Clade

[Loudmouth]

Clades are used in this study to find new potential resevoirs for C. jejuni, an important human pathogen.

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):16043-8. Epub 2005 Oct 17.

Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source.

Champion OL1, Gaunt MW, Gundogdu O, Elmi A, Witney AA, Hinds J, Dorrell N, Wren BW.

Abstract

Campylobacter jejuni is the predominant cause of bacterial gastroenteritis worldwide, but traditional typing methods are unable to discriminate strains from different sources that cause disease in humans. We report the use of genomotyping (whole-genome comparisons of microbes using DNA microarrays) combined with Bayesian-based algorithms to model the phylogeny of this major food-borne pathogen. In this study 111 C. jejuni strains were examined by genomotyping isolates from humans with a spectrum of C. jejuni-associated disease (70 strains), chickens (17 strains), bovines (13 strains), ovines (5 strains), and the environment (6 strains). From these data, the Bayesian phylogeny of the isolates revealed two distinct clades unequivocally supported by Bayesian probabilities (P = 1); a livestock clade comprising 31/35 (88.6%) of the livestock isolates and a "nonlivestock" clade comprising further clades of environmental isolates. Several genes were identified as characteristic of strains in the livestock clade. The most prominent was a cluster of six genes (cj1321 to cj1326) within the flagellin glycosylation locus, which were confirmed by PCR analysis as genetic markers in six additional chicken-associated strains. Surprisingly these studies show that the majority (39/70, 55.7%) of C. jejuni human isolates were found in the nonlivestock clade, suggesting that most C. jejuni infections may be from nonlivestock (and possibly nonagricultural) sources. This study has provided insight into a previously unidentified reservoir of C. jejuni infection that may have implications in disease-control strategies. The comparative phylogenomics approach described provides a robust methodological prototype that should be applicable to other microbes.
Comparative phylogenomics of the fo... [Proc Natl Acad Sci U S A. 2005] - PubMed - NCBI
​

 

[juvenissun]

Naturally you will see it as useless if you don't understand it.

A question you might ask yourself. Why is it used so much in science if it is so useless? Scientists apparently see a lot of use for it. That you don't see a use for it or that it is not useful to you is irrelevant. It is the opinion of scientists that counts here.

Dizredux

YOU do not understand.

It is useful because it is a classification system. It is used for effectively label life forms in an orderly way. Although I have to say that it may not be the best system we can make due to its fatal restriction right from the beginning.

I said it is useless because it genetically bears the meaning of ancestry relationship among life forms. This is absolutely unnecessary in any classification system. The cladistic system will still work if the ancestry implication is all taken off. People refused to do that because this doing will collapse the concept of evolution theory.

What I like to see is a practical application on that ancestry idea. So far, I have seen none.

 

[juvenissun]

Going back to the OP, I think I see your problem. Cladistics is not designed to solve practical questions but scientific ones. Apparently it does a pretty job of that as it is used a lot by scientists.

Dizredux

Scientific questions include practical questions.

Are you saying that the ancestry idea of this classification system is only theoretical? That is exactly what I think.

 

[juvenissun]

Clades are used in this study to find new potential resevoirs for C. jejuni, an important human pathogen.

Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):16043-8. Epub 2005 Oct 17.

Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source.

Champion OL1, Gaunt MW, Gundogdu O, Elmi A, Witney AA, Hinds J, Dorrell N, Wren BW.

