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Topic: Bremer (Read 1447 times) previous topic - next topic

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  • socrates1
Bremer
Notice the abysmally low Bremer support values:
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf

Maniraptoriformes--is only poorly supported (Bremer support of 1 and jackknife percentage of less than 50%), and relationships at its base are unresolved. There is a basal polytomy consisting of four clades: Ornitholestes, Compsognathidae, Ornithomimosauria, and Maniraptora (i.e., the clade of all taxa more closely related to birds than to Ornithomimus: [S52]).

Maniraptora--the clade defined as all taxa closer to birds than to Ornithomimus--is comprised in the present study of Alvarezsauroidea, Therizinosauroidea, Oviraptorosauria, and Paraves. This clade is supported by a Bremer value of 2 but a jackknife percentage of less than 50%.

Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less than 50%.

Paraves--consisting of dromaeosaurids, troodontids, and avialans--is also poorly supported, as it also has a Bremer value of 1 and a jackknife of less than 50%.

http://ib.berkeley.edu/courses/ib200a/labs/ib200a_lab10_bootstrap_jackknife_bremer.pdf
As a rule of thumb, a Bremer score of 3 is good and a score of 5 is "highly supported."


  • socrates1
Re: Bremer
Reply #1
It would be absurd to move this somewhere else given that this is simply a statement from a scientific published article. But the discriminatory decisions here are made on personal animus and not on scientific considerations.
Or perhaps they will suspend some people for posting scientific published material.
  • Last Edit: June 20, 2017, 06:24:09 AM by socrates1

  • socrates1
Re: Bremer
Reply #2
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

  • VoxRat
  • wtactualf
Re: Bremer
Reply #3
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.
Who is "you" ?

(Note that threads get moved, not just on the basis of whether there's something "scientific" in them, but also on the basis of the ability or willingness of participants to engage in discussion.)
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • MikeS
Re: Bremer
Reply #4
Publish or Die socrates.  Publish or Die.

  • socrates1
Re: Bremer
Reply #5
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
  • Last Edit: June 20, 2017, 06:52:14 AM by socrates1

  • MikeS
Re: Bremer
Reply #6
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Write it up for publication socrates.

  • socrates1
Re: Bremer
Reply #7
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Write it up for publication socrates.

Care to contribute? Particularly if you have some expertise in this area.

  • VoxRat
  • wtactualf
Re: Bremer
Reply #8
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Nothing you have written here contradicts the "dinosaur to bird hypothesis".
This would be blindingly obvious if you were ever to muster the courage to actually engage in discussion.
Like, for instance, explaining why you think anything you have written points to such a contradiction.
But you won't.
Which is why this thread does not belong in a Science discussion forum.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • MikeS
Re: Bremer
Reply #9
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Write it up for publication socrates.

Care to contribute? Particularly if you have some expertise in this area.
I will contribute to the discussion of your analysis and findings in whatever format you choose to submit.

All I see is your pointing at numbers and saying "SEE, LOOK, THERE."  But there is no analysis, comparative or contrasting evaluations and original ideas on proper modifications.

You say there's a "mistake", so spell it out already.

  • socrates1
Re: Bremer
Reply #10
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Write it up for publication socrates.

Care to contribute? Particularly if you have some expertise in this area.
I will contribute to the discussion of your analysis and findings in whatever format you choose to submit.

All I see is your pointing at numbers and saying "SEE, LOOK, THERE."  But there is no analysis, comparative or contrasting evaluations and original ideas on proper modifications.

You say there's a "mistake", so spell it out already.

What do you understand so far as the problems I have pointed out?

  • RAFH
  • Have a life, already.
Re: Bremer
Reply #11
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Write it up for publication socrates.

Care to contribute? Particularly if you have some expertise in this area.
Sucky my old chew toy, are you suggesting you have some expertise in this area?

Which university was it you got your Masters and Doctorates in paleontology and/or some other relevant field? Oh, wait, that's right, you don't have any such education.

How about the research organizations you've worked for? Oh, wait, that's right, you haven't.

Papers you've had published? Oops. Papers you've submitted? Double oops!

But, hey, you do have that crappy vanity blog, that's got to count for something, right?
Don;t feel too bad, though, you do serve some slightly useful societal purpose, providing a bit of entertainment.
Are we there yet?

  • Faid
Re: Bremer
Reply #12
Wow. "Socrates" is NOT quoting himself, and actually RESPONDING to others!

Let's see if the trend lasts.

Reposting DeanW's post from the "Classification" thread:


Let's begin the discussion with the highest Bremer value of the entire cladogram "12" supporting the clade containing Coelophysis, Dilophosaurus, Allosaurus, and Velociraptor. (For reference, Socrates considers Velociraptor to be a member of what he dubs "Euparaves".  "Euparaves" are presumeably closely related to the pterosaurs, way at the other end of the figure.)

The next highest Bremer value "9" supports Allosaurus and Velociraptor* as sister taxa.

Tied for next highest Bremer value "8" are Ornithodira (whew, finally pterosaurs figure into the picture), Diosauriformes, and the clade uniting Silesauridae, Ornithischia, Sauropodomorpha, and Theropoda.

And on and on it goes.  Socrates's pteroidiocy is ludicrously unsupported by the evidence.

End of the line.

