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Forensic evolution.

Discussion in 'Creation & Evolution' started by Cheeky Monkey, Jul 25, 2013.

  1. Cheeky Monkey

    Cheeky Monkey Newbie

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    Go to ERV blog for the whole story CSI: Virology – erv
    The long and the short of it is that an anaesthetist was convicted of professional malpractice because he had infected nearly 300 patients with Hep C. How did they know for sure? Evolution. Because viruses evolve quite rapidly they were able to construct a phylogenetic tree showing that the different infections were related by descent to the infection carried by the anaesthetist. Neat huh?

    Of course the creationists here argue that genetic similarity doesn't prove descent so I suppose god might have created all of the infections in such a way that they all just happen to look related. I guess a YEC jury couldn't find him guilty beyond reasonable doubt.

    Just so we're clear, the methods and science that underpin the conviction are well tested, for example

    Science 25 October 1991:
    Vol. 254. no. 5031, pp. 554 - 558

    Gene trees and the origins of inbred strains of mice

    WR Atchley and WM Fitch

    Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains. Partitioning these loci into structured subsets representing loci coding for proteins, the immune system and endogenous viruses give incongruent phylogenetic results. The gene tree based on protein loci provides an accurate picture of the genealogical relationships among strains; however, gene trees based upon immune and viral data show significant deviations from known genealogical affinities.

    ======================

    Science, Vol 255, Issue 5044, 589-592

    Experimental phylogenetics: generation of a known phylogeny

    DM Hillis, JJ Bull, ME White, MR Badgett, and IJ Molineux
    Department of Zoology, University of Texas, Austin 78712.

    Although methods of phylogenetic estimation are used routinely in comparative biology, direct tests of these methods are hampered by the lack of known phylogenies. Here a system based on serial propagation of bacteriophage T7 in the presence of a mutagen was used to create the first completely known phylogeny. Restriction-site maps of the terminal lineages were used to infer the evolutionary history of the experimental lines for comparison to the known history and actual ancestors. The five methods used to reconstruct branching pattern all predicted the correct topology but varied in their predictions of branch lengths; one method also predicts ancestral restriction maps and was found to be greater than 98 percent accurate.

    ==================================

    Science, Vol 264, Issue 5159, 671-677

    Application and accuracy of molecular phylogenies

    DM Hillis, JP Huelsenbeck, and CW Cunningham
    Department of Zoology, University of Texas, Austin 78712.

    Molecular investigations of evolutionary history are being used to study subjects as diverse as the epidemiology of acquired immune deficiency syndrome and the origin of life. These studies depend on accurate estimates of phylogeny. The performance of methods of phylogenetic analysis can be assessed by numerical simulation studies and by the experimental evolution of organisms in controlled laboratory situations. Both kinds of assessment indicate that existing methods are effective at estimating phylogenies over a wide range of evolutionary conditions, especially if information about substitution bias is used to provide differential weightings for character transformations.


    And these methods that were applied successfully in these papers and in this court case have also been used to trace primate evolution which includes us

    Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo

    "Here we compare ≈90 kb of coding DNA nucleotide sequence from 97 human genes to their sequenced chimpanzee counterparts and to available sequenced gorilla, orangutan, and Old World monkey counterparts, and, on a more limited basis, to mouse. The nonsynonymous changes (functionally important), like synonymous changes (functionally much less important), show chimpanzees and humans to be most closely related, sharing 99.4% identity at nonsynonymous sites and 98.4% at synonymous sites. "



    Mitochondrial Insertions into Primate Nuclear Genomes Suggest the Use of numts as a Tool for Phylogeny

    "Moreover, numts identified in gorilla Supercontigs were used to test the human–chimp–gorilla trichotomy, yielding a high level of support for the sister relationship of human and chimpanzee."



    A Molecular Phylogeny of Living Primates

    "Once contentiously debated, the closest human relative of chimpanzee (Pan) within subfamily Homininae (Gorilla, Pan, Homo) is now generally undisputed. The branch forming the Homo andPanlineage apart from Gorilla is relatively short (node 73, 27 steps MP, 0 indels) compared with that of thePan genus (node 72, 91 steps MP, 2 indels) and suggests rapid speciation into the 3 genera occurred early in Homininae evolution. Based on 54 gene regions, Homo-Pan genetic distance range from 6.92 to 7.90×10−3 substitutions/site (P. paniscus and P. troglodytes, respectively), which is less than previous estimates based on large scale sequencing of specific regions such as chromosome 7[50]. "



    Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.

