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Author Topic:   Convergent Evolution - Reasonable conclusion? or convenient excuse?
RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 6 of 107 (563876)
06-07-2010 7:51 AM
Reply to: Message 5 by Wounded King
06-07-2010 5:59 AM


Re: Another possibility
Hi Wounded King,
I don't see that this has much bearing on my previous comments though in terms of genetic support for the nested hierarchy.
There's another element to consider. From the first abstract:
Convergent sequence evolution between echolocating bats and dolphins - PubMed
quote:
... The motor protein Prestin is expressed in mammalian outer hair cells (OHCs) and is thought to confer high frequency sensitivity and selectivity in the mammalian auditory system [2]. We previously reported that the Prestin gene has undergone sequence convergence among unrelated lineages of echolocating bat [3]. Here we report that this gene has also undergone convergent amino acid substitutions in echolocating dolphins, which group with echolocating bats in a phylogenetic tree of Prestin. ...
If the changes result in sensitivity to certain frequencies used in echolocation, it could be a matter of resonance fitting: the amino acid substitutions changing the resonance response. For the same response in other species, the same substitutions would result in the same resonance fitting, while different substitutions would not. Selection for the resonance response would result in selection for the same sequences.
Enjoy.
Edited by RAZD, : /qs

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 5 by Wounded King, posted 06-07-2010 5:59 AM Wounded King has replied

Replies to this message:
 Message 7 by Wounded King, posted 06-07-2010 8:54 AM RAZD has replied

  
RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 12 of 107 (564009)
06-07-2010 6:31 PM
Reply to: Message 7 by Wounded King
06-07-2010 8:54 AM


Re: Another possibility
Hi Wounded King, it's just a thought.
I'm not sure how that is another element to consider, since it is the whole point of both articles. They both posit convergent protein sequence evolution of Prestin as a result of selective pressures associated with echolocation.
It's the issue of resonance, like a vibrating string ...
quote:
... The motor protein Prestin is expressed in mammalian outer hair cells (OHCs) ...
Presumably the hair vibrates in response to sound. This is how sound is normally sensed, yes?
Different mutations would cause different resonance frequencies (length, folding, weight distribution of the protein and change the hair), so selection for specific frequencies would result in selection for specific amino acid sequences.
But as I have been pointing out, protein sequences and amino acid substitutions are not really genetic data in and of themselves. Selection for the resonance response only selects for the same amino acid sequences not the same DNA sequences. While this selection will affect the DNA sequences to some extent it still allows a lot more variability than at the amino acid level.
I would not be surprised if you could compare any convergent species and find some similarities at this level (rather than the genetic level).
For Bob's argument to make any sense the nested hierarchy really needs to fall apart at the genetic level, it is no good him just choosing an arbitrary phenotypic level and then saying, look at these supposedly convergent traits they blow a major hole in the darwinian nested hierarchy approach.
I would think there would have to be a failure of any other nested hierarchy.
If evidence of some kind of intelligent design "reuse" of features is being sought, then there should be multiple examples of features "borrowed" from multiple other species, to the point where no consistent nested hierarchy could be derived.
Enjoy.

we are limited in our ability to understand
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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 21 of 107 (564317)
06-09-2010 7:55 PM
Reply to: Message 18 by BobTHJ
06-09-2010 6:31 PM


superficial similarity but differences in the details
Hi BobTHJ, and welcome to the fray.
Just a small point or two.
The overall evidence for a nested hierarchy is not high - the many cases of 'convergent evolution' demonstrate this.
Do you know how many different species are currently living? This list is less than 1% of the NEW species recently added to the catalog of life:
Number of Earth's species known to scientists rises to 1.9 million | Wildlife | The Guardian
quote:
The number of species on the planet that have been documented by scientists has risen to 1.9 million, according to the world's most comprehensive catalogue of plants and animals.
The new figure has been boosted by 114,000 new species discovered since the catalogue was last compiled by Australian researchers three years ago — a 6.3% increase.
And evidently we still don't know all of them.
While there are only 100 instances listed in the wiki article, and I don't call 100/1.9X10^6 = 0.005% a significant problem.
What does have a lot of evidence is the conclusion that creatures with similar morphological features will share similar genes.
Which is why, when you look at the details for animals that appear similar at the gross level, they show convergent evolution from different branches of life.
One from your - actual wiki's - list is the thylacine and wolf:
quote:
The skulls of the Thylacine (left) and the Grey Wolf, Canis lupus, are almost identical, although the species are only very distantly related (different infraclasses). The skull shape of the Red Fox, Vulpes vulpes, is even closer to that of the Thylacine.[1]
If you look closely you will see differences in each picture that are due to different hereditary ancestry. These differences are why biologists know that this is a case of convergent evolution.
We had a thread here a while ago that went into detail on the actual anatomical differences between these two organisms, and this showed that the basic detail level (number and type of teeth for instance) the characteristics of the thylacine were closer to the other marsupials than to the placental mammal wolf and that the grey wolf were closer to other placental mammals than to the marsupial thylacine.
Unfortunately the last time I checked for it, it appeared that the photos were no longer showing (the links were not working).
Curiously, the nested hierarchies of animals based on their morphological traits put these two animals in different clades, the grey wolf with the placental mammals and the thylacine with the marsupials, because of the morphological details.
We see similar detail differences in sugar-gliders and flying squirrels (also on the list):
When we look at the details once again, we see that the sugar-glider is clearly a marsupial and the flying squirrel is clearly a placental mammal, and these detailed differences are what the nested hierarchies are based on.
The same holds for the other organisms on this list.
However, as I mentioned in my previous post, where do you draw the line? Not all traits fit neatly into a nested hierarchy.
Where you draw the line is based on the preponderance of evidence at the detail level.
Interestingly, the same kind of nested hierarchy can be formed from genetic information, and if evolution is not the correct explanation, then there is no reason for a genetic hierarchy to match the one developed on the morphological details.
Fascinatingly, these two versions of nested hierarchies agree to phenomenal levels of comparison with very little error.
However, this conclusion does not support common ancestry and more than it supports baraminology.
Amusingly you don't show how "it supports baraminology" but just make an unfounded assertion.
Enjoy

