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DATE 2016-09-01

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Key: archive_learn Value: 2016-09-01

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MESSAGE
DATE 2016-09-25
FROM ruben safir
SUBJECT Subject: [Learn] Fwd: Cladistics and Computational Math
From learn-bounces-at-nylxs.com Sun Sep 25 03:05:42 2016
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From: ruben safir
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Please not this entire thread as it points us to where the paleontology
field is currently holding with regard to the use of computers in
producing cladistic trees.

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From: Popping mad
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Subject: Cladistics and Computational Math
Date: Sat, 24 Sep 2016 13:37:19 +0000 (UTC)
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So, I've been given the go ahead to do my thesis on Machine Learning and
Computational Mathematics in developing Cladistic Models of Evolution. I
discussed here, previously, how map theory might be helpful in producing
accurate interpretations of species relations. And it was told to me
that such attempts have been made before and papers were notated in that
discussion. Can someone give me, please, sources for previous work in
this area and also a basic work on cladistics?


Ruben

http://www.nylxs.com/thesis/

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Subject: Re: Cladistics and Computational Math
Newsgroups: sci.bio.paleontology
References:
From: John Harshman
Date: Sat, 24 Sep 2016 06:46:08 -0700
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On 9/24/16 6:37 AM, Popping mad wrote:
> So, I've been given the go ahead to do my thesis on Machine Learning and
> Computational Mathematics in developing Cladistic Models of Evolution. I
> discussed here, previously, how map theory might be helpful in producing
> accurate interpretations of species relations. And it was told to me
> that such attempts have been made before and papers were notated in that
> discussion. Can someone give me, please, sources for previous work in
> this area and also a basic work on cladistics?

I don't know what map theory is, so can't point to any previous work. A
basic work on cladistics, by which I assume you mean phylogenetics, is
Inferring Phylogenies by Joe Felsenstein. (If you really do mean
cladistics, which in this context is generally assumed to mean strict
parsimony, that's in there too, but it's a small part.)

You might want to look up some of the programs used for inference. Try
searching on PHYLIP, PAUP, RaxML, GARLI, BEAST, MrBayes.


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From: Popping mad
Newsgroups: sci.bio.paleontology
Subject: Re: Cladistics and Computational Math
Date: Sat, 24 Sep 2016 17:48:46 +0000 (UTC)
Organization: PANIX Public Access Internet and UNIX, NYC
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On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote:

>> So, I've been given the go ahead to do my thesis on Machine Learning
>> and Computational Mathematics in developing Cladistic Models of
>> Evolution. I
>> discussed here, previously, how map theory might be helpful in
>> producing accurate interpretations of species relations. And it was
>> told to me that such attempts have been made before and papers were
>> notated in that discussion. Can someone give me, please, sources for
>> previous work in this area and also a basic work on cladistics?
>
> I don't know what map theory is, so can't point to any previous work.

We spent quite a bit of time discussing it and cladistics are a form of
map theory so maybe you can clarify what you mean when you say that you
don't know what map theory is.

Maybe i would be clearer if I said Graph Theory similar to Dijkstra's
algorithm?



> A
> basic work on cladistics, by which I assume you mean phylogenetics, is
> Inferring Phylogenies by Joe Felsenstein. (If you really do mean
> cladistics, which in this context is generally assumed to mean strict
> parsimony, that's in there too, but it's a small part.)
>

I'd dealing with the morphology of fossils only. So that would not be
cladistics?

> You might want to look up some of the programs used for inference. Try
> searching on PHYLIP, PAUP, RaxML, GARLI, BEAST, MrBayes.

Thank You!

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On Sat, 24 Sep 2016 17:48:46 +0000 (UTC), Popping mad
wrote:

>On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote:
>
>>> So, I've been given the go ahead to do my thesis on Machine Learning
>>> and Computational Mathematics in developing Cladistic Models of
>>> Evolution. I
>>> discussed here, previously, how map theory might be helpful in
>>> producing accurate interpretations of species relations. And it was
>>> told to me that such attempts have been made before and papers were
>>> notated in that discussion. Can someone give me, please, sources for
>>> previous work in this area and also a basic work on cladistics?
>>
>> I don't know what map theory is, so can't point to any previous work.
>
>We spent quite a bit of time discussing it and cladistics are a form of
>map theory so maybe you can clarify what you mean when you say that you
>don't know what map theory is.
>
>Maybe i would be clearer if I said Graph Theory similar to Dijkstra's
>algorithm?
>
>

You are a computer scientist talking with a biologist. You come from
different backgrounds and assume rather different levels of assumed
knowledge in different subjects.

Just because biologists talk about trees doesn't mean that biologists
are up on graph theory and data structures.



