Author Topic: Taxonomy: What are we?  (Read 2911 times)

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Charles Pegge

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Taxonomy: What are we?
« on: June 14, 2011, 09:12:43 PM »
A sample of the tree of life:

Code: OxygenBasic
  1.  
  2.  
  3.   cr=chr(13)+chr(10)
  4.   '
  5.  '=============
  6.  class organism
  7.   '=============
  8.  '
  9.  sys id
  10.   sys ty
  11.   string formal
  12.   string informal
  13.   string descript
  14.   '
  15.  method name(sys n) as string
  16.   '===========================
  17.  if n=0 then
  18.     if len formal then return formal cr
  19.   else
  20.     if len informal then return informal cr
  21.   end if
  22.   end method
  23.   '
  24.  method describe() as string
  25.   '==========================
  26.  if len descript then return descript cr
  27.   end method
  28.   '
  29.  method lineage(sys n) as string
  30.   '==============================
  31.  sys a
  32.   string lnk
  33.   organism * o
  34.   if n=0 then exit method
  35.   @o=n
  36.   do
  37.     if o.id=0 then exit do
  38.     method= o.name(0) o.name(1) o.describe() lnk cr method
  39.     lnk="-->"
  40.     a=o.ty
  41.     if a=0 then exit do
  42.     'method+=cr
  43.    @o=a
  44.   end do
  45.   end method
  46.   '
  47.  end class
  48.  
  49.   '
  50.  organism oa[1000]
  51.   '
  52.  function f(sys n) as sys
  53.   '=======================
  54.  if n then return  @oa(n)
  55.   end function
  56.   '
  57.  def in oa[%1]<=f(%1),f(%2),%3,%4,%5
  58.   '
  59.  '  ID  TYP FORMAL             INFORMAL              DESCRIPTION
  60.  '========================================================================================
  61.  in 009 000 ""                 "Virtual entity"      ""
  62.   in 010 000 ""                 "Physical entity"     ""
  63.   in 011 009 ""                 "Command"             ""
  64.   in 012 009 ""                 "Maths"               ""
  65.   in 013 009 ""                 "Memory"              ""
  66.   in 016 010 ""                 "Magnetic"            ""
  67.   in 017 010 ""                 "Electromagnetic"     ""
  68.   in 018 010 ""                 "Electrical"          ""
  69.   in 019 010 ""                 "Atomic"              ""
  70.   in 020 010 ""                 "Molecular"           ""
  71.   in 029 020 ""                 "Inorganic chemistry" ""
  72.   in 030 020 ""                 "Organic chemistry"   ""
  73.   in 040 030 ""                 "Self replicator"     ""
  74.   '----------------------------------------------------------------------------------------
  75.  in 050 040 ""                 "Organism"            "Organic life with metabolism"
  76.   in 051 040 ""                 "virus"               "Organic life without metabolism"
  77.   in 060 050 "Bacteria"         "Bacteria"            "cells without nucleus"
  78.   in 061 050 "Archaea"          "Extremophiles"       "Cells tolerant of extreme conditions"
  79.   in 062 050 "Eukarya"          "Eukaryotes"          "cells with nucleus"
  80.   in 063 062 "Protozoa"         ""                    ""
  81.   in 064 062 "Chromista"        ""                    ""
  82.   in 071 063 ""                 "other protists"      ""
  83.   in 072 064 ""                 "Euglenoids"          ""
  84.   in 073 064 ""                 "Apicomplexa"         ""
  85.   in 074 064 ""                 "Haptophytes"         ""
  86.   in 075 064 ""                 "Brown Algae"         ""
  87.   in 076 064 ""                 "Diatoms"             ""
  88.   in 077 064 ""                 "Glaucophytes"        ""
  89.   in 078 062 "Fungi"            "Fungi"               ""
  90.   in 079 062 "Animalia"         "Animals"             ""
  91.   '----------------------------------------------------------------------------------------
  92.  in 080 064 "Rhodophyta"       "Red Algae"           ""
  93.   in 081 064 "Chlorophyta"      "Green Algae"         "green algae (desmids & charophytes)"
  94.   in 110 062 "Plantae"          "Plants"              "green multicellular organisms"
  95.   in 120 110 "Marchantiophyta"  "Bryophytes"          "liverworts"
  96.   in 121 110 "Anthocerotophyta" "Bryophytes"          "hornworts"
  97.   in 122 110 "Bryophyta"        "Bryophytes"          "mosses"
  98.   in 123 110 "Lycopodiophyta"   "Pteridophytes"       "club mosses"
  99.   in 124 110 "Pteridophyta"     "Pteridophytes"       "Ferns, Wisk ferns & horsetails"
  100.   in 125 110 "Cycadophyta"      "Seed plants"         "cycads"
  101.   in 126 110 "Ginkgophyta"      "Seed plants"         "ginkgo"
  102.   in 127 110 "Pinophyta"        "Seed plants"         "conifers"
  103.   in 128 110 "Gnetophyta"       "Seed plants"         "gnetophytes"
  104.   in 129 110 "Magnoliophyta"    "Seed plants"         "flowering plants"
  105.   '----------------------------------------------------------------------------------------
  106.  in 200 079 "Parazoa"          ""                    ""
  107.   in 201 200 "Porifera"         ""                    ""
  108.   in 202 200 "Placozoa"         ""                    ""
  109.   in 203 079 "Eumetazoa"        ""                    ""
  110.   in 204 203 "Radiata"          ""                    ""
  111.   in 205 203 "Bilateria"        ""                    ""
  112.   in 206 205 "Orthonectida"     ""                    ""
  113.   in 207 205 "Rhombozoa"        ""                    ""
  114.   in 208 205 "Acoelomorpha"     ""                    ""
  115.   in 209 205 "Chaetognatha"     ""                    ""
  116.   in 210 205 "Deuterostomia"    ""                    ""
  117.   in 211 210 "Chordata"         ""                    ""
  118.   in 212 210 "Hemichordata"     ""                    ""
  119.   in 213 210 "Echinodermata"    ""                    ""
  120.   in 214 210 "Xenoturbellida"   ""                    ""
  121.   in 215 210 "Vetulicolia"      ""                    ""
  122.   in 300 211 "Tunicata"         ""                    "tunicates; 3,000 species"
  123.   in 310 211 "Cephalochordata"  ""                    "lancelets; 30 species"