I counted the list by changing the bullet to numbers by global substitution. The thylacine is #3 and the sugar-glider is #9.
Many items on this list are only specific traits (see opposum opposable thumb) rather than whole organisms.
List of examples of convergent evolution - Wikipedia
  1. The pronghorn antelope of North America, while not a true antelope and only distantly related to them, closely resembles the true antelopes of the Old World, both behaviorally and morphologically. It also fills a similar ecological niche and is found in the same biomes.
  2. Members of the two clades Australosphenida and theria evolved tribosphenic molars independently.
  3. The marsupial thylacine (Tasmanian Tiger) had many resemblances to the placental canids.
  4. Several mammal groups have independently evolved prickly protrusions of the skin — echidnas (monotremes), the insectivorous hedgehogs, some tenrecs (a diverse group of shrew-like Madagascan mammals), Old World porcupines (rodents) and New World porcupines (another biological family of rodents). In this case, because the two groups of porcupines are closely related, they would be considered to be examples of parallel evolution; however, neither echidnas, nor hedgehogs, nor tenrecs are close relatives of the Rodentia. In fact, the last common ancestor of all of these groups was a contemporary of the dinosaurs.
  5. Cat-like sabre-toothed predators evolved in three distinct lineages of mammals — sabre-toothed cats, Nimravids ("false" sabre-tooths), and the marsupial "lion" thylacosmilus. Gorgonopsids and creodonts also developed long canine teeth, but with no other particular physical similarities.
  6. A number of mammals have developed powerful fore claws and long, sticky tongues that allow them to open the homes of social insects (e.g., ants and termites) and consume them (myrmecophagy). These include the four species of anteater, more than a dozen armadillos, eight species of pangolin (plus fossil species), the African aardvark, one echidna (an egg-laying monotreme), the enigmatic Fruitafossor, the singular Australian marsupial known as the numbat, the aberrant aardwolf, and possibly also the sloth bear of South Asia, all not related.
  7. Koalas of Australasia have evolved fingerprints, indistinguishable from those of humans. Apes' fingerprints are very similar to those too.
  8. The Australian honey possums acquired a long tongue for taking nectar from flowers, a structure similar to that of butterflies, some moths, and hummingbirds, and used to accomplish the very same task.
  9. Marsupial sugar glider and squirrel glider of Australia are like the placental flying squirrel.
  10. The North American kangaroo rat, Australian hopping mouse, and North African and Asian jerboa have developed convergent adaptations for hot desert environments; these include a small rounded body shape with very large hind legs and long thin tails, a characteristic bipedal hop, and nocturnal, burrowing and seed-eating behaviours. These rodent groups fill similar niches in their respective ecosystems.
  11. Opossums have evolved an opposable thumb, a feature which is also commonly found in the non-related primates.
  12. Marsupial mole has many resemblances to the placental mole.
  13. Marsupial mulgara has many resemblances to the placental mouse.
  14. Planigale has many resemblances to the deer mouse.
  15. Marsupial Tasmanian devil has many resemblances to the placental wolverine.
  16. Kangaroo has many resemblances to the Patagonian cavy.
  17. The Marsupial lion had retractable claws, the same way the placental felines (cats) do today.
  18. Microbats, toothed whales and shrews developed sonar-like echolocation systems used for navigation and for locating prey. DNA study has shown that echolocation in two types of bats, megachiroptera and microchiroptera, came about independently.
  19. Both the aye-aye lemur and the striped possum have an elongated finger used to get invertebrates from trees. There are no woodpeckers in Madagascar or Australia where the species evolved, so the supply of invertebrates in trees was large.
  20. Castorocauda and beaver both have webbed feet and a flattened tail, but are not related.
  21. Prehensile tails came in to a number of unrelated species New World monkeys, kinkajous, porcupines, tree-anteaters, marsupial opossums, and the salamander Bolitoglossa pangolins, treerats, skinks and chameleons.
  22. Pig form, large-headed, pig-snouted and hoofs are independent in true pigs in Eurasia and Peccary and Entelodonts.
