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Topic: Bremer (Read 1446 times) previous topic - next topic

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  • socrates1
Re: Bremer
Reply #50
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?

I guess Mike S has lost interest.

  • VoxRat
  • wtactualf
Re: Bremer
Reply #51
He's waiting for you to identify some "problem" or "mistake".

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

  • Faid
Re: Bremer
Reply #52

As I said, you folks amaze me with your misconceptions. You believe your misconceptions and then take them as proven. It is my policy to not correct every misconception you folks have. That could go on forever.
If anyone is actually serious, read what I have posted.
But you are still in the "pretending not to understand the subject or pretending not to understand that there is a problem" stage.

Yawn.

Here is something people could contribute on. Why do the bootstrap/jackknife values have high values (when they are closer to archosaurs) and totally non-supportive values at Euparaves? I do not really expect any contribution on this but who knows?
Here's another question- Why is the grass blue and the sky green?

Look at that chart (that you've supposedly "studied") again, "socrates":

There are consecutive 99% jackknife values for Therizinosauroidea groups. are those "closer to archosaurs"?

There is an 85% value for the node for all avialae excluding Archie. Are those "closer to archosaurs"?

There is a 93% value for the hesperornithes clade, and a 97%value for Galliformes. Are THOSE "closer to archosaurs"?

Nice try.

Try again.

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.

  • Faid
Re: Bremer
Reply #53
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."

Worth repeating since everyone seems to be ignoring this. Or more precisely," pretending not to understand it or pretending it is not a problem".
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.
In your source, there is a 'support calculation' with a Bremer value of 3 for a coelurosauria node that includes Paraves.

Where does THAT lead, "socrates"?
Worth repeating since "socrates" seems to be ignoring this. Or more precisely, "pretending not to understand it or pretending it is not a problem".
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.

  • socrates1
Re: Bremer
Reply #54
As I have said when people are in Stage 1 there is not much that can be done until someone acknowledges (admits) the problem. The pattern is then for others to say they always knew that, but did not feel they would acknowledge it.

  • socrates1
Re: Bremer
Reply #55
When people point to the higher support values in the earlier nodes it is hard to tell whether they are acknowledging the problem of the huge polytomy as being a problem or not. If they are acknowledging the huge polytomy as a problem, then they are in the "Yes but" stage. But nobody has actually acknowledged that the huge polytomy is any kind of problem so it is hard to tell.
As a sidenote if they are actually acknowledging the problem and are in the "yes but" stage then they bypassed the "Denial" stage. Which would be interesting.
But nobody has actually acknowledged that the huge polytomy is any kind of problem so it is hard to tell.
  • Last Edit: June 21, 2017, 08:11:00 AM by socrates1

  • Faid
Re: Bremer
Reply #56
Lol.

"Low support values obviously mean that nodes are not supported... What's that? there are HIGH support values in the earlier [sic] nodes? OMG nevermind that LOOK AT THE HUGE POLYTOMY!!!1".

You're not fooling anyone, champ. We can smell your cowardice from here.
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.

Re: Bremer
Reply #57
As I have said when people are in Stage 1 there is not much that can be done until someone acknowledges (admits) the problem. The pattern is then for others to say they always knew that, but did not feel they would acknowledge it.

What stage of untreated syphillis are you at, Socrates?

  • Faid
Re: Bremer
Reply #58
When people point to the higher support values in the earlier nodes it is hard to tell whether they are acknowledging the problem of the huge polytomy as being a problem or not. If they are acknowledging the huge polytomy as a problem, then they are in the "Yes but" stage. But nobody has actually acknowledged that the huge polytomy is any kind of problem so it is hard to tell.
As a sidenote if they are actually acknowledging the problem and are in the "yes but" stage then they bypassed the "Denial" stage. Which would be interesting.
But nobody has actually acknowledged that the huge polytomy is any kind of problem so it is hard to tell.
Lol. "socrates" is so lost within his own psychobabble about "people here", he's essentialy arguing with himself about the derived inconsistencies in his made-up "stages".

Can it really get any better than that? I guess we'll see. :popcorn:
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.

  • socrates1
Re: Bremer
Reply #59
Concerning the huge polytomy:
This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of Paraves.
It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.

  • Faid
Re: Bremer
Reply #60
Concerning the huge polytomy:
This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of Paraves.
It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.
Lol. Notice the sleight of hand here. "Socrates" goes from "not telling the relationship between oviraptorids and Paraves" to talking about "transitionals between dinosaurs and Paraves".

Did everyone catch that?

It was very smart.

(Well, not really, no.)

