Molecular phylogeny - a problem instead of a solution

[lee_merrill]

Surely if the tree of life is true, we ought to see it in the DNA. But molecular phylogeny has turned out to be a problem, instead of a solution.

Source: Evolution News

... the problem has only grown worse as more data have accumulated. In 2005, three biologists who compared 50 DNA sequences from 17 animal groups concluded that “different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support.” In 2012, four evolutionary biologists reported “incongruence between phylogenies derived from…different subsets of molecular sequences has become pervasive.”

Source

© Copyright Original Source

Blessings,
Lee

[shunyadragon]

Surely if the tree of life is true, we ought to see it in the DNA. But molecular phylogeny has turned out to be a problem, instead of a solution.

Source: Evolution News

... the problem has only grown worse as more data have accumulated. In 2005, three biologists who compared 50 DNA sequences from 17 animal groups concluded that “different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support.” In 2012, four evolutionary biologists reported “incongruence between phylogenies derived from…different subsets of molecular sequences has become pervasive.”

Source

© Copyright Original Source

Blessings,
Lee

Again . . .

A non-scientific source with a religious agenda. How about some references from per reviewed research journals.

[rogue06]

[cite=Evolution News]

Like a pig returning to its slop.

[Roy]

Surely if the tree of life is true, we ought to see it in the DNA.

We do see that. Your source is quote-mining, knowing that you are too trusting and gullible to check their citations.

The context of their first quote is this:

Source: https://www.science.org/doi/10.1126/science.1116759?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Furthermore, although increasing the gene number greatly reduces sampling error, the vulnerability to systematic error artefacts also increases, perhaps explaining how different phylogenetic analyses can reach contradicting inferences with absolute support

© Copyright Original Source

[lee_merrill]

We do see that.

How so?

Your source is quote-mining, knowing that you are too trusting and gullible to check their citations.

The context of their first quote is this:

Source: https://www.science.org/doi/10.1126/science.1116759?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed

Furthermore, although increasing the gene number greatly reduces sampling error, the vulnerability to systematic error artefacts also increases, perhaps explaining how different phylogenetic analyses can reach contradicting inferences with absolute support

© Copyright Original Source

For starters, they say "perhaps explaining", showing that their explanation is not certain. They are not sure they have explained the problem. So I think Evolution News is justified in pointing out that "different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support".

Blessings,
Lee

[TheLurch]

Surely if the tree of life is true, we ought to see it in the DNA. But molecular phylogeny has turned out to be a problem, instead of a solution.

Source: Evolution News

... the problem has only grown worse as more data have accumulated. In 2005, three biologists who compared 50 DNA sequences from 17 animal groups concluded that “different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support.” In 2012, four evolutionary biologists reported “incongruence between phylogenies derived from…different subsets of molecular sequences has become pervasive.”

Source

© Copyright Original Source

I won't accuse Lee of lying, but he has a habit of consistently quoting obvious liars.

The short summary of the liars at Evolution News is something like this: "we've found a single set of circumstances where molecular phylogenies don't produce reliable results, and therefore we think we should throw out the entire concept of the tree of life." (I feel dumber for having had to type something so mindbogglingly idiotic.)

The key sentence in the paper Roy looked up is the last one in the abstract: "given adequate sequence data, the lack of resolution in phylogenetic trees is a signature of closely spaced series of cladogenetic events." In less technical terms, if there's a rapid radiation, then everything doing the radiating will look extremely similar on the DNA level, so it can be impossible to tease the precise sequence of events apart using the DNA of their ancestors. The inability to make a molecular phylogeny work should therefore be interpreted as evidence of a rapid radiation.

That's it. All other molecular phylogenies typically produce consistent results. So, Evo News naturally cherry picks a few prominent cases of rapid radiations, and tries to pretend that represents all molecular phylogeny. They are terrible people who intentionally mislead the gullible.

[rogue06]

I won't accuse Lee of lying, but he has a habit of consistently quoting obvious liars.