  124.   in 320 211 "Vertebrata"       ""                    "vertebrates"
  125.   in 330 320 "Gnathostomata"    ""                    "jawed vertebrates"
  126.   in 340 330 "Placodermi"       ""                    "Paleozoic armoured forms"
  127.   in 350 330 "Chondrichthyes"   ""                    "cartilaginous fish; 900+ species"
  128.   in 360 330 "Acanthodii"       ""                    "Paleozoic spiny sharks"
  129.   in 370 330 "Osteichthyes"     ""                    "bony fish; 30,000+ species"
  130.   in 380 370 "Actinopterygii"   ""                    "ray-finned fish; about 30,000 species"
  131.   in 390 370 "Sarcopterygii"    ""                    "lobe-finned fish: 8 species"
  132.   in 400 330 "Tetrapoda"        ""                    "four-legged vertebrates; 28,000+ species"
  133.   in 410 400 "Amphibia"         ""                    "amphibians; 6,000 species"
  134.   in 420 400 "Reptilia"         ""                    "reptiles; 8,225+ species"
  135.   in 430 400 "Anapsida"         ""                    "extinct "proto-reptiles" and possibly turtles"
  136.   in 440 400 "Diapsida"         ""                    "majority of reptiles, progenitors of birds"
  137.   in 450 400 "Aves"             ""                    "birds; 8,800–10,000 species"
  138.   in 460 400 "Synapsida"        ""                    "mammal-like "reptiles"; 4,500+ species, progenitors of mammals"
  139.   in 470 400 "Mammalia"         ""                    "mammals; 5,800 species"
  140.   '----------------------------------------------------------------------------------------
  141.  in 500 470 "Prototheria"      "monotremes"          "echidnas and the Platypus"
  142.   in 510 470 "Theriiformes"     ""                    "live-bearing mammals and their prehistoric relatives"
  143.   in 520 470 "Allotheria"       "multituberculates"   ""
  144.   in 530 470 "Triconodonta"     "triconodonts"        ""
  145.   in 540 470 "Holotheria"       ""                    "modern live-bearing mammals and their prehistoric relatives"
  146.   in 550 540 "Theria"           ""                    "live-bearing mammals"
  147.   in 560 550 "Marsupialia"      "marsupials"          ""
  148.   in 570 560 "Australidelphia"  ""                    "Australian marsupials and the Monito del Monte"
  149.   in 580 560 "Ameridelphia"     ""                    "New World marsupials"
  150.   in 590 540 "Placentalia"      "placentals"          ""
  151.   in 600 540 "Xenarthra"        "xenarthrans"         ""
  152.   in 610 540 "Epitheria"        "epitheres"           ""
  153.   in 620 610 "Anagalida"        ""                    "lagomorphs, rodents, and elephant shrews"
  154.   in 630 610 "Ferae"            ""                    "carnivorans, pangolins, †creodonts, and relatives"
  155.   in 640 610 "Lipotyphla"       "insectivorans"       ""
  156.   in 650 610 "Archonta"         ""                    "bats, primates, colugos, and treeshrews"
  157.   in 670 610 "Ungulata"         "ungulates"           ""
  158.   in 680 670 "Tubulidentata"    ""                    "incertae sedis: aardvark"
  159.   in 690 670 "Eparctocyona"     ""                    "condylarths, whales, and artiodactyls (even-toed ungulates)"
  160.   in 700 670 "Meridiungulata"   ""                    "South American ungulates"
  161.   in 710 670 "Altungulata"      ""                    "perissodactyls (odd-toed ungulates), elephants, manatees, and hyraxes"
  162.   '----------------------------------------------------------------------------------------
  163.  in 800 650 "Primates"         ""                    ""
  164.   in 810 800 "Strepsirrhini"    ""                    "non-tarsier prosimians"
  165.   in 820 810 "Lemuriformes"     ""                    ""
  166.   in 822 820 "Cheirogaleidae"   ""                    "dwarf lemurs and mouse-lemurs 32 species"
  167.   in 824 820 "Daubentoniidae"   ""                    "aye-aye 1 species"
  168.   in 826 820 "Lemuridae"        ""                    "lemurs 22 species"
  169.   in 828 820 "Lepilemuridae"    ""                    "sportive lemurs 26 species"
  170.   in 830 820 "Indriidae"        ""                    "woolly lemurs and allies 19 species"
  171.   in 840 810 "Lorisiformes"     ""                    ""
  172.   in 842 840 "Lorisidae"        ""                    "lorises, pottos and allies 9 species"
  173.   in 844 840 "Galagidae"        ""                    "galagos 19 species"
  174.   in 850 800 "Haplorhini"       ""                    "tarsiers, monkeys and apes"
  175.   in 852 850 "Tarsiiformes"     ""                    ""
  176.   in 854 852 "Tarsiidae"        ""                    "tarsiers 9 species"
  177.   in 860 850 "Anthropoidea"     ""                    ""
  178.   in 862 850 "Parvorder"        "Platyrrhini"         "New World monkeys"
  179.   in 864 862 "Callitrichidae"   ""                    "marmosets and tamarins 42 species"
  180.   in 866 862 "Cebidae"          ""                    "capuchins and squirrel monkeys 17 species"
  181.   in 868 862 "Aotidae"          ""                    "night or owl monkeys (douroucoulis) 10 species"
  182.   in 870 862 "Pitheciidae"      ""                    "titis, sakis and uakaris 42 species"
  183.   in 872 862 "Atelidae"         ""                    "howler, spider and woolly monkeys 28 species"
  184.   in 880 850 "Catarrhini"       ""                    ""
  185.   in 882 880 "Cercopithecoidea" ""                    ""
  186.   in 884 882 "Cercopithecidae"  ""                    "Old World monkeys 135 species"
  187.   in 886 880 "Hominoidea"       ""                    ""
  188.   in 888 886 "Hylobatidae"      ""                    "gibbons or lesser apes 13 species"
  189.   in 900 886 "Hominidae"        ""                    "great apes, including humans 7 species"
  190.   '========================================================================================
  191.  '
  192.  'TEST
  193.  '====
  194.  
  195.   pr="TAXONOMY" cr cr
  196.   pr+=oa.lineage f 900
  197.  
  198.   print pr
  199.  
  200.  
  201.  