What the ACTUAL data shows, however, is that we may not know the exact relationship BETWEEN oviraptors and Paraves, but we certainly DO know that they are both coelurosaur dinosaurs- As the ENTIRE "polytomy" is included in the coelurosauria clade, whose node has HIGH support values.

And that is what makes our old friend shit his pants.
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.

  • socrates1
Re: Bremer
Reply #61
Concerning the huge polytomy:
This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of Paraves.
It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.

As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?
  • Last Edit: June 21, 2017, 08:59:04 AM by socrates1

  • VoxRat
  • wtactualf
Re: Bremer
Reply #62
Non sequitur.

And...
If something is in the publication- Supplementary or otherwise- it is MORE than just "acknowledged".
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Bremer
Reply #63
No, sucko. It shows that animals ANCESTRAL to oviraptorosaurs were transitional between the rest of the Coelurosauria and Paraves. There's no indication that they were similar at all, just that they also possessed the synapomorphies of both Paraves and Oviraptorosauria. Nobody thinks they had beaks, or bony create or anything else that we see in derived oviraptorosaurs.

And no, the polytomy does not mean that Oviraptorosauria is a subset of Paraves. It means that, therizinosaurs, for example, might be more closely related to Paraves than Oviraptorosauria is. It means we have difficulty resolving the relationships within Maniraptora, and Maniraptoriformes. But it most certainly doesn't mean that they're not members of Coelurosauria, and therefore nothing to do with Pterosauria.

The Nesbitt paper that includes pterosaurs and Velociraptor makes that abundantly clear.
Why do I bother?

  • socrates1
Re: Bremer
Reply #64
Concerning the huge polytomy:
This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of Paraves.
It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.

As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less
than 50%.

Just to remind people, a Bremer value of 1 is the lowest possible value and nodes of jackknife percentage of less than 50% are collapsed.

If researchers took Bremer and bootstrap/jackknife seriously, they are left with a huge polytomy which means that they know absolutely nothing about the purported evolution from tyrannosauroids to basal paraves.
  • Last Edit: June 21, 2017, 09:18:49 AM by socrates1

  • Faid
Re: Bremer
Reply #65
The clade of coelurosauria INCLUDING Paraves is supported by a Bremer value of 3 and a jackknife percentage of 94%.

We accept your apology.
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.

  • Faid
Re: Bremer
Reply #66
Here you go, dave, in terms even an uneducated B&B owner can understand:

We see a group of children. Just by looking at them, we can make out some resemblance between some of them, but we cannot use it to define specific relationships between them. Some may be brothers/sisters, other cousins, others more distantly related, but we can just not tell for sure.
What we can tell for sure, however, is that they're all human children (and not, say, puppies or kittens).

That "node" has a quite high support.

Gettit?

Of course you do. You're just pretending.

And as we all know, it is not possible to have a discussion with someone who is pretending.
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.

  • socrates1
Re: Bremer
Reply #67
Concerning the huge polytomy:
This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of Paraves.
It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.

As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less
than 50%.

Just to remind people, a Bremer value of 1 is the lowest possible value and nodes of jackknife percentage of less than 50% are collapsed.

If researchers took Bremer and bootstrap/jackknife seriously, they are left with a huge polytomy which means that they know absolutely nothing about the purported evolution from tyrannosauroids to basal paraves.

What makes this all the more ironic is that a large number of studies purport to trace the evolution of bird-like characters across nodes - when those nodes should all be collapsed. To add to the irony the Brusatte et al study is entitled:
"Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition"

Re: Bremer
Reply #68
There's a whole stack of stuff in there about morphospace. Did you read or understand any of it? That's what the title is referring to. Did you even try puttin pterosaurs into the dataset and seeing what that gave you?
Why do I bother?

  • socrates1
Re: Bremer
Reply #69
Concerning the huge polytomy:
This means (to take one example) that we cannot tell what the relationship is between oviraptorids and Paraves from the cladistic analysis. The two possibilities are that creatures similar to oviraptorids were transitional between dinosaurs and Paraves OR that oviraptorids were secondarily flightless members of Paraves.
It is important to note that the cladistic analyses cannot tell us which one is more credible.
Consequently we have to look for other indicators as to which is more credible.

As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?
http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less
than 50%.

Just to remind people, a Bremer value of 1 is the lowest possible value and nodes of jackknife percentage of less than 50% are collapsed.

If researchers took Bremer and bootstrap/jackknife seriously, they are left with a huge polytomy which means that they know absolutely nothing about the purported evolution from tyrannosauroids to basal paraves.

