MESSAGE
| DATE | 2016-09-25 |
| FROM | ruben safir
|
| SUBJECT | Subject: [Learn] Fwd: Cladistics and Computational Math
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From learn-bounces-at-nylxs.com Sun Sep 25 03:05:42 2016
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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
Newsgroups: sci.bio.paleontology
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)
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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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From: RSNorman
Newsgroups: sci.bio.paleontology
Subject: Re: Cladistics and Computational Math
Date: Sat, 24 Sep 2016 14:19:49 -0400
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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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NNTP-Posting-Date: Sat, 24 Sep 2016 14:40:30 -0500
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
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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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NNTP-Posting-Date: Sat, 24 Sep 2016 18:12:09 -0500
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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