  23. Plankton feeding filters, baleen: Whale sharks and baleen whales, like the humpback and blue whale independent have very sophisticated ways of sifting plankton from marine waters.
  24. There are five species of river/freshwater dolphins, which are not closely related.
  25. Platypus have what looks like a bird's Beak (hence its scientific name Ornithorhynchus), but is a mammal.
    [edit] Dinosaurs
  26. Ornithischian (bird-hipped) dinosaurs had a pelvis shape similar to that of birds, or avian dinosaurs, which evolved from saurischian (lizard-hipped) dinosaurs.
  27. The Heterodontosauridae evolved a tibiotarsus which is also found in modern birds. These groups aren't closely related.
  28. Ankylosaurs and glyptodont mammals both had spiked tails.
  29. Horned snouts independently is on non-related dinosaurs like ceratopsians and Triceratops, also rhinos and the brontotheres of the Cenozoic.
  30. Billed snouts on the duck-billed dinosaurs hadrosaurs strikingly convergent with ducks and duck-billed platypus.
  31. Ichthyosaurs a marine reptile of the Mesozoic era looked strikingly like dolphins.
  32. Beaks are independent in ceratopsian dinosaurs like Triceratops, birds and marine mollusks like squid and octopus.
  33. The Pelycosauria and the Ctenosauriscidae beared striking resemblance to each other because they both had a sail-like fin on their back. The Pelycosaurs are more closely related to mammals while the Ctenosauriscids are closely related to pterosaurs and dinosaurs.
    [edit] Other reptiles
  34. The thorny devil (Moloch horridus) is similar in diet and activity patterns to the Texas horned lizard (Phrynosoma cornutum), although the two are not particularly closely related.
  35. Modern Crocodilians resemble prehistoric phytosaurs, champsosaurs, certain labyrinthodont amphibians, and perhaps even the early whale Ambulocetus. The resemblance between the crocodilians and phytosaurs in particular is quite striking; even to the point of having evolved the graduation between narrow- and broad-snouted forms, due to differences in diet between particular species in both groups.
  36. The body shape of the prehistoric fish-like reptile Ophthalmosaurus is similar to those of other ichthyosaurians, dolphins (aquatic mammals), and tuna (scombrid fish).
  37. Death Adders strongly resemble true vipers, but are elapids.
  38. The Glass Snake is actually a lizard but is mistaken as a snake .
  39. Large Tegu lizards of South America have converged in form and ecology with monitor lizards, which are not present in the Americas.
  40. legless lizard-Pygopodidae are snake like lizard are much like true snakes.
  41. Mosasaurs of the Mesozoic era are like whales but are closely related to living monitor lizards and the Komodo Dragon.
  42. Anolis lizards are one of the best examples of both adaptive radiation and convergent evolution.
  43. Tuataras resemble lizards but in fact are in an order of their own, the Rhynchocephalia. The Tuatara has the sockets behind the eyes and has jagged extensions of the jaws instead of teeth.
    [edit] Avian
  44. The Little Auk of the north Atlantic (Charadriiformes) and the diving-petrels of the southern oceans (Procellariiformes) are remarkably similar in appearance and habits.
  45. Penguins in the Southern Hemisphere evolved similarly to flightless wing-propelled diving auks in the Northern Hemisphere: the Atlantic Great Auk and the Pacific mancallines.
  46. Vultures are a result of convergent evolution: both Old World vultures and New World vultures eat carrion, but Old World vultures are in the eagle and hawk family (Accipitridae) and use mainly eyesight for discovering food; the New World vultures are of obscure ancestry, and some use the sense of smell as well as sight in hunting. Birds of both families are very big, search for food by soaring, circle over sighted carrion, flock in trees, and have unfeathered heads and necks.
    Nubian Vulture, an Old World vulture
    Turkey Vulture, a New World vulture
    Hummingbird, a New World bird, with a sunbird, an Old World bird
  47. Hummingbirds resemble sunbirds. The former live in the Americas and belong to an order or superorder including the swifts, while the latter live in Africa and Asia and are a family in the order Passeriformes.
  48. In an odd cross-species example, an insect, the Hummingbird Hawk-moth (Macroglossum stellatarum), also feeds by hovering in front of flowers and drinking their nectar in the same way as the above mentioned birds.