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Subject: Re: Cladistics and Computational Math
Newsgroups: sci.bio.paleontology
References:


From: John Harshman
Date: Sat, 24 Sep 2016 12:41:20 -0700
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On 9/24/16 11:19 AM, RSNorman wrote:
> On Sat, 24 Sep 2016 17:48:46 +0000 (UTC), Popping mad
> wrote:
>
>> On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote:
>>
>>>> So, I've been given the go ahead to do my thesis on Machine Learning
>>>> and Computational Mathematics in developing Cladistic Models of
>>>> Evolution. I
>>>> discussed here, previously, how map theory might be helpful in
>>>> producing accurate interpretations of species relations. And it was
>>>> told to me that such attempts have been made before and papers were
>>>> notated in that discussion. Can someone give me, please, sources for
>>>> previous work in this area and also a basic work on cladistics?
>>>
>>> I don't know what map theory is, so can't point to any previous work.
>>
>> We spent quite a bit of time discussing it and cladistics are a form of
>> map theory so maybe you can clarify what you mean when you say that you
>> don't know what map theory is.
>>
>> Maybe i would be clearer if I said Graph Theory similar to Dijkstra's
>> algorithm?
>>
>>
>
> You are a computer scientist talking with a biologist. You come from
> different backgrounds and assume rather different levels of assumed
> knowledge in different subjects.
>
> Just because biologists talk about trees doesn't mean that biologists
> are up on graph theory and data structures.

Well, I'm up a little on data structures. Data structures are generally
the way trees are represented in programs.


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Subject: Re: Cladistics and Computational Math
Newsgroups: sci.bio.paleontology
References:


From: John Harshman
Date: Sat, 24 Sep 2016 12:40:30 -0700
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On 9/24/16 10:48 AM, Popping mad wrote:
> On Sat, 24 Sep 2016 06:46:08 -0700, John Harshman wrote:
>
>>> So, I've been given the go ahead to do my thesis on Machine Learning
>>> and Computational Mathematics in developing Cladistic Models of
>>> Evolution. I
>>> discussed here, previously, how map theory might be helpful in
>>> producing accurate interpretations of species relations. And it was
>>> told to me that such attempts have been made before and papers were
>>> notated in that discussion. Can someone give me, please, sources for
>>> previous work in this area and also a basic work on cladistics?
>>
>> I don't know what map theory is, so can't point to any previous work.
>
> We spent quite a bit of time discussing it and cladistics are a form of
> map theory so maybe you can clarify what you mean when you say that you
> don't know what map theory is.
>
> Maybe i would be clearer if I said Graph Theory similar to Dijkstra's
> algorithm?

No. All I know is how phylogenetics works, not what sort of mathematics
you would like to use on it. If that's map theory or graph theory, fine,
but not a concern of mine.

>> A
>> basic work on cladistics, by which I assume you mean phylogenetics, is
>> Inferring Phylogenies by Joe Felsenstein. (If you really do mean
>> cladistics, which in this context is generally assumed to mean strict
>> parsimony, that's in there too, but it's a small part.)
>
> I'd dealing with the morphology of fossils only. So that would not be
> cladistics?

Depends on what you mean by cladistics. What do you mean? There are
methods used for morphological phylogeny that do not rely on strict
parsimony, though parsimony is still probably the most common.

>> You might want to look up some of the programs used for inference. Try
>> searching on PHYLIP, PAUP, RaxML, GARLI, BEAST, MrBayes.
>
> Thank You!
>


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From: ruben safir
Newsgroups: sci.bio.paleontology
Subject: Re: Cladistics and Computational Math
Date: Sat, 24 Sep 2016 17:21:08 -0400
Organization: PANIX Public Access Internet and UNIX, NYC
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On 09/24/2016 03:40 PM, John Harshman wrote:
>
> Depends on what you mean by cladistics. What do you mean? There are
> methods used for morphological phylogeny that do not rely on strict
> parsimony, though parsimony is still probably the most common.


What is the definition of the word parsimony in regards to evolutionary
biology. It can't be the economics term I'm used to.



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Subject: Re: Cladistics and Computational Math
Newsgroups: sci.bio.paleontology
References:




From: John Harshman
Date: Sat, 24 Sep 2016 16:12:09 -0700
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On 9/24/16 2:21 PM, ruben safir wrote:
> On 09/24/2016 03:40 PM, John Harshman wrote:
>>
>> Depends on what you mean by cladistics. What do you mean? There are
>> methods used for morphological phylogeny that do not rely on strict
>> parsimony, though parsimony is still probably the most common.
>
> What is the definition of the word parsimony in regards to evolutionary
> biology. It can't be the economics term I'm used to.
>

These are the buzzwords you have to learn if you want to deal with
phylogenetics. Here's a short primer, beginning with a detour.

