Clade

[juvenissun]

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)? Since evolutionists will certainly oppose this idea, so 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.

 

[OllieFranz]

IThe idea of a clade is useful for DNA comparison between different species. There are occasional differences from classical Linnean taxonomy, but for the most part it confirms the tree of life that was derived from that taxonomy.

It also gives us a useful analog of the creationist idea of a kind. Many creationists have come to accept the idea of speciation. They accept that, for example, dogs and wolves have a common ancestor, and perhaps that other canines do as well. "Kind," for them no longer equates to species, but to a related group descended from a "created kind" created during the First Week in Genesis. They simply refuse to accept the so-called "molecule-to-man" evolution.

A clade is defined as an arbitrary species, called a root species, and all of its descendents, extant and extinct. A kind has thus been re-defined as a clade whose root species is one of the ones created during the First Week. Some creationists welcome the idea of a clade, since it gives a point of commonality with evolution to focus discussions on, and other creationists don't like clades because it allows too much compromise with evolution.

 

[Dizredux]

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)? Since evolutionists will certainly oppose this idea, so 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.

This is not my field but as I understand it from reading, cladistics allows more precise predictions of what we find than the older Linnaean taxonomy.

I do not know a lot about cladistics but what I do know, I like.

Dizredux

 

[CabVet]

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)? Since evolutionists will certainly oppose this idea, so 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.

Cladistics makes a lot more sense to evolutionary biologists than traditional Linnean taxonomy does.

 

[juvenissun]

IThe idea of a clade is useful for DNA comparison between different species. There are occasional differences from classical Linnean taxonomy, but for the most part it confirms the tree of life that was derived from that taxonomy.

Why should comparison use the idea of ancestry?

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

 

[juvenissun]

This is not my field but as I understand it from reading, cladistics allows more precise predictions of what we find than the older Linnaean taxonomy.

I do not know a lot about cladistics but what I do know, I like.

Dizredux

I do not accept that argument. Paleontological "prediction" is simply a joke. When the object is found, they claimed the prediction is wonderful. When it is not found, they argued it is "to be found".

And the nature of prediction is like this: If a and c are found, they predict b must be somewhere. This kind of prediction can be done by a three-year old.

 

[juvenissun]

Cladistics makes a lot more sense to evolutionary biologists than traditional Linnean taxonomy does.

Make sense is not good enough. Any practical use? The usefulness determines if it (the idea of ancestry) makes sense of not.

 

[OllieFranz]

Why should comparison use the idea of ancestry?

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

We see speciation in real time. We know it happens, and we know the effects that are seen in the DNA of related species. So it is evidence of relatedness and ancestry.

Creationists are correct in stating that we don't have "proof" of what they refer to as "molecule-to-man" evolution. Both the rules of evolution and the actual evidence would be the same if "Last Thursdayism" were true. But then there is the problem of when "Last Thursday" was. There is nothing in the scientific evidence to show when it was. Genesis, according to YEC's, tells us when it was, but it is not scientific evidence..

Science theories need to be consistent, must match the evidence, and must be elegant. An important element, perhaps the most important element, of an elegant theory is that there are no unsubstantiated assumptions. There is no scientific reason to assume any "Last Thursday," not even one 6,000 years ago.

 

[juvenissun]

We see speciation in real time. We know it happens, and we know the effects that are seen in the DNA of related species. So it is evidence of relatedness and ancestry.

I am not sure we do. The cases I have heard are either changes on bacteria or minor reversible changes on habit in a tightly controlled lab environment. If we do see speciation happened naturally in front of our eyes, then the creation/evolution debate should be over long time ago.

Besides, when we see A changed to B, then we found the DNA of A and B are related. However, we can not make a backward statement. When we find C and D are 98% identical in DNA, we can not say they have ancestral relationship.

Before that happen, the idea of ancestry in cladistics is simply useless.

 

[Mr Strawberry]

The cases I have heard are either changes on bacteria or minor reversible changes on habit in a tightly controlled lab environment. If we do see speciation happened naturally in front of our eyes, then the creation/evolution debate should be over long time ago.

The debate has been over for a very, very long time. This is not news.

And interesting that you dismiss speciation in bacteria. Where do you think you are most likely to see speciation "in front of our eyes"? In populations of very small organisms with very fast life cycles or in very large ones with very slow life cycles?

 

[Mr Strawberry]

Besides, when we see A changed to B, then we found the DNA of A and B are related. However, we can not make a backward statement. When we find C and D are 98% identical in DNA, we can not say they have ancestral relationship.

Why not?

Before that happen, the idea of ancestry in cladistics is simply useless.

What are you talking about?

 

[OllieFranz]

I am not sure we do. The cases I have heard are either changes on bacteria or minor reversible changes on habit in a tightly controlled lab environment. If we do see speciation happened naturally in front of our eyes, then the creation/evolution debate should be over long time ago.
.

Then explain Ring Species. They are neither "tightly controlled lab environment(s)" nor "minor reversible changes." The population at one end can not interbreed with the population at the other end, so there is no way to reverse the separation. And if one of the intermediate populations goes extinct, as happened in Siberia with the Greenish Warbler, then even the theoretical possibility of re-integrating the population through successive breedings with the intermediate populations is gone. Western Warblers are completely and permanently cut off from the original stock and the eastern Warblers.

We do see speciation happen naturally in front of our eyes. The debate continues only because the YECs are willfully ignorant of that fact. Shutting one's eyes and complaining that one does not see any evidence is directly comparable to the childish tactic of putting ones fingers in ones ears and shouting in orderto avoid hearing evidence one wishes not to acknowledge.