  49. Certain longclaws (Macronyx) and meadowlarks (Sturnella) have essentially the same striking plumage pattern. The former inhabit Africa and the latter the Americas, and they belong to different lineages of Passerida. While they are ecologically quite similar, no satisfying explanation exists for the convergent plumage; it is best explained by sheer chance.
  50. Resemblances between swifts and swallows is due to convergent evolution.
  51. Downy Woodpecker and Hairy Woodpecker look almost the same, as do some Chrysocolaptes and Dinopium flamebacks, the Smoky-brown Woodpecker and some Veniliornis species, and other Veniliornis species and certain "Picoides" and Piculus. In neither case are the similar species particularly close relatives.
  52. Many birds of Australia, like wrens and robins, look like northern hemisphere birds but are not related.
  53. Oilbird like microbats and toothed whales developed sonar-like echolocation systems used for locating prey.
  54. The brain structure, forebrain, of hummingbirds, songbirds, and parrots responsible for vocal learning (not by instinct) is very similar. These types of birds are not related.
    [edit] Fish
  55. Goby dorsal finned like the lumpsuckers, yet they are not related.
  56. Sandlance fish and chameleons have independent eye movements and focusing by use of the cornea.
  57. Cichlids of South America and the "sunfish" of North America are strikingly similar in morphology, ecology and behavior.
  58. The Peacock Bass and Largemouth Bass are excellent examples.
  59. The Antifreeze protein of fish in the arctic and Antarctic, came about independently.
  60. Eel form are independent in the North American brook lamprey, neotropical eels, and the African spiny eel.
  61. Stickleback fish, there is widespread convergent evolution in Sticklebacks.
    [edit] Amphibians
  62. Plethodontid salamanders and Chameleons have evolved a harpoon-like tongue to catch insects.
  63. Two lineages of frogs among the Neobatrachia are due for convergent evolution.
  64. The Neotropical poison dart frog and the Mantella of Madagascar have independently developed similar mechanisms for obtaining alkaloids from a diet of mites and storing the toxic chemicals in skin glands. They have also independently evolved similar bright skin colors that warn predators of their toxicity (by the opposite of crypsis, namely aposematism).
  65. Caecilian are Lissamphibians that secondarly lost their limbs, resembling snakes
    [edit] Arthropods
  66. Assassin spiders comprise two lineages that evolved independently. They have very long necks and fangs proportionately larger than those of any other spider, and they hunt other spiders by snagging them from a distance.
  67. The smelling organs of the terrestrial coconut crab are similar to those of insects.
  68. Silk: Spiders, silk moths, larval caddis flies, and the weaver ant all produce silken threads.
  69. The praying mantis body type — raptorial forelimb, prehensile neck, and extraordinary snatching speed - has evolved not only in mantid insects but also independently in neuropteran insects Mantispidae.
  70. Agriculture some kinds of ants, termites, and ambrosia beetles have for a long time cultivated and tend fungi for food. These insects sow, fertilize, and weed their crops. A damselfish also takes care of red algae carpets on its piece of reef; the damselfish actively weeds out invading species of algae by nipping out the newcomer.
    [edit] Molluscs
  71. Bivalves and the gastropods in the family Juliidae have very similar shells.
  72. There are limpet-like forms in several lines of gastropods: "true" limpets, pulmonate siphonariid limpets and several lineages of pulmonate freshwater limpets.
  73. Cuttlefish show similarities between cephalopod (nautili, octopods and squid) and vertebrate (Mammalia...) eyes.
  74. Swim bladders — Buoyant bladders independently evolved in fishes, female octopus and siphonophores such as the Portuguese Man o' War.
  75. The phylum Mollusca members such as bivalves, and Phylum brachiopoda members, the brachiopods aka lampshells, independently evolved paired hinged shells for protection. The anatomy of their soft body parts is so dissimilar, however, that they are classified in separate, independent phyla. Biologists think that clams are more closely related to earthworms than they are to brachiopods.