The short summary of the liars at Evolution News is something like this: "we've found a single set of circumstances where molecular phylogenies don't produce reliable results, and therefore we think we should throw out the entire concept of the tree of life." (I feel dumber for having had to type something so mindbogglingly idiotic.)

The key sentence in the paper Roy looked up is the last one in the abstract: "given adequate sequence data, the lack of resolution in phylogenetic trees is a signature of closely spaced series of cladogenetic events." In less technical terms, if there's a rapid radiation, then everything doing the radiating will look extremely similar on the DNA level, so it can be impossible to tease the precise sequence of events apart using the DNA of their ancestors. The inability to make a molecular phylogeny work should therefore be interpreted as evidence of a rapid radiation.

That's it. All other molecular phylogenies typically produce consistent results. So, Evo News naturally cherry picks a few prominent cases of rapid radiations, and tries to pretend that represents all molecular phylogeny. They are terrible people who intentionally mislead the gullible.

Many of those gullible are willingly so, hence I'm not sure that's the proper descriptor.

[TheLurch]

using the DNA of their ancestors.

That should be descendants; I apologize for the error.

[lee_merrill]

The inability to make a molecular phylogeny work should therefore be interpreted as evidence of a rapid radiation.

"Might be interpreted" would be more accurate: "perhaps explaining how different phylogenetic analyses can reach contradicting inferences with absolute support." (Rokas et al.)

All other molecular phylogenies typically produce consistent results.

Source: Science

Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.

Source

© Copyright Original Source

Evo News naturally cherry picks a few prominent cases of rapid radiations...

No, they quoted general statements about the state of molecular phylogeny.

Blessings,
Lee

[TheLurch]

Source: Science

Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.

Source

© Copyright Original Source

No, they quoted general statements about the state of molecular phylogeny.

If you'd actually read and understand the paper, you'd realize that what you're saying is completely wrong. They're not talking about the trees within major metazoan phyla - those all resolve just fine. They're talking about the tree of the major phyla - their relationships to each other and the order of their diversification. So no, the paper is not making a general statement - it refers only to the earliest branches of the metazoan tree.

Really, why do you keep talking about biology when you clearly don't understand it, and aren't at all interested in learning from anyone who actually understands biology? Couldn't you focus on something more appropriate for your knowledge base? Or take a few classes in biology and develop a knowledge base first? Does it not bother you to make false statements so often?

[Roy]

For starters, they say "perhaps explaining", showing that their explanation is not certain. They are not sure they have explained the problem. So I think Evolution News is justified in pointing out that "different phylogenetic analyses can reach contradicting inferences with [seemingly] absolute support".

So you don't mind ENV omitting that the person who obtained the results they're citing thinks they may be errors.

Are you willing to accept lies by omission from anyone, or only those you have common ground with?

[rogue06]

If you'd actually read and understand the paper, you'd realize that what you're saying is completely wrong.

By now you should realize that won't happen. He'll continue to turn to Evolution News and Behe to tell him what to and how to think.

[lee_merrill]

They're not talking about the trees within major metazoan phyla - those all resolve just fine. They're talking about the tree of the major phyla - their relationships to each other and the order of their diversification. So no, the paper is not making a general statement - it refers only to the earliest branches of the metazoan tree.

Could you give me a quote that demonstrates this? The abstract sure sounds like a general statement.

Source: Science

The phylogenetic relationships among most metazoan phyla remain uncertain. We obtained large numbers of gene sequences from metazoans, including key understudied taxa. Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.

© Copyright Original Source

Blessings,
Lee

[lee_merrill]

So you don't mind ENV omitting that the person who obtained the results they're citing thinks they may be errors.

I think that could be part of the reason Evolution News put [seemingly] in the quote.

Blessings,
Lee

[TheLurch]

Could you give me a quote that demonstrates this? The abstract sure sounds like a general statement.

Source: Science

The phylogenetic relationships among most metazoan phyla remain uncertain. We obtained large numbers of gene sequences from metazoans, including key understudied taxa. Despite the amount of data and breadth of taxa analyzed, relationships among most metazoan phyla remained unresolved.

© Copyright Original Source

Uhm, that quote demonstrates it. Relationships among phyla, not within phyla.