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DATE 2016-10-01

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MESSAGE
DATE 2016-10-05
FROM ruben safir
SUBJECT Subject: [Learn] Fwd: Re: Check List of Texts to learn Cladistics and
From learn-bounces-at-nylxs.com Wed Oct 5 00:39:25 2016
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-------- Forwarded Message --------
Subject: Re: Check List of Texts to learn Cladistics and Computational Math
Date: Tue, 4 Oct 2016 18:13:07 -0700
From: John Harshman
Newsgroups: sci.bio.paleontology
References:











On 10/4/16 6:02 PM, ruben safir wrote:
> On 10/04/2016 08:51 PM, John Harshman wrote:
>> On 10/4/16 5:33 PM, ruben safir wrote:
>>> On 10/03/2016 11:13 PM, John Harshman wrote:
>>>>> I don't know that with certainty. Do you have a specific suggestion?
>>>>>
>>>> I would have to know your intentions first.
>>>
>>> all men are dogs. You know my intentions.
>>>
>> I have no idea how that was supposed to help me.
>
> my intention is to learn how researches currently quantify and create
> the data they get from fossils to create cladistic, phylogenic trees,
> how they create those trees, and to use that knowledge in order to try
> to analyze their current methods from the prespective of machine
> learning and AI applications which can improve it.

Then in order to talk about improving methods, you need to find a group
for which you are willing to say that the true phylogeny is known and
then compare various methods of analysis to see which most reliably
produce that true phylogeny. Tyrannosaurids might not be the best for
that purpose. Within archosaurs, you might try looking at the
relationships of gharials to other living crocodylians, for which I
think the molecular data are conclusive but the morphological analyses
mostly systematically in error. Similarly, the position of whales within
artiodactyls has been difficult to morphology to deal with but easy for
molecular data.

Or you could try another route: simulated data on a known tree,, or
manufactured data like the caminalcules.

A concentration on character coding might be interesting; perhaps
machine learning could help with it. I don't see how machine learning
could help the analysis step. Though there is a phylogenetic program,
GARLI, that uses a genetic algorithm; perhaps that's something like you
propose?

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  1. 2016-10-04 ruben safir <ruben-at-mrbrklyn.com> Re: [Learn] Check List of Texts to learn Cladistics and
  2. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Library access
  3. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Library access
  4. 2016-10-04 Christopher League <christopher.league-at-liu.edu> Re: [Learn] phylogenetics
  5. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] 3rd scans and displays for msueums
  6. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] =?utf-8?q?Residual_diversity_estimates=E2=80=99_do_not_co?=
  7. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] another paper on this topic to dig through
  8. 2016-10-04 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] Basic Phylogeny and Systematics
  9. 2016-10-04 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Library access
  10. 2016-10-05 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] 3rd scans and displays for msueums
  11. 2016-10-05 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: Check List of Texts to learn Cladistics and
  12. 2016-10-06 From: "Ruben.Safir" <ruben.safir-at-my.liu.edu> Subject: [Learn] TNT - Boom
  13. 2016-10-06 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] tomorrow
  14. 2016-10-09 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: phylogeny tyrannosauroid dinosaurs
  15. 2016-10-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: phylogeny tyrannosauroid dinosaurs
  16. 2016-10-09 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: [dinosaur] phylogeny tyrannosauroid dinosaurs
  17. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Paleo meeting time
  18. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] phylogeny tyrannosauroid dinosaurs
  19. 2016-10-10 Steve Brusatte <brusatte-at-gmail.com> Re: [Learn] phylogeny tyrannosauroid dinosaurs
  20. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] phylogeny tyrannosauroid dinosaurs
  21. 2016-10-10 From: =?UTF-8?B?RGF2aWQgxIxlcm7DvQ==?= <david.cerny1-at-gmail.com> Re: [Learn] [dinosaur] phylogeny tyrannosauroid dinosaurs
  22. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] [dinosaur] phylogeny tyrannosauroid dinosaurs
  23. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] [dinosaur] phylogeny tyrannosauroid dinosaurs
  24. 2016-10-10 Dalton Meyer <paleonerd12-at-gmail.com> Re: [Learn] [dinosaur] phylogeny tyrannosauroid dinosaurs
  25. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] AI research
  26. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] CTScan in paelo
  27. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Re: [dinosaur] phylogeny tyrannosauroid dinosaurs
  28. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] http://palaeos.com/phylogeny/index.html
  29. 2016-10-10 Ruben Safir <ruben.safir-at-my.liu.edu> Subject: [Learn] maxillary fenestra and promaxillary fenestra
  30. 2016-10-10 Christopher League <league-at-contrapunctus.net> Subject: [Learn] Paleo meeting time
  31. 2016-10-10 Christopher League <league-at-contrapunctus.net> Subject: [Learn] Paleo meeting time
  32. 2016-10-10 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] promaxillary fenestra
  33. 2016-10-13 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Invitation: Phylogenetics project mtg -at- Thu 2016-10-13
  34. 2016-10-13 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Library access
  35. 2016-10-13 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: access to the screen
  36. 2016-10-13 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: access to the screen
  37. 2016-10-13 ruben safir <ruben-at-mrbrklyn.com> Subject: [Learn] graphics
  38. 2016-10-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] a new generation discovers freedom
  39. 2016-10-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Check out this picture...
  40. 2016-10-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Check out this picture...
  41. 2016-10-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Check out this picture...
  42. 2016-10-14 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Fwd: Check out this picture...
  43. 2016-10-15 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] 3d scanning in the field
  44. 2016-10-15 Ruben Safir <mrbrklyn-at-panix.com> Subject: [Learn] 3d scanning in the field
  45. 2016-10-16 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Jobs
  46. 2016-10-19 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] tomorrows schedule and plan got the week
  47. 2016-10-20 Christopher League <league-at-contrapunctus.net> Re: [Learn] tomorrows schedule and plan got the week
  48. 2016-10-21 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] tomorrows schedule and plan got the week
  49. 2016-10-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] publication
  50. 2016-10-21 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] thesis resources
  51. 2016-10-25 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Phylogenetics educational links
  52. 2016-10-27 Christopher League <league-at-contrapunctus.net> Re: [Learn] Phylogenetics educational links
  53. 2016-10-27 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Phylogenetics educational links
  54. 2016-10-27 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Phylogenetics educational links
  55. 2016-10-27 Ruben Safir <ruben-at-mrbrklyn.com> Re: [Learn] Phylogenetics educational links
  56. 2016-10-27 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] Phylogenetics educational links
  57. 2016-10-30 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] Orders for the Thesis,
  58. 2016-10-31 Christopher League <league-at-contrapunctus.net> Re: [Learn] cuda kernels
  59. 2016-10-31 Ruben Safir <ruben.safir-at-my.liu.edu> Re: [Learn] cuda kernels
  60. 2016-10-31 Christopher League <league-at-contrapunctus.net> Re: [Learn] cudaMallac
  61. 2016-10-31 Ruben Safir <mrbrklyn-at-panix.com> Re: [Learn] cudaMallac
  62. 2016-10-31 Christopher League <league-at-contrapunctus.net> Subject: [Learn] Computational evolution
  63. 2016-10-31 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] cuda kernels
  64. 2016-10-31 Ruben Safir <ruben-at-mrbrklyn.com> Subject: [Learn] cudaMallac

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