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*To*: dinosaur-l@usc.edu*Subject*: Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida*From*: Ruben Safir <ruben@mrbrklyn.com>*Date*: Fri, 24 Mar 2017 01:42:48 -0400*Delivered-to*: dinosaur-l@mymaillists.usc.edu*In-reply-to*: <CADHyUaTBnUJhNtVjjY6tewOYXxUPuxsmJ6Jfkx+khtSjgXvE+A@mail.gmail.com>*List-archive*: <http://mymaillists.usc.edu/sympa/arc/dinosaur-l>*List-help*: <mailto:sympa@mymaillists.usc.edu?subject=help>*List-id*: <dinosaur-l.mymaillists.usc.edu>*List-owner*: <mailto:dinosaur-l-request@mymaillists.usc.edu>*List-post*: <mailto:dinosaur-l@mymaillists.usc.edu>*List-subscribe*: <mailto:sympa@mymaillists.usc.edu?subject=subscribe%20dinosaur-l>*List-unsubscribe*: <mailto:sympa@mymaillists.usc.edu?subject=unsubscribe%20dinosaur-l>*References*: <CAMR9O1L_q6CQDtBB37zQptg2sbbtSqC9W90y_M8bj1WbF28r0A@mail.gmail.com> <CA+nnY_FhjRvvOmmOzAFOFJuMXLpA4QgUfsF7_qjYugRGqhYY2Q@mail.gmail.com> <0c2ee9c6-1bfc-8bf2-edb6-084aa4d8727a@mrbrklyn.com> <trinity-66683511-2367-4fa6-9cdb-99cc1025cd93-1490297389707@3capp-gmx-bs06> <CADHyUaS0ESz5NaKYd39=959HyPpxSRCzb3-OMHGjgmE2Jexr9g@mail.gmail.com> <fd4b85a6-433f-6e27-213c-0bb22aa860f7@mrbrklyn.com> <CADHyUaTBnUJhNtVjjY6tewOYXxUPuxsmJ6Jfkx+khtSjgXvE+A@mail.gmail.com>*Reply-to*: Ruben Safir <ruben@mrbrklyn.com>*Sender*: dinosaur-l-request@usc.edu*User-agent*: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Thunderbird/45.8.0