Phylogenetic analyses act on data sets to produce favored trees. Most
methods do this by first setting a numerical optimality criterion,
assessing that criterion for lots and lots of candidate trees, and
picking the one that's best by that criterion. Parsimony is one such
criterion. Briefly, a tree's parsimony score is the minimum number of
character state changes, somewhere on the tree, necessary to explain the
distribution of all character states in the terminal taxa. Parsimony
algorithms perform the calculations necessary to determine the parsimony
score. The lower the score, that is, the fewer the required changes, the
better.

(Let's leave aside the historical reasons for the name "parsimony". It
has to do with philosophy of science, specifically Karl Popper.)

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  1. 2016-09-01 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: LIU CS course
  2. 2016-09-04 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] LIU Brooklyn Student Update
  3. 2016-09-04 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] LIU Brooklyn Student Update
  4. 2016-09-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Lockout
  5. 2016-09-08 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Computer Sciences
  6. 2016-09-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] LIU Lock Out
  7. 2016-09-10 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] [Hangout-NYLXS] Fwd: LIU Lock Out
  8. 2016-09-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] LIU Lock Out
  9. 2016-09-12 Amy Rothenberg <Amy.Rothenberg-at-liu.edu> Re: [Learn] LIU Lock Out
  10. 2016-09-13 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: [isoc-ny] ISOC-NY joins coalition of groups supporting
  11. 2016-09-14 From: "Ruben.Safir" <ruben.safir-at-my.liu.edu> Subject: [Learn] Fwd: Calendar Update
  12. 2016-09-19 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: Thesis option
  13. 2016-09-21 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Fossil computational oppurtunities
  14. 2016-09-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fossil computational oppurtunities
  15. 2016-09-22 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] Sad News
  16. 2016-09-23 Christopher League <league-at-contrapunctus.net> Re: [Learn] Thesis - topic Machine learning in the determination of
  17. 2016-09-23 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Thesis - topic Machine learning in the determination of the
  18. 2016-09-25 ruben safir <ruben-at-mrbrklyn.com> Re: [Learn] Cladistics and Computational Math
  19. 2016-09-25 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Thesis
  20. 2016-09-25 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Thesis - topic Machine learning in the determination of
  21. 2016-09-25 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Cladistics and Computational Math
  22. 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Proposed Thesis
  23. 2016-09-26 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] Proposed Thesis
  24. 2016-09-26 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] Proposed Thesis
  25. 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Proposed Thesis
  26. 2016-09-26 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Proposed Thesis
  27. 2016-09-27 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] phylip
  28. 2016-09-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] phylip
  29. 2016-09-27 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] t-rex web server
  30. 2016-09-28 From: "Pinsdorf, Michelle" <PinsdorfM-at-si.edu> Re: [Learn] little can be better
  31. 2016-09-28 From: "Pinsdorf, Michelle" <PinsdorfM-at-si.edu> Re: [Learn] little can be better
  32. 2016-09-28 league-at-contrapunctus.net Re: [Learn] meet up for thesis?
  33. 2016-09-28 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] meet up for thesis?
  34. 2016-09-28 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] meet up for thesis?
  35. 2016-09-28 Maneesh Kongara <maneeshkongara-at-gmail.com> Re: [Learn] meet up for thesis?
  36. 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] meet up for thesis?
  37. 2016-09-28 Christopher League <league-at-contrapunctus.net> Re: [Learn] Thesis - topic Machine learning in the determination of
  38. 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] meet up for thesis?
  39. 2016-09-28 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Notice: Learn Mailing List for LIU
  40. 2016-09-28 Ben Creisler <bcreisler-at-gmail.com> Subject: [Learn] [dinosaur] T. rex tail CT scan + Utahraptor quicksand death
  41. 2016-09-28 Ben Creisler <bcreisler-at-gmail.com> Subject: [Learn] [dinosaur] T. rex tail CT scan + Utahraptor quicksand death
  42. 2016-09-29 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] Announcing LIU Votes 2016!
  43. 2016-09-29 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] phylogenetics
  44. 2016-09-29 Jon Tennant <jon.tennant.2-at-gmail.com> Re: [Learn] phylogenetics
  45. 2016-09-29 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] two textbooks
  46. 2016-09-30 league-at-contrapunctus.net Re: [Learn] Thesis data
  47. 2016-09-30 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Thesis data
  48. 2016-09-30 league-at-contrapunctus.net Re: [Learn] Thesis data
  49. 2016-09-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Thesis data

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