What makes this all the more ironic is that a large number of studies purport to trace the evolution of bird-like characters across nodes - when those nodes should all be collapsed. To add to the irony the Brusatte et al study is entitled:
"Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition"

Nobody is denying that according to all the support indices the nodes should be collapsed. That is something.

  • socrates1
Re: Bremer
Reply #70
Quote
As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?

http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less
than 50%.

Just to remind people, a Bremer value of 1 is the lowest possible value and nodes of jackknife percentage of less than 50% are collapsed.

If researchers took Bremer and bootstrap/jackknife seriously, they are left with a huge polytomy which means that they know absolutely nothing about the purported evolution from tyrannosauroids to basal paraves.

What makes this all the more ironic is that a large number of studies purport to trace the evolution of bird-like characters across nodes - when those nodes should all be collapsed. To add to the irony the Brusatte et al study is entitled:
"Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition"

Nobody is denying that according to all the support indices the nodes should be collapsed. That is something.

And by now some people are probably understanding the significance of a huge polytomy like that. That is something.

  • socrates1
Re: Bremer
Reply #71
Quote
As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?

http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less
than 50%.

Just to remind people, a Bremer value of 1 is the lowest possible value and nodes of jackknife percentage of less than 50% are collapsed.

If researchers took Bremer and bootstrap/jackknife seriously, they are left with a huge polytomy which means that they know absolutely nothing about the purported evolution from tyrannosauroids to basal paraves.

What makes this all the more ironic is that a large number of studies purport to trace the evolution of bird-like characters across nodes - when those nodes should all be collapsed. To add to the irony the Brusatte et al study is entitled:
"Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition"

Nobody is denying that according to all the support indices the nodes should be collapsed. That is something.

And by now some people are probably understanding the significance of a huge polytomy like that. That is something.

And it is likely that almost everybody here realizes that when you collapse the nodes that you get a huge polytomy like the one they got.

  • socrates1
Re: Bremer
Reply #72
Quote
As everyone knows, all the cladograms that are regularly presented show the unsubstantiated conclusion that creatures similar to oviraptorids were transitional between dinosaurs and Paraves. That is because they do not acknowledge the huge polytomy that they themselves include in their Supplementary Information. This is not particularly complicated. Does everyone understand that point? Does anyone?

http://www.cell.com/cms/attachment/2019474733/2039573094/mmc1.pdf
The clade consisting of Oviraptorosauria and Paraves is supported by a Bremer value of 1 and a jackknife percentage of less
than 50%.

Just to remind people, a Bremer value of 1 is the lowest possible value and nodes of jackknife percentage of less than 50% are collapsed.

If researchers took Bremer and bootstrap/jackknife seriously, they are left with a huge polytomy which means that they know absolutely nothing about the purported evolution from tyrannosauroids to basal paraves.

What makes this all the more ironic is that a large number of studies purport to trace the evolution of bird-like characters across nodes - when those nodes should all be collapsed. To add to the irony the Brusatte et al study is entitled:
"Gradual Assembly of Avian Body Plan Culminated in Rapid Rates of Evolution across the Dinosaur-Bird Transition"

Nobody is denying that according to all the support indices the nodes should be collapsed. That is something.

And by now some people are probably understanding the significance of a huge polytomy like that. That is something.

And it is likely that almost everybody here realizes that when you collapse the nodes that you get a huge polytomy like the one they got.
And some people here (perhaps not too many) realize that when you have a huge polytomy like that, you cannot tell the relationships of the branches.

  • VoxRat
  • wtactualf
Re: Bremer
Reply #73
"Socrates" appears to be talking to himself.

Here you go, dave, in terms even an uneducated B&B owner can understand:

We see a group of children. Just by looking at them, we can make out some resemblance between some of them, but we cannot use it to define specific relationships between them. Some may be brothers/sisters, other cousins, others more distantly related, but we can just not tell for sure.
What we can tell for sure, however, is that they're all human children (and not, say, puppies or kittens).

That "node" has a quite high support.

Gettit?

Of course you do. You're just pretending.

And as we all know, it is not possible to have a discussion with someone who is pretending.
The thing is...
There might be all kinds of uncertainty about who those kids' great-grandparents were.
Most of us, in fact, are pretty fuzzy about exactly who was who, going back just a handful of generations.
But we can be extremely certain that we are all Homo sapiens.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

Re: Bremer
Reply #74
But you can tell that they're all more closely related to each other than any of them is to anything else. And, depending on the support for clades within the polytony you can tell that they form monophyletic groups rather than being subsets of each other. So we can say that Oviraptorosauria does not belong within Paraves.

If you have a point you wish to make, rather than intimate, then do so. Fucking get on with it you miserable fuck.
Why do I bother?