    "The Superfamily Hominoidea for apes and humans is reduced to family Hominidae within Superfamily Cercopithecoidea, with all living hominids placed in subfamily Homininae; and (4) chimpanzees and humans are members of a single genus, Homo, with common and bonobo chimpanzees placed in subgenus H. (Pan) and humans placed in subgenus H. (Homo). It may be noted that humans and chimpanzees are more than 98.3% identical in their typical nuclear noncoding DNA and probably more than 99.5% identical in the active coding nucleotide sequences of their functional nuclear genes (Goodman et al., 1989, 1990). In mammals such high genetic correspondence is commonly found between sibling species below the generic level but not between species in different genera."

    H/T nmanning
     
  2. AV1611VET

    AV1611VET SCIENCE CAN TAKE A HIKE Supporter

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    Hispid, you guys like to think like us, don't you?

    And in so doing, very seldom do I see you guys get it right -- but you do at times, and I'm impressed.

    For the record, we believe in microevolution -- but not macroevolution.

    So if you can draw some phylogenetic tree and trace something to Hep C, go for it.

    But then don't say it was macroevolution that saved the day.

    When it comes to similarities, there are two kinds:

    1. Similarities due to common ancestor -- such as my great great grandpa having the same characteristics as my barber.
    2. Similarities due to common design -- such as whales and humans having lungs.
    Pan and Homo are examples of common design.
    Homo and Homo are examples of common descent.
     
  3. Cheeky Monkey

    Cheeky Monkey Newbie

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    How come the hypothetical design similarities look just like similarities due to common descent? Could the defense have said that it is just as reasonable to assume that the Hep C in the patients was designed to look like it came from the defendant.?
     
  4. AV1611VET

    AV1611VET SCIENCE CAN TAKE A HIKE Supporter

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    Goodyear makes rubber tires; so does Dunlop.

    Yet despite the fact that they are two different designers, they are still rubber tires.
    No.

    AFAIK, Hepatitis C is an example of microevolution (common ancestor).
     
  5. Cheeky Monkey

    Cheeky Monkey Newbie

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    Can you subject the genes of tyres to a phylogenetic analysis?
    That's my point. The gene trees obtained look just like and are based on the same methods and data as the phylogenies that you say are designed. Shouldn't the designed phylogenies look different? Shouldn't there be breaks in the nested hierarchies where it switches from descent to design?
     
  6. AV1611VET

    AV1611VET SCIENCE CAN TAKE A HIKE Supporter

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    God did not design Hepatitis C.

    The Hepatitis C virus comes from something that existed before the Fall, then it "trickled down" to Hepatitis C over 6000 years.

    Put another way, the viruses that existed in Genesis 1 were friendly viruses until after the Fall, when malevolent viruses started showing up.
     
  7. Cheeky Monkey

    Cheeky Monkey Newbie

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    Ok. This important to the question how?
     
  8. CabVet

    CabVet Question everything

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    Assuming for a second that this is correct, somebody must have designed what the viruses would look like (and do) after a possible fall. Same thing for carnivores. Lions have teeth, they are encoded in their DNA, something must have designed that. If not God, I wonder who could that be. Are you really given that much credit to the bad one?
     
  9. AV1611VET

    AV1611VET SCIENCE CAN TAKE A HIKE Supporter

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    What's your point?

    God warned us we would start dying.
     
  10. CabVet

    CabVet Question everything

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    What is my point? If he warned us he knew what was coming because he designed it. What makes this incorrect:

     
  11. AV1611VET

    AV1611VET SCIENCE CAN TAKE A HIKE Supporter

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    Foreknowledge ≠ Design
     
  12. CabVet

    CabVet Question everything

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    Who designed it then? Who was powerful enough to design a "fail safe" mechanism that changed life in the entire planet?
     
  13. Coelo

    Coelo Newbie

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    Actually tires are made out of a Synthetic rubber that is invariably a polymer. Each company has their own chemists and their own formula that they use.
     
  14. SkyWriting

    SkyWriting Member

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    YEC's would have no problem.
    You make the most excellent scientific point ever made,
    that unless it's repeatable and testable, it's not science.

    It's Science-Fiction.
     
  15. SkyWriting

    SkyWriting Member

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    Every polymer is identical. That's what a "mer" is.
    Each blend of identical additives can be unique.
     
  16. BarryDesborough

    BarryDesborough New Member

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    The procedures were indeed repeatable and testable. Part of the reason we can be confident that the anaesthetist was the source.
     
  17. Cheeky Monkey

    Cheeky Monkey Newbie

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    Cool. As you see in the OP I have only presented testable repeatable science.
     
  18. SkyWriting

    SkyWriting Member

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    Then it was real science.

    Not sludge science that can't be double checked:
    Origins and DNA evidence
     
  19. SkyWriting

    SkyWriting Member

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    Then YEC"S are not the problem. Your attitude toward them is.
     
  20. BarryDesborough

    BarryDesborough New Member

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    What is his "attitude to YECs", and what has it got to do with the truth?
     
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