  76. Jet propulsion in squids and in scallops: these two groups of mollusks have very different ways of squeezing water through their bodies in order to power rapid movement through a fluid. (Dragonfly larvae in the aquatic stage also use an anal jet to propel them, and Jellyfish have used jet propulsion for a very long time.)
    [edit] Other
  77. The notochords in chordates are like the stomochords in hemichordates.
  78. Elvis taxon in the fossil record developed a similar morphology through convergent evolution.
  79. Venomous sting: To inject poison with a hypodermic needle, a sharppointed tube, has shown up independently 10+ times: jellyfish, spiders, scorpions, centipedes, various insects, cone shell, snakes, stingrays, stonefish, the male duckbill platypus, and stinging nettles plant.
  80. Bioluminescence: A symbiotic partnerships with light-emitting bacteria developed many times independently in deep-sea fish, jellyfish, and in fireflies and glow worms.
  81. Parthenogenesis: Some lizards and insects have independent the capacity for females to produce live young from unfertilized eggs. Some species are entirely female.
    [edit] In plants
  82. Leaves have evolved multiple times - see Evolutionary history of plants.
  83. Prickles, thorns and spines are all modified plant tissues that have evolved to prevent or limit herbivory, these structures have evolved independently a number of times.
  84. Hallucinogenic toxins: Plants as diverse as the peyote cactus and the ayahuasca vine produce the same form of chemical toxin to deter predators.
  85. Stimulant toxins: Plants which are only distantly related to each other, such as coffee and tea, produce caffeine to deter predators.
  86. The aerial rootlets found in ivy (Hedera) are similar to those of the climbing hydrangea (Hydrangea petiolaris) and some other vines. These rootlets are not derived from a common ancestor but have the same function of clinging to whatever support is available.
  87. Flowering plants (Delphinium, Aerangis, Tropaeolum and others) from different regions form tube-like spur which contains nectar (that's why insect from one place sometimes can feed on plant from other which has such structure like the flower which is the traditional source of food for the animal).
  88. Both some dicots (Anemone) and monocots (Trillium) in inhospitable environments are able to form underground organs such as corms, bulbs and rhizomes for reserving of nutrition and water till the conditions become better.
  89. Insectivorous plants: Nitrogen-deficient plants have in at least 7 distinct times become insectivorous, like: flypaper traps\sundew, spring traps-Venus fly trap, and pitcher traps in order to capture and digest insects to obtain scarce nitrogen.
  90. Similar-looking rosette succulents have arisen separately among plants in the families Asphodelaceae (formerly Liliaceae) and Crassulaceae.
  91. The Orchids, the Birthwort family and Stylidiaceae have evolved independently the specific organ known as gynostemium, more popular as column.
  92. The Euphorbia of deserts in Africa and southern Asia, and the Cactaceae of the New World deserts have similar modifications (see picture below for one of many possible examples).
  93. Sunflower: some types of Sunflower and Pericallis are due to convergent evolution.
    Euphorbia obesa
    Astrophytum asterias
    [edit] Enzymes and biochemical pathways
  94. The existence of distinct families of carbonic anhydrase is believed to illustrate convergent evolution.
  95. The use of (Z)-7-dodecen-1-yl acetate as a sex pheromone by the Asian elephant (Elephas maximus) and by more than 100 species of Lepidoptera.
  96. The independent development of the catalytic triad in serine proteases independently with subtilisin in prokaryotes and the chymotrypsin clan in eukaryotes.
  97. The repeated independent evolution of nylonase in two different strains of Flavobacterium and one strain of Pseudomonas.
  98. The biosynthesis of plant hormones such as gibberellin and abscisic acid by different biochemical pathways in plants and fungi.[2][3]
  99. ABAC is a database of convergently evolved protein interaction interfaces. Examples comprise fibronectin/long chain cytokines, NEF/SH2, cyclophilin/capsid proteins. Details are described here.
  100. The independent development of three distinct hydrogenases exemplifies convergent evolution.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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This message is a reply to:
 Message 18 by BobTHJ, posted 06-09-2010 6:31 PM BobTHJ has replied