ETA *Deep within the Allosaurus/Velociraptor clade some studies have recovered a polytomy.  Socrates has creamed over this excitedly in other threads.  As all can see, it is irrelevant to the discussion at hand regarding the relationship of pterosaurs vis a vis Velociraptor.  But Socrates loves to harp on inconsequential ephemera.

And in the source "socrates" gave us, the coelurosauria node has a Bremer value of 3 (Which "socrates" accepts as "good", and it's the same as some of the best values we see WITHIN Avialae. The Avialae node itself has a value of 1, if archie is included ::)).

Your turn, "socrates". Discuss.

  • Last Edit: June 20, 2017, 07:38:25 AM by Faid
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • borealis
  • Administrator
Re: Bremer
Reply #13
ADMIN NOTE

SOCRATES1:

Since you refuse to respond to PMs, I'm addressing you here. You do not have permission to post threads in the Science forum, for reasons stated in previous PMs to you. If you haven't read them, that's your problem.

Next time, expect a 24 hour ban.

  • socrates1
Re: Bremer
Reply #14
What a laugh. Another interesting thread hits the end of the line.

  • borealis
  • Administrator
Re: Bremer
Reply #15
You could always go join another forum.

  • socrates1
Re: Bremer
Reply #16
What a laugh.

  • VoxRat
  • wtactualf
Re: Bremer
Reply #17
Another interesting thread ...

"Socrates"'s idea of an "interesting thread" is one where he makes unsupported pronouncements and declines to engage in any discussion of them.

What a laugh.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • RAFH
  • Have a life, already.
Re: Bremer
Reply #18
What a laugh. Another interesting thread hits the end of the line.
Ah, good to see even you agree you're entertaining.
Are we there yet?

  • Brother Daniel
  • Global Moderator
  • predisposed to antagonism
Re: Bremer
Reply #19
[relevant content snipped]
Your turn, "socrates". Discuss.
So what does "socrates" do when faced with substantive responses?
What a laugh. Another interesting thread hits the end of the line.
run away!

Re: Bremer
Reply #20
To this point I have not been mentioning the absurdly low Bremer support values because you have not even been able to take in the resampling test results (bootstrap, jackknife) and the huge polytomy they produce.

Every time we look at the published material and the statistical tests, they contradict the dinosaur to bird hypothesis.
Write it up for publication socrates.

Care to contribute? Particularly if you have some expertise in this area.
I will contribute to the discussion of your analysis and findings in whatever format you choose to submit.

All I see is your pointing at numbers and saying "SEE, LOOK, THERE."  But there is no analysis, comparative or contrasting evaluations and original ideas on proper modifications.

You say there's a "mistake", so spell it out already.

What do you understand so far as the problems I have pointed out?

For anybody unfamiliar with his method, this is classic Socrates.  It's as clear as day that he doesn't have a clue about any purported problem, and even if he did he couldn't express it coherently.  Socrates is fishing for Mike to make some cogent point which he will then pretend was what he meant all along, and that "finally, someone here is showing some honesty about the problem."

He's used this tactic countless times in the past.  Does anybody remember the hammerhead trait going to fixation in the entire shark population?

Pathetic.

  • socrates1
Re: Bremer
Reply #21
Mike S
If you are interested send me a private message. If you have some expertise that would be interesting. But if that does not appeal to you, that is fine also.

  • socrates1
Re: Bremer
Reply #22
For those interested, the Bremer values are another indication that the nodes are to be collapsed into the huge polytomy. Both the bootstrap/jackknife values and the Bremer numbers confirm the collapse of the nodes.
All the different support calculations lead to Euparaves.
  • Last Edit: June 20, 2017, 09:32:12 AM by socrates1

Re: Bremer
Reply #23
For those interested, the Bremer values are another indication that the nodes are to be collapsed into the huge polytomy. Both the bootstrap/jackknife values and the Bremer numbers confirm the collapse of the nodes.



Which nodes?  Are you talking about nodes deep within the Allosaurus/Velociraptor branch?  Or perhaps you mean that the Allosaurus/Velociraptor branch, since it only has a Bremer value of 9, and since the Allosaurus/Velociraptor/Dilophosaurus branch only has a value of 7, it as well should be collapsed into a polytomy with Coelophysis?  Hopefully, we can all agree that the Coelophysis/Dilophosaurus/Allosaurus/Velociraptor branch, with a Bremer value of 12, should be retained.  And naturally, that any proposed branch containg either or both pterosaurs with Velociraptor to the exclusion of Velociraptor's fellow theropods is completely contradicted by the results.

Here's a thought.  Since you have the TNT software you could import the Nesbitt matrix data and run it. And then run the bootstrap and jackknife support calculations and see if you get basically the same results as he did.  Oh, wait, you were pretending when you claimed to have done that for the Yu and Brusatte studies.  That's why you couldn't produce any evidence for having done it.  But go ahead, claim that you could've provided such evidence, but didn't because you ...yada...yada...yada.  A whiny four-year-old could make better excuses when caught in a blatant lie.

End of the line.
  • Last Edit: June 20, 2017, 09:43:00 AM by Dean W

  • socrates1
Re: Bremer
Reply #24
For those who want to pretend that they do not understand the problem I will post this again (from yesterday):

Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.