Quote

TAXONOMY

physical entity
-->
molecular
-->
organic chemistry
-->
self replicator
-->
organism
organic life with metabolism
-->
eukarya
eukaryotes
cells with nucleus
-->
animalia
animals
-->
eumetazoa
-->
bilateria
-->
deuterostomia
-->
chordata
-->
vertebrata
vertebrates
-->
gnathostomata
jawed vertebrates
-->
tetrapoda
four-legged vertebrates; 28,000+ species
-->
mammalia
mammals; 5,800 species
-->
holotheria
modern live-bearing mammals and their prehistoric relatives
-->
epitheria
epitheres
-->
archonta
bats, primates, colugos, and treeshrews
-->
primates
-->
haplorhini
tarsiers, monkeys and apes
-->
catarrhini
-->
hominoidea
-->
hominidae
great apes, including humans 7 species


Charles
« Last Edit: June 14, 2011, 09:16:16 PM by Charles Pegge »

Peter

  • Guest
Re: Taxonomy: What are we?
« Reply #1 on: June 15, 2011, 03:09:53 AM »

  Hi charles, is this your  doctoral thesis?   :D

kryton9

  • Guest
Re: Taxonomy: What are we?
« Reply #2 on: June 15, 2011, 07:32:19 PM »
I agree with Peter, looks like some sort of thesis project!

Charles Pegge

  • Guest
Re: Taxonomy: What are we?
« Reply #3 on: June 15, 2011, 10:19:19 PM »
It's a tree!

With an extra field this would also work for family trees.

Charles