On 03/23/2017 11:11 PM, David Černý wrote: > > Right, because no serious mathematicians currently work in the field I can't answer that but that is a real possibility. When I confronted the Math department with papers and texts, they immediately ripped it apart in confusion. For example chapter three of Felsenstein's text went though 2 EDITIONS with a fundamental error on the computation calculating out the numbers of trees occur which was finally corrected on pg 23 of the third addition. I mean, what is that about?!? No serious work on this subject in mathematics work would ever have such a fundemental error escape narly a decade before correction, let alone be released on the first edition. > or > contributed to its development in the past. Mike Steel, who has spent the > last 30 years exploring the math behind phylogenetic inference I'm an old man so I'm not impressed with 30 years of anything. Everyone I know has spent 30 years studying. I'm surrounded by people like that and they don't produce garbage like the like a complete lack of understanding NP completeness in papers I've read in journals. What I'm telling you, and not debating, is that the understanding of mathematics in the field is lacking. Instead of worrying about Mike Steel, just try to first grasp the fundamentals of algorithms, with a text like Cormen, Leiserson. And then spend some serious time with George Strung. It's not like these guys who created the mathematics for trees, paths and graph theory, starting with Euler, were idiots and that any paleo expert can pick this stuff up on a Sunday afternoon. And while you are on your way to that, understand that publishing journals doesn't produce an developed area of knowledge. Slapping together bits and pieces of partially understood mathematics areas doesn't formulate a body of knowledge and YES, I don't trust the software and I do question both the application and basis for the theorem that these applications are coded on. It's not like these guys who revolutionized humanity through computer engineering and computational mathematics are stupid, which is what you are implying here. Finally, and this is DEFINITELY the last I have to say about this topic, the code examples I have seen around the net have fundamental programming and algorithm flaws in them. I've seen problems with concurrency, algorithms logic, static memory bugs and more. So that magic box that you depend on for results needs to be explored, discussed with experts in the field, debated, and rewritten. And listen David, don't worry so much about what you think you know. Education is about learning what you don't KNOW, and what I have learned in the last year of investigating the computational mathematics of phylogenies is that there is a LOT more that I don't know then I thought I knew. Furthermore and the literature on the topic is in chaos, with incorrectly applied theorems, mistranslated texts and proofs, misunderstood proofs and applications, and full of editing errors. Have you ever made the effort to actually trace original articles in the literature? I have found that supposed papers that state things don't actually exist, but mere notations of announcements for lectures. That articles that are quoted as to supposedly proving something or proposing something simply don't do that at all. I can't imagine where that leaves others who have nearly ZERO foundation in the essentials of the very mathematics they are professing to ply. ( > www.math.canterbury.ac.nz/~m.steel/Non_UC/publications.html), presumably > doesn't count. Nor does Jerzy Neyman, who was the first to apply maximum > likelihood to phylogenetic analysis of nucleotide sequences back in 1971. Try learning Knuth, Landau, Fibonacci, De Moirvre, Verma, Euler, Aslam, Preparata and Shamos, Bellman, Hu and Shing, William Pugh, Dorit Hochbaum, Robert Floyd, Driscoll, John Chambers, Bill Joy, Dewer, Kenneth Rosen, Alonzo Church, and most of all probably, simply understanding EW Dijkstra. BTW - Neyman may have first tackled the problem with maximum likelihood with nucleotides, but the problem predates that by almost 10 years, if not more. And yet, most of that work has been problematic and it is yet to be shown how to best solved the application of this theorem, a theorem which rarely anyone understands, let alone code in Python. A large part of the problem is that the working solutions fail to recognize that the theoretical math has been already explored for a little more than a century, long before Watson met Crick. It just sucks having to reinvent the wheel constantly. What is needed is more mathematicians and computer scientists applying themselves to the problem and a free software code base that is under constant peer review. A consensus needs to be build on knowledge, not speculation. We need consistency in terminology, a translation from one paper to the next, and an application of an over all methodology to simplify the syntax and formulation of problems. You need a bible, so to speak. ~~fini. Ruben -- So many immigrant groups have swept through our town that Brooklyn, like Atlantis, reaches mythological proportions in the mind of the world - RI Safir 1998 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mrbrklyn.com&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=sk0N4FoRcZckolPGB9KsrgI7nz4HME67dSZTqfOwdX8&s=K7tg_U8L1sNWNOOh45BN1-MUfiVT7BhSwfCXiOiO1A8&e= DRM is THEFT - We are the STAKEHOLDERS - RI Safir 2002 https://urldefense.proofpoint.com/v2/url?u=http-3A__www.nylxs.com&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=sk0N4FoRcZckolPGB9KsrgI7nz4HME67dSZTqfOwdX8&s=9zzGMehpJJkmZ97uUC1CqXk7wqtCTQWD2oMZcVpU-iA&e= - Leadership Development in Free Software https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.mrbrklyn.com_resources&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=sk0N4FoRcZckolPGB9KsrgI7nz4HME67dSZTqfOwdX8&s=NcDYPK453f9QCuFieomxfP8BfRxfjFsMCljepPA3fAY&e= - Unpublished Archive https://urldefense.proofpoint.com/v2/url?u=http-3A__www.coinhangout.com&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=sk0N4FoRcZckolPGB9KsrgI7nz4HME67dSZTqfOwdX8&s=Tp1KTep874PRiRaf2jOUc3H3J_jegYr9Axdv9YZT0lE&e= - coins! https://urldefense.proofpoint.com/v2/url?u=http-3A__www.brooklyn-2Dliving.com&d=DwIDaQ&c=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI&r=Ry_mO4IFaUmGof_Yl9MyZgecRCKHn5g4z1CYJgFW9SI&m=sk0N4FoRcZckolPGB9KsrgI7nz4HME67dSZTqfOwdX8&s=2LiVdBM_8QSe_lW_QR525tr0hNAnFciClS2qbZlMpOs&e= Being so tracked is for FARM ANIMALS and and extermination camps, but incompatible with living as a free human being. -RI Safir 2013

**Follow-Ups**:**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*David Černý <david.cerny1@gmail.com>

**References**:**[dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*Ben Creisler <bcreisler@gmail.com>

**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*Tim Williams <tijawi@gmail.com>

**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*Ruben Safir <ruben@mrbrklyn.com>

**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*"David Marjanovic" <david.marjanovic@gmx.at>

**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*David Černý <david.cerny1@gmail.com>

**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*Ruben Safir <ruben@mrbrklyn.com>

**Re: [dinosaur] Dinosauria reclassification joins Ornithischia and Theropoda in Ornithoscelida***From:*David Černý <david.cerny1@gmail.com>

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