How do we apply evidence of Common Descent?

[Mung]

@T_aquaticus

Something as simple as BLAST or KALIGN will do.

Are those the programs that are used for paternity testing?

[Mung]

@Dan_Eastwood

The principle is the same, even some of the methods.

See what you started!

[pnelson (Paul A Nelson)]

@T_aquaticus

In common parlance, differences are due to mutations while shared sequence is due to common ancestry.

In other words, (2). All DNA sequences, whatever their composition, are due to descent with modification from a common ancestor.

That looks like a geometry that cannot be tested. Common ancestry is true, come what may.

[Mung]

@pnelson

Common ancestry is true, come what may.

All my brothers are sisters!

[T_aquaticus]

@Mung

Are those the programs that are used for paternity testing?

For paternity tests, I believe they use PCR to amplify short tandem repeats and use gel electrophoresis to measure the size of the amplified bands. They then enter the genotype as the size of the DNA and not the sequence. If there are 4 possible alleles at each STR and you have even mixing of STR alleles then you can find just one person out of billions with relatively few STR’s. The same logic could also apply to endogenous retroviruses between species where matches between randomly inserted retroviruses could indicate common ancestry.

[Timothy_Horton]

@Dan_Eastwood

The two are not the same.

The principle is the same, even some of the methods. What do you propose is not the same?

This thread is one more example of Nathan’s observation on Creationist / troll tactics.

@NLENTS

At its best, it’s semantic, and it’s worst, it’s about trying to score cheap debate points with slick rhetoric. (which is not nearly as slick as they think it is.)

[T_aquaticus]

@pnelson

In other words, (2). All DNA sequences, whatever their composition, are due to descent with modification from a common ancestor.

If the base is the same at an orthologous position it is considered to be unmodified.

@pnelson

That looks like a geometry that cannot be tested. Common ancestry is true, come what may.

There should also be a phylogenetic signal, and there is.

[Timothy_Horton]

@pnelson

In other words, (2). All DNA sequences, whatever their composition, are due to descent with modification from a common ancestor.

That looks like a geometry that cannot be tested. Common ancestry is true, come what may.

…and another example appears.

@NLENTS

At its best, it’s semantic, and it’s worst, it’s about trying to score cheap debate points with slick rhetoric. (which is not nearly as slick as they think it is.)

[Mung]

Actually, Dan had a legitimate question and he probably really wants to know. It would help if people could just admit that BLAST is not used for paternity testing.

[Michael_Callen (Herculean Skeptic)]

@Timothy_Horton

This thread is one more example of Nathan’s observation on Creationist / troll tactics.

There’s a discussion going on here. I don’t see how this is helpful at all.

[pnelson (Paul A Nelson)]

@T_aquaticus

There should also be a phylogenetic signal, and there is.

Except when there isn’t a signal.

See, for a striking example, the study on mitochondrial DNA by Emilie Richards et al., just published in Systematic Biology, and covered by Jeremy Brown at the 38:00 mark of the talk I linked above.

[Mung]

@Timothy_Horton

Nit picking the simple and correct observation DNA similarities can be used to test for common descent.

I have not argued that DNA similarities cannot be used to test for common descent. So this must be about someone else.

[Dan_Eastwood]

@pnelson

More data alone will not resolve the Tree of Life.

Some disambiguation is needed here: Phylogenetic methods are well grounded in statistics, yes, but that does not mean there are no questions to to resolve about the correctness of data and which models to apply. This is a good talk, but it’s discussing issues of statistical model fit, not the general fit of a Tree of Life pattern. These models CAN resolve phylogenetic trees to the extent of statistical power; there may be open questions about which model is correct for given data.
In simpler terms, we have strong resolution for some branches, and less resolution for others. The statistics methods are sound, but we do not yet have good models for all forms of evolution.

[pnelson (Paul A Nelson)]

@Dan_Eastwood

This is a good talk, but it’s discussing issues of statistical model fit, not the general fit of a Tree of Life pattern.

The data conflicts discussed in Brown’s talk raise the question (which he does not address, not surprisingly, given that he accepts the existence of some monophyletic tree as a given) of when a “Tree of Life” pattern would fail. I think most biologists who haven’t looked into the matter would be stunned by the conflicts in mitochondrial data revealed in the Richards et al. study.

[Mung]

@T_aquaticus

We observe that siblings and cousins have the same endogenous retrovirus insertions due to common ancestry. The same logic applies to shared ERVs between humans and chimps, as well as to other primates.

I don’t believe that ERVs are used for paternity testing. Are you saying that they are?

Here’s the logic as I see it. If another human shares the same ERVs that I have, that person and I must be cousins. And since humans and chimps share the same ERVs that means humans and chimps are cousins.

If i find the same ERV in a chimp that I find in my cousin, does it follow that the chimp and I are cousins?

[Dan_Eastwood]

@Mung

See what you started!

I have poked the hornets nest, haven’t i?

I have to step away a while, but I urge everyone to carefully consider your replies, and focus on points of agreement FIRST, with disagreements second. When I get back I may move the less constructive replies to side-comments.

[Timothy_Horton]

@Mung

Nit picking the simple and correct observation DNA similarities can be used to test for common descent.

I have not argued that DNA similarities cannot be used to test for common descent. So this must be about someone else.

That DNA similarities can be used as evidence for common descent was the only point of the gbrooks9 post you decided to strawman and attack in a whole new thread. But I’m sure your motives were as pure as they always are.

[Dan_Eastwood]

Go easy, @Timothy_Horton. I started this thread because it seemed like a legitimate question which deserved to be rescued from obscurity. It IS interesting too, if we don’t use it as an excuse to fight.

[T_aquaticus]

@pnelson

Except when there isn’t a signal.

See, for a striking example, the study on mitochondrial DNA by Emilie Richards et al., just published in Systematic Biology , and covered by Jeremy Brown at the 38:00 mark of the talk I linked above.

Is there a peer reviewed paper we could look at instead of going through hours of videos?

[T_aquaticus]

@Mung

I don’t believe that ERVs are used for paternity testing. Are you saying that they are?

I am saying that the same concepts that apply for STR’s in paternity testing apply to shared ERV’s among primates.

@Mung

Here’s the logic as I see it. If another human shares the same ERVs that I have, that person and I must be cousins. And since humans and chimps share the same ERVs that means humans and chimps are cousins.

If i find the same ERV in a chimp that I find in my cousin, does it follow that the chimp and I are cousins?

We can readily observe that cousins and siblings share orthologous ERV’s through common ancestry. The same logic would apply to chimps which would be more distantly related cousins.