 

[Dizredux]

If you deny speciation, and findings of paleontology then of course cladistics will not make sense to you.

If you deny geology, astronomy, astrophysics and biology then evolution will not make sense to you as seems to be the case.

Simple enough when seen from that viewpoint.

Dizredux

 

[juvenissun]

If you deny speciation, and findings of paleontology then of course cladistics will not make sense to you.

If you deny geology, astronomy, astrophysics and biology then evolution will not make sense to you as seems to be the case.

Simple enough when seen from that viewpoint.

Dizredux

I did not say it does not make sense. I said it is useless. Do not shift the goalpost.

 

[Subduction Zone]

I did not say it does not make sense. I said it is useless. Do not shift the goalpost.

Speciation is extremely useful. It is what allows life to survive.


It seems you should have said that you do not understand how speciation is useful.

In fact that should be a rule for all creationists when it comes to evolution. Instead of every claiming that evolution does not make sense in any way at all you should instead simply say that you do not understand how a certain process would happen with evolution. Occasionally you would find that scientists would be saying the same thing you are. Scientists have not solved all of the problems of evolution. That is what keeps a subject interesting.

 

[juvenissun]

Then explain Ring Species. They are neither "tightly controlled lab environment(s)" nor "minor reversible changes." The population at one end can not interbreed with the population at the other end, so there is no way to reverse the separation. And if one of the intermediate populations goes extinct, as happened in Siberia with the Greenish Warbler, then even the theoretical possibility of re-integrating the population through successive breedings with the intermediate populations is gone. Western Warblers are completely and permanently cut off from the original stock and the eastern Warblers.

We do see speciation happen naturally in front of our eyes. The debate continues only because the YECs are willfully ignorant of that fact. Shutting one's eyes and complaining that one does not see any evidence is directly comparable to the childish tactic of putting ones fingers in ones ears and shouting in orderto avoid hearing evidence one wishes not to acknowledge.

I am not trying to debate the speciation. That is another issue. Give you the benefit of doubt. Assume the few known examples of speciation are true, then how would that help your argument?

I am questioning the usefulness of cladistic classification. I have not seen any example yet. I am more confident now that the idea of "common ancestor" is basically an ideology and is impractical.

Prove me wrong, please.

 

[Dizredux]

I did not say it does not make sense. I said it is useless. Do not shift the goalpost.

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

 

[Loudmouth]

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)? Since evolutionists will certainly oppose this idea, so 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.

Clades are phylogenies. The phylogenomics method, which use phylogenies, us a very useful and practical method of pulling information out of genomes. The authors of this paper use the phylogenomics method to accurately predict protein function, which is a very useful.

PLoS Comput Biol. 2005 Oct;1(5):e45. Epub 2005 Oct 7.

Protein molecular function prediction by Bayesian phylogenomics.

Engelhardt BE1, Jordan MI, Muratore KE, Brenner SE.

Abstract

We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent molecular function predictions across 100 Pfam families in comparison to the Gene Ontology annotation database, BLAST, GOtcha, and Orthostrapper. We performed a more detailed exploration of functional predictions on the adenosine-5'-monophosphate/adenosine deaminase family and the lactate/malate dehydrogenase family, in the former case comparing the predictions against a gold standard set of published functional characterizations. Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods such as BLAST (75%), GeneQuiz (64%), GOtcha (89%), and Orthostrapper (11%). We also experimentally characterized the adenosine deaminase from Plasmodium falciparum, confirming SIFTER's prediction. The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors.
Protein molecular function prediction by Ba... [PLoS Comput Biol. 2005] - PubMed - NCBI​

You can read the full paper here:
Protein Molecular Function Prediction by Bayesian Phylogenomics

Another important quote from the paper:

Phylogenomics is a methodology for annotating the specific molecular function of a protein using the evolutionary history of that protein as captured by a phylogenetic tree [17].​

That phylogenetic tree is a product of cladistics.

 

[Dizredux]

Is this system only ideologic and has no practical use (except labeling)? Since evolutionists will certainly oppose this idea, so I really like to learn even a single case that this ancestry-focused classification system is useful to solve a practical question.

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

 

[Loudmouth]

Clades were used in this study to find potential virulence factors in C. difficile:

J Bacteriol. 2006 Oct;188(20):7297-305.

Comparative phylogenomics of Clostridium difficile reveals clade specificity and microevolution of hypervirulent strains.

Stabler RA1, Gerding DN, Songer JG, Drudy D, Brazier JS, Trinh HT, Witney AA, Hinds J, Wren BW.

Abstract

Clostridium difficile is the most frequent cause of nosocomial diarrhea worldwide, and recent reports suggested the emergence of a hypervirulent strain in North America and Europe. In this study, we applied comparative phylogenomics (whole-genome comparisons using DNA microarrays combined with Bayesian phylogenies) to model the phylogeny of C. difficile, including 75 diverse isolates comprising hypervirulent, toxin-variable, and animal strains. The analysis identified four distinct statistically supported clusters comprising a hypervirulent clade, a toxin A(-) B(+) clade, and two clades with human and animal isolates. Genetic differences among clades revealed several genetic islands relating to virulence and niche adaptation, including antibiotic resistance, motility, adhesion, and enteric metabolism. Only 19.7% of genes were shared by all strains, confirming that this enteric species readily undergoes genetic exchange. This study has provided insight into the possible origins of C. difficile and its evolution that may have implications in disease control strategies.
Comparative phylogenomics of Clostridium diffici... [J Bacteriol. 2006] - PubMed - NCBI​