Abstract

Campylobacter jejuni is the predominant cause of bacterial gastroenteritis worldwide, but traditional typing methods are unable to discriminate strains from different sources that cause disease in humans. We report the use of genomotyping (whole-genome comparisons of microbes using DNA microarrays) combined with Bayesian-based algorithms to model the phylogeny of this major food-borne pathogen. In this study 111 C. jejuni strains were examined by genomotyping isolates from humans with a spectrum of C. jejuni-associated disease (70 strains), chickens (17 strains), bovines (13 strains), ovines (5 strains), and the environment (6 strains). From these data, the Bayesian phylogeny of the isolates revealed two distinct clades unequivocally supported by Bayesian probabilities (P = 1); a livestock clade comprising 31/35 (88.6%) of the livestock isolates and a "nonlivestock" clade comprising further clades of environmental isolates. Several genes were identified as characteristic of strains in the livestock clade. The most prominent was a cluster of six genes (cj1321 to cj1326) within the flagellin glycosylation locus, which were confirmed by PCR analysis as genetic markers in six additional chicken-associated strains. Surprisingly these studies show that the majority (39/70, 55.7%) of C. jejuni human isolates were found in the nonlivestock clade, suggesting that most C. jejuni infections may be from nonlivestock (and possibly nonagricultural) sources. This study has provided insight into a previously unidentified reservoir of C. jejuni infection that may have implications in disease-control strategies. The comparative phylogenomics approach described provides a robust methodological prototype that should be applicable to other microbes.
Comparative phylogenomics of the fo... [Proc Natl Acad Sci U S A. 2005] - PubMed - NCBI
​

This study only used clade as a simple classification scheme (in fact, a very very simple application). It said NOTHING about using the idea of ancestry or, if you like, the common descendent.

I am not a biologist nor a geneticist. Do not just thrown an abstract to me and have me read it carefully. Shame on you. If you continue to do that, I will not read your post.

 

[Loudmouth]

This study only used clade as a simple classification scheme (in fact, a very very simple application). It said NOTHING about using the idea of ancestry or, if you like, the common descendent.

The simple classification scheme is based on common ancestry. That is what a phylogeny is.

I am not a biologist nor a geneticist. Do not just thrown an abstract to me and have me read it carefully.

Then how can you claim that the methods they are using do not include common ancestry?

Do you know what a phylogeny is?

"In biology, phylogenetics /faɪlɵdʒɪˈnɛtɪks/ is the study of evolutionary relationships among groups of organisms (e.g. species, populations), which are discovered through molecular sequencing data and morphological data matrices."
Phylogenetics - Wikipedia, the free encyclopedia

Phylogenies are clades. What do these studies use?

"We report the use of genomotyping (whole-genome comparisons of microbes using DNA microarrays) combined with Bayesian-based algorithms to model the phylogeny of this major food-borne pathogen."

They are using genome sequencing and common ancestry (i.e. clades and phylogenies) in their study. It states it as plain as day.

 

[Loudmouth]

Scientific questions include practical questions.

I have shown you the practical applications of evolution, phylogenies, clades, phylogenomics, etc.

 

[PsychoSarah]

Why should comparison use the idea of ancestry?

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

Because not all creatures that look alike have common ancestry as close as they appear. It helps clear that up.

 

[juvenissun]

Because not all creatures that look alike have common ancestry as close as they appear. It helps clear that up.

What is the practical purpose to clear that up?

 

[juvenissun]

The simple classification scheme is based on common ancestry.

That is what a phylogeny is.

That is my question. Why should it based on that? If one does not, then what would happen?

 

[PsychoSarah]

What is the practical purpose to clear that up?

Making medicine for animals and knowing what will be effective and what diseases certain creatures are likely susceptible to. This is important especially when keeping many different animals in close proximity, such as in a zoo or on a farm.

To be honest though, sometimes I just like to know crap for the laughs or for the entertainment. Not the case here though.

 

[PsychoSarah]

That is my question. Why should it based on that? If one does not, then what would happen?

What should it be based on besides that?

 

[juvenissun]

What should it be based on besides that?

Logic, for example. Or, practical function. Such as cow and sheep are both grazers. Don't give the useless (and may be wrong) information such as their common ancestor. Why should anyone care about that?

 

[juvenissun]

Making medicine for animals and knowing what will be effective and what diseases certain creatures are likely susceptible to. This is important especially when keeping many different animals in close proximity, such as in a zoo or on a farm.