Replies to this message:
 Message 38 by BobTHJ, posted 06-14-2010 1:07 PM RAZD has replied
 Message 100 by barbara, posted 07-19-2010 5:18 PM RAZD has replied

  
RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 46 of 107 (565124)
06-14-2010 9:35 PM
Reply to: Message 44 by BobTHJ
06-14-2010 6:24 PM


Hi again BobTHJ,
Cases of common morphology without common genetics does not make common design an unreasonable conclusion.
Silly Design Institute: Let's discuss BOTH sides of the Design Controversy... ... at issue is the purpose of design that we can infer from the evidence.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 44 by BobTHJ, posted 06-14-2010 6:24 PM BobTHJ has seen this message but not replied

  
RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 47 of 107 (565131)
06-14-2010 10:07 PM
Reply to: Message 38 by BobTHJ
06-14-2010 1:07 PM


Re: superficial similarity but differences in the details
Hi again BobTHJ,
I haven't looked, but it is probably safe to assume that the vast majority of these species are the result of recent variation (we may define 'recent' differently, but suffice it to say that they have very close relatives) so it seems your figure should be substantially less. I also doubt that the wikipedia article is comprehensive in nature as I've seen mentions of several hundred or more cases of convergency. As a result it is likely the percentage is substantially higher than .005%.
Except that (1a) all the convergent evolution examples include living species AND some fossil bits of evidence PLUS (1b) some of the examples are only specific traits (such as opposable thumbs) rather than the appearance of the whole organisms, as in the example of the flying squirrel and sugar glider, WHILE (2) "The number of species on the planet that have been documented by scientists has risen to 1.9 million" is only currently living species.
Therefore a proper comparison would be much lower than 0.005% (take out the fossil examples, take out the single feature examples).
As I stated in another thread - I suspect the phylogenetic tree to be a 95%+ accurate categorization of living organisms (ontology only - no common descent implied) - with these non-conforming cases composing the other <5%. Just stating this for the record so everyone knows where I stand.
Of course, and you also must realize that opinion is completely impotent at altering reality in any way. You are free to hold whatever opinion you wish, but if you are ignoring reality and evidence that contradicts your opinion, the only one you are fooling is yourself.
Yes - and that seems to be what happens. Organisms are placed into the phylogenetic tree at the location where they show the most similarity to the surrounding organisms. This reflects a good ontology model - though it does lead to some inconsistency since some organisms classed in different clades still share similarities not shared by other closely classed organisms.
Perhaps you would like to offer some evidence to show what you mean? Are you talking about lost traits?
Nobody is claiming that the nested hierarchies are necessarily true, just that they are the best known explanation of life as we know it, based on the information available.
Curiously, these nested hierarchies can be developed (a) in the traditional morphological detailed study method that has been used in biology since Linnaeus, and (b) based on genetic information.
With design there is no reason for these two trees to be the same.
With evolution the two trees must be the same, and they are.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 38 by BobTHJ, posted 06-14-2010 1:07 PM BobTHJ has replied

Replies to this message:
 Message 55 by BobTHJ, posted 06-16-2010 11:21 AM RAZD has replied

  
RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 64 of 107 (565440)
06-16-2010 7:25 PM
Reply to: Message 63 by Taq
06-16-2010 1:58 PM


Re: What is the ID Explanation?
Hi Taq,
Fish and squid share the same exact environment, and their eyes serve the same exact function. Their eyes are significantly different in their design. Remember what you said earlier?
Better still, compare the octopus eye to the nautilus eye, same environment, similar behavior, both use tentacles to capture prey, and need eyes to see the prey.
The octopus eye has a lens.
The nautilus eye does not - it has a small opening that functions like a "pin-hole" to focus images.
Enjoy.
Edited by RAZD, : images addedded

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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 67 of 107 (565446)
06-16-2010 8:58 PM
Reply to: Message 55 by BobTHJ
06-16-2010 11:21 AM


Re: superficial similarity but differences in the details
Hi BobTHJ, thanks.
Of course. You disagree with my opinion that the phylogenetic tree correctly models similarity (both morphological and genetic) to a degree higher than 95%? I didn't think many people would fight me on that assumption.
Amusingly, that is not the opinion that flies against scientific evidence. This issue is the 5% where you think there is wiggle room for your opinion to differ from science.
Sure, echolocating in bats and dolphins. They are not classed together in the phylogenetic tree (nor should they be if you want the most accurate ontological model possible) yet share a similarity not shared by other closely grouped organisms.
Except that this is not an example of where the 5% of the phylogenetic can be wrong.
The phylogeny is based on hereditary traits rather than developed traits. The "most accurate ontological model" would be based on inherited traits, and it would recognize that traits that appear similar because of independent development do not interfere with the phylogeny.
Homologies and analogies - Understanding Evolution
quote:
Since a phylogenetic tree is a hypothesis about evolutionary relationships, we want to use characters that are reliable indicators of common ancestry to build that tree. We use homologous characterscharacters in different organisms that are similar because they were inherited from a common ancestor that also had that character. An example of homologous characters is the four limbs of tetrapods. Birds, bats, mice, and crocodiles all have four limbs. Sharks and bony fish do not. The ancestor of tetrapods evolved four limbs, and its descendents have inherited that featureso the presence of four limbs is a homology.
Not all characters are homologies. For example, birds and bats both have wings, while mice and crocodiles do not. Does that mean that birds and bats are more closely related to one another than to mice and crocodiles? No. When we examine bird wings and bat wings closely, we see that there are some major differences.
Bat wings consist of flaps of skin stretched between the bones of the fingers and arm. Bird wings consist of feathers extending all along the arm. These structural dissimilarities suggest that bird wings and bat wings were not inherited from a common ancestor with wings. This idea is illustrated by the phylogeny below, which is based on a large number of other characters.

