthero]

It is immoral to have me read your paper. I do not even have genetics 101.
But, for sake of learning something new, I will try. It is going to be slow.

Immoral? Immoral?

What is wrong with you?

 

[Mr Strawberry]

What is wrong with you?

A question that has occurred to many of us.

 

[sfs]

It is immoral to have me read your paper. I do not even have genetics 101.
But, for sake of learning something new, I will try. It is going to be slow.

I've never had Genetics 101 either; in fact, I haven't taken a class in biology since 9th grade. I learned a great deal of genetics working on the paper in question.

 

[juvenissun]

I've never had Genetics 101 either; in fact, I haven't taken a class in biology since 9th grade. I learned a great deal of genetics working on the paper in question.

What is your comment to this report?

http://www.biologydirect.com/content/pdf/1745-6150-5-64.pdf

 

[PsychoSarah]

What is your comment to this report?

http://www.biologydirect.com/content/pdf/1745-6150-5-64.pdf

It doesn't disprove or reduce evidence in support of evolution or common ancestry.

 

[Loudmouth]

What is your comment to this report?

http://www.biologydirect.com/content/pdf/1745-6150-5-64.pdf

The reviewers comments are worth a read. They cover most of the points that need to be covered.

The main point is that Theobald's methodology is incapable of finding a real phylogenetic signal since it produced a false positive when "statistically similar but phylogenetically unrelated sequences" were used.

 

[sfs]

What is your comment to this report?

http://www.biologydirect.com/content/pdf/1745-6150-5-64.pdf

It sounds about right. You can formally compare two models, but you can't formally show that your model is better than all possible models. But, as the authors note, the evidence for common descent remains overwhelming and the alternative model they were able to dream up is almost certainly ruled out by other data. So we're left where we've always been: common descent is by far the best model available, and will continue to be the consensus until someone comes up with a better one, which is highly unlikely to happen.

 

[In situ]

Here a non-biology creationist talks again.

The biological classification used the idea of Clade. (link) It bears the meaning of ancestral history, and thus is a system support the idea of evolution.

Is this system only ideologic and has no practical use (except labeling)? I really like to learn even a single case that this ancestry-focused classification system is useful to solve a practical question. What I meant is that if we do not involve the use of ancestry, then this classification system won't work in a practical sense.

Please.

Are you asserting that clustering algorithms are ideologies? Then I am sorry, it will not be possible for you to learn anything because you have already made up your own answer.

 

[In situ]

Why should comparison use the idea of ancestry?

Why do you assume that which is not true? Ancestry is an observation.

When compare, we concluded the percentage of similarity. Why is it not enough?

What is "concluded the percentage of similarity" supposed to mean?

 

[In situ]

I really like to learn even a single case that this ancestry-focused classification system is useful to solve a practical question.

You can start here: Neighbor joining

What I meant is that if we do not involve the use of ancestry, then this classification system won't work in a practical sense.

Like I said as long you assume their exists a world wide conspiracy that somehow secretly rigged every single cluster algorithm is such way as to prevent loops to be created when investigating the distance matrix, this without anyone noticed this, with the purpose to make it look like common ancestor exists then you will learn noting.

If you assume this, then I challenge you to show us where this rigging occurred in the algorithms so we can use the proper cluster methods on the distance matrix (and by the way you can also tell use how evolutionist Carl von Linne rigged his classification to create the same relations as current algorithms produces).

If you cannot do that then next step is to investigate if the evolutionist conspired to rig every single of the distance algorithm uses, for instance where did the pesky evolutionist Euclides assumed a common ancestor when he came up with his famous distance formula:

A^2 = B^2 + C^2

Because what you actually say when you claim that common ancestor is assumed in cladistics is that the evolutionist Euclides assume a common ancestor in order to be able calculate the length of the diagonal in a triangle.

However, it is not obvious how he did this, so his assumption must somehow be very cleverly hidden in the formula because nobody, for well over two thousands years, has yet seen it.

This is your chance! You may here go to history as the first creationist who uncovered the evolutionists worldwide conspiracy and showed how the theory of evolution was all based on a false assumptions of an common ancestor.

Not to mention that you also will be the person that made the revolutionary discovery in mathematics that 1+1 cannot possible be equal to 2 unless a common ancestor is assumed for all life on Earth.

If none of all this silliness is your assumptions (and I guess it is not if you are at least half as sane I suspect you are) then I challenge you to come up with a clustering algorithm that when apply on the distance matrix will not produce a nested hierarchy. If you cannot do that, then you must accept the fact that shared common ancestor is an observational fact - or continue deny the facts (which I suspect you will do).

 

[In situ]

where did the pesky evolutionist Euclides assumed a common ancestor when he came up with his famous distance formula:

A^2 = B^2 + C^2

Oops, that was of course Pythagoras which came up with that. However, it is an euclidean distance measurement which still makes Euclides a pesky evolutionist (and Pythagoras as well).

 

[juvenissun]

If none of all this silliness is your assumptions (and I guess it is not if you are at least half as sane I suspect you are) then I challenge you to come up with a clustering algorithm that when apply on the distance matrix will not produce a nested hierarchy. If you cannot do that, then you must accept the fact that shared common ancestor is an observational fact - or continue deny the facts (which I suspect you will do).

I don't really understand these two terms. Do you mind to explain it?

If I could guess their meaning, how about:

God creates A, B, C, D, ...
A, B, etc. do not need any common ancestor.