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  #1  
Unread 25th July 2013, 04:39 PM
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Forensic evolution.

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
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  #2  
Unread 25th July 2013, 06:15 PM
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Originally Posted by Cheeky Monkey View Post
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.
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.
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  #3  
Unread 25th July 2013, 06:35 PM
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Originally Posted by AV1611VET View Post
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.
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.?
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Unread 25th July 2013, 06:53 PM
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Originally Posted by Cheeky Monkey View Post
How come the hypothetical design similarities look just like similarities due to common descent?
Goodyear makes rubber tires; so does Dunlop.

Yet despite the fact that they are two different designers, they are still rubber tires.
Originally Posted by Cheeky Monkey View Post
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.?
No.

AFAIK, Hepatitis C is an example of microevolution (common ancestor).
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Unread 25th July 2013, 07:02 PM
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Originally Posted by AV1611VET View Post
Goodyear makes rubber tires; so does Dunlop.

Yet despite the fact that they are two different designers, they are still rubber tires.
Can you subject the genes of tyres to a phylogenetic analysis?
No.

AFAIK, Hepatitis C is an example of microevolution (common ancestor).
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?
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Unread 25th July 2013, 07:19 PM
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Originally Posted by Cheeky Monkey View Post
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?
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.
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Unread 25th July 2013, 07:44 PM
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Originally Posted by AV1611VET View Post
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.
Ok. This important to the question how?
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Unread 26th July 2013, 12:56 AM
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Originally Posted by AV1611VET View Post
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.
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?
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Unread 26th July 2013, 01:02 AM
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Originally Posted by CabVet View Post
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?
What's your point?

God warned us we would start dying.
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Unread 26th July 2013, 01:05 AM
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Originally Posted by AV1611VET View Post
What's your point?

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

Originally Posted by AV1611VET View Post
God did not design Hepatitis C.
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