Bird and bat wings are analogousthat is, they have separate evolutionary origins, but are superficially similar because they evolved to serve the same function. Analogies are the result of convergent evolution.
The echolocation in bats and dolphins are developed analogous features, not inherited homologous features, and thus this does not interfere with the phylogenetic tree based on hereditary development.
A high degree of correlation between genomes and morpholocial features fits well with a design hypothesis. Just because darwinian evolution fails without that correlation doesn't mean it is the more reasonable conclusion.
A question for you is how you can distinguish your design hypothesis from the evolutionary hypothesis, not just telling yourself that the evidence shows design.
Message 52:
quote:
So if we found examples of non-convergence this would be evidence against a common designer?
If we failed to find significant similarity between life forms it would evidence against a common designer.
Message 53
quote:
Can you think of anything that would? And does it make a more reasonable conclusion than the one we already have which is supported by the material processes we can observe and understand?
Of course - if organisms lacked significant similarity to each other then you would have evidence against common design. For example, if organisms didn't share a similar cell structure but instead most used a basic anatomical unit that was different from other organisms this would be evidence against common design. Or if organisms didn't all use DNA/RNA but instead each used its own method of storing data - that would be evidence against common design.
Both are fairly reasonable conclusions - they both fit the data.
What I take issue with on these claims are:
  1. that they do not differentiate any observations from what is expected from evolution,
  2. that the scenarios you suggest would invalidate your design hypothesis would also invalidate evolution, and
  3. that this just appears to be your way of explaining the results of evolution to yourself, without risking any prediction that would falsify your design hypothesis.
By this means you avoid confrontation with evidence that invalidates belief, you just brush it away by telling yourself "oh it's consistent with (some kind of undefined generic) design hypothesis so it's okay" ... but it's no different than saying "god-did-it" and it doesn't predict any answers that would not be provided by evolution.
In a nutshell, you have failed to show how convergent evolution is due to design rather than evolution, or that evolution fails to explain convergence.
To maintain the thread topic here, I have continued my reply on the thread Silly Design Institute: Let's discuss BOTH sides of the Design Controversy..., Message 164.
Enjoy.
ps - with special thanks to Berkeley University for providing such an excellent resource:
Evolution 101
Evolution 101 - Understanding Evolution
Edited by RAZD, : clrty

we are limited in our ability to understand
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Rebel American Zen Deist
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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 78 of 107 (565880)
06-21-2010 7:06 PM
Reply to: Message 70 by BobTHJ
06-21-2010 4:39 PM


Thanks for playing.
Hi again BobTHJ,
To clarify my comments on the phylogenetic tree (referenced by Taq in Message 58, Catholic Scientist in Message 62, and Percy in Message 66, and RAZD in Message 67): The ontology is a useful tool to group organisms on similarities. Those similarities may occur at the genetic level, the morphological level, the behavioral level, etc. Since the inception of phylogentics similarities determine how organisms are grouped.
Based on hereditary traits, rather than arbitrary grouping because it looks nice. These homologous traits are similar because of descent from common ancestors, and they can be traced back to a common ancestor that had the same traits.
My point is that this leads to cases (such as bat/dolphin echolocation) where organisms that share one or more similarities at some level are not closely grouped. My statement is not made to validate or invalidate common ancestry (the conclusion many draw) - I am simply referring to the ontological model.
And your point fails because these are analogous traits arrived at independently, rather than inherited through a common ancestor. When you trace the hereditary lineages back in time, these traits disappear from the ancestral traits before a common ancestor is reached.
Dissimilarity in a single feature is not significant. Note that cephalopods and vertebrates still share the same cellular structure, the same DNA structure, etc. There is a host of similarities - it reeks of common design.
Curiously all life "still share the same cellular structure, the same DNA structure, etc." so you have not stated anything other than a mundane truth that makes you similar to a tree. Yeah, that reeks.
Amusingly this little equivocation means that your bat/dolphin echolocation example is completely useless in making your point, because you have revealed yourself as intellectually dishonest (whether consciously or not) by applying a double standard:
One little similarity in a part of one feature is highly significant, even though the rest of the features show dissimilarities.
One little dissimilarity in one feature is not significant at all, because the rest of the features show similarities.
Riiiight. Don't pay attention to the man behind the curtain ....
Enjoy.
Edited by RAZD, : clr

we are limited in our ability to understand
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Rebel American Zen Deist
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This message is a reply to:
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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 88 of 107 (566082)
06-22-2010 10:20 PM
Reply to: Message 85 by Dr Jack
06-22-2010 10:30 AM


Tree Lengths
Hi Mr Jack and Wounded Knee (and Percy makes three),
What does "tree length" mean?
The tree length is the number of individual changes required to form the tree, this is, each time we swap a single letter to another to make the tree the tree length increases by one. The most parsimonious tree(s) for a given set of data is the one with the lowest tree length - in other words, the one that applies the same mutation the least number of times.
Doesn't Percy's original tree only have a length of 3?
I'm curious why the original tree was not reproduced by this analysis. Certainly it should be the most parsimonious solution, yes?
Enjoy.