To be honest though, sometimes I just like to know crap for the laughs or for the entertainment. Not the case here though.

That is fine. But we do not have to know their common ancestor(s) to do that.

If you take the idea of common ancestor out of the classification system, then the idea of evolution broke or vanished. However, everything else still goes fine.

 

[PsychoSarah]

Logic, for example. Or, practical function. Such as cow and sheep are both grazers. Don't give the useless (and may be wrong) information such as their common ancestor. Why should anyone care about that?

Like I said earlier, it is important in examining disease risks. Say one animal catches a new disease and dies. The closer another being's genetics match the one of the creature that died, the more likely they can catch the devastating infection. Diseases that prey upon only one species are uncommon (small pox was able to be eradicated because the disease only afflicted humans).

It also can be predictive of disease progress and likely vectors.

As far as I am concerned, it is extremely important in the health fields.

 

[PsychoSarah]

That is fine. But we do not have to know their common ancestor(s) to do that.

If you take the idea of common ancestor out of the classification system, then the idea of evolution broke. However, everything else still goes fine.

Not necessarily. By the logic of kinds, would you think a bird disease could infect humans?

 

[juvenissun]

Not necessarily. By the logic of kinds, would you think a bird disease could infect humans?

If so, bird and human are the same kind. Is this your logic?

 

[OllieFranz]

If you take the idea of common ancestor out of the classification system, then the idea of evolution broke or vanished. However, everything else still goes fine.

Totally wrong.

In order to "take the idea of common ancestor out of the classification system," you have to add in a few of those scientifically unsubstantiated assumptions I mentioned in an earlier post. And those assumptions change the way the equations for geology work, necessitating even more unsubstantiated assumptions. And those assumptions necessitate even more unsubstantiated assumptions in Cosmology, and in Celestial Mechanics, Organic Chemistry, etc. In the end, you have not only broken evolution, you have broken every single branch of science, and every single sub-branch. The beauty of science is how one equation complements the next. An insistence on a specific "Last Thursday" scenario, especially without substantiation breaks all of those equations. Science is all about following the evidence where it leads, not trying to force it into a predetermined mold that it refuses to fit.

 

[juvenissun]

Totally wrong.

In order to "take the idea of common ancestor out of the classification system," you have to add in a few of those scientifically unsubstantiated assumptions I mentioned in an earlier post. And those assumptions change the way the equations for geology work, necessitating even more unsubstantiated assumptions. And those assumptions necessitate even more unsubstantiated assumptions in Cosmology, and in Celestial Mechanics, Organic Chemistry, etc. In the end, you have not only broken evolution, you have broken every single branch of science, and every single sub-branch. The beauty of science is how one equation complements the next. An insistence on a specific "Last Thursday" scenario, especially without substantiation breaks all of those equations. Science is all about following the evidence where it leads, not trying to force it into a predetermined mold that it refuses to fit.

I guess you are not giving up on your ring species argument.

Let's assume the ring species argument is valid, how would this idea be "practical" and solve practical problems? If a farmer managed all the animals related by a ring, should he do anything differently by knowing the relationship? If not, then why do we NEED this idea?

 

[Dizredux]

I guess you are not giving up on your ring species argument.

Let's assume the ring species argument is valid, how would this idea be "practical" and solve practical problems? If a farmer managed all the animals related by a ring, should he do anything differently by knowing the relationship? If not, then why do we NEED this idea?

What practical problem does cladistics solve?. To help understand how the natural world works.

Why do we need this idea? Same answer.

Why do we need science? Same answer.

Dizredux

 

[juvenissun]

What practical problem does cladistics solve?. To help understand how the natural world works.

Why do we need this idea? Same answer.

Why do we need science? Same answer.

Dizredux

In fact, it does not.
Because without the understanding, everything we do STILL work, not a bit short.

What I am asking is simply an example which is able to demonstrate the opposite. Just ONE!

I just wonder where do those knowledgeable evolutionists go? Are they simply chickened out?