we are limited in our ability to understand
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Rebel American Zen Deist
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This message is a reply to:
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Replies to this message:
 Message 89 by Wounded King, posted 06-23-2010 4:11 AM RAZD has replied
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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 94 of 107 (566131)
06-23-2010 7:08 AM
Reply to: Message 89 by Wounded King
06-23-2010 4:11 AM


Re: Tree Lengths
Thanks Wounded King, Mr. Jack, Percy
Adding in the ancestral sequence as an outgroup still doesn't give me Percy's tree exactly, but it does produce a tree with a length of 14.
And Mr. Jack had one with a tree length of 12 (Message 81).
I had wondered if making an outgroup would help, and if adding a lot more 'a's to the lineages (to more completely model the relatively small proportion of the genome that mutates).
Mr. Jack Message 90: The outgroup is important because it helps the program determine which states are later mutations and which states were there originally. The second reason is that Percy's example happens to have multiple mutations at the same site, specifically the first mutation on the left branch is then overwritten by the second mutation on the leftmost branch (AAAAAAA->AAAAABA->AAAAAGA).
Which would be a rare occurrence in a real world example, so we can avoid this in making future models (or use a longer genome and a random generator for location and change).
Percy Message 91: I can pretty easily write a program to generate genomes for the PARS program to analyze, but I need feedback on a few things. This list is for producing a final population through normal reproductive descent:
  1. I'll go with the standard 4 nucleotides: CAGT
  2. Genome size as measured by number of nucleotides will be large. This will be settable per program run.
  3. Mutations will be restricted to single nucleotide substitutions, with no additions or deletions.
  4. Number of mutations per offspring will be random with a settable upper and lower bound.
  5. Number of offspring produced by a single organism per generation would be random with a settable upper and lower bound.
  6. Position of mutations will be random.
  7. Number of generations will be settable.
What would be a good genome size in nucleotides for the PARS program to analyze? What would be a good number of generations? What would be a good number of offspring produced per organism per generation? What would be a good final population size?
For the designer case I'll start with a certain number of individuals, then take them through enough generations to give the same size final population as in the evolution case. I could use Bob's feedback on this. How many original individuals should I start with? How many nucleotide sequences should they have in common?
Given that this thread is about convergent evolution, perhaps we need to start with two different genomes and run the mutations/generations, with come mechanism to select for a specific output?
For the designer model we would also need to see some predictions of what the design would cause:
  1. start with a set of different genomes
  2. copy of a mutation from one genome to another to model reuse of design
  3. fewer generations should be needed for the designer model
Perhaps work backwards from the final results of the evolution model, so we have the same end but different hypothetical beginnings.
Enjoy.

we are limited in our ability to understand
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Rebel American Zen Deist
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This message is a reply to:
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Replies to this message:
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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 98 of 107 (566456)
06-24-2010 6:23 PM
Reply to: Message 97 by ramoss
06-24-2010 11:58 AM


LOW convergence rate: What is the ID Explanation?
Hi ramoss, good question, hope you get an answer.
And why would that be evidence against 'darwinism'.
Because he said so. Of course this would be 'darwinism' according to his interpretation, and not necessarily evolution as used in science.
Please define 'significant quantity'.
A lot more than we have seen:
quote:
My Message 21:
Page Not Found | The Guardian
quote:
The number of species on the planet that have been documented by scientists has risen to 1.9 million, according to the world's most comprehensive catalogue of plants and animals. ...

...
While there are only 100 instances listed in the wiki article, and I don't call 100/1.9X10^6 = 0.005% a significant problem.
BobTHJ has not really answered my previous post on this issue, but has gone off on other tangents.
And I would say that the (documented) extremely LOW incidence of convergent evolution examples is evidence against the IDologist claims of "reuse of design" - especially when there are numerous examples of opportunities for "reuse of design" to have been used that have been missed.
Enjoy.

we are limited in our ability to understand
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Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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This message is a reply to:
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RAZD
Member (Idle past 1426 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 102 of 107 (569049)
07-19-2010 10:43 PM
Reply to: Message 100 by barbara
07-19-2010 5:18 PM


Re: superficial similarity but differences in the details
Hi barbara, and welcome to the fray.
I wouldn't use natural selection to describe the vast differences across species especially when it lists the same type of animal that is classified as such based almost identical features in appearance and then state they are unrelated.
Not sure I understand you here, could you expand your argument some, and provide reference to an example from my post?
This list does not make any sense whatsoever and if it is suppose to be presented as the facts then good luck on convincing anyone of this crap.
Well that's one way to deal with not understanding the issue.
It's just a list of instances where some similarities have evolved in different species, some of them with a high degree of similar appearance.
Again, I'm not sure what your issue is, so you may want to expand on this as well.
Enjoy.
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we are limited in our ability to understand
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Rebel American Zen Deist
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